bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inadvertent human genomic bycatch and intentional capture raise beneficial applications and ethical concerns with environmental DNA
Authors: Whitmore Liam , McCauley Mark , Farrell Jessica A. , Stammnitz Maximilian R. , Koda Samantha A. , Mashkour Narges , Summers Victoria , Osborne Todd , Whilde Jenny , Duffy David J. 
Published: May 2023

AbstractThe field of environmental DNA (eDNA) is advancing rapidly, yet human eDNA applications remain underutilized and underconsidered. Broader adoption of eDNA analysis will produce many well-recognized benefits for pathogen surveillance, biodiversity monitoring, endangered and invasive species detection, and population genetics. Here we show that deep-sequencing-based eDNA approaches capture genomic information from humans (Homo sapiens) just as readily as that from the intended target species. We term this phenomenon human genetic bycatch (HGB). Additionally, high-quality human eDNA could be intentionally recovered from environmental substrates (water, sand and air), holding promise for beneficial medical, forensic and environmental applications. However, this also raises ethical dilemmas, from consent, privacy and surveillance to data ownership, requiring further consideration and potentially novel regulation. We present evidence that human eDNA is readily detectable from ‘wildlife’ environmental samples as human genetic bycatch, demonstrate that identifiable human DNA can be intentionally recovered from human-focused environmental sampling and discuss the translational and ethical implications of such findings.
Reconstruction of the personal information from human genome reads in gut metagenome sequencing data
Authors: Tomofuji Yoshihiko , Sonehara Kyuto , Kishikawa Toshihiro , Maeda Yuichi , Ogawa Kotaro , Kawabata Shuhei , Nii Takuro , Okuno Tatsusada , Oguro-Igashira Eri , Kinoshita Makoto , Takagaki Masatoshi , Yamamoto Kenichi , Kurakawa Takashi , Yagita-Sakamaki Mayu , Hosokawa Akiko , Motooka Daisuke , Matsumoto Yuki , Matsuoka Hidetoshi , Yoshimura Maiko , Ohshima Shiro , Nakamura Shota , Inohara Hidenori , Kishima Haruhiko , Mochizuki Hideki , Takeda Kiyoshi , Kumanogoh Atsushi , Okada Yukinori 
Published: May 2023

AbstractHuman DNA present in faecal samples can result in a small number of human reads in gut shotgun metagenomic sequencing data. However, it is presently unclear how much personal information can be reconstructed from such reads, and this has not been quantitatively evaluated. Such a quantitative evaluation is necessary to clarify the ethical concerns related to data sharing and to enable efficient use of human genetic information in stool samples, such as for research and forensics. Here we used genomic approaches to reconstruct personal information from the faecal metagenomes of 343 Japanese individuals with associated human genotype data. Genetic sex could be accurately predicted based on the sequencing depth of sex chromosomes for 97.3% of the samples. Individuals could be re-identified from the matched genotype data based on human reads recovered from the faecal metagenomic data with 93.3% sensitivity using a likelihood score-based method. This method also enabled us to predict the ancestries of 98.3% of the samples. Finally, we performed ultra-deep shotgun metagenomic sequencing of five faecal samples as well as whole-genome sequencing of blood samples. Using genotype-calling approaches, we demonstrated that the genotypes of both common and rare variants could be reconstructed from faecal samples. This included clinically relevant variants. Our approach can be used to quantify personal information contained within gut metagenome data.
Tectonic evolution of the Nootka fault zone and deformation of the shallow subducted Explorer plate in northern Cascadia as revealed by earthquake distributions and seismic tomography
Authors: Hutchinson Jesse , Kao Honn , Riedel Michael , Obana Koichiro , Wang Kelin , Kodaira Shuichi , Takahashi Tsutomu , Yamamoto Yojiro 
Published: May 2023

