Niche-dependent forest and savanna fragmentation in Tropical South America during the Last Glacial Maximum

The refugia hypothesis, often used to explain Amazonia's high biodiversity, initially received ample support but has garnered increasing criticism over time. Palynological, phylogenetic, and vegetation model reconstruction studies have been invoked to support the opposing arguments of extensive fragmentation versus a stable Amazonian Forest during Pleistocene glacial maxima. Here, we test the past existence of forest fragments and savanna connectivity by bias-correcting vegetation distributions from a Dynamic Vegetation Model (DVM) driven by paleoclimate simulations for South America during the Last Glacial Maximum (LGM). We find evidence for fragmented forests akin to refugia with extensive tropical humid forests to the west and forest islands in central/southern Amazonia. Drier ecosystems of Northern Llanos, Caatinga and Cerrado may have merged into continuous savanna/grasslands that dominated the continent. However, our reconstructions suggest taller, dense woodland/tropical savanna vegetation and areas of similar bioclimate connected disparate forest fragments across Amazonia. This ecotonal biome may have acted as a corridor for generalist forest and savanna species, creating connectivity that allows for range expansion during glacial periods. Simultaneously, it could have served as a barrier for specialists, inducing diversification through the formation of 'semi-refugia'.

The Complete Genome Sequence of Chlorophonia sclateri (Fringillidae, Passeriformes), the Puerto Rican Euphonia

The Puerto Rican Euphonia (Chlorophonia sclateri) was recognized as an endemic species in 2023 based solely on morphological differences. A brightly plumaged finch that inhabits a variety of habitats, including lowland dry, scrub forests and shade-coffee plantations (Carlo et. al 2004). To provide molecular evidence for the genetic comparison of Antillean Euphonias, we present the whole genome sequence of Chlorophonia sclateri. Illumina paired-end reads were assembled by a de novo method followed by a finishing step. The raw and assembled data are publicly available via GenBank: Sequence Read Archive (SRR28963854) and assembled genome (JBFPDU000000000).

A pilot feasibility study comparing large language models in extracting key information from ICU patient text records from an Irish population

BACKGROUND

Artificial intelligence, through improved data management and automated summarisation, has the potential to enhance intensive care unit (ICU) care. Large language models (LLMs) can interrogate and summarise large volumes of medical notes to create succinct discharge summaries. In this study, we aim to investigate the potential of LLMs to accurately and concisely synthesise ICU discharge summaries.

METHODS

Anonymised clinical notes from ICU admissions were used to train and validate a prompting structure in three separate LLMs (ChatGPT, GPT-4 API and Llama 2) to generate concise clinical summaries. Summaries were adjudicated by staff intensivists on ability to identify and appropriately order a pre-defined list of important clinical events as well as readability, organisation, succinctness, and overall rank.

RESULTS

In the development phase, text from five ICU episodes was used to develop a series of prompts to best capture clinical summaries. In the testing phase, a summary produced by each LLM from an additional six ICU episodes was utilised for evaluation. Overall ability to identify a pre-defined list of important clinical events in the summary was 41.5 ± 15.2% for GPT-4 API, 19.2 ± 20.9% for ChatGPT and 16.5 ± 14.1% for Llama2 (p = 0.002). GPT-4 API followed by ChatGPT had the highest score to appropriately order a pre-defined list of important clinical events in the summary as well as readability, organisation, succinctness, and overall rank, whilst Llama2 scored lowest for all. GPT-4 API produced minor hallucinations, which were not present in the other models.

CONCLUSION

Differences exist in large language model performance in readability, organisation, succinctness, and sequencing of clinical events compared to others. All encountered issues with narrative coherence and omitted key clinical data and only moderately captured all clinically meaningful data in the correct order. However, these technologies suggest future potential for creating succinct discharge summaries.

Major trauma patients and their outcomes - A retrospective observational study of critical care trauma admissions to a trauma unit with special services

INTRODUCTION

International data describes a changing pattern to trauma over the last decade, with an increasingly comorbid population presenting challenges to trauma management and resources. In Ireland, resource provision and management of trauma is being transformed to deliver a trauma network, in line with international best practice. Our hospital plays a crucial role within this network and is designated a Trauma Unit with Specialist Services (TUSS) to distinguish it from standard trauma units.

METHODS

This study aims to describe the characteristics of patients and injuries and assess trends in mortality rates. It is a retrospective observational study of adult ICU trauma admissions from August 2010 to July 2021. Primary outcome was all-cause mortality at 30-days, 90-days, and 1 year. Secondary outcomes included length of stay, disposition, and complications. Patients were categorised by age, injury severity score (ISS), and mechanism of injury.

