bluuebunny/crossref_metadata_2025_split huggingface dataset:
VariPred: Enhancing Pathogenicity Prediction of Missense Variants Using Protein Language Models
Authors: Lin Weining , Wells Jude , Wang Zeyuan , Orengo Christine , Martin Andrew C.R. 
Published: July 2023

Abstract
Computational approaches for predicting the pathogenicity of genetic variants have advanced in recent years. These methods enable researchers to determine the possible clinical impact of rare and novel variants. Historically these prediction methods used hand-crafted features based on structural, evolutionary, or physiochemical properties of the variant. In this study we propose a novel framework that leverages the power of pre-trained protein language models to predict variant pathogenicity. We show that our approach VariPred (Variant impact Predictor) outperforms current state-of-the-art methods by using an end-to-end model that only requires the protein sequence as input. By exploiting one of the best-performing protein language models (ESM-1b), we established a robust classifier, VariPred, requiring no pre-calculation of structural features or multiple sequence alignments. We compared the performance of VariPred with other representative models including 3Cnet, Polyphen-2, FATHMM and ‘ESM variant’. VariPred outperformed all these methods on the ClinVar dataset achieving an MCC of 0.727 vs. an MCC of 0.687 for the next closest predictor.
Investigation of The Possible Effects of Curative Radiochemotherapy on Muscle Oxygen Saturation Dynamics With Moxy Oxygen Monitor in Individuals With Local Advanced Lung Cancer Diagnosis
Authors: Sahin Yılmaz , Zortul Abdulsamet , Ozturk Deniz 
Published: July 2023

Abstract
Objective
This study was conducted to investigate the possible effects of curative radiochemotherapy on muscle oxygen saturation dynamics with moxy oxygen monitor in individuals with locally advanced lung cancer.
Materials and Methods
The study was conducted prospectively at Atatürk University Sports Sciences Application and Research Center. From the cases with locally advanced lung cancer in the Radiation Oncology Clinic of Erzurum Regional Training and Research Hospital, It was conducted with male patients aged 30–70 years diagnosed with locally advanced lung cancer. Before and after curative radiochemotherapy, patients were walked on a treadmill for 10 minutes by the low-intensity acute aerobic walking exercise protocol and with a Moxy monitor device, muscle oxygen saturation and total hemoglobin levels were monitored in the rectus femoris muscle with near-infrared spectroscopy both during and after the test. The analysis of the data obtained from the research was made in the SPSS 26.0 (SPSS, Inc., Chicago, IL, USA) program.
Results
According to the findings of the study, Sig. Although there was no significant difference since the (2-tailed) values were higher than 0.05, it was determined that the participants' right and left leg total hemoglobin values increased after curative radiochemotherapy application.
Conclusion
Curative radiochemotherapy showed a curative effect on muscle oxygen saturation and total hemoglobin.
Multi-Spatial Scale Spatio-Temporal Transformer: A Refined Traffic Data Forecasting Method
Authors: 张 悦 , Zhang Lei , Liu Bailong , Liang Zhizhen , Zhang Xuefei 
Published: July 2023

Abstract
Accurate traffic data forecasting is essential to improve the efficiency of intelligent transportation systems. Existing traffic prediction models only model spatial dependency based on the connectivity of roads, which overlooks the characteristic information of hidden spatial dependency and leads to a loss of prediction accuracy. In addition, there exists a strict relative positional relationship in the temporal dependency between traffic data, which is often overlooked by existing models, making it difficult to accurately model the temporal dependency. To solve these problems, this paper proposes a traffic data prediction method (MSS-STT) based on Multi-Spatial Scale Spatio-Temporal Transformer. MSS-STT first employs multiple specialized spatial Transformer networks to model different spatial scales in order to capture spatial dependencies and patterns at various levels. It also utilizes graph convolutional neural networks to extract static spatial structural features. Then, a gating mechanism is used to fuse the spatial dependencies from different spatial scales and the static spatial features. Finally, MSS-STT extracts different temporal dependencies by considering the order of time points and the varying contributions to the prediction from different relative positions between time points in historical traffic data. Experiments on three real-world datasets from the Caltrans Performance Measurement System (PeMS) show that the proposed MSS-STT model outperforms the state-of-the-art methods.
VAT Credit Refund, Financial Flexibility and Enterprise Innovation Incentives
Authors: Chen Jiangyan , Ye Aizhong , Guo Minrong , Guo Ju 
Published: July 2023

