bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reconstruction of 100-year dynamics in Daphnia spawning activity revealed by sedimentary DNA
Authors: Tsugeki Narumi , Nakane Kai , Doi Hideyuki , Ochi Natsuki , Kuwae Michinobu 
Published: February 2022

AbstractEnvironmental DNA (eDNA) is currently developing as a powerful tool for assessing aquatic species dynamics. However, its utility as an assessment tool for quantification remain under debate as the sources of eDNA for different species is not always known. Therefore, accumulating information about eDNA sources from different species is urgently required. The objective of our study was to evaluate whether sedimentary DNA targeting two Daphnia species, D. galeata and D. pulicaria, could track Daphnia population dynamics and resting egg production. Applying a quantitative PCR targeting the mitochondrial 12S rRNA gene on sediment cores collected in Lake Biwa, Japan, we compared sedimentary DNA concentration of Daphnia with the abundance of remains and ephippia, reflecting their abundance and resting egg production, respectively. We found that the sedimentary DNA concentrations of Daphnia for the past century were inconsistent with their population abundance. However, the concentration was highly correlated with the resting egg production. Our results provide evidence that ephippia with resting eggs, released during spawning activities, was a significant source of Daphnia DNA archived in sediments. Our work provides critical insights for using sedimentary DNA as a monitoring tool for egg production dating back 100 years.
Systematic comparative analysis of strand-specific RNA-seq library preparation methods for low input samples
Authors: Naphade Swati , Bhatnagar Rajat , Hanson-Smith Victor , Choi Irene , Zhang Alice 
Published: February 2022

AbstractDespite the recent precipitous decline in the cost of genome sequencing, library preparation for RNA-seq is still laborious and expensive for applications such as high throughput screening. Limited availability of RNA generated by some experimental workflows poses an additional challenge and increases the cost of RNA library preparation. In a search for low cost, automation-compatible RNA library preparation kits that maintain strand specificity and are amenable to low input RNA quantities, we systematically tested two recent commercial technologies—Swift RNA and Swift Rapid RNA, presently offered by Integrated DNA Technologies (IDT) —alongside the Illumina TruSeq stranded mRNA, the de facto standard workflow for bulk transcriptomics. We used the Universal Human Reference RNA (UHRR) (composed of equal quantities of total RNA from 10 human cancer cell lines) to benchmark gene expression in these kits, at input quantities ranging between 10 to 500 ng. We found normalized read counts between all treatment groups to be in high agreement. Compared to the Illumina TruSeq stranded mRNA kit, both Swift RNA library kits offer shorter workflow times enabled by their patented Adaptase technology. We also found the Swift RNA kit to produce the fewest number of differentially expressed genes and pathways directly attributable to input mRNA amount.
Unprecedently large 37Cl/35Cl equilibrium isotopic fractionation on nano-confinement of chloride anion
Authors: Pokora Mateusz , Paneth Agata , Paneth Piotr 
Published: February 2022

AbstractConfinement can result in unusual properties leading to new, exciting discoveries in the nano-realm. One such consequence of confinement at the nanoscale is extremally large isotopic fractionation, especially at sub-van der Waals distances. Herein, on the example of chlorine isotope effects, we show that at conditions of nanoencapsulation these effects may reach values by far larger than observed for the bulk environment, which in the case of nanotubes can lead to practical applications (e.g., in isotopic enrichment) and needs to be considered in analytical procedures that employ nanomaterials.
Generation mechanism and prediction of an observed extreme rogue wave
Authors: Gemmrich Johannes , Cicon Leah 
Published: February 2022

AbstractRogue waves are individual ocean surface waves with crest height $$\eta$$
η
or trough-to-crest height H that are large compared to the significant wave height $$H_s$$

H
s

of the underlying sea state: $$H/H_s>2.2$$

H
/

H
s

>
2.2

or $$\eta /H_s>1.25$$

η
/

H
s

>
1.25

. The physics of rogue wave generation and the potential of predicting the rogue wave risk are open questions. Only a few rogue waves in high sea states have been observed directly, but they can pose a danger to marine operations, onshore and offshore structures, and beachgoers. Here we report on a 17.6m high rogue wave in coastal waters with $$\eta /H_s=1.98$$