RESULTS

In all, 709 patients were identified for final analysis. Annual admissions doubled since 2010/11, with a trough of 41 admissions, increasing to peak at 95 admissions in 2017/18. Blunt trauma accounted for 97.6% of cases. Falls <2 m (45.4%) and RTAs (29.2%) were the main mechanisms of injury. Polytrauma comprised 41.9% of admissions. Traumatic brain injury accounted for 30.2% of cases; 18.8% of these patients were transferred to a neurosurgical centre. The majority of patients, 58.1%, were severely injured (ISS ≥ 16). Patients ≥ 65 years of age accounted for 45.7% of admissions, with falls <2 m their primary mechanism of injury. The primary outcome of all-cause mortality reduced with an absolute risk reduction (ARR) of 8.0% (95% CI: -8.37%, 24.36%), 12.9% (95% CI: -4.19%, 29.94%) and 8.2% (95% CI: -9.64%, 26.09%) for 30-day, 90-day and 1-year respectively. Regression analysis demonstrated a significant reduction in mortality for 30-days and 90-days post presentation to hospital (P-values of 0.018, 0.033 and 0.152 for 30-day, 90-day and 1-year respectively).

CONCLUSION

The burden of major trauma in our hospital is considerable and increasing over time. Substantial changes in demographics, injury mechanism and mortality were seen, with outcomes improving over time. This is consistent with international data where trauma systems have been adopted.

Unsupervised representation learning on high-dimensional clinical data improves genomic discovery and prediction

Although high-dimensional clinical data (HDCD) are increasingly available in biobank-scale datasets, their use for genetic discovery remains challenging. Here we introduce an unsupervised deep learning model, Representation Learning for Genetic Discovery on Low-Dimensional Embeddings (REGLE), for discovering associations between genetic variants and HDCD. REGLE leverages variational autoencoders to compute nonlinear disentangled embeddings of HDCD, which become the inputs to genome-wide association studies (GWAS). REGLE can uncover features not captured by existing expert-defined features and enables the creation of accurate disease-specific polygenic risk scores (PRSs) in datasets with very few labeled data. We apply REGLE to perform GWAS on respiratory and circulatory HDCD-spirograms measuring lung function and photoplethysmograms measuring blood volume changes. REGLE replicates known loci while identifying others not previously detected. REGLE are predictive of overall survival, and PRSs constructed from REGLE loci improve disease prediction across multiple biobanks. Overall, REGLE contain clinically relevant information beyond that captured by existing expert-defined features, leading to improved genetic discovery and disease prediction.

The Complete Genome Sequences of 37 Bird Species from the Ecuadorian Andes

We present the complete genome sequences of 37 Ecuadorian bird species widespread throughout the tropical Andes.

The Complete Genome Sequences of 23 Finch Species (Fringillidae, Passeriformes)

We present complete genome sequences of 23 species of finches from 6 genera.

Marine sulfated glycans inhibit the interaction of heparin with S-protein of SARS-CoV-2 Omicron XBB variant

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a worldwide COVID-19 pandemic, leading to 6.8 million deaths. Numerous variants have emerged since its outbreak, resulting in its significantly enhanced ability to spread among humans. As with many other viruses, SARS‑CoV‑2 utilizes heparan sulfate (HS) glycosaminoglycan (GAG) on the surface of host cells to facilitate viral attachment and initiate cellular entry through the ACE2 receptor. Therefore, interfering with virion-HS interactions represents a promising target to develop broad-spectrum antiviral therapeutics. Sulfated glycans derived from marine organisms have been proven to be exceptional reservoirs of naturally existing HS mimetics, which exhibit remarkable therapeutic properties encompassing antiviral/microbial, antitumor, anticoagulant, and anti-inflammatory activities. In the current study, the interactions between the receptor-binding domain (RBD) of S-protein of SARS-CoV-2 (both WT and XBB.1.5 variants) and heparin were applied to assess the inhibitory activity of 10 marine-sourced glycans including three sulfated fucans, three fucosylated chondroitin sulfates and two fucoidans derived from sea cucumbers, sea urchin and seaweed Saccharina japonica, respectively. The inhibitory activity of these marine derived sulfated glycans on the interactions between RBD of S-protein and heparin was evaluated using Surface Plasmon Resonance (SPR). The RBDs of S-proteins from both Omicrion XBB.1.5 and wild-type (WT) were found to bind to heparin, which is a highly sulfated form of HS. All the tested marine-sourced sulfated glycans exhibited strong inhibition of WT and XBB.1.5 S-protein binding to heparin. We believe the study on the molecular interactions between S-proteins and host cell glycosaminoglycans provides valuable insight for the development of marine-sourced, glycan-based inhibitors as potential anti-SARS-CoV-2 agents.

