bluuebunny/crossref_metadata_2025_split huggingface dataset:
A systematic comparison of data- and knowledge-driven approaches to disease subtype discovery
Authors: Rintala Teemu J , Federico Antonio , Latonen Leena , Greco Dario , Fortino Vittorio 
Published: August 2021

AbstractTypical clustering analysis for large-scale genomics data combines two unsupervised learning techniques: dimensionality reduction and clustering (DR-CL) methods. It has been demonstrated that transforming gene expression to pathway-level information can improve the robustness and interpretability of disease grouping results. This approach, referred to as biological knowledge-driven clustering (BK-CL) approach, is often neglected, due to a lack of tools enabling systematic comparisons with more established DR-based methods. Moreover, classic clustering metrics based on group separability tend to favor the DR-CL paradigm, which may increase the risk of identifying less actionable disease subtypes that have ambiguous biological and clinical explanations. Hence, there is a need for developing metrics that assess biological and clinical relevance. To facilitate the systematic analysis of BK-CL methods, we propose a computational protocol for quantitative analysis of clustering results derived from both DR-CL and BK-CL methods. Moreover, we propose a new BK-CL method that combines prior knowledge of disease relevant genes, network diffusion algorithms and gene set enrichment analysis to generate robust pathway-level information. Benchmarking studies were conducted to compare the grouping results from different DR-CL and BK-CL approaches with respect to standard clustering evaluation metrics, concordance with known subtypes, association with clinical outcomes and disease modules in co-expression networks of genes. No single approach dominated every metric, showing the importance multi-objective evaluation in clustering analysis. However, we demonstrated that, on gene expression data sets derived from TCGA samples, the BK-CL approach can find groupings that provide significant prognostic value in both breast and prostate cancers.
UPLC–MS/MS Method Validation for Estimation of Resveratrol in Rat Skin from Liposphere Gel Formulation and Its Application to Dermatokinetic Studies in Rats
Authors: Rahman Mahfoozur , Afzal Obaid , Panda Sunil K , Kazmi Imran , Ali Ahmed Mahmoud Abdelhaleem , Alossaimi Manal A , Al-Abbasi Fahad A , Almalki Waleed H , Katouah Hanadi A , Kumar Vikas , Barkat Md Abul , Rub Rehan A , Beg Sarwar 
Published: August 2021

Abstract
For the quantification of resveratrol (RV) in the Wistar rat skin, an ultra-performance liquid chromatography-mass spectrometric (UPLC–MS/MS) method was developed and validated on ACQUITY UPLC BEH C18 column (1.7 μm). The mobile phase ratio of methanol (A) and 2% formic acid (B) (ratio 10: 90% v/v, 80: 20 v/v) at isocratic elution with flow rate 0.3 mL/min, and run time 3 min was used for analysis. In addition, the use of multiple reaction monitoring (MRM)/ES+ mode to detect the analytes and to track parents to daughter ion transition of 229.17 &gt; 107.04 m/z (time scan 3 min, retention time 1.48) for RV and curcumin as an internal standard shows 369.16 &gt; 176.93m/z (scan time is 2.80 min, retention time is 1.11), respectively. Linearity was observed in the range of 2.5 to 2,000 ng/mL (R2 = 0.987). Precision and accuracy on rat skin were within the acceptability range (RE%: ±15; RSD%: ±15). Moreover, it showed a good percentage recovery and found within acceptance limit 90–110%. Lower limit of detection and quantitation for the method observed to be 2.5 and 20 ng.mL−1, respectively. Method application indicated successful determination of dermatokinetics parameters of RV from lipospheres gel and suspension in the rats.
An Algorithm to Construct Completely Independent Spanning Trees in Line Graphs
Authors: Wang Yifeng , Cheng Baolei , Fan Jianxi , Qian Yu , Jiang Ruofan 
Published: August 2021

