bluuebunny/crossref_metadata_2025_split huggingface dataset:
Loading equine oocytes with cryoprotective agents captured with a finite element method model
Authors: Içli Sercan , Soleimani Meisam , Oldenhof Harriëtte , Sieme Harald , Wriggers Peter , Wolkers Willem F. 
Published: October 2021

AbstractCryopreservation can be used to store equine oocytes for extended periods so that they can be used in artificial reproduction technologies at a desired time point. It requires use of cryoprotective agents (CPAs) to protect the oocytes against freezing injury. The intracellular introduction of CPAs, however, may cause irreversible osmotic damage. The response of cells exposed to CPA solutions is governed by the permeability of the cellular membrane towards water and the CPAs. In this study, a mathematical mass transport model describing the permeation of water and CPAs across an oocyte membrane was used to simulate oocyte volume responses and concomitant intracellular CPA concentrations during the exposure of oocytes to CPA solutions. The results of the analytical simulations were subsequently used to develop a phenomenological finite element method (FEM) continuum model to capture the response of oocytes exposed to CPA solutions with spatial information. FEM simulations were used to depict spatial differences in CPA concentration during CPA permeation, namely at locations near the membrane surface and towards the middle of the cell, and to capture corresponding changes in deformation and hydrostatic pressure. FEM simulations of the multiple processes occurring during CPA loading of oocytes are a valuable tool to increase our understanding of the mechanisms underlying cryopreservation outcome.
Possible vertebral brucellosis infection in a Neanderthal
Authors: Rothschild Bruce , Haeusler Martin 
Published: October 2021

AbstractThe La Chapelle-aux-Saints 1 skeleton of an old (>60-year-old) male Neanderthal is renowned for the advanced osteoarthritis of its spinal column and hip joint, and their implications for posture and lifestyle in these Mid- to Late Pleistocene humans. Reassessment of the pathologic lesions reveals erosions at multiple non-contiguous vertebrae and reactive bone formation extending far beyond the left hip joint, which suggests the additional diagnosis of brucellosis. This implies the earliest secure evidence of this zoonotic disease in hominin evolution. Brucellosis might have been transmitted via butchering or eating raw meat and is well compatible with the range of prey animals documented for Neanderthals. The associated infertility could have represented an important aspect of health in these late archaic humans.
Demography of a Eurasian lynx (Lynx lynx) population within a strictly protected area in Central Europe
Authors: Palmero Stefano , Belotti Elisa , Bufka Luděk , Gahbauer Martin , Heibl Christoph , Premier Joe , Weingarth-Dachs Kirsten , Heurich Marco 
Published: October 2021

AbstractLarge carnivores promote crucial ecosystem processes but are increasingly threatened by human persecution and habitat destruction. Successful conservation of this guild requires information on long-term population dynamics obtained through demographic surveys. We used camera traps to monitor Eurasian lynx between 2009 and 2018 in a strictly protected area in the Bohemian Forest Ecosystem, located in the core of the distribution of the Bohemian–Bavarian–Austrian lynx population. Thereby, we estimated sex-specific demographic parameters using spatial capture–recapture (SCR) models. Over 48,677 trap nights, we detected 65 unique lynx individuals. Density increased from 0.69 to 1.33 and from 1.09 to 2.35 individuals/100 km2for open and closed population SCR models, respectively, with corresponding positive population growth rates (mean = 1.06). Estimated yearly sex-specific survival probabilities for the entire monitoring period were high (females 82%, males 90%) and per capita recruitment rate was low (females 12%, males 9%), indicating a low yearly population turnover. We ascertained an average number of recruits of 1.97 and a generation time of 2.64 years when considering resident reproducing females. We confirmed that reproduction in the study area took place successfully every year. Despite the overall increase in local lynx densities, the number of detected family groups remained constant throughout the study period. These results indicated that the strictly protected study area acts as a source for the multi-use landscapes in its surroundings. In this first open population SCR study on lynx, we provide sex-specific demographic parameters that are fundamental information for lynx management in the study area as well as in similar contexts Europe-wide.
Generation of knock-in lampreys by CRISPR-Cas9-mediated genome engineering
Authors: Suzuki Daichi G. , Wada Hiroshi , Higashijima Shin-ichi 
Published: October 2021

