bluuebunny/crossref_metadata_2025_split huggingface dataset:
SPOP promotes cervical cancer progress by inducing PD-1 move away from PD-L1 in spatial localization
Authors: Wu Jiangchun , Wu Yong , Guo Qinhao , Chen Siyu , Wang Simin , Zhu Jun , Wu Xiaohua , Ju Xingzhu 
Published: April 2022

Abstract
Background
Metastasis is a major obstacle in treatment of cervical cancer (CC), and gene SPOP mediated regulatory effect is found to be involved in metastasis. However, its mechanisms have not been fully elucidated.
Methods
We performed proteomic sequencing, immunohistochemical staining (IHC) and scoring of SPOP in cancer tissues of 180 patients with 2009 FIGO stage IB1-IIA2 CC, and compared the expression of SPOP between pelvic lymph node (pLN) metastasis group and non-pLN metastasis group. We divided the data into two groups by SPOP expression, compared overall survival (OS) and relapse- free survival (RFS) of patients. In vitro, cells were carried out to determine whether SPOP overexpression or knockdown could affect the proliferation, cloning, wounding and Tanswell assays. Finally, the possible mechanism of pLN metastasis of CC was explored by analyzing the differences in the number and distance of various immune targets.
Results
SPOP is upregulated in CC with pLN metastasis and negatively associated with patient outcome. In vitro, SPOP promotes CC cell proliferation, invasion. Through further analysis, we found that there was no significant difference in the number of PD-1 and PD-L1 between the two groups, but the number of PD-1 in the range of PD-L1 100um was significantly increased.
Conclusion
This study presents that SPOP can inhibit the immune microenvironment by promoting PD-1 to move away from PD-L1, thereby promoting pLN metastasis of CC, resulting in worse OS and RFS in patients.
Prognostic factors for renal function deterioration during palliative first-line chemotherapy for metastatic colorectal cancer
Authors: Lim Ah Reum , Kim Jwa Hoon , Hyun Myung Han , Kim Yeul Hong , Lee Soohyeon 
Published: April 2022

Abstract
Purpose
Effective first-line therapy is a key determinant of long-term treatment outcomes in patients with metastatic colorectal cancer (mCRC). We assessed changes in renal function for 1 year among patients diagnosed with mCRC who received first-line chemotherapy. Further, we analyzed the prognostic factors and effect of each chemotherapy regimen on the renal function of the patients.
Methods
We retrospectively investigated patients with mCRC who were treated with a standard triplet regimen (FOLFOX/FOLFIRI with bevacizumab/cetuximab) in the first-line setting at Korea University Anam Hospital from 2015 to 2020. We checked renal function at 3-month intervals for 12 months. We calculated changes in eGFR (△eGFR, estimated glomerular filtration rate) and compared them with clinical factors such as age, sex, chronic disease, body mass index (BMI), disease status, baseline proteinuria, and first-line chemotherapy regimen.
Results
Among 472 patients with mCRC, the median eGFR at baseline was 90.9 mL/min/1.73 m2; it was significantly lower (80.1 mL/min/1.73 m2, p < 0.001) at 12 months after chemotherapy initiation. Particularly, the eGFR of patients treated with FOLFIRI + Bevacizumab was 74.9 mL/min/1.73 m2. The 1-year incidence rate of acute kidney injury (AKI) was 9.1%, with the lowest occurrence in patients receiving FOLFOX/cetuximab (2.1%) and the highest in those receiving FOLFIRI + bevacizumab (19.2%). Renal dysfunction was more frequent with FOLFIRI + bevacizumab as compared to the other regimens. Additionally, old age, low BMI, and proteinuria at baseline were also associated with a decreased eGFR.
Conclusions
These findings can serve as important factors when selecting the first-line chemotherapy regimen for patients with mCRC.
Project Emery: Humanizing Patient Experience through Arts Expressive Activity among Clinically Isolated Patients in a Large Referral Hospital in Qatar
Authors: Logrono Kenneth Jun , Narag Katrina , Capaspas April Vincent , Mulla Jakir , Zu'bi Belal Salem , Swallmeh Esmat , Piol Diana Lynn , Sarmiento Djoanne 
Published: April 2022

