bluuebunny/crossref_metadata_2025 huggingface dataset:
Relationship between the heterogeneity of low-permeability reservoirs and the dynamic evolution of fractures under uniaxial compression conditions by CT scanning: A case study in the jiyang depression of Bohai Bay Basin, China
Authors: Li Li , Shi Guangyao , Zhang Yixin , Liu Xiangwei
Published: January 2023

Based on an analysis of core fractures and computed tomography scanning by X-ray under uniaxial compression tests with loading and unloading, this study investigated the three-dimensional evolution of fracture initiation and propagation in different heterogeneity conditions of low-permeability reservoirs. Reservoir heterogeneity affected the 3D dynamic development of fractures. With increasing loading value, fractures with strong heterogeneity in low-permeability reservoirs followed the development sequence from shallow to deep depth in the profile. When the fracture tip reached the incompetent layer, propagation stopped. Subsequently, when the deformation continued to increase, the fracture crossed the incompetent layer and initiated a new fracture at the front end. Therefore, the across-bedding and through-going macro fractures formed in conjugate sets or were Y-shaped, with roughly equal spacing. In the plane, the fractures initiated along the pre-existing bedding parallel fracture and further propagated into large fractures. Consequently, they formed a net-shaped fracture from the edge to the center, with a long development period. These fractures intersected to form a complex, interconnected, and high-fracture-density system in three dimensions. Under the same loading value, owing to uniform lithology, the formation of micro-fractures in the weak heterogeneity of low-permeability reservoirs is difficult. Furthermore, long shear fractures were only produced in a relatively short formation period with a low fracture density. In the plane, the fractures stepped in an en-énchelon and terminated with horse-tailing microfractures. Moreover, the strong heterogeneity of low-permeability reservoirs was more favorable for producing fractures. The fracture volume was 13.17% of the total sample volume compared to 0.67% in the weak-heterogeneity reservoir under the same loading compression. Furthermore, a better fracturing effect was achieved by fracturing along the direction >50° with the natural fracture and under the condition of small differential horizontal stresses.
Shear wave velocity prediction based on deep neural network and theoretical rock physics modeling
Authors: Feng Gang , Zeng Hua-Hui , Xu Xing-Rong , Tang Gen-Yang , Wang Yan-Xiang
Published: January 2023

Shear wave velocity plays an important role in both reservoir prediction and pre-stack inversion. However, the current deep learning-based shear wave velocity prediction methods have certain limitations, including lack of training dataset, poor model generalization, and poor physical interpretability. In this study, the theoretical rock physics models are introduced into the construction of the labeled dataset for deep learning algorithms, and a forward simulation of the theoretical rock physics models is utilized to supplement the dataset that incorporates geological and geophysical knowledge. This markedly increases the physical interpretability of the deep learning algorithm. Theoretical rock physics models for two different types of reservoirs, i.e., conventional sandstone and tight sandstone reservoirs, are first established. Then, a full-sample labeled dataset is constructed using these two types of theoretical rock physics models to traverse the elasticity parameter space of the two types of reservoirs through random variation and combination of parameters in the theoretical models. Finally, based on the constructed full-sample labeled dataset, four parameters (P-wave velocity, clay content, porosity, and density) that are highly correlated with the shear wave velocity are selected and combined with a deep neural network to build a deep shear wave velocity prediction network with good generalization and robustness, which can be directly applied to field data. The errors between the predicted shear wave velocity using the deep neural network and the measured shear wave velocity data in the laboratory and the logging data in three real field work areas are less than 5%, which are much smaller than the errors predicted by both Han’s and Castagna’s empirical formula. Furthermore, the prediction accuracy and generalization performance are better than those of these two common empirical formulas. The forward simulation based on theoretical models supplements the training dataset and provides high-quality labels for machine learning. This can considerably improve the interpretability and generalization of models in real applications of a machine learning algorithm.
Analyzing the seismic attributes, structural and petrophysical analyses of the Lower Goru Formation: A case study from Middle Indus Basin Pakistan
Authors: Tounkara Fode , Ehsan Muhsan , Nasar Iqbal Muhammad , Al-Ansari Nadhir , Hajana Muhammad Iqbal , Shafi Ahsan , Elbeltagi Ahmed
Published: January 2023

The purpose of this research is to delineate the structures of the Lower Goru Formation, investigate fluid properties, and clarify the hydrocarbon-prone areas through seismic attributes analysis. First, the acquired data was matched by the interpretation datum. Structural analysis was done by performing horizon interpretation, fault interpretation, and contour mapping on the C-Interval of the Lower Goru Formation. Hydrocarbon zones were marked with the help of attribute analysis on seismic sections and were justified by petrophysical analysis. An integrated approach such as seismic structural interpretation, seismic attribute, spectral decomposition, and petrophysical analyses was used in current research to better understand geological structure and features. This research showed that normal faults are present in the area showing negative flower structure, horst and graben, and faults oriented north-west to south-east. The contour map shows structural inclination and faults bound closure near well locations. Variance attribute and spectral decomposition attribute were used to verify horizon lineation and fault behavior. Instantaneous amplitude and instantaneous phase attributes justify hydrocarbon bearing zones, and bright spots are present on seismic sections at C–Interval of Lower Goru Formation. Petrophysical analysis of the available wells showed a number of significant hydrocarbon zones having more than 55% of hydrocarbon saturation at the C-Interval of the Lower Goru Formation. The four possible reservoir zones in Sawan-02 well, two zones in Sawan-07 well, and three zones in Sawan-09 well are identified based on well data interpretation. Based on these analyses, the area of interest has a very good reservoir potential, structural closure, and visible bright spots. The current finding of this research will be helpful for future exploration and development of the Sawan area.
Comparison of time-dependent viscosity slurry and cement-clay slurry for anti-seepage grouting on faults
Authors: Zhang Jiaxing , Pei Xiangjun , He Zhihao , Pei Zuan , Zheng Guoxun
Published: January 2023

