bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implementation and Evaluation of Irrigation Techniques in the Community Land Model
Authors: Yao Yi , Vanderkelen Inne , Lombardozzi Danica , Swenson Sean , Lawrence David , Jägermeyr Jonas , Grant Luke , Thiery Wim 
Published: November 2022

AbstractSeveral previous studies have highlighted the irrigation‐induced impacts on the global and regional water cycle, energy budget, and near‐surface climate. While land models are widely used to address this question, the implementations of irrigation in these models vary in complexity. Here, we expand the representation of irrigation in Community Land Model to enable six different irrigation methods. We find that using a combination of irrigation methods, including default, sprinkler, flood and paddy techniques performs best as determined by evaluating the simulated irrigation water withdrawals against observations, and therefore select this combination as the new irrigation scheme. Then, the impact of the new irrigation scheme on surface fluxes is evaluated and detected using single‐point simulations. Finally, the global and regional irrigation‐induced impacts on surface energy and water fluxes are compared using both the original and the new irrigation scheme. The new irrigation scheme substantially reduces the bias and root‐mean‐square error of simulated irrigation water withdrawal in the USA and other countries, but considerably overestimates withdrawals in Central China. Results of single‐point experiments show that different irrigation methods have different effects on surface fluxes, while the magnitudes are small. At the global scale, the new scheme enlarges the irrigation‐induced impacts on water and energy variables relative to the original scheme, with varying magnitudes across regions. Overall, our results suggest that this newly developed scheme is a better tool for simulating irrigation‐induced impacts on climate, and highlight the added value of incorporating human water management in Earth system models.
Data‐Worth Analysis for Heterogeneous Subsurface Structure Identification With a Stochastic Deep Learning Framework
Authors: Zhan Chuanjun , Dai Zhenxue , Soltanian Mohamad Reza , de Barros Felipe P. J. 
Published: November 2022

AbstractReliable characterization of subsurface structures is essential for earth sciences and related applications. Data assimilation‐based identification frameworks can reasonably estimate subsurface structures using available lithological (e.g., borehole core, well log) and dynamic (e.g., hydraulic head, solute concentration) observations. However, a reasonable selection of the observation type and frequency is essential for accurate structure identification. To achieve this, we extended a recently developed stage‐wise stochastic deep learning inversion framework by coupling it with non‐isothermal flow and transport simulations. With the extended framework, the worth of three common observations (hydraulic head, concentration, and temperature) are compared under different observation noise and frequency. The framework combines the emerging deep‐learning (DL)‐based framework with the traditional stochastic approaches. This combination makes it possible to simultaneously compare the ability of these two methods to assimilate observation data. Our results show that including at least one type of dynamic observation strongly improves subsurface structure identifiability and reduces the uncertainty. However, the DL‐based framework is able to identify subsurface structures more accurately than stochastic identification methods under the same scenarios. Assimilation of certain types of dynamic observations could reduce the prediction error for related dynamic responses, but not necessarily for other uncorrelated dynamic responses. Observation data worth is affected by the observation noise and frequency. High observation noise increases the uncertainty of the prediction and reduces the estimation accuracy. However, the higher observation frequency can significantly improve the temporal dynamic information of observations. This information can compensate for negative impacts of high observation noise.
A database of 5305 healthy Korean individuals reveals genetic and clinical implications for an East Asian population
Authors: Lee Jeongeun , Lee Jean , Jeon Sungwon , Lee Jeongha , Jang Insu , Yang Jin Ok , Park Soojin , Lee Byungwook , Choi Jinwook , Choi Byung-Ok , Gee Heon Yung , Oh Jaeseong , Jang In-Jin , Lee Sanghyuk , Baek Daehyun , Koh Youngil , Yoon Sung-Soo , Kim Young-Joon , Chae Jong-Hee , Park Woong-Yang , Bhak Jong Hwa , Choi Murim 
Published: November 2022

