bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic modulations of urinary sphingolipid and glycerophospholipid levels in COVID-19 and correlations with COVID-19-associated kidney injuries
Authors: Kurano Makoto , Jubishi Daisuke , Okamoto Koh , Hashimoto Hideki , Sakai Eri , Morita Yoshifumi , Saigusa Daisuke , Kano Kuniyuki , Aoki Junken , Harada Sohei , Okugawa Shu , Doi Kent , Moriya Kyoji , Yatomi Yutaka 
Published: November 2022

Abstract
Background
Among various complications of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), renal complications, namely COVID-19-associated kidney injuries, are related to the mortality of COVID-19.

Methods
In this retrospective cross-sectional study, we measured the sphingolipids and glycerophospholipids, which have been shown to possess potent biological properties, using liquid chromatography-mass spectrometry in 272 urine samples collected longitudinally from 91 COVID-19 subjects and 95 control subjects without infectious diseases, to elucidate the pathogenesis of COVID-19-associated kidney injuries.

Results
The urinary levels of C18:0, C18:1, C22:0, and C24:0 ceramides, sphingosine, dihydrosphingosine, phosphatidylcholine, lysophosphatidylcholine, lysophosphatidic acid, and phosphatidylglycerol decreased, while those of phosphatidylserine, lysophosphatidylserine, phosphatidylethanolamine, and lysophosphatidylethanolamine increased in patients with mild COVID-19, especially during the early phase (day 1–3), suggesting that these modulations might reflect the direct effects of infection with SARS-CoV-2. Generally, the urinary levels of sphingomyelin, ceramides, sphingosine, dihydrosphingosine, dihydrosphingosine l-phosphate, phosphatidylcholine, lysophosphatidic acid, phosphatidylserine, lysophosphatidylserine, phosphatidylethanolamine, lysophosphatidylethanolamine, phosphatidylglycerol, lysophosphatidylglycerol, phosphatidylinositol, and lysophosphatidylinositol increased, especially in patients with severe COVID-19 during the later phase, suggesting that their modulations might result from kidney injuries accompanying severe COVID-19.

Conclusions
Considering the biological properties of sphingolipids and glycerophospholipids, an understanding of their urinary modulations in COVID-19 will help us to understand the mechanisms causing COVID-19-associated kidney injuries as well as general acute kidney injuries and may prompt researchers to develop laboratory tests for predicting maximum severity and/or novel reagents to suppress the renal complications of COVID-19.
Chemoradiation and consolidation chemotherapy for rectal cancer provides a high rate of organ preservation with a very good long-term oncological outcome: a single-center cohort series
Authors: Asoglu Oktar , Bulut Alisina , Aliyev Vusal , Piozzi Guglielmo Niccolò , Guven Koray , Bakır Barıs , Goksel Suha 
Published: November 2022

Abstract
Aim
To report long-term oncological outcomes and organ preservation rate with a chemoradiotherapy-consolidation chemotherapy (CRT-CNCT) treatment for locally advanced rectal cancer (LARC).

Method
Retrospective analysis of prospectively maintained database was performed. Oncological outcomes of mid-low LARC patients (n=60) were analyzed after a follow-up of 63 (50–83) months. Patients with clinical complete response (cCR) were treated with the watch-and-wait (WW) protocol. Patients who could not achieve cCR were treated with total mesorectal excision (TME) or local excision (LE).

Results
Thirty-nine (65%) patients who achieved cCR were treated with the WW protocol. TME was performed in 15 (25%) patients and LE was performed in 6 (10%) patients. During the follow-up period, 10 (25.6%) patients in the WW group had regrowth (RG) and 3 (7.7%) had distant metastasis (DM). Five-year overall survival (OS) and disease-free survival (DFS) were 90.1% and 71.6%, respectively, in the WW group. Five-year OS and DFS were 94.9% (95% CI: 88–100%) and 80% (95% CI: 55.2–100%), respectively, in the RG group. For all patients (n=60), 5-year TME-free DFS was 57.3% (95% CI: 44.3–70.2%) and organ preservation-adapted DFS was 77.5% (95% CI: 66.4–88.4%). For the WW group (n=39), 5-year TME-free DFS was 77.5% (95% CI: 63.2–91.8%) and organ preservation-adapted DFS was 85.0% (95% CI: 72.3–97.8%).