AbstractIn the past few years, much importance and attention have been attached to completely independent spanning trees (CISTs). Many results, such as edge-disjoint Hamilton cycles, traceability, number of spanning trees, structural properties, topological indices, etc., have been obtained on line graphs, and researchers have applied the line graphs of some interconnection networks such as generalized hypercubes, augmented cubes, crossed cubes, etc., into data center networks, such as SWCube, AQLCube, BCDC, etc. At the meanwhile, few results of CISTs are reported on the line graphs. In this paper, we establish the relation of edge-disjoint spanning trees in an interconnection network $G$’ with its line graph $G$ by proposing a general algorithm for the first time. By this method, more CISTs can be obtained comparing with results in the literature. Then, the decrease of diameter is discussed and simulation experiments are shown on the line graphs of hypercubes.
A Method for Building the Quantitative and Qualitative Part of Bayesian Networks for Intelligent Tutoring Systems
Authors: Ramírez-Noriega Alan , Juárez-Ramírez Reyes , Leyva-López Juan Carlos , Jiménez Samantha , Figueroa-Pérez J Francisco 
Published: August 2021

Abstract
The Bayesian network (BN) is an important technique to represent and infer knowledge in an Intelligent Tutoring System (ITS); however, ITSs are complex to build. Diverse authors have built BNs based on ontologies to accelerate the building process; nonetheless, they did not fully automate the process, and did not follow the ontologies standard Web Ontology Language, or simplified the final domain. This work proposes a method to build BNs based on ontologies and Wikipedia information to be employed on ITSs. The proposed method constructs the qualitative part of the BN through classes and relations of ontologies; the quantitative part is created based on frequencies, hops, and a measure of similarity between concepts of the ontology represented by Wikipedia articles. This study carried out an experiment to determine the correlation of our method against domain experts opinions; the method obtained a positive correlation of $0.647$ according to the Spearman test. The method constructs a BN to represent the knowledge in ITSs, in a similar way as experts would, supporting the automatic build of these systems.
Peptipedia: a user-friendly web application and a comprehensive database for peptide research supported by Machine Learning approach
Authors: Quiroz Cristofer , Saavedra Yasna Barrera , Armijo-Galdames Benjamín , Amado-Hinojosa Juan , Olivera-Nappa Álvaro , Sanchez-Daza Anamaria , Medina-Ortiz David 
Published: August 2021

Abstract
Peptides have attracted attention during the last decades due to their extraordinary therapeutic properties. Different computational tools have been developed to take advantage of existing information, compiling knowledge and making available the information for common users. Nevertheless, most related tools available are not user-friendly, present redundant information, do not clearly display the data, and usually are specific for particular biological activities, not existing so far, an integrated database with consolidated information to help research peptide sequences. To solve these necessities, we developed Peptipedia, a user-friendly web application and comprehensive database to search, characterize and analyse peptide sequences. Our tool integrates the information from 30 previously reported databases with a total of 92 055 amino acid sequences, making it the biggest repository of peptides with recorded activities to date. Furthermore, we make available a variety of bioinformatics services and statistical modules to increase our tool’s usability. Moreover, we incorporated a robust assembled binary classification system to predict putative biological activities for peptide sequences. Our tools’ significant differences with other existing alternatives become a substantial contribution for developing biotechnological and bioengineering applications for peptides. Peptipedia is available for non-commercial use as an open-access software, licensed under the GNU General Public License, version GPL 3.0. The web platform is publicly available at peptipedia.cl.
Database URL: Both the source code and sample data sets are available in the GitHub repository https://github.com/ProteinEngineering-PESB2/peptipedia
Personalized paroxysmal atrial fibrillation ablation by tailoring ablation index to the left atrial wall thickness: the ‘Ablate by-LAW’ single-centre study—a pilot study
Authors: Teres Cheryl , Soto-Iglesias David , Penela Diego , Jáuregui Beatriz , Ordoñez Augusto , Chauca Alfredo , Carreño Jose Miguel , Scherer Claudia , San Antonio Rodolfo , Huguet Marina , Roque Albert , Ramírez Carlos , Oller Guillermo , Jornet Agustí , Palet Jordi , Santana David , Panaro Alejandro , Maldonado Giuliana , de Leon Gustavo , Jiménez Gustavo , Evangelista Arturo , Carballo Julio , Ortíz-Pérez José-Tomás , Berruezo Antonio 
Published: August 2021

Abstract

Aims
To determine if adapting the ablation index (AI) to the left atrial wall thickness (LAWT), which is a determinant of lesion transmurality, is feasible, effective, and safe during paroxysmal atrial fibrillation (PAF) ablation.