AbstractDespite substantial advances in disease genetics, studies to date have largely focused on individuals of European descent. This limits further discoveries of novel functional genetic variants in other ethnic groups. To alleviate the paucity of East Asian population genome resources, we established the Korean Variant Archive 2 (KOVA 2), which is composed of 1896 whole-genome sequences and 3409 whole-exome sequences from healthy individuals of Korean ethnicity. This is the largest genome database from the ethnic Korean population to date, surpassing the 1909 Korean individuals deposited in gnomAD. The variants in KOVA 2 displayed all the known genetic features of those from previous genome databases, and we compiled data from Korean-specific runs of homozygosity, positively selected intervals, and structural variants. In doing so, we found loci, such as the loci ofADH1A/1BandUHRF1BP1, that are strongly selected in the Korean population relative to other East Asian populations. Our analysis of allele ages revealed a correlation between variant functionality and evolutionary age. The data can be browsed and downloaded from a public website (https://www.kobic.re.kr/kova/). We anticipate that KOVA 2 will serve as a valuable resource for genetic studies involving East Asian populations.
Chemicals of concern in personal care products used by women of color in three communities of California
Authors: Johnson Paula I. , Favela Kristin , Jarin Jennifer , Le Amy M. , Clark Phyllis Y. , Fu Lisa , Gillis April D. , Morga Norma , Nguyen Caroline , Harley Kim G. 
Published: November 2022

Abstract
Background
Personal care products (PCPs) may contain chemicals associated with adverse health effects. Prior studies found differences in product use by race/ethnicity and suggest some women are disproportionately exposed to chemicals of concern (CoCs).

Objective
We quantified chemicals linked to cancer, reproductive or developmental harm, or endocrine disruption in PCPs used by women of color.

Methods
We documented PCPs in stores frequented by Black, Latina, and Vietnamese women in their communities in California and CoCs on ingredient labels of 546 unique hair, skin, makeup, nail, deodorant/perfume, and intimate care products. Community partners chose 31 products for a combined targeted and suspect screen (National Institute of Standards and Technology mass spectral library search) two-dimensional gas chromatography time-of-flight mass spectrometry (GCxGC-TOFMS) analysis to detect chemicals not on ingredient labels.

Results
We found that 65% of labels included CoCs, and 74% of labels had undisclosed ingredients listed as “fragrance.” The most prevalent chemicals were parabens, cyclosiloxanes, and formaldehyde releasers. GCxGC-TOFMS found additional CoCs, including fragrances, solvents, preservatives, ultraviolet filters, and contaminants.

Significance
These findings contribute to awareness of potentially hazardous chemicals in PCPs, can help estimate disparities in chemical exposure, and complement research on health inequities due to chemical exposures from various contributors.

Impact statement
This study is one of the first detailed assessments of chemicals of concern found in various types of PCPs used by several racial/ethnic groups. We found that over half of the 546 products selected by community partners as marketed to and/or used by them contained ingredients linked to cancer, reproductive or developmental harm, or endocrine disruption. Laboratory analysis identified additional chemicals in a subset of products, including unlabeled fragrance chemicals and contaminants. Elucidating exposures to chemicals in PCPs is important for risk assessment and health inequity research.
Cap-dependent translation initiation monitored in living cells
Authors: Gandin Valentina , English Brian P. , Freeman Melanie , Leroux Louis-Philippe , Preibisch Stephan , Walpita Deepika , Jaramillo Maritza , Singer Robert H. 
Published: November 2022

AbstractmRNA translation is tightly regulated to preserve cellular homeostasis. Despite extensive biochemical, genetic, and structural studies, a detailed understanding of mRNA translation regulation is lacking. Imaging methodologies able to resolve the binding dynamics of translation factors at single-cell and single-mRNA resolution were necessary to fully elucidate regulation of this paramount process. Here live-cell spectroscopy and single-particle tracking were combined to interrogate the binding dynamics of endogenous initiation factors to the 5’cap. The diffusion of initiation factors (IFs) changed markedly upon their association with mRNA. Quantifying their diffusion characteristics revealed the sequence of IFs assembly and disassembly in cell lines and the clustering of translation in neurons. This approach revealed translation regulation at high spatial and temporal resolution that can be applied to the formation of any endogenous complex that results in a measurable shift in diffusion.
Pathogenome comparison and global phylogeny of Escherichia coli ST1485 strains
Authors: Hammad Ahmed M. , Gonzalez-Escalona Narjol , El Tahan Amira , Abbas Nasser H. , Koenig Sara S.K. , Allué-Guardia Anna , Eppinger Mark , Hoffmann Maria 
Published: November 2022

