bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical manifestations and approach to the management of patients with common variable immunodeficiency and liver disease
Authors: Daza-Cajigal Vanessa , Segura-Guerrero Marina , López-Cueto María , Robles-Marhuenda Ángel , Camara Carmen , Gerra-Galán Teresa , Gómez-de-la-Torre Ricardo , Avendaño-Monje Carmen L. , Sánchez-Ramón Silvia , Bosque-Lopez María J. , Quintero-Duarte Adriana , Bonet-Vidal María L. , Pons Jaime
Published: June 2023

Purpose

The clinical spectrum of common variable immunodeficiency (CVID) includes predisposition to infections, autoimmune/inflammatory complications and malignancy. Liver disease is developed by a proportion of patients with CVID, but limited evidence is available about its prevalence, pathogenesis and prognostic outcome. This lack of evidence leads to the absence of guidelines in clinical practice. In this study, we aimed at defining the characteristics, course and management of this CVID complication in Spain.

Methods

Spanish reference centers were invited to complete a cross-sectional survey. Thirty-eight patients with CVID-related liver disease from different hospitals were evaluated by a retrospective clinical course review.

Results

In this cohort, abnormal liver function and thrombocytopenia were found in most of the patients (95% and 79% respectively), in keeping with the higher incidence of abnormal liver imaging and splenomegaly. The most common histological findings included nodular regenerative hyperplasia (NRH) and lymphocytic infiltration, which have been associated with portal hypertension (PHTN) leading to a poorer prognosis. Autoimmune/inflammatory complications occurred in 82% of the CVID patients that developed liver disease and 52% of the patients treated with immunomodulators showed a reduction in the liver function tests’ abnormalities during treatment. Among the experts that conducted the survey, there was 80% or more consensus that the workup of CVID-related liver disease requires liver profile, abdominal ultrasound and transient elastography. The majority agreed that liver biopsy should be essential for diagnosis. There was 94% consensus that endoscopic studies should be performed in the presence of PHTN. However, there was 89% consensus that there is insufficient evidence on the management of these patients.

Conclusion

Liver disease varies in severity and may contribute substantially to morbidity and mortality in patients with CVID. Hence the importance of close follow-up and screening of this CVID complication to prompt early targeted intervention. Further research is needed to evaluate the pathophysiology of liver disease in patients with CVID to identify personalized treatment options. This study emphasizes the urgent need to develop international guidelines for the diagnosis and management of this CVID complication.
Immune-related adverse effects of checkpoint immunotherapy and implications for the treatment of patients with cancer and autoimmune diseases
Authors: Ibis Betul , Aliazis Konstantinos , Cao Carol , Yenyuwadee Sasitorn , Boussiotis Vassiliki A.
Published: June 2023

During the past decade, there has been a revolution in cancer therapeutics by the emergence of antibody-based immunotherapies that modulate immune responses against tumors. These therapies have offered treatment options to patients who are no longer responding to classic anti-cancer therapies. By blocking inhibitory signals mediated by surface receptors that are naturally upregulated during activation of antigen-presenting cells (APC) and T cells, predominantly PD-1 and its ligand PD-L1, as well as CTLA-4, such blocking agents have revolutionized cancer treatment. However, breaking these inhibitory signals cannot be selectively targeted to the tumor microenvironment (TME). Since the physiologic role of these inhibitory receptors, known as immune checkpoints (IC) is to maintain peripheral tolerance by preventing the activation of autoreactive immune cells, IC inhibitors (ICI) induce multiple types of immune-related adverse effects (irAEs). These irAEs, together with the natural properties of ICs as gatekeepers of self-tolerance, have precluded the use of ICI in patients with pre-existing autoimmune diseases (ADs). However, currently accumulating data indicates that ICI might be safely administered to such patients. In this review, we discuss mechanisms of well established and newly recognized irAEs and evolving knowledge from the application of ICI therapies in patients with cancer and pre-existing ADs.
The role of Nrf2 in the pathogenesis and treatment of ulcerative colitis
Authors: Peng Shuai , Shen Lei , Yu Xiaoyun , Zhang Li , Xu Ke , Xia Yuan , Zha Lanlan , Wu Jing , Luo Hesheng
Published: June 2023

Ulcerative colitis (UC) is a chronic inflammatory bowel disease involving mainly the colorectal mucosa and submucosa, the incidence of which has been on the rise in recent years. Nuclear factor erythroid 2-related factor 2 (Nrf2), known for its key function as a transcription factor, is pivotal in inducing antioxidant stress and regulating inflammatory responses. Numerous investigations have demonstrated the involvement of the Nrf2 pathway in maintaining the development and normal function of the intestine, the development of UC, and UC-related intestinal fibrosis and carcinogenesis; meanwhile, therapeutic agents targeting the Nrf2 pathway have been widely investigated. This paper reviews the research progress of the Nrf2 signaling pathway in UC.
A cytocompatible microporous Sr-doped titanium dioxide coating fabricated by plasma electrolytic oxidation
Authors: Zheng Hongming , He Shuangjun , Zhou Lijian , Yuan Jintao , Jiang Boyi , Ni Xiaohui , Lu Kaihang , Zhang Pengpeng , Zhao Quanming
Published: June 2023