The complex rock mass structure in fault fracture zone weakens the permeability of strata. This has led to curtain grouting being used to improve the anti-seepage properties of fault zones. This study evaluates the groutability and impermeability of a time-dependent viscosity slurry and a cement-clay slurry in a shattered fault zone. Rheology, setting time, mechanism, and permeability were tested to evaluate the groutability, and Lugeon and grouting field tests were carried out to evaluate the anti-seepage grouting characteristics of a fault zone. The results show that the time-dependent viscosity slurry had higher initial fluidity, a shorter and more controllable setting time, and higher strength than cement-clay slurry, better ensuring the slurry diffusion radius, pores filling rate, and bearing capacity and durability of the consolidated body. The permeability coefficient of the two grouts was less than 1×10−7 cm/s, and the blocking rate of heavy metal ions was more than 98%, sufficient to effectively control the leakage of sewage. The P∼Q curve of the Lugeon test showed that the original strata were of the washout type (>200 Lu), and the rock mass quality grade was the D grade (Poor). Under the same grouting depth, the amount of time-dependent viscosity slurry required was 72.6% of that of cement-clay slurry, and the permeability decreased to 10 Lu, far lower than the 50 Lu of the cement-clay slurry. The time-dependent viscosity slurry improved the quality of the rock mass from D to B-C grade, while the cement-clay slurry test area is remained C-D grade. In general, the time-dependent viscosity slurry performed better than cement-clay slurry in the water-bearing fault zone.
Analysis on fracture mechanics theory of roof cutting instability mechanism with large mining height face in shallow coal seam
Authors: Yang Dengfeng
Published: January 2023

The roof in a fully-mechanized face of a shallow coal seam with large mining height is prone to form a combined cantilever—articulated rock beam structure. When the support resistance is insufficient, the articulated rock beam will sink. This will make the combined cantilever beam rotate and fracture. It is then easy to induce the sliding and instability of the articulated rock beam, which results in large-scale roof cutting and the support crushing. Taking the combined cantilever beam structure as the main research object, and considering the mining damaged characteristics of cantilever beam rock stratum, the rock beam was regarded as a finite plate model with an edge crack of arbitrary dip angle. In addition, a fracture mechanics model controlled by a set of structural planes was established, the instability conditions of rock beam and the main control factors were analyzed, and the method of determining the support resistance were discussed. The results show that the cantilever beam rotates and fractures. This causes a chain reaction of the rock beam that leads to fracture. The combined cantilever beam then loses stability with the increase of the length of the crack length and the crack dip angle, and therefore it is easier to penetrate the cantilever beam and cause roof instability. The necessary condition for rock beam instability was crack activation, and the sufficient condition was the airfoil branch crack propagate through the rock beam. The influence degree of each parameter on the support resistance was thus determined: crack length a > crack dip angle β > rock thickness h > weighting interval l. The theoretical analysis results were proven to be reasonable by an in situ monitoring example of no. 22,310 working face in the Daliuta coal mine, China. On this basis, the reasonable value of support resistance was obtained. The conclusions of this research provide a new method for researching the roof instability mechanism. They are also conducive to the green and sustainable development of mines.
Thyroid autoimmunity and its negative impact on female fertility and maternal pregnancy outcomes
Authors: Tańska Kamila , Gietka-Czernel Małgorzata , Glinicki Piotr , Kozakowski Jarosław
Published: January 2023

Thyroid autoimmunity (TAI) is commonly defined as the presence of thyroperoxidase antibodies (TPOAbs) and/or thyroglobulin antibodies (TgAbs), which predisposes an individual to hypothyroidism. TAI affects nearly 10% of women of reproductive age and evokes great interest from clinicians because of its potentially negative impact on female fertility and pregnancy course. In this mini-review, we review the current literature concerning the influence of TPOAb or TPOAb/TgAb positivity without thyroid dysfunction on reproduction. TAI may negatively affect female fertility; several studies have found an increased prevalence of TAI in infertile women, especially in those with unexplained infertility and polycystic ovary syndrome. According to some observations, TAI might also be connected with premature ovarian insufficiency and endometriosis. The relationship between TAI and an increased risk of pregnancy loss is well documented. The pathophysiological background of these observations remains unclear, and researchers hypothesize on the direct infiltration of reproductive organs by thyroid antibodies, co-existence of TAI with other autoimmune diseases (either organ specific or systemic), immunological dysfunction leading to inhibition of immune tolerance, and relative thyroid hormone deficiency. Interestingly, in the current literature, better outcomes of assisted reproductive technology in women with TAI have been reported compared with those reported in earlier publications. One plausible explanation is the more widespread use of the intracytoplasmic sperm injection method. The results of randomized clinical trials have shown that levothyroxine supplementation is ineffective in preventing adverse pregnancy outcomes in women with TAI, and future research should probably be directed toward immunotherapy.
Numerical investigation of unsteady pressure pulsation characteristics in an ultra-low specific-speed centrifugal pump as a turbine
Authors: Wei Yangyang , Shi Yuhui , Zhang Qing , Shi Weidong
Published: January 2023

