Abstract
Owning to the rapid development of computer technologies, an increasing number of relational data have been emerging in modern biomedical research. Many network-based learning methods have ...been proposed to perform analysis on such data, which provide people a deep understanding of topology and knowledge behind the biomedical networks and benefit a lot of applications for human healthcare. However, most network-based methods suffer from high computational and space cost. There remain challenges on handling high dimensionality and sparsity of the biomedical networks. The latest advances in network embedding technologies provide new effective paradigms to solve the network analysis problem. It converts network into a low-dimensional space while maximally preserves structural properties. In this way, downstream tasks such as link prediction and node classification can be done by traditional machine learning methods. In this survey, we conduct a comprehensive review of the literature on applying network embedding to advance the biomedical domain. We first briefly introduce the widely used network embedding models. After that, we carefully discuss how the network embedding approaches were performed on biomedical networks as well as how they accelerated the downstream tasks in biomedical science. Finally, we discuss challenges the existing network embedding applications in biomedical domains are faced with and suggest several promising future directions for a better improvement in human healthcare.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Tubulointerstitial fibrosis (TIF) is caused by the progressive loss of renal tubular cells and the consequent replacement of the extracellular matrix. The progressive depletion of renal tubular cells ...results from apoptosis and necroptosis; however, the relative significance of each of these cell death mechanisms at different stages during the progression of chronic kidney disease (CKD) remains unclear. We sought to explore the mechanisms of renal tubular cell death during the early and intermediate stages of chronic renal damage of subtotal nephrectomied (SNx) rats. The results of tissue histological assays indicated that the numbers of necrotic dying cells and apoptotic cells were significantly higher in kidney tissues derived from a rat model of CKD. In addition, there was a significant increase in necroptosis observed by transmission electron microscopy (TEM) and an increase in the proportion of TUNEL-positive cells in kidney tissues from SNx rats compared with control rats, and necrostatin-1 (Nec-1) could inhibit necroptosis and reduce the proportion of TUNEL-positive cells. More importantly, we observed a significant increase in the incidence of necroptosis compared with apoptosis by TEM in vivo and in vitro and a significant increase in the proportion of TUNEL-positive tubular epithelial cells that did not express caspase-3 compared with those expressing cleaved caspase-3 in vitro. Furthermore, treatment with Nec-1 and zVAD strongly reduced necroptosis- and apoptosis-mediated renal tubular cell death and decreased the levels of blood urea nitrogen and serum creatinine and tubular damage scores of SNx rats. These results suggest that necroptotic cell death plays a more significant role than apoptosis in mediating the loss of renal tubular cells in SNx rats and that effectively blocking both necroptosis and apoptosis improves renal function and tubular damage at early and intermediate stages of CKD.
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The drip irrigation under mulch has become one of significant supporting technologies for cotton industry development in Xinjiang, and has shown the good economic and ecological benefits. With the ...rapid development of society and economy in Southern Xinjiang, the conventional mode of large-quota winter and spring irrigation, salt leaching and alkali decreasing is difficult to support sustainable development of land and water resources in Southern Xinjiang. This study tries to adjust soil moisture and salt content regulation mode of massive water salt leaching and drip irrigation under mulch in the non-growing period of cotton field in Southern Xinjiang, explores interannual soil salinity change features of drip irrigation cotton field without winter and spring irrigation, and provides experimental basis for drip irrigation technology under mulch which can reduce and exempt cotton irrigation in winter and spring. According to ET0, the dual-factor complete combination experiment involving 3 irrigating water quotas (I1, I2, I3) and 2 irrigation times (T12, T16) was designed, and 6 treatments were involved in total(I1T12,I2T12,I3T12,I1T16,I2T16 and I3T16). The investigation results of four-year (2012-2015) field positioning experiment showed that, under the condition of "germination under drip irrigation" without winter and spring irrigation, increasing irrigation quota and irrigation times could lower 0-100cm soil salinity accumulation, but the soil salinity accumulation degree was 40-100cm, and less than 0-30cm. In the seedling stage, bud stage, blossom and boll-forming stage, and boll opening stage, the average salinity of 0-100cm soil increased by 39.81%, 31.91%, 26.85% and 29.47%, respectively. Increasing irrigation quota and irrigation times could ease interannual soil salinity accumulation degree of cotton field with drip irrigation under mulch, without winter and spring irrigation. 0-100cm soil salinity before sowing was related to the irrigation quota of cotton in the growing stage of the last year. The larger the irrigation quota was, the smaller the soil salinity before sowing would be. The accumulation amount of soil salinity at the end of growing stage under different treatments was lower than that before sowing. The drip irrigation of cotton under mulch in the growing stage could effectively regulate soil salinity distribution and space-time migration process in the growing stage of cotton. Compared with the beginning of 2012, 0-100cm average soil salinity under 3 irrigation quotas (I1, I2, I3) was 33.66%, 5.60% and 1.24%, respectively. Salt accumulating rates under 12 irrigations and 16 irrigations were 20.66% and 6.33%, respectively. The soil had the risk of salinization when the "germination under drip irrigation" without winter and spring irrigation was used. Such results can provide the reference for prevention and treatment of soil moisture and salt content of cotton field with drip irrigation under mulch in the arid region.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
An increasing number of medical journals are using social media to promote themselves and communicate with their readers. However, little is known about how medical journals use Twitter and what ...their social media management strategies are.
