bluuebunny/crossref_metadata_2025 huggingface dataset:
47 High-resolution ribosome profiling reveals translational selectivity in the mammalian blastocyst
Authors: Zhu L. K. , Ming H. , Liu S. C. , Iyyappan R. , Llano E. D. , Dvoran M. , Chen Q. , Susor A. , Zhou T. , Jiang Z. L.
Published: January 2021

Transcriptomic analyses of early mammalian embryos from multiple species have been comprehensively conducted in the last decade. However, mRNAs detected from overall transcriptomic profile of an embryo or a single cell do not necessarily represent their functional status, as there is a gap between the overall transcriptome and mRNAs that are actively translated. Ribosome profiling has been developed to infer the translational status of a specific mRNA species and thus analyse the genome-wide translatome. However, the broad application of ribosome profiling has been slowed by its complexity and the difficulty of adapting it to low-input samples such as embryos. In this study, we developed an ultra-low-input ribosome profiling protocol optimized for mammalian embryos and systematically analysed both polysome- and non-polysome-bound mRNA profiles of invitro-produced bovine blastocysts. Ten equal fractions were collected by means of sucrose density gradient and ultracentrifugation of lysates from 100 pooled blastocysts (n=2 pools), and subjected to RNA isolation and RNA sequencing. Our bioinformatics analyses of the mRNA profiles from each fraction along with the whole-transcriptome data revealed that compared with the overall transcriptome, there is a strong selection of mRNAs in the ribosome- and polysome-associated fractions, including transcriptional factors (e.g. POU5F1, ESRRB, AQP3, and APOA1) and genes involved in ribosome biogenesis, oxidative phosphorylation, and metabolic pathways, many of which are essential for the function of embryo implantation. We also identified novel epigenetic regulators selectively translated, including regulatory enzymes on histone modifications and RNA modifications (e.g. JMJD7, ALKBH4, ALKBH7, and METTL26). In addition, we confirmed the translation of the highly expressed, yet developmentally essential pathways in the blastocysts (e.g. Wnt and Notch signalling pathways). The selectively translated mRNAs were further validated by immunofluorescent staining at the protein level and cross-validated in both bovine and mouse blastocysts. Some of these genes show only modest expression in the overall transcriptome data. Their selective translation at the blastocyst stage is only being revealed by the ribosome fractions analyses, and their functions warrant future detailed investigations. In conclusion, this study reveals bona fide active translating mRNAs in the mammalian blastocyst. The low-input ribosome profiling protocol and the data presented here set an example and open future avenues for detailed ribosome fraction–based translatome analyses to reveal novel cellular/embryonic functional regulators beyond transcriptomic data.
49 The dynamic changes in uterine morphology and function during the proestrus-diestrus transition in beef cattle
Authors: da Silva F. A. C. C. , da Silva G. F. , Vieira B. S. , Neto A. L. , Junior G. A. Arantes , Silva A. G. , Nogueira G. P. , Pugliesi G. , Binelli M.
Published: January 2021

In cattle, early development of the non-attaching embryo depends exclusively on the biochemical properties of the intrauterine milieu. As the embryo transitions from the oviduct to the tip of the uterine horn around 4 days after oestrus, little is known about uterine functions that modulate the milieu composition and potentially determine pregnancy success. The objective was to characterise changes in uterine luminal fluid (ULF) accumulation and absorption, endometrial vascularity, and endometrial thickness in response to progesterone fluctuations during the peri-ovulatory period in beef heifers. Fourteen Bos indicus heifers that presented a prostaglandin F2α (PGF2α) responsive CL received 500µg of PGF2α analogue i.m. (PGF) and were examined daily by rectal B-mode and pulse-wave colour-Doppler ultrasonography until the fifth day after oestrus (oestrus=Day 0). Plasma progesterone (P4) concentrations were measured daily. Uterine luminal fluid score was given based on the accumulation of fluid throughout the entire organ (0, no fluid, to 4). Measurement of the main ovarian structures, endometrial thickness, uterine luminal fluid score, and luminal fluid area of the cranial portion of the uterine horn ipsilateral to the preovulatory follicle and subsequent CL were executed by B-mode ultrasonography and endometrial vascularity by colour Doppler. The fixed effect of day was analysed by ANOVA. There was an effect of day on endometrial vascularity, endometrial thickness, and uterine luminal fluid score (P≤0.01) as well as uterine luminal fluid area (P≤0.05). Endometrial vascularity and endometrial thickness increased after PGF injection to peak on Day −1, whereas uterine fluid score peaked on Day 0. Interestingly, cranial uterine luminal fluid area peaked twice, on Day −1 and Day 5. Vascularity, thickness, and fluid accumulation decreased gradually from Day 0 to Day 5. There was a negative correlation (r=−0.55) between the sum of daily P4 concentrations during proestrus (i.e. from PGF to oestrus) and the greatest ULF score measured (P=0.05). Length of proestrus was correlated negatively (r=−0.69) with the increase in uterine body thickness during proestrus (P=0.03). The sum of daily luminal fluid scores, from PGF injection to Day 5, was double for heifers grouped within the upper third for that variable compared with those grouped within the lower third. In conclusion, peri-ovulatory transformations in uterine morphology and function are dramatic and vary in duration and in intensity among animals. Temporal changes in intraluminal fluid accumulation and absorption at the site of embryo arrival may change its biochemical composition. Potential implications for embryo receptivity and reproductive outcomes deserve further investigation.
55 Donor age has the least influence on recovery, quality, and in vitro developmental competence of ovum pickup–based Holstein Friesian oocytes under subtropical conditions
Authors: Yaseen M. , Saleem M. , Nawaz M. , Ahmad N. , Riaz A.
Published: January 2021