Abstract
Project Emery is a project and a strategy aimed to humanize the patient experience at Hamad General Hospital (HGH), which emphasized the need to translate compassionate and safe care into a tangible experience specifically for patients in isolation rooms. The evolving concept of "humanizing patient care" create a value improvement initiative for patients, treating them as individuals rather than just patients. Nearly all patients (80%) experienced anxiety as a result of isolation during the pandemic, and two-thirds (60%) reported a significant high level of anxiety, stress, and worry. To address the mental health challenges, art therapy inspired by patient Emery is offered as a tool to support patients during periods of isolation. The project is aimed to improve the patient engagement through increasing access to the arts as a means of expressing their thoughts and feelings about treatment and being hospitalized. The IHI Model of Improvement was utilized on this quality improvement initiative. A qualitative method was conducted using individual, semi-structured interviews. All interviews were transcribed verbatim for thematic analysis. Results have showed that 99% of 166 patients who voluntarily participate the arts activity had high engagement scores and would highly recommend the activity to the others. There are four common themes taken from patient interviews, 1) strengthens patient’s positive feelings, 2.) vent out feelings and concerns through storytelling, and narratives, 3.) optimizes nurse-patient communication; and 4.) activity for patient engagement.
Long-term comparative outcome analysis of a Robot-Assisted Laparoscopic Prostatectomy with Retropubic Radical Prostatectomy by a single surgeon
Authors: Tillu Neeraja , Kulkarni Jagdeesh 
Published: April 2022

Abstract
ObjectiveWe aimed to give a comprehensive outcome analysis of robot assisted laparoscopic prostatectomies (RALP) performed by a single surgeon and compared it to retropubic radical prostatectomies (RRP) done by the same surgeon in a high-volume center.Materials and MethodsPreoperative, perioperative, and postoperative data were collected prospectively and compared with retrospective retropubic radical prostatectomy data. Perioperative, oncological data and functional results in the first year were compared between the two groups. There were 547 RARPs between 4th August 2011 to 31st December 2018, and 428 RRPs between 1st January 1996 to 31st December 2009 which were included in this review.ResultsWhile the operation time was in favor of the open group (196 vs 160 min, p<0.01), the estimated blood loss (188 vs 316ml, p<0.01), blood transfusion rate (3% vs 7% p=0.021), hospital stay (4 days vs 7 days) and mean catheter duration (12 vs 15 days) were in favor of the robotic group. Majority of the complications belonged to Clavien-Dindo group II in both groups and rates were not significantly different. (p=0.33) 12-month continence rate was in favor of RALP group (98.3% vs 99.2%, p <0.01). Overall survival of the RALP cohort at 24 months was 99.8%, 60 months 96.1%, 84 months 87.3% , 96 months 81.3%), 108 months was 79.5%. Overall survival at 24 months was 99.8%, 60 months 96.1%, 84 months 87.3%, 96 months 81.3%, and 108 months was 79.5%.ConclusionRALP is a safe, minimally invasive technically feasible procedure with comparable functional and oncological outcomes. Our study showed superior perioperative and continence outcomes in RALP. However, despite its growing popularity, RRP still remains the gold standard in India due to its affordability and accessibility.
Malacoplakia of the bladder combined with infected renal calculi: A case report
Authors: Xu Wujun , He Qunjun , Wang Yi , Chen Xian , Xia Baopiao , Zeng Xuqiang , Wang Binhui , Fang Yong , Liu Shulin 
Published: April 2022

Abstract
Introduction: The malacoplakia of the bladder is a rare chronic acquired infection- associated granulomatous disease and even less common in combination with urinary stones. Case Presentation: We report the case of a 58-year-old female patient with malacoplakia of the bladder combined with renal calculi. The patient was admitted to the hospital with bilateral low back pain for one month and space-occupying lesions of the bladder for three days. Preoperative imaging suggested space-occupying lesions of the bladder: high probability of bladder cancer. Following the anti-infection treatment, the transurethral electrodesiccation was performed on the space-occupying lesions of the bladder. Pathological examination confirmed the diagnosis of malacoplakia of the bladder. Left-sided percutaneous nephrolithotomy was performed electively to remove the predisposing factors of infection. After the operation, the patient continued to receive anti-infection treatment for two months. The patient had a good prognosis in the six-month follow-up.Conclusions: Malacoplakia of the bladder is easily misdiagnosed as bladder cancer before operation, and the diagnosis depends on pathological diagnosis. Complete removal of urinary calculi, infection and other inducing factors, is beneficial to the treatment of malacoplakia of the bladder.
Superresolving, artifact-free optical coherence tomography with deconvolution-random phase modulation
Authors: liu linbo , Ge Xin , chen Si , kan lin , ni guangming , bo en , wang lulu 
Published: April 2022

