bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expression characteristics, immune signature, and prognostic value of the SOCS family identified by multiomics integrative analysis in liver cancer
Authors: Dong Zhitao , Dai Binghua , Fang Kunpeng , Duan Kecai , Sui Chengjun , Geng Li , Yang Jiamei 
Published: January 2023

Abstract
Objective
Hepatocellular carcinoma is one of the most common malignancies in the world, and the death rate is very high. The members of the SOCS family are the key factors in the regulation of various cytokines and growth factors. It is not clear, however, whether the level of the SOCS family will affect the prognosis in patients with HCC.
Methods
Firstly, we studied the expression levels of the SOCS family genes in the HCC and the relationship between the expression level of the SOCS family and different clinicopathological characteristics. Then the public database was used to analyze the changes of expression, potential function, transcription factors and immune invasion of SOCS family members. Finally, we analyzed the prognostic value of the patients with SOC family with HCC and the correlation with SOC family and ferroptosis-related genes.
Results
The expression of SOCS2-7 and CISH was downregulated in HCC. The SOCS4, SOCS5 and SOCS7 genes were all related to the clinicopathological features of HCC patients. SOCS family genes are mainly related to PIK3R3, GHR, TNS4, TNS4 pathway. We found that STAT3, PPAR-gamma 2 and IRF-2 are important transcription factors in regulating SOCS family members. We also confirmed that the expression level of SOCS family members are closely related to the immune infiltration of liver cancer. Then, we clarified that SOCS2 and SOCS4 are risk-related gene in predicting the prognosis of patients with liver cancer. Finally, we found that SOCS2 gene may be involved in the development and progression of hepatocellular carcinoma, but the mechanism needs further experimental verification.
Conclusion
Our study may expand upon the understanding of SOCS gene function in liver cancer and help clinicians select appropriate drugs and predict the prognosis of patients with liver cancer.
miR-122 dysregulation is associated to the type2 diabetes mellitus-induced dyslipidemia and hyperglycemia independently to its variant rs17669
Authors: Behrouj Hamid , Moridi Heresh , Moradi Mohamad Nabi , Ghasemi Hassan 
Published: January 2023

Abstract
Background: miR-122 is a liver specific micro RNA that participates in the regulation of carbohydrate and lipid metabolism. rs17669 variant positioned at the flanking region of miR-122 and may be affects its stability and maturation. Therefore, this study was aimed to investigates the association between rs17669 polymorphism with the miR-122 circulating level, risk of type 2 diabetes mellitus (T2DM) development and biochemical parameters in these patients and matched healthy controls.
Methods and Results: Two hundred and ninety-five subjects (controls; n=145 and T2DM; n=150) enrolled in this study. rs17669 variant genotyping was done by ARMS-PCR. Serum biochemical parameters including lipid profile and glucose were measured by colorimetric kits. Insulin and Glycated hemoglobin (HbA1c) were assayed by using capillary electrophoresis and ELISA methods respectively. miR-122 expression was measured by real-time PCR. There was no significant difference in allele and genotype distribution between study groups (P>0.05). rs17669 variant has not any significant association with miR-122 gene expression and biochemical parameters (P>0.05). miR-122 expression level in T2DM patients was considerably higher than that in control subjects (5.7±2.4 vs 1.4±0.78) (P>0.05). Furthermore, there were a positive and significant correlation between miR-122 fold change with LDL-C, sdLDL, FBS and insulin resistance (P>0.05).
Conclusions: It can be concluded that miR-122 rs17669 variant is not associated to the miR-122 expression and T2DM-associated serum parameters. Furthermore, it can be suggesting that miR-122 dysregulation involved in T2DM development through the inducing dyslipidemia, hyperglycemia as well as resistance to insulin.
Salivary Osteopontin was associated with lesion size in patients with oral lichen planus
Authors: Sharifi Sara , Hoseini Elaheh Ghasemzadeh , Rahimi Habibollah , Lotfinia Majid 
Published: January 2023