Methods and results
Consecutive patients referred for PAF first ablation. Left atrial wall thickness three-dimensional maps were obtained from multidetector computed tomography and integrated into the CARTO navigation system. Left atrial wall thickness was categorized into 1 mm layers and AI was titrated to the LAWT. The ablation line was personalized to avoid thicker regions. Primary endpoints were acute efficacy and safety, and freedom from atrial fibrillation (AF) recurrences. Follow-up (FU) was scheduled at 1, 3, 6, and every 6 months thereafter. Ninety patients [60 (67%) male, age 58 ± 13 years] were included. Mean LAWT was 1.25 ± 0.62 mm. Mean AI was 366 ± 26 on the right pulmonary veins with a first-pass isolation in 84 (93%) patients and 380 ± 42 on the left pulmonary veins with first-pass in 87 (97%). Procedure time was 59 min (49–66); radiofrequency (RF) time 14 min (12.5–16); and fluoroscopy time 0.7 min (0.5–1.4). No major complication occurred. Eighty-four out of 90 (93.3%) patients were free of recurrence after a mean FU of 16 ± 4 months.

Conclusion
Personalized AF ablation, adapting the AI to LAWT allowed pulmonary vein isolation with low RF delivery, fluoroscopy, and procedure time while obtaining a high rate of first-pass isolation, in this patient population. Freedom from AF recurrences was as high as in more demanding ablation protocols. A multicentre trial is ongoing to evaluate reproducibility of these results.
Olfaction and Physical Functioning in Older Adults: A Longitudinal Study
Authors: Yuan Yaqun , Li Chenxi , Luo Zhehui , Simonsick Eleanor M , Shiroma Eric J , Chen Honglei 
Published: August 2021

Abstract

Background
Poor olfaction is associated with worse functional performance in older adults, but longitudinal evidence is lacking. We investigated poor olfaction in relation to longitudinal changes in physical functioning among community-dwelling older adults.

Method
The analysis included 2 319 participants from the Health, Aging and Body Composition study (aged 71–82 years, 47.9% men, and 37.3% Blacks) who completed the Brief Smell Identification Test in 1999–2000. Olfaction was defined as good (test score 11–12), moderate (9–10), or poor (0–8). Physical functioning was assessed up to 4 times over 8 years, using the Short Physical Performance Battery (SPPB) and the Health Aging and Body Composition Physical Performance Battery (HABCPPB). We conducted joint model analyses and reported the differences in annual declines across olfaction groups.

Results
During the follow-up, compared to those with good olfaction, older adults with poor olfaction had greater annual declines in both the SPPB score (−0.137, 95% CI: −0.186, −0.088) and all its subscales: standing balance (−0.068, 95% CI: −0.091, −0.044), chair stand (−0.046, 95% CI: −0.070, −0.022), and gait speed (−0.022, 95% CI: −0.042, −0.001). A similar observation was made for the HABCPPB score (difference in annual decline: −0.032, 95% CI: −0.042, −0.021). These findings are robust and cannot be explained by measured confounding from demographics, lifestyle factors, and chronic diseases or by potential biases due to death and loss of follow-up. Similar associations were observed across subgroups of sex, race, and self-reported general health status.

Conclusion
This study provides the first epidemiological evidence that poor olfaction predicts a faster decline in physical functioning. Future studies should investigate potential mechanisms.
A testbed for geomagnetic data assimilation
Authors: Gwirtz K , Morzfeld M , Kuang W , Tangborn A 
Published: August 2021

