bluuebunny/crossref_metadata_2025_split huggingface dataset:
Developing and validating a multivariable prediction model which predicts progression of intermediate to late age-related macular degeneration—the PINNACLE trial protocol
Authors: Sutton Janice , Menten Martin J. , Riedl Sophie , Bogunović Hrvoje , Leingang Oliver , Anders Philipp , Hagag Ahmed M. , Waldstein Sebastian , Wilson Amber , Cree Angela J. , Traber Ghislaine , Fritsche Lars G. , Scholl Hendrik , Rueckert Daniel , Schmidt-Erfurth Ursula , Sivaprasad Sobha , Prevost Toby , Lotery Andrew 
Published: May 2022

Abstract
Aims
Age-related macular degeneration (AMD) is characterised by a progressive loss of central vision. Intermediate AMD is a risk factor for progression to advanced stages categorised as geographic atrophy (GA) and neovascular AMD. However, rates of progression to advanced stages vary between individuals. Recent advances in imaging and computing technologies have enabled deep phenotyping of intermediate AMD. The aim of this project is to utilise machine learning (ML) and advanced statistical modelling as an innovative approach to discover novel features and accurately quantify markers of pathological retinal ageing that can individualise progression to advanced AMD.

Methods
The PINNACLE study consists of both retrospective and prospective parts. In the retrospective part, more than 400,000 optical coherent tomography (OCT) images collected from four University Teaching Hospitals and the UK Biobank Population Study are being pooled, centrally stored and pre-processed. With this large dataset featuring eyes with AMD at various stages and healthy controls, we aim to identify imaging biomarkers for disease progression for intermediate AMD via supervised and unsupervised ML. The prospective study part will firstly characterise the progression of intermediate AMD in patients followed between one and three years; secondly, it will validate the utility of biomarkers identified in the retrospective cohort as predictors of progression towards late AMD. Patients aged 55–90 years old with intermediate AMD in at least one eye will be recruited across multiple sites in UK, Austria and Switzerland for visual function tests, multimodal retinal imaging and genotyping. Imaging will be repeated every four months to identify early focal signs of deterioration on spectral-domain optical coherence tomography (OCT) by human graders. A focal event triggers more frequent follow-up with visual function and imaging tests. The primary outcome is the sensitivity and specificity of the OCT imaging biomarkers. Secondary outcomes include sensitivity and specificity of novel multimodal imaging characteristics at predicting disease progression, ROC curves, time from development of imaging change to development of these endpoints, structure-function correlations, structure-genotype correlation and predictive risk models.

Conclusions
This is one of the first studies in intermediate AMD to combine both ML, retrospective and prospective AMD patient data with the goal of identifying biomarkers of progression and to report the natural history of progression of intermediate AMD with multimodal retinal imaging.
Pan-cancer analyses reveal the genetic and pharmacogenomic landscape of transient receptor potential channels
Authors: Pan Tao , Gao Yueying , Xu Gang , Zhou Ping , Li Si , Guo Jing , Zou Haozhe , Xu Qi , Huang Xiaoyan , Xu Juan , Li Yongsheng 
Published: May 2022

AbstractTransient-receptor potential (TRP) channels comprise a diverse family of ion channels, which play important roles in regulation of intracellular calcium. Emerging evidence has revealed the critical roles of TRP channels in tumor development and progression. However, we still lack knowledge about the genetic and pharmacogenomics landscape of TRP genes across cancer types. Here, we comprehensively characterized the genetic and transcriptome alterations of TRP genes across >10,000 patients of 33 cancer types. We revealed prevalent somatic mutations and copy number variation in TRP genes. In particular, mutations located in transmembrane regions of TRP genes were likely to be deleterious mutations (p-values < 0.001). Genetic alterations were correlated with transcriptome dysregulation of TRP genes, and we found that TRPM2, TRPM8, and TPRA1 showed extent dysregulation in cancer. Patients with TRP gene alterations were with significantly higher hypoxia scores, tumor mutation burdens, tumor stages and grades, and poor survival. The alterations of TRP genes were significantly associated with the activity of cancer-related pathways. Moreover, we found that the expression of TRP genes were potentially useful for development of targeted therapies. Our study provided the landscape of genomic and transcriptomic alterations of TPRs across 33 cancer types, which is a comprehensive resource for guiding both mechanistic and therapeutic analyses of the roles of TRP genes in cancer. Identifying the TRP genes with extensive genetic alterations will directly contribute to cancer therapy in the context of predictive, preventive, and personalized medicine.
Qubit teleportation between non-neighbouring nodes in a quantum network
Authors: Hermans S. L. N. , Pompili M. , Beukers H. K. C. , Baier S. , Borregaard J. , Hanson R. 
Published: May 2022