Abstract
Introduction: Osteopontin (OPN) is recognized as a potent biomarker of Oral lichen planus (OLP) because of vital role in inflammation and repair process. The aim of present study is assessment of OPN in OLP in comparison with healthy controls (HC).
Material and Methods: To explore salivary levels of OPN, a group of 20 subjects with OLP were compared with 20 HC. Salivary OPN levels was measured by enzyme-linked immunosorbent (ELISA) assay.
Results: Results indicated elevated OPN levels in lesion size < 1 cm compared with 1 - 3 cm lesion size of OLP (p= 0.02). In contrast, we did not find a significant difference in OPN expression level in saliva from OLP patients and healthy controls (P = 0.96).
Discussion: The above results suggest that maybe OPN may serve as a potential biomarker for the monitoring of repair process in OLP.
Impact of fracture properties on the performance of engineered geothermal systems in the crystalline basement of Kuujjuaq (Canadian Shield)
Authors: Miranda Mafalda M. , Raymond Jasmin , Dezayes Chrystel , Wigston Andrew , Perreault Serge 
Published: January 2023

Abstract
Understanding the natural fracture network is essential for geothermal-related investigations. However, the geometrical attributes depend on the scale of observation. Therefore, a multiscale characterization of the fracture network is essential to ensure that forward heat and flow simulations are based on stochastically generated discrete fracture network models representative of the natural fracture system observed. This was the goal of this work. Fracture data was collected from satellite imagery, outcrops and well cores to evaluate the scale effect and to study the impact of fracture size and density on the performance of engineered geothermal systems by numerical modeling. The numerical simulations highlighted that networks made of small fractures (0.08 to 27 m) tend to decrease the performance of the system compared to a network made of large fractures (22 to 1,437 m). However, thermal short-circuiting is easily reached in the latter scenario. Thus, the simulations suggest that the best-case network is made of fractures ranging between 1.57 to 135 m with fractures spaced by 5 m. This scenario provides the best compromise between heat extraction, water losses, hydraulic impedance and thermal drawdown. Despite the uncertainties, the fracture data used highlights the importance of multiscale fracture analysis for heat-flow simulations of geothermal reservoirs.
Age, sex, primary tumor type and site are associated with mortality after pathological fractures: An observational study of 1,453 patients from the Swedish Fracture Register
Authors: Wänman Johan , Kjartansdóttir Sonja , Wolf Olof , Sundkvist Jonas , Wennergren David , Mukka Sebastian 
Published: January 2023

Abstract
Background
Pathological fractures are challenging in orthopedic surgery and oncology, with implications for the patient’s quality of life, mobility and mortality. The efficacy of oncological treatment on life expectancy for cancer patients has improved, but the metastatic pattern for bone metastases and survival is diverse for different tumor types. This study aimed to evaluate survival in relation to age, sex, primary tumor and site of the pathological fractures.
Methods
All pathological fractures due to cancer between 1 September 2014 and 31 December 2021 were included in this observational study from the Swedish Fracture Register (SFR). Data on age, sex, tumor type, fracture site and mortality were collected.
Results
1,453 patients with pathological fractures were included (48% women, median age 73, range 18-100 years). Unknown primary tumors were the most common primary site (n=308). The lower extremities were the most common site of pathological fractures. Lung cancer had the shortest median survival of 78 days (range 54-102) and multiple myeloma had the longest median survival of 432 days (range 232-629). The site at the lower extremity had the shortest (187 days, range 162-212) and the spine had the longest survival (386 days, range 211-561). Age, sex, primary type and site of the pathological fractures were all associated with mortality.
Interpretation
Age, sex, primary tumor type and site of pathological fractures significantly impact survival. Survival time is short and correlated to primary tumor type, with lung cancer as the strongest negative predictor of survival.
Assessments of tree-ring intra-annual δ18O record for reconstructing hydroclimate with high temporal resolution
Authors: Watanabe Yumiko , Katayama Yoshito , Li Zhen , Nakatsuka Takeshi , Tazuru Suyako 
Published: January 2023

