bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mitogenome evolution in Trichoderma afroharzianum strains: for a better understanding of distinguishing genus
Authors: Özkale Evrim , Doğan Özgül , Budak Mahir , Mahir Korkmaz Ertan 
Published: December 2023

Trichoderma afroharzianum ( Hypocreales) is known as an important mycoparasite and biocontrol fungus and feeds on fungal material by parasitizing other fungi. Recent studies indicate that this species is also an ear rot pathogen in Europe. Here, the complete mitochondrial genome of three T. afroharzianum strains was sequenced using next-generation sequencing and comparatively characterized by the reported Trichoderma mitogenomes. T. afroharzianum mitogenomes were varying between 29 511 bp and 29 517 bp in length, with an average A + T content of 72.32%. These mitogenomes contain 14 core protein coding genes (PCGs), 22 tRNAs, two rRNAs, one gene encoding the ribosomal protein S3, and three or four genes including conserved domains for the homing endonucleases (HEGs; GIY-YIG type and LAGLIDADG type). All PCGs are initiated by ATG codons, except for atp8, and all are terminated with TAA. A significant correlation was observed between nucleotide composition and codon preference. Four introns belonging to the group I intron class were predicted, accounting for about 14.54% of the size of the mitogenomes. Phylogenetic analyses confirmed the positions of T. afroharzianum strains within the genus of Trichoderma and supported a sister group relationship between T. afroharzianum and T. simmonsii. The recovered trees also supported the monophyly of all included families and of the genus of Acremonium. The characterization of mitochondrial genome of T. afroharzianum contributes to the understanding of phylogeny and evolution of Hypocreales.
Traceable Group-Wise Self-Optimizing Feature Transformation Learning: A Dual Optimization Perspective
Authors: Xiao Meng , Wang Dongjie , Wu Min , Liu Kunpeng , Xiong Hui , Zhou Yuanchun , Fu Yanjie 
Published: December 2023

Feature transformation aims to reconstruct an effective representation space by mathematically refining the existing features. It serves as a pivotal approach to combat the curse of dimensionality, enhance model generalization, mitigate data sparsity, and extend the applicability of classical models. Existing research predominantly focuses on domain knowledge-based feature engineering or learning latent representations. However, these methods, while insightful, lack full automation and fail to yield a traceable and optimal representation space. An indispensable question arises: Can we concurrently address these limitations when reconstructing a feature space for a machine learning task? Our initial work took a pioneering step towards this challenge by introducing a novel self-optimizing framework. This framework leverages the power of three cascading reinforced agents to automatically select candidate features and operations for generating improved feature transformation combinations. Despite the impressive strides made, there was room for enhancing its effectiveness and generalization capability. In this extended journal version, we advance our initial work from two distinct yet interconnected perspectives: 1) We propose a refinement of the original framework, which integrates a graph-based state representation method to capture the feature interactions more effectively and develop different Q-learning strategies to alleviate Q-value overestimation further. 2) We utilize a new optimization technique (actor-critic) to train the entire self-optimizing framework in order to accelerate the model convergence and improve the feature transformation performance. Finally, to validate the improved effectiveness and generalization capability of our framework, we perform extensive experiments and conduct comprehensive analyses. These provide empirical evidence of the strides made in this journal version over the initial work, solidifying our framework’s standing as a substantial contribution to the field of automated feature transformation. To improve the reproducibility, we have released the associated code and data by the Github link https://github.com/coco11563/TKDD2023_code.
A structural heart-brain axis mediates the association between cardiovascular risk and cognitive function
Authors: Jaggi Akshay , Conole Eleanor L.S. , Raisi-Estabragh Zahra , Gkontra Polyxeni , McCracken Celeste , Szabo Liliana , Neubauer Stefan , Petersen Steffen E. , Cox Simon R. , Lekadir Karim 
Published: December 2023