AbstractFuture quantum internet applications will derive their power from the ability to share quantum information across the network1,2. Quantum teleportation allows for the reliable transfer of quantum information between distant nodes, even in the presence of highly lossy network connections3. Although many experimental demonstrations have been performed on different quantum network platforms4–10, moving beyond directly connected nodes has, so far, been hindered by the demanding requirements on the pre-shared remote entanglement, joint qubit readout and coherence times. Here we realize quantum teleportation between remote, non-neighbouring nodes in a quantum network. The network uses three optically connected nodes based on solid-state spin qubits. The teleporter is prepared by establishing remote entanglement on the two links, followed by entanglement swapping on the middle node and storage in a memory qubit. We demonstrate that, once successful preparation of the teleporter is heralded, arbitrary qubit states can be teleported with fidelity above the classical bound, even with unit efficiency. These results are enabled by key innovations in the qubit readout procedure, active memory qubit protection during entanglement generation and tailored heralding that reduces remote entanglement infidelities. Our work demonstrates a prime building block for future quantum networks and opens the door to exploring teleportation-based multi-node protocols and applications2,11–13.
Lidar reveals pre-Hispanic low-density urbanism in the Bolivian Amazon
Authors: Prümers Heiko , Betancourt Carla Jaimes , Iriarte José , Robinson Mark , Schaich Martin 
Published: May 2022

AbstractArchaeological remains of agrarian-based, low-density urbananism1–3have been reported to exist beneath the tropical forests of Southeast Asia, Sri Lanka and Central America4–6. However, beyond some large interconnected settlements in southern Amazonia7–9, there has been no such evidence for pre-Hispanic Amazonia. Here we present lidar data of sites belonging to the Casarabe culture (aroundad 500 toad 1400)10–13in the Llanos de Mojos savannah–forest mosaic, southwest Amazonia, revealing the presence of two remarkably large sites (147 ha and 315 ha) in a dense four-tiered settlement system. The Casarabe culture area, as far as known today, spans approximately 4,500 km2, with one of the large settlement sites controlling an area of approximately 500 km2. The civic-ceremonial architecture of these large settlement sites includes stepped platforms, on top of which lie U-shaped structures, rectangular platform mounds and conical pyramids (which are up to 22 m tall). The large settlement sites are surrounded by ranked concentric polygonal banks and represent central nodes that are connected to lower-ranked sites by straight, raised causeways that stretch over several kilometres. Massive water-management infrastructure, composed of canals and reservoirs, complete the settlement system in an anthropogenically modified landscape. Our results indicate that the Casarabe-culture settlement pattern represents a type of tropical low-density urbanism that has not previously been described in Amazonia.
Outcomes of simultaneous laparoscopic, hybrid, and open resection in colorectal cancer with synchronous liver metastases: a propensity score-matched study
Authors: Lim Han-Ki , Kim Minjung , Park Ji Won , Ryoo Seung-Bum , Park Kyu Joo , Yi Nam-Joon , Lee Kwang-Woong , Suh Kyung-Suk , Oh Heung-Kwon , Kim Duck-Woo , Kang Sung-Bum , Cho Jai Young , Lee Dong-Woon , Park Sung Chan , Oh Jae Hwan , Shin Aesun , Jeong Seung-Yong 
Published: May 2022

