bluuebunny/crossref_metadata_2025_split huggingface dataset:
Definer: A computational method for accurate identification of RNA pseudouridine sites based on deep learning
Authors: Feng Xin , Wang Ping , Ma Zhansen , Wu Jiezhang , Xin Ruihao 
Published: July 2023

Abstract
Background
RNA molecules are important biomolecules in cells and play a crucial role in processes such as genetic information transfer and gene expression regulation. However, in addition to their basic nucleotide composition, RNA molecules undergo various modifications, including pseudouridine. Pseudouridine is a critical site of alteration that is found in many non-coding RNAs and has a role in a number of biological processes, including gene expression, RNA structural stability, and the development of several illnesses. Accurate identification of pseudouridine sites in RNA molecules is of significant importance for understanding their functionality and regulatory mechanisms. Traditional experimental methods often rely on techniques such as chemical modifications and mass spectrometry analysis. However, these methods are costly, time-consuming, and limited in terms of sample size. Therefore, the development of an efficient and accurate computational method for identifying pseudouridine sites in RNA holds great scientific significance and practical application value.
Results
In this study, we propose a deep learning-based computational method, Definer, to accurately identify RNA pseudouridine loci in three species, H. sapiens, S. cerevisiae and M. musculus. The method incorporates two sequence coding schemes, including NCP and One-hot, and then feeds the extracted RNA sequence features into a deep learning model constructed from CNN, GRU and Attention. The benchmark dataset contained data from three species, namely H. sapiens, S. cerevisiae and M. musculus, and the results using 10-fold cross-validation showed that the model accuracy reached 82.95, 86.01 and 87.15 for the three species, respectively, with Definer significantly outperforming other existing methods. Meanwhile, the data sets of two species, H. sapiens and S. cerevisiae, were tested independently to further demonstrate the predictive ability of the model.
Conclusion
It is well known that RNA modifications are an important component of gene regulation and most biological processes depend on RNA modifications. Among them, pseudouridine modification is one of the crucial modification sites, and the accurate identification of pseudouridine sites in RNA is important for understanding their functions and regulatory mechanisms. Therefore, this paper proposes a new predictor, Definer, which can accurately identify pseudouridine sites in three species: H. sapiens, S. cerevisiae, and M. musculus. results on benchmark and independent test sets show that Definer has good performance over other existing methods and can accurately identify pseudouridine sites in cross-species data sets. set can accurately identify pseudouridine loci. In addition, we have developed software that runs on a local computer to provide users with a better presentation of the pseudouridine site prediction process and results for the three species datasets.
An enteroendocrine-microbial axis in the large intestine controls host metabolism
Authors: Burstein Ezra , Tan Shuai , Santolaya Jacobo , Wright Tiffany , Liu Qi , Fujikawa Teppei , Chi Sensen , Bergstrom Colin , Lopez Adam , Chen Qing , Vale Goncalo , McDonald Jeffrey , Jia Da , Elmquist Joel , Sifuentes-Dominguez Luis 
Published: July 2023

Abstract

Nutrient handling is an essential function of the gastrointestinal tract. Most nutrient absorption occurs in the small intestine and is coordinated by hormone-producing intestinal epithelial cells known as enteroendocrine cells (EECs). In contrast, the colon mostly reclaims water and electrolytes, and handles the influx of microbially-derived metabolites, including short chain fatty acids (SCFA). Hormonal responses of small intestinal EECs have been extensively studied but much less in known about the role of colonic EECs in metabolic regulation. To address this core question, we investigated a mouse model deficient in colonic EECs. We found that colonic EEC deficiency leads to hyperphagia and obesity. Surprisingly, colonic EEC deficiency results in altered microbiota composition and metabolism, which we found through antibiotic treatment and transfer to germ free recipients, to be both necessary and sufficient for the development of obesity. Moreover, studying stool and blood metabolomes, we found that differential glutamate production by intestinal microbiota corresponds to increase appetite due to EEC loss. Finally, we show that colonic glutamate administration can directly increase food intake and activate appetite centers in the central nervous system. These observations shed light on an unanticipated host-microbiota axis in the colon, part of a larger gut-brain axis, that regulates host metabolism and body weight.
Establishment of a prediction model for haemorrhage after semi-tubeless PCNL
Authors: Liu Jingbang , Zhang Yi , Liu Qing , Shi yaxing 
Published: July 2023