Titanium has broad application prospects in the field of hard bone tissue repair and replacement due to its low density, an elastic modulus similar to that of human bone, and better biocompatibility than stainless steel and cobalt-based alloys. However, titanium is a biologically inert material with low biological activity. After implantation, it only physically bonds with bone instead of chemically bonding, which causes complications such as implant loosening. In this study, a strontium-doped titanium dioxide coating was prepared on a titanium surface with micro-arc oxidation. Based on a systematic study of the surface properties of the strontium-doped titanium dioxide coating, the biocompatibility and bioactivity of the coating were evaluated with in vitro cell experiments. The results showed that the strontium-doped titanium dioxide coating was successfully prepared on the titanium surface and exhibited strong bonding with the substrate. The coating surface had a porous structure, and the strontium was dispersed on the surface and inside the coating. The strontium ions were released slowly, which improved the corrosion and wear resistance of the titanium. In vitro cell experiments showed that the coating had good cell compatibility; it promoted the adhesion, proliferation and differentiation of MC3T3-E1 cells and exhibited good biological activity. These results showed that preparation of a strontium-doped titanium dioxide coating by micro-arc oxidation is feasible. The coating had a good surface morphology, improved the biological activity of the titanium and has good potential for clinical application.
Case report: Post-traumatic Tourette syndrome resolving with treatment of jugular venous narrowing; reconciling organic brain dysfunction following whiplash trauma with the absence of direct brain injury
Authors: Higgins J. Nicholas P. , Kirker Stephen
Published: June 2023

We describe a man aged 33 years who developed multiple symptoms, personality change, and a severe tic disorder following a road traffic accident, which were undiminished for 3 years until jugular venous narrowing between the styloid process of the skull and the transverse process of the C1 vertebra was treated by surgical decompression. Immediately following surgery, his abnormal movements almost completely resolved, with no regression in 5 years of follow-up. Vigorously debated at the time was whether or not his condition represented a functional disorder. Unrecognized throughout his illness, however, was a complaint of intermittent, profuse discharge of clear fluid from his nose that began on the day of the accident and continued up to the time of surgery, after which it was substantially reduced. This outcome reinforces the idea that jugular venous narrowing can cause or perpetuate a cerebrospinal fluid leak. It suggests that the interaction between these two pathological defects may have a profound effect on brain function in the absence of any demonstrable brain lesion. It invites a reevaluation of normal head and neck venous anatomy. It should strike a cautionary note in the diagnosis of functional illness. It invites exploration of a remediable structural cause for Tourette syndrome.
A novel visual brain-computer interfaces paradigm based on evoked related potentials evoked by weak and small number of stimuli
Authors: Xiao Xiaolin , Gao Runyuan , Zhou Xiaoyu , Yi Weibo , Xu Fangzhou , Wang Kun , Xu Minpeng , Ming Dong
Published: June 2023

Introduction

Traditional visual Brain-Computer Interfaces (v-BCIs) usually use large-size stimuli to attract more attention from users and then elicit more distinct and robust EEG responses, which would cause visual fatigue and limit the length of use of the system. On the contrary, small-size stimuli always need multiple and repeated stimulus to code more instructions and increase separability among each code. These common v-BCIs paradigms can cause problems such as redundant coding, long calibration time, and visual fatigue.

Methods

To address these problems, this study presented a novel v-BCI paradigm using weak and small number of stimuli, and realized a nine-instruction v-BCI system that controlled by only three tiny stimuli. Each of these stimuli were located between instructions, occupied area with eccentricities subtended 0.4°, and flashed in the row-column paradigm. The weak stimuli around each instruction would evoke specific evoked related potentials (ERPs), and a template-matching method based on discriminative spatial pattern (DSP) was employed to recognize these ERPs containing the intention of users. Nine subjects participated in the offline and online experiments using this novel paradigm.

Results

The average accuracy of the offline experiment was 93.46% and the online average information transfer rate (ITR) was 120.95 bits/min. Notably, the highest online ITR achieved 177.5 bits/min.

Discussion

These results demonstrate the feasibility of using a weak and small number of stimuli to implement a friendly v-BCI. Furthermore, the proposed novel paradigm achieved higher ITR than traditional ones using ERPs as the controlled signal, which showed its superior performance and may have great potential of being widely used in various fields.
A touch-free human-robot collaborative surgical navigation robotic system based on hand gesture recognition
Authors: Wang Jie , Zhang Xinkang , Chen Xinrong , Song Zhijian
Published: June 2023

Robot-assisted minimally invasive surgery (RAMIS) has gained significant traction in clinical practice in recent years. However, most surgical robots rely on touch-based human-robot interaction (HRI), which increases the risk of bacterial diffusion. This risk is particularly concerning when surgeons must operate various equipment with their bare hands, necessitating repeated sterilization. Thus, achieving touch-free and precise manipulation with a surgical robot is challenging. To address this challenge, we propose a novel HRI interface based on gesture recognition, leveraging hand-keypoint regression and hand-shape reconstruction methods. By encoding the 21 keypoints from the recognized hand gesture, the robot can successfully perform the corresponding action according to predefined rules, which enables the robot to perform fine-tuning of surgical instruments without the need for physical contact with the surgeon. We evaluated the surgical applicability of the proposed system through both phantom and cadaver studies. In the phantom experiment, the average needle tip location error was 0.51  mm, and the mean angle error was 0.34 degrees. In the simulated nasopharyngeal carcinoma biopsy experiment, the needle insertion error was 0.16  mm, and the angle error was 0.10 degrees. These results indicate that the proposed system achieves clinically acceptable accuracy and can assist surgeons in performing contactless surgery with hand gesture interaction.
Biomarkers and the outcomes of ischemic stroke
Authors: Huang Ying , Wang Zhenzhen , Huang Zhi-Xin , Liu Zhenguo
Published: June 2023