AbstractWe aimed to compare the short- and long-term outcomes of simultaneous laparoscopic, hybrid, and open resection for colorectal cancer and synchronous liver metastases. We retrospectively analyzed the data of 647 patients with simultaneous resection of colorectal cancer and liver metastases between January 2006 and December 2018 at three tertiary referral hospitals. Patient’s baseline characteristics, perioperative outcomes, pathological examination results, liver-specific recurrence rate and survivals were compared between the propensity score-matched groups. Forty-two and 81 patients were selected for the laparoscopic vs. hybrid groups, and 48 and 136 patients for laparoscopic vs. open groups, respectively. The laparoscopic group had fewer wound complications (2.1 vs. 13.2%; p = 0.028) than the open group, and a shorter postoperative hospital stay than the hybrid and open groups (8 vs. 11 days, p < 0.001 for both). The 5-year liver-specific recurrence rates were 38.7% and 46.0% in the laparoscopic and hybrid groups, respectively (p = 0.270), and 34.0% and 37.0% in the laparoscopic and open groups, respectively (p = 0.391). Simultaneous laparoscopic resection for colorectal cancer and liver metastases can be performed safely with significantly enhanced postoperative recovery and comparable long-term outcomes compared to hybrid and open resection.
An exposome-wide association study on body mass index in adolescents using the National Health and Nutrition Examination Survey (NHANES) 2003–2004 and 2013–2014 data
Authors: Haddad Nadine , Andrianou Xanthi , Parrish Christa , Oikonomou Stavros , Makris Konstantinos C. 
Published: May 2022

AbstractExcess weight is a public health challenge affecting millions worldwide, including younger age groups. The human exposome concept presents a novel opportunity to comprehensively characterize all non-genetic disease determinants at susceptible time windows. This study aimed to describe the association between multiple lifestyle and clinical exposures and body mass index (BMI) in adolescents using the exposome framework. We conducted an exposome-wide association (ExWAS) study using U.S. National Health and Nutrition Examination Survey (NHANES) 2003–2004 wave for discovery of associations between study population characteristics and zBMI, and used the 2013–2014 wave to replicate analysis. We included non-diabetic and non-pregnant adolescents aged 12–18 years. We performed univariable and multivariable linear regression analysis adjusted for age, sex, race/ethnicity, household smoking, and income to poverty ratio, and corrected for false-discovery rate (FDR). A total of 1899 and 1224 participants were eligible from 2003–2004 and 2013–2014 survey waves. Weighted proportions of overweight were 18.4% and 18.5% whereas those for obese were 18.1% and 20.6% in 2003–2004 and 2013–2014, respectively. Retained exposure agents included 75 laboratory (clinical and biomarkers of environmental chemical exposures) and 64 lifestyle (63 dietary and 1 physical activity) variables. After FDR correction, univariable regression identified 27 and 12 predictors in discovery and replication datasets, respectively, while multivariable regression identified 22 and 9 predictors in discovery and replication datasets, respectively. Six were significant in both datasets: alanine aminotransferase, gamma glutamyl transferase, segmented neutrophils number, triglycerides; uric acid and white blood cell count. In this ExWAS study using NHANES data, we described associations between zBMI, nutritional, clinical and environmental factors in adolescents. Future studies are warranted to investigate the role of the identified predictors as early-stage biomarkers of increased BMI and associated pathologies among adolescents and to replicate findings to other populations.
Heat transfer analysis of Cu and Al2O3 dispersed in ethylene glycol as a base fluid over a stretchable permeable sheet of MHD thin-film flow
Authors: Zeeshan  , Khan Ilyas , Weera Wajaree , Mohamed Abdullah 
Published: May 2022

