bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Value of VFA (Vertebral Fracture Assessment) in Routine DXA Scanning
Authors: Byrne Maria , Jose Josy , Mulholland Doug , Darby Sharon , Dockery Frances 
Published: September 2024

Abstract

Background
Low-trauma vertebral fractures are strongly predictive of future fracture risk so are generally given osteoporosis treatment regardless of bone density readings, and for every vertebral fracture presenting clinically, it is estimated that there are another two which are ‘silent’ or may have been ascribed to mechanical back pain. VFA (vertebral fracture assessment) during DXA scanning is a means of assessing the lateral spine for evidence of fractures which may have been undiagnosed prior. The International Society of Clinical Densitometry (ISCD) recommends a VFA in those with a T score &lt;-1.0 plus one of: women ≥70 years, men ≥80 years, historical height loss &gt;4cm, self-reported but undocumented prior vertebral fracture, regular use of steroids.

Methods
We developed a nurse-led DXA service in late 2021, conducting all scans in according with ISCD and HIQA guidelines however we do VFA on all patients aged over 50 years as it adds minimal time and negligible radiation exposure. In 2023 we commenced recording whether VFA fractures were previously diagnosed, in order to evaluate the benefits of VFA and so determine ongoing practice. To this end, we reviewed all DXA results since service launch for VFA evidence of fractures, and for patients from the calendar year 2023, we noted questionnaire responses and referral information as to whether any vertebral fracture was known of prior.

Results
There were 3,759 DXA scans conducted over the 24-month period 2022-2023 of whom n=3,299 had VFA performed. N=470/3,299 (14%) had a fracture identified on VFA. In the year 2023 only, of the n=289/1,795 (16%) who had a fracture on VFA, n=96 of these had not been diagnosed previously, representing a screening pick up rate of 5%.

Conclusion
VFA is a high-yield investigation for detecting undiagnosed vertebral fractures. As these fractures have definite treatment implications, wider use of VFA should be considered with routine DXA.
SENSE-Cog Lewy: Investigating the Impact of Sensory Loss on the Diagnosis, Clinical Features and Prognosis of Lewy Body Dementia
Authors: Roche Adam , Fitzpatrick Rachel , Chai Sin , Leroi Iracema 
Published: September 2024

Abstract

Background
Lewy Body Dementia (LBD) accounts for 20% of the nearly 65,000 people with dementia in Ireland, but fewer than 5% of those affected receive a formal diagnosis. LBD includes both Parkinson’s disease dementia (PDD) and dementia with Lewy bodies (DLB) and can be characterised by fluctuating and progressive cognitive difficulties, vivid visual hallucinations and REM sleep behaviour disturbances. Sensory function such hearing, vision and olfactory function declines with age—but increasing evidence shows that abnormal patterns of sensory dysfunction can be one of the earliest clinical signs and predictors of progression of neurodegenerative diseases such as Lewy body dementia and Parkinson’s disease dementia.

Methods
A scoping review was undertaken using Embase, CINAHL, PsychINFO and PubMed. Only reports on people with LBD (DLB and PDD) from any stage, prodromal to late stage were considered. Papers primarily addressing other forms of neurocognitive disorders were excluded. Sensory loss was conceptualised as the loss of smell, vision and hearing. Two reviewers independently assessed each study for inclusion, and disagreements were resolved by a third reviewer.

Results
Reports on sensory loss in LBD were very few and most often were comparing sensory loss across different dementia types. Strong associations were observed between olfactory loss and particular visual impairment patterns and the severity of both cognitive and non-cognitive DLB symptoms. Olfactory impairment is a potential early biomarker of DLB and PDD and severity of olfactory dysfunction can predict cognitive decline. Visual hallucinations, for example, were found to be closely linked to visual impairment patterns such as pareidolia.

