bluuebunny/crossref_metadata_2025 huggingface dataset:
A Critical Analysis of Prosthetic Augmentation of Autologous Microvascular Breast Reconstruction
Authors: Piper Merisa L. , Lentz Rachel , Gomez-Sanchez Clara , Withers Jacquelyn , Hu Allison , Sbitany Hani
Published: November 2019

Introduction

The combined approach using both an implant and autologous tissue for breast reconstruction has become more common over the last 10 years. We sought to provide a systematic review and outcomes analysis of this technique.

Methods

We searched PubMed and the Cochrane Library database to identify studies that described implant augmentation of autologous flaps for breast reconstruction. The references of selected articles were also reviewed to identify any additional pertinent articles.

Results

We identified 11 articles, which included 230 patients and 378 flaps. Implants used ranged in size from 90 to 510 cc, with an average size of 198 cc. Implants were more frequently placed at the time of autologous reconstruction and in the subpectoral plane. There were no total flap losses, and partial flap loss occurred in 3 patients (1%). There were no cases of venous or arterial thrombosis and no early return to the operating room for flap compromise. Eight implants (2%) were lost because of infection or extrusion, and capsular contracture occurred in 9 breasts (3%). When stratified by the timing of implant placement (immediate vs delayed), there were no significant differences in any postoperative outcomes except the immediate group had a higher infection rate.

Conclusions

The criteria for women to be candidates for autologous tissue breast reconstruction can be expanded by adding an implant underneath the flap. We found the overall flap loss rate is comparable with standard autologous flap reconstruction, and the implant loss rate is lower than that in patients who undergo prosthetic reconstruction alone.
Analgesic Use Following Bilateral Breast Reduction
Authors: Fisher Alec H. , Powelson Ian A. , Wampler Ariel T. , Doughty Hayden , Freed Gary L.
Published: November 2019

The opioid epidemic in the United States resulted in 42,000 deaths in 2016, 40% of which involved a prescription opioid. It is estimated that 2 million patients become opioid-dependent after elective, ambulatory surgery each year. There has been increased interest in quantifying the need for postoperative narcotic pain medications for a variety of surgical procedures. However, studies have been limited. We sought to quantify the analgesic usage after one of the most common operations performed in plastic surgery, bilateral breast reduction.

In this prospective, observational study, sequential breast reduction patients were contacted by telephone on the evening of postoperative days 3 and 7. Patients were queried as to which analgesic medications were used on the day of the phone call. Data relating to dosage, frequency, and satisfaction with pain control were sought. Patients taking chronic narcotics, postoperative complications requiring surgical intervention, and those unable to be reached after multiple attempts were excluded.

Complete data were obtained for 40 patients. Narcotic prescriptions were written for oxycodone, hydromorphone and tramadol, with the number prescribed ranging from 0 to 20 tablets. The median total number used was 6 tablets. Eighty percent of patients used a total of 10 tablets or less. Fifty percent of patients were using only nonnarcotic analgesia by postoperative day 3. Patient-reported satisfaction with pain control was overwhelmingly positive, with 95% being either somewhat satisfied or very satisfied with postoperative pain control. Of those taking any medication on postoperative day 3, only half were using a nonsteroidal anti-inflammatory drug (NSAID) as part of their pain regimen.

The number of tablets prescribed after breast reduction surgery varies considerably, and there is no consensus regarding the appropriate number to prescribe. Currently, few patients use all the medication prescribed to them, indicating a high rate of overprescribing. The overwhelming majority are satisfied with their pain control. Most patients use less than 10 tablets of narcotic pain medication after surgery. Acetaminophen is widely used as an adjunct but NSAIDs remain underutilized. Based on these data, we recommend that breast reduction patient's pain is best managed with acetaminophen, NSAIDs, and expectation management.
Surgery of Cerebral Cavernous Angiomas With Navigational Support
Authors: Gao Yang , Zheng Hui , Hao Bin , Chen Xin , Cao Yiqun
Published: November 2019

Objective:

Accurate localization and removal of deep-seated cavernomas through a less invasive approach is still a challenge. The aim of this study is to compare the efficacy of neuronavigation and ultrasound in guiding surgery for resection of deep-seated cavernomas by transsulcal microsurgical approach.

Methods:

A total of 38 consecutive patients who suffered from deep-seated cavernomas underwent surgery via a transsulcal microsurgical approach in our hospital between September 2016 and March 2018. Patients were randomly divided into 2 groups (20 cases in neuronavigation group and 18 cases in ultrasound group). The clinical features, character of images, and surgical outcome were analyzed.

Results:

There was no significant difference between the 2 groups in diameter (16.6 ± 2.7 mm versus 19.6 ± 2.0 mm, P > 0.05) and depth (19.2 ± 2.4 mm versus 22.0 ± 4.6 mm, P > 0.05) of lesions. The ultrasound group had a similar tumor resection rate (100% versus 80%, P = 0.11) and shorter operation time (119.7 ± 4.5 minutes versus 137.3 ± 4.9 minutes, P < 0.05) than that in the neuronavigation group. There was no significant difference between in the symptomatic improvement rate, complication, postoperative hospital stay, and period of follow-up (P > 0.05). No death and recurrence appeared in both groups.

