bluuebunny/crossref_metadata_2025 huggingface dataset:
KLF9 and EPYC acting as feature genes for osteoarthritis and their association with immune infiltration
Authors: Zhang Jiayin , Zhang Shengjie , Zhou Yu , Qu Yuan , Hou Tingting , Ge Wanbao , Zhang Shanyong
Published: July 2022

Background

Osteoarthritis, a common degenerative disease of articular cartilage, is characterized by degeneration of articular cartilage, changes in subchondral bone structure, and formation of osteophytes, with main clinical manifestations including increasingly serious swelling, pain, stiffness, deformity, and mobility deficits of the knee joints. With the advent of the big data era, the processing of mass data has evolved into a hot topic and gained a solid foundation from the steadily developed and improved machine learning algorithms. Aiming to provide a reference for the diagnosis and treatment of osteoarthritis, this paper using machine learning identifies the key feature genes of osteoarthritis and explores its relationship with immune infiltration, thereby revealing its pathogenesis at the molecular level.

Methods

From the GEO database, GSE55235 and GSE55457 data were derived as training sets and GSE98918 data as a validation set. Differential gene expressions of the training sets were analyzed, and the LASSO regression model and support vector machine model were established by applying machine learning algorithms. Moreover, their intersection genes were regarded as feature genes, the receiver operator characteristic (ROC) curve was drawn, and the results were verified using the validation set. In addition, the expression spectrum of osteoarthritis was analyzed by immunocyte infiltration and the co-expression correlation between feature genes and immunocytes was construed.

Conclusion

EPYC and KLF9 can be viewed as feature genes for osteoarthritis. The silencing of EPYC and the overexpression of KLF9 are associated with the occurrence of osteoarthritis and immunocyte infiltration.
Association of low-dose glucocorticoid use and infection occurrence in systemic lupus erythematosus patients: a prospective cohort study
Authors: Abe Kazuya , Ishikawa Yuichi , Kita Yasuhiko , Yajima Nobuyuki , Inoue Eisuke , Sada Ken-ei , Miyawaki Yoshia , Yoshimi Ryusuke , Shimojima Yasuhiro , Ohno Shigeru , Kajiyama Hiroshi , Ichinose Kunihiro , Sato Shuzo , Fujiwara Michio
Published: July 2022

Background

Infection is a major cause of mortality in patients with systemic lupus erythematosus (SLE). Therefore, minimizing the risk of infection is an important clinical goal to improve the long-term prognosis of SLE patients. Treatment with ≥7.5 mg prednisolone (PSL) or equivalent has been reported to increase the risk of infections. However, it remains unclear whether <7.5 mg PSL or equivalent dose affects the risk of infection in SLE patients. This study evaluated the association between the occurrence of infection in patients with SLE and low-dose glucocorticoid (GC) usage, especially <7.5 mg PSL or equivalent, to explore the GC dose that could reduce infection occurrence.

Methods

This prospective cohort study included patients from the Japanese multicenter registry of patients with SLE (defined as ≥4 American College of Rheumatology 1997 revised criteria) over 20 years of age. The PSL dose was categorized as PSL 0–2.5, 2.6–5.0, 5.1–7.5, and 7.6–15.0 mg. The primary outcome was infection requiring hospitalization. We conducted a multivariable analysis using time-dependent Cox regression analysis to assess the hazard ratio of infection occurrence compared with a dose of 0–2.5 mg PSL or equivalent in the other three PSL dose groups. Based on previous reports and clinical importance, the covariates selected were age, sex, and concurrent use of immunosuppressants with GC. In addition, two sensitivity analyses were conducted.

Results

The mean age of the 509 SLE patients was 46.7 years; 89.0% were female, and 77.2% used multiple immunosuppressants concomitantly. During the observation period, 52 infections requiring hospitalization occurred. The incidence of infection with a PSL dose of 5.0–7.5 mg was significantly higher than that in the PSL 0–2.5 mg group (adjusted hazard ratio: 6.80, 95% confidence interval: 2.17–21.27). The results of the two sensitivity analyses were similar.

Conclusions

Our results suggested that the use of 5.0–7.5 mg PSL or equivalent could pose an infection risk in SLE patients. This finding indicates that PSL dose should be reduced to as low as possible in SLE patients to avoid infection.
Dataset for classifying and estimating the position, orientation, and dimensions of a list of primitive objects
Authors: Makki Alireza , Hadi Alireza , Tarvirdizadeh Bahram , Teimouri Mehdi
Published: July 2022

Objectives

Robotic systems are moving toward more interaction with the environment, which requires improving environmental perception methods. The concept of primitive objects simplified the perception of the environment and is frequently used in various fields of robotics, significantly in the grasping challenge. After reviewing the related resources and datasets, we could not find a suitable dataset for our purpose, so we decided to create a dataset to train deep neural networks to classify a primitive object and estimate its position, orientation, and dimensions described in this report.

Data description

This dataset contains 8000 virtual data for four primitive objects, including sphere, cylinder, cube, and rectangular sheet with dimensions between 10 to 150 mm, and 200 real data of these four types of objects. Real data are provided by Intel Realsense SR300 3D camera, and virtual data are generated using the Gazebo simulator. Raw data are generated in.pcd format in both virtual and real types. Data labels include values of the object type and its position, orientation, and dimensions.
Spatial differences in Casuarina equisetifolia L. endophyte community structure
Authors: Lin Qi , Xu Zhixia , Li Miaomiao , Wang Ying , Li Lei
Published: July 2022

Purpose

Casuarina equisetifolia, a fast-growing, abundant tree species on the southeastern coast of China, plays an important role in protecting the coastal environment, but the ecological processes that govern microbiome assembly and within-plant microorganism transmission are poorly known.

