bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic and Morphological Differentiation and Phylogeny in the Australo-Papuan Scrubwrens (Sericornis, Acanthizidae)
Authors: Christidis Leslie , Schodde Richard , Baverstock Peter R. 
Published: October 2019

Abstract
The interrelationships of 13 of the 14 species currently recognized in the Australo-Papuan oscinine scrubwrens, Sericornis, were assessed by protein electrophoresis, screening 44 presumptive loci. Consensus among analyses indicated that Sericornis comprises two primary lineages of hitherto unassociated species: S. beccarii with S. magnirostris, S. nouhuysi and the S. perspicillatus group; and S. papuensis and S. keri with S. spilodera and the S. frontalis group. Both lineages are shared by Australia and New Guinea. Patterns of latitudinal and altitudinal allopatry and sequences of introgressive intergradation are concordant with these groupings, but many features of external morphology are not. Apparent homologies in face, wing and tail markings, used formerly as the principal criteria for grouping species, are particularly at variance and are interpreted either as coinherited ancestral traits or homoplasies.
Distribution patterns suggest that both primary lineages were first split vicariantly between Australia and New Guinea, and then radiated independently on each land mass under the influence of paleoclimatic change. Dispersal between Australia and New Guinea is indicated only in the magnirostris sublineage and is either very recent or just broken.
Cooperative bird discriminates between individuals based purely on their aerial alarm calls
Authors: Farrow Lucy F , Barati Ahmad , McDonald Paul G 
Published: October 2019

AbstractFrom an evolutionary perspective, the ability to recognize individuals provides great selective advantages, such as avoiding inbreeding depression during breeding. Whilst the capacity to recognize individuals for these types of benefits is well established in social contexts, why this recognition might arise in a potentially deadly alarm-calling context following predator encounters is less obvious. For example, in most avian systems, alarm signals directed toward aerial predators represent higher predation risk and vulnerability than when individuals vocalize toward a terrestrial-based predator. Although selection should favor simple, more effective alarm calls to these dangerous aerial predators, the potential of these signals to nonetheless encode additional information such as caller identity has not received a great deal of attention. We tested for individual discrimination capacity in the aerial alarm vocalizations of the noisy miner (Manorina melanocephala), a highly social honeyeater that has been previously shown to be able to discriminate between the terrestrial alarm signals of individuals. Utilizing habituation–discrimination paradigm testing, we found conclusive evidence of individual discrimination in the aerial alarm calls of noisy miners, which was surprisingly of similar efficiency to their ability to discriminate between less urgent terrestrial alarm signals. Although the mechanism(s) driving this behavior is currently unclear, it most likely occurs as a result of selection favoring individualism among other social calls in the repertoire of this cooperative species. This raises the intriguing possibility that individualistic signatures in vocalizations of social animals might be more widespread than currently appreciated, opening new areas of bioacoustics research.
γ-TRIS: a graph-algorithm for comprehensive identification of vector genomic insertion sites
Authors: Calabria Andrea , Beretta Stefano , Merelli Ivan , Spinozzi Giulio , Brasca Stefano , Pirola Yuri , Benedicenti Fabrizio , Tenderini Erika , Bonizzoni Paola , Milanesi Luciano , Montini Eugenio 
Published: October 2019

Abstract

Summary
Retroviruses and their vector derivatives integrate semi-randomly in the genome of host cells and are inherited by their progeny as stable genetic marks. The retrieval and mapping of the sequences flanking the virus-host DNA junctions allows the identification of insertion sites in gene therapy or virally infected patients, essential for monitoring the evolution of genetically modified cells in vivo. However, since ∼30% of insertions land in low complexity or repetitive regions of the host cell genome, they cannot be correctly assigned and are currently discarded, limiting the accuracy and predictive power of clonal tracking studies. Here, we present γ-TRIS, a new graph-based genome-free alignment tool for identifying insertion sites even if embedded in low complexity regions. By using γ-TRIS to reanalyze clinical studies, we observed improvements in clonal quantification and tracking.

Availability and implementation
Source code at https://bitbucket.org/bereste/g-tris.