Abstract
Elevated vascular disease risk associates with poorer cognitive function, but the mechanism for this link is poorly understood. A leading theory, the structural-functional model argues that vascular risk may drive adverse cardiac remodelling, which, in turn, leads to chronic cerebral hypoperfusion and subsequent brain structural damage. This model predicts that variation in heart and brain structure should associate with both greater vascular risk and lower cognitive function. This study tests that prediction in a large sample of the UK Biobank (N = 11,962). We assemble and summarise vascular risk factors, cardiac magnetic resonance radiomics, brain structural and diffusion MRI indices, and cognitive assessment. We also extract “heart-brain axes” capturing the covariation in heart and brain structure. Many heart and brain measures partially explain the vascular risk—cognitive function association, like left ventricular end-diastolic volume and grey matter volume. Notably, a heart-brain axis, capturing correlation between lower myocardial intensity, lower grey matter volume, and poorer thalamic white matter integrity, completely mediates the association, supporting the structural-functional model. Our findings also complicate this theory by finding that brain structural variation cannot completely explain the heart structure—cognitive function association. Our results broadly offer evidence for the structural functional hypothesis, identify imaging biomarkers for this association by considering covariation in heart and brain structure, and generate novel hypotheses about how cardiovascular risk may link to cognitive function.
Classification accuracy of structural and functional connectomes across different depressive phenotypes
Authors: Yeung Hon Wah , Stolicyn Aleks , Shen Xueyi , Adams Mark J. , Romaniuk Liana , Thng Gladi , Buchanan Colin R. , Tucker-Drob Elliot M. , Bastin Mark E. , McIntosh Andrew M. , Cox Simon R. , Smith Keith M. , Whalley Heather C. 
Published: December 2023

AbstractPhenotyping of major depressive disorder (MDD) can vary from study to study, which, together with heterogeneity of the disorder, may contribute to the inconsistent associations with neuroimaging features and underlie previous problems with machine-learning methods for MDD diagnostic applications. In this study, we examined the classification accuracy of structural and functional connectomes across different depressive phenotypes, including separating MDD subgroups into those with and without self-reported exposure to childhood trauma (CT) (one of the largest risk factors for MDD associated with brain development). We applied logistic ridge regression to classify control and MDD participants defined by six different MDD definitions in a large community-based sample (N=14,507). We used brain connectomic data based on six structural and two functional network weightings and conducted a comprehensive analysis to (i) explore how well different connectome modalities predict different MDD phenotypes commonly used in research, (ii) whether stratification of MDD based on self-reported exposure to childhood trauma (measured with the childhood trauma questionnaire (CTQ)) may improve the accuracies, and (iii) identify important predictive features across different MDD phenotypes. We found that functional connectomes outperformed structural connectomes as features for MDD classification across phenotypes. The highest accuracy of 64.8% (chance level 50.0%) was achieved in the Currently Depressed (defined by the presence of more than five symptoms of depression in the past 2 weeks) sample with additional CTQ criterion using partial correlation functional connectomes. The predictive feature overlap, measured using Jaccard index, indicated that there were neurobiological differences between MDD patients with and without childhood adversity. Further analysis of predictive features for different MDD phenotypes with hypergeometric tests revealed sensorimotor and visual subnetworks as important predictors of MDD. Our results suggest that differences in sensorimotor and visual subnetworks may serve as potential biomarkers of MDD.
From Data Doubles to Data Demons: Reflections on a CripTech
Collaboration
Authors: Forlano Laura , Barrio Itziar 
Published: December 2023

Abstract
This article describes a collaboration between the authors around a series of robotic sculptures that were created by Barrio with data from Forlano’s “smart” insulin pump and sensor system. Forlano, a type 1 diabetic for over 10 years, expands upon previous writing about her experience as a “disabled cyborg.” As CripTech art, the robotic sculptures, discussed here as data demons, complicate and expand contemporary discourses on artificial intelligence and design. By engaging themes such as data as labor, data as material, and data as relations, this article ultimately argues that both people and technologies are disabled.
Remote Access: Crip Nightlife, Artistry, and Technoscience
Authors: Gotkin Kevin , Hamraie Aimi 
Published: December 2023

Abstract
Since 2020, Kevin Gotkin has spearheaded disability nightlife events for the virtual Remote Access series for the Critical Design Lab, a multidisciplinary and multi-institution arts and design collaborative. Aimi Hamraie directs the Critical Design Lab and coined the term crip technoscience. Hamraie interviews Gotkin about the genesis of this disability arts and culture party and how it has evolved into an ongoing experiment in critical access-making. The authors focus on the elements of artistic production, presentation, and exhibition that required crip technoscience interventions before and during the COVID-19 pandemic.
Experimental Modalities: Crip Representation and Access with Electronic Arts Intermix
Authors: Martin Darrin 
Published: December 2023