AbstractEscherichia coli ST1485 strains belong to the clinically important phylogroup F and have disseminated worldwide in humans, animals, and the environment. Here, we elucidated the pathogenome of a global collection of E. coli ST1485 isolates from diverse sources retrieved from public databases and a high-quality sequenced complete genome of colistin-resistant E. coli strain CFSAN061771 isolated from raw milk cheese which designated as a reference strain. CFSAN061771 belongs to O83:H42-ST1485 pathotype and carries a conjugative ColV plasmid, pCFSAN061771_01, combining extraintestinal virulence genes (ompt, sitA, iroN, etsC, traT, cvaC, hylF, iss, tsh, mchf, iucC, iutA) with a multidrug resistance island (blaTEM-1, aph(6)-Id, aph(3″)-Ib, sul2, dfrA14). Comparative genomic analysis revealed a high frequency of pCFSAN061771_01-like plasmids in E. coli ST1485. A notable evolutionary genetic event in E. coli ST1485 strains is the acquisition of a pCFSAN061771_02-like plasmid, which confers resistance to several antimicrobials, tellurium, and quaternary ammonium compounds. The identical virulence and antibiotic resistance profiles identified in some human and animal strains are worrisome. This is the first study to emphasize the significance of E. coli ST1485 as a global high-risk virulent and multidrug-resistant clone with zoonotic potential.
Improving the filtration properties for manganese tetroxide mud utilizing perlite particles to drill wide-range permeability sandstone formation
Authors: Al Jaberi Jaber B. , Bageri Badr , Elkatatny Salaheldin 
Published: November 2022

AbstractA required feature of any drilling formulation is to mitigate the formation damage by having an excellent filtration and filter cake properties. The key factor for preventing and limiting formation damage is to improve the sealing qualities of the planned drilling fluid. In this study, a new novel filtration agent called “perlite” was introduced for improving the manganese tetroxide mud cake ability for better sealing features. The perlite particles were loaded to formulation containing the manganese tetroxide as weighting agent. The water-based drilling mud was designed at high densities (14.25 and 17.2 ppg). Perlite was added in varied concentrations to reach the optimum performance. The filtration test conducted at reservoir temperature of 250 °F and a differential pressure of 300 psi to form the filter cake. The tests were performed using sandstone cores with two different permeability categories (low and high permeabilities) as the filtration media. This gave the full picture of perlite performance as implemented for different formation properties and considering the drilling fluid properties. The formed filter cake structure and chemical composition was evaluated using scanning electron energy-dispersive X-ray (SEM–EDS). The presented results illustrated how the perlite was compatible to be added to the manganese tetroxide weighting agents in the same formulation. In addition, it has the capacity to improve the filter cake's sealing qualities, lowering the filtration volume by 41% and the filter cake internal and external layers permeability by 58% and 25%, respectively. Moreover, the EDS analysis showed that the perlite particles are concentrated generally in the internal layer of the filter cake.
Real world clinical feasibility of direct-from-specimen antimicrobial susceptibility testing of clinical specimens with unknown microbial load or susceptibility
Authors: Chen Jade , Navarro Eduardo , Mesich Brian , Gerstbrein Derek , Cruz Amorina , Faron Matthew L. , Gau Vincent 
Published: November 2022

