bluuebunny/crossref_metadata_2025 huggingface dataset:
An eco-friendly ultrasound-assisted deep eutectic solvent-based liquid–phase microextraction method for enrichment and quantification of nickel in environmental samples
Authors: Hameed Ahmed M.
Published: November 2022

An eco-friendly and easy ultrasound-assisted liquid phase microextraction approach using deep eutectic solvent (UA-DES-LPME) was established to preconcentrate and separate trace amount of nickel (Ni(II)) in various environmental samples before flame atomic absorption spectrometric estimation. In this method, Ni(II) was complexed with 2-(benzothiazolyl azo) orcinol reagent. The impacts various parameters on the microextarction of Ni(II) was investigated. The calibration graph is linear in the range of 1–500 µg L−1 and limits of detection and quantification were determined as 0.27 and 0.90 μg L−1, respectively. The RSD% and preconcentration factor were 2.30% and 100, respectively. The analysis of certified reference materials demonstrated the validity of the established procedure. The microextraction method provided here simple, rapid, cheap, green and was effectively used to determine nickel levels in a variety of environmental samples with recoveries ranged of 95.0–98.54%.
Z-Transform-Based Profile Matching to Develop a Learning-Free Keyword Spotting Method for Handwritten Document Images
Authors: Banerjee Debanshu , Bhowal Pratik , Malakar Samir , Cuevas Erik , Pérez‑Cisneros Marco , Sarkar Ram
Published: November 2022

For easy accessibility of the information from the digitized document images, optical character recognition (OCR)-based software can be used. But in the case of handwritten documents, the performance of the state-of-the-art OCR systems is not satisfactory owing to the complexity of the unconstrained handwriting. Hence, research affinity comes up with an alternative solution for this problem called keyword spotting (KWS) which is much more practical than an OCR-based solution. This work proposes a novel learning-free KWS method that can be applied to a heterogeneous collection of handwritten documents. In this work, we introduce a new way of profile matching to compare the query word profiles (i.e., both upper and lower) with the target words’ profiles. At first, both query and target words are binarized, and then two profiles from each such word are generated. Next, we formulate rules to filter out the irrelevant words concerning the query word and obtain the probable candidate query (i.e., target) words. Then we compare the profiles of the query and candidate query words in the Z-transform domain using the condition of resonance for the damped oscillator. However, before the match, we perform an affine transformation on the Bezier curve representation of the profiles of the candidate query words to reduce the effects like scaling, rotation, and shearing which might occur due to the variant writing styles of individuals. The proposed method achieves satisfactory performance compared to state-of-the-art learning-free methods when applied to four publicly available standard datasets namely ICFHR 2014 H-KWS competition Modern, IAM, ICFHR 2016 H-KWS competition Botany and ICFHR 2016 H-KWS competition Konzilsprotokolle datasets.
pulsar_spectra: A pulsar flux density catalogue and spectrum fitting repository
Authors: Swainston N. A. , Lee C. P. , McSweeney S. J. , Bhat N. D. R.
Published: November 2022

We present the
pulsar_spectra
software repository, an open-source pulsar flux density catalogue and automated spectral fitting software that finds the best spectral model and produces publication-quality plots. The python-based software includes features that enable users in the astronomical community to add newly published spectral measurements to the catalogue as they become available. The spectral fitting software is an implementation of the method described in Jankowski et al. (2018, MNRAS, 473, 4436) which uses robust statistical methods to decide on the best-fitting model for individual pulsar spectra.
pulsar_spectra
is motivated by the need for a centralised repository for pulsar flux density measurements to make published measurements more accessible to the astronomical community and provide a suite of tools for measuring spectra.
A RESPONSE TO COMMUNITY QUESTIONS ON THE MARINE20 RADIOCARBON AGE CALIBRATION CURVE: MARINE RESERVOIR AGES AND THE CALIBRATION OF 14C SAMPLES FROM THE OCEANS
Authors: Heaton T J , Bard E , Bronk Ramsey C , Butzin M , Hatté C , Hughen K A , Köhler P , Reimer P J
Published: November 2022