Methods

In this paper, we used ITS and 16S amplification techniques to study the diversity of fungal and bacterial endophytes in critical plant parts of this species: seeds, branchlets, and roots. Additionally, we examined the litter of this species to understand the process of branchlets from birth to litter.

Result

We uncovered a non-random distribution of endophyte diversity in which branchlets had the greatest and seeds had the lowest endophytic fungal diversity. In contrast, litter endophytic bacteria had the highest diversity, and branchlets had the lowest diversity. As for fungi, a large part of the seed microbiome was transmitted to the phyllosphere, while a large part of the bacterial microbiome in the seed was transmitted to the root.

Conclusion

Our study provides comprehensive evidence on diversity, potential sources, and transmission pathways for non-crop microbiome assembly and has implications for the management and manipulation of the non-crop microbiome in the future.
A comparison of Covid-19 early detection between convolutional neural networks and radiologists
Authors: Albiol Alberto , Albiol Francisco , Paredes Roberto , Plasencia-Martínez Juana María , Blanco Barrio Ana , Santos José M. García , Tortajada Salvador , González Montaño Victoria M. , Rodríguez Godoy Clara E. , Fernández Gómez Saray , Oliver-Garcia Elena , de la Iglesia Vayá María , Márquez Pérez Francisca L. , Rayo Madrid Juan I.
Published: July 2022

Background

The role of chest radiography in COVID-19 disease has changed since the beginning of the pandemic from a diagnostic tool when microbiological resources were scarce to a different one focused on detecting and monitoring COVID-19 lung involvement. Using chest radiographs, early detection of the disease is still helpful in resource-poor environments. However, the sensitivity of a chest radiograph for diagnosing COVID-19 is modest, even for expert radiologists. In this paper, the performance of a deep learning algorithm on the first clinical encounter is evaluated and compared with a group of radiologists with different years of experience.

Methods

The algorithm uses an ensemble of four deep convolutional networks, Ensemble4Covid, trained to detect COVID-19 on frontal chest radiographs. The algorithm was tested using images from the first clinical encounter of positive and negative cases. Its performance was compared with five radiologists on a smaller test subset of patients. The algorithm's performance was also validated using the public dataset COVIDx.

Results

Compared to the consensus of five radiologists, the Ensemble4Covid model achieved an AUC of 0.85, whereas the radiologists achieved an AUC of 0.71. Compared with other state-of-the-art models, the performance of a single model of our ensemble achieved nonsignificant differences in the public dataset COVIDx.

Conclusion

The results show that the use of images from the first clinical encounter significantly drops the detection performance of COVID-19. The performance of our Ensemble4Covid under these challenging conditions is considerably higher compared to a consensus of five radiologists. Artificial intelligence can be used for the fast diagnosis of COVID-19.
Niemann-Pick type A disease with new mutation: a case report
Authors: Aghamahdi Fatemeh , Nirouei Matineh , Savad Shahram
Published: July 2022

Background

Niemann-Pick type A (NP-A) is a congenital, hereditary disease caused by a deficiency in acid sphingomyelinase, a lysosomal enzyme. This deficiency results in an accumulation of sphingomyelin in lysosomes, leading to cellular apoptosis and ultimately to hepatosplenomegaly, neurodegenerative disorder and failure to thrive. Cherry-red spots in the macula and foamy cells in the bone marrow are other manifestations of the disease that help with diagnosis. Type A is a rare, untreatable disease with early manifestations and a poor prognosis, with newborns rarely surviving for 2–3 years.

Case presentation

A 1-year-old Persian boy was referred to our clinic due to abdominal distention and poor weight gain. He was the first male offspring of consanguineous parents. Other findings were neurodevelopmental delay, hepatosplenomegaly, severe hypotonia, difficulty in breathing, and a slightly coarse face with an open mouth and protruding tongue. The initial diagnosis was clinical mucopolysaccharidosis (MPS) based on the coarse facial features, but further workup ruled out this inherited disorder. Enzyme histochemistry revealed that the level of acid sphingomyelinase was lower than normal. In the genetic study, next-generation sequencing of all coding exons and flanking intronic regions of the patient’s DNA demonstrated a homozygous c.682T>G variant in the SMPD1 gene. This variant was classified as a variant of unknown significance. Further evaluation of DNA extract from his parents and examined using Sanger sequencing showed a heterozygous c.682T>G variant in the SMPD1 gene of both parents.

Conclusions

We describe a 1-year-old boy with neurodevelopmental delay, hepatosplenomegaly, and severe hypotonia. Further investigation demonstrated a new mutation for Niemann-Pick disease.
TAS2R supports odontoblastic differentiation of human dental pulp stem cells in the inflammatory microenvironment
Authors: Kang Wen , Wang Yiwen , Li Jiaying , Xie Weige , Zhao Dan , Wu Li , Wang Hongwei , Xie Sijing
Published: July 2022

Background

Inflammatory microenvironment promotes odontoblastic differentiation in human dental pulp stem cells (hDPSCs), but the regulatory mechanisms remain unclear. In this study, we aimed to explore the role of TAS2R in odontoblastic differentiation of hDPSCs in the inflammatory microenvironment.