The unsteady flow characteristics of pump as hydraulic turbine play a vital role in its safe and stable operation, while the ultra-low specific-speed centrifugal pump may face more stability problems due to the limitations of its flow conditions under the turbine working condition. Therefore, in this study, the unsteady characteristics of an ultra-low specific-speed centrifugal pump under turbine conditions are studied using a numerical simulation method, and the numerical simulation is verified using an experimental method. Based on the hydraulic losses of each flow passage component, the energy characteristics of pump as turbine (PAT) are established, and the distribution pattern of total pressure fluctuation in the turbine is studied. The results show that the rotor–stator interaction between the impeller and the tongue makes the hydraulic performance and the internal flow field change periodically. The pressure fluctuation intensities at the tongue, blade inlet edge, and balance hole are large, and the total pressure fluctuation in the three areas is intense in space and time. The internal flow characteristics at typical blade positions show that the secondary flow phenomena such as separation flow and wake flow near the tongue make the pressure gradient larger, which is an important influence mode of the rotor–stator interaction. This study provides a reference and guidance for the unsteady study of low specific-speed PAT.
Power-balancing compensation mechanism and method for controllable load reduction
Authors: Sun Yalu , Ding Kun , Du Wenlu , Yang Changhai , Li Yalong
Published: January 2023

In the coming renewable energy-dominated power systems, their uncertain nature calls for a controllable load to track the change of renewable energy. To achieve power balance during peak load, a compensation mechanism for the controllable load to reduce power consumption is constructed. First, a multi-round sequential auction method is used to determine the reduced and non-reduced loads. Second, based on the proportional distribution according to the reduction loss, a compensation method for the reduced load by the non-reduced load is proposed. Considering both the reduction of electricity consumption and the carbon emission rate indicator, a compensation method for the reduced load by new energy enterprises is proposed; then, the compensation method and process of the controllable load reduction are formed. Finally, simulations are performed on a practical test case, and the effectiveness of the proposed scheme is verified by the numerical results.
Prediction of sediment wear of francis turbine with high head and high sediment content
Authors: Pan Jun , Ma Jianfeng , Han Junzhao , Zhou Ye , Wu Lielong , Zhang Weiliang
Published: January 2023

Wear of runner blades is a common problem affecting the operational reliability of turbines with high head and high sediment content. In order to accurately predict the wear of the turbine runner blade, based on the solid-liquid two-phase flow equation and turbulence model, the full channel numerical simulation of the internal water and sediment flow was carried out, and the sediment volume distribution and sand water velocity on the turbine runner blade were obtained. Then, according to the digital simulation results and the operating parameters of the turbine runner, the sediment wear test scheme for the turbine blade material specimen is designed, and the sediment wear test is carried out on the runner material. According to the test results, the sediment wear curve of runner blade material is obtained and applied to numerical simulation, and the main position and wear degree of turbine blade sediment erosion are predicted. The inspection results of the runner blade wear after the unit has operated for a flood season show that obvious wear can be seen at the outlet edge of the lower band of the runner blade, and the wear position and wear amount are basically consistent with the simulation values. The study is of great importance for predicting the wear of turbine runner blades with high drop height and high sediment content, and for turbine maintenance under complex conditions.
Dynamic changes in human THP-1-derived M1-to-M2 macrophage polarization during Thelazia callipaeda MIF induction
Authors: Yin Changzhu , Cai Juan , Gou Yanting , Li Di , Tang Hongri , Wang Lingjun , Liu Hui , Luo Bo
Published: January 2023

Macrophages are innate immune cells with essential roles in the immune response during helminth infection. Particularly, the direction of macrophage polarization could contribute to pathogen trapping and killing as well as tissue repair and the resolution of type 2 inflammation. This study establishes that the recombinant protein of Thelazia callipaeda macrophage migration inhibitory factor (T.cp-MIF) induces THP-1-derived macrophages to undergo M1 to M2 type dynamic polarization, using the methods of flow cytometry, real-time quantitative PCR, differential transcriptomic analysis and western blot. Interestingly, there was an increase in protein and mRNA expression of M1-type proteins and cytokines after the use of PI3K inhibitors, suggesting that the polarization state tends to favor the M1 type after M2 type inhibition. In conclusion, the dynamic polarization mechanism of T.cp-MIF-induced human THP-1-derived macrophages from M1 to M2 type is related to the binding of TLR4. It can first affect the M1 type polarization of macrophages by activating its downstream NF-κB pathway. Activation of the PI3K/Akt pathway and inhibition of NF-κB phosphorylation affects the M2 type polarization of macrophages.
Checkpoint inhibitor immune-related adverse events: A focused review on autoantibodies and B cells as biomarkers, advancements and future possibilities
Authors: Taylor John , Gandhi Aesha , Gray Elin , Zaenker Pauline
Published: January 2023