Conclusion
This study highlights a knowledge gap regarding the patterns of sensory loss in LBD and their relationship with cognitive and non-cognitive LBD symptoms. Sensory assessments represent potentially valuable diagnostic and prognosis tool in LBD, with further research required to understand the aetiological mechanisms underlying sensory impairment in LBD and other dementias.
Untangling poikilohydry and desiccation tolerance: evolutionary and macroecological drivers in ferns
Authors: Aros-Mualin Daniela , Kessler Michael 
Published: September 2024

Abstract

Background and Aims
Poikilohydry describes the inability of plants to internally regulate their water content (hydroregulation), whereas desiccation tolerance (DT) refers to the ability to restore normal metabolic functions upon rehydration. The failure to clearly separate these two adaptations has impeded a comprehensive understanding of their unique evolutionary and ecological drivers. Unlike bryophytes and angiosperms, these adaptations in ferns are sometimes uncorrelated, offering a unique opportunity to navigate their intricate interplay.

Methods
We classified ferns into two syndromes: the Hymenophyllum-type (H-type), encompassing species with filmy leaves lacking stomata that experience extreme poikilohydry and varying degrees of DT, and the Pleopeltis-type (P-type), consisting of resurrection plants with variable hydroregulation but high DT.

Key Results
The H-type evolved during globally cool Icehouse periods, as an adaptation to low light levels in damp, shady habitats, and currently prevails in wet environments. Conversely, the P-type evolved predominantly under Greenhouse periods as an adaptation to periodic water shortage, with most extant species thriving in warm, seasonally dry habitats.

Conclusions
Out study underscores the fundamental differences between poikilohydry and DT, emphasizing the imperative to meticulously differentiate and qualify the strength of each strategy as well as their interactions, as a basis for understanding the genetic and evolutionary background of these ecologically crucial adaptations.
Using Neuropsychological Profiling to Tailor Mental Health Care for Children and Youth: a Quality Improvement Project to Measure Feasibility
Authors: Blais Angelica , Holahan Anne-Lise , Helleman Amanda , Pajer Kathleen , Honeywell Christina , Salehi Roxana , Anderson Peter , Vasserman Marsha 
Published: September 2024

Abstract

Objective
Precision child and youth mental healthcare has great potential to improve treatment success by tailoring interventions to individual needs. An innovative care pathway in a pediatric mental health outpatient clinic was designed to allow for neuropsychology data to be integrated in psychotherapeutic care. This paper describes the feasibility of this new pathway, including implementation outcomes, acceptability, and potential for future integration.

Method
The target population was outpatients 6–17 years old referred for individual treatment to a tertiary outpatient mental health (OPMH) clinic. The new care pathway was co-developed by neuropsychologists and mental health practitioners. A logic model was created to guide the evaluation, which was informed by the Reach Effectiveness Adoption Implementation Maintenance framework. As part of the logic model, a stepped assessment protocol was implemented, and reports on neuropsychological function were shared with patients, caregivers, and care providers. Evaluation data were collected from phone surveys, questionnaires, a focus group, and administrative records.

Results
Forty-two patients scheduled to receive therapy over a 6-month period were offered the opportunity to participate in the new care pathway and 39 (93%) agreed. Self-reported outcome data showed that 83% of patients and 94% of caregivers valued neuropsychology-informed care, with some describing it as transformative. Almost all practitioners (91%) reported that the project added value to their clinical care. There were no adverse effects on participants nor the flow of patients through the system.

Conclusions
Neuropsychology-informed pediatric OPMH care was feasible and well-received. Clinical effectiveness should be studied in an experimental trial.
Towards the accurate modelling of antibody−antigen complexes from sequence using machine learning and information-driven docking
Authors: Giulini Marco , Schneider Constantin , Cutting Daniel , Desai Nikita , Deane Charlotte M , Bonvin Alexandre M J J 
Published: September 2024

Abstract

Motivation
Antibody−antigen complex modelling is an important step in computational workflows for therapeutic antibody design. While experimentally determined structures of both antibody and the cognate antigen are often not available, recent advances in machine learning-driven protein modelling have enabled accurate prediction of both antibody and antigen structures. Here, we analyse the ability of protein−protein docking tools to use machine learning generated input structures for information-driven docking.

