bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increased expression of the immunoproteasome subunits PSMB8 and PSMB9 by cancer cells correlate with better outcomes for triple-negative breast cancers
Authors: Geoffroy Karen , Araripe Saraiva Bruna , Viens Melissa , Béland Delphine , Bourgeois-Daigneault Marie-Claude 
Published: February 2023

AbstractProteasome dependency is a feature of many cancers that can be targeted by proteasome inhibitors. For some cancer types, notably breast cancer and triple-negative breast cancer (TNBC), high mRNA expression of a modified form of the proteasome, called the immunoproteasome (ImP), correlates with better outcomes and higher expression of one ImP subunit was associated with slower tumor growth in a small patient cohort. While these findings are in line with an anti-tumoral role of the ImP in breast cancer, studies investigating ImP expression at the protein level in large patient cohorts are lacking. Furthermore, while ImPs can be found in both immune and non-immune cells, the cellular source is often ignored in correlative studies. In order to determine the impact of ImP expression on breast cancer outcomes, we assessed the protein expression and cellular source of the ImP subunits PSMB8 and PSMB9 in a cohort of 2070 patients. Our data show a clear correlation between high ImP expression and better outcomes, most notably for TNBC patients and when tumor cells rather than stromal or immune cells express PSMB8 or PSMB9. Our results therefore suggest that ImP expression by tumor cells could be used as prognostic markers of TNBC outcomes.
Exact solutions of $$\kappa$$-dependent Schrödinger equation with quantum pseudo-harmonic oscillator and its applications for the thermodynamic properties in normal and superstatistics
Authors: Okorie Uduakobong S. , Ikot Akpan N. , Okon Ituen B. , Obagboye Lewis F. , Horchani Ridha , Abdullah Hewa Y. , Qadir Karwan W. , Abdel-Aty Abdel-Haleem 
Published: February 2023

AbstractThe effects of the curvature parameters on the energy eigenvalues and thermodynamic properties of quantum pseudoharmonic oscillator are investigated within the framework of nonrelativistic quantum mechanics. By employing Nikiforov-Uvarov method, the energy spectra are obtained and used to study the ordinary statistics and q-deformed superstatistics as a function of temperature in the presence and absence of the curvature parameters. It is shown that the q-deformed supertatistics properties of the quantum pseudoharmonic oscillator reduce to the ordinary statistical properties in the absence of the deformation parameter. Finally, our results are illustrated graphically to show the behaviour of the energy spectra and thermodynamic properties for the three curvature parameters:$$\kappa = - 1,\,\,\kappa = 1\,\,{\text{and}}\,\,\kappa = 0$$

κ
=
-
1
,

κ
=
1

and

κ
=
0

.
An in-depth analysis of four classes of antidepressants quantification from human serum using LC–MS/MS
Authors: Fariha Ramisa , Deshpande Prutha S. , Rothkopf Emma , Jabrah Mohannad , Spooner Adam , Okoh Oluwanifemi David , Tripathi Anubhav 
Published: February 2023

AbstractDepression is a growing global crisis, with females at a higher rate of diagnosis than males. While the percentage of patients on prescribed antidepressants have tripled over the last two decades, we are still at a crossroad where the discrepancy lies between finding a drug to suit a patient and monitoring the abundance of it in the body to prevent unwanted side effects. Liquid Chromatography tandem mass spectrometry (LC–MS/MS) has garnered the attention of clinicians as a technique to accurately monitor therapeutic drugs in human serum with high specificity and accuracy. This may be a potential solution, but the challenge persists in the realm of sample preparation, where a method is automatable. We have developed and validated an LC–MS/MS-based assay for simultaneous quantification of 4 different classes of commonly prescribed antidepressants in women that is automated using a JANUS G3 Robotic Liquid Handler. Our method utilizes a simple sample preparation technique, utilizing only 20 μL of a serum sample, to accurately measure Bupropion, Citalopram, Desipramine, Imipramine, Olanzapine, Sertraline and Vilazodone across a range of 1.0 to 230 ng/mL. Our method exhibits a linearity of R2 ≥ 0.99 when detected in MRM mode and % CV of ≤ 20% for all analytes across the board. In addition, we have designed a prototype that can be utilized at a clinical mass spectrometry lab and assessed the long-term use of this prototype using an accelerated stability study. Overall, our developed method has the potential to be translated to clinical settings to monitor postpartum depression for a large number of patient samples using automation.
A nomogram for predicting postoperative urosepsis following retrograde intrarenal surgery in upper urinary calculi patients with negative preoperative urine culture
Authors: Yang Miaomiao , Li Yongchao , Huang Fang 
Published: February 2023