AbstractAt the northern Cascadia subduction zone, the subducting Explorer and Juan de Fuca plates interact across a transform deformation zone, known as the Nootka fault zone (NFZ). This study continues the Seafloor Earthquake Array Japan Canada Cascadia Experiment to a second phase (SeaJade II) consisting of nine months of recording of earthquakes using ocean-bottom and land-based seismometers. In addition to mapping the distribution of seismicity, including an MW 6.4 earthquake and aftershocks along the previously unknown Nootka Sequence Fault, we also conducted seismic tomography, which delineates the geometry of the shallow subducting Explorer plate (ExP). We derived hundreds of high-quality focal mechanism solutions from the SeaJade II data. The mechanisms manifest a complex regional tectonic state, with normal faulting of the ExP west of the NFZ, left-lateral strike-slip behaviour of the NFZ, and reverse faulting within the overriding plate above the subducting Juan de Fuca plate. Using data from the combined SeaJade I and II catalogs, we have performed double-difference hypocentre relocations and found seismicity lineations to the southeast of, and oriented 18° clockwise from, the subducted NFZ, which we interpret to represent less active small faults off the primary faults of the NFZ. These lineations are not optimally oriented for shear failure in the regional stress field, which we inferred from averaged focal mechanism solutions, and may represent paleo-configurations of the NFZ. Further, active faults interpreted from seismicity lineations within the subducted plate, including the Nootka Sequence Fault, may have originated as conjugate faults within the paleo-NFZ.
Exact solutions via Prabhakar fractional approach to investigate heat transfer and flow features of hybrid nanofluid subject to shape and slip effects
Authors: Asifa  , Anwar Talha , Kumam Poom , Almusawa Musawa Yahya , Lone Showkat Ahmad , Suttiarporn Panawan 
Published: May 2023

AbstractThe core devotion of this study is to develop a generalized model by means of a recently proposed fractional technique in order to anticipate the enhancement in the thermal efficiency of engine oil because of the dispersion of graphene and magnesia nanoparticles. In addition to investigating the synergistic attributes of the foregoing particles, this work evaluates shape impacts for column, brick, tetrahedron, blade, and lamina-like shapes. In the primary model, the flow equation is coupled with concentration and energy functions. This classical system is transmuted into a fractional environment by generalizing mathematical expressions of thermal and diffusion fluxes by virtue of the Prabhakar fractional operator. In this study, ramped flow and temperature slip conditions are simultaneously applied for the first time to examine the behavior of a hybrid nanofluid. The mathematical analysis of this problem involves the incorporation of dimension-independent parameters into the model and the execution of the Laplace transform for the consequent equations. By doing so, exact solutions are derived in the form of Mittag–Leffler functions. Multiple illustrations are developed by dint of exact solutions to chew over all aspects of temperature variations and flow dynamics. For the preparation of these illustrations, the details of parametric ranges are as follows: $$0.00 \le \varUpsilon \le 0.04$$

0.00
≤
Υ
≤
0.04

, $$2.0 \le Gr_1 \le 8.0$$

2.0
≤
G

r
1

≤
8.0

, $$0.5 \le Sc \le 2.0$$

0.5
≤
S
c
≤
2.0

, $$0.1 \le \uptau \le 4.0$$

0.1
≤
τ
≤
4.0

, $$0.1 \le d \le 0.6$$

0.1
≤
d
≤
0.6

, $$0.2 \le \lambda _1 \le 1.5$$

0.2
≤

λ
1

≤
1.5

, and $$1.0 \le Gr_2 \le 7.0$$

1.0
≤
G

r
2

≤
7.0

. The contribution of differently shaped nanoparticles, volume proportions, and fractional parameters in boosting the heat-transferring attributes of engine oil is also anticipated. In this regard, results for Nusselt number are provided in tabular form. Additionally, a brief analysis of shear stress is carried out for fractional parameters and various combinations of magnesia, graphene, and engine oil. This investigation anticipates that engine oil’s hybridization with magnesia and graphene would result in a 33% increase in its thermal performance, which evidently improves its industrial significance. The enhancement in Schmidt number yields an improvement in the mass transfer rate. An increment in collective volume fraction leads to raising the profile of the thermal field. However, the velocity indicates a decreasing behavior. Nusselt number reaches its highest value ($$Nu=8.1363$$