AbstractThe process of thin films is commonly utilized to improve the surface characteristics of materials. A thin film helps to improve the absorption, depreciation, flexibility, lighting, transport, and electromagnetic efficiency of a bulk material medium. Thin-film treatment can be especially helpful in nanotechnology. As a result, the current study investigates the computational process of heat relocation analysis in a thin-film MHD flow embedded in hybrid nanoparticles, which combines the spherical copper and alumina dispersed in ethylene glycol as the conventional heat transfer Newtonian fluid model over a stretching sheet. Important elements such as thermophoresis and Brownian movement are used to explain the characteristics of heat and mass transfer analysis. Nonlinear higher differential equations (ODEs) were attained by transforming partial differential equations (PDEs) into governing equations when implementing the similarity transformation technique. The resulting nonlinear ODEs have been utilized by using the homotopy analysis method (HAM). The natures of the thin-film flow and heat transfer through the various values of the pertinent parameters: unsteadiness, nanoparticle volume fraction, thin-film thickness, magnetic interaction, and intensity suction/injection are deliberated. The approximate consequences for flow rate and temperature distributions and physical quantities in terms of local skin friction and Nusselt number were obtained and analyzed via graphs and tables. As a consequence, the suction has a more prodigious effect on the hybrid nanofluid than on the injection fluid for all the investigated parameters. It is worth acknowledging that the existence of the nanoparticles and MHD in the viscous hybrid nanofluid tends to enhance the temperature profile but decays the particle movement in the thin-film flow. It is perceived that the velocity and temperature fields decline with increasing unsteadiness, thin-film thickness, and suction/injection parameters. The novel part of the present work is to investigate the hybrid nanofluid including Cu–Al2O3 dispersed in Ethylene glycol as a base fluid in the presence of a magnetic field, which has not been investigated yet. So, in limiting cases the present work is validated with published work and found in excellent agreement as shown in Table 3.
Radiomics utilization to differentiate nonfunctional adenoma in essential hypertension and functional adenoma in primary aldosteronism
Authors: Chen Po-Ting , Chang Dawei , Liu Kao-Lang , Liao Wei-Chih , Wang Weichung , Chang Chin-Chen , Wu Vin-Cent , Lin Yen-Hung 
Published: May 2022

AbstractWe performed the present study to investigate the role of computed tomography (CT) radiomics in differentiating nonfunctional adenoma and aldosterone-producing adenoma (APA) and outcome prediction in patients with clinically suspected primary aldosteronism (PA). This study included 60 patients diagnosed with essential hypertension (EH) with nonfunctional adenoma on CT and 91 patients with unilateral surgically proven APA. Each whole nodule on unenhanced and venous phase CT images was segmented manually and randomly split into training and test sets at a ratio of 8:2. Radiomic models for nodule discrimination and outcome prediction of APA after adrenalectomy were established separately using the training set by least absolute shrinkage and selection operator (LASSO) logistic regression, and the performance was evaluated on test sets. The model can differentiate adrenal nodules in EH and PA with a sensitivity, specificity, and accuracy of 83.3%, 78.9% and 80.6% (AUC = 0.91 [0.72, 0.97]) in unenhanced CT and 81.2%, 100% and 87.5% (AUC = 0.98 [0.77, 1.00]) in venous phase CT, respectively. In the outcome after adrenalectomy, the models showed a favorable ability to predict biochemical success (Unenhanced/venous CT: AUC = 0.67 [0.52, 0.79]/0.62 [0.46, 0.76]) and clinical success (Unenhanced/venous CT: AUC = 0.59 [0.47, 0.70]/0.64 [0.51, 0.74]). The results showed that CT-based radiomic models hold promise to discriminate APA and nonfunctional adenoma when an adrenal incidentaloma was detected on CT images of hypertensive patients in clinical practice, while the role of radiomic analysis in outcome prediction after adrenalectomy needs further investigation.
Predicting the quality of soybean seeds stored in different environments and packaging using machine learning
Authors: da Silva André Geovane , Coradi Paulo Carteri , Teodoro Larissa Pereira Ribeiro , Teodoro Paulo Eduardo 
Published: May 2022

AbstractThe monitoring and evaluating the physical and physiological quality of seeds throughout storage requires technical and financial resources and is subject to sampling and laboratory errors. Therefore, machine learning (ML) techniques could help optimize the processes and obtain accurate results for decision-making in the seed storage process. This study aimed to analyze the performance of ML algorithms from variables monitored during seed conditioning (temperature and packaging) and storage time to predict the physical and physiological quality of stored soybean seeds. Data analysis was performed using the Artificial Neural Networks, decision tree algorithms REPTree and M5P, Random Forest, and Linear Regression. In predicting seed quality, the combination of the input variables temperature and storage time for REPTree and Random Forest algorithms outperformed the linear regression, providing higher accuracy indices. Among the most important results, it was observed for apparent specific mass that T + P + ST, T + ST, P + ST, and ST had the highest r means and the lowest MAE means, however, Person's r coefficient for these inputs was 0.63 and the MAE between 9.59 to 10.47. The germination results for inputs T + P + ST and T + ST had the best results (r = 0.65 and r = 0.67, respectively) in the ANN, REPTree, M5P and RF models. Using computational intelligence algorithms is an excellent alternative to predict the quality of soybean seeds from the information of easy-to-measure variables.
Fabrication of benzoyl chloride treated tiger-nut fiber reinforced insect repellent hybrid composite
Authors: Babayo Hajara , Musa Haruna , Garba Mustapha D. 
Published: May 2022