Supplementary information
Supplementary data are available at Bioinformatics online.
Regulatory oversight, causal inference, and safe and effective health care machine learning
Authors: Stern Ariel Dora , Price W Nicholson 
Published: October 2019

SummaryIn recent years, the applications of Machine Learning (ML) in the health care delivery setting have grown to become both abundant and compelling. Regulators have taken notice of these developments and the U.S. Food and Drug Administration (FDA) has been engaging actively in thinking about how best to facilitate safe and effective use. Although the scope of its oversight for software-driven products is limited, if FDA takes the lead in promoting and facilitating appropriate applications of causal inference as a part of ML development, that leadership is likely to have implications well beyond regulated products.
Social Workers in a Modernising Welfare State: Professionals or Street-Level Bureaucrats?
Authors: Trappenburg Margo , Kampen Thomas , Tonkens Evelien 
Published: October 2019

AbstractSocial workers are often depicted as street-level bureaucrats (SLBs) or professionals interchangeably. However, to find out how social workers relate to new policy measures, a clear distinction between SLBs and professionals is helpful. Ideal–typical SLBs subscribe to new policies although they may diverge from them in practice, to accommodate clients. Ideal–typical professionals weigh new policies against their ethical code. If the new policy goes against their professional principles, they protest on behalf of their clients. In this article, we study Dutch social workers who have to implement a new policy that (i) obliges their clients to actively participate in society and (ii) obliges them to rely on family and friends when they need help. The data for this article are derived from two projects: interviews with twenty-nine experienced social workers and interviews with social workers in neighbourhood teams and observations of their interactions with clients in six municipalities. We found that Dutch social workers think as professionals: they weigh the new policy against their ethical code and have serious doubts about the second part of the new policy. Hence, they find ways to avoid implementation. However, they behave as SLBs, bending the rules in practice. They rarely confront policymakers or higher management.
Mutations in PCYT2 disrupt etherlipid biosynthesis and cause a complex hereditary spastic paraplegia
Authors: Vaz Frédéric M , McDermott John H , Alders Mariëlle , Wortmann Saskia B , Kölker Stefan , Pras-Raves Mia L , Vervaart Martin A T , van Lenthe Henk , Luyf Angela C M , Elfrink Hyung L , Metcalfe Kay , Cuvertino Sara , Clayton Peter E , Yarwood Rebecca , Lowe Martin P , Lovell Simon , Rogers Richard C ,   Deciphering Developmental Disorders Study, van Kampen Antoine H C , Ruiter Jos P N , Wanders Ronald J A , Ferdinandusse Sacha , van Weeghel Michel , Engelen Marc , Banka Siddharth 
Published: October 2019

AbstractCTP:phosphoethanolamine cytidylyltransferase (ET), encoded by PCYT2, is the rate-limiting enzyme for phosphatidylethanolamine synthesis via the CDP-ethanolamine pathway. Phosphatidylethanolamine is one of the most abundant membrane lipids and is particularly enriched in the brain. We identified five individuals with biallelic PCYT2 variants clinically characterized by global developmental delay with regression, spastic para- or tetraparesis, epilepsy and progressive cerebral and cerebellar atrophy. Using patient fibroblasts we demonstrated that these variants are hypomorphic, result in altered but residual ET protein levels and concomitant reduced enzyme activity without affecting mRNA levels. The significantly better survival of hypomorphic CRISPR-Cas9 generated pcyt2 zebrafish knockout compared to a complete knockout, in conjunction with previously described data on the Pcyt2 mouse model, indicates that complete loss of ET function may be incompatible with life in vertebrates. Lipidomic analysis revealed profound lipid abnormalities in patient fibroblasts impacting both neutral etherlipid and etherphospholipid metabolism. Plasma lipidomics studies also identified changes in etherlipids that have the potential to be used as biomarkers for ET deficiency. In conclusion, our data establish PCYT2 as a disease gene for a new complex hereditary spastic paraplegia and confirm that etherlipid homeostasis is important for the development and function of the brain.
Laxative Use Does Not Preclude Diagnosis or Reduce Disease Severity in Clostridiodes difficile Infection
Authors: White Nicole C , Mendo-Lopez Rafael , Papamichael Konstantinos , Cuddemi Christine A , Barrett Caitlin , Daugherty Kaitlyn , Pollock Nira , Kelly Ciaran P , Alonso Carolyn D 
Published: October 2019

Abstract

Background
To optimize utility of laboratory testing for Clostridiodes difficile infection (CDI), the 2017 Infectious Diseases Society of America–Society for Healthcare Epidemiology of America (IDSA-SHEA) clinical practice guidelines recommend excluding patients from stool testing for C. difficile if they have received laxatives within the preceding 48 hours. Sparse data support this recommendation.

