bluuebunny/crossref_metadata_2025 huggingface dataset:
Laparoscopic Liver Resections for Tumors in the Posterosuperior Segments: A Single-center Experience of 174 Consecutive Cases
Authors: Kirmizi Serdar , De Meyere Celine , Parmentier Isabelle , D’Hondt Mathieu
Published: August 2020

Background:

Laparoscopic posterosuperior liver resection is a technically difficult and complex surgery. These patients are seen as poor candidates for laparoscopic surgery. This study aimed to show the safe and effective applicability of the posterosuperior segment resections by experienced surgeons in advanced centers.

Materials and Methods:

Patients who underwent laparoscopic posterosuperior liver resection between October 2011 and October 2019 at the Groeninge Hospital were evaluated retrospectively. Demographic and perioperative data were obtained from the prospectively maintained database. Resection of at least 3 consecutive Couinaud segments was accepted as a major surgery (trisegmentectomy). Postoperative complications were registered according to the Clavien-Dindo classification.

Results:

The median age of the 174 patients was 68 years [interquartile range (IQR): 60 to 75]. The semiprone position was used in the majority of operations (82.2%). Nonanatomic resection was performed in more than half of the operations (55.1%). A total of 5 patients underwent major hepatic resection. The median time of surgery was 150 (IQR: 120 to 190) minutes. Median blood loss was determined to be 150 (IQR: 50 to 300) mL. Malignancy was detected in 95% of the cases. The surgical margin was reported to be R0 in 93.3% of the specimens. The median hospitalization time was 4 (IQR: 3 to 6) days. The major complication rate was 1.7%, and only 1 patient died. Overall survival rates for patients who underwent a resection for colorectal liver metastases in the first and fifth years were 97.5% and 62.2%, and disease-free survival rates were 69.8% and 35.5%, respectively.

Conclusion:

Laparoscopic resections in the posterosuperior segments can be performed safely in experienced hands with good short and long term (oncologial) outcomes.
Functional and Short-term Outcomes in Elective Laparoscopic Colectomy for Symptomatic Diverticular Disease With Either Low Ligation or Inferior Mesenteric Artery Preservation: A Randomized Trial
Authors: Mari Giulio , Montroni Isacco , Origi Matteo , Crippa Jacopo , Achilli Pietro , Costanzi Andrea , Ferrari Giovanni , Ugolini Giampaolo , Maggioni Dario
Published: August 2020

Background:

The current treatment of symptomatic diverticular disease is left colectomy/sigmoidectomy with low ligation of the inferior mesenteric artery versus the inferior mesenteric artery preservation. Up to now, there is no strong evidence in favor of one of the 2 strategies. The aim of this study is to compare the bowel-specific quality of life and functional outcomes between these 2.

Methods:

Between June 2015 and February 2019, patients were randomly assigned to inferior mesenteric artery low ligation or inferior mesenteric artery preservation during elective laparoscopic sigmoidectomy for diverticular disease. Gastrointestinal, genitourinary functions and surgical outcomes were compared postoperatively between groups.

Results:

One-hundred sixty-eight patients were randomized providing 2 homogenous groups. Gastrointestinal and genitourinary functions were not significantly different between groups after 1 and 6 months postoperative. In both groups, the function was restored to the preoperative level 6 months after surgery. There was no statistically significant difference in terms of conversion rate, blood loss, length of surgery, between groups. There was no difference in the overall complication rate and the anastomotic leak rate among groups.

Conclusions:

Inferior mesenteric artery low ligation or inferior mesenteric artery preservation during elective laparoscopic sigmoidectomy for a diverticular disease can be considered equivalent in affecting the postoperative bowel-related quality of life, genitourinary function, and surgical outcomes.
Uromodulin to Osteopontin Ratio in Deceased Donor Urine Is Associated With Kidney Graft Outcomes
Authors: Mansour Sherry G. , Liu Caroline , Jia Yaqi , Reese Peter P. , Hall Isaac E. , El-Achkar Tarek M. , LaFavers Kaice A. , Obeid Wassim , Rosenberg Avi Z. , Daneshpajouhnejad Parnaz , Doshi Mona D. , Akalin Enver , Bromberg Jonathan S. , Harhay Meera N. , Mohan Sumit , Muthukumar Thangamani , Schröppel Bernd , Singh Pooja , El-Khoury Joe M. , Weng Francis L. , Thiessen-Philbrook Heather R. , Parikh Chirag R.
Published: August 2020

Background.

Deceased-donor kidneys experience extensive injury, activating adaptive and maladaptive pathways therefore impacting graft function. We evaluated urinary donor uromodulin (UMOD) and osteopontin (OPN) in recipient graft outcomes.

Methods.

Primary outcomes: all-cause graft failure (GF) and death-censored GF (dcGF). Secondary outcomes: delayed graft function (DGF) and 6-month estimated glomerular filtration rate (eGFR). We randomly divided our cohort of deceased donors and recipients into training and test datasets. We internally validated associations between donor urine UMOD and OPN at time of procurement, with our primary outcomes. The direction of association between biomarkers and GF contrasted. Subsequently, we evaluated UMOD:OPN ratio with all outcomes. To understand these mechanisms, we examined the effect of UMOD on expression of major histocompatibility complex II in mouse macrophages.

Results.