Conclusion:

Ultrasound showed certain advantages than neuronavigation in guiding resection of deep-seated cavernomas by transsulcal microsurgical approach.
Optimal Pancreatic Surgery
Authors: Beane Joal D. , Borrebach Jeffrey D. , Zureikat Amer H. , Kilbane E. Molly , Thompson Vanessa M. , Pitt Henry A.
Published: November 2019

Objective:

Our aims were to assess North American trends in the management of patients undergoing pancreatoduodenectomy (PD) and distal pancreatectomy (DP), and to quantify the delivery of optimal pancreatic surgery.

Background:

Morbidity after pancreatectomy remains unacceptably high. Recent literature suggests that composite measures may more accurately define surgical quality.

Methods:

The 2013 to 2017 American College of Surgeons National Surgical Quality Improvement Program Participant Use Files were queried to identify patients undergoing PD (N = 16,222) and DP (N = 7946). Patient, process, procedure, and 30-day postoperative outcome variables were analyzed over time. Optimal pancreatic surgery was defined as the absence of postoperative mortality, serious morbidity, percutaneous drainage, and reoperation while achieving a length of stay equal to or less than the 75th percentile (12 days for PD and 7 days for DP) with no readmissions. Risk-adjusted time-trend analyses were performed using logistic regression, and the threshold for statistical significance was P ≤ 0.05.

Results:

The use of minimally invasive PD did not change over time, but robotic PD increased (2.5 to 4.2%; P < 0.001) and laparoscopic PD decreased (5.8% to 4.3%; P < 0.02). Operative times decreased (P < 0.05) and fewer transfusions were administered (P < 0.001). The percentage of patients with a drain fluid amylase checked on postoperative day 1 increased (P < 0.001), and a greater percentage of surgical drains were removed by postoperative day 3 (P < 0.001). Overall morbidity (P < 0.02), mortality (P < 0.05), and postoperative length of stay (P = 0.002) decreased. Finally, the rate of optimal pancreatic surgery increased for PD (53.7% to 56.9%; P < 0.01) and DP (53.3% to 58.5%; P < 0.001), and alspo for patients with pancreatic cancer (P < 0.01).

Conclusions:

From 2013 to 2017, pre, intra, and perioperative pancreatectomy processes have evolved, and multiple postoperative outcomes have improved. Thus, in 4 years, optimal pancreatic surgery in North America has increased by 3% to 5%.
Urinary Catheter Management Approaches Among Women Undergoing Benign Gynecologic Surgery: A Randomized Trial
Authors: Lang Patrick , Quezada Yarini , Whiteside James
Published: November 2019

Objective

The objective of this study was to identify differences in voiding trial success rates between delayed (postoperative day 1) and day of surgery catheter removal (“fast track”) among women undergoing benign gynecologic surgery. Rates of urinary tract infection, patient satisfaction, and lower urinary tract symptoms were compared between catheter management schemes.

Methods

Women undergoing benign gynecologic surgery were randomized to either “conventional” delayed urinary catheter care removal on postoperative day 1 or day of surgery catheter removal (fast track) 4 hours after surgery. Subjects were asked to complete a brief survey recording bladder function before and during their hospitalization and satisfaction with their catheter management. Subjects were contacted by phone 2 to 3 weeks after the index surgery to survey their bladder function including symptoms (eg, dysuria) or treatment indicative of a bladder infection.

Results

The median dwell time for Foley catheters in the “fast-track” group was 8.15 hours (SD = 375 minutes), whereas the median dwell time in the conventional group was 20.6 hours (SD = 265 minutes), which was significantly different (P < 0.001). Overall, 153 (93%) patients passed their voiding trial with significantly more patients passing their voiding trial in the conventional management group (P = 0.01). There was no difference in the Urogenital Distress Inventory scores at 2 weeks between catheter management cohorts (P = 0.81).

Conclusions

Foley dwell time is significantly reduced in the fast-track cohort. Voiding trial failure is higher with same-day catheter removal but that rate of failure rate is low. Patient satisfaction, the Urogenital Distress Inventory score, and postoperative urinary tract infection rates are not significantly different between cohorts.
Determining the clinical significance of the Chest Wall Injury Society taxonomy for multiple rib fractures
Authors: Clarke Peter T.M. , Simpson Rosalind B. , Dorman Jessica R. , Hunt William J. , Edwards John G.
Published: November 2019

BACKGROUND

The Chest Wall Injury Society (CWIS) proposals for standardized nomenclature for multiple rib fracture (MRF) classifications were derived by international expert Delphi consensus. This study aimed to validate the CWIS taxonomy using a single-instituion clinical database.

