bluuebunny/crossref_metadata_2025_split huggingface dataset:
A New Broad-Spectrum Drug Screen for 127 Analytes by LC-MS/MS
Authors: Smith Kathryn , Johnson-Davis Kamisha L , Shahrokh Kiumars 
Published: January 2023

Abstract

Background
Broad-spectrum drug screening is offered by many clinical laboratories to support investigation of possible drug exposures. The traditional broad-spectrum drug screen employed at our laboratory utilizes several different analytical platforms, thus requiring relatively high volumes of sample and a cumbersome workflow. Here we describe the development and validation of a consolidated broad-spectrum drug screen assay designed to qualitatively detect 127 compounds in urine (Ur) and serum/plasma (S/P) samples.

Methods
An LC-MS/MS method was developed using the Ultivo LC-MS/MS and designed to be qualitative with a 1-point calibration curve and 50% to 150% controls. Sample preparation included the addition of 122 internal standards (IS) followed by mixed-mode strong cation exchange solid-phase extraction and reverse-phase chromatographic separation on a biphenyl column.

Results
For the method described herein, ≥ 95% of analytes in urine and serum control samples had a CV of ≤20% for total imprecision. Accuracy testing included 46 external controls and demonstrated 99.9% accuracy. Method comparison studies to quantitative testing are discussed. The high level of coverage of the analytes with a stable isotope-labeled IS (SIL-IS) helped normalize for matrix effects when significant ion suppression (&gt;25%) was present. Analyte stability in the matrix, the impact of potentially interfering compounds, and method ruggedness were demonstrated. Method limitations include limited detection of glucuronidated drugs and potential cross-contamination with samples at very high concentrations (&gt;&gt;100 × cutoff).

Conclusions
The broad-spectrum drug screen method developed here qualitatively detected 127 drugs and select metabolites. This method could be used to support investigations of possible drug exposures in a clinical setting.
Application of the three-component transient electromagnetic method in gold exploration: a case study of the Heicigou gold deposit in east Kunlun
Authors: Wang Xingchun , Zhi Qingquan , Deng Xiaohong , Wu Junjie , Zhang Jie , Yu Zhonghong , Yang Yi 
Published: January 2023

Abstract
Heicigou gold mine is a gold polymetallic mine controlled by a northwest trending fault. The magnetic method and induced polarization results show that the gold-bearing alteration zone is distributed discontinuously in a northwest direction, but the spatial distribution characteristics of the alteration zone have not been effectively identified. Although some drilling work has been carried out in the latter, the number and the depths of the drillings have been insufficient to control the distribution of the alteration zone. According to the measured three-component transient electromagnetic anomaly characteristics, we designed corresponding models and carried out three-component forward simulation on the platform of EMIT Maxwell. We summarized the corresponding relationship between the three-component plane change characteristics and the orientation and occurrence of the low-resistivity medium subsurface. We applied this method to the Heicigou gold deposit and found that the occurrence of the ore-bearing alteration zone is northeast. This discovery solved the problem that the previous magnetic method and induced polarization method failed to solve. It corrected the geologists’ incorrect understanding of the spatial distribution of the alteration zone.
Petrophysical characteristics and identification parameters of the Jurassic continental shale oil reservoirs in the Central Sichuan Basin
Authors: Song Yichen , Zeng Lianbo , Gong Fei , Huang Ping , Lyu Wenya , Dong Shaoqun 
Published: January 2023