Radiocarbon (14C) concentrations in the oceans are different from those in the atmosphere. Understanding these ocean-atmospheric 14C differences is important both to estimate the calendar ages of samples which obtained their 14C in the marine environment, and to investigate the carbon cycle. The Marine20 radiocarbon age calibration curve is created to address these dual aims by providing a global-scale surface ocean record of radiocarbon from 55,000–0 cal yr BP that accounts for the smoothed response of the ocean to variations in atmospheric 14C production rates and factors out the effect of known changes in global-scale palaeoclimatic variables. The curve also serves as a baseline to study regional oceanic 14C variation. Marine20 offers substantial improvements over the previous Marine13 curve. In response to community questions, we provide a short intuitive guide, intended for the lay-reader, on the construction and use of the Marine20 calibration curve. We describe the choices behind the making of Marine20, as well as the similarities and differences compared with the earlier Marine calibration curves. We also describe how to use the Marine20 curve for calibration and how to estimate ΔR—the localized variation in the oceanic 14C levels due to regional factors which are not incorporated in the global-scale Marine20 curve. To aid understanding, illustrative worked examples are provided.
Description of Diegoglossidium maradonai n. g. and n. sp. (Digenea: Alloglossidiidae) through an integrative taxonomy approach, with an amended diagnosis of the family
Authors: Montes M.M. , Arredondo N.J. , Barneche J.A. , Balcazar D. , Reig Cardarella G. , Martorelli S.R. , Pérez-Ponce de León G.
Published: November 2022

This paper describes Diegloglossidium maradonai n. g., n. sp. a parasite of the intestine of Hoplosternum littorale (Hancock) from La Plata River basin. The new genus is morphologically similar to members of Alloglossidiidae and Macroderoidiidae although they also share some traits observed in both families. Those families can be differentiated from each other by the combination of morphological features, including the density and distribution of the tegumental spines, the distribution of the vitelline follicles and the extent of the post-testicular space. The molecular analyses based on the large subunit of the ribosomal RNA gene, and the internal transcribed spacer (ITS) regions including ITS1, 5.8S and ITS2 unequivocally place the new genus in the family Alloglossidiidae which is amended based on new observed features. Diegoglossidium n. g. is characterized by a combination of characteristics, being most notably the presence of a deeply lobed ovary. Lastly, the geographical distribution and host associations of the two closely related Neotropical genera of Alloglossidiidae: Magnivitellinum and Diegoglossidium are discussed, and the host and distribution range of Magnivitellinum saltaensis is expanded into Argentina.
Flying across Europe: the case of the spread of Chaunocephalus ferox on a black stork (Ciconia nigra)
Authors: Gonzálvez M. , Muñoz-Hernández C. , Gómez de Ramón A. , Buendía A. , Escribano F. , Martínez-Carrasco C.
Published: November 2022

The annual migration of birds involves a very large number of inter-continental and intra-continental movements in which thousands of bird species participate. These migrations have been associated with the spread of pathogens worldwide, including bacteria, viruses and parasites. This study describes the case of a black stork (Ciconia nigra) that was ringed at the nest in Latvia and died five months later in the south-east of the Iberian Peninsula. Post-mortem examination revealed that the cause of death was electrocution. In addition, a massive infection by the trematode Chaunocephalus ferox (Digenea: Echinostomatidae) causing severe granulomatous lesions throughout the small intestine was detected. This is the first report of C. ferox infection in a black stork in the Iberian Peninsula, a trematode that, due to the severe lesions it causes, can affect the health of C. ferox-infected wild birds, particularly in severely infected long-distance migrants. The dispersal of platyhelminths associated with migratory birds is discussed. After the ringing at the nest, the black stork was sighted in Central Europe one month before its capture, and the trematodes found by necropsy were mostly mature adults. Consequently, we estimate that this juvenile animal acquired the infection during its migration in a European area other than the Iberian Peninsula, evidencing a long-distance parasite spread through its migratory host. Our study highlights that bird ringing can be used to understand the epidemiological implications that bird migratory behaviour may have on the dispersal of parasites.
Experimental investigation of stereocamera's error to optimize dust observation on HL-2A tokamak
Authors: Ma Zhuang , Li Wei , Li Zhengyang , Huang Zhihui , Shen Jue , Huang Dong , Huang Yu , Liu Zhuang , Gu Liang , Lu Shaoyu , He Xiaoxue , Yan Longwen , Xu Min , Feng Yan
Published: November 2022