Methods

Microarray analysis was performed to explore the differential mRNA profiles in inflammatory and healthy pulp tissues from the patients. hDPSCs isolated from the healthy pulp tissues were stimulated by LPS, TNFα and IL-6, respectively, to verify the effect of TAS2R. The expression markers related to odontoblastic differentiation of hDPSCs were observed by qPCR and chemical staining methods. TAS2R10 was overexpressed or silenced to observe the effect on odontoblastic differentiation of hDPSCs under LPS stimulation. The G protein and intracellular Ca2+were detected, respectively, by qPCR and Fluo-4AM Ca2+fluorescent probe.

Results

The expression of TAS2R was significantly upregulated in the inflammatory pulp tissues. In vitro, 5 subtypes of TAS2R mRNA expressions including TAS2R10, TAS2R14, TAS2R19, TAS2R30 and TAS2R31 in hDPSCs increased under the stimulation of LPS, TNFα or IL-6. In odontoblastic differentiation medium, we found LPS, TNFα or IL-6 stimulation promoted odontoblastic differentiation of hDPSCs. TAS2R10 overexpression in hDPSCs significantly increased the expression markers related to odontoblastic differentiation, whereas TAS2R10 silencing revealed the opposite effect. Furthermore, G protein was activated, and at the same time, intracellular Ca2+enhanced when TAS2R10 was overexpressed, but decreased when TAS2R10 was silenced.

Conclusions

This study demonstrated that TAS2R was found to be expressed in hDPSCs, and TAS2R promoted odontoblastic differentiation of hDPSCs by mediating the increase in intracellular Ca2+via the G protein-coupled receptors (GPCR) conventional signaling pathway in inflammatory microenvironment, which may be a potential target for the development of effective conservative treatments for dental pulp repair.
Chain-structure time-delay reservoir computing for synchronizing chaotic signal and an application to secure communication
Authors: Jin Leisheng , Liu Zhuo , Li Lijie
Published: July 2022

In this work, a chain-structure time-delay reservoir (CSTDR) computing, as a new kind of machine learning-based recurrent neural network, is proposed for synchronizing chaotic signals. Compared with the single time-delay reservoir, our proposed CSTDR computing shows excellent performance in synchronizing chaotic signal achieving an order of magnitude higher accuracy. Noise consideration and optimal parameter setting of the model are discussed. Taking the CSTDR computing as the core, a novel scheme of secure communication is further designed, in which the “smart” receiver is different from the traditional in that it can synchronize to the chaotic signal used for encryption in an adaptive manner. The scheme can solve the issues such as design constrains for identical dynamical systems and couplings between transmitter and receiver in conventional settings. To further manifest the practical significance of the scheme, the digital implementation using field-programmable gate array is conducted and tested experimentally with real-world examples including image and video transmission. The work sheds light on developing machine learning-based signal processing and communication applications.
Feasibility of a tele-prehabilitation program in high-risk patients with colon or rectal cancer undergoing elective surgery: a feasibility study
Authors: Franssen Ruud F. W. , Bongers Bart C. , Vogelaar F. Jeroen , Janssen-Heijnen Maryska L. G.
Published: July 2022

Background

Prehabilitation appears to be an effective strategy to reduce postoperative complications and enhance recovery after colorectal surgery. Although many patients prefer (unsupervised) home-based prehabilitation, adherence can be problematic. Combining home-based prehabilitation with tele-monitoring might demonstrate a higher adherence than unsupervised prehabilitation; however, evidence on its feasibility and effectiveness in patients with colorectal cancer scheduled for elective surgery who are at high risk for postoperative complications is lacking. The aim of this study was to assess the feasibility of a bimodal tele-prehabilitation program in patients with colorectal cancer at high risk for postoperative complications.

Methods

High-risk patients (oxygen uptake at the ventilatory anaerobic threshold ≤11 mL/kg/min or oxygen uptake at peak exercise ≤ 18 mL/kg/min) with colorectal cancer were included in a home-based bimodal tele-prehabilitation program. The program consisted of a personalized tele-monitored moderate to high-intensity interval training intervention and nutritional counseling. Feasibility was measured by participation rate, dropout rate, adherence to the physical exercise training session’s frequency, intensity, and time, and retention rate. Patient appreciation was measured by a patient appreciation questionnaire. Changes in preoperative physical fitness as secondary outcomes were quantified by time to exhaustion on a constant work rate (cycle) test, number of repetitions on the 30-s chair-stand test, and walking speed on the 4-m gait speed test.

Results

The participation rate was 81%, there were no adverse events, and all participants managed to complete the tele-prehabilitation program (retention rate of 100%). Adherence with regard to the exercise program’s frequency, intensity, and time was respectively 91%, 84%, and 100%. All participants appreciated the tele-prehabilitation program. Time to exhaustion on the constant work rate test improved (not statistically significant) from a pre-prehabilitation median score of 317 seconds to a post-prehabilitation median score of 412 seconds (p= 0.24). Median number of repetitions on the 30-s chair-stand test improved from 12 to 16 (p= 0.01).

Conclusions

Tele-prehabilitation seems feasible in high-risk patients with colorectal cancer, but efforts should be made to further improve adherence to physical exercise training intensity. More research is needed to establish the (cost-)effectiveness of tele-prehabilitation regarding preoperative improvements in preoperative aerobic fitness and postoperative reduction of complications.