Abstract
Objectives: To establish a prediction model to predict the risk of severe hemorrhage after semi-tubeless percutaneous nephroscopy(PCNL).
Methods: The data of 464 patients (464 semi-tubeless PCNL procedures) were retrospectively analyzed at Shenyang Red Cross Hospital from January 1st,2016 to January 1st,2023.The following factors were analyzed: blood pressure,stone score,expansion method,visualization,
Guys grades,avasculararea,diabetes,age,history of PCNL,duration,solid kidney,preoperative nephrostomy ,number of channel,channel size,BMI and gender.We established a prediction model by using the data above and we collect 50 additional patients as the test group to verify the accuracy of the model.
Results: For all the 464 patients, 91 patients had postoperative haemorrhage and 373 had no haemorrhage.The average hemoglobin drop for all the procedures was 23 .5±6.1g/L (range 20.1–38.1g/L), whereas the average hematocritdrop was 5.46±4.08% (range 0.4%–29%).We collect 16 variables.Univariate regression analysis was performed in SPSS and independent factors(P<0.2)affecting haemorrhage were selected.Gender(P=0.301),dilation method(P=0.455) and age(P=0.214) are excluded.We performed a logistic regression in the R studio.The nomogram was constructed to present the prediction model and the decision curve analysis(DCA) was conducted to evaluate the model efficiency.
Conclusion: For patients after semi-tubeless PCNL, High blood pressure,high stone score,non-visualization,high Guys grade,non-avascular area,diabet,advanced age,history of PCNL,long operation time ,solid kidney,non-preoperative nephrostomy,multiple channels,large channel size and high BMI are alarming variables for haemorrhage after semi-tubeless PCNL.Preoperative assessment of haemorrhage risk is necessary.
How do Gendered Laws Affect Women’s Decisions among Education, Family and Career? The Case of Taiwan
Authors: Tang Meng-Chi , Wang Zi-Xuan 
Published: July 2023

Abstract
This paper studies how women’s life decisions were affected by the passage of the Act of Gender Equality in Employment, legislation concerning workplace gender equality in Taiwan. Using a difference-in-differences estimation, we first showed that the act increased women’s education relative to men. We then separated women by their college education into the treatment and control groups in a bivariate probit model, considering their education decisions to be related with women’s other life decisions. Empirical results show that the effects of the act are conditional on college degree. The act increased the likelihood of women with a college degree to marry earlier, have children and start a job earlier. But the act increased the labor force participation of the women without a college degree more than the women with one. Our interpretation of the results is that the act enhanced the family prospects of the college-educated women and promoted the career prospects for the women without college degrees.
JEL classification: J16, K38
Biomimetic Artificial Bone Marrow Niches for the Scale Up of Hematopoietic Stem Cells
Authors: Gautrot Julien , Bosch-Fortea Minerva , Marciano Daniele 
Published: July 2023

Abstract
Hematopoietic stem cell (HSC) transplantation to treat haematological disorders is greatly restricted by poor cell availability. Ex vivo expansion of HSCs as a strategy to overcome this limitation has shown limited success so far, due to the loss of stem cell properties in culture. Therefore, engineering of culture platforms that mimic the physiological properties of the bone marrow (BM) in a scalable format is an important target to enable the translation of HSC therapies. Here, we report the design of biomimetic BM niches that enable the culture of HSCs in a scalable 3D platform. Beyond cellular and biochemical components (e.g., matrix and growth factors), an important element of the BM microenvironment is its architecture, dense in adipocytes, with relatively limited matrix and anisotropic mechanical properties. To capture this context, we propose the use of bioemulsions1,2 in which oil microdroplets and associated mechanical anisotropy recreate important architectural features of the hematopoietic niche. Mesenchymal stem cells (MSCs) grown at the surface of such bioemulsion remodelled this environment, assembling an interstitial matrix mimicking that of the BM microenvironment composition. In addition, MSCs secreted important factors underpinning the crosstalk between stromal cells and HSCs in the native environment. HSCs cultured in the resulting artificial BM niches maintained stemness whilst expanding significantly (> 33-fold compared to HSCs cultured in suspension) and enabling scale up of expansion in conical flask bioreactors, to produce 2M cells in a single batch. This platform therefore harnesses engineered BM microenvironments and the processability of bioemulsions and microdroplet technologies to produce HSCs in a scalable format, for application in cell-based therapies.
Laparoscopic multivisceral resection for advanced colorectal cancer: multicenter analysis of short-term and long-term outcomes
Authors: NAMBARA SHO , Nakanishi Ryota , Nonaka Kentaro , Fujimoto Yoshiaki , Hu Qinjiang , Nakanoko Tomonori , Sugiyama Masahiko , Ota Mitsuhiko , Kimura Yasue , Oki Eiji , Toh Yasushi , Yoshizumi Tomoharu 
Published: July 2023