Biomarkers are measurable substances that could be used as objective indicators for disease diagnosis, responses to treatments, and outcomes predictions. In this review, we summarized the data on a number of important biomarkers including glutamate, S100B, glial fibrillary acidic protein, receptor for advanced glycation end-products, intercellular adhesion molecule-1, von willebrand factor, matrix metalloproteinase-9, interleukin-6, tumor necrosis factor-a, activated protein C, copeptin, neuron-specific enolase, tau protein, gamma aminobutyric acid, blood glucose, endothelial progenitor cells, and circulating CD34-positive cells that could be potentially used to indicate the disease burden and/or predict clinical outcome of ischemic stroke. We examined the relationship between specific biomarkers and disease burden and outcomes and discussed the potential mechanisms underlying the relationship. The clinical significance and implications of these biomarkers were also discussed.
Partially brain effects of injection of human umbilical cord mesenchymal stem cells at injury sites in a mouse model of thoracic spinal cord contusion
Authors: Hu Haijun , Long Houqing , Ren Zhenxiao , Liu Tianhua , Xu Jinghui , Xiao Fan
Published: June 2023

Purpose

The pain caused by spinal cord injury (SCI) poses a major burden on patients, and pain management is becoming a focus of treatment. Few reports have described changes in the brain after SCI. Particularly, the exact mechanism through which brain regions affect post-injury pain remains unclear. In this study, we aimed to determine the potential therapeutic mechanisms of pain. A mouse model of spinal cord contusion was established, and molecular expression in the anterior cingulate cortex (ACC) and periaqueductal gray (PAG) in the brain and animal behavior was observed after local injection of human umbilical cord mesenchymal stem cells (HU-MSCs) at the site of SCI.

Method

Sixty-three female C57BL/6J mice were divided into four groups: a sham operation group (n = 15); a spinal injury group (SCI, n = 16); an SCI + HU-MSCs group (n = 16) and an SCI + PBS group (n = 16), in which the SCI site was injected with HU-MSCs/phosphate buffer. The BMS score was determined, and the von Frey test and Hargreaves test were used to assess behavior every week after surgery. Mice were sacrificed in the fourth week after operation, and samples were collected. The expression of CGRP, Substance P, C-Fos and KCC2 in the ACC and PAG were observed with immunohistochemistry. Chromic cyanine staining was used to observe transverse sections of the injured spinal cord.

Result

In the ACC and PAG after SCI, the expression of CGRP, SP and C-Fos increased, and the expression of KCC2 decreased, whereas after HU-MSC injection, the expression of CGRP, SP and C-Fos decreased, and the expression of KCC2 increased. The SCI + HU-MSC group showed better exercise ability from 2 to 4 weeks after surgery than the SCI/SCI + PBS groups (P < 0.001). Local injection of HU-MSCs significantly improved the mechanical hyperalgesia caused by SCI in the fourth week after surgery (P < 0.0001), and sensation was significantly recovered 2 weeks after surgery (P < 0.0001); no improvement in thermal hypersensitivity was observed (P > 0.05). The HU-MSC group retained more white matter than the SCI/SCI + PBS groups (P < 0.0001).

Conclusion

Local transplantation of HU-MSCs at the site of SCI partially relieves the neuropathic pain and promotes recovery of motor function. These findings suggest a feasible direction for the future treatment of SCI.
Assessment of serum, dietary zinc levels, and other risk factors during the third trimester among pregnant women with and without pregnancy-induced hypertension: a case-control study
Authors: El Bilbeisi Abdel Hamid , Abo Khosa Sahar M. , Taleb Mahmoud H. , El Afifi Amany M.
Published: June 2023

Background

This study assessed serum, dietary zinc levels, and other risk factors during the third trimester among pregnant women with and without pregnancy-induced hypertension (PIH).

Methods

This case-control study was conducted in 2022, in the three main Obstetrics and Gynecology departments in Gaza Strip, Palestine. One hundred sixty pregnant women, during the third trimester, aged ≥20 years, were selected using a convenient sampling method. Data were obtained using an interview-based questionnaire, food frequency questionnaire, anthropometric measures, and biochemical tests. Statistical analysis was performed using SPSS version 24.