Trial registration

ISRCTN,ISRCTN64482109. Registered 09 November 2021 - Retrospectively registered.
Capacity utilization, factor substitution, and productivity growth in Canadian food processing sector
Authors: Gamtessa Samuel
Published: July 2022

The food processing industry has been confronted with unprecedented challenges as the costs of raw materials have risen rapidly, owing in part to the increased use of grains for ethanol. It is critical to comprehend how these trends affect the industry and potential coping techniques. This study estimates capacity utilization, which is a measurement that is well-suited to identify how input prices affect productivity in the short-run. The results show that capacity utilization decreased significantly after the year 2005 when raw materials input prices skyrocketed. TFP growth has also slowed significantly because of this. According to the estimated elasticities, the industry has little potential to deal with the cost challenge through factor substitution. Another conclusion is that capacity utilization has a positive elasticity with respect to the cost of raw materials. Because it is related to induced capital stock adjustment, which is only achievable in the long run, this is an indicator of how the industry will be affected in the long-run.
Supercarriers of antibiotic resistome in a world’s large river
Authors: Wang Jiawen , Pan Rui , Dong Peiyan , Liu Shufeng , Chen Qian , Borthwick Alistair G. L. , Sun Liyu , Xu Nan , Ni Jinren
Published: July 2022

Background

Antibiotic resistome has been found to strongly interact with the core microbiota in the human gut, yet little is known about how antibiotic resistance genes (ARGs) correlate with certain microbes in large rivers that are regarded as “terrestrial gut.”

Results

By creating the integral pattern for ARGs and antibiotic-resistant microbes in water and sediment along a 4300-km continuum of the Yangtze River, we found that human pathogen bacteria (HPB) share 13.4% and 5.9% of the ARG hosts in water and sediment but contribute 64% and 46% to the total number of planktonic and sedimentary ARGs, respectively. Moreover, the planktonic HPB harbored 79 ARG combinations that are dominated by “natural” supercarriers (e.g., Rheinheimera texasensis and Noviherbaspirillum sp. Root189) in river basins.

Conclusions

We confirmed that terrestrial HPB are the major ARG hosts in the river, rather than conventional supercarriers (e.g., Enterococcus spp. and other fecal indicator bacteria) that prevail in the human gut. The discovery of HPB as natural supercarriers in a world’s large river not only interprets the inconsistency between the spatial dissimilarities in ARGs and their hosts, but also highlights the top priority of controlling terrestrial HPB in the future ARG-related risk management of riverine ecosystems globally.
Long-term nitrogen deposition enhances microbial capacities in soil carbon stabilization but reduces network complexity
Authors: Ma Xingyu , Wang Tengxu , Shi Zhou , Chiariello Nona R. , Docherty Kathryn , Field Christopher B. , Gutknecht Jessica , Gao Qun , Gu Yunfu , Guo Xue , Hungate Bruce A. , Lei Jiesi , Niboyet Audrey , Le Roux Xavier , Yuan Mengting , Yuan Tong , Zhou Jizhong , Yang Yunfeng
Published: July 2022

Background

Anthropogenic activities have increased the inputs of atmospheric reactive nitrogen (N) into terrestrial ecosystems, affecting soil carbon stability and microbial communities. Previous studies have primarily examined the effects of nitrogen deposition on microbial taxonomy, enzymatic activities, and functional processes. Here, we examined various functional traits of soil microbial communities and how these traits are interrelated in a Mediterranean-type grassland administrated with 14 years of 7 g m−2 year−1 of N amendment, based on estimated atmospheric N deposition in areas within California, USA, by the end of the twenty-first century.

Results

Soil microbial communities were significantly altered by N deposition. Consistent with higher aboveground plant biomass and litter, fast-growing bacteria, assessed by abundance-weighted average rRNA operon copy number, were favored in N deposited soils. The relative abundances of genes associated with labile carbon (C) degradation (e.g., amyA and cda) were also increased. In contrast, the relative abundances of functional genes associated with the degradation of more recalcitrant C (e.g., mannanase and chitinase) were either unchanged or decreased. Compared with the ambient control, N deposition significantly reduced network complexity, such as average degree and connectedness. The network for N deposited samples contained only genes associated with C degradation, suggesting that C degradation genes became more intensely connected under N deposition.

Conclusions

We propose a conceptual model to summarize the mechanisms of how changes in above- and belowground ecosystems by long-term N deposition collectively lead to more soil C accumulation.
Barriers and opportunities to accessing social support in the transition from community to prison: a qualitative interview study with incarcerated individuals in Northern Norway
Authors: Solbakken Line Elisabeth , Wynn Rolf
Published: July 2022

Background

Incarcerated individuals have poor mental health compared to the general population. Social support has a beneficial effect on mental health. The buffering model proposes that social support facilitates coping under stressful conditions, while the main effects model suggests that belonging to social networks and having positive social interactions are beneficial for mental health. Prisons are a highly interesting context for studying social support, as imprisonment is perceived as stressful and disrupts social relationships and the availability of support. This study aims to explore incarcerated individuals' perceptions of social support from various sources in the transition from community to prison, its perceived significance for mental health, and the opportunities and barriers to accessing social support in a Norwegian prison context.