η
/

H
s

=
1.98

and $$H/H_s=2.9$$

H
/

H
s

=
2.9

which are likely the largest normalized heights ever recorded. Simulations of random superposition of Stokes waves in intermediate water depth show good agreement with the observation. Non-linear wave modulational instability, a well known cause for rogue waves in laboratory settings, did not contribute significantly to the rogue wave generation. A parameter obtained from a routine spectral wave forecast provides a practical risk prediction for rogue waves. These results confirm that probabilistic prediction of oceanic rogue waves based on random superposition of steep waves are possible and should replace predictions based on modulational instability.
Identification of novel leads as potent inhibitors of HDAC3 using ligand-based pharmacophore modeling and MD simulation
Authors: Kumbhar Navanath , Nimal Snehal , Barale Sagar , Kamble Subodh , Bavi Rohit , Sonawane Kailas , Gacche Rajesh 
Published: February 2022

AbstractIn the landscape of epigenetic regulation, histone deacetylase 3 (HDAC3) has emerged as a prominent therapeutic target for the design and development of candidate drugs against various types of cancers and other human disorders. Herein, we have performed ligand-based pharmacophore modeling, virtual screening, molecular docking, and MD simulations to design potent and selective inhibitors against HDAC3. The predicted best pharmacophore model ‘Hypo 1’ showed excellent correlation (R2 = 0.994), lowest RMSD (0.373), lowest total cost value (102.519), and highest cost difference (124.08). Hypo 1 consists of four salient pharmacophore features viz. one hydrogen bond acceptor (HBA), one ring aromatic (RA), and two hydrophobic (HYP). Hypo 1 was validated by Fischer's randomization with a 95% of confidence level and the external test set of 60 compounds with a good correlation coefficient (R2 = 0.970). The virtual screening of chemical databases, drug-like properties calculations followed by molecular docking resulted in identifying 22 representative hit compounds. Performed 50 ns of MD simulations on top three hits were retained the salient π-stacking, Zn2+ coordination, hydrogen bonding, and hydrophobic interactions with catalytic residues from the active site pocket of HDAC3. Total binding energy calculated by MM-PBSA showed that the Hit 1 and Hit 2 formed stable complexes with HDAC3 as compared to reference TSA. Further, the PLIP analysis showed a close resemblance between the salient pharmacophore features of Hypo 1 and the presence of molecular interactions in co-crystallized FDA-approved drugs. We conclude that the screened hit compounds may act as potent inhibitors of HDAC3 and further preclinical and clinical studies may pave the way for developing them as effective therapeutic agents for the treatment of different cancers and neurodegenerative disorders.
Completely predatory development is described in a braconid wasp
Authors: Ranjith A. P. , Quicke Donald L. J. , Manjusha K. , Butcher Buntika A. , Nasser M. 
Published: February 2022

AbstractHymenopteran parasitoids are well known for their ubiquitous diversity, important ecological roles and biocontrol potential. We report the first detailed documentation of mite predation by a parasitoid wasp,Bracon predatoriusRanjith & Quicke sp. nov., (Insecta: Hymenoptera), first case of obligate predatory behaviour in the family Braconidae and first case of mite feeding within the superfamily Ichneumonoidea. Larvae of a new wasp species are shown to develop entirely as predators of eriophyid mites that induce leaf galls in a commercially important plant. They display highly modified head capsule morphology that we interpret as being associated with this atypical life style. We propose that the new feeding strategy evolved separately from recently described entomophytophagy in another species of the same genus. The divergent larval morphological adaptations of both species indicate a high degree of evolutionary developmental plasticity in the developmental stage.
Purification and characterization of human adipose-resident microvascular endothelial progenitor cells
Authors: Saito Natsumi , Shirado Takako , Funabashi-Eto Hitomi , Wu Yunyan , Mori Masanori , Asahi Rintaro , Yoshimura Kotaro 
Published: February 2022