Abstract
The Sichuan Basin in south-western China is rich in shale oil in the Jurassic strata. Due to its complex geological characteristics, reservoir identification using current log-constrained seismic inversion methods is difficult. Characteristics of the shale oil reservoirs were tested on the basis of the petrophysical experimentation of core samples from the said strata. Thin sections and logging data analysis showed the influencing factors on petrophysical characteristics and clarified the sensitive geophysical parameters for reservoir identification. The Da'anzhai Member reservoirs were determined to have high acoustic velocities, Vp/Vs ratios and Young's moduli, and low Poisson's ratios. Several geological factors have influenced the petrophysical properties of the reservoirs. The Da'anzhai Member reservoirs are characterized by a low content of clay minerals and the development of fractures and laminae. The presence of clay minerals caused general high acoustic velocities of the reservoirs; the presence of fractures and laminae in high-quality reservoirs results in a decrease of the acoustic velocities. Therefore, the relatively low value against the background of high acoustic velocity can be used as the criteria for high-quality reservoirs. Poisson's ratio is obviously different in reservoirs and non-reservoirs. When it is &lt;0.269, the reservoirs can be fully identified. In addition, the combination of the Lame constant and shear modulus (λ &gt; 25.277 and μ &gt; 20.72 GPa), P-wave and S-wave velocity (Vp &gt; 4967 and Vs &gt; 2781 m s−1), wave impedance and Vp/Vs ratio (AI &gt; 13.319 g · cm3 · km · s−1 and Vp/Vs &gt; 1.792) can also provide references for reservoir identification.
A lithofacies prediction method based on stochastic simulation
Authors: Li Jingnan , Sun Zhentao , Liu Chanjuan , Zhu Tong , Cao Huilan , Li Feifei 
Published: January 2023

AbstractLithofacies prediction can facilitate the search for hydrocarbon reservoirs and is, therefore, crucial for seismic exploration. We proposed a new approach for lithofacies prediction based on stochastic simulation of pseudo-wells. First, we performed a pseudo-well simulation using a continuous-time Markov chain (CTMC), which can accurately describe geological deposition and can be created using logging, core or geological data. We used the CTMC to randomly generate many pseudo-wells with different lithofacies columns. The corresponding reservoir and elasticity parameters for these lithofacies columns were determined using the Monte Carlo random sampling method. Second, we used seismic modeling and seismic matching to predict the lithofacies. We applied the elastic parameters for each pseudo-well to calculate the reflection coefficients and performed seismic modeling to generate synthetic seismic data. Thereafter, we used a weighted matching function based on prior geological constraints to match the synthetic seismic data with actual seismic data. We predicted the lithofacies based on numerous pseudo-wells with the best fit and tested the influencing factors of the method using model data. Finally, we applied this method to the field data, and the predicted lithofacies agreed well with the wells. Compared to conventional methods, the proposed method can use prior information in the log and the geology data, and detects thin layers better.
Exploring how cultural and structural elements relate to communal coping for separated Latina/o/x immigrant families
Authors: Mendez Murillo Roselia , Kam Jennifer A 
Published: January 2023

AbstractFamily immigration-related separation is incredibly stressful; however, Latina/o/x separated families might engage in communal coping to help mitigate those stressors. Utilizing the extended theoretical model of communal coping, we conducted semi-structured interviews with 20 family triads (i.e., separated parent, separated child, primary caregiver) who were experiencing or had recently experienced immigration-related family separation. We explored cultural and structural elements associated with communally or individually coping, and we considered why family members, all of whom experienced separation stress, might cope differently. Among the different types of family members, gender norms were related to communally coping, relying on extended family for support, and protective buffering. Physical distance, as well as limited technology access and literacy also hindered communal coping. When exploring within-family-triad experiences, three themes were apparent: (a) one-sided communal coping, (b) protective buffering at the cost of one’s own needs, and (c) communal coping impeded by relational strain. Our findings emphasize the importance of considering the multidimensional nature of a stressor (i.e., family separation) when determining whether people are communally coping; how cultural and structural elements relate to coping; and including multiple family members’ perspectives.
Postoperative transverse colon necrosis due to mesenteric injury during laparoscopic surgery for endometrial carcinoma
Authors: Kaji Kentaro , Tsubouchi Hirofumi , Mori Masahiko , Suzuki Shiro 
Published: January 2023

Abstract
Hemorrhage and organ injury have been frequently reported as complications associated with trocar puncture in laparoscopic surgery. This report presents a case of delayed intestinal necrosis due to mesenteric injury. A 76-year-old woman who had a history of distal gastrectomy and adrenal insufficiency was diagnosed with stage IA endometrial cancer. We performed laparoscopic total hysterectomy and bilateral salpingo-oophorectomy. The upper abdominal wall and mesentery were adhered, and bleeding from the mesentery was noted during the first trocar puncture of the umbilical region, resulting in ligation and hemostasis. Abdominal pain and fever developed on the third postoperative day, and contrast-enhanced computed tomography demonstrated transverse colon perforation. Emergency laparotomy showed necrosis in the proximal transverse colon and a defect in the marginal artery. Mesenteric injury can lead to delayed intestinal necrosis without intraoperative macroscopic findings. In laparoscopic cases where adhesion is expected, trocar placement should be carefully considered.
Traumatic spigelian hernia complicated by caecal perforation and retroperitoneal haematoma—an unusual concurrence in blunt trauma
Authors: Syed Faisal , Quah Gaik si , Di Re Angelina 
Published: January 2023