Conclusion
CRT-CNCT provides cCR as high as 2/3 of LARC patients. Regrowths, developed during follow-up, can be successfully salvaged without causing oncological disadvantage if strict surveillance is performed.
Gene flow and introgression are pervasive forces shaping the evolution of bacterial species
Authors: Diop Awa , Torrance Ellis L. , Stott Caroline M. , Bobay Louis-Marie 
Published: November 2022

Abstract
Background
Although originally thought to evolve clonally, studies have revealed that most bacteria exchange DNA. However, it remains unclear to what extent gene flow shapes the evolution of bacterial genomes and maintains the cohesion of species.

Results
Here, we analyze the patterns of gene flow within and between >2600 bacterial species. Our results show that fewer than 10% of bacterial species are truly clonal, indicating that purely asexual species are rare in nature. We further demonstrate that the taxonomic criterion of ~95% genome sequence identity routinely used to define bacterial species does not accurately represent a level of divergence that imposes an effective barrier to gene flow across bacterial species. Interruption of gene flow can occur at various sequence identities across lineages, generally from 90 to 98% genome identity. This likely explains why a ~95% genome sequence identity threshold has empirically been judged as a good approximation to define bacterial species. Our results support a universal mechanism where the availability of identical genomic DNA segments required to initiate homologous recombination is the primary determinant of gene flow and species boundaries in bacteria. We show that these barriers of gene flow remain porous since many distinct species maintain some level of gene flow, similar to introgression in sexual organisms.

Conclusions
Overall, bacterial evolution and speciation are likely shaped by similar forces driving the evolution of sexual organisms. Our findings support a model where the interruption of gene flow—although not necessarily the initial cause of speciation—leads to the establishment of permanent and irreversible species borders.
Great saphenous vein aneurysm mimicking inguinal hernia: a case report
Authors: Ghoddusi Johari Hamed , Malekhosseini Hamidreza , Erfani Amirhossein , Shahriarirad Reza 
Published: November 2022

Abstract
Background
Diagnosis of venous aneurysm may be difficult and can be misjudged as mass-like lesions, including hernias. Here we present the case of a patient with a great saphenous vein aneurysm misdiagnosed and operated as an inguinal hernia.

Case presentation
A 39-year-old Middle Eastern/Persian male presented with left inguinal bulging 15 years ago, which was misdiagnosed and operated on with a diagnosis of inguinal hernia. He was referred to our clinic, in which color Doppler sonography revealed left-sided saphenofemoral junction incompetence with severe flow reversal during the Valsalva maneuver, in favor of a great saphenous vein aneurysm. Ligation of left saphenofemoral junction and stripping of saphenous vein, and stab avulsion phlebotomy of left lower extremity varicose veins, were done. He was discharged the next day after the operation with an uneventful postoperative course or complication on follow-up.

Conclusion
Venous aneurysms can be misdiagnosed as other, more common, mass-like lesions, such as inguinal hernias. Therefore, our report emphasizes the consideration of thorough assessment and utilization of color duplex sonography to prevent further misdiagnosis and unnecessary intervention and operations.
Understanding the role of stress, personality and coping on learning motivation and mental health in university students during a pandemic
Authors: Gibbons Chris 
Published: November 2022