Methods

The experiences of eight incarcerated individuals from a prison in Northern Norway were gathered through conducting individual in-depth interviews. The data analysis was inspired by Charmaz’s version of Grounded Theory.

Results

Social support from peers was perceived to be important for the well-being and preserving of mental health in prison. Support from informal sources outside prison and prison officers were not granted the same significance by the participants. Although prison life was perceived as stressful, social support in the form of companionship, the feeling of belonging, shared activities, and everyday conversations were more important for the participants than support focusing on coping with the stress of incarceration.

Conclusions

Peers are perceived to be the most important source of social support, and vital for well-being and mental health in prison. Barriers to support from family, friends and prison officers may amplify the significance of support from peers.
A randomized, double-blind, phase III, non-inferiority clinical trial comparing the efficacy and safety of TA4415V (a proposed Trastuzumab biosimilar) and Herceptin (Trastuzumab reference product) in HER2-positive early-stage breast Cancer patients
Authors: Nodehi Reza Safaei , Kalantari Behjat , Raafat Jahangir , Ansarinejad Nafiseh , Moazed Vahid , Mortazavizadeh Seyed Mohammad Reza , Hosseinzadeh Mehran , Ghaderi Bayazid , Jenabian Arash , Qadyani Mojtaba , Haghighat Shirin , Allahyari Abolghasem , Mirzania Mehrzad , Seghatoleslami Mohammad , Payandeh Mehrdad , Alikhasi Afsaneh , Kafi Hamidreza , Shahi Farhad
Published: July 2022

Background

This study compared efficacy and safety of TA4415V, a trastuzumab biosimilar, with reference trastuzumab in patients with human epidermal growth factor receptor 2–positive (HER2-positive) early-stage breast cancer treated in the neoadjuvant setting in Iran.

Methods

Patients were randomly assigned to receive neoadjuvant TA4415V or reference trastuzumab concurrently with docetaxel (TH phase) for 4 cycles after treatment with 4 cycles of doxorubicin and cyclophosphamide (AC phase). Chemotherapy was followed by surgery. The primary endpoint was the comparison of pathologic complete response (pCR) rate in the per-protocol population. Secondary endpoints included comparisons of overall response rate (ORR), breast-conserving surgery (BCS), safety, and immunogenicity.

Results

Ninety-two participants were analyzed in the per-protocol population (TA4415V, n = 48; reference trastuzumab, n = 44). The pCR rates were 37.50% and 34.09% with TA4415V and reference drug, respectively. The 95% CI of the estimated treatment outcome difference (− 0·03 [95% CI − 0.23 to 0.16]) was within the non-inferiority margin. No statistically significant difference was observed between the groups for other efficacy variables in the ITT population: ORR (89.13% vs. 83.33%; p = 0.72) and BCS (20.37% vs. 12.96%; p = 0.42) in the TA4415V and reference drug group, respectively.

At least one grade 3 or 4 adverse events occurred in 27 (50%) patients in the TA4415V group versus 29 (53.70%) in the reference trastuzumab group (p = 0.70). The decrease in left ventricular ejection fraction (LVEF), as an adverse event of special interest (AESI) for trastuzumab, was compared between treatment groups in TH phase. Results demonstrated an LVEF decrease in 7 (12.96%) and 9 (16.67%) patients in TA4415V and reference trastuzumab groups, respectively (p = 0.59). Anti-drug antibodies (ADA) were not detected in any samples of groups.

Conclusions

Non-inferiority for efficacy was demonstrated between TA4415V and Herceptin based on the ratio of pCR rates in HER2-positive early breast cancer patients. In addition, ORR and BCS, as secondary endpoints, were not significantly different. Safety profile and immunogenicity were also comparable between the two groups.
Extrachromosomal circular DNA (eccDNA): an emerging star in cancer
Authors: Li Ruomeng , Wang Ying , Li Jing , Zhou Xikun
Published: July 2022

Extrachromosomal circular DNA (eccDNA) is defined as a type of circular DNA that exists widely in nature and is independent of chromosomes. EccDNA has attracted the attention of researchers due to its broad, random distribution, complex biogenesis and tumor-relevant functions. EccDNA can carry complete gene information, especially the oncogenic driver genes that are often carried in tumors, with increased copy number and high transcriptional activity. The high overexpression of oncogenes by eccDNA leads to malignant growth of tumors. Regardless, the exact generation and functional mechanisms of eccDNA in disease progression are not yet clear. There is, however, an emerging body of evidence characterizing that eccDNA can be generated from multiple pathways, including DNA damage repair pathways, breakage-fusion-bridge (BFB) mechanisms, chromothripsis and cell apoptosis, and participates in the regulation of tumor progression with multiplex functions. This up-to-date review summarizes and discusses the origins, biogenesis and functions of eccDNA, including its contribution to the formation of oncogene instability and mutations, the heterogeneity and cellular senescence of tumor cells, and the proinflammatory response of tumors. We highlight the possible cancer-related applications of eccDNA, such as its potential use in the diagnosis, targeted therapy and prognostic assessment of cancer.
A practical workflow for the 3D reconstruction of complex historic sites and their decorative interiors: Florence As It Was and the church of Orsanmichele
Authors: Bent George R. , Pfaff David , Brooks Mackenzie , Radpour Roxanne , Delaney John
Published: July 2022