The use of immune checkpoint inhibitors (ICIs) has evolved rapidly with unprecedented treatment benefits being obtained for cancer patients, including improved patient survival. However, over half of the patients experience immune related adverse events (irAEs) or toxicities, which can be fatal, affect the quality of life of patients and potentially cause treatment interruption or cessation. Complications from these toxicities can also cause long term irreversible organ damage and other chronic health conditions. Toxicities can occur in various organ systems, with common observations in the skin, rheumatologic, gastrointestinal, hepatic, endocrine system and the lungs. These are not only challenging to manage but also difficult to detect during the early stages of treatment. Currently, no biomarker exists to predict which patients are likely to develop toxicities from ICI therapy and efforts to identify robust biomarkers are ongoing. B cells and antibodies against autologous antigens (autoantibodies) have shown promise and are emerging as markers to predict the development of irAEs in cancer patients. In this review, we discuss the interplay between ICIs and toxicities in cancer patients, insights into the underlying mechanisms of irAEs, and the involvement of the humoral immune response, particularly by B cells and autoantibodies in irAE development. We also provide an appraisal of the progress, key empirical results and advances in B cell and autoantibody research as biomarkers for predicting irAEs. We conclude the review by outlining the challenges and steps required for their potential clinical application in the future.
Polystyrene as a vector of heavy metals in hard clam Meretrix lusoria under various salinities
Authors: Barus Beta Susanto , Zhu Zuhao , Cheuch Chih-Yang , Chen Kai , Wang Jun , Cai Minggang , Cheng Sha-Yen , Wei Huihua
Published: January 2023

Microplastics and heavy metals are the two main contaminants that are often found in aquatic environments and can lead to major issues for aquatic organisms. Polystyrene (PS) is a type of microplastic that is commonly found in aquatic environments. Hard clams are one of the organisms that are often used as a bioindicator of water pollution, and they can live in a certain salinity range. The objective of this study is to investigate the potential of PS particles as heavy metal vectors in M. lusoria influenced by differences in salinity. The result showed that the highest increase in concentrations of all heavy metals in hard clams was found in those placed at higher salinities. Hard clams that were placed at higher salinity required more water, allowing more PS particles to enter the clams’ bodies. Hard clams placed at salinity 30‰ always gathered significantly more PS particles (p<0.05) than hard clams placed at the other two salinities (20 and 25‰). This is also corroborated by water depletion at a salinity of 30‰, which is significantly higher (p<0.05) than the other two salinities. Our findings indicate that PS particles have the potential as vectors for heavy metal pollutants in hard clams in environments of varying salinity.
Human shellfish poisoning: Implementation of a national surveillance program in France
Authors: Sinno-Tellier Sandra , Abadie Eric , Guillotin Sophie , Bossée Anne , Nicolas Marina , Delcourt Nicolas
Published: January 2023

Toxic algae and their toxins represent an emerging public health issue, particularly due to global warming. The toxicological mechanisms of neurotoxic phycotoxins and their human health effects have been widely described (paralytic, neurological, amnesic, and ciguateric toxins). Food poisoning by bivalve shellfish (mussels, oysters…) can cause serious or even fatal neurological disorders, as bivalves accumulate toxins by feeding on harmful algae. However, retrospective study of human shellfish poisoning highlighted the difficulties in identifying cases related to neurotoxic phycotoxins by gathering clinical and biological diagnostic confirmations on the one hand, as well as environmental contaminations on the other. To improve the collection of shellfish poisoning data, the French Agency for Food, Environmental and Occupational Health and Safety (ANSES), French Poison Control Centers (PCCs), the French Research Institute for Exploitation of the Sea (Ifremer) and the French Defense Procurement Agency (DGA) have developed a prospective surveillance of neurotoxins from algal origin that combines monitoring of poisoning cases (clinical monitoring), of harmful algae and their toxins in shellfish production areas (environmental monitoring), as well as of toxins levels in seafood leftovers and in biological samples from poisoned subjects. This original clinical and environmental monitoring will allow us to have a more complete view of phycotoxin human exposures that are underreported, and to implement measures to protect consumers.
Sarcopenia is associated with mortality in non-critical elderly patients visiting the emergency department
Authors: Liao Mei-Chen , Yen Cheng-Chang , Lin Yuh-Te , Huang Fong-Dee , Chang Yun-Te
Published: January 2023

Introduction

Geriatric syndrome (GS) increases risk of disability and mortality in older adults. Sarcopenia is a predominant illness of GS and accelerate its progression. This study aimed to investigate associations between mortality, emergency department (ED) re-visits and GS-related illnesses among older adults who visited the ED.

Method

This retrospective observational study enrolled elderly patients who visited the ED in our hospital between January 2018 and October 2020. Patients were evaluated for potential sarcopenia, which was defined by both low handgrip strength and calf circumference. Follow-up was at least 6 months. Data of age, gender, mortality, ED re-visits, and GS-related illnesses were collected and analyzed for associations.