AbstractHuman adipose tissue is a rich source of adipose-derived stem cells (ASCs) and vascular endothelial progenitor cells (EPCs). However, no standardized method has been established for the isolation and purification of adipose-derived EPCs (AEPCs). The aim of this study was to establish a method for the isolation and purification of AEPCs. The stromal vascular fraction (SVF) was extracted from human lipoaspirates, and the CD45−CD31+ fraction of the SVF was collected by magnetic-activated cell sorting (MACS). The CD45−CD31+ fraction was cultured for 4.5 days, followed by a second MACS separation to collect the CD31+ fraction. Purified AEPCs were expanded without being overwhelmed by proliferating ASCs, indicating that a high level (> 95%) of AEPC purification is a key factor for their successful isolation and expansion. AEPCs exhibited typical endothelial markers, including CD31, von Willebrand factor, and the isolectin-B4 binding capacity. AEPCs formed colonies, comparable to cultured human umbilical vein endothelial cells (HUVECs). Both AEPCs and HUVECs formed capillary-like networks in the tube formation assay, with no significant difference in network lengths. We are the first to establish a purification and expansion method to isolate these cells. Because adipose tissue is a clinically accessible and abundant tissue, AEPCs may have potential advantages as a therapeutic tool for regenerative medicine.
β-III-spectrin N-terminus is required for high-affinity actin binding and SCA5 neurotoxicity
Authors: Denha Sarah A. , Atang Alexandra E. , Hays Thomas S. , Avery Adam W. 
Published: February 2022

AbstractRecent structural studies of β-III-spectrin and related cytoskeletal proteins revealed N-terminal sequences that directly bind actin. These sequences are variable in structure, and immediately precede a conserved actin-binding domain composed of tandem calponin homology domains (CH1 and CH2). Here we investigated in Drosophila the significance of the β-spectrin N-terminus, and explored its functional interaction with a CH2-localized L253P mutation that underlies the neurodegenerative disease spinocerebellar ataxia type 5 (SCA5). We report that pan-neuronal expression of an N-terminally truncated β-spectrin fails to rescue lethality resulting from a β-spectrin loss-of-function allele, indicating that the N-terminus is essential to β-spectrin function in vivo. Significantly, N-terminal truncation rescues neurotoxicity and defects in dendritic arborization caused by L253P. In vitro studies show that N-terminal truncation eliminates L253P-induced high-affinity actin binding, providing a mechanistic basis for rescue. These data suggest that N-terminal sequences may be useful therapeutic targets for small molecule modulation of the aberrant actin binding associated with SCA5 β-spectrin and spectrin-related disease proteins.
In vitro regeneration and Agrobacterium-mediated genetic transformation of Dragon’s Head plant (Lallemantia iberica)
Authors: Ebrahimzadegan Rahman , Maroufi Asad 
Published: February 2022

AbstractDragon’s head plant (Lallemantia iberica), is a flowering species belongs to the mint family (Lamiaceae). The species contains valuable essential oils, mucilage and oil which are used in pharmaceutical and food industries. Tissue culture is a feasible strategy to attain large‐scale production of plantlets with a huge potential to produce plants with superior quality. The objective of this study was to develop a simple and efficient method for regeneration and transformation of L. iberica. To reach this goal, the regeneration ability of various explants including leaf, cotyledonary node, hypocotyl and cotyledon segments was investigated in MS medium supplemented with diverse concentrations of NAA (Naphthalene acetic acid) and BAP (6-Benzyl Amino Purine). According to the results, cotyledonary nodes showed the best regeneration response. The maximum rate of regeneration (and number of induced shoots was achieved in 1 mg l−1 BAP in combination with 0.05 mg l−1 NAA from the cotyledonary nodes. Additionally, through the optimized regeneration technique Agrobacterium-mediated transformation of L. iberica was successfully accomplished. Gene transfer was assessed on leaf samples from regenerated plantlets under a fluorescent microscope to detect the GFP signals. Moreover, transgene integration and its expression were confirmed by PCR and RT-PCR analysis, respectively. The establishment of these efficient regeneration and genetic transformation methods paved the way for further application such as plant improvement, functional analysis and gene editing.
m6A-related lncRNAs predict prognosis and indicate immune microenvironment in acute myeloid leukemia
Authors: Zhong Fangmin , Yao Fangyi , Cheng Ying , Liu Jing , Zhang Nan , Li Shuqi , Li Meiyong , Huang Bo , Wang Xiaozhong 
Published: February 2022