The use of oocytes obtained from younger donors for invitro fertilization followed by embryo transfer represents an opportunity to accelerate genetic gain by reducing generation interval. The present study was designed to evaluate the effect of age of donor on the follicular population, recovery, quality and invitro developmental competence of ovum pickup based Holstein Friesian oocytes under subtropical conditions. A total of eight (n=8) Holstein Friesian (with proper oestrus cyclicity) were selected for the study and divided into 2 groups based on animal age: (1) heifers (n=4), 1.5 to 2 years of age, and (2) adults (n=4), 5 to 6 years of age. The study was conducted near Lahore (31°33′ N, 74°19′ E), Punjab, Pakistan, from November 2019 to February 2020. The animals were wave synchronized using the physiological method of wave synchronization. After 4 days of second dominant follicle puncture, the first ovum pickup was carried out and a total of nine (n=9) OPU sessions were held for each group. The COCs from the follicles were aspirated using a transvaginal ultrasound–guided needle. Following searching and grading, COCs of grade A, B and C were processed for IVM in 100-µL droplets of BO-IVM under mineral oil at 37°C, 5% CO2, and 95% humidity for 24h. The frozen semen of a high-pedigree bull was thawed at 37°C and observed for post-thaw sperm motility. The semen samples of the same bull having motility >50% were processed using the sperm swim-up method throughout the study. The IVF was carried out by placing the COCs and required amount of sperm in 100-µL droplets of BO-IVF at similar conditions for a maximum of 18h. The presumptive zygotes were denuded by gentle pipetting and cultured for a period of 7 days after placing in 100-µL drops of BO-IVC at 37°C, 5% CO2, 5% O2, and maximum humidity. The presumptive zygotes were observed for cleavage rate and blastocyst rate on Days 2 and 7 following COCs-sperm co-incubation. Data on the follicular population, oocytes recovered, and viable oocytes were analysed by the PROC GLIMMIX of SAS (SAS Institute Inc.), and proportional data were analysed by the Chi-squared method using SAS 9.1. COCs of grade AB (35.2 vs. 25.4%) were higher (P>0.05) in the adult group than in the heifer group, respectively. Similarly, COCs with grade CD (57.5 vs. 71.9%) were lower (P<0.05) in the adult group compared with the heifer group, respectively. However, the total follicles (6.55±0.42 vs. 6.39±0.39), number of COCs recovered (3.33±0.32 vs. 3.17±0.41), viable oocytes (3.08±0.29 vs. 3.08±0.39), cleavage rate (60.3 vs. 68.7%), and blastocyst rate (38.7 vs. 48.8%) did not differ (P>0.05) between the groups. To conclude, donor age up to third lactation, under subtropical conditions, does not affect invitro embryo production in Holstein Friesian undergoing repeated OPU.
69 Invitro production of ovine embryos using either fresh or frozen-thawed semen
Authors: Márquez-Márquez G. , Velázquez-Roque A. , Villaseñor-González F. , Kjelland M. , Álvarez-Gallardo H. , Romo S.
Published: January 2021