N
u
=
8.1363

) for the lamina shape of considered particles. When the intensity of the buoyancy force augments, it causes the velocity to increase.
Mediation of the mediolateral ground reaction force profile to maintain straight running among unilateral transfemoral amputees
Authors: Tang Ying Wai , Murai Akihiko , Hobara Hiroaki 
Published: May 2023

AbstractThe mediolateral ground reaction force (M-L GRF) profile that realizes a symmetrical mediolateral ground reaction impulse (M-L GRI) between both limbs is essential for maintaining a straight movement path. We aimed to examine the M-L GRF production across different running speeds in unilateral transfemoral amputees (TFA) to identify strategies for maintaining straight running. The average medial and lateral GRF, contact time (tc), M-L GRI, step width, and center of pressure angle (COPANG) were analyzed. Nine TFAs performed running trials at 100% speed on an instrumented treadmill. Trials were set at 30–80% speed with an increment of 10%. Seven steps from the unaffected and affected limbs were analyzed. Overall, the unaffected limbs exhibited a higher average medial GRF than the affected limbs. The M-L GRI were similar between both limbs at all speeds, implying that the participants were able to maintain a straight running path. The affected limb exhibited a longer tc and a lower M-L GRF profile than the unaffected limb. The results showed that unilateral TFAs adopted limb-specific strategies to maintain a straight running path, and that these limb-specific strategies were consistent across different running speeds.
Behavioral and cellular responses to circadian disruption and prenatal immune activation in mice
Authors: Delorme Tara C. , Ozell-Landry William , Cermakian Nicolas , Srivastava Lalit K. 
Published: May 2023

AbstractMost individuals with neurodevelopmental disorders (NDDs), including schizophrenia and autism spectrum disorders, experience disruptions in sleep and circadian rhythms. Epidemiological studies indicate that exposure to prenatal infection increases the risk of developing NDDs. We studied how environmental circadian disruption contributes to NDDs using maternal immune activation (MIA) in mice, which models prenatal infection. Pregnant dams were injected with viral mimetic poly IC (or saline) at E9.5. Adult poly IC- and saline-exposed offspring were subjected to 4 weeks of each of the following: standard lighting (LD1), constant light (LL) and standard lighting again (LD2). Behavioral tests were conducted in the last 12 days of each condition. Poly IC exposure led to significant behavioral differences, including reduced sociability (males only) and deficits in prepulse inhibition. Interestingly, poly IC exposure led to reduced sociability specifically when males were tested after LL exposure. Mice were exposed again to either LD or LL for 4 weeks and microglia were characterized. Notably, poly IC exposure led to increased microglial morphology index and density in dentate gyrus, an effect attenuated by LL exposure. Our findings highlight interactions between circadian disruption and prenatal infection, which has implications in informing the development of circadian-based therapies for individuals with NDDs.
Layer-dependent stability of 2D mica nanosheets
Authors: Kim Jae-Hun , Kulish Vadym. V. , Wu Shunnian , Wu Ping , Shi Yue , Osada Minoru , Kim Hyoun Woo , Kim Sang Sub 
Published: May 2023

AbstractWe report on the layer-dependent stability of muscovite-type two-dimensional (2D) mica nanosheets (KAl3Si3O10(OH)2). First-principles calculations on mica nanosheets with different layer thicknesses (n = 1, 2, and 3) reveal their layer-dependent stability; odd-numbered 2D mica nanosheets are more stable than even-numbered ones, and the preferable stability of odd-numbered layers originates from electronic effects. A core-shielding model is proposed with a reasonable assumption, successfully proving the instability of the even-numbered mica nanosheets. Raman imaging supports that the population of odd-numbered mica nanosheets is predominant in exfoliated mica products. The alternating charge states with odd/even layers were evidenced by Kelvin probe force microscopy. We also demonstrate a unique photocatalytic degradation, opening new doors for environmental applications of mica nanosheets.
Mutational signatures association with replication timing in normal cells reveals similarities and differences with matched cancer tissues
Authors: Yaacov Adar , Rosenberg Shai , Simon Itamar 
Published: May 2023