Doubling of UMOD increased dcGF risk (adjusted hazard ratio [aHR], 1.1; 95% confidence interval [CI], 1.02-1.2), whereas OPN decreased dcGF risk (aHR, 0.94; 95% CI, 0.88-1). UMOD:OPN ratio ≤3 strengthened the association, with reduced dcGF risk (aHR, 0.57; 0.41-0.80) with similar associations for GF, and in the test dataset. A ratio ≤3 was also associated with lower DGF (aOR, 0.73; 95% CI, 0.60-0.89) and higher 6-month eGFR (adjusted β coefficient, 3.19; 95% CI, 1.28-5.11). UMOD increased major histocompatibility complex II expression elucidating a possible mechanism behind UMOD’s association with GF.

Conclusions.

UMOD:OPN ratio ≤3 was protective, with lower risk of DGF, higher 6-month eGFR, and improved graft survival. This ratio may supplement existing strategies for evaluating kidney quality and allocation decisions regarding deceased-donor kidney transplantation.
Living Kidney Donors’ Financial Expenses and Mental Health
Authors: Barnieh Lianne , Arnold Jennifer B. , Boudville Neil , Cuerden Meaghan S. , Dew Mary Amanda , Dipchand Christine , Feldman Liane S , Gill John S. , Karpinski Martin , Klarenbach Scott , Knoll Greg , Lok Charmaine , Miller Matt , Monroy Mauricio , Nguan Chris , Prasad G.V. Ramesh , Sontrop Jessica M. , Storsley Leroy , Garg Amit X. ,   for the Donor Nephrectomy Outcomes Research (DONOR) Network
Published: August 2020

Background.

Living kidney donors incur donation-related expenses, but how these expenses impact postdonation mental health is unknown.

Methods.

In this prospective cohort study, the association between mental health and donor-incurred expenses (both out-of-pocket costs and lost wages) was examined in 821 people who donated a kidney at one of the 12 transplant centers in Canada between 2009 and 2014. Mental health was measured by the RAND Short Form-36 Health Survey along with Beck Anxiety Inventory and Beck Depression Inventory.

Results.

A total of 209 donors (25%) reported expenses of >5500 Canadian dollars. Compared with donors who incurred lower expenses, those who incurred higher expenses demonstrated significantly worse mental health–related quality of life 3 months after donation, with a trend towards worse anxiety and depression, after controlling for predonation mental health–related quality of life and other risk factors for psychological distress. Between-group differences for donors with lower and higher expenses on these measures were no longer significant 12 months after donation.

Conclusions.

Living kidney donor transplant programs should ensure that adequate psychosocial support is available to all donors who need it, based on known and unknown risk factors. Efforts to minimize donor-incurred expenses and to better support the mental well-being of donors need to continue. Further research is needed to investigate the effect of donor reimbursement programs, which mitigate donor expenses, on postdonation mental health.
The Introduction of cPRA and Its Impact on Access to Deceased Donor Kidney Transplantation for Highly Sensitized Patients in Australia
Authors: Sypek Matthew P. , Kausman Joshua Y. , Watson Narelle , Wyburn Kate , Holt Stephen G. , Hughes Peter , Clayton Philip A.
Published: August 2020

Background.

In March 2016, Australia’s deceased donor kidney allocation program introduced calculated panel reactive antibody (cPRA) based on antibody exclusions using multiplex assays to define sensitization for waitlisted candidates. We aimed to assess the impact of this change and review access to transplantation for highly sensitized patients under the current allocation rules.

Methods.

Registry data were used to reconstruct changes in panel reactive antibody (PRA)/cPRA for all patients active on the waiting list between 2013 and 2018. A multilevel, mixed-effects negative binomial regression model was used to determine the association between sensitization and transplantation rate in the cPRA era.

Results.

Following the introduction of cPRA, there was an increase in the percentage of the waiting list classified as highly sensitized (PRA/cPRA ≥80%) from 7.2% to 27.8% and very highly sensitized (PRA/cPRA ≥99%) from 2.7% to 15.3%. Any degree of sensitization was associated with a decreased rate of transplantation with a marked reduction for those with cPRA 95%–98% (adjusted incidence rate ratio, 0.36 [95% confidence interval, 0.28-0.47], P < 0.001) and cPRA ≥99% (adjusted incidence rate ratio, 0.09 [95% confidence interval, 0.07-0.12], P < 0.001).

Conclusions.

The proportion of the waiting list classified as highly sensitized increased substantially following the introduction of cPRA, and despite current prioritization, very highly sensitized patients have markedly reduced access to deceased donor transplantation.
Dextromethorphan Abuse Among Opioid-Dependent Patients
Authors: Windhab Laura G. , Gastberger Salome , Hulka Lea M. , Baumgartner Markus R. , Soyka Michael , Müller Thomas J. , Seifritz Erich , Mutschler Jochen
Published: August 2020

Background

Among opioid-dependent patients on maintenance therapy, concomitant drug abuse is a serious problem. Dextromethorphan, an over-the-counter antitussive agent that can be purchased without prescription, is a drug with a high potential for misuse, especially when consumed in high doses.

The objective of this study was to investigate possible abuse of dextromethorphan among substituted opioid-dependent patients and comparison of subjective and objective findings.

Due to its ability to increase serotonin levels, opioid-dependent patients may be particularly susceptible to dextromethorphan misuse. Dextromethorphan misuse may have side effects, including psychiatric symptoms and serotonin syndrome, and may induce assault, suicide, or homicide.

Methods

A total of 104 opioid-dependent patients in maintenance treatment were included in this cross-sectional study conducted in the outpatient department of the Psychiatric Hospital, University of Zurich. Study participants were divided into 2 groups based on laboratory results: dextromethorphan abusers (n = 12) and nonabusers (n = 92). The objective use and concentrations of dextromethorphan was detected using 3-month hair toxicology analysis.