Abstract
Deconvolution is widely used to improve resolution in microscopy. Unfortunately, deconvolution in optical coherence tomography (OCT) is sensitive to noise which inherently results in additive artifacts. These artifacts severely impair the fidelity of deconvolved images and limit its use in OCT imaging. Here we propose a framework that encodes numerical random phase masks in the Fourier space of a deconvolved OCT image, to produce a sub-resolution image with the artifacts removed. The optimized joint operation of an iterative Richardson-Lucy deconvolution and a numerical synthesis of random phase masks (RPM), termed as Deconv-RPM, enables a 2.7-fold enhancement in both transverse and axial resolutions. We demonstrate that the Deconv-RPM method allows imaging previously unresolved cellular-level details in the human labial mucosa in vivo with significantly improved clarity.
Effect of a uterine manipulator on the incidence of lymphovascular propagation (LVSI) in treatment of endometrial cancer
Authors: Dókuš Karol , Hudec Boris , Urdzík Peter , Školka Richard , Koňarčíková Tatiana , Smitka Michal 
Published: April 2022

Abstract
Background Endometrial cancers are among the epithelial malignancies of the lining in the uterine cavity. The invasion of carcinoma into the lymphovascular space (LVSI – lymphovascular space invasion) is considered a risk factor for the course of the disease. In our study, we investigated the potential effect of an intrauterine manipulator on the presence of LVSI in a definitive preparation.Methods Based on the inclusion and exclusion criteria, we were retrospectively evaluating 170 female patients. During endoscopic procedures we use a uterine manipulator. As the primary objectives were determined to be the finding of the difference in the incidence of LVSI in female patients with and without an intrauterine manipulator. As the secondary objective was set to determine the effect of a type of an intrauterine manipulator on the incidence of LVSI. Tertiary we analysed grading of tumor, myometrial invasion and method of obtaining primary histology in connection to the incidence of LVSI. Results We used logistic regression to identify the risk factors for LVSI. Using a manipulator during a surgery was not associated with the occurrence of LVSI (with a manipulator vs. without, 11.5% vs. 21.7%; OR 1.8; 95% CI 0.73–4.39; p = 0.199). The type of method used to obtain the primary histology had a statistically significant effect on the incidence of LVSI in our set (hysteroscopy vs. curettage; OR 4.27; 95% CI 1.39–13.07; p value = 0.011); grading and TNM (especially the grading G2 and G3 and TNM 1b).Conclusions In our study we have not confirmed the effect of a uterine manipulator on the possible increase of LVSI positive cases. Similar results have been published in other studies. The secondary analysis indicated a higher incidence of LVSI in the female patients diagnosed with curettage than in those who underwent hysteroscopy. Further studies will be needed to confirm this phenomenon.
Multi-level cellular and functional annotation of single-cell transcriptomes
Authors: Han Hong , Mikolajewicz Nicholas , Brown Kevin , Moffat Jason 
Published: April 2022

Abstract
Single-cell RNA-sequencing (scRNA-seq) offers unprecedented insight into heterogenous biology, allowing for the interrogation of cellular populations and gene expression programs at single-cell resolution. Here, we introduce scPipeline, a single-cell analytic toolbox that offers modular workflows for multi-level cellular annotation and user-friendly analysis reports. Novel methods that are introduced to facilitate scRNA-seq annotation include: (i) co-dependency index (CDI)-based differential expression; (ii) cluster resolution optimization using a marker-specificity criterion; (iii) marker-based cell-type annotation with Miko scoring; and (iv) gene program discovery using scale-free shared nearest neighbor network (SSN) analysis. Our unsupervised and supervised procedures were validated using a diverse collection of scRNA-seq datasets and we provide illustrative examples of cellular and transcriptomic annotation of developmental and immunological scRNA-seq atlases. Overall, scPipeline provides a flexible computational framework for in-depth scRNA-seq analysis.
Construction of a transposase accessible chromatin landscape reveals chromatin state of repeat elements and potential causal variant for complex traits in pigs
Authors: Jiang Tao , Ling Ziqi , Zhou Zhimin , Chen Xiaoyun , Chen Liqing , Liu Sha , Sun Yingchun , Yang Jiawen , Yang Bin , Huang Jianzhen , Huang Lusheng 
Published: April 2022

