bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immunoadsorption versus double-dose methylprednisolone in refractory multiple sclerosis relapses
Authors: Pfeuffer Steffen , Rolfes Leoni , Wirth Timo , Steffen Falk , Pawlitzki Marc , Schulte-Mecklenbeck Andreas , Gross Catharina C. , Brand Marcus , Bittner Stefan , Ruck Tobias , Klotz Luisa , Wiendl Heinz , Meuth Sven G. 
Published: September 2022

Abstract
Objective
Intravenous methylprednisolone is the standard treatment for a multiple sclerosis relapse; however, this fails to improve symptoms in up to one quarter of patients. Immunoadsorption is an accepted treatment for refractory relapses, but prospective comparator-controlled studies are missing.

Methods
In this observational study, patients with steroid-refractory acute multiple sclerosis relapses receiving either six courses of tryptophan-immunoadsorption or double-dose methylprednisolone therapy were analysed. Outcomes were evaluated at discharge and three months later. Immune profiling of blood lymphocytes and proteomic analysis were performed by multi-parameter flow cytometry and Olink analysis, respectively (NCT04450030).

Results
42 patients were enrolled (methylprednisolone: 26 patients; immunoadsorption: 16 patients). For determination of the primary outcome, treatment response was stratified according to relative function system score changes (“full/best” vs. “average” vs. “worse/none”). Upon discharge, the adjusted odds ratio for any treatment response (“full/best” + ”average” vs. “worse/none”) was 10.697 favouring immunoadsorption (p = 0.005 compared to methylprednisolone). At follow-up, the adjusted odds ratio for the best treatment response (“full/best” vs. “average” + ”worse/none”) was 103.236 favouring IA patients (p = 0.001 compared to methylprednisolone). Similar results were observed regarding evoked potentials and quality of life outcomes, as well as serum neurofilament light-chain levels. Flow cytometry revealed a profound reduction of B cell subsets following immunoadsorption, which was closely correlated to clinical outcomes, whereas methylprednisolone had a minimal effect on B cell populations. Immunoadsorption treatment skewed the blood cytokine network, reduced levels of B cell-related cytokines and reduced immunoglobulin levels as well as levels of certain coagulation factors.

Interpretation
Immunoadsorption demonstrated favourable outcomes compared to double-dose methylprednisolone. Outcome differences were significant at discharge and follow-up. Further analyses identified modulation of B cell function as a potential mechanism of action for immunoadsorption, as reduction of B cell subsets correlated with clinical improvement.
Cross-validation of predictive models for functional recovery after post-stroke rehabilitation
Authors: Campagnini Silvia , Liuzzi Piergiuseppe , Mannini Andrea , Basagni Benedetta , Macchi Claudio , Carrozza Maria Chiara , Cecchi Francesca 
Published: September 2022

Abstract
Background
Rehabilitation treatments and services are essential for the recovery of post-stroke patients’ functions; however, the increasing number of available therapies and the lack of consensus among outcome measures compromises the possibility to determine an appropriate level of evidence. Machine learning techniques for prognostic applications offer accurate and interpretable predictions, supporting the clinical decision for personalised treatment. The aim of this study is to develop and cross-validate predictive models for the functional prognosis of patients, highlighting the contributions of each predictor.

Methods
A dataset of 278 post-stroke patients was used for the prediction of the class transition, obtained from the modified Barthel Index. Four classification algorithms were cross-validated and compared. On the best performing model on the validation set, an analysis of predictors contribution was conducted.

Results
The Random Forest obtained the best overall results on the accuracy (76.2%), balanced accuracy (74.3%), sensitivity (0.80), and specificity (0.68). The combination of all the classification results on the test set, by weighted voting, reached 80.2% accuracy. The predictors analysis applied on the Support Vector Machine, showed that a good trunk control and communication level, and the absence of bedsores retain the major contribution in the prediction of a good functional outcome.