Results

The participants’ mean age was 30.7 ± 5.6 years. A total of 47 (58.8%) of cases and 6 (7.5%) of controls were insufficiently active; and the mean of blood pressure (mmHg) was 133.3 ± 11.9/85.11 ± 10.0 for cases and 112.8 ± 9.5/68.02 ± 7.2 for controls with significant differences between the two groups (P = <0.005). The mean serum zinc level (μg/dl) was 67.15 ± 16.5 for cases and 68.45 ± 18.0 for controls without significant differences between the two groups (P = 0.636). For newborns, the mean birth weight (g) was 2,904.6 ± 486 for cases, and 3,128.3 ± 501 for controls, and the mean Apgar score was 8.03 ± 0.62 for cases and 8.30 ± 1.17 for controls, with significant differences between the two groups (P = <0.005). Furthermore, 43 (53.8%) of cases have family history of hypertension; 5 (6.2%) were primiparous; 19 (23.8%) have previous caesarian section; 33 (41.2%) have history of preeclampsia; and 62 (77.5%) have edema, with significant differences between the two groups (P = <0.005). Additionally, the total zinc dietary daily intake (mg/day) was 4.15 ± 2.10 for cases and 4.88 ± 3.02 for controls, with significant differences between the two groups (P = 0.041). After adjustment for confounding variables, participants in the case group have higher odds of having low total zinc dietary intake compared to those in the control group [OR = 1.185, 95% CI = (1.016–1.382), P = 0.030].

Conclusion

The current study showed the main risk factors of PIH among pregnant women in the Gaza Strip, Palestine. Furthermore, low maternal dietary zinc intake was associated with a high level of PIH. Moreover, having PIH could increase the risk of low birth weight and low Apgar scores. Therefore, reducing the main risk factors of PIH could reduce the adverse effect on both mother and birth outcomes.
Identification of a novel MYC target gene set signature for predicting the prognosis of osteosarcoma patients
Authors: Gong Deliang , Zhao Qingzhong , Liu Jun , Zhao Shibing , Yi Chengfeng , Lv Jianwei , Yu Hang , Bian Erbao , Tian Dasheng
Published: June 2023

Osteosarcoma is a primary malignant tumor found mainly in teenagers and young adults. Patients have very little long-term survival. MYC controls tumor initiation and progression by regulating the expression of its target genes; thus, constructing a risk signature of osteosarcoma MYC target gene set will benefit the evaluation of both treatment and prognosis. In this paper, we used GEO data to download the ChIP-seq data of MYC to obtain the MYC target gene. Then, a risk signature consisting of 10 MYC target genes was developed using Cox regression analysis. The signature indicates that patients in the high-risk group performed poorly. After that, we verified it in the GSE21257 dataset. In addition, the difference in tumor immune function among the low- and high-risk populations was compared by single sample gene enrichment analysis. Immunotherapy and prediction of response to the anticancer drug have shown that the risk signature of the MYC target gene set was positively correlated with immune checkpoint response and drug sensitivity. Functional analysis has demonstrated that these genes are enriched in malignant tumors. Finally, STX10 was selected for functional experimentation. STX10 silence has limited osteosarcoma cell migration, invasion, and proliferation. Therefore, these findings indicated that the MYC target gene set risk signature could be used as a potential therapeutic target and prognostic indicator in patients with osteosarcoma.
Colorectal polyps increase the glycolytic activity
Authors: Rebane-Klemm Egle , Reinsalu Leenu , Puurand Marju , Shevchuk Igor , Bogovskaja Jelena , Suurmaa Kulliki , Valvere Vahur , Moreno-Sanchez Rafael , Kaambre Tuuli
Published: June 2023

In colorectal cancer (CRC) energy metabolism research, the precancerous stage of polyp has remained rather unexplored. By now, it has been shown that CRC has not fully obtained the glycolytic phenotype proposed by O. Warburg and rather depends on mitochondrial respiration. However, the pattern of metabolic adaptations during tumorigenesis is still unknown. Understanding the interplay between genetic and metabolic changes that initiate tumor development could provide biomarkers for diagnosing cancer early and targets for new cancer therapeutics. We used human CRC and polyp tissue material and performed high-resolution respirometry and qRT-PCR to detect changes on molecular and functional level with the goal of generally describing metabolic reprogramming during CRC development. Colon polyps were found to have a more glycolytic bioenergetic phenotype than tumors and normal tissues. This was supported by a greater GLUT1, HK, LDHA, and MCT expression. Despite the increased glycolytic activity, cells in polyps were still able to maintain a highly functional OXPHOS system. The mechanisms of OXPHOS regulation and the preferred substrates are currently unclear and would require further investigation. During polyp formation, intracellular energy transfer pathways become rearranged mainly by increasing the expression of mitochondrial adenylate kinase (AK) and creatine kinase (CK) isoforms. Decreased glycolysis and maintenance of OXPHOS activity, together with the downregulation of the CK system and the most common AK isoforms (AK1 and AK2), seem to play a relevant role in CRC development.
An improved nomogram including elastography for the prediction of non-sentinel lymph node metastasis in breast cancer patients with 1 or 2 sentinel lymph node metastases
Authors: Duan Hongtao , Zhang Jiawei , Zhang Guanxin , Zhu Xingmeng , Wang Wenjia
Published: June 2023

Background

The rate of breast-conserving surgery is very low in China, compared with that in developed countries; most breast cancer patients receive mastectomy. It is great important to explore the possibility of omitting axillary lymph node dissection (ALND) in early-stage breast cancer patients with 1 or 2 positive sentinel lymph nodes (SLNs) in China. The aim of this study was to develop a nomogram based on elastography for the prediction of the risk of non-SLN (NSLN) metastasis in early-stage breast cancer patients with 1 or 2 positive SLNs.