AbstractThe lamprey represents the oldest group of living vertebrates and has been a key organism in various research fields such as evolutionary developmental biology and neuroscience. However, no knock-in technique for this animal has been established yet, preventing application of advanced genetic techniques. Here, we report efficient generation of F0 knock-in lampreys by CRISPR-Cas9-mediated genome editing. A donor plasmid containing a heat-shock promoter was co-injected with a short guide RNA (sgRNA) for genome digestion, a sgRNA for donor plasmid digestion, and Cas9 mRNA. Targeting different genetic loci, we succeeded in generating knock-in lampreys expressing photoconvertible protein Dendra2 as well as those expressing EGFP. With its simplicity, design flexibility, and high efficiency, we propose that the present method has great versatility for various experimental uses in lamprey research and that it can also be applied to other “non-model” organisms.
Optogenetic stimulation of striatal patches modifies habit formation and inhibits dopamine release
Authors: Nadel J. A. , Pawelko S. S. , Scott J. R. , McLaughlin R. , Fox M. , Ghanem M. , van der Merwe R. , Hollon N. G. , Ramsson E. S. , Howard C. D. 
Published: October 2021

AbstractHabits are inflexible behaviors that develop after extensive repetition, and overreliance on habits is a hallmark of many pathological states. The striatum is involved in the transition from flexible to inflexible responding, and interspersed throughout the striatum are patches, or striosomes, which make up ~15% of the volume of the striatum relative to the surrounding matrix compartment. Previous studies have suggested that patches are necessary for normal habit formation, but it remains unknown exactly how patches contribute to habit formation and expression. Here, using optogenetics, we stimulated striatal patches in Sepw1-NP67 mice during variable interval training (VI60), which is used to establish habitual responding. We found that activation of patches at reward retrieval resulted in elevated responding during VI60 training by modifying the pattern of head entry and pressing. Further, this optogenetic manipulation reduced subsequent responding following reinforcer devaluation, suggesting modified habit formation. However, patch stimulation did not generally increase extinction rates during a subsequent extinction probe, but did result in a small ‘extinction burst’, further suggesting goal-directed behavior. On the other hand, this manipulation had no effect in omission trials, where mice had to withhold responses to obtain rewards. Finally, we utilized fast-scan cyclic voltammetry to investigate how patch activation modifies evoked striatal dopamine release and found that optogenetic activation of patch projections to the substantia nigra pars compacta (SNc) is sufficient to suppress dopamine release in the dorsal striatum. Overall, this work provides novel insight into the role of the patch compartment in habit formation, and provides a potential mechanism for how patches modify habitual behavior by exerting control over dopamine signaling.
One-pot three-component tandem annulation of 4-hydroxycoumarine with aldehyde and aromatic amines using graphene oxide as an efficient catalyst
Authors: Singha Rabindranath , Islam Aminul , Ghosh Pranab 
Published: October 2021

AbstractA convenient and efficient solvent-free, facile, one-pot three-component graphene oxide catalysed approach has been described for the synthesis of chromeno-[4,3-b]quinolin-6-one derivatives from 4-hydroxycoumarin with aldehydes and aromatic amines. Graphene oxide (GO) has proved to be a new class of heterogeneous carbocatalyst which could be easily recovered and reused up to 5th run without significant loss of its catalytic activity. A broad scope of substrate applicability is offered and a plausible mechanism is also suggested for this developed protocol.
Influence of normal tide and the Great Tsunami as recorded through hourly-resolution micro-analysis of a mussel shell
Authors: Sano Yuji , Okumura Tomoyo , Murakami-Sugihara Naoko , Tanaka Kentaro , Kagoshima Takanori , Ishida Akizumi , Hori Masako , Snyder Glen T. , Takahata Naoto , Shirai Kotaro 
Published: October 2021