Conclusions
Despite a more comprehensive assessment of the patients is needed, this work paves the way for the implementation of solutions for clinical decision support in the rehabilitation of post-stroke patients. Indeed, offering good prognostic accuracies for class transition and patient-wise view of the predictors contributions, it might help in a personalised optimisation of the patients’ rehabilitation path.
Soybean cyst nematode detection and management: a review
Authors: Arjoune Youness , Sugunaraj Niroop , Peri Sai , Nair Sreejith V. , Skurdal Anton , Ranganathan Prakash , Johnson Burton 
Published: September 2022

AbstractSoybeans play a key role in global food security. U.S. soybean yields, which comprise $$32\%$$

32
%

of the total soybeans planted in the world, continue to experience unprecedented grain loss due to the soybean cyst nematode (SCN) plant pathogen. SCN remains one of the primary disruptive pests despite the existence of advanced management techniques such as crop rotation and SCN-resistant varieties. SCN detection is a key step in managing this disease; however, early detection is challenging because soybeans do not show any above ground symptoms unless they are significantly damaged. Direct soil sampling remains the most common method for SCN detection, however, this method has several problems. For example, the threshold damage methods—adopted by most of the laboratories to make recommendations—is not reliable as it does not consider soil pH, N, P, and K values and relies solely on the egg count instead of assessment of the root infection. To overcome the challenges of manual soil sampling methods, deep learning and hyperspectral imaging are important current topics in precision agriculture for plant disease detection and have been proposed as cost-effective and efficient detection methods that can work at scale. We have reviewed more than 150 research papers focusing on soybean cyst nematodes with an emphasis on deep learning techniques for detection and management. First: we describe soybean vegetation and reproduction stages, SCN life cycles, and factors influencing this disease. Second: we highlight the impact of SCN on soybean yield loss and the challenges associated with its detection. Third: we describe direct sampling methods in which the soil samples are procured and analyzed to evaluate SCN egg counts. Fourth: we highlight the advantages and limitations of these direct methods, then review computer vision- and remote sensing-based detection methods: data collection using ground, aerial, and satellite approaches followed by a review of machine learning methods for image analysis-based soybean cyst nematode detection. We highlight the evaluation approaches and the advantages of overall detection workflow in high-performance and big data environments. Lastly, we discuss various management approaches, such as crop rotation, fertilization, SCN resistant varieties such as PI 88788, and SCN’s increasing resistance to these strategies. We review machine learning approaches for soybean crop yield forecasting as well as the influence of pesticides, herbicides, and fertilizers on SCN infestation reduction. We provide recommendations for soybean research using deep learning and hyperspectral imaging to accommodate the lack of the ground truth data and training and testing methodologies, such as data augmentation and transfer learning, to achieve a high level of detection accuracy while keeping costs as low as possible.
Predictors of major adverse events and complications after ventricular septal defects surgical closure in children less than 10 kg
Authors: Abdelrehim Ayman R. , Al-Muhaya Mustafa , Alkodami Alassal A. , Baangood Luna S. , Al-Mutairi Mansour , Quadeer Abdul , Alabsi Fath A. , Alashwal M. , Morsy Mohamed Mofeed F. , Alnajjar Abdulhameed A. , Salem Sherif S. 
Published: September 2022

Abstract
Background
Ventricular septal defect (VSD) is the most common congenital cardiac defect for which outcomes are not uniform. There is a lack of consensus on the risk factors for the unfavorable outcomes following surgical VSD closure.

Aim
The aim of this study was to determine the risk factors and the predictors of major adverse events (MAEs) and complications following surgical closure of VSD in children weighing less than 10 kg.

Methods
This retrospective cohort study included children less than 10 kg who underwent surgical closure of congenital VSD of any type with or without associated congenital heart diseases. Patients with associated major cardiac anomalies were excluded. Preoperative, operative and postoperative data were collected from medical records.

Results
This study included 127 patients 52.8% were males, the median age was 8.0 months (IQR = 6.0–11.0 months), and their median weight was 5.7 kg (IQR = 4.8–7.0). Mortality was in one patient (0.8%) Multivariable logistic regression analysis revealed that male sex group (observational data), previous pulmonary artery banding (PAB), and significant intraoperative residual VSD were significant risk factors for the development of MAEs (odds ratios were 3.398, 14.282, and 8.634, respectively). Trisomy 21 syndrome (odds ratio: 5.678) contributed significantly to prolonged ventilation. Pulmonary artery banding (odds ratio: 14.415), significant intraoperative (3 mm) residual VSD (odds ratio: 11.262), and long cross-clamp time (odds ratio: 1.064) were significant predictors of prolonged ICU stay, whereas prolonged hospital stay was observed significantly in male sex group (odds ratio: 12.8281), PAB (odds ratio: 2.669), and significant intraoperative (3 mm) residual VSD (odds ratio: 19.551).