Abstract
Blunt abdominal injury can be a cause of significant morbidity and mortality in patients who have sustained trauma even at low velocity. We report on an unusual case of a 50-year-old male who developed a traumatic spigelian hernia and caecal perforation after falling off a pushbike and impacting on the handlebar. We have also discussed some of the considerations taken in the assessment and surgical management of this case.
Mutation ofDEFECTIVE EMBRYO SAC1results in a low seed-setting rate in rice by regulating embryo sac development
Authors: Hu Xia , Yu Ping , Zhang Yingxin , Gao Zhiqiang , Sun Bin , Wu Weixun , Deng Chenwei , Abbas Adil , Hong Yongbo , Sun Lianping , Liu Qunen , Xue Pao , Wang Beifang , Zhan Xiaodeng , Cao Liyong , Cheng Shihua 
Published: January 2023

AbstractThe seed-setting rate has a significant effect on grain yield in rice (Oryza sativa L.). Embryo sac development is essential for seed setting; however, the molecular mechanism underlying this process remains unclear. Here, we isolated defective embryo sac1 (des1), a rice mutant with a low seed-setting rate. Cytological examination showed degenerated embryo sacs and reduced fertilization capacity in des1. Map-based cloning revealed a nonsense mutation in OsDES1, a gene that encodes a putative nuclear envelope membrane protein (NEMP)-domain-containing protein that is preferentially expressed in pistils. The OsDES1 mutation disrupts the normal formation of functional megaspores, which ultimately results in a degenerated embryo sac in des1. Reciprocal crosses showed that fertilization is abnormal and that the female reproductive organ is defective in des1. OsDES1 interacts with LONELY GUY (LOG), a cytokinin-activating enzyme that acts in the final step of cytokinin synthesis; mutation of LOG led to defective female reproductive organ development. These results demonstrate that OsDES1 functions in determining the rice seed-setting rate by regulating embryo sac development and fertilization. Our study sheds light on the function of NEMP-type proteins in rice reproductive development.
Degradation of glutathione and glutathione conjugates in plants
Authors: Ito Takehiro , Ohkama-Ohtsu Naoko 
Published: January 2023

Abstract
Glutathione (GSH) is a ubiquitous, abundant, and indispensable thiol for plants that participates in various biological processes, such as scavenging reactive oxygen species, redox signaling, storage and transport of sulfur, detoxification of harmful substances, and metabolism of several compounds. Therefore knowledge of GSH metabolism is essential for plant science. Nevertheless, GSH degradation has been insufficiently elucidated, and this has hampered our understanding of plant life. Over the last five decades, the γ-glutamyl cycle has been dominant in GSH studies, and the exoenzyme γ-glutamyl transpeptidase has been regarded as the major GSH degradation enzyme. However, recent studies have shown that GSH is degraded in cells by cytosolic enzymes such as γ-glutamyl cyclotransferase or γ-glutamyl peptidase. Meanwhile, a portion of GSH is degraded after conjugation with other molecules, which has also been found to be carried out by vacuolar γ-glutamyl transpeptidase, γ-glutamyl peptidase, or phytochelatin synthase. These findings highlight the need to re-assess previous assumptions concerning the γ-glutamyl cycle, and a novel overview of the plant GSH degradation pathway is essential. This review aims to build a foundation for future studies by summarizing current understanding of GSH/glutathione conjugate degradation.
The transcription factor AtMYB12 is part of a feedback loop regulating cell division orientation in the root meristem vasculature
Authors: Wybouw Brecht , Arents Helena E , Yang Baojun , Nolf Jonah , Smet Wouter , Vandorpe Michael , Minne Max , Luo Xiaopeng , De Clercq Inge , Van Damme Daniël , Glanc Matouš , De Rybel Bert 
Published: January 2023