Abstract
In collaboration with Electronic Arts Intermix (EAI), a nonprofit video arts distributor, the author has found videos in EAI’s collection that may reflect upon themes of disability and/or engage modes of access like captioning and audio description. The video/film works referenced in conceptual and performance practices have been broadly tethered to the word “experimental” and situated in this context to engage with accessibility even for works that resist and challenge the very nature of legibility. This essay is the author’s first attempt to explore an archive to identify video artworks that represent disability (whether deliberately or not) and present alternative modes of access (whether deliberately or not) with the intent of laying a groundwork for curations that tap into possibilities within accessibility formats.
Rejecting an Additive Solution to Regan’s Lifeboat Case
Authors: Kary Daniel 
Published: December 2023

Abstract
This paper considers a solution to a scenario found in Tom Regan’s Case for Animal Rights, offered by Daniel Kary. Regan considers a case where either one human or any number of dog’s must be sacrificed. He chooses the human because they would be harmed more than any dog would be. This is initially puzzling since Regan claims that humans and dogs have equal inherent value (the objective value as an end that entities have). Kary’s solution argues the human should be saved since their possible experiences have greater intrinsic value (the objective value as an end that experiences have) than those of any number of dogs’. The rationale is that dog experiences are too similar to be additive. The paper acknowledges that Kary’s alternative solution is more plausible than Regan’s, but it ultimately fails to be convincing.
The Small-Amplitude Dynamics of Spontaneous Tropical Cyclogenesis. Part I: Experiments with Amplified Longwave Radiative Feedback
Authors: Fu Hao , O’Neill Morgan 
Published: December 2023

Abstract
What determines the vortex size at the small-amplitude stage of spontaneous tropical cyclogenesis remains unclear. A doubly periodic domain is a standard setup for numerically studying this problem, but the convectively coupled standing waves inherent to the setup could directly trigger vortices, rendering an unrealistic path for tropical cyclogenesis. We increase the Coriolis parameter to suppress the wave and double the longwave radiative feedback to make the more realistic moisture–radiation instability dominant. Experiments show that the moisture–radiation instability has a short-wavelength cutoff due to the smoothing effect of convective dynamics, which includes the nonlocal convective triggering by cold pools and the nonlocal longwave radiative effect of anvil clouds. By approximating the spread of convective activity as a Gaussian filter on the column humidity, we derive a bulk convective spreading length lcp+av to parameterize the combined effect of cold pools and anvils. Using a novel diagnostic method, lcp+av is shown to be around 10 km. The contribution of cold pools and anvil clouds to convective spreading is comparable in the doubled radiative feedback experiments. An extrapolation to the normal radiative feedback state shows the anvil clouds play a smaller yet nonnegligible role.
The Effects of Cognitive Ability, Mental Health, and Self-Quarantining on Functional Ability of Older Adults During the COVID-19 Pandemic: Results From the Canadian Longitudinal Study on Aging
Authors: Gregory Madeline A. , Schaeffer Morgan J. , Reeves Jennifer T. H. , Griffith Lauren E. , Wolfson Christina , Basta Nicole E. , McMillan Jacqueline M. , Kirkland Susan , Raina Parminder , Paterson Theone S. E. ,   on behalf of the Canadian Longitudinal Study on Aging (CLSA) Team
Published: December 2023