Methods
Patients with new-onset diarrhea (≥3 bowel movements in any 24-hour period in the 48 hours before stool collection) and a positive stool C. difficile nucleic acid amplification test were enrolled. Laxative use within 48 hours before stool testing, severity of illness (defined by 4 distinct scoring methods), and clinical outcomes were recorded.

Results
209 patients with CDI were studied, 65 of whom had received laxatives. There were no significant differences in the proportion of patients meeting severe CDI criteria by 4 severity scoring methods in patients receiving versus not receiving laxatives (66.2% vs 56.3%, respectively; P = .224) by IDSA-SHEA, the primary scoring system. Similar rates of serious outcomes attributable to CDI, including death, intensive care unit admission, and colectomy, were observed in the laxative and no laxative groups.

Conclusions
Our study found similar rates of severe CDI and serious CDI-attributable clinical outcomes in CDI-diagnosed patients who did or did not receive laxatives. Precluding recent laxative users from CDI testing, as proposed by the IDSA-SHEA guideline, carries a potential for harm due to delayed diagnosis and treatment.
Deprivation and kidney disease—a predictor of poor outcomes
Authors: Guthrie Greg D , Bell Samira 
Published: October 2019

Abstract
There is a growing body of evidence for the role of deprivation in a broad spectrum of diseases including renal disease. Deprivation has been demonstrated to be associated with poorer outcomes across a range of renal diseases including acute kidney injury (AKI), chronic kidney disease and transplantation. In this issue of Clinical Kidney Journal, Hounkpatin et al. describe the association of socioeconomic deprivation with incidence, mortality and resolution of AKI in a large UK cohort. Investigating deprivation as a factor influencing either incidence or outcome of disease is challenging due to variations in measures of deprivation used and other confounding factors that may be contributing to the observed differences. In this editorial, we review the current literature examining the role of deprivation in renal disease.
Duration of early systolic lengthening: prognostic potential in the general population
Authors: Brainin Philip , Biering-Sørensen Sofie Reumert , Møgelvang Rasmus , Jensen Jan Skov , Biering-Sørensen Tor 
Published: October 2019

Abstract

Background
When the left ventricle pressure rises during early systole, myocardial fibres with reduced contractility tend to stretch instead of shortening. This interval is known as duration of early systolic lengthening (DESL). We sought to investigate if DESL provides prognostic information on cardiovascular events.

Methods and results
In this prospective study we included 1210 participants from a low-risk general population who underwent speckle tracking echocardiography (men 41%, mean age 56 years, SD 16). Primary endpoints were incident heart failure (HF), myocardial infarction (MI), and cardiovascular death (CVD). We defined DESL as time from onset of Q-wave on the electrocardiogram to peak positive systolic strain. In addition, we assessed the ratio between DESL and duration of cardiac systole, DESLsystole.
During median follow-up of 16 years, 90 (7%) developed HF, 50 (4%) MI, and 70 (6%) experienced CVD. Both DESL [hazard ratio (HR) 1.58 95%CI 1.16–2.15, P = 0.004 per 10 ms increase] and DESLsystole (HR 1.74 95%CI 1.24–2.47, P = 0.001 per 1% increase) were predictors of HF. Similarly, DESL (HR 1.40 95%CI 1.09–1.78, P = 0.007 per 10 ms increase) and DESLsystole (HR 1.58 95%CI 1.01–2.49, P = 0.047 per 1% increase) were predictors of MI. No associations were found with CVD. After adjusting for clinical and echocardiographic parameters, the associations remained significant. DESLsystole was superior to systolic echocardiographic parameters for predicting HF (P = 0.012).