METHODS

Computed tomography (CT) scans, of 539 consecutive patients with MRFs admitted to a regional major trauma center over a 33-month period, were reviewed (blinded for clinical outcomes). Every rib fracture in every patient was assessed according to each of the CWIS criteria (the degree of displacement, characterization of the fracture line, location of each fracture, and the relationship to neighboring fractures). The clinical significance of the proposed CWIS definitions were determined from independently coded, routinely collected Hospital Episodes Statistics data.

RESULTS

The radiologic aspects of 3,944 individual rib fractures were assessed. Indicators of injury severity (severe displacement greater series length, and flail segment) were positively associated with other fractures (p < 0.001), hemopneumothorax (p < 0.001), pulmonary complications (p = 0.002), adverse outcomes (p = 0.006), mechanical ventilation (p < 0.001) and prolonged hospital and intensive therapy unit length of stay (p = 0.006, p = 0.007 respectively). Four of the CWIS-proposed definitions were correlated with pulmonary complications and adverse outcomes: the categories of displacement, the definition of individual fracture characterization, the presence of a flail segment. Two definitions for which there was CWIS consensus were not correlated with clinical outcomes: the definition of a series to describe associated fractures on neighboring ribs, the inclusion of a paravertebral sector for fracture localization.

CONCLUSION

The CWIS rib fracture taxonomy demonstrates clinical relevance. There were associations between the severity of category groups within three of the proposed definitions, based on the clinical outcomes observed. Clinical outcome assessment proved inconclusive for four agreed definitions. Comprehensive, multiinstitutional data collection would be required to provide validation for all the CWIS-proposed definitions.

LEVELS OF EVIDENCE

Level IV.
Pediatric Donor Glomerulopathy Is a Possible Cause of Abnormal Urinalysis in Adults Receiving Small Pediatric Donor Kidneys
Authors: Jiang Zeying , Liang Yuling , Zhong Tingting , Yang Shicong , Chen Yanyang , Huang Gang , Wang Changxi , Chen Wenfang
Published: November 2019

Background.

Reports about prognosis of adults receiving small pediatric-donor kidneys (PDK) as compared to those receiving elder pediatric or adult donor kidneys (ADKs) are controversial. This study aimed to examine the outcomes of adults receiving small PDK and possible prognostic factors.

Methods.

The records of adults who received kidneys from donors < 10 years old at our center from July 1, 2011 to June 30, 2018 were reviewed.

Results.

A total of 121 adults were small PDK recipients. Twenty-three patients received 29 biopsies or nephrectomy between 6 and 896 days posttransplantation days. Seven patients (30.4%) had pediatric donor glomerulopathy (PDG), which developed from 113 to 615 days posttransplantation. The incidence of proteinuria and hematuria was significantly higher in the PDG group. The characteristic pathological finding in PDG was irregular lamination and splintering of the glomerular basement membrane (GBM). Donor age, donor weight, and donor kidney volume were significantly less in PDG cases compared with the non-PDG cases. For the risk factors of PDG, increasing urinary RBC count during follow-up was an independent predictor, while increasing donor age and body weight were protective factors. PDG was not a significant risk factor for Scr increasing of PDKs.

Conclusions.

PDG is a potential cause of abnormal urinalysis in adults receiving small PDKs. The pathological characteristic change of PDG is splitting and lamination of GBM. Persistent hematuria after transplantation in recipients of PDK is a predictor of PDG development.
Calcium signaling in brain microvascular endothelial cells and its roles in the function of the blood–brain barrier
Authors: Ma Xingjie , Liu Weili
Published: November 2019

The blood–brain barrier (BBB) plays critical roles in maintaining the stability of the brain's internal milieu, providing nutrients for the brain, and preventing toxic materials from the blood from entering the brain. The cellular structure of the BBB is mainly composed of brain microvascular endothelial cells (BMVECs), which are surrounded by astrocytic endfeet that are connected by tight junction proteins, pericytes and astrocytes. Recently, several studies have shown that aberrant increase in intracellular calcium levels in BMVECs lead to cellular metabolic disturbances and subsequent impairment of BBB integrity. Although multiple stresses can lead to intracellular calcium accumulation, inherent protective mechanisms in affected cells are subsequently activated to maintain calcium homeostasis. However, once the increase in intracellular calcium goes beyond a certain threshold, disturbances in cellular structures, protein expression, and the BBB permeability are inevitable. Here, we review recent research on the different factors regulating intracellular calcium concentrations and the mechanisms related to how calcium signaling cascades protect the BMVECs from outside injury. We also consider the potential of calcium signaling regulators as therapeutic targets for modulating intracellular calcium homeostasis and ameliorating BBB disruption in patients with calcium-related pathologies.
A conservation palaeobiological perspective on Chesapeake Bay oysters
Authors: Lockwood Rowan , Mann Roger
Published: November 2019