Whole genome sequencing reveals stepping-stone dispersal buffered against founder effects in a range expanding seabird

Many species are shifting their ranges in response to climate-driven environmental changes, particularly in high-latitude regions. However, the patterns of dispersal and colonization during range shifting events are not always clear. Understanding how populations are connected through space and time can reveal how species navigate a changing environment. Here, we present a fine-scale population genomics study of gentoo penguins (Pygoscelis papua), a presumed site-faithful colonial nesting species that has increased in population size and expanded its range south along the Western Antarctic Peninsula. Using whole genome sequencing, we analysed 129 gentoo penguin individuals across 12 colonies located at or near the southern range edge. Through a detailed examination of fine-scale population structure, admixture, and population divergence, we inferred that gentoo penguins historically dispersed rapidly in a stepping-stone pattern from the South Shetland Islands leading to the colonization of Anvers Island, and then the adjacent mainland Western Antarctica Peninsula. Recent southward expansion along the Western Antarctic Peninsula also followed a stepping-stone dispersal pattern coupled with limited post-divergence gene flow from colonies on Anvers Island. Genetic diversity appeared to be maintained across colonies during the historical dispersal process, and range-edge populations are still growing. This suggests large numbers of migrants may provide a buffer against founder effects at the beginning of colonization events to maintain genetic diversity similar to that of the source populations before migration ceases post-divergence. These results coupled with a continued increase in effective population size since approximately 500-800 years ago distinguish gentoo penguins as a robust species that is highly adaptable and resilient to changing climate.

Frontal sinus stenting in endoscopic sinus surgery: the 10-year Oxford experience

BACKGROUND

Frontal sinus stents have been introduced to reduce frontal sinus re-stenosis after surgery and to improve outcomes.

METHOD

This study was a retrospective analysis of 19 patients who had endoscopic sinus surgery with approach to the frontal sinus and insertion of a soft sinus stent.

RESULTS

The frontal recess was patent in 78.9 per cent and stenosed in 21.1 per cent of patients; no completely closed recesses were observed. Mean follow up was 20.7 months, and time period of stenting was 9.8 months on average; complications were observed in 47.4 per cent of the patients, with post-operative sinonasal infection being the most common.

CONCLUSION

In the authors' experience, indications for frontal sinus stenting include recalcitrant chronic rhinosinusitis after multiple functional endoscopic sinus surgeries (especially in chronic rhinosinusitis with nasal polyps), patients with history of important craniofacial surgery or trauma, and recurrent mucoceles. The stent was overall well tolerated as only minor complications were observed. Close clinical follow up is mandatory.

Specimen collection is essential for modern science

Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection.

Hearing Outcomes in Cisplatin or Cetuximab Combined with Radiation for Patients with HPV-Associated Oropharyngeal Cancer in NRG/RTOG 1016

PURPOSE/OBJECTIVE(S)

NRG/RTOG 1016 was a noninferiority phase 3 trial comparing the efficacy of radiation with either cisplatin (RT+Cisp) or cetuximab (RT+Cetux) for patients with HPV+ oropharyngeal cancer (OPC). Perceived hearing handicap was included as a patient-reported outcome (PRO) secondary endpoint. The primary hypothesis was that perceived hearing handicap would be greater for patients receiving RT+Cisp compared to RT+Cetux.

MATERIALS/METHODS

Perceived hearing handicap was measured at baseline, end of treatment, 3, 6, and 12-months post-treatment using the Hearing Handicap Inventory for Adults Screening Version (HHIA-S), a 10-item self-assessment questionnaire designed to measure patients' reactions to their hearing loss. Total HHIA-S scores range from 0 to 40; higher total score indicates more severe perceived hearing handicap. Hearing handicap categories (none, mild/moderate, and severe) were also analyzed. Mixed ordinal logistic models were used to analyze the raw HHIA-S scores and handicap categories (2-sided alpha 0.05).