Results

A total of 273 older adults aged 74 years or older were included, of whom 194 were diagnosed with possible sarcopenia. Older adults with possible sarcopenia also had significantly lower body mass index (BMI); a higher proportion needed assistance with daily activities; more had malnutrition, frailty, and history of falls (allp< 0.001) and acute decline in activities of daily living (p= 0.027). Multivariate analysis showed that possible sarcopenia [adjusted hazard ratio, aHR): 9.89, 95% confidence interval (CI): 1.17–83.81,p= 0.036], living in residential institutions (aHR: 2.85, 95% CI: 1.08–7.50,p= 0.034), and frailty (aHR: 7.30, 95% CI: 1.20–44.62,p= 0.031) were associated with mortality. Aged over 85 years (adjusted odds ratio: 2.44, 95% CI: 1.25–4.80,p= 0.02) was associated with ED re-visits.

Conclusion

Sarcopenia is associated with mortality among older adults who visit ED. Initial screening for sarcopenia and relevant risk factors among older adults in the ED may help with early intervention for those at high-risk and may improve their prognosis.
Global excellence in rheumatology in Latin America: The case of systemic lupus erythematosus
Authors: Ugarte-Gil Manuel F. , Fuentes-Silva Yurilis , Pimentel-Quiroz Victor R. , Pons-Estel Guillermo J. , Quintana Rosana , Pons-Estel Bernardo A. , Alarcón Graciela S.
Published: January 2023

Systemic lupus erythematosus (SLE) affects more severely non-White populations, due to their genetic background and sociodemographic characteristics. Several studies have evaluated Latin American SLE patients to determine their genetic and clinical characteristics as well as prognostic factors; these studies have not only allowed the development of treatment guidelines aimed at the region but also to support regional and global projects. Additionally, educational activities in Spanish and Portuguese have been started to reduce our patients’ health illiteracy. Despite the relatively low research output from Latin American countries, we consider that studies from our region coupled with the networks developed to increase our capabilities, could be a model for other rare autoimmune diseases.
Naso-oropharyngeal microbiome from breast cancer patients diagnosed with COVID-19
Authors: Viana Maria Carolina , Curty Gislaine , Furtado Carolina , Singh Bhavya , Bendall Matthew L. , Viola João P. B. , de Melo Andreia Cristina , Soares Marcelo A. , Moreira Miguel A. M.
Published: January 2023

Due to immunosuppressive cancer therapies, cancer patients diagnosed with COVID-19 have a higher chance of developing severe symptoms and present a higher mortality rate in comparison to the general population. Here we show a comparative analysis of the microbiome from naso-oropharyngeal samples of breast cancer patients with respect to SARS-CoV-2 status and identified bacteria associated with symptom severity. Total DNA of naso-oropharyngeal swabs from 74 women with or without breast cancer, positive or negative for SARS-CoV-2 were PCR-amplified for 16S-rDNA V3 and V4 regions and submitted to massive parallel sequencing. Sequencing data were analyzed with QIIME2 and taxonomic identification was performed using the q2-feature-classifier QIIME2 plugin, the Greengenes Database, and amplicon sequence variants (ASV) analysis. A total of 486 different bacteria were identified. No difference was found in taxa diversity between sample groups. Cluster analysis did not group the samples concerning SARS-CoV-2 status, breast cancer diagnosis, or symptom severity. Three taxa (Pseudomonas, Moraxella, and Klebsiella,) showed to be overrepresented in women with breast cancer and positive for SARS-CoV-2 when compared to the other women groups, and five bacterial groups were associated with COVID-19 severity among breast cancer patients: Staphylococcus, Staphylococcus epidermidis, Scardovia, Parasegitibacter luogiensis, and Thermomonas. The presence of Staphylococcus in COVID-19 breast cancer patients may possibly be a consequence of nosocomial infection.
Metabolic turnover of cysteine-related thiol compounds at environmentally relevant concentrations by Geobacter sulfurreducens
Authors: Gutensohn Mareike , Schaefer Jeffra K. , Maas Torben J. , Skyllberg Ulf , Björn Erik
Published: January 2023

Low-molecular-mass (LMM) thiol compounds are known to be important for many biological processes in various organisms but LMM thiols are understudied in anaerobic bacteria. In this work, we examined the production and turnover of nanomolar concentrations of LMM thiols with a chemical structure related to cysteine by the model iron-reducing bacterium Geobacter sulfurreducens. Our results show that G. sulfurreducens tightly controls the production, excretion and intracellular concentration of thiols depending on cellular growth state and external conditions. The production and cellular export of endogenous cysteine was coupled to the extracellular supply of Fe(II), suggesting that cysteine excretion may play a role in cellular trafficking to iron proteins. Addition of excess exogenous cysteine resulted in a rapid and extensive conversion of cysteine to penicillamine by the cells. Experiments with added isotopically labeled cysteine confirmed that penicillamine was formed by a dimethylation of the C-3 atom of cysteine and not via indirect metabolic responses to cysteine exposure. This is the first report of de novo metabolic synthesis of this compound. Penicillamine formation increased with external exposure to cysteine but the compound did not accumulate intracellularly, which may suggest that it is part of G. sulfurreducens’ metabolic strategy to maintain cysteine homeostasis. Our findings highlight and expand on processes mediating homeostasis of cysteine-like LMM thiols in strict anaerobic bacteria. The formation of penicillamine is particularly noteworthy and this compound warrants more attention in microbial metabolism studies.
The microbial communities and natural fermentation quality of ensiling oat (Avena sativa L.) harvest from different elevations on the Qinghai-Tibet Plateau
Authors: Bao Yuhong , Yangzong Zhaxi , Yuan Zhenjie , Shi Ruizhi , Feng Ke , Xin Pengcheng , Song Tianzeng
Published: January 2023