Conclusion
DESL and the novel index of DESLsystole provide independent and novel prognostic information on the risk of HF and MI in the general population. Evaluation of DESL should be explored in future echocardiographic studies.
Endothelial SIRT6 blunts stroke size and neurological deficit by preserving blood–brain barrier integrity: a translational study
Authors: Liberale Luca , Gaul Daniel S , Akhmedov Alexander , Bonetti Nicole R , Nageswaran Vanasa , Costantino Sarah , Pahla Jürgen , Weber Julien , Fehr Vera , Vdovenko Daria , Semerano Aurora , Giacalone Giacomo , Kullak-Ublick Gerd A , Sessa Maria , Eriksson Urs , Paneni Francesco , Ruschitzka Frank , Montecucco Fabrizio , Beer Jürg H , Lüscher Thomas F , Matter Christian M , Camici Giovanni G 
Published: October 2019

Abstract

Aims
Aging is an established risk factor for stroke; genes regulating longevity are implicated in the pathogenesis of ischaemic stroke where to date, therapeutic options remain limited. The blood–brain barrier (BBB) is crucially involved in ischaemia/reperfusion (I/R) brain injury thus representing an attractive target for developing novel therapeutic agents. Given the role of endothelial cells in the BBB, we hypothesized that the endothelial-specific expression of the recently described longevity gene SIRT6 may exhibit protective properties in stroke.

Methods and results
SIRT6 endothelial expression was reduced following stroke. Endothelial-specific Sirt6 knockout (eSirt6−/−) mice, as well as animals in which Sirt6 overexpression was post-ischaemically induced, underwent transient middle cerebral artery occlusion (tMCAO). eSirt6−/− animals displayed increased infarct volumes, mortality, and neurological deficit after tMCAO, as compared to control littermates. Conversely, post-ischaemic Sirt6 overexpression decreased infarct size and neurological deficit. Analysis of ischaemic brain sections revealed increased BBB damage and endothelial expression of cleaved caspase-3 in eSIRT6−/− mice as compared to controls. In primary human brain microvascular endothelial cells (HBMVECs), hypoxia/reoxygenation (H/R) reduced SIRT6 expression and SIRT6 silencing impaired the barrier function (transendothelial resistance) similar to what was observed in mice exposed to I/R. Further, SIRT6-silenced HBMVECs exposed to H/R showed reduced viability, increased cleaved caspase-3 expression and reduced activation of the survival pathway Akt. In ischaemic stroke patients, SIRT6 expression was higher in those with short-term neurological improvement as assessed by NIHSS scale and correlated with stroke outcome.

Conclusion
Endothelial SIRT6 exerts a protective role in ischaemic stroke by blunting I/R-mediated BBB damage and thus, it may represent an interesting novel therapeutic target to be explored in future clinical investigation.
Transcatheter aspiration of large pacemaker and implantable cardioverter-defibrillator lead vegetations facilitating safe transvenous lead extraction
Authors: Starck Christoph T , Schaerf Raymond H M , Breitenstein Alexander , Najibi Sasan , Conrad John , Berendt Joseph , Esmailian Fardad , Eulert-Grehn Jürgen , Dreizler Thomas , Falk Volkmar 
Published: October 2019

Abstract

Aims
Treatment of patients with systemic cardiac implantable electronic device (CIED) infection with large lead vegetations is challenging and associated with relevant morbidity and mortality. To avoid complications from open surgical extraction, a novel approach with percutaneous aspiration of large vegetations prior to transvenous lead extraction was instituted. The results of this treatment concept were retrospectively analysed in this multicentre study.

Methods and results
One hundred and one patients [mean age 68.2 ± 13.1 (30–92) years] were treated in four centres for endovascular CIED infection with large lead vegetations. Mean lead vegetation size was 30.7 ± 13.5 mm. Two hundred and forty-seven leads were targeted for extraction (170 pacemaker leads, 77 implantable cardioverter-defibrillator leads). Mean lead implant duration was 81.7 (1–254) months. The transcatheter aspiration system with a specialized long venous drainage cannula and a funnel-shaped tip was based on a veno-venous extracorporeal circuit with an in-line filter. The aspiration of vegetations showed complete procedural success in 94.0% (n = 95), partial success in 5.0% (n = 5). Three major complications (3.0%) were encountered. Complete procedural success (per lead) of the subsequently performed transvenous lead extraction procedure was 99.2% (n = 245). Thirty-day mortality was 3.0% (n = 3). Five patients (5.0%) died in the further course on Days 51, 54, 68, 134, and 182 post-procedure (septic complications: n = 4; heart failure: n = 1).