AbstractRetrograde intrarenal surgery (RIRS) is one of the main surgical methods for upper urinary calculi, but severe complications of infection may occur after surgery. This study aimed to establish and validate a preoperative nomogram for predicting postoperative urosepsis following retrograde intrarenal surgery to treat upper urinary calculus in patients with a negative preoperative urine culture. We retrospectively recruited 1767 patients with negative preoperative urine cultures who underwent retrograde intrarenal surgery to treat upper urinary calculi from January 2017 to April 2022. The independent risk factors for urosepsis include a solitary kidney, positive urine nitrite, operative time ≥ 75 min, history of recurrent urinary tract infections, and history of diabetes were identified by univariate analysis and multivariate binary logistic regression analysis, which construct a nomogram. The receiver operating characteristic curve of the nomogram for predicting urosepsis was 0.887 in the training cohort and 0.864 in the validation cohort, respectively. The calibration curve and decision curve analysis demonstrated great consistency and clinical utility of the nomogram. Therefore, the nomogram combining preoperative independent risk factors can predict the probability of a postoperative urosepsis following retrograde intrarenal surgery in patients with a negative preoperative urine culture, which could help urologists take preventive measures in advance after surgery to avoid more serious complications of infection.
Risk of mortality in COVID-19 patients: a meta- and network analysis
Authors: Kowsar Rasoul , Rahimi Amir Mohammad , Sroka Magdalena , Mansouri Alireza , Sadeghi Khaled , Bonakdar Elham , Kateb Sayed Farshad , Mahdavi Amir Hossein 
Published: February 2023

AbstractUnderstanding the most relevant hematological/biochemical characteristics, pre-existing health conditions and complications in survivors and non-survivor will aid in predicting COVID-19 patient mortality, as well as intensive care unit (ICU) referral and death. A literature review was conducted for COVID-19 mortality in PubMed, Scopus, and various preprint servers (bioRxiv, medRxiv and SSRN), with 97 observational studies and preprints, consisting of survivor and non-survivor sub-populations. This meta/network analysis comprised 19,014 COVID-19 patients, consisting of 14,359 survivors and 4655 non-survivors. Meta and network analyses were performed using META-MAR V2.7.0 and PAST software. The study revealed that non-survivors of COVID-19 had elevated levels of gamma-glutamyl transferase and creatinine, as well as a higher number of neutrophils. Non-survivors had fewer lymphocytes and platelets, as well as lower hemoglobin and albumin concentrations. Age, hypertension, and cerebrovascular disease were shown to be the most influential risk factors among non-survivors. The most common complication among non-survivors was heart failure, followed by septic shock and respiratory failure. Platelet counts, creatinine, aspartate aminotransferase, albumin, and blood urea nitrogen levels were all linked to ICU admission. Hemoglobin levels preferred non-ICU patients. Lower levels of hemoglobin, lymphocytes, and albumin were associated with increased mortality in ICU patients. This meta-analysis showed that inexpensive and fast biochemical and hematological tests, as well as pre-existing conditions and complications, can be used to estimate the risk of mortality in COVID-19 patients.
Recombinant anti-HIV MAP30, a ribosome inactivating protein: against plant virus and bacteriophage
Authors: Amirzadeh Nafiseh , Moghadam Ali , Niazi Ali , Afsharifar Alireza 
Published: February 2023