Abstract
Tree-ring cellulose oxygen isotopic ratios have been widely studied as a hydrological proxy in monsoonal Asia. There has been, however, little attempt to perform proxy assessment of the intra-annual isotopic data to reconstruct hydroclimate with higher temporal resolution. We presented new intra-annual cellulose oxygen isotopic record of Japanese cedar trees spanning A.D. 1918 to 2017, and validated it as a hydrological proxy by comparing with meteorological data. There are significant negative correlations between intra-annual isotopic ratios and summer precipitation/relative humidity, as similar to annual-resolution data of earlier studies. Notably on intra-annual scales, the period showing the highest correlation gradually shifted from May to August, in corresponding to the location within the annual ring. Principal component regression analyses show the regression was more accurate over a wider duration than single regression analysis using the annual data, therefore indicating that the subdivision of the annual ring could contribute to reconstruct higher-resolution hydroclimate.
The future of pre-exposure prophylaxis (PrEP) for HIV prevention: Provider perspectives
Authors: Henderson Mary , Schmidt Heather-Marie A , Chitembo Lastone , Hortencia Peralta , Sabry Ahmed , Johnson Cheryl , Baggaley Rachel , Schaefer Robin 
Published: January 2023

Abstract
Background: Differentiated service delivery and new products, such as long-acting injectable cabotegravir (CAB-LA) and the dapivirine vaginal ring (DVR), could increase uptake and use of pre-exposure prophylaxis (PrEP) for HIV prevention. We explored PrEP provider perspectives on innovations in service delivery and products to inform World Health Organization (WHO) guidelines and programme implementation.
Methods: 150 PrEP providers who participated in a WHO online survey were randomly selected and 67 were invited for interviews based on geographic representation, provider cadre, gender, experience with community-based PrEP service delivery, and familiarity with new PrEP products. Semi-structured interviews were conducted via video calls. Key themes were inductively extracted relating to differentiated service delivery and benefits and concerns regarding new PrEP products.
Results: 30 PrEP providers from 24 countries were interviewed. Across regions, providers were supportive of differentiated service delivery to respond to clients’ needs and preferences, maintain services during COVID-19, and ensure access for hard-to-reach populations. Providers welcomed prospects of offering an CAB-LA to their clients but had concerns about HIV testing, costs, and the need for clinic-based services, including staff who can administer injections. Providers felt the DVR was potentially important for some women, especially young clients and female sex workers, and raised fewer concerns compared to injectable PrEP.
Conclusions: Providers’ views are critical for the development of guidelines and implementing programmes that will best serve PrEP users. Understanding areas where provider capacities and biases may create barriers can define opportunities for training and support to ensure that providers can deliver effective programmes.
Performance assessment of helicon wave heating andcurrent drive in EXL-50 spherical torus plasmas
Authors: Qiao G.J. , Luo D. , Song S.D. , Dong J.Q. , Shi Y.J. , Li J. C. , Du D. , Peng Y. K. Martin 
Published: January 2023

Abstract
Analysis of helicon wave heating and current drive capability in EXL-50spherical torus plasmas has been conducted. It is found that the drivencurrent increases with the launched parallel refractive index n|| and peaksaround n|| = 4.0 when the frequency of the helicon wave is between 300 MHzand 380 MHz. The helicon wave current drive efficiency shows a relativelystable upward trend with increasing plasma temperature. Moreover, thedriven current decreases as the plasma density increases. We also analyzedthe current drive with helicon waves of 150 MHz and 170 MHz and foundthat the driven current at a lower frequency was lower than that at a higherfrequency. A positive proportional relationship exists between the drivencurrent and n||. Besides, as n|| increases, the profile of the driven currentbecomes wider. Finally, the effect of the scrape-off layer (SOL) region on thehelicon wave current drive was also investigated.
Field-measured canopy height may not be as accurate and heritable as believed – Evidence from advanced 3D sensing
Authors: Zang Jingrong , Jin Shichao , Zhang Songyin , Li Qing , Mu Yue , Li Ziyu , Li Shaochen , Wang Xiao , Su Yanjun , Jiang Dong 
Published: January 2023