Abstract
Technological innovation is the primary driving force. This paper uses a difference-in-differences model, based on data from non-financial A-share listed companies, to demonstrate the impact of the 2018 value-added tax (VAT) refund policy on corporate innovation. The evaluation results found that: (1) Compared with the control group, the VAT refund policy significantly increased the innovation investment of the experimental group companies. (2) The VAT refund policy mainly encourages corporate innovation by affecting corporate financial flexibility. (3) From the perspective of corporate characteristics, the innovative incentive effect of the VAT refund policy is more pronounced for non-state-owned enterprises, smaller enterprises, growth-stage enterprises, and enterprises with a low inventory turnover rate. In addition to encouraging corporate innovation, the VAT refund policy also significantly improves corporate innovation efficiency. Based on the research conclusions, this paper proposes further expanding the scope of the VAT refund policy, differentiating tax subjects, and other related suggestions.
Factors associated with renal oxygen extraction in mechanically ventilated children after the Norwood operation: insights from high fidelity hemodynamic data
Authors: loomba rohit , Villarreal Enrique , Farias Juan S. , Flores Saul , Wong Joshua 
Published: July 2023

Abstract
Background
As the human body and its constituent organs require oxygen to function, maintaining the adequacy of systemic oxygen delivery is of utmost importance, particularly in critically ill children. Renal oxygen extraction can be utilized as a metric of the balance between systemic oxygen delivery and oxygen consumption. The primary aim of this study was to determine what clinical factors are associated with renal oxygen extraction in children with parallel circulation after the Norwood operation.
Methods
Mechanically ventilated children who underwent a Norwood operation from September 1, 2022 to March 1, 2023 were identified as these patients had data collected and stored with high fidelity by the T3 software. Data regarding hemodynamic values, fluid balance, and airway pressure were collected. These data were analyzed using Bayesian regression to determine the association of the individual metrics with renal oxygen extraction.
Results
A total of 27,270 datapoints were included in the final analyses. The resulting top two models explained had nearly 80% probability of being true and explained over 90% of the variance in renal oxygen extraction.
Conclusion
Increased milrinone, epinephrine, mean arterial pressure, and systemic blood flow were associated with decreased (improved) renal oxygen extraction while increased mean airway pressure, central venous pressure, arterial saturation by pulse oximetry, and systemic vascular resistance were associated with increased (worsened) renal oxygen extraction.
A Method of Overtourism Optimisation for national parks (Case: Stołowe Mts. National Park, Poland)
Authors: Rogowski Mateusz 
Published: July 2023

Abstract
The increasing popularity of national parks in recent years results from the reopened of tourism after the Covid-19 pandemic and the increasing for outdoor activities in such areas. In many national parks face overtourism which has a negative impact on nature, residents, the economy of the region and visitors. The aim is provide the new Method of Overtourism Optimisation in national park. The Method consist of nine tasks that have include the diagnose of overtourism in spatio-temporal terms by visitors and residents, the analysis of hourly visitors data and develop the Tourism Carrying Capacity of trails. The results of the survey carried out among the visitors and residents diagnosed overtourism in spatio-temporal terms, discussed with the National Park managers and the Scientific Council. The Method delivers the diagnosis and management of overtourism by determination of entry limits preceded by participation in the co-decision in residents, visitors and national park managers.
Isolation, Purification and Characterization of Xylanase produced by Bacillus sp. NIORKP76 strain under solid state fermentation and its application in saccharification of various agro-residues into fermentable sugars
Authors: Parab Pankaj D. , Khandeparker Rakhee D. , Amberkar Ujwala 
Published: July 2023