AbstractTranscriptional networks are crucial to integrate various internal and external signals into optimal responses during plant growth and development. In Arabidopsis thaliana, primary root vasculature patterning and proliferation are controlled by a network centred around the basic Helix-Loop-Helix transcription factor complex, formed by TARGET OF MONOPTEROS 5 (TMO5) and LONESOME HIGHWAY (LHW), which control cell proliferation and division orientation by modulating the cytokinin response and other downstream factors. Despite recent progress, many aspects of the TMO5/LHW pathway are not fully understood. In particular, the upstream regulators of TMO5/LHW activity remain unknown. Here, using a forward genetics approach to identify new factors of the TMO5/LHW pathway, we discovered a novel function of the MYB-type transcription factor, MYB12. MYB12 physically interacts with TMO5 and dampens the TMO5/LHW-mediated induction of direct target gene expression, as well as the periclinal/radial cell divisions. The expression of MYB12 is activated by the cytokinin response, downstream of TMO5/LHW, resulting in a novel MYB12-mediated negative feedback loop that restricts TMO5/LHW activity, to ensure optimal cell proliferation rates during root vascular development.
Shoot-root interaction in control of camalexin exudation in Arabidopsis
Authors: Koprivova Anna , Schwier Melina , Volz Vanessa , Kopriva Stanislav 
Published: January 2023

Abstract
Plants exude secondary metabolites from the roots to shape the composition and function of their microbiome. Many of these compounds are known for their anti-microbial activities and play a role in plant immunity, such as the indole-derived phytoalexin camalexin. Here we studied the dynamics of camalexin synthesis and exudation upon interaction of Arabidopsis thaliana with the plant growth promoting bacteria Pseudomonas sp. CH267 or the bacterial pathogen Burkholderia glumae PG1. We show that while camalexin accumulation and exudation is more rapidly but transiently induced upon interaction with the growth promoting bacteria, the pathogen induces higher and more stable camalexin levels. By combination of experiments with cut shoots and roots, and grafting of wild-type plants with mutants in camalexin synthesis, we showed that while camalexin can be produced and released by both organs, in intact plants exuded camalexin originates in the shoots. We also reveal that the root specific CYP71A27 protein specifically affects the outcome of the interaction with the plant growth promoting bacteria and that its transcript levels are controlled by a shoot derived signal. In conclusion, camalexin synthesis seems to be controlled on a whole plant level and is coordinated between the shoots and the roots.
Exploring the antimicrobial effects of a phenolic-rich extract from jabuticaba depulping waste against enterotoxigenic Escherichia coli
Authors: Lima Maiara da Costa , Magnani Marciane , Lima Marcos dos Santos , Macarisin Dumitru , de Sousa Cristina Paiva , Dubreuil J Daniel , de Souza Evandro Leite 
Published: January 2023

Abstract
This study evaluated the effects of a phenolic-rich extract from jabuticaba [Myrciaria jaboticaba (Vell.) Berg] depulping waste (PEJ) on the survival, antibiotic susceptibility, virulence, and cellular functions of various enterotoxigenic Escherichia coli (ETEC) strains.
The minimum inhibitory concentration of PEJ against the five tested ETEC strains was 125 mg mL−1. PEJ at 125 and 250 mg mL−1 caused reductions in viable cell counts of ≥ 3 and ≥ 5 log CFU mL−1 in ETEC over 24 h, respectively. PEJ at subinhibitory concentrations (31.25 and 62.5 mg mL−1) reduced the viable cell counts of ETEC when exposed to in vitro gastrointestinal conditions, besides decreasing the biofilm formation, cell surface hydrophobicity, mucin adhesion, and swimming and swarming motility. PEJ (31.25 and 62.5 mg mL−1) increased the susceptibility of the tested ETEC strains to various clinically relevant antibiotics. The exposure to PEJ (62.5 and 125 mg mL−1) impaired the membrane permeability and enzymatic and efflux pump activities in ETEC cells. PEJ effectively reduces survival, increases antibiotic susceptibility, and attenuates virulence in ETEC. These effects could be linked to a PEJ multi-target action disturbing various cellular functions in ETEC cells. PEJ could be a candidate for developing innovative solutions to prevent and treat ETEC infections.
Towards 21-cm intensity mapping at z = 2.28 with uGMRT using the tapered gridded estimator – II. Cross-polarization power spectrum
Authors: Elahi Kh Md Asif , Bharadwaj Somnath , Ghosh Abhik , Pal Srijita , Ali Sk Saiyad , Choudhuri Samir , Chakraborty Arnab , Datta Abhirup , Roy Nirupam , Choudhury Madhurima , Dutta Prasun 
Published: January 2023