Abstract
Background
In response to the rising use of laparoscopic surgery, recent studies have shown that laparoscopic multivisceral resection (MVR) for advanced colorectal cancer is safe, feasible, and provides acceptable oncological outcomes. However, the usefulness of laparoscopic MVR remains controversial. Here, we aimed to compare short-term and long-term outcomes between the laparoscopic and open MVR approaches for patients with advanced colorectal cancer.
Methods
We retrospectively collected data on 3571 consecutive patients admitted to the Kyushu University National Kyushu Cancer Center for surgical treatment of colorectal cancer between 2004 and 2020. We ultimately analyzed 84 patients who underwent a colectomy with MVR for advanced colorectal cancer. We assessed invasiveness in terms of operating time, blood loss, and complications. Oncological outcomes included 5-year overall survival and recurrence-free survival rates.
Results
Among the 84 patients analyzed, 29 were treated with a laparoscopic approach, and 55 were treated with an open approach. Compared to the open surgery group, the laparoscopic surgery group had significantly less blood loss (median volume: 167 vs 1058 g, P < 0.005) and shorter hospital stays (15 vs 18 days, P < 0.05). After patients with stage Ⅳ colorectal cancer were excluded from the analysis (laparoscopic surgery group, n = 25; open surgery group, n = 38), the groups showed similar pathologic outcomes and no significant differences in 5-year overall survival (P = 0.87) or recurrence-free survival (P = 0.86).
Conclusion
A laparoscopic MVR approach for advanced colorectal cancer could be less invasive than an open MVR approach without affecting oncological outcomes in selected patients.
Arylhydrazine salt-selenium: a novel and efficient reagent system for arylselenenylation of unprotected uracil and its derivatives
Authors: Wang Cong , Wu Yi , Peng Qi-Yun , He Yan-Ling , Zheng Xiao-He , Chen Yan-Qin , Wang Hai-Bo , Wang Bing , Xie Jun , Tang Lei 
Published: July 2023

Abstract
A convenient and efficient reagent system of arylhydrazine salt-selenium was developed to directly synthesize 5-selenium uracil from uracil, arylhydrazine salt and selenium powder. This procedure provides diverse 5-arylselanyluracils with good yields and functional group tolerance and selectively constructs different types of selenopyrimidine. The advantages of this protocol involve the use of commercial available, stable, cheap and easy to handle selenating reagents, not require catalysts and ligands, good regional selectivity, the tolerance of a variety of functional groups and the practicality.
Computational Comparison of CNN Based Methods for Violence Detection
Authors: Singh Shubhangi , Tyagi Bhawana 
Published: July 2023

Abstract
In this paper, we approach with four different CNN-based models i.e., VGG-19, VGG-16, InceptionV3 and MobileNetV3 with an improved version of the previous models for violence detection and recognition from videos. The proposed models use the pre-trained models as the base model for feature extraction and for classification after freezing the rest of the layer, the head model is prepared with averagepooling2D of (5, 5), and after flattening only one dense layer having 512 nodes with ‘ReLU’ activation function, dropout layer of 0.5 and last output layer with only 2 classes and ‘softmax’ activation function. This head model of fully connected layers was used in the proposed models. These models are trained and evaluated on the Hockey fight dataset and Real life violence situations detection datasets. The experimental results are far better in terms of accuracy and other performance metrics and the models have reduced parameters and less computational time than previous models.
Oxophilic Ce single atoms-triggered active sites reverse for superior alkaline hydrogen evolution
Authors: Zhou Kebin , Shen Fengyi , Zhang Zhihao , Wang Zhe , Ren Hao , Liang Xinhu , Cai Zengjian , Yang Shitu , Sun Guodong , cao yanan , Yang Xiaoxin , Hu Mingzhen , Hao Zhengping 
Published: July 2023