RESULTS

Participation in the PRO assessments was optional, with 368 patients participating in the hearing PRO. No significant differences in patient/tumor characteristics were found between PRO participants/non-participants. Pre-treatment (mean [SD]) HHIA-S scores were not different for RT+Cisp (3.23 [6.28]) and RT+Cetux (4.77 [8.14]) groups. Post-treatment HHIA-S scores increased for RT+Cisp, and remained stable at the later follow-up time points. RT+Cetux scores remained stable from baseline. Change score from pre- to post-treatment was higher for RT+Cisp (4.32, 95% CI = [2.57, 6.07]) than RT+Cetux (0.08, 95% CI = [-1.15, 1.31]; p < 0.001). For hearing handicap category, post-treatment RT+Cisp had a significantly higher percentage of mild/moderate and severe cases (32%) compared to RT+Cetux (20%). From pre- to post-treatment, worsening of hearing handicap category from normal to mild/moderate or severe was greater for RT+Cisp (24%) than for RT+Cetux (9%). The conditional odds of being in a higher self-perceived hearing handicap category in the RT+Cisp arm were 3.57 (95% CI [2.04, 6.25]) times that in the RT+Cetux arm. Averaging over patients, the marginal odds ratio was 2.46 (95% CI [1.65, 3.66]).

CONCLUSION

Patients receiving concurrent RT+Cisp for HPV-associated OPC have significantly higher odds of worsening self-perceived hearing handicap after treatment than with RT+Cetux. This was consistent across time through one-year post-treatment. These findings inform hearing-related outcomes for patients with HPV-associated OPC.

Unsupervised representation learning improves genomic discovery and risk prediction for respiratory and circulatory functions and diseases

High-dimensional clinical data are becoming more accessible in biobank-scale datasets. However, effectively utilizing high-dimensional clinical data for genetic discovery remains challenging. Here we introduce a general deep learning-based framework, REpresentation learning for Genetic discovery on Low-dimensional Embeddings (REGLE), for discovering associations between genetic variants and high-dimensional clinical data. REGLE uses convolutional variational autoencoders to compute a non-linear, low-dimensional, disentangled embedding of the data with highly heritable individual components. REGLE can incorporate expert-defined or clinical features and provides a framework to create accurate disease-specific polygenic risk scores (PRS) in datasets which have minimal expert phenotyping. We apply REGLE to both respiratory and circulatory systems: spirograms which measure lung function and photoplethysmograms (PPG) which measure blood volume changes. Genome-wide association studies on REGLE embeddings identify more genome-wide significant loci than existing methods and replicate known loci for both spirograms and PPG, demonstrating the generality of the framework. Furthermore, these embeddings are associated with overall survival. Finally, we construct a set of PRSs that improve predictive performance of asthma, chronic obstructive pulmonary disease, hypertension, and systolic blood pressure in multiple biobanks. Thus, REGLE embeddings can quantify clinically relevant features that are not currently captured in a standardized or automated way.

The Complete Genome Sequences of 19 Species of Snipes (Scolopacidae, Charadriiformes, Aves)

We present the complete genome sequences of 19 species of snipes from 7 genera. Illumina sequencing was performed on genetic material from museum specimens. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via Genbank.

Evaluation of a training programme for critical incident debrief facilitators

BACKGROUND

Critical incident debriefs are a commonly used occupational health tool for supporting staff after traumatic work incidents. However, there is a dearth of literature evaluating training programmes for debrief facilitators.

AIMS

To evaluate a 5-day training programme to equip healthcare, social care and voluntary, community and social enterprise sector staff to act as post-incident peer supporters and debrief facilitators.

METHODS

A mixed-methods, single-arm, before-and-after study. Data were collected at baseline and post-training. The quantitative outcome measure was 'Confidence'; the sum of two items measuring confidence in (i) supporting peers after critical incidents and (ii) facilitating post-incident structured team discussions. At post-training, quantitative and qualitative feedback regarding experiences and perceptions of the training was also gathered.

RESULTS

We recruited 45 participants between October 2021 and January 2022. Confidence in supporting peers following incidents and facilitating post-incident structured team discussions increased significantly following the training, t(35) = -6.77, P < 0.001. A majority of participants reported they would do things differently because of the training and that they found the training relevant, useful and engaging. Summative content analysis of qualitative feedback indicated that participants (i) believed the role plays were an important learning tool and (ii) thought it was important that the trainer was engaging. Some participants would have preferred in-person delivery.

CONCLUSIONS

Participants valued training in post-incident peer support and debriefing skills. Organizations implementing post-incident support pathways could usefully include this training and ensure optimal uptake and engagement by (i) providing in-person and online delivery options and (ii) including role play as a learning technique.