Methods

A total of 601 breast cancer patients were initially recruited. According to the inclusion and exclusion criteria, 118 early-stage breast cancer patients with 1 or 2 positive SLNs were finally enrolled and were assigned to the training cohort (n=82) and the validation cohort (n=36), respectively. In the training cohort, the independent predictors were screened by logistic regression analysis and then were used to conducted the nomogram for the prediction of NSLN metastasis in early-stage breast cancer patients with 1 or 2 positive SLNs. The calibration curves, concordance index (C-index), the area under the receiver operating characteristic (ROC) curve (AUC), and Decision curve analysis (DCA) were used to verified the performance of the nomogram.

Results

The multivariable analysis showed that the enrolled patients with positive HER2 expression (OR=6.179, P=0.013), Ki67≥14% (OR=8.976, P=0.015), larger lesion size (OR=1.038, P=0.045), and higher Emean (OR=2.237, P=0.006) were observed to be the independent factors of NSLN metastasis. Based on the above four independent predictors, a nomogram was conducted to predict the risk of the NSLN metastasis in early-stage breast cancer patients with 1 or 2 positive SLNs. The nomogram showed good discrimination in the prediction of NSLN metastasis, with bias-corrected C-index of 0.855 (95% CI, 0.754-0.956) and 0.853 (95% CI, 0.724-0.983) in the training and validation cohorts, respectively. Furthermore, the AUC was 0.877 (95%CI: 0.776- 0.978) and 0.861 (95%CI: 0.732-0.991), respectively, indicating a good performance of the nomogram. The calibration curve suggested a satisfactory agreement between the predictive and actual risk in both the training (χ2 = 11.484, P=0.176, HL test) and validation (χ2 = 6.247, p = 0.620, HL test) cohorts, and the obvious clinical nets were revealed by DCA.

Conclusions

We conducted a satisfactory nomogram model to evaluate the risk of NSLN metastasis in early-stage breast cancer patients with 1 or 2 SLN metastases. This model could be considered as an ancillary tool to help such patients to be selectively exempted from ALND.
Physical, psychological, and behavioral problems among children and adolescents in countries with different economic statuses during the COVID-19 pandemic: a systematic review and meta-analysis
Authors: Peng Bo , Reeves Kara K. L. , Lee Shara W. Y. , Chung Tina H. Y. , Hui Heidi W. L. , Leung Alfred H. L. , Pang Johnson C. Y.
Published: June 2023

Introduction

The COVID-19 pandemic has impacted children and adolescents’ physical activity (PA), sleeping patterns, and psychological and behavioral health. Yet, little is known about the differences between those in countries with various economic statuses.

Methods

Articles published from database inception through 16 March 2022 were retrieved using CINAHL Complete, Cochrane Library, EMBASE, Medline, PubMed, and PsycINFO. High-quality studies that reported the number of participants with parameters associated with PA, sleeping patterns, and psychological and behavioral problems in young people aged under 18 years during the pandemic were included. We referenced the Canadian 24-Hour Movement Guidelines for PA and sleep duration to provide the event rate for young people who were not compliant with the guidelines. The event rate of young people who had decreased sleep quality and experienced psychological and behavioral problems were also investigated. A subgroup analysis was conducted to identify the differences in those in countries with diverse economic statuses. Funnel plot analysis and Egger's test were also conducted to identify any risk of publication bias.

Result

A total of 66 studies with 1,371,168 participants aged between 0 and 18 years, involving 27 countries, were included. During the pandemic, we identified that 41% (95% CI: 39%, 43%; I2 = 96.62) and 43% (95% CI: 34%, 52%; I2 = 99.42) of young people did not meet the PA and sleep duration recommendation guidelines. In addition, 31% (95% CI: 28%, 35%; I2 = 99.66) of young people had decreased their sleep quality. Yet, no significant difference was found across countries with different economic statuses. However, the event rates of participants with psychological and behavioral problems were 32% (95% CI: 28%, 36%; I2 = 99.85) and 19% (95% CI: 14%, 25%; I2 = 99.72), respectively. In addition, the rate of psychological problems was more severe in those who live in lower middle-income countries (p < 0.001), while the rate of behavioral problems was more severe in those who live in high-income countries (p = 0.001).

Discussion

During the pandemic, the discouragement of PA, poor sleep quality, and high risk of psychological and behavioral problems are concerning. A large number of young people did not comply with the recommendation guidelines. Timely implementation of recovery plans is critical to address the adverse effects on young people.

Systematic review registration

https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=309209, identifier CRD42022309209.
Identifying vital nodes in recovering dynamical process of networked system
Authors: Fu Jiale , Jiang Xiaoya , Shao Qi , Chen Duxin , Yu Wenwu
Published: June 2023

Vital nodes identification is the problem of identifying the most significant nodes in complex networks, which is crucial in understanding the property of the networks and has applications in various fields such as pandemic controlling and energy saving. Traditional methods mainly focus on some types of centrality indices, which have restricted application cases. To improve the flexibility of the process and enable simultaneous multiple nodes mining, a deep learning-based vital nodes identification algorithm is proposed in this study, where we train the influence score of each node by using a set of nodes to approximate the rest of the network via the graph convolutional network. Experiments are conducted with generated data to justify the effectiveness of the proposed algorithm. The experimental results show that the proposed method outperforms the traditional ways in adaptability and accuracy to recover the dynamical process of networked system under different classes of network structure.
Impacts of climate change and human activities on vegetation coverage variation in mountainous and hilly areas in Central South of Shandong Province based on tree-ring
Authors: Yin Tingting , Zhai Yinuo , Zhang Yan , Yang Wenjun , Dong Jinbin , Liu Xiao , Fan Peixian , You Chao , Yu Linqian , Gao Qun , Wang Hui , Zheng Peiming , Wang Renqing
Published: June 2023