AbstractWe report here hourly variations of Mg/Ca, Sr/Ca, and Ba/Ca ratios in a Mediterranean mussel shell (Mytilus galloprovincialis) collected at the Otsuchi bay, on the Pacific coast of northeastern Japan. This bivalve was living in the intertidal zone, where such organisms are known to form a daily or bidaily growth line comprised of abundant organic matter. Mg/Ca ratios of the inner surface of the outer shell layer, corresponding to the most recent date, show cyclic changes at 25–90 μm intervals, while no interpretable variations are observed in Sr/Ca and Ba/Ca ratios. High Mg/Ca ratios were probably established by (1) cessation of the external supply of Ca and organic layer forming when the shell is closed at low tide, and (2) the strong binding of Mg to the organic layer, but not of Sr and Ba. Immediately following the great tsunami induced by the 2011 Tohoku earthquake, Mg/Ca enrichment occurred, up to 10 times that of normal low tide, while apparent Ba/Ca enrichment was observed for only a few days following the event, therefore serving a proxy of the past tsunami. Following the tsunami, periodic peaks and troughs in Mg/Ca continued, perhaps due to a biological memory effect as an endogenous clock.
Combining experiments and in silico modeling to infer the role of adhesion and proliferation on the collective dynamics of cells
Authors: Melo Hygor P. M. , Maia F. Raquel , Nunes André S. , Reis Rui L. , Oliveira Joaquim M. , Araújo Nuno A. M. 
Published: October 2021

AbstractThe collective dynamics of cells on surfaces and interfaces poses technological and theoretical challenges in the study of morphogenesis, tissue engineering, and cancer. Different mechanisms are at play, including, cell–cell adhesion, cell motility, and proliferation. However, the relative importance of each one is elusive. Here, experiments with a culture of glioblastoma multiforme cells on a substrate are combined with in silico modeling to infer the rate of each mechanism. By parametrizing these rates, the time-dependence of the spatial correlation observed experimentally is reproduced. The obtained results suggest a reduction in cell–cell adhesion with the density of cells. The reason for such reduction and possible implications for the collective dynamics of cancer cells are discussed.
miR-27b antagonizes BMP signaling in early differentiation of human induced pluripotent stem cells
Authors: Lim Jaeeun , Sakai Eiko , Sakurai Fuminori , Mizuguchi Hiroyuki 
Published: October 2021

AbstractHuman induced pluripotent stem (hiPS) cells are feasible materials for studying the biological mechanisms underlying human embryogenesis. In early embryogenesis, definitive endoderm and mesoderm are differentiated from their common precursor, mesendoderm. Bone morphogenetic protein (BMP) signaling is responsible for regulating mesendoderm and mesoderm formation. Micro RNAs (miRNAs), short non-coding RNAs, broadly regulate biological processes via post-transcriptional repression. The expression of miR-27b, which is enriched in somatic cells, has been reported to increase through definitive endoderm and hepatic differentiation, but little is known about how miR-27b acts during early differentiation. Here, we used miR-27b-inducible hiPS cells to investigate the roles of miR-27b in the undifferentiated and early-differentiated stages. In undifferentiated hiPS cells, miR-27b suppressed the expression of pluripotency markers [alkaline phosphatase (AP) and nanog homeobox (NANOG)] and cell proliferation. Once differentiation began, miR-27b expression repressed phosphorylated SMAD1/5, the mediators of the BMP signaling, throughout definitive endoderm differentiation. Consistent with the above findings, miR-27b overexpression downregulated BMP-induced mesendodermal marker genes [Brachyury, mix paired-like homeobox 1 (MIXL1) and eomesodermin (EOMES)], suggesting that miR-27b had an inhibitory effect on early differentiation. Collectively, our findings revealed a novel antagonistic role of miR-27b in the BMP signaling pathway in the early differentiation of hiPS cells.
Effect of gamma irradiation on filtering facepiece respirators and SARS-CoV-2 detection
Authors: Al-Hadyan Khaled , Alsbeih Ghazi , Al-Harbi Najla , Judia Sara Bin , Al-Ghamdi Maha , Almousa Akram , Alsharif Ibtihaj , Bakheet Razan , Al-Romaih Khaldoun , Al-Mozaini Maha , Al-Ghamdi Salem , Moftah Belal , Alhmaid Rashed 
Published: October 2021