The Digital Humanities project Florence As It Was (http://florenceasitwas.wlu.edu) seeks to reconstruct the architectural and decorative appearance of late Medieval and early Modern buildings by combining 3D point cloud models of buildings (i.e. extant structures such as chapels, churches, etc.) with 3D rendered models of artworks that were installed inside them during the fourteenth and fifteenth centuries. This paper documents a novel bifurcated workflow that allows the construction of such integrated 3D models as well as an example case study of a church in Florence, Italy called Orsanmichele (https://3d.wlu.edu/v21/pages/orsanmichele2.html). The key steps worked out in the optimized workflow include: (1) art historical research to identify the original artworks in each building, (2) the use of LiDAR scanners to obtain 3D data (along with associated color information) of the interiors and exteriors of buildings, (3) the use of high resolution photogrammetry of works of art (i.e. paintings and sculptures) which have been removed from those buildings and are now in public collections, (4) the generation of point clouds from the 3D data of the buildings and works of art, (5) the editing and cojoining of a textured polygon model of artworks with a reduced size (using novel algorithms) point cloud model of the buildings in an open-source software tool called Potree so that artworks can be embedded in their original architectural settings, and (6) the annotation of these models with scholarly art historical texts that present viewers immediate access to information, archival evidence, and historical descriptions of these spaces. The integrated point cloud and textured models of buildings and artworks, respectively, plus annotations are then published with Potree. This process has resulted in the development of highly accurate virtual reconstructions of key monuments from the Florentine Middle Ages and Renaissance (like the fourteenth century building of Orsanmichele and the multiple paintings that were once inside it) as they originally appeared. The goal of this project is to create virtual models for scholars and students to explore research questions while providing key information that may assist in generating new projects. Such models represent a significant tool to allow improved teaching of art and architectural history. Furthermore, since the assigned location of some of the historic artworks within these sites are not always firmly known, the virtual model allows users to experiment with potential arrangements of objects in and on the buildings they may have originally decorated.
Predicting implementation of active learning by tenure-track teaching faculty using robust cluster analysis
Authors: Denaro Kameryn , Kranzfelder Petra , Owens Melinda T. , Sato Brian , Zuckerman Austin L. , Hardesty Rebecca A. , Signorini Adriana , Aebersold Andrea , Verma Mayank , Lo Stanley M.
Published: July 2022

Background

The University of California system has a novel tenure-track education-focused faculty position called Lecturer with Security of Employment (working titles: Teaching Professor or Professor of Teaching). We focus on the potential difference in implementation of active-learning strategies by faculty type, including tenure-track education-focused faculty, tenure-track research-focused faculty, and non-tenure-track lecturers. In addition, we consider other instructor characteristics (faculty rank, years of teaching, and gender) and classroom characteristics (campus, discipline, and class size). We use a robust clustering algorithm to determine the number of clusters, identify instructors using active learning, and to understand the instructor and classroom characteristics in relation to the adoption of active-learning strategies.

Results

We observed 125 science, technology, engineering, and mathematics (STEM) undergraduate courses at three University of California campuses using the Classroom Observation Protocol for Undergraduate STEM to examine active-learning strategies implemented in the classroom. Tenure-track education-focused faculty are more likely to teach with active-learning strategies compared to tenure-track research-focused faculty. Instructor and classroom characteristics that are also related to active learning include campus, discipline, and class size. The campus with initiatives and programs to support undergraduate STEM education is more likely to have instructors who adopt active-learning strategies. There is no difference in instructors in the Biological Sciences, Engineering, or Information and Computer Sciences disciplines who teach actively. However, instructors in the Physical Sciences are less likely to teach actively. Smaller class sizes also tend to have instructors who teach more actively.

Conclusions

The novel tenure-track education-focused faculty position within the University of California system represents a formal structure that results in higher adoption of active-learning strategies in undergraduate STEM education. Campus context and evolving expectations of the position (faculty rank) contribute to the symbols related to learning and teaching that correlate with differential implementation of active learning.
Induction of severe hypoxemia and low lung recruitability for the evaluation of therapeutic ventilation strategies: a translational model of combined surfactant-depletion and ventilator-induced lung injury
Authors: Boerger Emilia , Russ Martin , von Platen Philip , Taher Mahdi , Hinken Lea , Pomprapa Anake , Koebrich Rainer , Konietschke Frank , Graw Jan Adriaan , Lachmann Burkhard , Braun Wolfgang , Leonhardt Steffen , Pickerodt Philipp A. , Francis Roland C. E.
Published: July 2022

Background

Models of hypoxemic lung injury caused by lavage-induced pulmonary surfactant depletion are prone to prompt recovery of blood oxygenation following recruitment maneuvers and have limited translational validity. We hypothesized that addition of injurious ventilation following surfactant-depletion creates a model of the acute respiratory distress syndrome (ARDS) with persistently low recruitability and higher levels of titrated “best” positive end-expiratory pressure (PEEP) during protective ventilation.

Methods

Two types of porcine lung injury were induced by lung lavage and 3 h of either protective or injurious ventilation, followed by 3 h of protective ventilation (N = 6 per group). Recruitment maneuvers (RM) and decremental PEEP trials comparing oxygenation versus dynamic compliance were performed after lavage and at 3 h intervals of ventilation. Pulmonary gas exchange function, respiratory mechanics, and ventilator-derived parameters were assessed after each RM to map the course of injury severity and recruitability.