Conclusions
Surgical VSD repair is considered a safe procedure with very low mortality. Trisomy 21 was a significant risk factor for prolonged ventilation. Further, PAB, significant intraoperative residual of 3 mm or more that required a second pulmonary bypass, and a greater cross-clamp time were significant predictors of MAE and associated complications with prolonged ICU and hospital stay.
Spatiotemporal Pavlovian head-fixed reversal learning task for mice
Authors: Yamamoto Kohei , Yamada Kota , Yatagai Saya , Ujihara Yusuke , Toda Koji 
Published: September 2022

AbstractOur world is full of uncertainty. Animals, including humans, need to behave flexibly to adjust to ever-changing environments. Reversal learning tasks have been used to assess behavioral flexibility in many species. However, there are some limitations in the traditional free-moving methodology, including (1) sessions to train the animals, (2) within-session number of trials associated with reversals, (3) factors of physical movement unrelated to the task in the maze or operant box, and (4) incompatibility with techniques, such as two-photon imaging. Therefore, to address these limitations, we established a novel spatiotemporal Pavlovian head-fixed reversal learning task for mice. Six experimentally naive adult C57BL/6J mice were used in this study. First, we trained head-fixed mice on a fixed-time schedule task. Sucrose solution was delivered every 10 s with a single drinking spout placed within the licking distance of the mice. After the mice showed anticipatory licking toward the timing of sucrose solution delivery, we began training the mice on the fixed-time schedule reversal learning task with two licking spouts. In this task, sucrose solution was delivered through one of the two drinking spouts. The rewarding spout was switched every 10 trials. Mice quickly learned to switch anticipatory licking to the rewarding side of the spouts, suggesting that they learned this head-fixed reversal learning task. Using the head-fixed experimental design, behavioral measures can be simplified by eliminating the complex behavioral sequences observed in free-moving animals. This novel head-fixed reversal learning task is a useful assay for studying the neurobiological mechanism of behavioral flexibility that is impaired in various psychopathological conditions.
The role of DNA damage repair (DDR) system in response to immune checkpoint inhibitor (ICI) therapy
Authors: Shi Congqi , Qin Kaiyu , Lin Anqi , Jiang Aimin , Cheng Quan , Liu Zaoqu , Zhang Jian , Luo Peng 
Published: September 2022

AbstractAs our understanding of the mechanisms of cancer treatment has increased, a growing number of studies demonstrate pathways through which DNA damage repair (DDR) affects the immune system. At the same time, the varied response of patients to immune checkpoint blockade (ICB) therapy has prompted the discovery of various predictive biomarkers and the study of combination therapy. Here, our investigation explores the interactions involved in combination therapy, accompanied by a review that summarizes currently identified and promising predictors of response to immune checkpoint inhibitors (ICIs) that are useful for classifying oncology patients. In addition, this work, which discusses immunogenicity and several components of the tumor immune microenvironment, serves to illustrate the mechanism by which higher response rates and improved efficacy of DDR inhibitors (DDRi) in combination with ICIs are achieved.
Novel tri-specific tribodies induce strong T cell activation and anti-tumor effects in vitro and in vivo
Authors: Passariello Margherita , Yoshioka Asami , Takahashi Kota , Hashimoto Shu-ichi , Inoue Toshikazu , Nakamura Koji , De Lorenzo Claudia 
Published: September 2022

Abstract
Background
Immunotherapy based on Bi-specific T Cell Engagers (TCE) represents one of the most attractive strategy to treat cancers resistant to conventional therapies. TCE are antibody-like proteins that simultaneously bind with one arm to a Tumor Associated Antigen (TAA) on cancer cells and with the other one to CD3 complex on a T-cell to form a TCR-independent immune synapse and circumvent Human Leucocyte Antigen restriction. Among them, the tribodies, such as Tb535H, a bi-specific molecule, made up of a Fab and a scFv domain both targeting 5T4 and another scFv targeting CD3, have demonstrated anti-tumor efficacy in preclinical studies.