AbstractTo cope with the shortage of filtering facepiece respirators (FFRs) during the coronavirus (COVID-19) pandemic, healthcare institutions were forced to reuse FFRs after applying different decontamination methods including gamma-irradiation (GIR). The aim of this study was to evaluate the effect of GIR on the filtration efficiency (FE) of FFRs and on SARS-CoV-2 detection. The FE of 2 FFRs types (KN95 and N95-3 M masks) was assessed at different particle sizes (0.3–5 µm) following GIR (0–15 kGy) delivered at either typical (1.65 kGy/h) or low (0.5088 kGy/h) dose rates. The detection of two SARS-CoV-2 RNA genes (E and RdRp4) following GIR (0–50 kGy) was carried out using RT-qPCR assay. Both masks showed an overall significant (P < 0.001) reduction in FE with increased GIR doses. No significant differences were observed between GIR dose rates on FE. The GIR exhibited significant increases (P ≤ 0.001) in the cycle threshold values (ΔCt) of both genes, with no detection following high doses. In conclusion, complete degradation of SARS-CoV-2 RNA can be achieved by high GIR (≥ 30 kGy), suggesting its potential use in FFRs decontamination. However, GIR exhibited adverse effects on FE in dose- and particle size-dependent manners, rendering its use to decontaminate FFRs debatable.
Intention-based and sensory-based predictions
Authors: Darriba Álvaro , Hsu Yi-Fang , Van Ommen Sandrien , Waszak Florian 
Published: October 2021

AbstractWe inhabit a continuously changing world, where the ability to anticipate future states of the environment is critical for adaptation. Anticipation can be achieved by learning about the causal or temporal relationship between sensory events, as well as by learning to act on the environment to produce an intended effect. Together, sensory-based and intention-based predictions provide the flexibility needed to successfully adapt. Yet it is currently unknown whether the two sources of information are processed independently to form separate predictions, or are combined into a common prediction. To investigate this, we ran an experiment in which the final tone of two possible four-tone sequences could be predicted from the preceding tones in the sequence and/or from the participants’ intention to trigger that final tone. This tone could be congruent with both sensory-based and intention-based predictions, incongruent with both, or congruent with one while incongruent with the other. Trials where predictions were incongruent with each other yielded similar prediction error responses irrespectively of the violated prediction, indicating that both predictions were formulated and coexisted simultaneously. The violation of intention-based predictions yielded late additional error responses, suggesting that those violations underwent further differential processing which the violations of sensory-based predictions did not receive.
Comparison of mitral regurgitation severity assessments based on magnetic resonance imaging and echocardiography in patients with hypertrophic cardiomyopathy
Authors: Śpiewak Mateusz , Kłopotowski Mariusz , Kowalik Ewa , Mazurkiewicz Łukasz , Kożuch Katarzyna , Petryka-Mazurkiewicz Joanna , Miłosz-Wieczorek Barbara , Witkowski Adam , Klisiewicz Anna , Marczak Magdalena 
Published: October 2021

AbstractMitral regurgitation (MR), which is one of the factors responsible for heart failure symptoms and the development of atrial fibrillation, is an important feature of hypertrophic cardiomyopathy (HCM), and its presence affects which treatment options are chosen. Although cardiac magnetic resonance imaging (MRI) is considered the reference standard for assessing the regurgitant volume (RV) and fraction (RF), echocardiography is the most common method for assessing MR severity. Accordingly, the aim of this study was to compare the results of echocardiography and cardiac MRI for assessing MR severity in a cohort of patients with HCM. MR severity was assessed in 53 patients using cardiac MRI by determining the mitral RV (MRV) and mitral RF (MRF). The results were graded according to thresholds recommended in current guidelines. MR severity assessed by echocardiography was graded by integrating indices of severity. Greater than mild MR, as assessed using echocardiography, was present in 22 patients (41.5%) with HCM and in none of the control patients (p = 0.001). In all, 31 patients (58.5%) had no more than mild MR. When MR severity was assessed using different methods, either moderate (kappa = 0.44, 95% confidence interval = 0.21–0.67), poor or no agreement was found between MRI-derived and echocardiography-derived grades. HCM patients with echocardiography-derived moderate and severe MR had similar median MRVs and MRFs (p = 0.59 and p = 0.11, respectively). In HCM patients, cardiac MRI and echocardiography were at most in modest agreement in assessing MR severity. Importantly, echocardiography-derived moderate and severe MR were not distinguishable by either MRV or MRF.
A case series shows independent vestibular labyrinthine function after major surgical trauma to the human cochlea
Authors: Plontke Stefan K. , Rahne Torsten , Curthoys Ian S. , Håkansson Bo , Fröhlich Laura 
Published: October 2021