Abstract

Microbial xylanases are xylan hydrolyzing enzymes which has congregated attention due to their immense potential in many industries. Increasing demand for these enzymes versus inadequate supply makes these biomolecules a value-added product. The current study is focused on xylanase from bacterial isolate identified as Bacillus sp. NIORKP76. The bacterial isolate used in this study showed ability to produce xylanase on an inexpensive agro-industrial waste (wheat bran) under solid-state fermentation. The isolate showed maximum xylanase production in growth media supplemented with phosphate, NaCl and NH4Cl concentration of 64 mM, 15 mg/mL and 0.3 mg/mL respectively. The maximum xylanase titer volume was obtained with 1:3 substrate to moisture ratio (w/v). Using optimized conditions maximum xylanase production in wheat bran was achieved in 72 h at room temperature 28 ±2°C. Xylanase exhibited pH optima of 8.0 and retained 92% of its residual activity after 24h incubation period at pH 8.0, thus proving its high stability at alkaline pH. Xylanase displayed optimum activity at 60°C. Xylanase stability at 30°C and 40 °C remained unhindered even after 12h of incubation period. The xylanase isolated in this study was purified up to homogeneity and its molecular weight was found to be ~28kDa. Xylanase produced by Bacillus sp. NIORKP76 strain was found to have essential qualities required for saccharification of various agro-residues to generate fermentable sugars which can be a raw-material for biofuel production. Wheat bran with heat pre-treatment was found to be par excellence agro-waste as compared to other heat pre-treated and untreated lignocellulosic agro-wastes in production of fermentable reducing sugars. 141mg/g fermentable sugars were whipped up when reaction mixture of pre-treated wheat bran with 5U/g partially purified xylanase incubated at 40°C for 8h, which was found to be best results among all agro-residues studied.
A Confirmed Case of Xylazine-Induced Skin Ulcers in a Person Who Injects Drugs in Miami, Florida, USA
Authors: Warp Peyton V. , Hauschild Maia , Tookes Hansel E. , Ciraldo Katrina , Serota David P. , Cruz Irasema 
Published: July 2023

Abstract
Background Xylazine is an alpha-2 adrenergic receptor agonist that has emerged as a contaminant in the street drug supply of fentanyl. Xylazine use may be suspected in naloxone-resistant overdoses and atypical, chronic wounds in people who inject drugs (PWID). This case is unique because it is the first case to our knowledge describing wound care for a xylazine-induced wound with a confirmatory xylazine test strip (XTS) in the setting of a syringe services program (SSP) and in the state of Florida.Case Presentation A 43-year-old woman with a past medical history of severe opioid use disorder and stimulant use disorder presented to a student-run clinic at the IDEA Miami SSP for wound care. She had multiple ulcerations diffusely over her bilateral forearms with surrounding erythema and warmth. Seven weeks later, she presented to clinic again for wound care because her wounds had progressed. At this visit, a XTS was used to confirm the presence of xylazine in her urine. Wound care management and harm reduction strategies employed at both visits are discussed below. Wound outcomes are unknown as the patient has not returned to clinic.Conclusions Many PWID at highest risk for acute and chronic health consequences of xylazine-adulterated fentanyl do not have access to healthcare outside of low barrier clinics and SSPs due to lack of insurance or mistrust of the traditional healthcare system. There is an urgent need for access to XTS for PWID and clinical practice guidelines for the treatment of xylazine-related wounds in outpatient clinics.
Deterioration Mechanism and Statistical Damage Constitutive Model of Red-Bed Soft Rock with Different Moisture Contents
Authors: Wu Yizhe , Wang Huanling , Zhang Yanjie , Lyu Changhao , Liu Yuxuan , Wang Wenxiu 
Published: July 2023

Abstract

The mechanical properties of red-bed soft rock, widely encountered in the Central Yunnan Water Diversion Project, deteriorate significantly upon contact with water, impacting the safety of the project. The objective of this paper is to investigate the effects of moisture content on the mechanical properties of red-bed soft rock by conducting triaxial compression tests under varying confining pressure. Degradation mechanisms associated with distinct moisture content levels are determined. Deformation and deterioration mechanisms are investigated from the mineral compositions using X-ray diffraction. Modification of the Drucker-Prager criterion is studied to incorporate the Lode parameter. Utilizing the Weibull distribution, this study establishes a statistical damage constitutive model for red-bed soft rock. The triaxial compression test results of red-bed soft rock are used for the purpose of model validation. It is demonstrated that there is a strong concurrence between the theoretical model and empirical findings, indicating its suitability for analyzing the mechanical behavior of red-bed soft rock under varying moisture content. Findings in this paper can provide valuable insights into the investigation of large deformation occurring in surrounding red-bed soft rocks within the context of Central Yunnan Water Diversion Project.
A novel nomogram to identify the III-N2 non-small cell lung cancer patients who may benefit from adjuvant radiotherapy
Authors: Yi Xinglin , Deng Caixia , He Yi , Zhou Xiangdong , Luo Hu 
Published: July 2023