Abstract
Canopy height (CH) is an important trait for crop breeding and production. The rapid development of 3D sensing technologies shed new light on high-throughput height measurement. However, a systematic comparison of the accuracy and heritability of different 3D sensing technologies is seriously lacking. Moreover, it is questionable whether the field-measured height is as reliable as believed. This study uncovered these issues by comparing traditional height measurement with four advanced 3D sensing technologies, including terrestrial laser scanning (TLS), backpack laser scanning (BLS), gantry laser scanning (GLS), and digital areal photogrammetry (DAP). A total of 1920 plots covering 120 varieties were selected for comparison. Cross-comparisons of different data sources were performed to evaluate their performances in CH estimation concerning different CH, leaf area index (LAI), and growth stage (GS) groups. Results showed that 1) All 3D sensing data sources had high correlations with field measurement (r>0.82), while the correlations between different 3D sensing data sources were even better (r>0.87). 2) The prediction accuracy between different data sources decreased in subgroups of CH, LAI, and GS. 3) Canopy height showed high heritability from all datasets, and 3D sensing datasets had even higher heritability (H2=0.79-0.89) than FM (H2=0.77). Finally, outliers of different datasets are analyzed. The results provide novel insights into different methods for canopy height measurement that may ensure the high-quality application of this important trait.
Design of a Few End-Capped Donor-Acceptor Inorganic-Organic Hybrid Nickel Dithiolene Derivatives for Efficient NLO Response
Authors: Ghosh Prokash , Majumder Manoj , Sutradhar Tanushree , Misra Anirban 
Published: January 2023

Abstract
The NLO property of a few designed inorganic-organic hybrid materials based on Nickel dithiolenes end-capped with donor-acceptor groups has been studied theoretically. All the designed molecules possess high first hyperpolarizability values indicating their potential use in optics, photonics, and as photosensitizers. Among the four designed systems, the BODIPY-containing systems significantly reduce the HOMO-LUMO energy gap resulting in a massive trek in the first hyperpolarizability (β) values. To judge their high NLO response, transition dipole moment (TDM) density has been plotted and it has been found that electron dissipation occurs through the molecular network with a large Δr index value. It is to be noted that high Δr index values are quantitative measurements to understand the type of transitions, and we noticed that a charge transfer transition occurs in all of our designed systems. Hence a nice correlation between the first hyperpolarizability, TDM density, and Δr index value has been observed. The global reactivity parameters are also studied and correlated nicely with polarizability and hole-electron transport ability.
Prevalence of neural tube defects among pregnant women in Addis Ababa: A community-based study using prenatal ultrasound examination
Authors: Tirsit Abenezer , Zewdneh Daniel , Yigeremu Mahlet , Legese Aga , Moen Bente E. , Lie Rolv T. , Lund-Johansen² Morten , Mahesparan Rupavathana 
Published: January 2023

Abstract
Purpose
The primary aim of this study was to estimate the prevalence of NTDs at ultrasound examination in communities of Addis Ababa and secondarily to provide a description of the dysmorphology of the NTD cases.
Methods
We enrolled 958 pregnant women from 20 randomly selected health centers in Addis Ababa during the period from October 1, 2018 to April 30, 2019. Of these 958 women, 891 had an ultrasound examination after enrollment, with special focus on NTDs. We estimated the prevalence of NTDs and compared it with previously reported hospital-based birth prevalence estimates from Addis Ababa.
Results
Among 891 women, 13 had twin pregnancies. We identified 15 NTD cases among 904 fetuses, corresponding to an ultrasound-based prevalence of 166 per 10,000 (95% CI: 100–274). There were no NTD-cases among the 26 twins. Eleven had spina bifida (122 per 10,000, 95% CI: 67–219). Among the 11 fetuses with spina bifida, three had a cervical and one had a thoracolumbar defect while the anatomical site for 7 was not registered. Seven of the 11 spina bifida defects had skin covering, while two of the cervical lesions were uncovered.
Conclusion
We report a high prevalence of NTDs among pregnancies in communities of Addis Ababa based on screening by ultrasound. The prevalence was higher than previous hospital-based studies in Addis, and the prevalence of spina bifida was particularly high.
Mixed-methods education of mechanical ventilation for residents in the era of the COVID- 19 pandemic: preliminary interventional study
Authors: Takeda Kenichiro , Kasai Hajime , Tajima Hiroshi , Furukawa Yutaka , Imaeda Taro , Suzuki Takuji , Ito Shoichi 
Published: January 2023