Abstract
Background
The receptors for hearing and balance are housed together in the labyrinth of the inner ear and share the same fluids. Surgical damage to either receptor system was widely believed to cause certain permanent loss of the receptor function of the other. That principle, however, has been called into question because there have been anecdotal reports in individual patients of at least partial preservation of cochlear function after major surgical damage to the vestibular division and vice versa.

Methods
We performed specific objective vestibular function tests before and after surgical trauma (partial or subtotal cochlear removal) for treatment of intracochlear tumors in 27 consecutive patients in a tertiary referral center. Vestibular function was assessed by calorics (low-frequency response of the lateral semicircular canal), vestibulo-ocular reflex by video head impulse test (vHIT) of the three semicircular canals, cervical and ocular vestibular evoked myogenic potentials (cVEMP, saccule and oVEMP, utricle). Preoperative and postoperative distributions were compared with paired t-tests.

Results
Here we show that there was no significant difference between pre- and post-operative measures for all tests of the five vestibular organs, and that after major surgical cochlear trauma, the vestibular receptors continue to function independently.

Conclusions
These surprising observations have important implications for our understanding of the function and the surgery of the peripheral auditory and vestibular system in general and open up new possibilities for the development, construction and evaluation of neural interfaces for electrical or optical stimulation of the peripheral auditory and vestibular nervous system.
Searching for an additional high-energy component in Fermi-LAT GRB afterglows
Authors: He Xin-Bo , Thomas Tam Pak-Hin , Long Guang-Bo , Sarathi Pal Partha , Zhang Yong , Zhang Li-Jun 
Published: October 2021

Context. The very high-energy (VHE; ≥100 GeV) component from at least two gamma-ray bursts (GRBs), that is, GRB 180720B and GRB 190114C, has been detected in the afterglow phase. It is widely discussed that the GeV to TeV emission originated from a synchrotron self-Compton (SSC) process. The VHE component may cause an upturn at the high-energy spectral ends in the Fermi-Large Area Telescope (Fermi-LAT) observing band.
Aims. We aim to find out whether an additional high-energy component commonly exists in the afterglows of Fermi-LAT GRBs. This study will help us to better understand how common it is for a GRB afterglow detected by Fermi-LAT to involve a VHE component.
Methods. First, we selected the GRBs that emit ≥10 GeV photons. The ≥10 GeV photons can be considered as a plausible proxy for a VHE component. We systematically analyzed 199 GRBs detected by Fermi-LAT from 2008–2019. If an additional high-energy component exists in the afterglows of Fermi-LAT GRBs, the best-fit spectral model could be a broken power law (BPL) model with an upturn above a break energy. We compared the afterglow spectra using power-law (PL) and BPL representations.
Results. Out of the 30 GRBs with ≥10 GeV photons that arrived after T90 (the time duration when 90% of the prompt emission was detected), 25 GRBs are tentatively or significantly detected at 0.1–200 GeV after 2 ×  T90. The spectrum of GRB 131231A shows an upturn above an energy break of 1.6 ± 0.8 GeV, supporting the BPL model. For GRB 131231A, we performed a modeling of its X-ray and γ-ray spectra and found that the SSC model can explain the upturn with acceptable parameter values. In the cases of GRB 190114C, GRB 171210A, GRB 150902A, GRB 130907A, GRB 130427A, and GRB 090902B, the improvement of the BPL fit compared to the PL fit is tentative or marginal.
Conclusions. There is no conclusive evidence that an additional higher energy component commonly exists in Fermi-LAT GRB afterglows, except for the group of Fermi-LAT GRBs mentioned above. Such an additional high-energy component may be explained by the SSC mechanism. Current and future VHE observations will provide important constraints on the issue.