Results
In an information-driven scenario, we find that HADDOCK can generate accurate models of antibody−antigen complexes using an ensemble of antibody structures generated by machine learning tools and AlphaFold2 predicted antigen structures. Targeted docking using knowledge of the complementary determining regions on the antibody and some information about the targeted epitope allows the generation of high-quality models of the complex with reduced sampling, resulting in a computationally cheap protocol that outperforms the ZDOCK baseline.

Availability and implementation
The source code of HADDOCK3 is freely available at github.com/haddocking/haddock3. The code to generate and analyse the data is available at github.com/haddocking/ai-antibodies. The full runs, including docking models from all modules of a workflow have been deposited in our lab collection (data.sbgrid.org/labs/32/1139) at the SBGRID data repository.
DockQ v2: improved automatic quality measure for protein multimers, nucleic acids, and small molecules
Authors: Mirabello Claudio , Wallner Björn 
Published: September 2024

Abstract

Motivation
It is important to assess the quality of modeled biomolecules to benchmark and assess the performance of different prediction methods. DockQ has emerged as the standard tool for assessing the quality of protein interfaces in model structures against given references. However, as predictions of large multimers with multiple chains become more common, DockQ needs to be updated with more functionality for robustness and speed. Moreover, as the field progresses and more methods are released to predict interactions between proteins and other types of molecules, such as nucleic acids and small molecules, it becomes necessary to have a tool that can assess all types of interactions.

Results
Here, we present a complete reimplementation of DockQ in pure Python. The updated version of DockQ is more portable, faster and introduces novel functionalities, such as automatic DockQ calculations for multiple interfaces and automatic chain mapping with multi-threading. These enhancements are designed to facilitate comparative analyses of protein complexes, particularly large multi-chain complexes. Furthermore, DockQ is now also able to score interfaces between proteins, nucleic acids, and small molecules.

Availability and implementation
DockQ v2 is available online at: https://wallnerlab.org/DockQ.
Waifs and strays of office automation
Authors: Williams John 
Published: September 2024

Abstract
Think of a department in your company. It is staffed by highly paid professionals who are responsible for ensuring the profitable exploitation of company assets worth millions of pounds. The results of their efforts can give your company an edge over your competitors either in new products or in more efficient operation of the company as a whole. And yet this department probably makes less use of office automation to help it than, say, your accounts department. Who is this waif of office automation; this group whose contribution to the company is being limited by the tools they use? Surprisingly, it’s the Management Information Systems department. They have probably been pioneering office automation within the company but have often got left behind themselves, using tools that are inadequate, and rarely reflect the needs of the department today. The tragedy is that it is not their fault; with limited resources they have put their customers – the user departments – first, and most of the office automation systems around just haven’t met their special requirements.
IPSE: the office of the educated professional
Authors: Sartain David 
Published: September 2024

Abstract
Automated office systems used to conjure up a picture of typists and clerical workers sitting in front of keyboards and screens. Effectively, their main activity was word processing. The chief benefit of such an arrangement, for most professional staff, was probably to eliminate the need for accuracy in the preparation of manuscript drafts or in dictation! Obviously there are many cases where the use of word processors has resulted in a genuine increase in productivity. However, whilst it is desirable to increase productivity and job satisfaction of typing staff, are we addressing those areas which lead to the greatest financial saving? In most office environments, certainly in education, the typists are amongst the lowest paid. In addition the number of typists may be small when compared with the number of professionally qualified staff. Thus it is surely more sensible to increase the productivity of the latter; since they are more expensive and frequently scarce.
The effect of technology on organisations
Authors: Tuffield David 
Published: September 2024