AbstractThe ribosome inactivating proteins (RIPs) efficiently decrease the microbial infections in plants. Momordicacharantia MAP30 is a type I RIP that has not been investigated against plant viruses or bacteriophages. To evaluate of these activities, the recombinant MAP30 (rMAP30) was produced in the hairy roots of Nicotianatabacum. Inoculation of 3 μg of transgenic total protein or 0.6 μg of rMAP30 against 0.1 μg of TMV reduced the leaf necrotic spots to 78.23% and 82.72%, respectively. The treatment of 0.1 μg of CMV with rMAP30 (0.6 μg) showed the reduction in the leaf necrotic spots to 85.8%. While the infection was increased after rMAP30 dilution. In the time interval assays, the leaves were first inoculated with 1 μg of rMAP30 or 0.1 μg of purified TMV or CMV agent for 6 h, then virus or protein was applied in order. This led the spot reduction to 35.22% and 67% for TMV, and 38.61% and 55.31% for CMV, respectively. In both the pre- and co-treatments of 1:10 or 1:20 diluted bacteriophage with 15 μg of transgenic total protein, the number and diameter of the plaques were reduced. The results showed that the highest inhibitory effect was observed in the pre-treatment assay of bacteriophage with transgenic total protein for 24 h. The decrease in the growth of bacteriophage caused more growth pattern of Escherichiacoli. The results confirm that rMAP30 shows antibacterial activity against Streptococcusaureus and E.coli, antifungal activity against Candidaalbicans, and antiviral activity against CMV and TMV. Moreover, rMAP30 exhibits anti-phage activity for the first time. According to our findings, rMAP30 might be a valuable preservative agent in foods and beverages in the food industry as well as an antiviral and antimicrobial mixture in agriculture.
Monocyte subsets and monocyte-related chemokines in Takayasu arteritis
Authors: de Aguiar Mariana Freitas , Torquato Heron , Salu Bruno Ramos , Oliveira Ana Cecília Diniz , Oliva Maria Luiza Vilela , Paredes-Gamero Edgar Julian , Abdulahad Wayel H. , Brouwer Elisabeth , de Souza Alexandre W. S. 
Published: February 2023

AbstractThe pathogenesis of Takayasu arteritis (TAK) is poorly understood and no previous studies have analyzed monocytes in TAK. This study evaluated monocyte subsets and monocyte-related chemokines in the peripheral blood of TAK patients and healthy controls (HC). Monocyte subsets were identified as classical (CD14+CD16−), intermediate (CD14+CD16dim), and non-classical (CD14dimCD16high) in the peripheral blood. The chemokines CCL (C–C chemokine ligand)2, CCL3, CCL4, CCL5, CCL7, CXCL (C-X-C motif ligand)10, and CX3CL (C-X3-C motif ligand)1 were measured in the sera. Thirty-two TAK patients and 30 HC were evaluated. Intermediate monocytes were higher in TAK than HC [25.0 cells ×106/L (16.7–52.0) vs. 17.2 cells ×106/L (9.2–25.3); p = 0.014]. Active disease was associated with monocytosis (p = 0.004), increased classical (p = 0.003), and intermediate (p < 0.001) subsets than HC. Prednisone reduced the percentage of non-classical monocytes (p = 0.011). TAK patients had lower CCL3 (p = 0.033) and CCL4 (p = 0.023) levels than HC, whereas CCL22 levels were higher in active TAK compared to the remission state (p = 0.008). Glucocorticoids were associated with lower CXCL10 levels (p = 0.012). In TAK, CCL4 correlated with total (Rho = 0.489; p = 0.005), classical and intermediate monocytes (Rho = 0.448; p = 0.010 and Rho = 0.412; p = 0.019). In conclusion, TAK is associated with altered counts of monocyte subsets in the peripheral blood compared to HC and CCL22 is the chemokine with the strongest association with active disease in TAK.
Ovicidal toxicity of plant essential oils and their major constituents against two mosquito vectors and their non-target aquatic predators
Authors: Moungthipmalai Tanapoom , Puwanard Cheepchanok , Aungtikun Jirapon , Sittichok Sirawut , Soonwera Mayura 
Published: February 2023

AbstractPlant essential oil (EO) is a natural alternative to synthetic chemical insecticides for mosquito control. EOs from Citrus aurantium L., Cymbopogon citratus (Stapf.), and Cinnamomum verum (J. Presl.) were selected for topical assay of their ovicidal activity against Aedes aegypti (Linnaeus) and Aedes albopictus (Skuse). Their efficacy was compared to that of 1% (w/w) temephos. In addition, their non-toxicity against aquatic mosquito predators, Poecilia latipinna and Poecilia reticulata, was tested. Found by GC–MS analysis, the major constituent of C. verum EO was trans-cinnamaldehyde, of C. aurantium EO was d-limonene, and of C. citratus EO was geranial. Both C. verum EO and trans-cinnamaldehyde at a high concentration (30,000 ppm) exhibited high ovicidal activity against Ae. aegypti and Ae. albopictus eggs after 48 h of incubation with an inhibition rate of 91.0–93.0% for C. verum EO and 96.7–95.2% for trans-cinnamaldehyde. The combination of C. verum EO + geranial exhibited the strongest synergistic inhibition activity (100%) against the two mosquito vectors and was five times more effective than temephos. Moreover, they were not toxic to the non-target fishes. As a safe ovicidal agent for mosquito egg control, the combination of C. verum EO + geranial has excellent potential.
Three-dimensional visualization of the total mesorectal excision plane for dissection in rectal cancer surgery and its ability to predict surgical difficulty
Authors: Nagai Yuzo , Kawai Kazushige , Nozawa Hiroaki , Sasaki Kazuhito , Murono Koji , Emoto Shigenobu , Yokoyama Yuichiro , Matsuzaki Hiroyuki , Abe Shinya , Sonoda Hirofumi , Yoshioka Yuichiro , Shinagawa Takahide , Ishihara Soichiro 
Published: February 2023