Introduction

It is of great significance to understand the characteristics and influencing factors of vegetation coverage variation in the warm temperate zone. As a typical region of the warm temperate zone in eastern China, the mountainous and hilly region in central-south Shandong Province has fragile ecological environment and soil erosion problem. Studying on vegetation dynamics and its influencing factors in this region will help to better understand the relationship between climate change and vegetation cover change in the warm temperate zone of eastern China, and the influence of human activities on vegetation cover dynamics.

Methods

Based on dendrochronology, a standard tree-ring width chronology was established in the mountainous and hilly region of central-south Shandong Province, and the vegetation coverage from 1905 to 2020 was reconstructed to reveal the dynamic change characteristics of vegetation cover in this region. Secondly, the influence of climate factors and human activities on the dynamic change of vegetation cover was discussed through correlation analysis and residual analysis.

Results and discussion

In the reconstructed sequence, 23 years had high vegetation coverage and 15 years had low vegetation coverage. After low-pass filtering, the vegetation coverage of 1911–1913, 1945–1951, 1958–1962, 1994–1996, and 2007–2011 was relatively high, while the vegetation coverage of 1925–1927, 1936–1942, 2001–2003, and 2019–2020 was relatively low. Although precipitation determined the variation of vegetation coverage in this study area, the impacts of human activities on the change of vegetation coverage in the past decades cannot be ignored. With the development of social economy and the acceleration of urbanization, the vegetation coverage declined. Since the beginning of the 21st century, ecological projects such as Grain-for-Green have increased the vegetation coverage.
A YOLOv7 incorporating the Adan optimizer based corn pests identification method
Authors: Zhang Chong , Hu Zhuhua , Xu Lewei , Zhao Yaochi
Published: June 2023

Major pests of corn insects include corn borer, armyworm, bollworm, aphid, and corn leaf mites. Timely and accurate detection of these pests is crucial for effective pests control and scientific decision making. However, existing methods for identification based on traditional machine learning and neural networks are limited by high model training costs and low recognition accuracy. To address these problems, we proposed a YOLOv7 maize pests identification method incorporating the Adan optimizer. First, we selected three major corn pests, corn borer, armyworm and bollworm as research objects. Then, we collected and constructed a corn pests dataset by using data augmentation to address the problem of scarce corn pests data. Second, we chose the YOLOv7 network as the detection model, and we proposed to replace the original optimizer of YOLOv7 with the Adan optimizer for its high computational cost. The Adan optimizer can efficiently sense the surrounding gradient information in advance, allowing the model to escape sharp local minima. Thus, the robustness and accuracy of the model can be improved while significantly reducing the computing power. Finally, we did ablation experiments and compared the experiments with traditional methods and other common object detection networks. Theoretical analysis and experimental result show that the model incorporating with Adan optimizer only requires 1/2-2/3 of the computing power of the original network to obtain performance beyond that of the original network. The mAP@[.5:.95] (mean Average Precision) of the improved network reaches 96.69% and the precision reaches 99.95%. Meanwhile, the mAP@[.5:.95] was improved by 2.79%-11.83% compared to the original YOLOv7 and 41.98%-60.61% compared to other common object detection models. In complex natural scenes, our proposed method is not only time-efficient and has higher recognition accuracy, reaching the level of SOTA.
Cellular response of Parachlorella kessleri to a solid surface culture environment
Authors: Miyauchi Hiroki , Ishikawa Tomoharu , Hirakawa Yutaro , Sudou Ayumu , Okada Katsuhiko , Hijikata Atsushi , Sato Norihiro , Tsuzuki Mikio , Fujiwara Shoko
Published: June 2023

Attached culture allows high biomass productivity and is a promising biomass cultivating system because neither a huge facility area nor a large volume of culture medium are needed. This study investigates photosynthetic and transcriptomic behaviors in Parachlorella kessleri cells on a solid surface after their transfer from liquid culture to elucidate the physiological and gene-expression regulatory mechanisms that underlie their vigorous proliferation. The chlorophyll content shows a decrease at 12 h after the transfer; however, it has fully recovered at 24 h, suggesting temporary decreases in the amounts of light harvesting complexes. On PAM analysis, it is demonstrated that the effective quantum yield of PSII decreases at 0 h right after the transfer, followed by its recovery in the next 24 h. A similar changing pattern is observed for the photochemical quenching, with the PSII maximum quantum yield remaining at an almost unaltered level. Non-photochemical quenching was increased at both 0 h and 12 h after the transfer. These observations suggest that electron transfer downstream of PSII but not PSII itself is only temporarily damaged in solid-surface cells just after the transfer, with light energy in excess being dissipated as heat for PSII protection. It thus seems that the photosynthetic machinery acclimates to high-light and/or dehydration stresses through its temporal size-down and functional regulation that start right after the transfer. Meanwhile, transcriptomic analysis by RNA-Seq demonstrates temporary upregulation at 12 h after the transfer as to the expression levels of many genes for photosynthesis, amino acid synthesis, general stress response, and ribosomal subunit proteins. These findings suggest that cells transferred to a solid surface become stressed immediately after transfer but can recover their high photosynthetic activity through adaptation of photosynthetic machinery and metabolic flow as well as induction of general stress response mechanisms within 24 h.
Rapid detection of Yunnan Xiaomila based on lightweight YOLOv7 algorithm
Authors: Wang Fenghua , Jiang Jin , Chen Yu , Sun Zhexing , Tang Yuan , Lai Qinghui , Zhu Hailong
Published: June 2023