Objectives Determine whether levels of anxiety and depression, cognitive ability, and self-quarantining during and prior to the pandemic predict decreases in perceived functional ability. Design and Setting Longitudinal data collected from the Canadian Longitudinal Study on Aging (CLSA) COVID-19 Questionnaire Study (2020) and core CLSA study (Follow-Up 1; 2014-2018). Participants 17 541 CLSA participants. Measurements Self-quarantining behaviours from questionnaires administered at Baseline (April 2020), Monthly, and Exit (December 2020) time points of the CLSA COVID-19 Questionnaire Study, levels of anxiety and depression at Baseline, perceived change in functional ability at Exit, and performance on neuropsychological tests (Rey Auditory Verbal Learning Task, Mental Alternation Task, Animal Fluency Test) and functional ability (Older Americans Resources and Services [OARS] Multidimensional Assessment Questionnaire) from the core CLSA study. Results Greater cognitive ability pre-pandemic ( B = −.003, P < .01), higher levels of anxiety ( B = −.024, P < .01) and depressive symptoms ( B = −.110, P < .01) at Baseline, and higher frequency of engaging in self-quarantining throughout the COVID-19 survey period ( B = −.098, P < .01) were associated with perceived loss in functional ability at Exit. Self-quarantining behaviour was associated with perceived loss in functional ability only at average and high levels of depressive symptoms ( B = −.013, P < .01). Conclusions Older adults with higher cognitive and lower functional ability prior to the pandemic were at greater risk of decreased perceived functional ability during the first year of the pandemic, as were those who experienced greater levels of anxiety and depressive symptoms during the pandemic. Strategies/interventions to preserve functional ability in older adults with cognitive independence prior to future pandemics are warranted.
Sterility of antibiotic-admixed peritoneal dialysis solution over time
Authors: Tan Ken-Soon , Rogers Robyn , Shephard Deanna , Lewis Amanda , George Narelle , Johnson David W 
Published: December 2023

Background: Intraperitoneal antibiotics may be required daily for up to three weeks to treat peritoneal dialysis (PD)-related peritonitis. In some jurisdictions, antibiotic-admixed PD solutions are required to be used within 24 h due to concerns regarding microbial contamination and growth. This requires patients to attend the PD unit daily or alternatively for staff to perform home delivery with associated transport, staffing and cost implications. Objective: The aim of this study was to determine if significant microbial growth occurs in PD solutions following their injection with antibiotic or sterile water. Methods: Twelve PD solution bags were admixed with cefazolin sodium 1 g, diluted in 10 mL sterile water, while a further 12 PD solution bags were admixed with 10 mL sterile water using aseptic technique (AT) under supervision. All bags were stored at room temperature. Three bags from each experimental group were sampled for microbiologic culture at 0-, 24-, 48- and 72-h intervals. Results: One sterile water admixed bag sampled at 24 h yielded a Corynebacterium spp. after microbiologic culture. A repeat specimen from the same bag at day nine returned a negative culture result. All other sterile water and cefazolin admixed bags returned negative culture results at all time points. Conclusions: Antibiotic-admixed PD solutions prepared using AT and stored at room temperature remained sterile for up to 72 h. This suggests that patients can be safely issued with a supply of antibiotic-admixed PD bags for up to three days at a time.
Severity, interference, qualities, and correlates of severe pain: Descriptive cross-sectional study on pain experience of cancer patients in Sri Lanka
Authors: Edirisinghe N. P. , Makuloluwa P. T. R. , Amarasekara A. A. T. D. , Goonewardena C. S. E. 
Published: December 2023

Objective Pain is the most debilitating and subjective experience of cancer patients. This study examines the severity, interference, characteristics, and associations of severe pain in Sri Lankan cancer patients. Methods A descriptive study was conducted in Sri Lanka on 384 patients at age 18 or older who had cancer pain for 3 months or more due to the initial lesion, secondaries, radiation, or chemotherapy. Patients with non-cancerous pain or brain metastases were excluded. Data was collected using a validated Sinhala version of the Short-Form Brief Pain Inventory and the Short-Form McGill Pain Questionnaire-2. Logistic regression was used to identify severe pain correlations. Results The mean of the “worst pain” experience was 7.97, and 73.2% reported their “worst pain” as severe. The “normal works” (62.5%) and “sleep” (58.3%) were severely influenced by pain. “Aching pain,” was the most reported pain quality. A statistically significant association was shown between severe pain and male gender (adjusted odds ratio (AOR) = 1.723), being in marriage (AOR = 1.947), absence of family commitments (AOR = 1.8), and pain of 3 months or more duration (AOR = 1.76). Conclusion The experiences of cancer pain vary, with the majority suffering from severe pain.
Preoperative and Postoperative Segmental and Overall Range of Motion in Patients Undergoing Lumbar Spinal Fusion Using HA-Infused PEEK and HA-Treated Titanium Alloy Interbody Cages
Authors: Kazarian Gregory S. , Du Jerry , Gang Catherine Himo , Shahi Pratysuh , Asada Tomoyuki , Lu Amy , Korsun Maximillian , Tuma Olivia , Singh Nishtha , Araghi Kasra , Maayan Omri , Singh Sumedha , Iyer Sravisht 
Published: December 2023