AbstractWithin healthcare settings, physicians use antibiograms, which offer information on local susceptibility rates, as an aid in selecting empirical antibiotic therapy and avoiding the prescription of potentially ineffective drugs. While antibiograms display susceptibility and resistance data at hospital, city, or region-specific levels and ultimately enable the initiation of antibiogram-based empirical antibiotic treatment, AST reports at the individual patient level and guides treatments away from broad-spectrum antibiotics towards narrower-spectrum antibiotics or the removal of antibiotics entirely. Despite these advantages, AST traditionally requires a 48- to 72-h turn-around; this window of time can be critical for some antimicrobial therapeutic interventions. Herein, we present a direct-from-specimen AST to reduce the time between patient sampling and receipt of lab AST results. The biggest challenge of performing AST directly from unprocessed clinical specimens with an unknown microbial load is aligning the categorical susceptibility report with CLSI reference methods, which start from a fixed inoculum of 0.5 McFarland units prepared using colonies from a sub-culture. In this pilot clinical feasibility study using de-identified remnant specimens collected from MCW, we observed the high and low ends of microbial loads, demonstrating a final categorical agreement of 87.5% for ampicillin, 100% for ciprofloxacin, and 100% for sulfamethoxazole-trimethoprim.
Taxonomic response of bacterial and fungal populations to biofertilizers applied to soil or substrate in greenhouse-grown cucumber
Authors: Wu Jiajia , Shi Zhaoai , Zhu Jiahong , Cao Aocheng , Fang Wensheng , Yan Dongdong , Wang Qiuxia , Li Yuan 
Published: November 2022

AbstractReductions in the quality and yield of crops continuously produced in the same location for many years due to annual increases in soil-borne pathogens. Environmentally-friendly methods are needed to produce vegetables sustainably and cost effectively under protective cover. We investigated the impact of biofertilizers on cucumber growth and yield, and changes to populations of soil microorganisms in response to biofertilizer treatments applied to substrate or soil. We observed that some biofertilizers significantly increased cucumber growth and decreased soil-borne pathogens in soil and substrate. Rhizosphere microbial communities in soil and substrate responded differently to different biofertilizers, which also led to significant differences in microbial diversity and taxonomic structure at different times in the growing season. Biofertilizers increase the prospects of re-using substrate for continuously producing high-quality crops cost-effectively from the same soil each year while at the same time controlling soil-borne disease.
Design of amino acid- and carbohydrate-based anticancer drugs to inhibit polymerase η
Authors: Kalhor Sepideh , Fattahi Alireza 
Published: November 2022

AbstractDNA polymerase η (polη) is of significant value for designing new families of anticancer drugs. This protein takes a role in many stages of the cell cycle, including DNA replication, translesion DNA synthesis, and the repairing process of DNA. According to many studies, a high level of expression of polη in most cases has been associated with low rates of patients' survival, regardless of considering the stage of tumor cells. Thus, the design of new drugs with fewer side effects to inhibit polη in cancerous cells has attracted attention in recent years. This project aims to design and explore the alternative inhibitors for polη, which are based on carbohydrates and amino acids. In terms of physicochemical properties, they are similar to the traditional anticancer drugs such as Cytarabine (cytosine arabinose). These alternative inhibitors are supposed to disrupt the DNA replication process in cancerous cells and prevent the tumor cells from mitosis. These newly designed structures, which are based on natural products, are expected to be non-toxic and to have the same chemotherapeutic impact as the traditional agents. The combinatorial use of quantum mechanics studies and molecular dynamic simulation has enabled us to precisely predict the inhibition mechanism of the newly designed structure, which is based on carbohydrates and amino acids, and compare it with that of the traditional chemotherapeutic drugs such as Cytarabine. Our results suggest that the inhibitors containing the natural building blocks of amino acid and carbohydrate could be considered alternative drugs for Cytarabine to block polη.
A novel cuproptosis-related immune checkpoint gene signature identification and experimental validation in hepatocellular carcinoma
Authors: Xie Yusai , Zhang Wei , Sun Jia , Sun Lingyan , Meng Fanjie , Yu Huiying 
Published: November 2022