AbstractTotal mesorectal excision (TME) for rectal cancer is often technically challenging. We aimed to develop a method for three-dimensional (3D) visualization of the TME dissection plane and to evaluate its ability to predict surgical difficulty. Sixty-six patients with lower rectal cancer who underwent robot-assisted surgery were retrospectively analyzed. A 3D TME dissection plane image for each case was reconstructed using Ziostation2. Subsequently, a novel index that reflects accessibility to the deep pelvis during TME, namely, the TME difficulty index, was defined and measured. Representative bony pelvimetry parameters and clinicopathological factors were also analyzed. The operative time for TME was used as an indicator of surgical difficulty. Univariate regression analysis revealed that sex, body mass index, mesorectal fat area, and TME difficulty index were associated with the operative time for TME, whereas bony pelvimetry parameters were not. Multivariate regression analysis found that TME difficulty index (β = − 0.398, P = 0.0025) and mesorectal fat area (β = 0.223, P = 0.045) had significant predictability for the operative time for TME. Compared with conventional bony pelvimetry parameters, the TME difficulty index and mesorectal fat area might be more useful in predicting the difficulty of rectal cancer surgery.
Genetic distance from wolves affects family dogs’ reactions towards howls
Authors: Lehoczki Fanni , Andics Attila , Kershenbaum Arik , Kubinyi Enikő , Passilongo Daniela , Root-Gutteridge Holly , Range Friederike , Sánchez Vicente Palacios , Schmidt Lori , Townsend Simon W. , Watson Stuart K. , Faragó Tamás 
Published: February 2023

AbstractDomestication dramatically changes behaviour, including communication, as seen in the case of dogs (Canis familiaris) and wolves (Canis lupus). We tested the hypothesis that domestication may affect an ancient, shared communication form of canids, the howling which seems to have higher individual variation in dogs: the perception and usage of howls may be affected by the genetic relatedness of the breeds to their last common ancestor with wolves (‘root distance’) and by other individual features like age, sex, and reproductive status. We exposed 68 purebred dogs to wolf howl playbacks and recorded their responses. We identified an interaction between root distance and age on the dogs’ vocal and behavioural responses: older dogs from more ancient breeds responded longer with howls and showed more stress behaviours. Our results suggest that domestication impacts vocal behaviour significantly: disintegrating howling, a central, species-specific communication form of canids and gradually eradicating it from dogs’ repertoire.
Self‐supervised non‐rigid structure from motion with improved training of Wasserstein GANs
Authors: Wang Yaming , Peng Xiangyang , Huang Wenqing , Ye Xiaoping , Jiang Mingfeng 
Published: February 2023

AbstractThis study proposes a self‐supervised method to reconstruct 3D limbic structures from 2D landmarks extracted from a single view. The loss of self‐consistency can be reduced by performing a random orthogonal projection of the reconstructed 3D structure. Thus, the training process can be self‐supervised by using geometric self‐consistency in the reconstruction–projection–reconstruction process. The self‐supervised network mainly consists of graph convolution and Transformer encoders. This network is called the SS‐Graphformer. By adding a discriminator, the SS‐Graphformer is used as a generator to form a Wasserstein Generative Adversarial Network architecture with a Gradient Penalty to improve the accuracy of the reconstruction. It is experimentally demonstrated that the addition of the 2D structure discriminator can significantly improve the accuracy of the reconstruction.
The impact of feature selection techniques on effort‐aware defect prediction: An empirical study
Authors: Li Fuyang , Lu Wanpeng , Keung Jacky Wai , Yu Xiao , Gong Lina , Li Juan 
Published: February 2023