Study Design Retrospective observational radiographic analysis. Objective Determine how single level lumbar interbody fusion (LIF) alters segmental range of motion (ROM) at adjacent levels and decreases overall ROM. Methods This study included 54 patients who underwent single-level anterior (ALIF, 39%), thoraco-LIF (TLIF, 26%), posterior LIF (PLIF, 22%), or lateral LIF (LLIF, 13%) (L2-3/L3-4/L4-5/L5-S1: 4%/13%/35%/48%). Segmental ROM from L1-2 to L5-S1 and the overall lumbar ROM (L1-S1) were assessed from preoperative and postoperative flexion-extension radiographs. K-means cluster analysis was used to identify ROM subgroups. Results The overall L1-S1 ROM decreased 14% (25.5 ± 20.4° to 22.0 ± 17.2°, P = .104) postoperatively. ROM at the fusion level decreased 77% (4.8 ± 5.0° to 1.1 ± 1.1°, P < .001). Caudal adjacent segment ROM decreased 12% (5.2 ± 5.7° to 4.6 ± 4.4°, P = .345) and cranially ROM increased 34% (4.3 ± 5.0° to 5.7 ± 5.7°, P = .05). K-cluster analysis identified 3 distinct clusters ( P < .05). Cluster 1 lost more ROM and had less improvement in patient-reported outcomes measures (PROMs) than average. Cluster 2 had less ROM loss than average with worse PROMs improvement. Cluster 3 did not have changes in ROM and better improvement in PROMs than average. Successful fusion was verified in 96% of all instrumented segments with >6 months follow-up (ROM <4°). Conclusion Following single-level L IF, patients should expect a loss of 3.3°, or 14% of overall lumbar motion with increases in ROM of the cranial segment. However, specific clusters of patients exist that experience different relative changes in ROM and PROMs.
Oral nitrate supplementation improves cardiovascular risk markers in COPD: ON-BC, a randomised controlled trial
Authors: Alasmari Ali M. , Alsulayyim Abdullah S. , Alghamdi Saeed M. , Philip Keir E.J. , Buttery Sara C. , Banya Winston A.S. , Polkey Michael I. , Armstrong Paul C. , Rickman Matthew J. , Warner Timothy D. , Mitchell Jane A. , Hopkinson Nicholas S. 
Published: December 2023

BackgroundShort-term studies suggest that dietary nitrate (NO3−) supplementation may improve the cardiovascular risk profile, lowering blood pressure (BP) and enhancing endothelial function. It is not clear if these beneficial effects are sustained and whether they apply in people with COPD, who have a worse cardiovascular profile than those without COPD. Nitrate-rich beetroot juice (NR-BRJ) is a convenient dietary source of nitrate.MethodsThe ON-BC trial was a randomised, double-blind, placebo-controlled parallel group study in stable COPD patients with home systolic BP (SBP) measurement ≥130 mmHg. Participants were randomly allocated (1:1) using computer-generated, block randomisation to either 70 mL NR-BRJ (400 mg NO3−) (n=40) or an otherwise identical nitrate-depleted placebo juice (0 mg NO3−) (n=41), once daily for 12 weeks. The primary end-point was between-group change in home SBP measurement. Secondary outcomes included change in 6-min walk distance (6MWD) and measures of endothelial function (reactive hyperaemia index (RHI) and augmentation index normalised to a heart rate of 75 beats·min−1(AIx75)) using an EndoPAT device. Plasma nitrate and platelet function were also measured.ResultsCompared with placebo, active treatment lowered SBP (Hodges–Lehmann treatment effect −4.5 (95% CI −5.9– −3.0) mmHg), and improved 6MWD (30.0 (95% CI 15.7–44.2) m; p<0.001), RHI (0.34 (95% CI 0.03–0.63); p=0.03) and AIx75 (−7.61% (95% CI −14.3– −0.95%); p=0.026).ConclusionsIn people with COPD, prolonged dietary nitrate supplementation in the form of beetroot juice produces a sustained reduction in BP, associated with an improvement in endothelial function and exercise capacity.