Methods
Here, we generated five novel tri-specific and multi-functional tribodies, called 53X tribodies, composed of a 5T4 binding Fab arm and a CD3 binding scFv, but differently from the parental Tb535H, they contain an additional scFv derived from an antibody specific for an immune checkpoint, such as PD-1, PD-L1 or LAG-3.

Results
Compared with the parental Tb535H bi-specific T cell engager targeting 5T4, the novel 53X tribodies retained similar binding properties of Tb535H tribody, but showed enhanced anti-tumor potency due to the incorporation of the checkpoint inhibitory moiety. In particular, one of them, called 53L10, a tri-specific T cell engager targeting 5T4, CD3 and PD-L1, showed the most promising anti-tumor efficacy in vitro and led to complete tumor regression in vivo.

Conclusions
The novel tribodies have the potential to become strong and safe therapeutic drugs, allowing to reduce also the cost of production as one single molecule contains three different specificities including the anti-TAA, anti-CD3 and anti-IC binding arms.
Hsa_circ_0000098 is a novel therapeutic target that promotes hepatocellular carcinoma development and resistance to doxorubicin
Authors: Li Yi , Wu Anqi , Chen Lin , Cai Aiting , Hu Yuhao , Zhou Zhou , Qi Qianyi , Wu Yixuan , Xia Donglin , Dong Peixin , Ju Shaoqing , Wang Feng 
Published: September 2022

Abstract
Background
Circular RNA (circRNA) is crucial to the progression of hepatocellular cancer (HCC). In addition, Mitochondrial calcium uniporter regulatory factor 1 (MCUR1) is commonly overexpressed in HCC to increase cellular ATP levels. Due to the highly aggressive characteristics of HCC, it is essential to identify new diagnostic biomarkers and therapeutic targets that may facilitate the diagnosis of HCC and the development of effective anti-HCC treatments.

Methods
A series of in vitro and in vivo experiments were undertaken to investigate the biological importance and underlying mechanisms of circ_0000098 in HCC.

Results
The expression of circ_0000098 was higher in HCC tissues compared to paired adjacent tissues. According to the receiver-operating characteristic curves, circ_0000098 functioned as a potential diagnostic tumor marker in HCC. Our experiments indicated that circ_0000098 served as a key oncogenic circRNA to increase HCC cell proliferation and invasion in vitro and HCC progression in vivo. Furthermore, mechanistic investigation demonstrated that by sequestering miR-383 from the 3′-UTR of MCUR1, circ_0000098 positively regulated MCUR1 expression in HCC cells and finally promoted HCC progression. On the other hand, inhibiting circ_0000098 in HCC cells could diminish doxorubicin (DOX) resistance by decreasing P-glycoprotein (P-gp, MDR1) expression and intracellular ATP levels. Either downregulation of MCUR1 or overexpression of miR-383 improved DOX sensitivity in HCC cells. Subsequently, a short hairpin RNA targeting circ_0000098 (referred to as sh-1) and doxorubicin (DOX) were encapsulated into platelets (PLTs), referred to as DOX/sh-1@PLT. Activated DOX/sh-1@PLT through HCC cells resulted in the creation of platelet-derived particles that were capable of delivering the DOX/sh-1 combination into HCC cells and promoting intracellular DOX accumulation. Furthermore, our in vivo experiments showed that DOX/sh-1@PLT can effectively reduce P-gp expression, promote DOX accumulation, and reverse DOX resistance.

Conclusions
Our results demonstrated that circ_0000098 is an oncogenic circRNA that promotes HCC development through the miR-383/MCUR1 axis and targeting circ_0000098 with DOX/sh-1@PLT may be a promising and practical therapeutic strategy for preventing DOX resistance in HCC.
Glutathione metabolism in Cryptocaryon irritans involved in defense against oxidative stress induced by zinc ions
Authors: Zhong Zhi-Hong , Li Zhi-Cheng , Li Han , Guo Qing-Kai , Wang Chen-Xi , Cao Ji-Zhen , Li An-Xing 
Published: September 2022

Abstract
Background
Cryptocaryon irritans is a fatal parasite for marine teleosts and causes severe economic loss for aquaculture. Galvanized materials have shown efficacy in controlling this parasite infestation through the release of zinc ions to induce oxidative stress.