AbstractMutational signatures’ association with replication timing (RT) has been studied in cancer samples, but the RT distribution of somatic mutations in non-cancerous cells was only minimally explored. Here, we performed comprehensive analyses of mutational signatures in 2.9 million somatic mutations across multiple non-cancerous tissues, stratified by early and late RT regions. We found that many mutational processes are active mainly or solely in early RT, such as SBS16 in hepatocytes and SBS88 in the colon, or in late RT, such as SBS4 in lung and hepatocytes, and SBS18 across many tissues. The two ubiquitous signatures, SBS1 and SBS5, showed late and early bias, respectively, across multiple tissues and in mutations representing germ cells. We also performed a direct comparison with cancer samples in 4 matched tissue-cancer types. Unexpectedly, while for most signatures the RT bias was consistent in normal tissue and in cancer, we found that SBS1’s late RT bias is lost in cancer.
Transcriptomic and glycomic analyses highlight pathway-specific glycosylation alterations unique to Alzheimer’s disease
Authors: Tang Xinyu , Tena Jennyfer , Di Lucente Jacopo , Maezawa Izumi , Harvey Danielle J. , Jin Lee-Way , Lebrilla Carlito B. , Zivkovic Angela M. 
Published: May 2023

AbstractGlycosylation has been found to be altered in the brains of individuals with Alzheimer’s disease (AD). However, it is unknown which specific glycosylation-related pathways are altered in AD dementia. Using publicly available RNA-seq datasets covering seven brain regions and including 1724 samples, we identified glycosylation-related genes ubiquitously changed in individuals with AD. Several differentially expressed glycosyltransferases found by RNA-seq were confirmed by qPCR in a different set of human medial temporal cortex (MTC) samples (n = 20 AD vs. 20 controls). N-glycan-related changes predicted by expression changes in these glycosyltransferases were confirmed by mass spectrometry (MS)-based N-glycan analysis in the MTC (n = 9 AD vs. 6 controls). About 80% of glycosylation-related genes were differentially expressed in at least one brain region of AD participants (adjusted p-values < 0.05). Upregulation of MGAT1 and B4GALT1 involved in complex N-linked glycan formation and galactosylation, respectively, were reflected by increased concentrations of corresponding N-glycans. Isozyme-specific changes were observed in expression of the polypeptide N-acetylgalactosaminyltransferase (GALNT) family and the alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase (ST6GALNAC) family of enzymes. Several glycolipid-specific genes (UGT8, PIGM) were upregulated. The critical transcription factors regulating the expression of N-glycosylation and elongation genes were predicted and found to include STAT1 and HSF5. The miRNA predicted to be involved in regulating N-glycosylation and elongation glycosyltransferases were has-miR-1-3p and has-miR-16-5p, respectively. Our findings provide an overview of glycosylation pathways affected by AD and potential regulators of glycosyltransferase expression that deserve further validation and suggest that glycosylation changes occurring in the brains of AD dementia individuals are highly pathway-specific and unique to AD.
Changes in the epidemiological characteristics of prehospital emergency services before and during the COVID-19 pandemic, Chengdu, 2016–2021
Authors: Zhang Bihua , Kang Wenchao , Xiong Shiqiang , Huang Xia , Chen Pei , Huang Jinmin , Hou Yufei , Ma Lin , Xiang Tao 
Published: May 2023

AbstractThe coronavirus disease 2019 (COVID-19) brought a healthy crisis all around the world. It’s not only affected healthcare utilization, but also some disease’s incidence. We collected pre-hospital emergency data in Chengdu from January 2016 to December 2021, and studied the demand for emergency medical services (EMSs), emergency response times (ERTs), and the disease spectrum in the city proper of Chengdu as a whole. A total of 1,122,294 prehospital emergency medical service (EMS) instances met the inclusion criteria. Under the influence of COVID-19, notably in 2020, the epidemiological characteristics of prehospital emergency services in Chengdu were considerably altered. However, as the pandemic was brought under control, they returned to normal or even earlier in 2021.The COVID-19 pandemic had an effect on people's medical care-seeking behavior and the performance of prehospital emergency services. Although the indicators associated with prehospital emergency services eventually recovered as the epidemic was brought under control, they remained marginally different from before the outbreak.
Effect of inclined magnetic field on radiative heat and mass transfer in chemically reactive hybrid nanofluid flow due to dual stretching
Authors: Arshad Mubashar , Alharbi Fahad M. , Hassan Ali , Haider Qusain , Alhushaybari Abdullah , Eldin Sayed M. , Ahmad Zubair , Al-Essa Laila A. , Galal Ahmed M. 
Published: May 2023