Abstract
Technology is purported to be either benign and beneficial or harmful and socially retrogressive. Whether we are on one side or the other of this argument there is little doubt that we are in the early phases of a radical change in our lives due to electronic technologies. Some people are afraid that work itself may be under threat. Jeremy Seabrook has written ‘In the 1930’s, those who wanted work had a sense that they only had to wait before their labour would be required again… Now, on the other hand, there is a terminal sense of the extinction of work itself.’ [1], while the American economist Wassily Leontieff in a recent New Scientist article has written ‘Human labour from time immemorial has played the role of the principal factor of production. There are reasons to believe that human labour may not retain this status in the future.’[2]
Distributed speech recegnition
Authors: Ellis Chris 
Published: September 2024

Abstract
The latest experimental speech recognition systems can take dictation at normal speed, with no special techniques required of the speaker, and they can support large, generalised vocabularies. Some of these systems may soon appear as commercial offerings. However, they must run on powerful workstations to deliver anything like real-time performance, and they need bundreds of megabytes of RAM and large amounts of disk storage. This puts full-function speech recognition in a cost class of its own, compared with any other office application.
Climatic variation and risk assessment in a highly seasonal mammal
Authors: Sanchez McKenna , Martin Julien G A , Blumstein Daniel T 
Published: September 2024

Abstract
Climate change and its resulting effects on seasonality are known to alter a variety of animal behaviors including those related to foraging, phenology, and migration. Although many studies focus on the impacts of phenological changes on physiology or fitness enhancing behaviors, fewer have investigated the relationship between variation in weather and phenology on risk assessment. Fleeing from predators is an economic decision that incurs costs and benefits. As environmental conditions change, animals may face additional stressors that affect their decision to flee and influence their ability to effectively assess risk. Flight initiation distance (FID)—the distance at which animals move away from threats—is often used to study risk assessment. FID varies due to both internal and external biotic and physical factors as well as anthropogenic activities. We asked whether variation in weather and phenology is associated with risk-taking in a population of yellow-bellied marmots (Marmota flaviventer). As the air temperature increased marmots tolerated closer approaches, suggesting that they either perceived less risk or that their response to a threat was thermally compromised. The effect of temperature was relatively small and was largely dependent upon having a larger range in the full data set that permitted us to detect it. We found no effects of either the date that snow disappeared or July precipitation on marmot FID. As global temperatures continue to rise, rainfall varies more and drought becomes more common, understanding climate-related changes in how animals assess risk should be used to inform population viability models.
Cardiovascular events following coronavirus disease 2019 vaccination in adults: a nationwide Swedish study
Authors: Xu Yiyi , Li Huiqi , Santosa Ailiana , Wettermark Björn , Fall Tove , Björk Jonas , Börjesson Mats , Gisslén Magnus , Nyberg Fredrik 
Published: September 2024

Abstract

Background and Aims
While the rationale for coronavirus disease 2019 (COVID-19) vaccination is to reduce complications and overall mortality, some cardiovascular complications from the vaccine itself have been demonstrated. Myocarditis and pericarditis are recognized as rare acute adverse events after mRNA vaccines in young males, while evidence regarding other cardiovascular events remains limited and inconsistent. This study assessed the risks of several cardiovascular and cerebrovascular events in a Swedish nationwide register-based cohort.

Methods
Post-vaccination risk of myocarditis/pericarditis, dysrhythmias, heart failure, myocardial infarction, and cerebrovascular events (transient ischaemic attack and stroke) in several risk windows after each vaccine dose were assessed among all Swedish adults (n = 8 070 674). Hazard ratios (HRs) with 95% confidence intervals (95% CIs) compared with unvaccinated were estimated from Cox regression models adjusted for potential confounders.