AbstractThe aims explored the associations between stress, personality and coping on student mental health and compared defensive-pessimism and optimism as influences on learning motivation. Most research construes ‘stress’ as ‘distress’, with little attempt to measure the stress that enhances motivation and wellbeing. Undergraduate psychology students (N = 162) were surveyed on student and pandemic-related stressors, personality, support, control, mental health and learning motivation. Overall, adverse mental health was high and the lack of motivation acute. While positive ratings of teaching and optimistic thinking were associated with good mental health, context control was key. Adverse ratings of teaching quality lowered learning motivation. Support and conscientiousness bolstered learning motivation and conscientiousness buffered against the adverse impact of stress on motivation. Openness was associated with the stress involved in learning. For those anxious-prone, defensive-pessimism was as effective as optimism was in stimulating learning motivation. Developing context control, support and strategies linked to personality could bolster student resilience during and post Covid-19.
Maladaptive personality traits as predictors of prosocial and trusting behavior in two economic games
Authors: Hepp Johanna , Mohr Melissa R. M. , Niedtfeld Inga 
Published: November 2022

AbstractBackgroundDimensional models of personality disorders postulate interpersonal dysfunction as the core feature of personality pathology, and describe maladaptive personality traits that characterize the specific pattern of dysfunction that is experienced. Herein, we examined whether maladaptive traits predict prosocial and trusting behavior, both of which are highly relevant behaviors for interpersonal functioning. Specifically, we examined antagonism as a predictor of prosocial behavior in a dictator game, and suspiciousness as a predictor of trust in the faith game.Materials and methodsThe study was preregistered and conducted online. The preregistration protocol is available athttps://osf.io/er43j. Data and code are available athttps://osf.io/2rvbg/. Participants (N = 445) completed the German version of the Personality Inventory for DSM-5 to measure antagonism and suspiciousness. Additionally, they played the dictator game (more money taken away from another person indicates less prosocial behavior) and the faith game (choosing the sure choice instead of the faith choice indicates less trust). We conducted a linear regression model to test whether antagonism is associated with prosocial behavior in the dictator game and a logistic regression model to test whether suspiciousness predicts selection of the sure choice in the faith game.ResultsAs hypothesized, higher levels of antagonism were associated with less prosocial behavior in the dictator game. The remaining hypotheses were not supported, as suspiciousness was not significantly associated with the likelihood of choosing the sure choice in the faith game. Exploratory analyses on participants’ estimates of the sure choice amount suggest successful experimental manipulation in the faith game.ConclusionsThe results on antagonism and prosocial behavior are consistent with those of previous studies that used categorial classification systems of personality disorders or examined non-pathological personality traits. Potential explanations for the non-significant effects of suspiciousness are discussed, including the small size and range of the sure choice payoff and that the anonymity of the game may have precluded suspicious traits from expressing. Future research with higher stakes and known interaction partners is needed to further probe the effects of suspiciousness.
Does diabetes mellitus affect the safety profile of valproic acid for the treatment of status epilepticus? A retrospective cohort study
Authors: Müller Annekatrin , von Hofen-Hohloch Judith , Awissus Carolin , Przybilla Jens , Mrestani Achmed , Classen Joseph 
Published: November 2022

Abstract
Background
In the treatment of status epilepticus less is known about the influence of comorbidities on the safety profile of anticonvulsive drugs. Especially patients with diabetes mellitus may be predisposed to certain adverse events that have been related to therapy with valproic acid. In this single-center retrospective cohort study we examined if the complications of the intravenous treatment with valproic acid is different in patients with or without diabetes.

Methods
Patients who were treated for status epilepticus with intravenous valproic acid between 2008 and 2020 were identified. Primary endpoint was the discontinuation of therapy with valproic acid due to adverse events. Relevant secondary endpoints were the functional status at the time of discharge from hospital in comparison to the premorbid state and the in-hospital mortality. Both groups (patients with or without diabetes) were compared by Mann–Whitney U-Test or Pearson´s Chi2 test. To identify therapy with valproic acid as a risk factor of in-hospital mortality, a binary regression model was used.

Results
During the study period 408 patients and 482 episodes of status epilepticus were treated with intravenous valproic acid. Group comparisons did not reveal a significant difference in the rates of discontinuation of therapy. A difference was found in the rate of thrombocytopenia (p = 0.015), which occurred more often in patients with diabetes. In total, 36 hypoglycemic episodes could be identified, two occurred spontaneously under intravenous valproic acid. After correction for potential confounders, continuous therapy with valproic acid could not be confirmed as an independent risk factor for in-hospital mortality (p = 0.079). In patients with diabetes, the proportion of patients with a good functional state, indicated by the modified Rankin Scale, was significantly lower in both times (premorbid: 55% vs. 69%, p = 0.008; at discharge: 22% vs. 36%, p = 0.004).