Statistical analysis was performed by using χ2 test, Student t test, Mann-Whitney U test, and Barnard exact test.

Results

Dextromethorphan was abused by 12 (11.5%) patients, 11 (91.7%) of whom did not report concomitant abuse of dextromethorphan but were identified through hair analysis. In general, there were significant differences among patients abusing dextromethorphan compared with nondextromethorphan consumers in terms of trauma due to sexual maltreatment/violence, multiple traumas, or harmful use of hallucinogenic drugs.

Conclusions

Further studies are necessary to examine dextromethorphan and its impact on patients with psychiatric comorbidities and psychiatric medication. According to literature, there is a significant drug interaction risk due to the impact of dextromethorphan misuse on serotonin syndrome and psychiatric symptoms.1–3 We recommend active inquiry into and testing for concomitant drug abuse among substituted opioid-dependent patients to reduce the risk of drug interactions and side effects in this especially vulnerable group of patients.
One Plus One Sometimes Equals More Than Two: Long-acting Injectable Aripiprazole Adjunction in Clozapine-Resistant Schizophrenia
Authors: Balcioglu Yasin Hasan , Gokcay Hasan , Yesilkaya Umit Haluk
Published: August 2020

In this report, we present a patient whose positive symptoms did not improve despite being treated with clozapine monotherapy at a therapeutic dose for 4 months, and whose symptoms began to resolve after aripiprazole long-acting injection adjunction to clozapine. A 22-year-old man was diagnosed as having schizophrenia last year in his first admission, with symptoms of auditory hallucinations, persecutory delusions, and associated social withdrawal. His positive symptoms did not improve despite being treated with risperidone, olanzapine, and paliperidone. Oral clozapine monotherapy was planned, and the daily dose was increased to provide a therapeutic plasma clozapine concentration and measured as effective (545 mg/dL). Aripiprazole long-acting injection 400 mg monthly was combined with the ongoing clozapine treatment for augmentation. One week after the third injection, a psychiatric examination revealed a significant improvement in the positive symptoms, and his caregivers confirmed an increase in the social interaction of the patient. Although we cannot postulate on a single exact mechanism for the increased efficacy of clozapine and aripiprazole combination, we may suggest that, at least for a subgroup of patients with schizophrenia who respond clinically to clozapine at a suboptimal level, combination with aripiprazole may be an effective therapeutic strategy.
The latitudinal gradient in rates of evolution for bird beaks, a species interaction trait
Authors: Freeman Benjamin G , Schluter Dolph , Tobias Joseph A
Published: August 2020

Where is evolution fastest? The biotic interactions hypothesis proposes that greater species richness creates more ecological opportunity, driving faster evolution at low latitudes, whereas the “empty niches” hypothesis proposes that ecological opportunity is greater where diversity is low, spurring faster evolution at high latitudes. Here we tested these contrasting predictions by analyzing rates of bird beak evolution for a global dataset of 1141 sister pairs of birds. Beak size evolves at similar rates across latitudes, while beak shape evolves faster in the temperate zone, consistent with the empty niches hypothesis. We show in a meta-analysis that trait evolution and recent speciation rates are faster in the temperate zone, while rates of molecular evolution are slightly faster in the tropics. Our results suggest that drivers of evolutionary diversification are more potent at higher latitudes, thus calling into question multiple hypotheses invoking faster tropical evolution to explain the latitudinal diversity gradient.
A new ischemic grading system to aid combat extremity vascular injury decision making
Authors: Ratnayake Amila , Reva Viktor A. , Bala Miklosh , Jayatilleke Achala U. , Thalgaspitiya Sujeewa P.B. , Kauvar David S. , Worlton Tamara J.
Published: August 2020

Introduction

In resource limited combat settings with frequent encounters of mass casualty incidents, the decision to attempt limb salvage versus primary amputation is refined over time based on experience. This experience can be augmented by grading systems and algorithms to assist in clinical decisions. Few investigators have attempted to explicitly grade limb ischemia according to clinical criteria and study the impact of limb ischemia on clinical outcome. We suggest a new ischemia grading system based on the Rutherford ischemic classification and the V. A. Kornilov classification which we adapted to apply to the combat setting. This new tool was then retrospectively applied to combat trauma patients from the Sri Lankan Civil War.

Method

We retrospectively queried a prospectively maintained, single surgeon registry containing 129 extremity vascular injuries managed at a Role 3 military base hospital (MBH) from 2008 December to June 2009 during the last phase of Sri Lankan Civil war. 89 patients were analyzed for early limb salvage according to the modified Kornilov extremity ischemia index (MKEII).

Result

According to the MKEII, subcohort analysis of C1 (viable), C2 (threatened), and C3 (irreversible) classified injuries demonstrated a statistically significant (P < 0.001) difference in limb salvage. Further statistical evaluation demonstrated injury to popliteal region (P=0.006), severe arterial injury (P=0.018) and venous injuries (P< 0.001) had statistically significant differences in distribution between C1, C2 and C3.

Conclusion

By application of the MKEII, combat surgeons can rapidly and correctly select and prioritize vascular injured extremities to optimally use limited resources to achieve realistic limb salvage goals. A rigid ankle was correlated with the worst index of extremity ischemia. Further investigation into this sign as an indication for primary amputation is warranted.
HOW, WHY AND UNDER WHAT CIRCUMSTANCES DOES A QUALITY IMPROVEMENT COLLABORATIVE BUILD KNOWLEDGE AND SKILLS IN CLINICIANS WORKING WITH PEOPLE WITH DEMENTIA? A REALIST INFORMED PROCESS EVALUATION
Authors: de la Perrelle Lenore , Cations Monica , Barbery Gaery , Radisic Gorjana , Kaambwa Billingsley , Crotty Maria , Fitzgerald Janna Anneke , Kurrle Susan , Cameron Ian D , Whitehead Craig , Thompson Jane , Laver Kate
Published: August 2020

In increasingly constrained health and aged care services, strategies are needed to improve quality and translate evidence into practice. In dementia care, recent failures in quality and safety have led the World Health Organisation to prioritise the translation of known evidence into practice. While quality improvement collaboratives have been widely used in healthcare, there are few examples in dementia care.