Abstract
Background
A comprehensive landscape of chromatin states for multiple mammalian tissues is essential for elucidating the molecular mechanism underlying regulatory variants on complex traits. However, the genome-wide chromatin accessibility has been only reported in limited tissue types in pigs.
Results
Here we report a genome-wide landscape of chromatin accessibility of 20 tissues in two female pigs at ages of 6 months using ATAC-seq, and identified 557,273 merged peaks, which greatly expanded the pig regulatory element repository. We revealed tissue-specific regulatory elements, which were associated with tissue-relevant biological function. We identified both positive and negative significant correlations between the regulatory elements and gene transcripts, which showed distinct distributions in terms of their strength and distances from corresponding genes. We investigated the presence of transposable elements in open chromatin regions across all tissues, these included identifications of porcine endogenous retroviruses exhibiting high accessibility in liver and homology of porcine specific virus sequences to universally accessible TEs. Furthermore, we prioritized a potential causal variant for polyunsaturated fatty acid in the muscle.
Conclusions
Our data provides a novel multi-tissue accessible chromatin landscape that serve as an important resource for interpreting regulatory sequences in tissue specific and conserved biological function, as well as regulatory variants underlying variation in complex traits associated loci in pigs.
Near‑infrared spectroscopy of plasma amino acids with chemometrics towards breast cancer discrimination
Authors: Zhu Liying , Qian Wen , Li Haizhi , Li Chengcheng , Huang Changyudong , Zhang Yiqiong , Duan Yunfeng , Wang Shuang , Xu YongJie , Zhang Jingzhi , Liu Mi , Li Xing , Pan Wei 
Published: April 2022

Abstract
Breast cancer(BC) is the most prevalent cancer and the second-leading cause of cancer-related death for women in the worldwide. BC cells need more amino acids to meet the demand of rapid proliferation. In this paper, we focus on the role of near‑infrared (NIR) spectroscopy to analyse blood plasma samples of breast cancer patients to differentiate healthy controls. The possibility of quantitative detection of 20 amino acids in breast cancer plasma by NIR spectroscopy was investigated for the first time in this study. 180 samples (80 BC patients, 30 benign breast disease patients and 70 healthy controls) were analysed. Canonical correlation analysis (CCA) was used to analyse the relationship between clinical biochemical parameters and amino acid metabolic profile for BC patients. In this study, plasma glutamine, histidine, threonine, proline, phenylalanine content of BC patients was higher than healthy control plasma (p < 0.05) by NIR spectroscopy. There was overall correlation (r = 0.935) between three clinical parameters(age, albumin, total triglyceride) and four amino acids (glutamic acid, tyrosine, valine and lysine) from BC patients. In this study，we have built quantitative and qualitative model which is used to detect plasma amino acids of BC patients by NIR spectroscopy has good performance. It fully demonstrated the great potential and advantages of NIR spectroscopy combined with chemometrics in breast cancer research, which can provide a new research strategy and technical platform for the study of plasma amino acid metabolism in breast cancer patients, and provide basic experimental data reference for clinical diagnosis and treatment of breast cancer patients.
Avalanche Criticality in LaAlO3: The Effect of Aspect Ratio
Authors: Scott John J. R. , Casals Blai , Luo King-Fa , Haq Atta , Mariotti Davide , Salje Ekhard K. H. , Arredondo Miryam 
Published: April 2022

Abstract
Ferroic domain dynamics, as a function of external stimuli, can be collectively described as scale-invariant avalanches characterised by a critical exponent that are sensitive to the complexity of the domain microstructure. The understanding and manipulation of these avalanches lies at the heart of developing novel applications such as neuromorphic computing. Here we combine in situ heating optical observations and mean-field analysis to investigate the collective domain behaviour in pure-ferroelastic lanthanum aluminate (LaAlO3) as a function of aspect ratio, the ratio of sample length to width, where the movement of the domains is predominantly driven by thermal stresses via thermal expansion/contraction during heat cycling. Our observations demonstrate that the aspect ratio induces i) distinctive domain microstructures at room temperature, ii) a deviation of dynamical behaviour at high temperatures and iii) critical exponent mixing in the higher aspect ratio samples that accompanies this behaviour. While the critical exponents of each aspect ratio fall within mean-field predicted values, we highlight the effect that the aspect ratio has in inducing exponent mixing. Hence, furthering our understanding towards tuning and controlling avalanches is crucial for fundamental and applied research.
Evaluation of the efficiency of DEEP-LSTM model in estimating evaporation from the pan in dry areas and its comparison with MLP model
Authors: Samii Amirhossein , Karami Hojat , Ghazvinian Hamidreza , Safari Amirsaeed , DadrasAjirlou Yashar 
Published: April 2022