AbstractThis research analyzes the three-dimensional magneto hydrodynamic nanofluid flow through chemical reaction and thermal radiation above the dual stretching surface in the presence of an inclined magnetic field. Different rotational nanofluid and hybrid nanofluids with constant angular velocity $${\upomega }^{*}$$

ω

∗

for this comparative study are considered. The constitutive relations are used to gain the equations of motion, energy, and concentration. This flow governing extremely non-linear equations cannot be handled by an analytical solution. So, these equations are transformed into ordinary differential equalities by using the similarity transformation and then handled in MATLAB by applying the boundary values problem practice. The outcomes for the considered problem are accessed through tables and graphs for different parameters. A maximum heat transfer amount is observed in the absence of thermal radiation and when the inclined magnetic field and axis of rotation are parallel.
Association between characteristics of swallowing-related muscles and trunk muscle mass
Authors: Yamaguchi Kohei , Nakagawa Kazuharu , Yoshimi Kanako , Ariya Chantaramanee , Nakane Ayako , Ishii Miki , Hasegawa Shohei , Tohara Haruka 
Published: May 2023

AbstractSwallowing function is associated with systemic factors. Whether trunk or appendicular skeletal muscle mass is a better indicator of swallowing-related muscle characteristics in community-dwelling older adults is not clear. Hence, we investigated the association between the characteristics of swallowing-related muscles (e.g., mass and quality) and trunk muscle mass. Community-dwelling older adults aged ≥ 65 years (n = 141; men: n = 45, women: n = 96) were recruited for this cross-sectional observational study via a health survey conducted in 2018. Trunk muscle mass index (TMI) and appendicular skeletal muscle mass index (SMI) were measured using bioelectrical impedance analysis. Cross-sectional areas (CSAs) and echo intensity (EI) of the geniohyoid muscle (GHM) and tongue were evaluated using an ultrasonic diagnostic apparatus. Multiple regression analysis was used to examine the relationship of the characteristics of swallowing-related muscle with TMI and SMI. Multiple regression analysis showed that CSA of the GHM was positively associated with both TMI (B = 24.9, p < 0.001) and SMI (B = 13.7, p = 0.002). EIs of swallowing-related muscles were not associated with TMI and SMI. Trunk muscle mass was associated with swallowing-related muscle mass and not muscle quality. The results of this study shed light on the elucidation of association of dysphagia with TMI and SMI.
Effects of antibiotic interaction on antimicrobial resistance development in wastewater
Authors: Sutradhar Indorica , Ching Carly , Desai Darash , Heins Zachary , Khalil Ahmad S. , Zaman Muhammad H. 
Published: May 2023

AbstractWhile wastewater is understood to be a critically important reservoir of antimicrobial resistance due to the presence of multiple antibiotic residues from industrial and agricultural runoff, there is little known about the effects of antibiotic interactions in the wastewater on the development of resistance. We worked to fill this gap in quantitative understanding of antibiotic interaction in constant flow environments by experimentally monitoring E. coli populations under subinhibitory concentrations of combinations of antibiotics with synergistic, antagonistic, and additive interactions. We then used these results to expand our previously developed computational model to account for the effects of antibiotic interaction. We found that populations grown under synergistic and antagonistic antibiotic conditions exhibited significant differences from predicted behavior. E. coli populations grown with synergistically interacting antibiotics developed less resistance than predicted, indicating that synergistic antibiotics may have a suppressive effect on resistance development. Furthermore E. coli populations grown with antagonistically interacting antibiotics showed an antibiotic ratio-dependent development of resistance, suggesting that not only antibiotic interaction, but relative concentration is important in predicting resistance development. These results provide critical insight for quantitatively understanding the effects of antibiotic interactions in wastewater and provide a basis for future studies in modelling resistance in these environments.