We describe a recent quality improvement collaborative to improve dementia care across Australia and assess the implementation outcomes of acceptability and feasibility of this strategy to translate known evidence into practice. A realist-informed process evaluation was used to analyse how, why and under what circumstances a quality improvement collaborative built knowledge and skills in clinicians working in dementia care.

This realist-informed process evaluation developed, tested, and refined the program theory of a quality improvement collaborative. Data were collected pre-and post-intervention using surveys and interviews with participants (n=24). A combined inductive and deductive data analysis process integrated three frameworks to examine the context and mechanisms of knowledge and skill building in participant clinicians.

A refined program theory showed how and why clinicians built knowledge and skills in quality improvement in dementia care. Seven mechanisms were identified: motivation, accountability, identity, collective learning, credibility, and reflective practice. Each of these mechanisms operated differently according to context.

A quality improvement collaborative designed for clinicians in different contexts and roles was acceptable and feasible in building knowledge and skills of clinicians to improve dementia care. A supportive setting and a credible, flexible, and collaborative process optimises quality improvement knowledge and skills in clinicians working with people with dementia.

Trial registration

Australian and New Zealand Clinical Trials Registry 21 February 2018 (ACTRN 12618000268246)
Aggregation Tool for Genomic Concepts (ATGC): A deep learning framework for somatic mutations and other sparse genomic measures
Authors: Anaya Jordan , Sidhom John-William , Mahmood Faisal , Baras Alexander S.
Published: August 2020

Deep learning can extract meaningful features from data given enough training examples. Large-scale genomic data are well suited for this class of machine learning algorithms; however, for many of these data the labels are at the level of the sample instead of at the level of the individual genomic measures. Conventional approaches to this data statically featurise and aggregate the measures separately from prediction. We propose to featurise, aggregate, and predict with a single trainable end-to-end model by turning to attention-based multiple instance learning. This allows for direct modelling of instance importance to sample-level classification in addition to trainable encoding strategies of genomic descriptions, such as mutations. We first demonstrate this approach by successfully solving synthetic tasks conventional approaches fail. Subsequently we applied the approach to somatic variants and achieved best-in-class performance when classifying tumour type or microsatellite status, while simultaneously providing an improved level of model explainability. Our results suggest that this framework could lead to biological insights and improve performance on tasks that aggregate information from sets of genomic data.
New insights of zoogeographical distribution of Himalayan goral (Naemorhedus goral) from Indian Himalayan Region
Authors: Joshi Bheem Dutt , Singh Vinay Kumar , Singh Hemant , Singh Ashutosh , Singh Sujeet Kumar , Chandra Kailash , Sharma Lalit Kumar , Thakur Mukesh
Published: August 2020

In the present study, we explored the intraspecific genetic variation and phylogeographic relationship among all the reported species in the genusNaemorhedusdistributed in a wide range of habitats. The Bayesian based phylogeny demonstrated that Himalayan goral, is a highly diverged species from the other reported species of gorals. We claim the presence of two valid sub-species of Himalayan goral, i.e.N. g. bedfordiandN. g. goral, distributed in the western and central Himalaya, respectively. The comparative analysis with the inclusion of data available from different ranges, suggests the presence of plausibly six species of gorals across the distribution with a few valid subspecies. Further, we report thatN. griseusis a valid species and not the synonyms ofN. goralconsidering the observed discrepancy in the available sequences. We recommend all the sub-species present at distant locations may be considered as Evolutionary Significant Units (ESUs) and, therefore, appeal to provide them special attention for long term conservation and management.
Genomic investigation of a suspected multi-drug resistantKlebsiella pneumoniaeoutbreak in a neonatal care unit in sub-Saharan Africa
Authors: Cornick Jennifer , Musicha Patrick , Peno Chikondi , Saeger Ezgi , Toh Pui-ying Iroh , Bennett Aisleen , Kennedy Neil , Feasey Nicholas , Heinz Eva , Cain Amy K.
Published: August 2020

A suspected outbreak of multi-drug resistant (MDR)Klebsiella pneumoniaein a Malawian neonatal unit was investigated using whole-genome sequencing. Strain-types, virulence and resistance genes ofK. pneumoniaeisolated from patients from the hospital over a four-year period were identified. A MDR ST340 clone was implicated as the likely outbreak cause.
Modelling the interaction between Infectious Bursal Disease Virus VP3 polypeptide and dsRNA: identification of key residues for ribonucleoprotein assembly and virus replication
Authors: Busnadiego Idoia , Martín Maria T , Ferrero Diego S , de la Blanca María G Millán , Broto Laura , Díaz-Beneitez Elisabeth , Fuentes Daniel , Rodríguez Dolores , Verdaguer Nuria , Kremer Leonor , Rodríguez José F.
Published: August 2020