Genomic architecture of autism from comprehensive whole-genome sequence annotation

Fully understanding autism spectrum disorder (ASD) genetics requires whole-genome sequencing (WGS). We present the latest release of the Autism Speaks MSSNG resource, which includes WGS data from 5,100 individuals with ASD and 6,212 non-ASD parents and siblings (total n = 11,312). Examining a wide variety of genetic variants in MSSNG and the Simons Simplex Collection (SSC; n = 9,205), we identified ASD-associated rare variants in 718/5,100 individuals with ASD from MSSNG (14.1%) and 350/2,419 from SSC (14.5%). Considering genomic architecture, 52% were nuclear sequence-level variants, 46% were nuclear structural variants (including copy-number variants, inversions, large insertions, uniparental isodisomies, and tandem repeat expansions), and 2% were mitochondrial variants. Our study provides a guidebook for exploring genotype-phenotype correlations in families who carry ASD-associated rare variants and serves as an entry point to the expanded studies required to dissect the etiology in the ∼85% of the ASD population that remain idiopathic.

The Complete Genome Sequences of 94 Species of Parrots (Psittaciformes, Aves)

We present the complete genome sequences of 94 species of parrots from 40 genera. Illumina sequencing was performed on genetic material from single individuals. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data is publicly available via Genbank.

The Complete Genome Sequence of Cyanopsitta spixii, the Spix's Macaw

The Spix's Macaw (Cyanopsitta spixii) is a critically endangered parrot that was once endemic to Brazil. We present the whole genome sequence of this species. Illumina sequencing was performed on a genetic sample from a single captive individual. The reads were assembled using a de novo method followed by a series of references from related species for finishing. The raw and assembled data is publicly available via Genbank: Sequence Read Archive (SRR15037507) and Assembly (GCA_024336845).

Digital Extended Specimens: Enabling an Extensible Network of Biodiversity Data Records as Integrated Digital Objects on the Internet

The early twenty-first century has witnessed massive expansions in availability and accessibility of digital data in virtually all domains of the biodiversity sciences. Led by an array of asynchronous digitization activities spanning ecological, environmental, climatological, and biological collections data, these initiatives have resulted in a plethora of mostly disconnected and siloed data, leaving to researchers the tedious and time-consuming manual task of finding and connecting them in usable ways, integrating them into coherent data sets, and making them interoperable. The focus to date has been on elevating analog and physical records to digital replicas in local databases prior to elevating them to ever-growing aggregations of essentially disconnected discipline-specific information. In the present article, we propose a new interconnected network of digital objects on the Internet—the Digital Extended Specimen (DES) network—that transcends existing aggregator technology, augments the DES with third-party data through machine algorithms, and provides a platform for more efficient research and robust interdisciplinary discovery.

Outcomes of Patients with a pH<7.0 Presenting to the Emergency Department (OPpHED Study)

Objectives The aim of this study was to assess the mortality and predictive factors in patients presenting with a pH<7.0 to the emergency department (ED). Methods A retrospective study of patients presenting to the ED of University Hospital Galway with a pH<7.0 from January 2014 to December 2017 was performed. A pH<7.0 on arrival to the ED from either an arterial or venous sample as measured by the blood gas analyser machine were assessed for inclusion. Results A total of 130 patients presented to ED over a 4-year period, with a mean age of 58 ±20 years. Eighty-one (63%) patients of the total cohort were male. In terms of aetiology of presentation, 66 (51%) cases were from cardiac arrest (CA), while the remaining 64 (49%) cases were non-cardiac arrest (NCA) related. Twenty-eight-day mortality was 69.5% overall, with significant mortality in the CA group (89%) compared to the NCA group (48%) (p<0.00). A modified early warning score (MEWS) (odds ratio [OR] 1.37, 95% CI: 1.18-1.59) and PCO2 ([OR] 1.35, 95% CI: 1.08-1.68.) were predictive of mortality. Conclusion In patients presenting to the ED with a pH of <7.0 the overall mortality was 69.5%, with survival more likely in NCA aetiologies. Mortality was associated with higher pCO2 and MEWS.

Ruptured Urinary Bladder Diagnosed by Point-of-care Ultrasound

Case Presentation

We describe a case of abdominal pain in a male patient who performed daily self-catheterization and developed a ruptured urinary bladder, which was diagnosed at bedside in the emergency department with point-of-care ultrasound (POCUS).

Discussion

Ruptured urinary bladder is commonly associated with blunt abdominal trauma. It is a rare complication of Foley catheter insertion. These images demonstrate that POCUS can be used as a screening tool to evaluate for bladder rupture when clinically suspected.