Results
For most studied outcomes, decreased risks of cardiovascular events post-vaccination were observed, especially after dose three (HRs for dose three ranging from .69 to .81), while replicating the increased risk of myocarditis and pericarditis 1–2 weeks after COVID-19 mRNA vaccination. Slightly increased risks, similar across vaccines, were observed for extrasystoles [HR 1.17 (95% CI 1.06–1.28) for dose one and HR 1.22 (95% CI 1.10–1.36) for dose two, stronger in elderly and males] but not for arrhythmias and for transient ischaemic attack [HR 1.13 (95% CI 1.05–1.23), mainly in elderly] but not for stroke.

Conclusions
Risk of myopericarditis (mRNA vaccines only), extrasystoles, and transient ischaemic attack was transiently increased after COVID-19 vaccination, but full vaccination substantially reduced the risk of several more severe COVID-19-associated cardiovascular outcomes, underscoring the protective benefits of complete vaccination.
Is dabigatran a good alternative to warfarin in patients with atrial fibrillation accompanied by valvular and nonvalvular heart diseases? A systematic review and meta-analysis
Authors: Youssef Eman , Daher Mohanad , Milad Abanoub , Gamal Aliaa , Elmezayen Rafeek Walid 
Published: September 2024

Abstract

Background
There is ongoing discussion regarding the terminology used when atrial fibrillation (AF) is present alongside either valvular heart disease (VHD) or non-valvular heart disease (NVHD). Warfarin has been used for decades for stroke (S) and systemic embolism (SE) prophylaxis in atrial fibrillation (AF) patients. However, due to its drug and food interactions, pharmacogenetic approach via VKORC1, narrow therapeutic window, frequent monitoring, and high risk of intracranial hemorrhage (ICH), it is not preferred as a first-line anticoagulant for AF patients. Is it time to retire warfarin and replace it with dabigatran?

Aim and objectives
We conducted this meta-analysis to assess the effectiveness and safety of dabigatran compared to warfarin and find out how likely it could be used instead of warfarin in AF patients with VHD and NVHD.

Methods
PubMed, SCOPUS, Web of Science, and Cochrane CENTRAL were searched online from inception till June 2023, and eligible randomized controlled trials (RCTs) were selected. The outcomes were analyzed and calculated using the risk ratio (RR), and its confidence interval (CI) using STATA software. The Cochrane Risk of Bias 2.0 tool (ROB2) was used to assess the included studies.

Results
In the NVHD subgroup, dabigatran 150 mg showed a significantly low risk of S and SE (RR 0.74, 95% CI: [0.62,0.88]), ICH (RR 0.38, 95% CI: [0.26,0.56]), death (RR 0.85, 95% CI: [0.74,0.99]), and high risk of gastrointestinal bleeding (GIB) (RR 1.47, 95% CI: [1.17,1.85]) compared to Warfarin. Dabigatran 110 mg showed a low risk of ICH (RR 0.31, 95% CI: [0.21,0.47]), and no significant differences in S/SE (RR 1.02, 95% CI: [0.87,1.19]) and death (RR 0.94, 95% CI: [0.82,1.09]) compared to warfarin. In the VHD subgroup, dabigatran showed no significant differences in S/SE (RR 2.57, 95% CI: [0.57,11.56]), major bleeding (RR 1.14, 95% CI: [0.35,3.68]), and death (RR 0.35, 95% CI: [0.07,1.81]) compared to warfarin. In the catheter ablation subgroup, dabigatran showed a significant reduction only in groin hematoma (RR 0.19, 95% CI: [0.05,0.73]), compared to warfarin.

Conclusion
Dabigatran 150 mg was superior to warfarin in AF patients with NVHD; except with GIB; otherwise, Dabigatran 110 mg was superior only to warfarin in reducing ICH. In catheter ablation, dabigatran only reduced the groin hematoma. In AF patients with VHD, dabigatran did not show either superiority or inferiority to warfarin, further studies are needed. “Non-valvular AF” term is outdated and should be replaced with “type II VHD” to differentiate it from other valvular heart diseases that are accompanied by AF.