AbstractAcute myeloid leukemia (AML) is a complex hematologic malignancy. Survival rate of AML patients is low. N6-methyladenosine (m6A) and long non-coding RNAs (lncRNAs) play important roles in AML tumorigenesis and progression. However, the relationship between lncRNAs and biological characteristics of AML, as well as how lncRNAs influence the prognosis of AML patients, remain unclear. In this study. In this study, Pearson correlation analysis was used to identify lncRNAs related to m6A regulatory genes, namely m6A-related lncRNAs. And we analyzed their roles and prognostic values in AML. m6A-related lncRNAs associated with patient prognosis were screened using univariate Cox regression analysis, followed by systematic analysis of the relationship between these genes and AML clinicopathologic and biologic characteristics. Furthermore, we examined the characteristics of tumor immune microenvironment (TIME) using different IncRNA clustering models. Using LASSO regression, we identified the risk signals related to prognosis of AML patients. We then constructed and verified a risk model based on m6A-related lncRNAs for independent prediction of overall survival in AML patients. Our results indicate that risk scores, calculated based on risk-related signaling, were related to the clinicopathologic characteristics of AML and level of immune infiltration. Finally, we examined the expression level of TRAF3IP2-AS1 in patient samples through real-time polymerase chain reaction analysis and in GEO datasets, and we identified a interaction relationship between SRSF10 and TRAF3IP2-AS1 through in vitro assays. Our study shows that m6A-related lncRNAs, evaluated using the risk prediction model, can potentially be used to predict prognosis and design immunotherapy in AML patients.
Analysis of antiretroviral therapy switch rate and switching pattern for people living with HIV from a national database in Japan
Authors: Naito Toshio , Mori Hirotake , Fujibayashi Kazutoshi , Fukushima Shinichi , Yuda Mayumi , Fukui Nobuyuki , Tsukamoto Shotaro , Suzuki Mai , Goto-Hirano Keiko , Kuwatsuru Ryohei 
Published: February 2022

AbstractTo report the status of switch rates and time-to-switch of antiretroviral therapy (ART) regimens by evaluating anchor drug classes and common switching patterns in Japanese people living with human immunodeficiency virus (HIV, PLWH). This cross-sectional cohort study extracted data of 28,089 PLWH from the National Database of Health Insurance Claims and Specific Health Checkups of Japan (NDB), which contains data representing the entire population of Japan. PLWH with first prescription records of ART administered between January 2011 and March 2019 were identified (n = 16,069). The median time-to-switch and switch rates of anchor drug classes were estimated by Kaplan–Meier analysis. Brookmeyer–Crowley and Greenwood methods were used to estimate 95% confidence intervals for switch rates and median days, respectively. Switch rates were compared between anchor drug classes by year using log-rank tests. A total of 3108 (19.3%) PLWH switched anchor drug classes from first to second regimens. Switch rates increased continuously over 8 years for non-nucleoside reverse transcriptase inhibitors (NNRTIs) (14.9–65.5%) and protease inhibitors (PIs) (13.2–67.7%), with median time-to-switch of 1826 and 1583 days, respectively. Integrase strand transfer inhibitors (INSTIs) maintained a low switch rate (3.0–7.6%), precluding median-days calculation. Overall, the majority of patients treated initially with NNRTIs and PIs switched to INSTIs regardless of switching times (< 1 year: 67.3% and 85.9%, respectively; ≥ 1 year: 95.5% and 93.6%, respectively). The foremost switching strategies for first-to-second ART regimens are from NNRTIs or PIs to INSTIs regimens that maintain low switch rates long term. There was no observable difference in trend between sex, age and status of AIDS disease at first ART regimen. INSTIs HIV agents may be the most durable anchor drug class for PLWH receiving ART.
Application of flexible pin for planetary gear set of wind turbine gearbox
Authors: Yoo Ho-Gil , Chung Woo-Jin , Kim Beom-Soo , Park Young-Jun , Kim Su-Chul , Lee Geun-Ho 
Published: February 2022