Results

Lung lavage impaired respiratory system compliance (Crs) and produced arterial oxygen tensions (PaO2) of 84±13 and 80±15 (FIO2 = 1.0) with prompt increase after RM to 270–395 mmHg in both groups. After subsequent 3 h of either protective or injurious ventilation, PaO2/FIO2 was 104±26 vs. 154±123 and increased to 369±132 vs. 167±87 mmHg in response to RM, respectively. After additional 3 h of protective ventilation, PaO2/FIO2 was 120±15 vs. 128±37 and increased to 470±68 vs. 185±129 mmHg in response to RM, respectively. Subsequently, decremental PEEP titration revealed that Crs peaked at 36 ± 10 vs. 25 ± 5 ml/cm H2O with PEEP of 12 vs. 16 cmH2O, and PaO2/FIO2 peaked at 563 ± 83 vs. 334 ± 148 mm Hg with PEEP of 16 vs. 22 cmH2O in the protective vs. injurious ventilation groups, respectively. The large disparity of recruitability between groups was not reflected in the Crs nor the magnitude of mechanical power present after injurious ventilation, once protective ventilation was resumed.

Conclusion

Addition of transitory injurious ventilation after lung lavage causes prolonged acute lung injury with diffuse alveolar damage and low recruitability yielding high titrated PEEP levels. Mimicking lung mechanical and functional characteristics of ARDS, this porcine model rectifies the constraints of single-hit lavage models and may enhance the translation of experimental research on mechanical ventilation strategies.
The Relationship Between Undulatory Underwater Kick Performance Determinants and Underwater Velocity in Competitive Swimmers: A Systematic Review
Authors: West Rani , Lorimer Anna , Pearson Simon , Keogh Justin W. L.
Published: July 2022

Background

Undulatory underwater swimming (UUS) has become an integral component of the start and turn phases in competitive swimming allowing higher velocities than can be achieved swimming at the surface. An understanding of the most important determinants for UUS performance and how these can be optimised to different swimmers is poorly understood.

Objective

The aim of this systematic review was to systematically assess the current peer-reviewed literature on the relationship between UUS performance determinants and underwater velocity in competitive swimmers.

Methods

An electronic search using AusSportMed, Embase, PubMed, SPORTDiscus and Biomechanics and Medicine in Swimming was performed. The methodological quality of the studies was evaluated using a biomechanics-specific checklist developed by Hindle and colleagues (Sports Med Open. 5(1):49, 2019.10.1186/s40798-019-0222-z).

Results

Twenty-five studies met the eligibility criteria. While UUS velocity was nearly perfectly related (r > 0.90) to foot resultant acceleration and kick frequency, several other biomechanical factors were also significant correlates. UUS velocity and frequency were typically higher in high-performance swimmers and during prone versus dorsal positions. UUS velocity, kick frequency and kick amplitude were also significantly correlated with high angular velocities of the hip, knee and ankle joints and knee range of motion.

Conclusion

While there appears to be evidence supporting some performance variables to be related to UUS, future research should examine how to optimise the kinematic and kinetic characteristics with respect to the imposed task constraints and organism constraints between swimmers. Additional research should also investigate the effect of biomechanically informed interventions to improve UUS performance.

Registration

Open Science Framework.
Persistence of African swine fever virus on porous and non-porous fomites at environmental temperatures
Authors: Nuanualsuwan Suphachai , Songkasupa Tapanut , Boonpornprasert Prakit , Suwankitwat Nutthakarn , Lohlamoh Walaiporn , Nuengjamnong Chackrit
Published: July 2022

Background

African swine fever (ASF) is a lethal contagious disease affecting both domestic pigs and wild boars. Even though it is a non-zoonotic disease, ASF causes economic loss in swine industries across continents. ASF control and eradication are almost impossible since effective vaccines and direct antiviral treatment are not available. The persistence of ASFV on fomites plays an important role in the indirect transmission of ASFV to pigs encountering ASFV-contaminated fomites. ASFV persistence on porous and non-porous fomites (glass, metal, rubber, and cellulose paper) at different environmental temperatures was determined. The persistence of ASFV of fomites was determined by the rate of ASFV inactivation in terms ofDT,or the time required to reduce ASFV per 1 log at each selected environmental temperature (T).DTis used to compare the persistence of ASFV on the fomites.

Results

The meanD25,D33, andD42, of dried infectious ASFV on glass, metal, rubber, and paper were in the ranges 1.42–2.42, 0.72–1.94, and 0.07–0.23 days, respectively. The multipleDTwere used to develop aDTmodel to predict theDTfor some other environmental temperatures. TheDTmodels to predict the persistence of dried infectious ASFV on glass, metal, rubber, and paper are logDT = (− T/21.51) + 1.34, logDT = (− T/20.42) + 1.47, logDT = (− T/14.91) + 2.03, and logDT = (− T/10.91) + 2.84, respectively. A spreadsheet as a quick and handy tool predicting the persistence time of dried infectious ASFV on fomites at various environmental temperatures based on theseDTmodels is available for public to download.