The eastern oyster plays a vital role in estuarine habitats, acting as an ecosystem engineer and improving water quality. Populations of Chesapeake Bay oysters have declined precipitously in recent decades. The fossil record, which preserves 500 000 years of once-thriving reefs, provides a unique opportunity to study pristine reefs to establish a possible baseline for mitigation. For this study, over 900 fossil oysters were examined from three Pleistocene localities in the Chesapeake region. Data on oyster shell lengths, lifespans and population density were assessed. Comparisons to modern
Crassostrea virginica
, sampled from monitoring surveys of similar environments, reveal that fossil oysters were significantly larger, longer-lived and more abundant than modern oysters from polyhaline salinity zones. This pattern results from the preferential harvesting of larger, reproductively more active females from the modern population. These fossil data, combined with modern estimates of age-based fecundity and mortality, make it possible to estimate ecosystem services in these long-dead reefs, including filtering capacity, which was an order of magnitude greater in the past than today. Conservation palaeobiology can provide us with a picture of not just what the Chesapeake Bay looked like, but how it functioned, before humans.

This article is part of a discussion meeting issue ‘The past is a foreign country: how much can the fossil record actually inform conservation?’
Consequences of past climate change and recent human persecution on mitogenomic diversity in the arctic fox
Authors: Larsson Petter , von Seth Johanna , Hagen Ingerid J. , Götherström Anders , Androsov Semyon , Germonpré Mietje , Bergfeldt Nora , Fedorov Sergey , Eide Nina E. , Sokolova Natalia , Berteaux Dominique , Angerbjörn Anders , Flagstad Øystein , Plotnikov Valeri , Norén Karin , Díez-del-Molino David , Dussex Nicolas , Stanton David W. G. , Dalén Love
Published: November 2019

Ancient DNA provides a powerful means to investigate the timing, rate and extent of population declines caused by extrinsic factors, such as past climate change and human activities. One species probably affected by both these factors is the arctic fox, which had a large distribution during the last glaciation that subsequently contracted at the start of the Holocene. More recently, the arctic fox population in Scandinavia went through a demographic bottleneck owing to human persecution. To investigate the consequences of these processes, we generated mitogenome sequences from a temporal dataset comprising Pleistocene, historical and modern arctic fox samples. We found no evidence that Pleistocene populations in mid-latitude Europe or Russia contributed to the present-day gene pool of the Scandinavian population, suggesting that postglacial climate warming led to local population extinctions. Furthermore, during the twentieth-century bottleneck in Scandinavia, at least half of the mitogenome haplotypes were lost, consistent with a 20-fold reduction in female effective population size. In conclusion, these results suggest that the arctic fox in mainland Western Europe has lost genetic diversity as a result of both past climate change and human persecution. Consequently, it might be particularly vulnerable to the future challenges posed by climate change.

This article is part of a discussion meeting issue ‘The past is a foreign country: how much can the fossil record actually inform conservation?’
Shifted distribution baselines: neglecting long-term biodiversity records risks overlooking potentially suitable habitat for conservation management
Authors: Monsarrat Sophie , Novellie Peter , Rushworth Ian , Kerley Graham
Published: November 2019

Setting appropriate conservation measures to halt the loss of biodiversity requires a good understanding of species' habitat requirements and potential distribution. Recent (past few decades) ecological data are typically used to estimate and understand species’ ecological niches. However, historical local extinctions may have truncated species–environment relationships, resulting in a biased perception of species' habitat preferences. This may result in incorrect assessments of the area potentially available for their conservation. Incorporating long-term (centuries-old) occurrence records with recent records may provide better information on species–environment relationships and improve the modelling and understanding of habitat suitability. We test whether neglecting long-term occurrence records leads to an underestimation of species’ historical niche and potential distribution and identify which species are more vulnerable to this effect. We compare outputs of species distribution models and niche hypervolumes built using recent records only with those built using both recent and long-term (post-1500) records, for a set of 34 large mammal species in South Africa. We find that, while using recent records only is adequate for some species, adding historical records in the analyses impacts estimates of the niche and habitat suitability for 12 species (34%) in our dataset, and that this effect is significantly higher for carnivores. These results show that neglecting long-term biodiversity records in spatial analyses risks misunderstanding, and generally underestimating, species' niches, which in turn may lead to ill-informed management decisions, with significant implications for the effectiveness of conservation efforts.