AbstractWind turbines are eco-friendly energy sources that generate electricity from wind power. Among their various components, gearboxes constitute the most critical loss owing to their longest downtime. To guarantee their durability, a flexible pin was designed based on the original straddle-mounted pin for enhanced tooth load sharing and distribution in the planetary gear set (PGS) of a wind turbine gearbox (WTGB). The improved durability was evaluated by calculating the mesh load factor and face load factor for contact stress and comparing these values with those of the original straddle-mounted pin. The mesh load factor decreased from 1.37 to 1.08, whereas the maximum face load factor decreased slightly, moderating the overall safety factor variation. Furthermore, the structure of the proposed flexible pin model was analyzed and verified that no static failure or interference occurred. Additionally, microgeometry optimization was applied to improve the load distribution. Therefore, it was verified that a flexible pin applied to a single helical-geared PGS, thus far considered impossible, enhances the durability of WTGBs by improving the load sharing and distribution of a PGS. Consequently, the possibility of designing single helical-geared planetary gearboxes with flexible pins to take advantages of both helical gears and flexible pins was shown analytically.
The effect of territorial awareness in a three-species cyclic predator–prey model
Authors: Wang Xiaoyue , Lu Yikang , Shi Lei , Park Junpyo 
Published: February 2022

AbstractRecognizing territories is essential to decide behavior of population either human or animals, and interaction between groups or individuals according to the territorial awareness is universal. Understanding various mechanisms which affect on such species behaviors can be possible by evolutionary games, and in particular, the rock–paper–scissors (RPS) game has been played a key role as a paradigmatic model to explore biodiversity from microbiota to societies. Among paramount mechanisms in systems of RPS, the role of intraspecific interaction has been recently noted in terms of promoting biodiversity. Since intraspecific interaction is defined by an invasive reaction between individuals in the same group, the interaction may be also sensitive to the territorial awareness. To explore how territorial awareness-based intraspecific interaction can affect species biodiversity, we endow species with the mechanism in the classic RPS game. By means of the Monte-Carlo method, we find the phenomenon that the presence of species’ territorial awareness has an impact on intraspecific interaction which ultimately affects species biodiversity. At the same time, we also find that territorial awareness can play a significant role to the average waiting time for extinction which is numerically elucidated by exploiting the quantity: interface width statistic. Unlike prior research that concentrated solely on the relationship between interaction frequency and species diversity, our results shed lights on the important role of territorial awareness in models of RPS, and they reveal fascinating evolutionary outcomes in structured populations that are a unique consequence of such awareness behavior.
Astrocytes deficient in circadian clock gene Bmal1 show enhanced activation responses to amyloid-beta pathology without changing plaque burden
Authors: McKee Celia A. , Lee Jiyeon , Cai Yuqi , Saito Takashi , Saido Takaomi , Musiek Erik S. 
Published: February 2022

AbstractAn emerging link between circadian clock function and neurodegeneration has indicated a critical role for the molecular clock in brain health. We previously reported that deletion of the core circadian clock gene Bmal1abrogates clock function and induces cell-autonomous astrocyte activation. Regulation of astrocyte activation has important implications for protein aggregation, inflammation, and neuronal survival in neurodegenerative conditions such as Alzheimer's disease (AD). Here, we investigated how astrocyte activation induced byBmal1deletion regulates astrocyte gene expression, amyloid-beta (Aβ) plaque-associated activation, and plaque deposition. To address these questions, we crossed astrocyte-specificBmal1knockout mice (Aldh1l1-CreERT2;Bmal1fl/fl, termed BMAL1 aKO), to the APP/PS1-21 and the APPNL-G-Fmodels of Aβ accumulation. Transcriptomic profiling showed that BMAL1 aKO induced a unique transcriptional profile affecting genes involved in both the generation and elimination of Aβ. BMAL1 aKO mice showed exacerbated astrocyte activation around Aβ plaques and altered gene expression. However, this astrogliosis did not affect plaque accumulation or neuronal dystrophy in either model. Our results demonstrate that the striking astrocyte activation induced byBmal1knockout does not influence Aβ deposition, which indicates that the effect of astrocyte activation on plaque pathology in general is highly dependent on the molecular mechanism of activation.