Introduction

Ensiling whole-crop oat (Avena sativa L.) has attracted a growing interest in the Qinghai-Tibet Plateau. The study aimed to investigate the microbial community and chemical composition of fresh and ensiling oat harvested from six different elevations of the Qinghai-Tibet Plateau.

Method

The oat (A. sativa L. cv. Qingyin No. 1) was planted in six different sites across Qinghai-Tibet Plateau (BM, Bomi County; BY, Bayi County; DZ, Dazi County; BR, Biru County; SC, Suo County; SN, Seni County), where the elevations were in the range of 2,800–4,500 m above sea level (a. s. l.). Oat was harvested at the milk stage and ensiled for 90 days.

Results

The highest crude protein (CP) and lowest water-soluble carbohydrate (WSC) were observed in fresh oat of SN and BM, respectively, however, no distinct gradient trend in WSC and CP concentrations along the elevation gradient. The lowest LAB counts in fresh oat from the highest elevational regions of SN. After 90 days of ensiling, the pH in all oat silages was lower than 4.2, and silages from SC and SN showed a lower pH and butyric acid concentration, and higher lactic acid (LA) concentration than silages of other regions. The oat silage from BR showed the lowest LA concentration and the highest pH. The bimodal distributions of fungal and bacterial richness in fresh oat along the elevation gradient were observed, while the elevation gradients did not affect the fungal Shannon index in fresh oat. Dioszegia, Cladosporium, and Vishniacozyma were the prevalent fungal genus in fresh oat, while Wickerhamomyces, Candida, and Saccharomyces dominated the fungal communities of silages. Wickerhamomyces and Candida were the dominant genera in oat silages from BM and SC, respectively. Erwinia, Paenibacillus, Pseudomonas, Leuconostoc, and Exiguobacterium dominated the bacterial community of fresh oat, while Lactobacillus and Kosakonia were the dominant bacterial genus in oat silages. Pantoea was the most dominant bacterial genus in fresh oat from low-elevational regions (BM, BY, and DZ). Oat from SN exhibited the best fermentation quality although fresh oat of SN hosted the lowest LAB counts, indicating that high-efficient LAB might be present in fresh oat sampled from high altitudes.
Toward a causal model of chronic back pain: Challenges and opportunities
Authors: Huie J. Russell , Vashisht Rohit , Galivanche Anoop , Hadjadj Constance , Morshed Saam , Butte Atul J. , Ferguson Adam R. , O'Neill Conor
Published: January 2023

Chronic low back pain (cLBP) afflicts 8. 2% of adults in the United States, and is the leading global cause of disability. Neuropsychiatric co-morbidities including anxiety, depression, and substance abuse- are common in cLBP patients. In particular, cLBP is a risk factor for opioid addiction, as more than 50% of opioid prescriptions in the United States are for cLBP. Misuse of these prescriptions is a common precursor to addiction. While associations between cLBP and neuropsychiatric disorders are well established, causal relationships for the most part are unknown. Developing effective treatments for cLBP, and associated co-morbidities, requires identifying and understanding causal relationships. Rigorous methods for causal inference, a process for quantifying causal effects from observational data, have been developed over the past 30 years. In this review we first discuss the conceptual model of cLBP that current treatments are based on, and how gaps in causal knowledge contribute to poor clinical outcomes. We then present cLBP as a “Big Data” problem and identify how advanced analytic techniques may close knowledge gaps and improve clinical outcomes. We will focus on causal discovery, which is a data-driven method that uses artificial intelligence (AI) and high dimensional datasets to identify causal structures, discussing both constraint-based (PC and Fast Causal Inference) and score-based (Fast Greedy Equivalent Search) algorithms.
Energy efficiency and coding of neural network
Authors: Li Shengnan , Yan Chuankui , Liu Ying
Published: January 2023

Based on the Hodgkin-Huxley model, this study explored the energy efficiency of BA network, ER network, WS network, and Caenorhabditis elegans neural network, and explained the development of neural network structure in the brain from the perspective of energy efficiency using energy coding theory. The numerical simulation results showed that the BA network had higher energy efficiency, which was closer to that of the C. elegans neural network, indicating that the neural network in the brain had scale-free property because of satisfying high energy efficiency. In addition, the relationship between the energy consumption of neural networks and synchronization was established by applying energy coding. The stronger the neural network synchronization was, the less energy the network consumed.
Characterization of lipid droplet metabolism patterns identified prognosis and tumor microenvironment infiltration in gastric cancer
Authors: Liu Mengxiao , Fang Xidong , Wang Haoying , Ji Rui , Guo Qinghong , Chen Zhaofeng , Ren Qian , Wang Yuping , Zhou Yongning
Published: January 2023

Background

Gastric cancer is one of the common malignant tumors of the digestive system worldwide, posing a serious threat to human health. A growing number of studies have demonstrated the important role that lipid droplets play in promoting cancer progression. However, few studies have systematically evaluated the role of lipid droplet metabolism-related genes (LDMRGs) in patients with gastric cancer.