Introduction

Real-time fruit detection is a prerequisite for using the Xiaomila pepper harvesting robot in the harvesting process.

Methods

To reduce the computational cost of the model and improve its accuracy in detecting dense distributions and occluded Xiaomila objects, this paper adopts YOLOv7-tiny as the transfer learning model for the field detection of Xiaomila, collects images of immature and mature Xiaomila fruits under different lighting conditions, and proposes an effective model called YOLOv7-PD. Firstly, the main feature extraction network is fused with deformable convolution by replacing the traditional convolution module in the YOLOv7-tiny main network and the ELAN module with deformable convolution, which reduces network parameters while improving the detection accuracy of multi-scale Xiaomila targets. Secondly, the SE (Squeeze-and-Excitation) attention mechanism is introduced into the reconstructed main feature extraction network to improve its ability to extract key features of Xiaomila in complex environments, realizing multi-scale Xiaomila fruit detection. The effectiveness of the proposed method is verified through ablation experiments under different lighting conditions and model comparison experiments.

Results

The experimental results indicate that YOLOv7-PD achieves higher detection performance than other single-stage detection models. Through these improvements, YOLOv7-PD achieves a mAP (mean Average Precision) of 90.3%, which is 2.2%, 3.6%, and 5.5% higher than that of the original YOLOv7-tiny, YOLOv5s, and Mobilenetv3 models, respectively, the model size is reduced from 12.7 MB to 12.1 MB, and the model’s unit time computation is reduced from 13.1 GFlops to 10.3 GFlops.

Discussion

The results shows that compared to existing models, this model is more effective in detecting Xiaomila fruits in images, and the computational complexity of the model is smaller.
Time to move beyond monological perspectives in health behavior change communication research and practice
Authors: Schöps Antje Maria , Skinner Timothy Charles , Fosgerau Christina Fogtmann
Published: June 2023

Chronic disease self-management and health behavior change programs are becoming increasingly important to health service delivery to prevent the development of chronic disease and optimize health outcomes for those who suffer from it. To train people to deliver these programs effectively, we need to understand both the what and how of program delivery. While there is an abundant literature on what, and a merging evidence about what techniques to use, such as goals setting and self-monitoring, the literature on how programs should be delivered is less well developed. This paper reviews emerging research in this area and identifies an underlying monological approach. We argue that this currently dominant model cannot address the key issues in this area. By considering the theoretical framework of Dialogism, we introduce the method of Conversation Analysis to the field of behavior change interventions. Extensive research into health communication has endeavored to show the importance of language and the organization of interactions. We demonstrate and discuss how a monological approach to interventions prevents exploration of what professionals do to deliver intervention content. In doing so, we show that techniques do not account for how successfully an intervention is delivered.
Paths towards parenthood after repeated treatment failures: a comparative study on predictors of psychological health outcomes in infertile couples persisting in treatments or opting for adoption
Authors: Zurlo Maria Clelia , Cattaneo Della Volta Maria Francesca , Vallone Federica
Published: June 2023

Introduction

Infertility literature suggests widespread recourse to long-term medical treatments despite evidence of high stress, costs, and adverse effects of repeated treatment failures. However, there is a lack of research comparing predictors of stress and psychological health outcomes between members of infertile couples who – after repeated failures – persist in pursuing medical treatments (PT) with those who opted for quitting treatments and adopting (QTA). Basing on a transactional and multidimensional approach to infertility-related stress and health, the present study aims at exploring individual (socio-demographics; coping strategies) and situational (infertility-related parameters; infertility-related stressors; couple’s dyadic adjustment dimensions) predictors of state-anxiety and depression in male and female partners of PT-infertile couples and of QTA-infertile couples.

Methods

Participants were both members of 176 couples with duration of infertility and a history of medical treatments for at least 3 years (76 PT-infertile couples, 100 QTA-infertile couples). The study variables were compared by study group across genders. Structural equation models (SEM) were used to test main and moderating effects of study variables on state-anxiety and depression by study group and across genders.

Results

Members of infertile couples quitting treatments and adopting (QTA) reported significantly lower levels of state-anxiety and depression, higher stress related to need for parenthood and rejection of childfree-lifestyle and lower stress related to social and couple’s relationship concerns than those who persist in pursuing medical treatments (PT). Members of infertile couples quitting treatments and adopting (QTA) recurred to a greater extent to active coping strategies (problem-solving/social-support) and to a lower extent to passive coping strategies (avoiding/turning-to-religion), and they reported higher levels of dyadic adjustment. Specificities in main and moderating factors related to state-anxiety and depression by study group and across genders were found.