Conclusions
Tolerability of the treatment with valproic acid was similar in patients with or without diabetes. Diabetes as a relevant comorbidity can signal a potentially increased risk of a poor outcome after status epilepticus.
Trial registration: The study was registered at the German Clinical Trials Register on 8 April 2022 (DRKS 00,027,836).
Sterol demethylation inhibitor fungicide resistance in Colletotrichum siamense from chili is caused by mutations in CYP51A and CYP51B
Authors: Chen Wenchan , Wei Lingling , Hou Rongxian , Zhao Yangyang , Zhao Yancun , Liu Fengquan 
Published: November 2022

AbstractAnthracnose, caused by fungi of the genus Colletotrichum, is a serious disease of chili worldwide. Sterol 14α-demethylation inhibitors (DMIs) are a class of chemical fungicides that can effectively control anthracnose diseases. In this study, 22 Colletotrichum isolates collected from commercial chili fields in Zhangzhou, Fujian Province, China, were identified as Colletotrichum siamense. The sensitivities of the 22 C. siamense isolates to tebuconazole were determined based on the EC50 (50% effective inhibition concentration) value. The results showed that the EC50 values of the two isolates to tebuconazole were 0.039 ± 0.0036 and 0.042 ± 0.0012 mg/L, while the other 20 isolates showed significantly decreased sensitivities to tebuconazole, with EC50 values ranging from 0.61 ± 0.056 to 1.94 ± 0.11 mg/L. Sequence analysis of CYP51A and CYP51B revealed five genotype mutations (i. e., CYP51AV46L, D115V, P163S, R306K, E397D, CYP51AD115V, S164Y, R306K, E397D, CYP51AD115V, R306K, P339T, E397D, CYP51AD115V, R306K, E397D, S400N, and CYP51AD115V, R306K, E397DCYP51BR266H) in the resistant isolates. The tebuconazole-resistant isolates of five genotypes suffered a fitness penalty and exhibited cross-resistance to difenoconazole, prochloraz, and propiconazole. Additionally, the five genotype mutations were validated as being responsible for tebuconazole-resistance in C. siamense by construction of replacement mutants. Overexpression of CYP51A and CYP51B was not detected in the replacement mutants of the five genotypes. Overall, the present study is the first to report DMI resistance in C. siamense and provides significant information for rational use of DMIs to control chili anthracnose.
Physics-driven self-supervised learning system for seismic velocity inversion
Authors: Liu Bin , Jiang Peng , Wang Qingyang , Ren Yuxiao , Yang Senlin , Cohn Anthony G. 
Published: November 2022

Seismic velocity inversion plays a vital role in various applied seismology processes. A series of deep learning methods have been developed that rely purely on manually provided labels for supervision; however, their performances depend heavily on using large training data sets with corresponding velocity models. Because no physical laws are used in the training phase, it is usually challenging to generalize trained neural networks to a new data domain. To mitigate these issues, we have embedded a seismic forward modeling step at the end of a network to remap the inversion result back to seismic data and thus train the neural network through self-supervised loss, i.e., the misfit between the network input and output. As a result, we eliminate the need for many labeled velocity models, and physical laws are introduced when back-propagating gradients through the seismic forward modeling step. We verify the effectiveness of our approach through comprehensive experiments on synthetic data sets, where self-supervised learning outperforms the fully supervised approach, which accesses much more labeled data. The superior performance is even more significant when compared with a new data domain that has velocity models with faults and more geologic layers. Finally, in case of unknown and more complex data types, we develop a network-constrained full-waveform inversion (FWI) method. This method refines the initial prediction of the network by iteratively optimizing network parameters other than the velocity model, as found with the conventional FWI method, and demonstrates clear advantages in terms of interface and velocity accuracy. With these measures (self-supervised learning and network-constrained FWI), our physics-driven self-supervised learning system successfully mitigates issues such as the dependence on large labeled data sets, the absence of physical laws, and the difficulty in adapting to new data domains.
Data-assimilated time-lapse visco-acoustic full-waveform inversion: Theory and application for injected CO2 plume monitoring
Authors: Huang Chao , Zhu Tieyuan , Xing Guangchi 
Published: November 2022