Methods

We identified two distinct molecular subtypes in the TCGA-STAD cohort based on LDMRGs expression. We then constructed risk prediction scoring models in the TCGA-STAD cohort by lasso regression analysis and validated the model with the GSE15459 and GSE66229 cohorts. Moreover, we constructed a nomogram prediction model by cox regression analysis and evaluated the predictive efficacy of the model by various methods in STAD. Finally, we identified the key gene in LDMRGs, ABCA1, and performed a systematic multi-omics analysis in gastric cancer.

Results

Two molecular subtypes were identified based on LDMRGs expression with different survival prognosis and immune infiltration levels. lasso regression models were effective in predicting overall survival (OS) of gastric cancer patients at 1, 3 and 5 years and were validated in the GEO database with consistent results. The nomogram prediction model incorporated additional clinical factors and prognostic molecules to improve the prognostic predictive value of the current TNM staging system. ABCA1 was identified as a key gene in LDMRGs and multi-omics analysis showed a strong correlation between ABCA1 and the prognosis and immune status of patients with gastric cancer.

Conclusion

This study reveals the characteristics and possible underlying mechanisms of LDMRGs in gastric cancer, contributing to the identification of new prognostic biomarkers and providing a basis for future research.
The evolving role of radiation in pancreatic cancer
Authors: Malla Midhun , Fekrmandi Fatemeh , Malik Nadia , Hatoum Hassan , George Sagila , Goldberg Richard M. , Mukherjee Sarbajit
Published: January 2023

Pancreatic cancer is the fourth leading cause of cancer mortality in the United States. Chemotherapy in resectable pancreatic cancer has improved survival by 10-20%. It only converted 10-30% of the borderline resectable and locally advanced pancreatic cancers to be surgically resectable. Radiation therapy has a documented role in managing localized pancreatic cancer, more so for borderline and locally advanced pancreatic cancer, where it can potentially improve the resectability rate of a given neoadjuvant treatment. The role of radiation therapy in resected pancreatic cancer is controversial, but it is used routinely to treat positive margins after pancreatic cancer surgery. Radiation therapy paradigms continue to evolve with advancements in treatment modalities, delivery techniques, and combination approaches. Despite the advances, there continues to be a controversy on the role of radiation therapy in managing this disease. In this review article, we discuss the recent updates, delivery techniques, and motion management in radiation therapy and dissect the applicability of this therapy in pancreatic cancer.
Disproportionality analysis of quinolone safety in children using data from the FDA adverse event reporting system (FAERS)
Authors: Kong Wenqiang , Mao Wei , Zhang Lin , Wu Yanyan
Published: January 2023

Background

Quinolones are widely prescribed for the treatment or prevention of infectious diseases in children. To gain further insight into quinolone-associated adverse event (AE) in children and better protect pediatric patients, continued surveillance of safety data is essential. The purpose of this study was to characterize the safety profiles of quinolone-associated AEs in children by mining the FDA adverse event reporting system (FAERS).

Methods

FAERS reports from quarter 1 of 2004 to quarter 1 of 2022 were included in the study. The Medical Dictionary for Regulatory Activities (MedDRA) was used to identify adverse events. Reporting odds ratios (ROR) corresponding 95% confidence intervals (CIs) and information component (IC) along with 95% CIs were calculated to detect drug–AE pairs with higher-than-expected reporting rates within the FAERS from System Organ Classes (SOCs) to Preferred Terms (PTs). Reports were considered as signals if the 95% conﬁdence interval did not contain the null value.

Results

After inclusion criteria were applied, a total of 4,704 reports associated with quinolones were considered. Most FAERS reports associated with ciprofloxacin (N = 2,706) followed by levofloxacin (N = 1,191), moxifloxacin (N = 375), oflaxacin (N = 245) and ozenoxacin (N = 187). The most common age group was 12–18 years. The median weight was 39.0 kilogram. The adverse effects of quinolones emerging for SOCs primarily included Infections and infestations, gastrointestinal symptoms, blood and lymphatic system disorders, cardiac disorders, nervous system disorders, musculoskeletal and connective tissue disorders and psychiatric disorders. The most frequently AE signals at the PT level were pyrexia (N = 236), febrile neutropenia (N = 120), off label use (N = 48), drug resistance (N = 18) and cardiac arrest (N = 22) following the use of ciprofloxacin, levofloxacin, moxifloxacin, ofloxacin, and ozenoxacin, respectively. Serious oznoxacin-associated AE signals were found and have not been documented in the package insert. They included cardiac arrest (N = 22; ROR = 19.83; IC = 3.68), overdose (N = 21; ROR = 4.98; IC = 2.07), seizure (N = 16; ROR = 6.01; IC = 2.29), small for dates baby (N = 9; ROR = 14.7; IC = 3.05), completed suicide (N = 15, ROR = 18.87; IC = 3.51), asthma (N = 9; ROR = 6.69; IC = 2.24;) and hypotension (N = 9; ROR = 3.83; IC = 1.68).