The interaction of the structural VP3 polypeptide of infectious bursal disease virus (IBDV) with virus-encoded dsRNA is essential both for the assembly of ribonucleoprotein complexes responsible for genome transcription and replication and for the evasion of host’s antiviral responses. Surface plasmon resonance analysis allowed us to determine the kinetic constants of the VP3-dsRNA interaction as well as to map the VP3 dsRNA bipartite dsRNA binding domain (dsRBD), uncovering the specific role of the previously described Patch1 and Patch2 dsRB subdomains. Here we show that the Patch1 domain plays a primary binding function while Patch2 exerts a subordinate role stabilizing VP3-dsRNA complexes. The use of a set of VP3 mutant versions facilitated the identification of K99 and K106 within Patch1 as the essential residues for the formation of VP3-dsRNA complexes. Furthermore, replacement of either one of these two residues by aspartic acid completely thwarts both evasion from host’s sensors and virus replication. Data presented here allow us to propose a VP3-dsRNA interaction model that should help to further elucidate the mechanics of IBDV morphogenesis and genome packaging as well as to better understand how VP3 counteracts recognition of virus-encoded dsRNA by specialized host’s sensors.
Characterization of a sex-determining region and its genomic context via statistical estimates of haplotype frequencies in daughters and sons sequenced in pools
Authors: Cordaux Richard , Chebbi Mohamed Amine , Giraud Isabelle , Pleydell David , Peccoud Jean
Published: August 2020

Sex chromosomes are generally derived from a pair of autosomes that have acquired a locus controlling sex. Sex chromosomes usually evolve reduced recombination around this locus and undergo a long process of molecular divergence. Although sex chromosomes have been intensively studied in several model taxa, the actual loci controlling sex are difficult to identify in highly diverged sex chromosomes, hence they are known in relatively few species. Taxa with evolutionarily young sex chromosomes can help fill this gap in knowledge. Here we aimed at pinpointing the sex-determining region (SDR) of Armadillidium vulgare, a terrestrial isopod with female heterogamety (ZW females and ZZ males) and which presumably presents evolutionarily young sex chromosomes. To locate the SDR, we assessed SNP allele frequencies in F1 daughters and sons sequenced in pools (pool-seq) in several families. We developed a Bayesian method that uses the SNP genotypes of individually sequenced parents and poolseq data from F1 siblings to estimate the genetic distance between a given genomic region (contig) and the SDR. This allowed us to assign more than 43 Megabases of contigs to sex chromosomes. By taking advantage of the several F1 families, we delineated a very short genomic region (~65 kilobases) that did not show evidence for recombination with the SDR. In this region, the comparison of sequencing depths between sexes outlined female-specific genes that may be involved in sex determination. Overall, our results provide strong evidence for an extremely low divergence of sex chromosomes in A. vulgare.
Genomic evolutionary analysis in R with geaR
Authors: Ward Christopher M. , Ludington Alastair J. , Breen James , Baxter Simon W.
Published: August 2020

The analysis and interpretation of datasets generated through sequencing large numbers of individual genomes is becoming commonplace in population and evolutionary genetic studies. Here we introduce geaR, a modular R package for evolutionary analysis of genome-wide genotype data. The package leverages the Genomic Data Structure (GDS) format, which enables memory and time efficient querying of genotype datasets compared to standard VCF genotype files. geaR utilizes GRange object classes to partition an analysis based on features from GFF annotation files, select codons based on position or degeneracy, and construct both positional and coordinate genomic windows. Tests of genetic diversity (eg.dXY,π, FST) and admixturealong with tree building and sequence output, can be carried out on partitions using a single function regardless of sample ploidy or number of observed alleles. The package and associated documentation are available on GitHub athttps://github.com/CMWbio/geaR.
Successful reproduction ofTrachemys scriptain the Altrhein of Kehl (Germany) and simultaneous increase of estimated population size
Authors: Schradin Carsten
Published: August 2020

The European Union categorised pond sliders (Trachemys scripta) as an invasive species for which all member countries have to develop an action plan. WhileT. scriptahas been released illegally in thousands of freshwaters in Europe, monitoring programs in Germany are missing. Based on short term surveys, anecdotal data, and assumptions, the action plan in Germany proposes thatT. scriptadoes not represent a problem as the cold weather causes high mortality and does not allow for successful reproduction. Here I present data of five years of monitoring at the Altrhein of Kehl, at the border between Germany and France showing: 1. Apart fromT. scripta, five additional species have been released (Pseudemys nelson, Pseudemys concinna, Graptemys pseudogeographica, Mauremys spec.,Chrysemys picta.). 2. Population size seemed to increase over the years, with 116 individuals being counted in 2020 compared to 33 individuals in 2016. 3. Successful reproduction of.T. scriptawas indicated by the observation of very small individuals and proved by the collection of hatchlings in two years. While the data presented here would benefit from more years of more intensive monitoring, they are sufficient to draw the conclusion that the German action plan is insufficient because individuals survive for long periods and do reproduce successfully. Similar results have been reported from other central European countries. Thus,T. scriptamight become invasive not only in south but also in central Europe. In sum, national action plans of how to deal with the invasiveT. scriptashould to be revised in Germany and many other European countries.
Diploid hepatocytes drive physiological liver renewal in adult humans
Authors: Heinke Paula , Rost Fabian , Rode Julian , Welsch Thilo , Alkass Kanar , Feddema Joshua , Salehpour Mehran , Possnert Göran , Druid Henrik , Brusch Lutz , Bergmann Olaf
Published: August 2020