AbstractCopper-induced death, also termed cuproptosis, is a novel form of programmed cell death and is promising as a new strategy for cancer therapeutics. Elevated copper levels in tumor cells are positively associated with high PD-L1 expression. Nonetheless, the prognostic significance of cuproptosis-related immune checkpoint genes (CRICGs) in hepatocellular carcinoma remains to be further clarified. This study aimed to construct the prognostic CRICG signature to predict the immunotherapy response and outcomes of HCC patients. The co-expressed CRICGs were first screened through Pearson correlation analysis. Based on the least absolute shrinkage and selection operator-COX regression analyses, we identified a prognostic 5-CRICGs model, which closely correlates with poor outcomes, cancer development, and immune response to hepatocellular carcinoma. External validation was conducted using the GSE14520 dataset. Lastly, qRT-PCR was performed to determine the expression of the CRICGs in HCC. In summary, we developed and validated a novel prognostic CRICG model based on 5 CRICGs. This prognostic signature could effectively forecast the outcomes and immune response of HCC patients, which may serve as biomarkers for anticancer therapy.
A study on the relationship between odor hedonic ratings and individual odor detection threshold
Authors: Bontempi Charlotte , Jacquot Laurence , Brand Gérard 
Published: November 2022

AbstractOdor hedonic perception (pleasant/unpleasant character) is considered as the first and one of the most prominent dimensions in olfaction and is known to depend on several parameters. Among them, the relation between the odorant concentration and the hedonic estimation has been widely studied. However, few studies have considered odor hedonic ratings (OHR) in relation to individual detection thresholds (IDT). Thus, the aim of this study was to determine olfactory detection thresholds and to describe hedonic rating variations from individual thresholds to higher concentrations. IDT were performed for two pleasant (apple and jasmine) and two unpleasant (durian and trimethylamine) odorant stimuli. The experimenter presented one by one in a randomized order, the different odorant concentrations above IDT. Participants rated odor hedonic valence of these stimuli on a visual analog scale. Results showed, except for trimethylamine, the same relationship between hedonic ratings and stimulus concentration, i.e., an increase of pleasantness (apple and jasmine)/unpleasantness (durian) ratings at low and middle concentrations followed by a plateau at high concentrations. Correlations between OHR and concentrations as well as between OHR and threshold steps were always significant. Moreover, comparisons between both conditions showed that the correlation coefficient was significantly higher for trimethylamine (and a trend for apple) when IDTs were considered, while no difference was found for jasmine and durian. Overall, results suggested that the relationship between OHR and IDT is odor specific. These findings contribute to explain the large variability of the hedonic tone (i.e., weakly vs. very pleasant, weakly vs. very unpleasant) at specific concentration in the general population and could serve future research in this field (e.g., olfactory preferences in nutrition studies, anhedonia in psychiatric disorders…).
Multiplexed base editing through Cas12a variant-mediated cytosine and adenine base editors
Authors: Chen Fangbing , Lian Meng , Ma Bingxiu , Gou Shixue , Luo Xian , Yang Kaiming , Shi Hui , Xie Jingke , Ge Weika , Ouyang Zhen , Lai Chengdan , Li Nan , Zhang Quanjun , Jin Qin , Liang Yanhui , Chen Tao , Wang Jiaowei , Zhao Xiaozhu , Li Lei , Yu Manya , Ye Yinghua , Wang Kepin , Wu Han , Lai Liangxue 
Published: November 2022

AbstractCas12a can process multiple sgRNAs from a single transcript of CRISPR array, conferring advantages in multiplexed base editing when incorporated into base editor systems, which is extremely helpful given that phenotypes commonly involve multiple genes or single-nucleotide variants. However, multiplexed base editing through Cas12a-derived base editors has been barely reported, mainly due to the compromised efficiencies and restricted protospacer-adjacent motif (PAM) of TTTV for wild-type Cas12a. Here, we develop Cas12a-mediated cytosine base editor (CBE) and adenine base editor (ABE) systems with elevated efficiencies and expanded targeting scope, by combining highly active deaminases with Lachnospiraceae bacterium Cas12a (LbCas12a) variants. We confirm that these CBEs and ABEs can perform efficient C-to-T and A-to-G conversions, respectively, on targets with PAMs of NTTN, TYCN, and TRTN. Notably, multiplexed base editing can be conducted using the developed CBEs and ABEs in somatic cells and embryos. These Cas12a variant-mediated base editors will serve as versatile tools for multiplexed point mutation, which is notably important in genetic improvement, disease modeling, and gene therapy.