Conclusion

This study provided additional evidence with respect to quinolones-related AEs for children. Generally, the findings of this study are compatible with AEs recorded in package inserts. The unexpected signals of ozenoxacin justify active vigilance by clinicians and timely monitoring by pharmacovigilance experts.
Bayesian optimisation for breeding schemes
Authors: Diot Julien , Iwata Hiroyoshi
Published: January 2023

Introduction

Advances in genotyping technologies have provided breeders with access to the genotypic values of several thousand genetic markers in their breeding materials. Combined with phenotypic data, this information facilitates genomic selection. Although genomic selection can benefit breeders, it does not guarantee efficient genetic improvement. Indeed, multiple components of breeding schemes may affect the efficiency of genetic improvement and controlling all components may not be possible. In this study, we propose a new application of Bayesian optimisation for optimizing breeding schemes under specific constraints using computer simulation.

Methods

Breeding schemes are simulated according to nine different parameters. Five of those parameters are considered constraints, and 4 can be optimised. Two optimisation methods are used to optimise those parameters, Bayesian optimisation and random optimisation.

Results

The results show that Bayesian optimisation indeed finds breeding scheme parametrisations that provide good breeding improvement with regard to the entire parameter space and outperforms random optimisation. Moreover, the results also show that the optimised parameter distributions differ according to breeder constraints.

Discussion

This study is one of the first to apply Bayesian optimisation to the design of breeding schemes while considering constraints. The presented approach has some limitations and should be considered as a first proof of concept that demonstrates the potential of Bayesian optimisation when applied to breeding schemes. Determining a general "rule of thumb" for breeding optimisation may be difficult and considering the specific constraints of each breeding campaign is important for finding an optimal breeding scheme.
Identification of major QTLs for soybean seed size and seed weight traits using a RIL population in different environments
Authors: Luo Shilin , Jia Jia , Liu Riqian , Wei Ruqian , Guo Zhibin , Cai Zhandong , Chen Bo , Liang Fuwei , Xia Qiuju , Nian Hai , Cheng Yanbo
Published: January 2023

Introduction

The seed weight of soybean [Glycine max (L.) Merr.] is one of the major traits that determine soybean yield and is closely related to seed size. However, the genetic basis of the synergistic regulation of traits related to soybean yield is unclear.

Methods

To understand the molecular genetic basis for the formation of soybean yield traits, the present study focused on QTLs mapping for seed size and weight traits in different environments and target genes mining.

Results

A total of 85 QTLs associated with seed size and weight traits were identified using a recombinant inbred line (RIL) population developed from Guizao1×B13 (GB13). We also detected 18 environmentally stable QTLs. Of these, qSL-3-1 was a novel QTL with a stable main effect associated with seed length. It was detected in all environments, three of which explained more than 10% of phenotypic variance (PV), with a maximum of 15.91%. In addition, qSW-20-3 was a novel QTL with a stable main effect associated with seed width, which was identified in four environments. And the amount of phenotypic variance explained (PVE) varied from 9.22 to 21.93%. Five QTL clusters associated with both seed size and seed weight were summarized by QTL cluster identification. Fifteen candidate genes that may be involved in regulating soybean seed size and weight were also screened based on gene function annotation and GO enrichment analysis.

Discussion

The results provide a biologically basic reference for understanding the formation of soybean seed size and weight traits.
Factors predicting secondary school language course enrollment and performance among U.S. heritage speakers of Spanish
Authors: Nguyen My V. H. , Serafini Ellen J. , Leeman Jennifer , Winsler Adam
Published: January 2023

Introduction

While a growing body of research indicates that Spanish language courses can promote Spanish maintenance and lead to overall improved educational outcomes among heritage speakers, there is little empirical or longitudinal evidence of factors that shape their enrollment in Spanish language courses at the secondary level. To address this issue, the current study takes a large-scale, longitudinal approach to investigate rates of enrollment in secondary school (6th–12th grade) Spanish and other non-English language courses, as well as factors that predict heritage speakers’ enrollment and performance in non-English language courses.

Method

We analyzed subsample data from the Miami School Readiness Project (MSRP), a large-scale, longitudinal study consisting of 17,341 heritage speakers of Spanish (47% female, 95.4% Hispanic/Latino, 82.8% received free/reduced-price lunch, and 18.3% with a disability) who were followed from 4 years old until the end of high school.

Results

In general, Heritage speakers enrolled in Spanish language courses at a higher rate than other non-English language courses (52.2 and 25.3%, respectively). Enrollment patterns varied across different type of languages and grade level. Student-level factors including disability status, poverty status, early behavioral problems, and prior academic achievement significantly predicted students’ enrollment in Spanish and performance in non-English language courses.

Discussion

Findings shed light on the long-term patterns of language study of this growing segment of the US school population with implications for future research and school policies that seek to improve heritage language learning and maintenance as well as equitable access to language education for language-minority students.