Physiological liver cell replacement is central to maintaining the organ’s high metabolic activity, although its characteristics are difficult to study in humans. Using retrospective14C birth dating of cells, we report that human hepatocytes show continuous and lifelong turnover, maintaining the liver a young organ (average age < 3 years). Hepatocyte renewal is highly dependent on the ploidy level. Diploid hepatocytes show an seven-fold higher annual exchange rate than polyploid hepatocytes. These observations support the view that physiological liver cell renewal in humans is mainly dependent on diploid hepatocytes, whereas polyploid cells are compromised in their ability to divide. Moreover, cellular transitions between these two subpopulations are limited, with minimal contribution to the respective other ploidy class under homeostatic conditions. With these findings, we present a new integrated model of homeostatic liver cell generation in humans that provides fundamental insights into liver cell turnover dynamics.
Multivalent interactions between eIF4G1, Pub1 and Pab1 drive the formation of protein condensates
Authors: Chaves-Arquero Belén , Martínez-Lumbreras Santiago , Sibille Nathalie , Camero Sergio , Bernadó Pau , Jiménez Ma Ángeles , Zorrilla Silvia , Pérez-Cañadillas José Manuel
Published: August 2020

Yeast eIF4G1 interacts with RNA binding proteins (RBPs) like Pab1 and Pub1 affecting its function in translation initiation and stress granules formation. We present an NMR and SAXS study of the intrinsically disordered region of eIF4G1, eIF4G11-249, and its interactions with Pub1 and Pab1. The conformational ensemble of eIF4G11-249shows an α-helix within the BOX3 conserved element and a dynamic network of fuzzy π-π and π-cation interactions involving arginine and aromatic residues. The Pab1 RRM2 domain interacts with eIF4G1 BOX3, the canonical interaction site, but also with BOX2, a conserved element of unknown function to date. In contrast, the Pub1 RRM3 domain interacts with the RNA1-1 and BOX1 regions of eIF4G1. Mixtures of Pub1, Pab1 and eIF4G1 form micrometer-size protein condensates that require the presence of the eIF4G1 BOX1 element. These homotypic interactions suggest a double key mechanism of eIF4G1 regulation, important for understanding the architecture of stress granule cores.
Ribosome fingerprinting with a solid-state nanopore
Authors: Raveendran Mukhil , Leach Anna Rose , Hopes Tayah , Aspden Julie L. , Actis Paolo
Published: August 2020

Nanopores hold great potential for the analysis of complex biological molecules at the single entity level. One particularly interesting macromolecular machine is the ribosome, responsible for translating mRNA into proteins. In this study, we use a solid-state nanopore to fingerprint 80S ribosomes and polysomes from a human neuronal cell line and,Drosophila melanogastercultured cells and ovaries. Specifically, we show that the peak amplitude and dwell time characteristics of 80S ribosomes are distinct from polysomes and can be used to discriminate ribosomes from polysomes in mixed samples. Moreover, we are able to distinguish large polysomes, containing more than 7 ribosomes, from those containing 2-3 ribosomes, and demonstrate a correlation between polysome size and peak amplitude. This study highlights the application of solid-state nanopores as a rapid analytical tool for the detection and characterization of ribosomal complexes.
Integron activity accelerates the evolution of antibiotic resistance
Authors: Souque Célia , Escudero José A. , MacLean R.Craig
Published: August 2020

Mobile integrons are widespread genetic platforms that allow bacteria to modulate the expression of antibiotic resistance cassettes by shuffling their position from a common promoter. Antibiotic stress induces the expression of an integrase that excises and integrates cassettes, and this unique recombination and expression system is thought to allow bacteria to ‘evolve on demand’ in response to antibiotic pressure. To test this hypothesis, we inserted a custom three cassette integron intoP. aeruginosa, and used experimental evolution to measure the impact of integrase activity on adaptation to gentamicin. Crucially, integrase activity accelerated evolution by increasing the expression of a gentamicin resistance cassette through duplications and by eliminating redundant cassettes. Importantly, we found no evidence of deleterious off-target effects of integrase activity. In summary, integrons accelerate resistance evolution by rapidly generating combinatorial variation in cassette composition while maintaining genomic integrity.
Genome Diversity in Ukraine
Authors: Oleksyk Taras K. , Wolfsberger Walter W. , Weber Alexandra , Shchubelka Khrystyna , Oleksyk Olga T. , Levchuk Olga , Patrus Alla , Lazar Nelya , Castro-Marquez Stephanie O. , Boldyzhar Patricia , Urbanovych Alina , Stakhovska Viktoriya , Malyar Kateryna , Chervyakova Svitlana , Podoroha Olena , Kovalchuk Natalia , Hasynets Yaroslava , Rodriguez-Flores Juan L. , Medley Sarah , Battistuzzi Fabia , Liu Ryan , Hou Yong , Chen Siru , Yang Huanming , Yeager Meredith , Dean Michael , Mills Ryan E. , Smolanka Volodymyr
Published: August 2020