Conclusion

Findings should be addressed to provide a comprehensive assessment of both members of infertile couples facing repeated treatment failures to identify risks and resources and develop tailored evidence-based interventions.
Metabolite-disease interaction prediction based on logistic matrix factorization and local neighborhood constraints
Authors: Zhao Yongbiao , Ma Yuanyuan , Zhang Qilin
Published: June 2023

Background

Increasing evidence indicates that metabolites are closely related to human diseases. Identifying disease-related metabolites is especially important for the diagnosis and treatment of disease. Previous works have mainly focused on the global topological information of metabolite and disease similarity networks. However, the local tiny structure of metabolites and diseases may have been ignored, leading to insufficiency and inaccuracy in the latent metabolite-disease interaction mining.

Methods

To solve the aforementioned problem, we propose a novel metabolite-disease interaction prediction method with logical matrix factorization and local nearest neighbor constraints (LMFLNC). First, the algorithm constructs metabolite-metabolite and disease-disease similarity networks by integrating multi-source heterogeneous microbiome data. Then, the local spectral matrices based on these two networks are established and used as the input of the model, together with the known metabolite-disease interaction network. Finally, the probability of metabolite-disease interaction is calculated according to the learned latent representations of metabolites and diseases.

Results

Extensive experiments on the metabolite-disease interaction data were conducted. The results show that the proposed LMFLNC method outperformed the second-best algorithm by 5.28 and 5.61% in the AUPR and F1, respectively. The LMFLNC method also exhibited several potential metabolite-disease interactions, such as “Cortisol” (HMDB0000063), relating to “21-Hydroxylase deficiency,” and “3-Hydroxybutyric acid” (HMDB0000011) and “Acetoacetic acid” (HMDB0000060), both relating to “3-Hydroxy-3-methylglutaryl-CoA lyase deficiency.”

Conclusion

The proposed LMFLNC method can well preserve the geometrical structure of original data and can thus effectively predict the underlying associations between metabolites and diseases. The experimental results show its effectiveness in metabolite-disease interaction prediction.
The Cajal body marker protein coilin is SUMOylated and possesses SUMO E3 ligase-like activity
Authors: Lett Katheryn E. , McLaurin Douglas M. , Tucker Sara K. , Hebert Michael D.
Published: June 2023

Cajal bodies (CBs) are subnuclear domains that contribute to the biogenesis of several different classes of ribonucleoproteins (RNPs), including small nuclear RNPs. Only some cell types contain abundant CBs, such as neuronal cells and skeletal muscle, but CBs are invariant features of transformed cells. In contrast, coilin, the CB marker protein, is a ubiquitously expressed nuclear protein, but the function of coilin in cell types that lack CBs is not well understood. We have previously shown that coilin promotes microRNA biogenesis by promoting phosphorylation of DGCR8, a component of the microprocessor. Here, we identify seven additional residues of DGCR8 with decreased phosphorylation upon coilin knockdown. In addition to phosphorylation, the addition of a small ubiquitin-like modifier (SUMO) to DGCR8 also increases its stability. Because of coilin’s role in the promotion of DGCR8 phosphorylation, we investigated whether coilin is involved in DGCR8 SUMOylation. We show that coilin knockdown results in global decrease of protein SUMOylation, including decreased DGCR8 and Sp100 (a PML body client protein) SUMOylation and decreased SMN expression. Alternatively, we found that coilin expression rescued Sp100 SUMOylation and increased DGCR8 and SMN levels in a coilin knockout cell line. Furthermore, we found that coilin facilitates RanGAP1 SUMOylation, interacts directly with components of the SUMOylation machinery (Ubc9 and SUMO2), and, itself, is SUMOylated in vitro and in vivo. In summary, we have identified coilin as a regulator of DGCR8 phosphorylation and a promotor of protein SUMOylation with SUMO E3 ligase-like activity.
Predicting streamflow with LSTM networks using global datasets
Authors: Wilbrand Katharina , Taormina Riccardo , ten Veldhuis Marie-Claire , Visser Martijn , Hrachowitz Markus , Nuttall Jonathan , Dahm Ruben
Published: June 2023

Streamflow predictions remain a challenge for poorly gauged and ungauged catchments. Recent research has shown that deep learning methods based on Long Short-Term Memory (LSTM) cells outperform process-based hydrological models for rainfall-runoff modeling, opening new possibilities for prediction in ungauged basins (PUB). These studies usually feature local datasets for model development, while predictions in ungauged basins at a global scale require training on global datasets. In this study, we develop LSTM models for over 500 catchments from the CAMELS-US data base using global ERA5 meteorological forcing and global catchment characteristics retrieved with the HydroMT tool. Comparison against an LSTM trained with local datasets shows that, while the latter generally yields superior performances due to the higher spatial resolution meteorological forcing (overall median daily NSE 0.54 vs. 0.71), training with ERA5 results in higher NSE in most catchments of Western and North-Western US (median daily NSE of 0.83 vs. 0.78). No significant changes in performance occur when substituting local with global data sources for deriving the catchment characteristics. These results encourage further research to develop LSTM models for worldwide predictions of streamflow in ungauged basins using available global datasets. Promising directions include training the models with streamflow data from different regions of the world and with higher quality meteorological forcing.