AbstractBackground In the current era of the severe acute respiratory syndrome-coronavirus-2 epidemic, the need for respiratory care, including mechanical ventilatory (MV) management, has increased. However, there are no well-developed educational strategies for training medical personnel dealing with respiratory care in MV management. Methods A novel mixed-methods hands-on seminar for learning MV management was conducted for the residents at Chiba University Hospital in March 2022. The seminar lasted approximately 2 hours. The learning goal for the residents was to develop skills and knowledge in performing basic respiratory care, including MV, during an outbreak of a respiratory infection. The seminar with a flipped classroom consisted of e-learning, including modules on respiratory physiology and MV management, hands-on training with a low-fidelity simulator (a lung simulator), and hands-on training with a high-fidelity simulator (a human patient simulator). Each training activity was supervised by respiratory physicians, an intensivist, or a clinical engineer. The effectiveness of the seminar was evaluated using closed questions (scored on a five-point Likert scale: 1 [minimum] to 5 [maximum]) and multiple-choice questions (maximum score: 6) at the pre- and post-seminar evaluations. Results Fourteen residents at Chiba University Hospital participated in the program. The questionnaire responses revealed that the participants’ motivation for learning about MV was relatively high in the pre-seminar period (seven participants [50%] selected level 5 [very strong]), and it increased in the post-seminar period (all participants selected level 5) (p = 0.016). However, most participants (n = 12, 86%) felt the psychological burden of providing respiratory care to patients needing MV management, and the level of the psychological burden did not change significantly from the pre- to post-seminar period (p = 0.328). The responses to the multiple-choice questions revealed that the participants did not have enough knowledge to operate a mechanical ventilator, but the total score significantly improved from the pre- to post-seminar period (pre-seminar: 3.3, post-seminar: 4.6,p = 0.003). Conclusions The seminar implemented in this study helped increase the residents’ motivation to learn about respiratory care and improved knowledge of MV management in a short time. In particular, the flipped classroom may promote the efficiency of education on MV management.
AttSec: protein secondary structure prediction by capturing local patterns from attention map
Authors: Kim Youjin , Kwon Junseok 
Published: January 2023

Abstract
Background: Protein secondary structures that link simple 1D sequences to complex 3D structures can be used as good features for describing the local properties of protein, but also can serve as key features for predicting the complex 3D structures of protein. Thus, it is very important to accurately predict the secondary structure of the protein, which contains a local structural property assigned by the pattern of hydrogen bonds formed between amino acids. In this study, we accurately predict protein secondary structure by capturing the local patterns of protein. For this objective, we present a novel prediction model, AttSec, based on transformer architecture. In particular, AttSec extracts self-attention maps corresponding to pairwise features between amino acid embeddings and passes them through 2D convolution blocks to capture local patterns. In addition, instead of using additional evolutionary information, it uses protein embedding as an input, which is generated by a language model.
Results: For the ProteinNet DSSP8 dataset, our model showed 11.8% better performance on the entire evaluation datasets compared with other no-evolutionary-information-based models. For the NetSurfP-2.0 DSSP8 dataset, it showed 0.8% better performance on average. There was an average performance improvement of 9.0% for the ProteinNet DSSP3 dataset and an average of 0.18% for the NetSurfP-2.0 DSSP3 dataset.
Conclusion: We accurately predict protein secondary structure by capturing the local patterns of protein. For this objective, we present a novel prediction model, AttSec, based on transformer architecture.Although there was no dramatic accuracy improvement compared with other models, the improvement on DSSP8 was greater than that on DSSP3. This result implies that using our proposed pairwise feature could have a remarkable effect for several challenging tasks that require finely subdivided classification.
Github package URL is https://github.com/youjin-DDAI/AttSec.