The main goal of this collaborative effort is to provide genome wide data for the previously underrepresented population in Eastern Europe, and to provide cross-validation of the data from genome sequences and genotypes of the same individuals acquired by different technologies. We collected 97 genome-grade DNA samples from consented individuals representing major regions of Ukraine that were consented for the public data release. DNBSEQ-G50 sequences, and genotypes by an Illumina GWAS chip were cross-validated on multiple samples, and additionally referenced to one sample that has been resequenced by Illumina NovaSeq6000 S4 at high coverage. The genome data has been searched for genomic variation represented in this population, and a number of variants have been reported: large structural variants, indels, CNVs, SNPs and microsatellites. This study provides the largest to-date survey of genetic variation in Ukraine, creating a public reference resource aiming to provide data for historic and medical research in a large understudied population. While most of the common variation is shared with other European populations, this survey of population variation contributes a number of novel SNPs and structural variants that have not been reported in the gnomAD/1KG databases representing global distribution of genomic variation. These endemic variants will become a valuable resource for designing future population and clinical studies, help address questions about ancestry and admixture, and will fill a missing place in the puzzle characterizing human population diversity in Eastern Europe. Our results indicate that genetic diversity of the Ukrainian population is uniquely shaped by the evolutionary and demographic forces, and cannot be ignored in the future genetic and biomedical studies. This data will contribute a wealth of new information bringing forth different risk and/or protective alleles. The newly discovered low frequency and local variants can be added to the current genotyping arrays for genome wide association studies, clinical trials, and in genome assessment of proliferating cancer cells.
The Pancreatic Tumor Microenvironment Compensates for Loss of GOT2
Authors: Kerk Samuel A. , Lin Lin , Myers Amy L. , Zhang Yaqing , Jiménez Jennifer A. , Sajjakulnukit Peter , Nelson Barbara S. , Chen Brandon , Robinson Anthony , Thurston Galloway , Kemp Samantha B. , Steele Nina G. , Hoffman Megan T. , Wen Hui-Ju , Long Daniel , Ackenhusen Sarah E. , Ramos Johanna , Gao Xiaohua , Zhang Li , Andren Anthony , Nwosu Zeribe C. , Galbán Stefanie , Halbrook Christopher J. , Lombard David B. , Piwnica-Worms David R. , Ying Haoqiang , Crawford Howard C. , di Magliano Marina Pasca , Shah Yatrik M. , Lyssiotis Costas A.
Published: August 2020

The tumor microenvironment (TME) in pancreatic ductal adenocarcinoma (PDA) restricts vascularization and, consequently, access to blood-derived nutrients and oxygen, which impacts tumor growth. Intracellular redox imbalance is another restraint on cellular proliferation, yet it is unknown if the TME contributes to the maintenance of redox homeostasis in PDA cells. Here, we demonstrate that the loss of mitochondrial glutamate-oxaloacetate transaminase 2 (GOT2), a component in the malate-aspartate shuttle, disturbs redox homeostasis and halts proliferation of PDA cells in vitro. In contrast, GOT2 inhibition has no effect on in vivo tumor growth or tumorigenesis in an autochthonous model. We propose that this discrepancy is explained by heterocellular pyruvate exchange from the TME, including from cancer associated fibroblasts. More broadly, pyruvate similarly confers resistance to inhibitors of mitochondrial respiration. Genetic or pharmacologic inhibition of pyruvate uptake or metabolism abrogated pyruvate-mediated alleviation of reductive stress from NADH buildup. In sum, this work describes a potential resistance mechanism mediated by metabolic crosstalk within the pancreatic TME. These findings have important implications for metabolic treatment strategies since several mitochondrial inhibitors are currently in clinical trials for PDA and other cancers.
Interstitial spaces are continuous across tissue and organ boundaries in humans
Authors: Cenaj Odise , Allison Douglas H. R. , Imam R , Zeck Briana , Drohan Lilly M. , Chiriboga Luis , Llewellyn Jessica , Liu Cheng Z , Park Young Nyun , Wells Rebecca G. , Theise Neil D.
Published: August 2020

Bodies have “reticular networks” comprising collagens, elastin, glycosaminoglycans, and other extracellular matrix components, that are continuous within and around all organs. Fibrous tissue coverings of nerves and blood vessels create structural continuity beyond organ boundaries. We recently described fluid flow through such human fibrous tissues. It remains unclear whether these interstitial spaces are continuous through the body or are discontinuous, confined within individual organs. We investigated IS continuity using two approaches. Non-biological particles (tattoo pigment, colloidal silver) were tracked within colon and skin interstitial spaces and into adjacent fascia. We also exploited hyaluronic acid, a macromolecular component of interstitial spaces. Both techniques demonstrate continuity of interstitial spaces within and across organ boundaries, including within perineurium and vascular adventitia traversing organs and the spaces between them. We suggest a body-wide network of fluid-filled interstitial spaces with significant implications for molecular signaling, cell trafficking, and the spread of malignant and infectious disease.
Engineered sex distortion in the global agricultural pestCeratitis capitata
Authors: Meccariello Angela , Krsticevic Flavia , Colonna Rita , Del Corsano Giuseppe , Fasulo Barbara , Papathanos Philippos Aris , Windbichler Nikolai
Published: August 2020

Genetic sex ratio distorters have potential for the area-wide control of harmful insect populations. Endonucleases targeting the X-chromosome and whose activity is restricted to male gametogenesis have recently been pioneered as a means to engineer such traits. Here we enabled endogenous CRISPR/Cas9 and CRISPR/Cas12a activity during spermatogenesis of the Mediterranean fruit flyCeratitis capitata, a worldwide agricultural pest of extensive economic significance. In the absence of a chromosome-level assembly, we analysed long and short-read genome sequencing data from males and females to identify two clusters of abundant and X-chromosome specific sequence repeats. When targeted by gRNAs in conjunction with Cas9 they yielded a significant and consistent distortion of the sex ratio in independent transgenic strains and a combination of distorters induced a strong bias towards males (~80%). Our results demonstrate the design of sex distorters in a non-model organism and suggest that strains with characteristics suitable for field application could be developed for a range of medically or agriculturally relevant insect species.
Impaired Fetal Lung Development can be Rescued by Administration of Extracellular Vesicles Derived from Amniotic Fluid Stem Cells
Authors: Antounians Lina , Catania Vincenzo D. , Montalva Louise , Liu Benjamin D. , Hou Huayun , Chan Cadia , Matei Andreea C. , Tzanetakis Areti , Li Bo , Figueira Rebeca Lopes , da Costa Karina Miura , Wong Amy P. , Mitchell Robert , David Anna L. , Patel Ketan , De Coppi Paolo , Neto Lourenço Sbragia , Wilson Michael D. , Rossant Janet , Zani Augusto
Published: August 2020