This article is part of a discussion meeting issue ‘The past is a foreign country: how much can the fossil record actually inform conservation?’
Complementarity, completeness and quality of long-term faunal archives in an Asian biodiversity hotspot
Authors: Turvey Samuel T. , Walsh Connor , Hansford James P. , Crees Jennifer J. , Bielby Jon , Duncan Clare , Hu Kaijin , Hudson Michael A.
Published: November 2019

Long-term baselines on biodiversity change through time are crucial to inform conservation decision-making in biodiversity hotspots, but environmental archives remain unavailable for many regions. Extensive palaeontological, zooarchaeological and historical records and indigenous knowledge about past environmental conditions exist for China, a megadiverse country experiencing large-scale biodiversity loss, but their potential to understand past human-caused faunal turnover is not fully assessed. We investigate a series of complementary environmental archives to evaluate the quality of the Holocene–historical faunal record of Hainan Island, China's southernmost province, for establishing new baselines on postglacial mammalian diversity and extinction dynamics. Synthesis of multiple archives provides an integrated model of long-term biodiversity change, revealing that Hainan has experienced protracted and ongoing human-caused depletion of its mammal fauna from prehistory to the present, and that past baselines can inform practical conservation management. However, China's Holocene–historical archives exhibit substantial incompleteness and bias at regional and country-wide scales, with limited taxonomic representation especially for small-bodied species, and poor sampling of high-elevation landscapes facing current-day climate change risks. Establishing a clearer understanding of the quality of environmental archives in threatened ecoregions, and their ability to provide a meaningful understanding of the past, is needed to identify future conservation-relevant historical research priorities.

This article is part of a discussion meeting issue ‘The past is a foreign country: how much can the fossil record actually inform conservation?’
Differing climatic mechanisms control transient and accumulated vegetation novelty in Europe and eastern North America
Authors: Burke Kevin D. , Williams John W. , Brewer Simon , Finsinger Walter , Giesecke Thomas , Lorenz David J. , Ordonez Alejandro
Published: November 2019

Understanding the mechanisms of climate that produce novel ecosystems is of joint interest to conservation biologists and palaeoecologists. Here, we define and differentiate transient from accumulated novelty and evaluate four climatic mechanisms proposed to cause species to reshuffle into novel assemblages: high climatic novelty, high spatial rates of change (displacement), high variance among displacement rates for individual climate variables, and divergence among displacement vector bearings. We use climate simulations to quantify climate novelty, displacement and divergence across Europe and eastern North America from the last glacial maximum to the present, and fossil pollen records to quantify vegetation novelty. Transient climate novelty is consistently the strongest predictor of transient vegetation novelty, while displacement rates (mean and variance) are equally important in Europe. However, transient vegetation novelty is lower in Europe and its relationship to climatic predictors is the opposite of expectation. For both continents, accumulated novelty is greater than transient novelty, and climate novelty is the strongest predictor of accumulated ecological novelty. These results suggest that controls on novel ecosystems vary with timescale and among continents, and that the twenty-first century emergence of novelty will be driven by both rapid rates of climate change and the emergence of novel climate states.

This article is part of a discussion meeting issue ‘The past is a foreign country: how much can the fossil record actually inform conservation?’
Anthropocene refugia: integrating history and predictive modelling to assess the space available for biodiversity in a human-dominated world
Authors: Monsarrat Sophie , Jarvie Scott , Svenning Jens-Christian
Published: November 2019

During periods of strong environmental change, some areas may serve as refugia, where components of biodiversity can find protection, persist and potentially expand from should conditions again become favourable. The refugia concept has previously been used in the context of climatic change, to describe climatically stable areas in which taxa survived past Quaternary glacial–interglacial oscillations, or where they might persist in the future under anthropogenic climate change. However, with the recognition that Earth has entered the Anthropocene, an era in which human activities are the dominant driving force on ecosystems, it is critical to also consider human pressures on the environment as factors limiting species distributions. Here, we present a novel concept, Anthropocene refugia, to refer to areas that provide spatial and temporal protection from human activities and that will remain suitable for a given taxonomic unit in the long-term. It integrates a deep-time perspective on species biogeography that provides information on the natural rather than current-day relictual distribution of species, with spatial information on modern and future anthropogenic threats. We define the concept and propose a methodology to effectively identify and map realized and potential current and future refugia, using examples for two megafaunal species as a proof of concept. We argue that identifying Anthropocene refugia will improve biodiversity conservation and restoration by allowing better prediction of key areas for conservation and potential for re-expansions today and in the future. More generally, it forms a new conceptual framework to assess and manage the impact of anthropogenic activities on past, current and future patterns of species distributions.

This article is part of a discussion meeting issue ‘The past is a foreign country: how much can the fossil record actually inform conservation?’
The Burramys Project: a conservationist's reach should exceed history's grasp, or what is the fossil record for?
Authors: Archer Michael , Bates Hayley , Hand Suzanne J. , Evans Trevor , Broome Linda , McAllan Bronwyn , Geiser Fritz , Jackson Stephen , Myers Troy , Gillespie Anna , Palmer Chris , Hawke Tahneal , Horn Alexis M.
Published: November 2019