AbstractAn insect repellent composite containing tiger nut particulate fibre, waste low density polyethene (LDPE) and castor oil alkyd resin was fabricated. Canarium schweinfurthii gum was used as insect repellent compound and maleic anhydride as compatibilizer. The tiger nut chaff was subjected to benzoylation using benzoyl chloride to increase the fibre-matrix interaction. The compound and composition was then moulded with LDPE as dual matrices for excellent physico-mechanical properties (pressed for 5 min, 130 °C and 25 bar and cured). The 10 wt.% treated composite exhibited a minimum water absorption of ~ 0.085%, optimal chemical resistance for both acids (HCl and H2SO4) and bases (NaOH and KOH) and no effect on thickness. Density measurement showed the lowest value of ~ 0.0096 g/cm3 for the treated fibre composite. However, the tensile strength, flexural stress, hardness and impact load were improved up to 35.08 Mpa, 456.3 Mpa, 95 and 730 J/m respectively with treated composites. Insect repellent tests against termites and cockroaches show repellent activity with time intervals. FTIR and SEM analysis showed fibre modification achieved.
RNA-binding proteins and their role in translational regulation in plants
Authors: Duarte-Conde José Antonio , Sans-Coll Gemma , Merchante Catharina 
Published: May 2022

Abstract
Translation is a fundamental process for life that needs to be finely adapted to the energetical, developmental and environmental conditions; however, the molecular mechanisms behind such adaptation are not yet fully understood. By directly recognizing and binding to cis-elements present in their target mRNAs, RBPs govern all post-transcriptional regulatory processes. They orchestrate the balance between mRNA stability, storage, decay, and translation of their client mRNAs, playing a crucial role in the modulation of gene expression. In the last years exciting discoveries have been made regarding the roles of RBPs in fine-tuning translation. In this review, we focus on how these RBPs recognize their targets and modulate their translation, highlighting the complex and diverse molecular mechanisms implicated. Since the repertoire of RBPs keeps growing, future research promises to uncover new fascinating means of translational modulation, and thus, of gene expression.
Evolution of resistance (R) gene specificity
Authors: Märkle Hanna , Saur Isabel M.L. , Stam Remco 
Published: May 2022

Abstract
Plant resistance (R) genes are members of large gene families with significant within and between species variation. It has been hypothesised that a variety of processes have shaped R gene evolution and the evolution of R gene specificity. In this review, we illustrate the main mechanisms that generate R gene diversity and provide examples of how they can change R gene specificity. Next, we explain which evolutionary mechanisms are at play and how they determine the fate of new R gene alleles and R genes. Finally, we place this in a larger context by comparing the diversity and evolution of R gene specificity within and between species scales.
Plant immunity by damage-associated molecular patterns (DAMPs)
Authors: De Lorenzo Giulia , Cervone Felice 
Published: May 2022

AbstractRecognition by plant receptors of microbe-associated molecular patterns (MAMPs) and pathogenicity effectors activates immunity. However, before evolving the capacity of perceiving and responding to MAMPs and pathogenicity factors, plants, like animals, must have faced the necessity to protect and repair the mechanical wounds used by pathogens as an easy passage into their tissue. Consequently, plants evolved the capacity to react to damage-associated molecular patterns (DAMPs) with responses capable of functioning also in the absence of pathogens. DAMPs include not only primarily cell wall (CW) fragments but also extracellular peptides, nucleotides and amino acids that activate both local and long-distance systemic responses and, in some cases, prime the subsequent responses to MAMPs. It is conceivable that DAMPs and MAMPs act in synergy to activate a stronger plant immunity and that MAMPs exploit the mechanisms and transduction pathways traced by DAMPs. The interest for the biology and mechanism of action of DAMPs, either in the plant or animal kingdom, is expected to substantially increase in the next future. This review focuses on the most recent advances in DAMPs biology, particularly in the field of CW-derived DAMPs.