This study aimed to understand how medical journals use Twitter from a global standpoint. We conducted a broad, in-depth analysis of all the available Twitter accounts of medical journals indexed by major indexing services, with a particular focus on their social networks and content.
The Twitter profiles and metadata of medical journals were analyzed along with the social networks on their Twitter accounts.
The results showed that overall, publishers used different strategies regarding Twitter adoption, Twitter use patterns, and their subsequent decisions. The following specific findings were noted: journals with Twitter accounts had a significantly higher number of publications and a greater impact than their counterparts; subscription journals had a slightly higher Twitter adoption rate (2%) than open access journals; journals with higher impact had more followers; and prestigious journals rarely followed other lesser-known journals on social media. In addition, an in-depth analysis of 2000 randomly selected tweets from 4 prestigious journals revealed that The Lancet had dedicated considerable effort to communicating with people about health information and fulfilling its social responsibility by organizing committees and activities to engage with a broad range of health-related issues; The New England Journal of Medicine and the Journal of the American Medical Association focused on promoting research articles and attempting to maximize the visibility of their research articles; and the British Medical Journal provided copious amounts of health information and discussed various health-related social problems to increase social awareness of the field of medicine.
Our study used various perspectives to investigate how medical journals use Twitter and explored the Twitter management strategies of 4 of the most prestigious journals. Our study provides a detailed understanding of medical journals' use of Twitter from various perspectives and can help publishers, journals, and researchers to better use Twitter for their respective purposes.
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Vascular calcification (VC) is regarded as an important pathological change lacking effective treatment and associated with high mortality. Sirtuin 6 (SIRT6) is a member of the Sirtuin family, a ...class III histone deacetylase and a key epigenetic regulator. SIRT6 has a protective role in patients with chronic kidney disease (CKD). However, the exact role and molecular mechanism of SIRT6 in VC in patients with CKD remain unclear. Here, we demonstrated that SIRT6 was markedly downregulated in peripheral blood mononuclear cells (PBMCs) and in the radial artery tissue of patients with CKD with VC. SIRT6-transgenic (SIRT6-Tg) mice showed alleviated VC, while vascular smooth muscle cell-specific (VSMC-specific) SIRT6 knocked-down mice showed severe VC in CKD. SIRT6 suppressed the osteogenic transdifferentiation of VSMCs via regulation of runt-related transcription factor 2 (Runx2). Coimmunoprecipitation (co-IP) and immunoprecipitation (IP) assays confirmed that SIRT6 bound to Runx2. Moreover, Runx2 was deacetylated by SIRT6 and further promoted nuclear export via exportin 1 (XPO1), which in turn caused degradation of Runx2 through the ubiquitin-proteasome system. These results demonstrated that SIRT6 prevented VC by suppressing the osteogenic transdifferentiation of VSMCs, and as such targeting SIRT6 may be an appealing therapeutic target for VC in CKD.
Understanding semantic relatedness and similarity between biomedical terms has a great impact on a variety of applications such as biomedical information retrieval, information extraction, and ...recommender systems. The objective of this study is to examine word2vec's ability in deriving semantic relatedness and similarity between biomedical terms from large publication data. Specifically, we focus on the effects of recency, size, and section of biomedical publication data on the performance of word2vec.
We download abstracts of 18,777,129 articles from PubMed and 766,326 full-text articles from PubMed Central (PMC). The datasets are preprocessed and grouped into subsets by recency, size, and section. Word2vec models are trained on these subtests. Cosine similarities between biomedical terms obtained from the word2vec models are compared against reference standards. Performance of models trained on different subsets are compared to examine recency, size, and section effects.
Models trained on recent datasets did not boost the performance. Models trained on larger datasets identified more pairs of biomedical terms than models trained on smaller datasets in relatedness task (from 368 at the 10% level to 494 at the 100% level) and similarity task (from 374 at the 10% level to 491 at the 100% level). The model trained on abstracts produced results that have higher correlations with the reference standards than the one trained on article bodies (i.e., 0.65 vs. 0.62 in the similarity task and 0.66 vs. 0.59 in the relatedness task). However, the latter identified more pairs of biomedical terms than the former (i.e., 344 vs. 498 in the similarity task and 339 vs. 503 in the relatedness task).
Increasing the size of dataset does not always enhance the performance. Increasing the size of datasets can result in the identification of more relations of biomedical terms even though it does not guarantee better precision. As summaries of research articles, compared with article bodies, abstracts excel in accuracy but lose in coverage of identifiable relations.
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Background and Aims
The optimal treatment for gastric varices (GVs) is a topic that remains open for study. This study compared the efficacy and safety of endoscopic cyanoacrylate injection and ...balloon‐occluded retrograde transvenous obliteration (BRTO) to prevent rebleeding in patients with cirrhosis and GVs after primary hemostasis.