Abstract
The importance of evaporation estimation in water resources and agricultural studies is undeniable. Evaporation pans (EP) are used as an indicator to determine the evaporation of lakes and reservoirs around the world due to the ease of interpreting its data. The purpose of this study is to evaluate the efficiency of the Long- Short Term Memory (LSTM) model to estimate evaporation from a pan and compare it with the Multilayer Perceptron (MLP) model in Semnan and Garmsar. For this purpose, daily meteorological data recorded between 2000 and 2018 (18 consecutive years) in Semnan and Garmsar synoptic stations were used. Minimum and maximum air temperature (Tmax, Tmin), wind speed (WS), sunshine hours (SH), air pressure (PA), relative humidity (RH) were selected as input data and evaporation data from the pan (EP) was considered as the output of the case. Also, in modeling both networks in the input section, 4 different scenarios were used. The two studied models were evaluated by the evaluation criteria of coefficient of determination (R2), root mean square error (RMSE) and mean absolute error (MAE). The results showed that among the studied scenarios, the fourth scenario (considering all input parameters) had the highest R2 and the lowest RMSE and MAE. In general, the two models performed well in predicting the rate of evaporation. Also, in both stations, the LSTM model had more R2 and less RMSE and MAE than the MLP model.
High-throughput Screening of Stable and Efficient Double Inorganic Halide Perovskite Materials by DFT
Authors: Diao Xinfeng , Diao Yongxin , Tang Yanlin , Zhao Gangling , Gu Qinzhong , Xie Yu , Shi Yebai , Zhang Liang , Zhu Ping 
Published: April 2022

Abstract
In this paper, the photoelectric conversion properties and stability of 42 inorganic double perovskite materials were studied based on density functional theory (DFT). Starting from the construction of double perovskite crystal structures, the data mining algorithm in informatics was introduced into the analysis of high-throughput computing data. The results show that the tolerance factors of 39 crystals are between 0.8 and 1.10, indicating that these crystals have a stable perovskite structure. Then, the important parameters such as dielectric function, PDOS, elastic modulus, shear modulus and Poisson's ratio of the crystal were analyzed. Considering the band gap structure and absorption spectrum, it is found that the light absorption curves of Cs2SeI6，Cs2SeBr6 Rb2SeI6，Rb2SeBr6，and Rb2SeCl6 fall in a relatively large range in the visible light region.Further considering the stability factor Cs2SeI6, Rb2SeI6, Cs2SeBr6 and Rb2SeBr6 can be considered as ideal candidates for light absorbing materials, providing a basis for the industrial application of solar cells.PACS: 78.56.-a 81.05.Fb 42.50.Nn
Synthesis of Flavonoids using ZnCr2O4 nanoparticle catalyst
Authors: Amiri Behnam , Nazarpour Roya , Mohave Fouad , Ghaemi Arezoo , Tavakkoli Haman 
Published: April 2022

Abstract
ZnCr2O4 nanoparticles with a high specific surface area has been fabricated using a hydrothermal synthetic process and was used as an effective catalyst to synthesize flavonoid derivatives. The textural and structural properties of the spinel were studied by X-ray diffraction (XRD), Field Emission scanning electron microscope (FE-SEM), nitrogen sorption techniques, and Fourier transform infrared spectroscopy (FT-IR). XRD confirmed the formation of cubic Zinc Chromite spinel with an average crystallite size of 5.04 nm. While textural analysis by N2 sorption revealed a disordered mesoporous system with a high specific surface of 215 m2/g for ZnCr2O4. Moreover, all desired flavonoids obtained in high yields under solvent-free conditions with the aid of the ZnCr2O4 catalyst. Structures of all flavonoid derivatives were confirmed by 1H-NMR, 13C-NMR, FT-IR and their melting points.