An experimental investigation of the stereocamera's systematic error is carried out to optimize three-dimensional (3-D) dust observation on the HL-2A tokamak. It is found that a larger 3-D region occupied by all calibration points is able to reduce the 3-D reconstruction systematic error of the stereocamera. In addition, the 3-D reconstruction is the most accurate around the region where the calibration points are located. Based on these experimental results, the design of the stereocamera on the HL-2A tokamak is presented, and a set of practical procedures to optimize the 3-D reconstruction accuracy of the stereocamera are proposed.
Early life nutrition and brain development: breakthroughs, challenges and new horizons
Authors: Georgieff Michael K.
Published: November 2022

The role of early life nutrition's impact on relevant health outcomes across the lifespan laid the foundation for the field titled the developmental origins of health and disease. Studies in this area initially concentrated on nutrition and the risk of adverse cardio-metabolic and cancer outcomes. More recently the role of nutrition in early brain development and the subsequent influence of later mental health has become more evident. Scientific breakthroughs have elucidated two mechanisms behind long-term nutrient effects on the brain, including the existence of critical periods for certain nutrients during brain development and nutrient-driven epigenetic modifications of chromatin. While multiple nutrients and nutritional conditions have the potential to modify brain development, iron can serve as a paradigm to understand both mechanisms. New horizons in nutritional medicine include leveraging the mechanistic knowledge of nutrient–brain interactions to propose novel nutritional approaches that protect the developing brain through better timing of nutrient delivery and potential reversal of negative epigenetic marks. The main challenge in the field is detecting whether a change in nutritional status truly affects the brain's development and performance in human subjects. To that end, a strong case can be made to develop and utilise bioindicators of a nutrient's effect on the developing brain instead of relying exclusively on biomarkers of the nutrient's status.
Genetic analysis of a 66-kDa protein-encoding gene of Angiostrongylus cantonensis and Angiostrongylus malaysiensis
Authors: Dumidae Abdulhakam , Subkrasae Chanakan , Ardpairin Jiranun , Thanwisai Aunchalee , Vitta Apichat
Published: November 2022

The rat lungworm Angiostrongylus cantonensis is globally known to be the cause of oeosinophilic meningitis in humans. Another congener, Angiostrongylus malaysiensis, is closely related to A. cantonensis and has been described as a potential human pathogenic parasite. These 2 worms are similar in terms of life cycle, host range and morphological and genetic information. However, there are limited studies about their genetic diversity based on the 66-kDa protein-encoding gene. The objective of this study was to explore the 66-kDa protein sequence variation of A. cantonensis and A. malaysiensis collected from Thailand. Two adult and 53 third-stage larval specimens of Angiostrongylus from 4 geographic locations in Thailand were molecularly identified using the 66-kDa protein gene. The phylogenetic trees (Bayesian inference tree and maximum-likelihood tree) showed that Angiostrongylus formed a monophyletic clade with a clear separation between A. cantonensis and A. malaysiensis. The genetic distance between A. cantonensis and A. malaysiensis varies from 0.82 to 2.86%, with a total of 16 variable sites. The analysis of genetic diversity revealed 1 and 5 new haplotypes of A. cantonensis and A. malaysiensis, respectively, and showed genetic differences between the populations of A. cantonensis and A. malaysiensis. The haplotype networks of A. cantonensis and A. malaysiensis populations in Thailand are similar to those of populations in some countries, indicating the range expansion of genomic origin between populations in different areas. In conclusion, the 66-kDa protein gene was a good genetic marker for studying genetic diversity and discriminating between A. cantonensis and A. malaysiensis.
Creating a culture that supports food security and health equity at higher education institutions
Authors: Savoie-Roskos Mateja R , Hood Lanae B , Hagedorn-Hatfield Rebecca L , Landry Matthew J , Patton-López Megan M , Richards Rickelle , Vogelzang Jody L , Qamar Zubaida , OoNorasak Kendra , Mann Georgianna
Published: November 2022