Approach and Results
Patients with cirrhosis and history of bleeding from gastroesophageal varices type 2 or isolated gastric varices type 1 were randomized to cyanoacrylate injection (n = 32) or BRTO treatment (n = 32). Primary outcomes were gastric variceal rebleeding or all‐cause rebleeding. Patient characteristics were well balanced between two groups. Mean follow‐up time was 27.1 ± 12.0 months in a cyanoacrylate injection group and 27.6 ± 14.3 months in a BRTO group. Probability of gastric variceal rebleeding was higher in the cyanoacrylate injection group than in the BRTO group (P = 0.024). Probability of remaining free of all‐cause rebleeding at 1 and 2 years for cyanoacrylate injection versus BRTO was 77% versus 96.3% and 65.2% versus 92.6% (P = 0.004). Survival rates, frequency of complications, and worsening of esophageal varices were similar in both groups. BRTO resulted in fewer hospitalizations, inpatient stays, and lower medical costs.
Conclusions
BRTO is more effective than cyanoacrylate injection in preventing rebleeding from GVs, with similar frequencies of complications and mortalities.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Metastasis is the main cause of death in individuals with cancer. Immune checkpoint blockade (ICB) can potentially reverse CD8+ cytotoxic T lymphocytes (CTLs) dysfunction, leading to significant ...remission in multiple cancers. However, the mechanism underlying the development of CTL exhaustion during metastatic progression remains unclear. Here, we established an experimental pulmonary metastasis model with melanoma cells and discovered a critical role for melanoma‐released exosomes in metastasis. Using genetic knockdown of nSMase2 and Rab27a, 2 key enzymes for exosome secretion, we showed that high levels of effector‐like tumor‐specific CD8+ T cells with transitory exhaustion, instead of terminal exhaustion, were observed in mice without exosomes; these cells showed limited inhibitory receptors and strong proliferation and cytotoxicity. Mechanistically, the immunosuppression of exosomes depends on exogenous PD‐L1, which can be largely rescued by pretreatment with antibody blockade. Notably, we also found that exosomal PD‐L1 acts as a promising predictive biomarker for ICB therapies during metastasis. Together, our findings suggest that exosomal PD‐L1 may be a potential immunotherapy target, suggesting a new curative therapy for tumor metastasis.
We demonstrate a crucial role for tumor‐released exosomes in promoting metastatic progression. We provide extensive evidence that exosomes from tumor cells act alone as contributors to driving tumor‐specific CD8+ T cell exhaustion in vivo. We also find that exosomal PD‐L1 acts as a promising predictive biomarker for ICB therapies during metastasis.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Advances in biomedical research using deep learning techniques have generated a large volume of related literature. However, there is a lack of scientometric studies that provide a bird's-eye view of ...them. This absence has led to a partial and fragmented understanding of the field and its progress.
This study aimed to gain a quantitative and qualitative understanding of the scientific domain by analyzing diverse bibliographic entities that represent the research landscape from multiple perspectives and levels of granularity.
We searched and retrieved 978 deep learning studies in biomedicine from the PubMed database. A scientometric analysis was performed by analyzing the metadata, content of influential works, and cited references.
In the process, we identified the current leading fields, major research topics and techniques, knowledge diffusion, and research collaboration. There was a predominant focus on applying deep learning, especially convolutional neural networks, to radiology and medical imaging, whereas a few studies focused on protein or genome analysis. Radiology and medical imaging also appeared to be the most significant knowledge sources and an important field in knowledge diffusion, followed by computer science and electrical engineering. A coauthorship analysis revealed various collaborations among engineering-oriented and biomedicine-oriented clusters of disciplines.
This study investigated the landscape of deep learning research in biomedicine and confirmed its interdisciplinary nature. Although it has been successful, we believe that there is a need for diverse applications in certain areas to further boost the contributions of deep learning in addressing biomedical research problems. We expect the results of this study to help researchers and communities better align their present and future work.
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Wireless visual sensor networks (WVSN) have been widely used to capture images in the fields of monitoring, intelligent transportation, and reconnaissance in recent years. Because of the wireless ...transmission mode and the huge amount of image data, major challenges in this application are frequent information stealing, big data problems, and harsh communication circumstances. Some encryption schemes based on compressive sensing (CS) and chaotic systems have been proposed to cope with these threats, but most of them are vulnerable against the chosen-plaintext attack (CPA). To remedy these defects, this paper designs a novel method based on non-uniform quantization (NQ). Then, in order to evaluate the true compression ratio (CR), our work takes into account limited data precision in cipher images, while most papers ignored this fact and calculated CR with the assumption of infinite data precision. Besides, to eliminate the periodic windows in the bifurcation diagram of the logistic map (LM), an optimized logistic map (OLM) is designed. Furthermore, simulation results prove that the performance of anti-jamming in the proposed cryptosystem is better than that in existing schemes under the condition of strong noise interference or severe data loss. In conclusion, the proposed method could improve the performance of security and anti-jamming for WVSN.
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