The fossil record provides important information about changes in species diversity, distribution, habitat and abundance through time. As we understand more about these changes, it becomes possible to envisage a wider range of options for translocations in a world where sustainability of habitats is under increasing threat. The Critically Endangered alpine/subalpine mountain pygmy-possum,Burramys parvus(Marsupialia, Burramyidae), is threatened by global heating. Using conventional strategies, there would be no viable pathway for stopping this iconic marsupial from becoming extinct. The fossil record, however, has inspired an innovative strategy for saving this species. This lineage has been represented over 25 Myr by a series of species always inhabiting lowland, wet forest palaeocommunities. These fossil deposits have been found in what is now the Tirari Desert, South Australia (24 Ma), savannah woodlands of the Riversleigh World Heritage Area, Queensland (approx. 24–15 Ma) and savannah grasslands of Hamilton, Victoria (approx. 4 Ma). This palaeoecological record has led to the proposal overviewed here to construct a lowland breeding facility with the goal of monitoring the outcome of introducing this possum back into the pre-Quaternary core habitat for the lineage. If this project succeeds, similar approaches could be considered for other climate-change-threatened Australian species such as the southern corroboree frog (Pseudophryne corroboree) and the western swamp tortoise (Pseudemydura umbrina).

This article is part of a discussion meeting issue ‘The past is a foreign country: how much can the fossil record actually inform conservation?’
Addressing priority questions of conservation science with palaeontological data
Authors: Kiessling Wolfgang , Raja Nussaïbah B. , Roden Vanessa Julie , Turvey Samuel T. , Saupe Erin E.
Published: November 2019

Palaeontologists often ask identical questions to those asked by ecologists. Despite this, ecology is considered a core discipline of conservation biology, while palaeontologists are rarely consulted in the protection of species, habitats and ecosystems. The recent emergence of conservation palaeobiology presents a big step towards better integration of palaeontology in conservation science, although its focus on historical baselines may not fully capture the potential contributions of geohistorical data to conservation science. In this essay we address previously defined priority questions in conservation and consider which of these questions may be answerable using palaeontological data. Using a statistical assessment of surveys, we find that conservation biologists and younger scientists have a more optimistic view of potential palaeontological contributions to the field compared to experienced palaeontologists. Participants considered questions related to climate change and marine ecosystems to be the best addressable with palaeontological data. As these categories are also deemed most relevant by ecologists and receive the greatest research effort in conservation, they are the natural choice for future academic collaboration.

This article is part of a discussion meeting issue ‘The past is a foreign country: how much can the fossil record actually inform conservation?’
Using historical and palaeoecological data to inform ambitious species recovery targets
Authors: Grace Molly , Akçakaya H. Resit , Bennett Elizabeth , Hilton-Taylor Craig , Long Barney , Milner-Gulland E. J. , Young Richard , Hoffmann Michael
Published: November 2019

Historical data are a valuable resource for addressing present-day conservation issues, for example by informing the establishment of appropriate recovery targets. However, while the recovery of threatened species is the end goal of many conservation programmes, data made available through the efforts of palaeoecologists and historical ecologists are rarely consulted. The proposal of a ‘Green List of Species’ by the International Union for Conservation of Nature (IUCN) will soon change this. The Green List of Species measures recovery against historical baselines; in particular, the method requires estimates of species range and abundance in previous centuries. In this paper, we present the case for why setting species recovery against a historical baseline is necessary to produce ambitious conservation targets, and we highlight examples from palaeoecology and historical ecology where fossil and archival data have been used to establish historical species baselines. Finally, we introduce Conservation Archive (https://conservationarchive.shinyapps.io/ConservationArchive/), a database of resources that can be used to infer baseline species conditions, and invite contributions to this database.

This article is part of a discussion meeting issue ‘The past is a foreign country: how much can the fossil record actually inform conservation?’
Genotypic diversity, circulation patterns and co-detections among rhinoviruses in Queensland, 2001
Authors: Arden Katherine E. , Greer Ristan M. , Wang Claire Y.T. , Mackay Ian M.
Published: November 2019

Purpose. Rhinoviruses (RVs) occur more frequently than other viruses and more often in people displaying symptoms than in those without. We sought to estimate the spectrum of RV diversity, RV species seasonality and to analyse RV involvement in respiratory virus co-detections.

Methodology. A convenience collection of 1179 airway sample extracts from patients with suspected respiratory infections, collected during 2001, was subjected to comprehensive molecular testing.

Results. RVs were the most common virus detected. We were able to genotype ~90 % of RV detections, identifying 70 distinct RVs, spanning all three species. RV-Bs were under-represented. We found RV species co-circulated at times, although one species usually dominated. Each species displayed a bimodal distribution.