SUMMARYGeomagnetic data assimilation merges past and present-day observations of the Earth’s magnetic field with numerical geodynamo models and the results are used to initialize forecasts. We present a new ‘proxy model’ that can be used to test, or rapidly prototype, numerical techniques for geomagnetic data assimilation. The basic idea for constructing a proxy is to capture the conceptual difficulties one encounters when assimilating observations into high-resolution, 3-D geodynamo simulations, but at a much lower computational cost. The framework of using proxy models as ‘gate-keepers’ for numerical methods that could/should be considered for more extensive testing on operational models has proven useful in numerical weather prediction, where advances in data assimilation and, hence, improved forecast skill, are at least in part enabled by the common use of a wide range of proxy models. We also present a large set of systematic data assimilation experiments with the proxy to reveal the importance of localization and inflation in geomagnetic data assimilation.
Poor feeding opportunities and reduced condition factor for salmon post-smolts in the Northeast Atlantic Ocean
Authors: Utne Kjell Rong , Pauli Beatriz Diaz , Haugland Monika , Jacobsen Jan Arge , Maoileidigh Niall , Melle Webjørn , Broms Cecilie Thorsen , Nøttestad Leif , Holm Marianne , Thomas Katie , Wennevik Vidar 
Published: August 2021

AbstractDuring the last few decades, many wild Atlantic salmon populations have declined dramatically. One possible contributing factor for the decline is reduced prey availability at sea. Here, we examine post-smolt diet and investigate if post-smolts show signs of selective feeding based on 2546 post-smolts sampled from west of Ireland to the northern Norwegian Sea over a 25-year period. We also test for changes over time in stomach fullness, diet, condition factor and body length. There was a clear reduction in condition factor for post-smolts sampled in the Norwegian Sea in the period 2003–2012. The post-smolt stomach fullness was also reduced in the same period. The reduction in condition factor is partly explained by reduced stomach fullness, including a reduction of highly energetic fish larvae and Amphipoda in the diet. Feeding on other prey, such as meso-zooplankton and insects, cannot substitute the high-quality fish larvae and Amphipoda in the post-smolt diet. This is the first study to document how salmon post-smolts feeding in the Norwegian Sea are affected by reduced feeding conditions. Possible causes for the observed changes in post-smolt feeding are ocean warming, decreased primary productivity, and reduced recruitment of important fish larvae.
Crohn’s and Colitis Canada’s 2021 Impact of COVID-19 and Inflammatory Bowel Disease in Canada: Epidemiology—The Trends of Disease Over Time
Authors: Coward Stephanie , Windsor Joseph W , Kuenzig M Ellen , Bitton Alain , Bernstein Charles N , Jones Jennifer L , Khanna Reena , Lee Kate , Murthy Sanjay K , Targownik Laura , Benchimol Eric , Huang James Guoxian , Mukhtar Mariam S , Tandon Parul , Kaplan Gilaad G 
Published: August 2021

AbstractAt the beginning of the coronavirus disease 2019 (COVID-19) pandemic, there were many unknowns: transmission vectors of the virus, appropriate intervention strategies and if being immunocompromised due to inflammatory bowel disease (IBD), for example, or medications put a person at increased risk for severe COVID-19. Imposing and relaxing of public health restrictions at different times and in different regions in Canada led to different epidemiologies of the virus in different provinces and territories. In order to understand the waxing and waning of waves of the COVID-19 pandemic, it is necessary to understand the effective reproductive number (Rt) and the countervailing forces that exert upward or downward pressure on the spread of the virus at a given point in time. As many regions in Canada deal with a third wave, the primary forces affecting the Rt of severe acute respiratory syndrome coronavirus 2 are variants of concern and the increasing vaccinations of Canadians leading to increased population-level immunity. Fortunately, for the IBD population, current research suggests that those with IBD are not at increased risk of contracting COVID-19, nor of having a more severe disease course when compared to the general population.
Factors affecting antler growth period and casting date in red deer
Authors: Gómez José Ángel , Pérez-Barbería Javier , García Andrés José , Cappelli Jamil , Chonco Louis , Ceacero Francisco , Pérez-Serrano Martina , Landete-Castillejos Tomás 
Published: August 2021