Continuous seismic monitoring for quantifying CO2 plume migration and detection of any potential leakages in the subsurface is essential for the security of long-term anthropogenic carbon dioxide geologic storage. Traditional time-lapse full-waveform inversion (TLFWI) methods aim to map the CO2 distribution by estimating seismic velocity changes, but recent studies find that CO2-induced attenuation is an important complement to seismic velocity for tracking the CO2 plumes and even quantifying the CO2 saturation. We have developed a novel data-assimilated TLFWI method to construct high-resolution time-lapse velocity and attenuation changes from dense time-lapse monitoring data. This method consists of two theoretical developments: visco-acoustic full-waveform inversion (QFWI) and multiparameter hierarchical matrix-powered extended Kalman filter (mHiEKF). The method is capable of (1) posing temporal constraints to retrieve time-lapse information from dense monitoring data by using mHiEKF, (2) accurately recovering high-spatial-resolution velocity and attenuation perturbations using first-order equation system-based QFWI, and (3) providing the model uncertainty by estimating their model standard deviation. With numerical examples, we first find the effectiveness of the new QFWI on estimating accurate velocity and attenuation models simultaneously. Then, a CO2 leakage case and a realistic Frio-II CO2 monitoring case are presented to find the advantages and applicability of our data-assimilated QFWI method for estimating time-lapse changes using dense time-lapse monitoring surveys. By assimilating time-lapse seismic monitoring data over time, our data-assimilated QFWI method can improve the resolution of velocity and attenuation changes and decrease their model uncertainties.
Interpretation of well logs and core data via Bayesian inversion
Authors: Deng Tianqi , Ambía Joaquín , Torres-Verdín Carlos 
Published: November 2022

Estimating in situ petrophysical and compositional properties of rocks (e.g., porosity, mineralogy, and fluid saturation) from well logs and core measurements is critical for the evaluation of subsurface fluid resources. Traditional multimineral analysis of well logs is susceptible to abnormal borehole and geometric conditions, such as shoulder-bed effects and tool/borehole-related biases. Moreover, traditional multimineral analysis rarely includes uncertainty quantification, much less assessments of the impact of measurement noise, borehole conditions, and/or inaccurate rock-physics models (RPMs) on estimated properties. Probabilistic formation evaluation with credible-interval estimations can improve the outcome of mineral and fluid evaluations from well logs by explicitly incorporating the effects of measurement biases and a priori compositional and petrophysical constraints in the estimation. A probabilistic workflow is developed to estimate petrophysical/compositional properties from well logs and available core data. The workflow consists of two sequential steps: borehole measurements (e.g., density, resistivity, and gamma ray) are first converted into a layer-by-layer earth model, which consists of piecewise constant property values, with associated uncertainty estimations. The estimated earth model is tool/borehole independent, allowing for a common baseline to effectively compare properties among neighboring wells. Next, the estimated earth-model physical properties are used to derive petrophysical properties (e.g., volumetric concentration of fluid and solid rock constituents) via petrophysical joint inversion. In each step, Bayesian inversion is implemented with Markov chain Monte Carlo sampling in contrast to deterministic algorithms used by traditional multimineral methods. The developed method has the following advantages over traditional approaches: (1) it propagates uncertainty from well logs to petrophysical properties by assimilating measurement noise, tool/borehole-related biases, and RPM errors and (2) it enables the implementation of a priori knowledge per rock class to constrain the petrophysical estimation, effectively integrating field-specific core/regional geologic data. Examples of thinly laminated and organic shale formations successfully verify the reliability, efficiency, and accuracy of our estimation method.