AbstractEffort‐Aware Defect Prediction (EADP) methods sort software modules based on the defect density and guide the testing team to inspect the modules with high defect density first. Previous studies indicated that some feature selection methods could improve the performance of Classification‐Based Defect Prediction (CBDP) models, and the Correlation‐based feature subset selection method with the Best First strategy (CorBF) performed the best. However, the practical benefits of feature selection methods on EADP performance are still unknown, and blindly employing the best‐performing CorBF method in CBDP to pre‐process the defect datasets may not improve the performance of EADP models but possibly result in performance degradation. To assess the impact of the feature selection techniques on EADP, a total of 24 feature selection methods with 10 classifiers embedded in a state‐of‐the‐art EADP model (CBS+) on the 41 PROMISE defect datasets were examined. We employ six evaluation metrics to assess the performance of EADP models comprehensively. The results show that (1) The impact of the feature selection methods varies in classifiers and datasets. (2) The four wrapper‐based feature subset selection methods with forwards search, that is, AdaBoost with Forwards Search, Deep Forest with Forwards Search, Random Forest with Forwards Search, and XGBoost with Forwards Search (XGBF) are better than other methods across the studied classifiers and the used datasets. And XGBF with XGBoost as the embedded classifier in CBS+ performs the best on the datasets. (3) The best‐performing CorBF method in CBDP does not perform well on the EADP task. (4) The selected features vary with different feature selection methods and different datasets, and the features noc (number of children), ic (inheritance coupling), cbo (coupling between object classes), and cbm (coupling between methods) are frequently selected by the four wrapper‐based feature subset selection methods with forwards search. (5) Using AdaBoost, deep forest, random forest, and XGBoost as the base classifiers embedded in CBS+ can achieve the best performance. In summary, we recommend the software testing team should employ XGBF with XGBoost as the embedded classifier in CBS+ to enhance the EADP performance.
Retracted: Intelligent design of rural residential environment guided by blockchain under the concept of green low carbon
Authors: Cheng Shuo , Lu Yao 
Published: February 2023

AbstractRetraction: [Shuo Cheng, Yao Lu, Intelligent design of rural residential environment guided by blockchain under the concept of green low carbon, IET Software 2023 (https://doi.org/10.1049/sfw2.12119)].The above article from IET Software, published online on 5 February 2023 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the Editor‐in‐Chief, Hana Chockler, the Institution of Engineering and Technology (the IET) and John Wiley and Sons Ltd. This article was published as part of a Guest Edited special issue. Following an investigation, the IET and the journal have determined that the article was not reviewed in line with the journal’s peer review standards and there is evidence that the peer review process of the special issue underwent systematic manipulation. Accordingly, we cannot vouch for the integrity or reliability of the content. As such we have taken the decision to retract the article. The authors have been informed of the decision to retract.
Galactic diffuse gamma rays meet the PeV frontier
Authors: De La Torre Luque P. , Gaggero D. , Grasso D. , Fornieri O. , Egberts K. , Steppa C. , Evoli C. 
Published: February 2023

Context. The Tibet ASγ and LHAASO collaborations recently reported the observation of a γ-ray diffuse emission with energy up to the PeV level from the Galactic plane.
Aims. We discuss the relevance of non-uniform cosmic-ray transport scenarios and the implications of these results for cosmic-ray physics.
Methods. We used the DRAGON and HERMES codes to build high-resolution maps and spectral distributions of that emission for several representative models under the condition that they reproduce a wide set of local cosmic-ray data up to 100 PeV.
Results. We show that the energy spectra measured by Tibet ASγ, LHAASO, ARGO-YBJ, and Fermi-LAT in several regions of interest in the sky can all be reasonably described in terms of the emission arising by the Galactic cosmic-ray “sea”. We also show that all our models are compatible with IceTop γ-ray upper limits.
Conclusions. We compare the predictions of conventional and space-dependent transport models with those data sets. Although the Fermi-LAT, ARGO-YBJ, and LHAASO preliminary data slightly favor this scenario, due to the still large experimental errors, the poorly known source spectral shape at the highest energies, the potential role of spatial fluctuations in the leptonic component, and a possible larger-than-expected contamination due to unresolved sources, a solid confirmation requires further investigations. We discuss which measurements will be most relevant in order to resolve the remaining degeneracy.