Food insecurity on college campuses is a major public health problem and has been documented for the last decade. Sufficient food access is a crucial social determinant of health, thus campuses across the country have implemented various programmes, systems and policies to enhance access to food which have included food pantries, campus gardens, farmers’ markets, meal share or voucher programmes, mobile food applications, campus food gleaning, food recovery efforts, meal deliveries and task force/working groups. However, little is understood about how to best address food insecurity and support students who are struggling with basic needs. The impact of food insecurity on students’ academic and social success, in addition to their overall well-being, should be investigated and prioritised at each higher education institution. This is especially true for marginalised students, such as minority or first-generation students, who are at heightened risk for food insecurity. In order to create a culture of health equity, in which most at-risk students are provided resources and opportunities to achieve optimal well-being, higher education institutions must prioritise mitigating food insecurity on the college campus. Higher education institutions could benefit from adopting comprehensive and individualised approaches to promoting food security for marginalised students in order to facilitate equal opportunity for optimal scholastic achievement among students of all socio-demographic backgrounds.
Acceptability and mechanisms of change associated with group cognitive behavioural therapy using the Recovering from Childhood Abuse Programme among women with CPTSD: a qualitative analysis
Authors: Hegarty Siobhan , Ehntholt Kimberly , Williams Dorothy , Kennerley Helen , Billings Jo , Bloomfield Michael
Published: November 2022

Survivors of childhood trauma are at increased risk of complex post-traumatic stress disorder (CPTSD). The Recovering from Child Abuse Programme (RCAP) is a cognitive behavioural therapy (CBT) group promoting adaptive coping strategies which may help overcome CPTSD symptoms in adult survivors of childhood trauma. We sought to explore patient experiences of factors influencing treatment acceptability and potential mechanisms of therapeutic change in a sample of participants in the RCAP programme. As the group was delivered during the COVID-19 pandemic, necessitating a transition to remote therapy, we further aimed to capture experiences of the transition to telehealth delivery of the programme. A naturalistic sample of 10 women with CPTSD attending a specialist out-patient psychological trauma service participated in the study. Therapy sessions were recorded, transcribed verbatim and group members completed written feedback forms following each session. Reflexive thematic analysis was used to analyse the written feedback and transcripts. The RCAP was acceptable to group members and several themes were identified related to the experience of change in the group. Key themes centred on group solidarity; safety in the psychotherapeutic process; schema changes related to the self, others and future catalysed by the shifting of self-blame; increased emotional regulation to feel safer in the present; and increased future optimism. Therapeutic progress continued following the transition to telehealth, although face-to-face delivery was generally preferred. The programme was acceptable and led to cognitive change, enabling increased emotional regulation in the present and improved self-concept, thereby addressing key symptoms of CPTSD.

Key learning aims

(1)

To identify potential mechanisms of therapeutic change related to participation in the Recovery from Childhood Abuse group CBT intervention.

(2)

To understand factors influencing acceptability of the group intervention among women with CPTSD to childhood sexual abuse.
Bayesian Confirmatory Factor Analysis of the Psychological Capital	PCQ-12 Scale
Authors: Tomás José M. , Martínez-Gregorio Sara , Oliver Amparo
Published: November 2022

Abstract: Psychological Capital (PsyCap) is a key construct in psychological research across the lifespan. Although the 12-item Psychological Capital Questionnaire (PCQ-12) is among the most used scales to approach its measurement, its factor structure and reliability remain controversial, particularly in samples of adolescents. Data came from a cross-sectional survey administered to 267 Spanish adolescents, 59.9% girls ( Mage = 13.96, SD = 1.56). Confirmatory Factor Analyses (CFAs) in Mplus 8.6 were used to compare three competitive models (one factor, four correlated factors, and a second order structure) estimated with Bayesian methods. Although Self-Efficacy, Hope, and Optimism significantly explained their indicators, and their cross-loadings were not statistically significant, Resilience operated differently. We obtained evidence supporting the second-order structure. Also, it becomes clear that the scale has difficulties measuring Resilience in adolescents. Consequently, further research should explore new adaptations or alternative measures to overcome these limitations when researching adolescents.
Ionospheric D Region: VLF‐Measured Electron Densities Compared With Rocket‐Based FIRI‐2018 Model
Authors: Thomson Neil R. , Clilverd Mark A. , Rodger Craig J.
Published: November 2022