ABSTRACT
Neutral hydrogen (H i) 21-cm intensity mapping (IM) offers an efficient technique for mapping the large-scale structures in the Universe. We introduce the ‘Cross’ Tapered Gridded Estimator (Cross TGE), which cross-correlates two cross-polarizations (RR and LL) to estimate the multifrequency angular power spectrum Cℓ(Δν). We expect this to mitigate several effects like noise bias, calibration errors, etc., which affect the ‘Total’ TGE that combines the two polarizations. Here, we apply the Cross TGE on $24.4 \text{-} \rm {MHz}$-bandwidth uGMRT (upgraded Giant Metrewave Radio Telescope) Band 3 data centred at $432.8 \, \rm {MHz}$ aiming H i IM at z = 2.28. The measured Cℓ(Δν) is modelled to yield maximum likelihood estimates of the foregrounds and the spherical power spectrum P(k) in several k bins. Considering the mean squared brightness temperature fluctuations, we report a 2σ upper limit $\Delta _{\mathrm{ UL}}^{2}(k) \le (58.67)^{2} \, {\rm mK}^{2}$ at $k=0.804 \, {\rm Mpc}^{-1}$, which is a factor of 5.2 improvement on our previous estimate based on the Total TGE. Assuming that the H i traces the underlying matter distribution, we have modelled Cℓ(Δν) to simultaneously estimate the foregrounds and $[\Omega _{\rm{ H}\, {\small {I}}} b_{\rm{ H}\, {\small {I}}}]$, where $\Omega _{\rm{ H}\, {\small {I}}}$ and $b_{\rm{ H}\, {\small {I}}}$ are the H i density and linear bias parameters, respectively. We obtain a best-fitting value of $[\Omega _{\rm{ H}\, {\small {I}}}b_{\rm{ H}\, {\small {I}}}]^2 = 7.51\times 10^{-4} \pm 1.47\times 10^{-3}$ that is consistent with noise. Although the 2σ upper limit $[\Omega _{\rm{ H}\, {\small {I}}}b_{\rm{ H}\, {\small {I}}}]_{\mathrm{ UL}} \le 0.061$ is ∼50 times larger than the expected value, this is a considerable improvement over earlier works at this redshift.
BD +30°549: a young helium-weak silicon star in the NGC 1333 star-forming region
Authors: Potravnov I , Mashonkina L , Ryabchikova T 
Published: January 2023

ABSTRACT
We present results of the spectroscopic study of the chemically peculiar star BD +30°549, which is a bona fide member of the young NGC 1333 star-forming region. We found that the star possesses negligible rotation and a helium-weak spectroscopic pattern with strongly enhanced Si ii and Si iii lines. The fundamental parameters of the star, Teff = 13 100 K and log (L/L⊙) = 2.1, indicate that its age is about 2.7 Myr and that its position on the Hertzsprung–Russell diagram is at the end of the pre-main-sequence evolutionary track, close to the zero-age main sequence. Abundance analysis reveals the modest deficit of almost all elements, with the exception of Si , Fe , Ca  and P,  which are overabundant. We performed non-local thermodynamic equilibrium (non-LTE) calculations for Si ii/Si iii, Mg ii and Ca ii in order to check the influence of departures from LTE on line formation. Non-LTE calculations lead to much better reproduction of individual silicon line profiles, but do not completely remove the abundance discrepancy between Si ii and Si iii lines. We also investigate the effects of possible chemical stratification in BD +30°549. We suspect that the ‘Si ii/Si iii anomaly’ observed in the BD +30°549 spectrum arises under the combined action of the vertical and horizontal abundance gradients and non-LTE effects. We suppose that the evolutionary status and phenomena observed in BD +30°549 indicate that conditions favourable for the selective diffusion and formation of the surface chemical composition peculiarities (slow rotation and stabilization of the atmosphere) could already be built up at the pre-main-sequence phase.