Abstract
The state-of-the-art alkaline HER catalyst of united Ru single atoms and small Ru nanoparticles (Ru1-Run) has sparked considerable research interest. However, it remains a serious problem that hydrogen evolution primarily occurs on the less active Ru single atoms instead of the more efficient small Ru nanoparticles in Ru1-Run, hence largely falling short of its full activity potential and unnecessarily increasing Ru usage amount. Here, we report that combining oxophilic Ce single atoms and fully-exposed Ru nanoclusters on a N functionalized carbon (Ce1-Run/NC) can facilely reverse alkaline hydrogen evolution centers to the more active fully-exposed Ru nanoclusters driven by the strong oxophilicity of Ce and thus greatly improves HER activity as well as Ru atom efficiency. Remarkably, the Ce1-Run/NC outperformed all the other Ru-based alkaline HER catalysts to date by its excellent mass activity. This finding is expected to shed new light on developing more efficient and cost-saving alkaline HER catalyst.
Projectile Energy and Entrance Channel Mass-Asymmetry Effects on Incomplete Fusion of 12C + 169Tm, 16O + 169Tm and 16O + 75As Systems at Energy Beam
Authors: Kebede Getahun 
Published: July 2023

Abstract
This study focus on the correlation between entrance channel properties and incomplete fusion reaction. The dynamics of heavy-ion fusion reactions involved in the interaction of 12C and 16O with 169Tm and 75As targets were examined at 3-8 MeV /nucleon specific energies. The influence of projectile energy and entrance channel mass-asymmetry on the incomplete fusion process in the interaction of 12C + 169Tm, 16O + 169Tm and 16O + 75As systems at energies ranging from 4-7.5 MeV /Nucleon was examined in this study. The PACE4 statistical model was used to compare and analyze the measured cross sections from the EXFOR data base. The values of level density parameter, which is a sensitive input parameter, were optimized using a representative non-a-emitting channel from the respective systems. The experimentally measured excitation functions for representative non α-emitting channels were found to be in good agreement with the theoretical predictions in general. However, for α-emitting channels in the current systems, the measured excitation functions were greater than the theoretical model code predictions, which could be attributed to incomplete fusion reaction at these energies. The observed enhancements in α-emitting channels were attributable to the contribution coming from incomplete fusion reactions. The incomplete fusion fraction, which explains the relative relevance of incomplete fusion processes, was attempted to be approximated. The incomplete fusion fraction was shown to be sensitive to the projectile energy and mass-asymmetry of the entrance channel. Further, the results showed that incomplete fusion reactions were higher for more mass-asymmetric systems than mass-symmetric one.
Cutaneous chronic expanding hematoma on the elbow mimicking a malignant tumor: report of a case and review of the literature
Authors: Hase Takahiro , Imafuku Keisuke 
Published: July 2023

Abstract
Chronic extended hematoma (CEH) is a rare condition characterized by slow mass growth over the course of a month after trauma or surgery. Clinically, it is important to distinguish CEH from malignancy, and characteristic findings on CT and MRI images have been reported. In this study, we explored the association of CEH with anemia, anticoagulant administration, and history of trauma/surgery on PubMed and conclude that a history of trauma or surgery can provide a diagnostic clue.
Enhanced Recovery After Surgery Facilitates Next Day Discharge for Laparoscopic Roux-en-Y Gastric Bypass: Experience from a Provincial Referral Program
Authors: Hardy Krista , Leung Caleb , Seto Jonathan , Tewes Simon , He Wenjing , Vergis Ashley 
Published: July 2023