Methods
In this study, the resistance mechanism in C. irritans against oxidative stress induced by zinc ions was investigated. Untargeted metabolomics analysis was used to determine metabolic regulation in C. irritans in response to zinc ion treatment by the immersion of protomonts in ZnSO4 solution at a sublethal dose (20 μmol). Eight differential metabolites were selected to assess the efficacy of defense against zinc ion stimulation in protomonts of C. irritans. Furthermore, the mRNA relative levels of glutathione metabolism-associated enzymes were measured in protomonts following treatment with ZnSO4 solution at sublethal dose.

Results
The results showed that zinc ion exposure disrupted amino acid metabolism, carbohydrate metabolism, lipid metabolism, and nucleotide metabolism in C. irritans. Four antioxidants, namely ascorbate, S-hexyl-glutathione, syringic acid, and ubiquinone-1, were significantly increased in the Zn group (P < 0.01), while the glutathione metabolism pathway was enhanced. The encystment rate of C. irritans was significantly higher in the ascorbate and methionine treatment (P < 0.05) groups. Additionally, at 24 h post-zinc ion exposure, the relative mRNA level of glutathione reductase (GR) was increased significantly (P < 0.01). On the contrary, the relative mRNA levels of glutathione S-transferase (GT) and phospholipid-hydroperoxide glutathione peroxidase (GPx) were significantly decreased (P < 0.05), thus indicating that the generation of reduced glutathione was enhanced.

Conclusions
These results revealed that glutathione metabolism in C. irritans contributes to oxidative stress resistance from zinc ions, and could be a potential drug target for controlling C. irritans infection.

Graphical Abstract
Effect of heat inactivation and bulk lysis on real-time reverse transcription PCR detection of the SARS-COV-2: an experimental study
Authors: Leta Dereje , Gutema Gadissa , Hagos Gebremedhin Gebremichael , Diriba Regasa , Bulti Gutema , Sura Tolawak , Ayana Desta , Chala Dawit , Lenjiso Boki , Bulti Jaleta , Abdella Saro , Tola Habteyes Hailu 
Published: September 2022

Abstract
Objective
This study aimed to investigate the effect of heat inactivation and chemical bulklysis on SARS-CoV-2 detection.

Results
About 6.2% (5/80) of samples were changed to negative results in heat inactivation at 60 °C and about 8.7% (7/80) of samples were changed to negative in heat inactivation at 100 °C. The Ct values of heat-inactivated samples (at 60 °C, at 100 °C, and bulk lysis) were significantly different from the temperature at 56 °C. The effect of heat on Ct value should be considered when interpreting diagnostic PCR results from clinical samples which could have an initial low virus concentration. The efficacy of heat-inactivation varies greatly depending on temperature and duration. Local validation of heat-inactivation and its effects is therefore essential for molecular testing.
Comparison and impact of associated anomalies on the anal position index in neonates with anorectal malformation
Authors: Pitaka Ririd Tri , Fauzi Aditya Rifqi , Makhmudi Akhmad , Gunadi  
Published: September 2022

Abstract
Objective
Some prognostic factors have affected the functional outcomes of patients with anorectal malformations (ARM) after definitive surgery, including the associated anomalies. Moreover, the anal position index (API) study in neonates from developing countries is minimal. We aimed to (1) compare the API between neonates with ARM and controls; and (2) determine the impact of associated anomalies on the API in neonates with ARM.

Results
We ascertained 68 subjects: 35 neonates with ARM and 33 controls. The API of neonates with ARM was similar to controls, either male or female neonates (p = 0.51 and 0.90, respectively). Interestingly, the API in ARM males with associated anomalies (0.42 ± 0.07) was significantly lower than in control males (0.48 ± 0.02) (p = 0.005). Moreover, the API of ARM neonates with vertebral anomalies (0.35 ± 0.04) was lower than ARM neonates without vertebral anomalies (0.47 ± 0.07) (p = 0.021). In conclusion, associated anomalies and sex might affect the API in neonates with ARM. These findings should be considered and informed during counseling to the parents regarding the prognosis of functional outcomes in ARM neonates, particularly with associated anomalies.