AbstractAntlers are unique structures because they grow rapidly and are cast annually, representing an important energetic and mineral cost for deer. Variables related to the timing of antler growth, such as date of antler casting and length of growth period, therefore, should be affected by somatic resources and availability of food. We examined the effects of body and antler weight, age, and climatic variables, on antler casting date and the period of time antlers were grown as well as possible random effects of individual, year, cohort, and pedigree, based on 244 antlers in a population of 109 males of Iberian red deer (Cervus elaphus) over a 17-year study from 1999 to 2016. Body weight affected casting date, with heavier males casting antlers earlier than lighter males. Antlers also grew faster and were cast earlier among older males than young males. Antler weight influenced casting date and the duration of the growth period: males with heavier antlers cast them earlier and grow them faster than males with light antlers. Nevertheless, age and antler weight interacted; as such, older males grew their antlers slower and delay casting date because they produce heavier antlers, in contrast to younger males, where those with the heaviest antlers grow them faster and cast first. The date of the end of antler growth also influenced casting date, so that antlers that took the longest to develop were cast later than those that finished growing early. We conclude that older and heavier males cast their antlers earlier and grow them faster than younger and lighter males, likely to correlate the subsequent antler growth with the spring peak in plant nutrients, but that this early development is limited physiologically by the size of the antlers.
Invasive wild boar’s distribution overlap with threatened native ungulate in Patagonia
Authors: Bercê William , Bello Carolina , Mendes Calebe P , Vancine Maurício H , Galetti Mauro , Ballari Sebastián A 
Published: August 2021

Abstract
Wild boar (Sus scrofa) is one of the most damaging invasive species in the world and can have a profound impact on the distribution of native species. Nevertheless, there still are limitations on the species’ current fine-scale spatial information, which is needed to develop effective management measures. Here, we used Species Distribution Models (SDMs) and niche overlap analysis to estimate potential conflict areas between the wild boar and the native southern pudu (Pudu puda), which is a bioindicator of the forest conservation status within the Nahuel Huapi National Park (NHNP), Argentina. The two species’ environmental niche overlaps by 40%, which results in a wide geographical overlap between wild boar and pudu distributions. The distribution model predicted that the wild boar potential distribution occupies 22% of the national park and overlaps up to 67% with the pudu distribution, which in turn occupies 20% of the park. Based on our models, we classified 12% of the park as extreme management priority areas, because both species are present. High priority areas, where wild boars have the potential to invade but will not overlap with pudu populations, represent 10% of the park. Medium priority areas, where wild boars do not threaten pudu populations, and low priority areas, with no potential presence of either species, are 8% and 68%, respectively. The results of this study show how SDMs developed at local scales can support the management and monitoring of native and invasive species and help guide the allocation of efforts and resources for management actions focused on protected areas.
Rapid, midline retroperitoneal exposure for four-level anterior lumbar interbody fusion—technical case atlas
Authors: Malik Rema J , Falahee Mark H , Kahn Elyne N , Heidenreich Michael J , Springstead David , Aziz Abdulhameed 
Published: August 2021

AbstractWe describe a novel, rapid midline retroperitoneal operative technique in a patient, with multi-level degenerative scoliosis, who underwent an extensive L2-S1 anterior lumbar interbody fusion in addition to posterior instrumentation. Uniquely, our approach enables an essentially midline approach to the rectus muscle and uses the diminution of the transversalis fascia-to-peritoneum transition in the pelvis to provide expedited exposure—making it particularly helpful for ALIF exposure, retraction and intraoperative radiography. We minimize morbidity around the rectus sheath by dissecting only the medial rectus muscle and then gently, bluntly mobilizing the retroperitoneum from the deep pelvis cranially.
Reconstruction for rupture of profunda femoris artery aneurysm in a patient with sarcopenia
Authors: Tanaka Chiharu , Furuya Hidekazu , Yamaguchi Masaomi , Kanabuchi Kazuo , Kuwaki Kenji 
Published: August 2021

Abstract
Profunda femoris artery aneurysm (PFAA) is rare and has a high incidence of rupture. Herein, we report the case of an 80-year-old man who developed sarcopenia after gastric surgery. The patient presented to our hospital with a reddish thigh and was diagnosed with PFAA rupture. We performed aneurysmectomy and graft interposition in emergency. Postoperative enhanced computed tomography revealed an interposed graft, and the patient was discharged on postoperative Day 7. We considered that the PFAA patients with sarcopenia has a high risk of rupture because the muscles surrounding the profunda femoris artery became weak, and should be followed-up closely.