Conclusion
The percutaneous aspiration procedure is highly effective and is associated with a low complication profile. The aspiration of vegetations immediately prior and during the lead extraction procedure may avoid septic embolization into the pulmonary circulation. This may potentially lead to a long-term survival benefit.
Evolution and Unprecedented Variants of the Mitochondrial Genetic Code in a Lineage of Green Algae
Authors: Žihala David , Eliáš Marek 
Published: September 2019

Abstract
Mitochondria of diverse eukaryotes have evolved various departures from the standard genetic code, but the breadth of possible modifications and their phylogenetic distribution are known only incompletely. Furthermore, it is possible that some codon reassignments in previously sequenced mitogenomes have been missed, resulting in inaccurate protein sequences in databases. Here we show, considering the distribution of codons at conserved amino acid positions in mitogenome-encoded proteins, that mitochondria of the green algal order Sphaeropleales exhibit a diversity of codon reassignments, including previously missed ones and some that are unprecedented in any translation system examined so far, necessitating redefinition of existing translation tables and creating at least seven new ones. We resolve a previous controversy concerning the meaning the UAG codon in Hydrodictyaceae, which beyond any doubt encodes alanine. We further demonstrate that AGG, sometimes together with AGA, encodes alanine instead of arginine in diverse sphaeroplealeans. Further newly detected changes include Arg-to-Met reassignment of the AGG codon and Arg-to-Leu reassignment of the CGG codon in particular species. Analysis of tRNAs specified by sphaeroplealean mitogenomes provides direct support for and molecular underpinning of the proposed reassignments. Furthermore, we point to unique mutations in the mitochondrial release factor mtRF1a that correlate with changes in the use of termination codons in Sphaeropleales, including the two independent stop-to-sense UAG reassignments, the reintroduction of UGA in some Scenedesmaceae, and the sense-to-stop reassignment of UCA widespread in the group. Codon disappearance seems to be the main drive of the dynamic evolution of the mitochondrial genetic code in Sphaeropleales.
Draft genome sequence of Solanum aethiopicum provides insights into disease resistance, drought tolerance, and the evolution of the genome
Authors: Song Bo , Song Yue , Fu Yuan , Kizito Elizabeth Balyejusa , Kamenya Sandra Ndagire , Kabod Pamela Nahamya , Liu Huan , Muthemba Samuel , Kariba Robert , Njuguna Joyce , Maina Solomon , Stomeo Francesca , Djikeng Appolinaire , Hendre Prasad S , Chen Xiaoli , Chen Wenbin , Li Xiuli , Sun Wenjing , Wang Sibo , Cheng Shifeng , Muchugi Alice , Jamnadass Ramni , Shapiro Howard-Yana , Van Deynze Allen , Yang Huanming , Wang Jian , Xu Xun , Odeny Damaris Achieng , Liu Xin 
Published: October 2019

Abstract

Background
The African eggplant (Solanum aethiopicum) is a nutritious traditional vegetable used in many African countries, including Uganda and Nigeria. It is thought to have been domesticated in Africa from its wild relative, Solanum anguivi. S. aethiopicum has been routinely used as a source of disease resistance genes for several Solanaceae crops, including Solanum melongena. A lack of genomic resources has meant that breeding of S. aethiopicum has lagged behind other vegetable crops.

Results
We assembled a 1.02-Gb draft genome of S. aethiopicum, which contained predominantly repetitive sequences (78.9%). We annotated 37,681 gene models, including 34,906 protein-coding genes. Expansion of disease resistance genes was observed via 2 rounds of amplification of long terminal repeat retrotransposons, which may have occurred ~1.25 and 3.5 million years ago, respectively. By resequencing 65 S. aethiopicum and S. anguivi genotypes, 18,614,838 single-nucleotide polymorphisms were identified, of which 34,171 were located within disease resistance genes. Analysis of domestication and demographic history revealed active selection for genes involved in drought tolerance in both “Gilo” and “Shum” groups. A pan-genome of S. aethiopicum was assembled, containing 51,351 protein-coding genes; 7,069 of these genes were missing from the reference genome.

Conclusions
The genome sequence of S. aethiopicum enhances our understanding of its biotic and abiotic resistance. The single-nucleotide polymorphisms identified are immediately available for use by breeders. The information provided here will accelerate selection and breeding of the African eggplant, as well as other crops within the Solanaceae family.