Abstract
Purpose
We aimed to develop a novel risk stratification system based on a prognostic nomogram to identify patients with pIII-N2 non-small cell lung cancer (NSCLC) who may benefit from postoperative radiotherapy (PORT) after complete resection.
Methods
We retrospectively enrolled 3,520 eligible NSCLC patients with pIII-N2 stage disease from the Surveillance, Epidemiology, and End Results database. Stabilized inverse probability of treatment weighting (sIPTW) was used to equilibrate the characteristic baseline to reduce bias. We established a risk stratification tool using a nomogram that incorporated independent factors identified using least absolute shrinkage and selection operator (LASSO) Cox regression. Kaplan–Meier and subgroup survival analyses were conducted to estimate the benefit of PORT in every risk stratification.
Results
Kaplan–Meier survival analysis observed that high-risk patients owned a significant improvement in overall survival (OS) after PORT (p = 0.002), while those in low- or intermediate-risk cohorts did not show such improvement. Subgroup survival analysis suggested that patients with a high lymph node ratio ≥ 0.56 (hazard ratio [HR] = 0.803; 95% confidence interval [CI]:0.661–0.975, p = 0.027), without postoperative chemotherapy (HR = 0.782; 95% CI: 0.619–0.989; p = 0.040), and those in the high-risk group (HR = 0.577; 95% CI: 0.410–0.812; p = 0.001) achieved a significant OS advantage from PORT.
Conclusion
This novel risk stratification system based on nomogram provides a preliminary identification of potential pIII-N2 NSCLC patients who are more likely to benefit from PORT.
Positive family history and girl sex might increase the risk of failure of abduction treatment in developmental dysplasia of the hip
Authors: Lankinen Vilma , Helminen Mika , Bakti Karim , Välipakka Jarmo , Laivuori Hannele , Hyvärinen Anna 
Published: July 2023

Abstract
Background. Mild Barlow positive but Ortolani negative developmental dysplasia of the hip (DDH) has a great spontaneous recovery potential. Despite that, in many cases abduction treatment is needed. Known risk factors of DDH include girl sex, family history and breech presentation. Risks of failure of the abduction treatment are not well established.
Material and methods. The Children with DDH diagnosis treated in Tampere University hospital in the years 1998-2018 were retrospectively found. Only the children with early evaluation (under 2 weeks of age) of pediatric surgeon or pediatric surgery resident were included in the analysis. Total of 759 children were included.
Results. Girl sex (p=0.008) and family history (p=0.003) were associated with the most sever forms of DDH in dynamic ultrasound at one month of age. Major hip instability in dynamic ultrasound (p=0.016), and not the alpha angles (p=0.426), was associated with the risk of operative and/or casting treatments. Watchful waiting strategy in mild DDH was safe regarding the major hip instability (p= 0.260) and duration of abduction treatment, as treatment duration was shorter in these children (p<0.001).
Conclusion. Family history and girl sex increase a risk of more severe form of DDH which increases the risk of failure of the abduction treatment. The observation period of four to six weeks seems safe in clinically diagnosed mild DDH regarding the risk of operative treatment and treatment duration.
Level of evidence: Level II Retrospective study
Graphene-based quad-port MIMO reconfigurable antennas for SATCOM and 5G applications
Authors: Kiani Narges , Hamedani Farzad Tavakkol , Rezaei Pejman 
Published: July 2023