Conclusion. Notably, RVs and influenza A viruses (IFAV) seldom co-occurred, supporting their roles as primary pathogens of the airway among acutely ill infants. Whether RV circulation has a moderating or controlling effect on the IFAV season or is controlled by it cannot be determined from these data. Despite the frequent perception that RVs commonly co-occur with another virus, our findings indicated this was not always the case. Nearly 80 % of RV detections occurred alone. Understanding more about population-level interference between viruses may allow us to harness aspects of it to generate a non-specific antiviral intervention that mimics a putative protective effect. For routine respiratory virus screening to best serve the patient, RV testing should be a principal component of any acute respiratory illness testing algorithm throughout the year.
Dengue virus capsid anchor modulates the efficiency of polyprotein processing and assembly of viral particles
Authors: Rana Jyoti , Slon Campos José Luis , Poggianella Monica , Burrone Oscar R.
Published: November 2019

The assembly and secretion of flaviviruses are part of an elegantly regulated process. During maturation, the viral polyprotein undergoes several co- and post-translational cleavages mediated by both viral and host proteases. Among these, sequential cleavage at the N and C termini of the hydrophobic capsid anchor (Ca) is crucial in deciding the fate of viral infection. Here, using a refined dengue pseudovirus production system, along with cleavage and furin inhibition assays, immunoblotting and secondary structure prediction analysis, we show that Ca plays a key role in the processing efficiency of dengue virus type 2 (DENV2) structural proteins and viral particle assembly. Replacement of the DENV2 Ca with the homologous regions from West nile or Zika viruses or, alternatively, increasing its length, improved cleavage and hence particle assembly. Further, we showed that substitution of the Ca conserved proline residue (P110) to alanine abolishes pseudovirus production, regardless of the Ca sequence length. Besides providing the results of a biochemical analysis of DENV2 structural polyprotein processing, this study also presents a system for efficient production of dengue pseudoviruses.
Opening the Black Box of Artificial Intelligence for Clinical Decision Support: A Study Predicting Stroke Outcome
Authors: Zihni Esra , Madai Vince Istvan , Livne Michelle , Galinovic Ivana , Khalil Ahmed A. , Fiebach Jochen B. , Frey Dietmar
Published: November 2019

Background

State-of-the-art machine learning (ML) artificial intelligence methods are increasingly leveraged in clinical predictive modeling to provide clinical decision support systems to physicians. Modern ML approaches such as artificial neural networks (ANNs) and tree boosting often perform better than more traditional methods like logistic regression. On the other hand, these modern methods yield a limited understanding of the resulting predictions. However, in the medical domain, understanding of applied models is essential, in particular, when informing clinical decision support. Thus, in recent years, interpretability methods for modern ML methods have emerged to potentially allow explainable predictions paired with high performance.

Methods

To our knowledge, we present in this work the first explainability comparison of two modern ML methods, tree boosting and multilayer perceptrons (MLPs), to traditional logistic regression methods using a stroke outcome prediction paradigm. Here, we used clinical features to predict a dichotomized 90 days post-stroke modified Rankin Scale (mRS) score. For interpretability, we evaluated clinical features’ importance with regard to predictions using deep Taylor decomposition for MLP, Shapley values for tree boosting and model coefficients for logistic regression.

Results

With regard to performance as measured by AUC values on the test dataset, all models performed comparably: Logistic regression AUCs were 0.82, 0.82, 0.79 for three different regularization schemes; tree boosting AUC was 0.81; MLP AUC was 0.81. Importantly, the interpretability analysis demonstrated consistent results across models by rating age and stroke severity consecutively amongst the most important predictive features. For less important features, some differences were observed between the methods.

Conclusions

Our analysis suggests that modern machine learning methods can provide explainability which is compatible with domain knowledge interpretation and traditional method rankings. Future work should focus on replication of these findings in other datasets and further testing of different explainability methods.
Mating enhances immune function of Drosophila melanogaster populations against bacterial pathogens
Authors: Bansal Nitin , Shit Biswajit , Aparajita  , Hegde Tejashwini , Dutta Rochishnu , Prasad Nagaraj Guru
Published: November 2019

Immunity and reproduction are two important processes that affect fitness of an organisms. Sexual activity has been previously shown to determine the degree to which a population is able to survive various infections. While many studies have demonstrated a trade-off between immune function and reproduction, many studies have found synergistic relation between the two fitness determinants. Besides it is generally hypothesised that sexes may differ in immunity due to relative cost they incur during reproduction with males losing in immunity to rather increase their reproductive success. In this study, we test the effect of immune function on the survival of mated and virgin replicates of a large outbred baseline D. melanogaster population that was infected with four different bacterial infections. We find enhanced survival in mated flies than virgin flies in response to all four bacterial infections across all replicates. While investigating sexual dimorphism in immune function, we find no difference in sexes in their ability to survive the imposed bacterial infections. Synergistic interaction between reproduction and immunity may exist if it improves Darwinian fitness of either sexes of a population under selection, and are not necessarily limited by each other due to trade-off over finite resources.
Afrotropical Tree Communities May Have Distinct Responses to Forecasted Climate Change
Authors: Nuñez Chase L. , Clark James S. , Poulsen John R.
Published: November 2019