Conclusion

Persistence of dried infectious ASFV on paper are significantly the longest at lower environmental temperatures whereas that of dried infectious ASFV on paper is significantly the shortest at higher environmental temperature.
Medaka, Oryzias latipes, egg envelopes are created by ovarian-expressed ZP proteins and liver-expressed choriogenins
Authors: Birk Devun S. , Onose Shinji , Kinoshita Masato , Murata Kenji
Published: July 2022

The medaka (Oryzias latipes) egg envelope (chorion) is composed of three major glycoproteins, Zona Interna (ZI)-1, -2, and -3, that originate in the spawning female liver as the precursor proteins Choriogenin (Chg.)H, Chg.Hm, and Chg.L, respectively. These ZI and Chg. proteins contain a structural ZP protein domain that is conserved among the egg envelope proteins of all animals. While ovarian expression of ZP proteins (e.g., ZPCs and ZPB) has been reported in medakas, the functions of these proteins remain unknown. Thus, the present study aimed to determine whether the ovary-expressed medaka ZP protein, mZPC5, is involved in forming the chorion matrix.

The mZPC5 gene (mzpc5) was expressed in the ovaries but not the livers of mature female medakas, as shown by reverse transcription-polymerase chain reaction assays with mzpc5-specific primers. In situ hybridization analysis revealed that ovarian mzpc5 expression was restricted to the ooplasm of early (stage I–III) previtellogenic oocytes, and its expression signal weakened with oocyte growth. Following sodium-dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and Western blotting analysis with anti-mZPC5 antibodies, two immunoreactive proteins were detected in the ovary and chorion extracts. These proteins were approximately 50 and 74 kDa in size, like ZI-3 and ZI-2, respectively.

Immunohistochemical assays using anti-mZPC5 and anti-Chg.H antibodies localized the mZPC5 protein in the ooplasm of early previtellogenic oocytes. With oocyte growth, mZPC5 tended to accumulate in the chorion, co-localizing with Chg.H.

We previously showed that ovary-expressed ZP proteins could not compensate for Chg.L function loss in gene knock-out (chg.l -/-) medakas. As in our previous study, the chg.l-/- females produced oocytes with thin chorions, resulting in infertile soft eggs. However, in the present study, mZPC5 and Chg.H were co-localized in the chg.l-/- chorions. These results suggested that in the medaka previtellogenic oocyte, 1) mZPC5 is secreted from the ooplasm and deposited on the outer surface of its plasma membrane, creating the thin chorion layer; and 2) following the accumulation of liver-derived Chgs., the 3D structure of the chorion matrix is formed cooperatively with mZPC5 and Chgs. during oogenesis. More research is needed to confirm the functions of mZPC5 in chorion structure and physiology.
Iliopsoas abscess in patients receiving hemodialysis: a case series and a literature survey
Authors: Oshida Takuma , Yoshida Tadashi , Itoh Hiroshi , Oya Mototsugu
Published: July 2022

Background

Iliopsoas abscess is a relatively rare but serious infectious disease. Infectious disease is one of the major causes of death among patients receiving hemodialysis for end-stage renal disease (ESRD).

Case presentation

We experienced three cases of iliopsoas abscess in patients receiving hemodialysis. The infection route was distinct in each case. A 79-year-old woman with ESRD due to autosomal dominant polycystic kidney disease exhibited bilateral iliopsoas abscesses caused by bacterial contamination during a lumbar epidural block procedure. A 60-year-old woman with ESRD due to diabetic nephropathy was diagnosed as having an iliopsoas abscess, caused by the direct invasion of bacteria from a renal abscess. A 78-year-old woman who started hemodialysis because of nephrosclerosis developed an iliopsoas abscess caused by the hematogenous spread of bacteria from emphysematous cystitis. All three cases were treated with antibiotics and/or percutaneous drainage. A survey of published reports suggested that iliopsoas abscess can be caused by infection through a variety of routes in hemodialysis patients.

Conclusion

Because hemodialysis patients are at a high risk of infection because of their immunocompromised state, physicians should pay close attention to infection prevention. If iliopsoas abscess is suspected, examinations such as computed tomography, magnetic resonance imaging, and blood culture sampling should be conducted promptly, followed by appropriate treatment with antibiotics and/or drainage.
Effects of individual and dyadic decision-making and normative reference on delay discounting decisions
Authors: Schwenke Diana , Wehner Peggy , Scherbaum Stefan
Published: July 2022

The tendency to devaluate delayed rewards, a phenomenon referred to as ‘discounting behaviour’, has been studied by wide-ranging research examining individuals choosing between sooner but smaller or later but larger rewards. Despite the fact that many real-life choices are embedded in a social context, the question of whether or not social collaboration can have an impact on such choices has not been addressed empirically. With this research, we aimed to fill this gap experimentally by implementing a novel choice selection procedure in order to study the interactive dynamics between two participants. This selection procedure allowed us to dissect the sequence of decision-making into its elements, starting from the very first individual preference to the solution of possible conflicting preferences in the dyad. In Experiment 1, we studied group decision-making on classical intertemporal choices to reveal the possible benefit of social collaboration on discounting and identified that the knowledge of the social situation in collective decision-making causes a reduction in discounting. In a pre-registered Experiment 2, we compared classical intertemporal choices with choices in a gamified version of a discounting paradigm in which the participants had a real-time experience trial by trial and for which a normative reference was present. We found that collective decision-making had a substantial impact on intertemporal decision-making, but was shaped by different types of choices. Classical intertemporal choices were rather susceptible to the contextual factors of decision-making, whereas in the gamified version that included a normative reference the decisions were reliably influenced by social collaboration and resulted in a lower discounting. The results in this paradigm replicate our original findings from former research.