Abstract
In this research, two graphene-based THz patch antenna structures for satellite communication and 5G applications is reported. In the unit cell analysis, it can be pointed out that the patch is made of graphene and the substrate is made of silicon dioxide. While its dielectric permittivity is 3.7. The operating frequency of the MIMO antenna is designed at 0.6 THz. In the plan of MIMO reconfigurable antenna, cells are arranged vertically. Reconfigurable conditions can be achieved by changing the chemical potential or in other words the bias voltage of graphene patches. The amount of chemical potential in the original project of both quad-port MIMO reconfigurable antennas is considered to be 0.6 eV. In the results of the first antenna, S11 is less than -10 dB in the range of 0.58786 THz through 0.63112 THz. In the results of the second antenna, S11 is less than -10 dB in the range of 0.57814 THz through 0.63391 THz. In the results of the first antenna, maximum efficiency is reported about 65%. In the results of the second antenna, maximum efficiency is reported about 72%. Finally, peak realized gains, radiation efficiencies, far-field 2D radiation patterns, VSWRs, current distributions, envelope correlation coefficients (port1-port2, port1-port3, port1-port4), and diversity gains (port1-port2, port1-port3, port1-port4) have all been reported over the operating frequency band for two antennas.
HGNNDR: Heterogeneous Graph Neural Network Recommendation Model based on Feature Aggregation
Authors: Norton Marlowe , Kingsley Arwen , Wellington Asher , Prescott Juniper 
Published: July 2023

Abstract
In recent years, with the rapid development of information technology such as big data, cloud computing, and the Internet of Things, the scale of data contained in the Internet has been growing explosively. The arrival of the big data era will bring more convenience to people. However, it will also bring people the problem of "information overload", that is, when people face a huge amount of information data, many redundant and useless data will be lost. Heterogeneous graphs have diverse and complex types of data structures, how to mine information effectively for heterogeneous graphs, whether the embedding of nodes contains neighborhood information and semantic information, and so on, are all challenges in the representation learning of heterogeneous graphs. In order to address the above shortcomings, this paper combines graph neural networks with heterogeneous networks to propose the deep recommendation model HGNNDR. In this paper, a multi-feature joint representation of information in heterogeneous information networks is given. Oriented to the two domains of user/item interaction and user socialization, the multi-order topology information in heterogeneous information networks is utilized to enhance the representation of node features in the case of sparse network connections.
A graph neural network recommendation method oriented to the attention mechanism is proposed. Through the effective fusion of multidimensional representation vectors of users, items, ratings, and socialization, the recommendation quality of the recommendation model is enhanced in the case of sparse rating matrices.
The recommended accuracy of the model in this paper is verified to be better than the baseline method on multiple public datasets.
Validation of a smartphone-based gait analysis focusing on waveform similarity
Authors: Arita Satoshi , Nishiyama Daisuke , Fukui Daisuke , Yamanaka Manabu , Yamada Hiroshi 
Published: July 2023

Abstract
Objective: Gait analysis using Inertial measurement units (IMUs) have gained attention owing to low economic and logistical constraints and obtaining spatiotemporal gait parameters with the same accuracy as that of conventional gait analysis. Most validation studies have focused on the agreement of spatiotemporal parameters calculated by integrating acceleration data with laboratory-based optical motion capture systems (OMCS), the gold standard of gait analysis. To legitimize analysis using acceleration waveforms, it is necessary to verify the parameters obtained from waveforms and their shapes; however, no research uses the similarity of waveform shape to validate the IMU gait analysis system. Thus, this study investigated the acceleration and angular velocity change waveforms obtained from the IMU as compared to a laboratory-based OMCS, the gold standard of gait analysis.
Method: Ten walkers were recorded three times each, using an IMU and a laboratory-based OMCS. Three-axis angular velocities and acceleration waveforms were verified for similarity using the cross-correlation function (CCF) and dynamic time warping (DTW).
Results: The derivative DTW distances between IMU and OMCS waveforms of the same gait were significantly smaller than those of the different gait groups in all directions. The acceleration waveforms toward gait, left-right direction, and vertical direction exhibited significant similarity, as did, angular velocities in pitch, yaw, and roll angular directions.
Conclusion: Analysis using the acceleration pattern of the IMU can be legitimized without complicated signal processing for attitude estimation. These results can inform 3D motion analysis using the angular velocity of the pelvis.