More refined knowledge of how tropical forests respond to changes in the abiotic environment and human disturbance is necessary to mitigating climate change, maintain biodiversity, and preserve ecosystem services. To evaluate the unique response of Afrotropical forests to changes in the abiotic environment and disturbance, we employ species inventories, remotely sensed historic climatic data, and future climate predictions collected from 104 1-ha plots in the central African country of Gabon. We forecast a 3 - 8% decrease in Afrotropical forest species richness by the end of the century, in contrast to the 30-50% loss of plant diversity predicted to occur with equivalent warming in the Neotropics. This work reveals that community forecasts are not generalizable across regions, and more representative studies are needed in understudied biomes like the Afrotropics. This study serves as an important counterpoint to work done in the Neotropics by providing contrasting predictions for Afrotropical forests with substantially different ecological, evolutionary, and anthropogenic histories.
Close relationship between coral-associated Chromera strains despite major differences within the Symbiodiniaceae
Authors: Mohamed Amin R. , Chan Cheong Xin , Ragan Mark A. , Zhang Jia , Cooke Ira , Ball Eldon E. , Miller David J.
Published: November 2019

Reef-building corals live in a mutualistic relationship with photosynthetic algae (family Symbiodiniaceae) that usually provide most of the energy required by the coral host. This relationship is sensitive to temperature stress; as little as a 1°C increase often leading to collapse of the association. This sensitivity has led to interest in the potential of more stress tolerant algae to supplement or substitute for the normal Symbiodiniaceae mutualists. In this respect, the apicomplexan-like microalga Chromera is of particular interest due to its greater temperature tolerance. We generated a de novo transcriptome for a Chromera strain isolated from a GBR coral (“GBR Chromera”) and compared to those of the reference strain of Chromera (“Sydney Chromera”), and to those of Symbiodiniaceae (Fugacium, Cladocopium and Breviolum), as well as the apicomplexan parasite, Plasmodium falciparum. By contrast with the Symbiodiniaceae, the two Chromera strains had a high level of sequence similarity evident by very low levels of divergence in orthologous genes. Although KEGG categories provide few criteria by which true coral mutualists might be identified, they do supply a molecular rationalization for the ubiquitous association of Cladocopium strains with Indo-Pacific reef corals. The presence of HSP20 genes may underlie the higher thermal tolerance of Chromera.
High complexity and degree of genetic variation inBrettanomyces bruxellensispopulation
Authors: Gounot Jean-Sébastien , Neuvéglise Cécile , Freel Kelle C. , Devillers Hugo , Piškur Jure , Friedrich Anne , Schacherer Joseph
Published: November 2019

Genome-wide characterization of genetic variants of a large population of individuals within the same species is essential to have a deeper insight into its evolutionary history as well as the genotype-phenotype relationship. Population genomic surveys have been performed in multiple yeast species, including the two model organisms,Saccharomyces cerevisiaeandSchizosaccharomyces pombe. In this context, we sought to explore an uncharacterized yeast species,Brettanomyces bruxellensis, which is a major cause of wine spoilage but also can contribute to the specific flavor profile of some Belgium beers. We have completely sequenced the genome of 53B. bruxellensisstrains isolated worldwide. The annotation of the reference genome allowed us to define the gene content of this species. As previously suggested, our genomic data clearly highlighted that genetic diversity variation is related to ploidy level, which is variable in theB. bruxellensisspecies. Genomes are punctuated by multiple loss-of-heterozygosity regions while aneuploidies as well as segmental duplications are uncommon. Interestingly, triploid genomes are more prone to gene copy number variation than diploids. Finally, the pangenome of the species was reconstructed and was found to be small with few accessory genes compared toS. cerevisiae. The pangenome is composed of 4,923 core ORFs and 303 ORFs that are variable within the population. All these results highlight the different trajectories of species evolution and consequently the interest of establishing population genomic surveys in more populations.
Neuro-computational account of arbitration between imitation and emulation during human observational learning
Authors: Charpentier Caroline C. , Iigaya Kiyohito , O’Doherty John P.
Published: November 2019

In observational learning (OL), organisms learn from observing the behavior of others. There are at least two distinct strategies for OL. Imitation involves learning to repeat the previous actions of other agents, while in emulation, learning proceeds from inferring the goals and intentions of others. While putative neural correlates for these forms of learning have been identified, a fundamental question remains unaddressed: how does the brain decides which strategy to use in a given situation? Here we developed a novel computational model in which arbitration between the strategies is determined by the predictive reliability, such that control over behavior is adaptively weighted toward the strategy with the most reliable prediction. To test the theory, we designed a novel behavioral task in which our experimental manipulations produced dissociable effects on the reliability of the two strategies. Participants performed this task while undergoing fMRI in two independent studies (the second a pre-registered replication of the first). Behavior manifested patterns consistent with both emulation and imitation and flexibly changed between the two strategies as expected from the theory. Computational modelling revealed that behavior was best described by an arbitration model, in which the reliability of the emulation strategy determined the relative weights allocated to behavior for each strategy. Emulation reliability - the model’s arbitration signal - was encoded in the ventrolateral prefrontal cortex, temporoparietal junction and rostral cingulate cortex. Being replicated across two fMRI studies, these findings suggest a neuro-computational mechanism for allocating control between emulation and imitation during observational learning.