Incomplete lung development, also known as pulmonary hypoplasia, is a recognized cause of neonatal death and poor outcome for survivors. To date, there is no effective treatment that promotes fetal lung growth and maturation. Herein, we describe a novel stem cell-based approach that enhances fetal lung development via the administration of extracellular vesicles (EVs) derived from amniotic fluid stem cells (AFSCs). In experimental models of pulmonary hypoplasia, administration of AFSC-EVs promoted lung branching morphogenesis and alveolarization, and stimulated pulmonary epithelial cell and fibroblast differentiation. This regenerative ability was confirmed in two models of injured human lung cells, where human AFSC-EVs obtained following good manufacturing practices restored pulmonary epithelial homeostasis. AFSC-EV beneficial effects were exerted via the release of RNA cargo, primarily miRNAs, that regulate the expression of genes involved in fetal lung development. Our findings suggest that AFSC-EVs hold regenerative ability for underdeveloped fetal lungs, demonstrating potential for therapeutic application.

One Sentence Summary

Fetal lung regeneration via administration of extracellular vesicles derived from amniotic fluid stem cells
Extrasynaptic volume transmission: A novel route for neuropeptide signaling in nematodes
Authors: Atkinson Louise E. , Liu Yang , McKay Fiona , Vandewyer Elke , Viau Charles , Irvine Allister , Rosa Bruce A. , Li Zihui , Marks Nikki J. , Maule Aaron G. , Mitreva Makedonka , Beets Isabel , Li Lingjun , Mousley Angela
Published: August 2020

Neural circuit synaptic connectivities (the connectome) provide the anatomical foundation for our understanding of nematode nervous system function. However, other non-synaptic routes of communication are known in invertebrates including extrasynaptic volume transmission (EVT), which enables short- and/or long-range communication in the absence of synaptic connections. Although EVT has been highlighted as a facet ofCaenorhabditis elegansneurosignaling, no experimental evidence identifies body cavity fluid (pseudocoelomic fluid; PCF) as a vehicle for either neuropeptide or biogenic amine transmission. In the parasitic nematodeAscaris suumFMRFamide-like peptides encoded onflp-18 potently stimulate female reproductive organs but are only expressed in cells that are anatomically distant from the reproductive organ, with no known synaptic connections to this tissue. Here we report a new non-synaptic mode of signaling in nematodes mediated by neuropeptides within the PCF. Our data show that: (i)A. suumPCF (As-PCF) contains a catalogue of neuropeptides including FMRFamide-like peptides and neuropeptide-like proteins; (ii) theA. suumFMRFamide-like peptide As-FLP-18A dominates the As-PCF peptidome; (iii) As-PCF potently modulates nematode reproductive muscle functionex vivo, mirroring the effects of synthetic FLP-18 peptides; (iv) As-PCF activates theC. elegansFLP-18 receptors NPR-4 and -5; (v) As-PCF altersC. elegansbehavior and, (vi) FLP-18 and FLP-18 receptors display pan-phylum distribution in nematodes. Here we provide the first direct experimental evidence that supports an extrasynaptic volume route for neuropeptide transmission in nematodes. These data demonstrate non-synaptic signaling within the nematode functional connectome and are pertinent to receptor deorphanisation approaches underpinning drug discovery programs for nematode pathogens.
Sialylation and fucosylation changes of cytidine monophosphate-Nacetylneuraminic acid hydroxylase (CMAH) and glycoprotein, alpha1,3-galactosyltransferase(GGTA1) knockout pig erythrocyte membranes
Authors: Choe Hak Myong , Luo Zhao-Bo , Xuan Mei-Fu , Quan Biao-Hu , Kang Jin-Dan , Oh Myung Jin , An Hyun Joo , Yin Xi-jun
Published: August 2020

The recent GGTA1 and CMAH DKO pigs have made it possible to resolve the immune barriers which are duo to xenoantigens on RBC such as αGal and Neu5Gc. Nevertheless, it still requires the detection of glycosylation alternation on the pig RBCs because even the minor changes would be unexpected xenoantigens.

DKO RBC immune reactivity with human serum was assessed by hemagglutination assay. Glycosylation alteration of RBC membranes was characterized by NanoLC-Q-TOF-MS system and lectin blotting assay.

Twelve GGTA1/CMAH DKO piglets were successfully produced. The immunoreactivity with human serum was remarkably reduced in DKO (less than 1:2 dilution), whereas wild type(WT) pigs showed agglutination (the least 1:256 dilution). The MS results showed that DKO increased neutral N-glycans as well as decreased total sialylated N-glycans, especially suggesting significant decrease of di-sialylated N-glycans (P < 0.05). Moreover, lectin blotting assay revealed that DKO pigs reduced the binding signals with AAL, AOL, LCA and SNA and increased the binding signal with MAL.

DKO pigs decreased the expression of total fucosylation and sialylated N-glycans on the erythrocyte membrane. Our findings will support further investigation into DKO pig RBC glycosylation and contribute to uncover the roles of glycan changes for xenotransfusion.

Summary statement

To detect glycosylation changes in red blood cells(RBC) of GGTA1/CMAH double knockout(DKO) pigs, comparative analysis of the glycan profiling was done.