Ground‐based very low frequency (VLF) radio propagation in the Earth‐ionosphere waveguide has enabled extensive electron number densities in the D region of the Earth's ionosphere to be determined, by day typically below heights of 70–80 km and by night in the height range ∼75–90 km. Many rocket‐based electron density measurements have also been reported in the literature from ∼60 km upwards using current probes, and radio propagation at a few MHz between the rocket and ground. Recently these rocket measurements have been summarized, and supplemented with D region production‐loss modeling, giving rise to a near global model named FIRI‐2018 (Faraday‐International Reference Ionosphere) which provides electron number densities as functions of height, latitude (<60°), solar zenith angle and F10.7 cm solar flux. These rocket‐based electron density values are here compared with corresponding values from VLF measurements, by day at a low‐latitude (∼20°) and a high mid‐latitude (∼55°), and by night mainly at mid‐latitudes. At night the average agreement (over 75–90 km) is remarkably good. By day, at low latitude the agreement is also fairly good (in the common height range ∼60–75 km), with the changes with solar zenith angle being moderately comparable. For daytime high mid‐latitudes, the agreement is less satisfactory, particularly at the lowest common altitudes, with the VLF measurements showing the expected effects of cosmic rays much more than the rocket‐based values. Overall, we find that the D region description in the FIRI‐2018 model is a significant advance on the earlier International Reference Ionosphere (IRI‐2016) model.
Experimental Modeling of Tsunamis Generated by Pyroclastic Density Currents: The Effects of Particle Size Distribution on Wave Generation
Authors: Lipiejko Natalia , Whittaker Colin N. , Lane Emily M. , White James D. L. , Power William L.
Published: November 2022

Volcanic tsunamis can expand the radius of hazards posed by a volcano well beyond the reach of the eruption itself; however, their source mechanisms are poorly understood. The tsunamigenic potential of pyroclastic density currents was studied experimentally by releasing a fluidized column of glass beads from a reservoir; the beads then ran down an inclined ramp into a water‐filled flume and generated waves. The effects of the particle size distribution on the generated waves were analyzed by comparing the waves generated by flows comprising different proportions of particles of diameters 63–90 μm and 600–850 μm. The flows comprising higher proportions of large particles travel more slowly down the ramp; however, all the flows impact the water at velocities greater than the shallow water wave speed, , where h is the still‐water depth. The entrance of the fluidized flow into the water generates a solitary‐like leading wave followed by a smaller trough and trailing waves. Upon impact, the flow separates into a part advected with the wave crest and a part which turbulently mixes with water and propagates along the bottom of the flume, forming an underwater gravity current. A higher proportion of large particles makes the flows more porous, allowing the water to penetrate through the flows more easily, slightly decreasing the efficiency of the energy transfer. While this affects the celerity of the waves, the results show that, over the studied range of particle size distributions, all the flows can generate waves of similar amplitudes regardless of the particle size distribution.
Impact of Clouds and Blowing Snow on Surface and Atmospheric Boundary Layer Properties Over Dome C, Antarctica
Authors: Ganeshan Manisha , Yang Yuekui , Palm Stephen. P.
Published: November 2022

Clouds and blowing snow (BLSN) occur frequently over Antarctica, where it is critical to understand their feedbacks to surface and atmospheric boundary layer processes. Dome C, an elevated East Antarctic station, dominated by lengthy periods of surface longwave (LW) radiative cooling, is selected to reveal cloud and BLSN impacts within a largely stable environment. The sky condition is classified as clear, cloudy, or BLSN, using 3 years of Cloud‐Aerosol Lidar and Infrared Pathfinder Satellite Observations satellite data. Co‐located and contemporaneous in situ observations are used to investigate the relationship of sky condition with surface and atmospheric boundary layer thermal structure, focusing on seasonal variability. Results show that increased downwelling LW radiation from clouds abate surface radiative cooling losses, contributing to warming during all seasons. An increase of 3°C in the mean surface air temperature is observed during spring, whereas, a more dramatic rise (around 10°C), due to accompanying large‐scale subsidence, is observed during fall and winter in association with clouds. For all seasons, the wind speed and wind speed shear are strongest during BLSN events, and the surface‐based inversion is weakened by cooling which peaks in a shallow above‐surface turbulent layer. The stronger background stability during fall and winter seasons, restricts turbulence and BLSN depths generally to the lowest tens of meters. The Earth's cryosphere is among the most rapidly evolving yet least well‐observed regions, and knowledge of clouds and BLSN interactions with the typical stable atmospheric boundary layer can help further understand energy and moisture exchanges.
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

Several 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

Reliable 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

Despite 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

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

mRNA 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

Escherichia 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

A 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

Within 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

Reductions 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

DNA 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

Copper-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

Odor 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

Cas12a 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.