Abstract
Introduction:
Laparoscopic Roux-en-Y gastric bypass (LRYGB) is a common bariatric procedure, but patients often experience extended inpatient stays. Enhanced recovery after surgery (ERAS) protocols aim to expedite recovery and discharge. In the province of Manitoba, Canada, the Centre for Metabolic and Bariatric Surgery (CMBS) is dedicated to providing bariatric care to the population. To enable earlier discharge, an overnight short-stay unit with ERAS protocols was introduced, along with transfer protocols for patients requiring prolonged care.
Methods
We retrospectively reviewed prospectively collected data on LRYGBs performed from November 2017 to December 2020. Surgical indications included BMI ≥ 35 with comorbidities or BMI 40–55 without comorbidities, approved by a multidisciplinary bariatric team. Postoperative evaluations were conducted 16–21 hours post-surgery. Patients were educated about potential complications and required to reside within one hour of a tertiary center for seven days. This study reports descriptive outcomes: length of stay (LOS), 30-day emergency room (ER) presentations, 7-day readmissions, and 30-day readmissions.
Results
Among the 439 LRYGB patients, the postoperative day 1 discharge rate was 94.8%, and day 2 discharge rate was 1.8%. A small proportion (2.7%, n = 12) required transfer due to anticipated prolonged LOS, primarily for delayed intraabdominal hemorrhage (66.7%) requiring reoperation and precautionary measures for technically challenging procedures (16.7%). Two brief ICU admissions occurred, with no mortalities. ER presentation rate within 30 days was 10.3% (n = 45), 7-day readmission rate was 2.7% (n = 12), and 30-day readmission rate was 4.1% (n = 18). Gastrointestinal intolerance was the most common reason for readmission.
Conclusion
Implementing an ERAS protocol for LRYGB enabled safe next-day discharge for 94.8% of patients. ER presentation and readmission rates aligned with existing literature, supporting the feasibility of next-day discharge for appropriately selected bariatric patients. These findings contribute to the evidence base for optimizing postoperative care and enhancing patient outcomes in bariatric surgery.
Therapeutic possibilities for secondary epithelial-endothelial corneal dystrophy using a portable device for local collagen crosslinking
Authors: Yani E. V. , Seliverstova K. E. 
Published: July 2023

Purpose: to evaluate the effectiveness of corneal collagen crosslinking (CCC) with a portable Keratolink device in patients with bullous keratopathy after cataract surgery.Materials and methods. 19 patients (19 eyes) aged 60 to 87 with secondary epithelial-endothelial corneal dystrophy, developed due to cataract surgery received three CCC procedures which lasted 20 minutes each, with intervals of 2 days between the procedures.Results. The mean corneal pain score according to verbal pain scale decreased to 4.5 from the initial 9 points and did not change significantly at subsequent visits. Optical coherence tomography data show that before the first procedure, the average corneal transparency score was 2.8 while by the 20th day of observation it fell to 1.4 points. After 3 CCC procedures, bullae continued to form in 3 patients only (3 eyes, 16 %) over the entire 3-month-long observation period. The best corrected visual acuity 3 months after CСC in patients was about 0.07 ± 0.02, which is slightly higher than the initial value (0.05 ± 0.03).Conclusion. A short course of ultraviolet CCC with a portable Keratolink device may be recommended as a palliative treatment for elderly patients with bullous keratopathy developed after cataract surgery.
Spatiotemporal succession of phosphorous accumulating biofilms during the first year of establishment
Authors: Villard Didrik , Nesbø Goa Inger Andrea , Leena Angell Inga , Eikaas Sondre , Saltnes Torgeir , Johansen Wenche , Rudi Knut 
Published: July 2023

Abstract

Many wastewater treatment plants are dependent on the utilization of microorganisms in biofilms. Our knowledge about the establishment of these biofilms is limited, particular with respect to biofilms involved in enhanced biological phosphorus removal (EBPR). These biofilms rely on polyphosphate-accumulating organisms (PAOs), requiring alternating oxic and anaerobic conditions for phosphorous uptake. This challenge has been solved using the Hias process, which combines moving-bed biofilm-reactor (MBBR) technology with physical transfer of biofilm-carriers from oxic to anaerobic zones. We combined biofilm fractionation with temporal analyses to unveil the establishment in the Hias process. A stable phosphorous removal efficiency of &gt;95% was reached within 16 weeks of operation. Phosphorus removal, however, was not correlated with the establishment of known PAOs. The biofilms seemed associated with an outer microbiota layer with rapid turnover and an inner layer with a slow expansion. The inner layer showed an overrepresentation of known PAOs. In conclusion, our spatiotemporal analyses of phosphorous accumulating biofilm establishment lead to a new model for biofilm growth, while the mechanisms for phosphorous removal remain largely unresolved.