Invitro embryo production (IVP) is an important tool for genetic improvement in small ruminants. Semen quality is one of the most important aspects to consider for the success of this assisted reproductive technique. With ovine IVP, it is a common practice to use fresh semen for IVF, but this could be a problem because the differences between ejaculates from the same animal are well documented and a source of variation in IVP results. The objective of this research was to compare the effect of fresh and frozen–thawed domestic sheep (Ovis aries) semen on IVF for ovine IVP. The research was carried out in the reproduction laboratory at the Palominos Ranch (Jalisco, México). The IVP was performed with a continuous invitro culture system. Ovaries (n=186) were collected from a slaughterhouse (León, México) and transported to the laboratory within 2h in physiological saline solution (0.9% NaCl) supplemented with penicillin G (100IU mL−1) and streptomycin sulphate (100µg mL−1). For IVP, IVF-Bioscience™ media were used for IVM, IVF, and invitro culture (IVC). For IVM, the cumulus–oocyte complexes (COCs) were selected (only grades 1 and 2) and matured for 24h at 38.5°C in 5% CO2 in air and 100% humidity. Matured oocytes (n=1000) were invitro fertilized using either fresh or frozen–thawed semen (Triladyl™; Minitube) from the same sheep, at a concentration of 2×106 sperm mL−1, for 18h in 38.5°C, 5% CO2 in air, and 100% humidity. The presumptive zygotes were denuded by pipetting and set in IVC until Day 7 at 38.5°C, 5% CO2, 5% O2, and 90% N2 at 100% humidity. The percentages of cleavage, embryos with more than 6 cells, and blastocysts on Day 7 of culture were evaluated, based on the initial number of oocytes entering into IVM. Statistical analyses were carried out with the GLM procedure of SAS software (version 9.3; SAS Institute Inc.) to evaluate the results of fresh versus frozen–thawed (α level=0.05). Rates of cleavage, embryos with more than 6 cells, and blastocysts on Day 7 were similar (P>0.05): fresh 52.3±3.0%, 43.6±2.6%, and 34.3±2.9%, respectively; frozen–thawed: 53.3%±3.0, 41.1±2.6%, and 33.3±2.9%, respectively. In conclusion, under the conditions of this research, the use of fresh and frozen–thawed semen had similar results for ovine IVP.
87 Population estimate and morphology of ovarian preantral follicles in fetal and adult alpacas (Vicugna pacos)
Authors: Dipaz-Berrocal D. J. , Rojas G. , Mamani C. , Figueiredo J. R. , Mellisho E.
Published: January 2021

Preantral follicles are the largest ovarian follicle population and represent an important source of potentially competent oocytes. During the lifespan of the female this large population becomes atretic during their growth. In alpacas, there are few studies that estimate the number of preantral follicles. Therefore, the objective of the present study was to compare the population and morphology of preantral follicles in the ovaries of fetal and adult alpacas. Ovaries from alpacas in fetal (fetus during the last third of gestation, n=5) and adult stage (3–4 years, n=5) were collected at a local slaughterhouse. The whole ovaries were individually fixed overnight at room temperature, and later dehydrated in alcohol, cleared with xylene, and embedded in paraffin. Tissue were sectioned at 7μm with a rotating microtome. Then, sections were processed and stained with periodic acid Schiff and haematoxylin. Preantral follicles were classified for their development stage as primordial, transitional, primary, or secondary, according to the layer number and form of granulosa cells. Estimation of the number of preantral follicles was made by counting all follicles in each histological section. Only follicles in which the oocyte nucleus was visible were counted. In addition, for each follicle category (n=30 per group), oocyte and follicle diameters were measured using Motic Images Plus 2.0 software. The population estimate and follicular diameter were compared using Kruskal–Wallis test with significance set at P ≤ 0.05 using SPSS v.2 2 software (IBM Corp.). A total of 2174 histologic sections were analysed. The results showed a higher (P=0.045) number of preantral follicles (80 516.1±3623.9) for fetal alpacas compared with adult alpacas (67 870.8±2267.4). Also, primordial follicles population (31 543.4±2690) and morphologically normal follicles (98.2%) were higher (P=0.04) in fetus compared with those in the adult stage (2244.7±355.37; 76.35%) respectively. On the contrary, the diameters of primordial, transitional, and primary follicles (45.34±3.76; 52.38±6.22; 59.79±5.22µm) from adult alpaca were greater (P=0.04) than those of fetal preantral follicles (33.305±7.2; 36.715±3; 77.985±15.8µm). In conclusion, the preantral follicle population declines dramatically in adult alpaca and animals of this age show an increased percentage of degenerate primordial follicles.
Mammalian cell proliferation requires noncatalytic functions of O-GlcNAc transferase
Authors: Levine Zebulon G. , Potter Sarah C. , Joiner Cassandra M. , Fei George Q. , Nabet Behnam , Sonnett Matthew , Zachara Natasha E. , Gray Nathanael S. , Paulo Joao A. , Walker Suzanne
Published: January 2021

Significance

Mammalian cells contain only one glycosyltransferase, OGT, that operates in the nucleus and cytoplasm rather than the secretory pathway. OGT is required for cell proliferation, but a basic unanswered question is which OGT functions are essential. This question is challenging to address because OGT has thousands of glycosylation substrates, two different enzymatic activities, and a large number of binding partners. Here, by establishing genetic tools to replace endogenous OGT with variants that preserve only a subset of its activities, we show that only a low level of glycosylation activity is required to maintain cell viability; however, cell proliferation requires noncatalytic OGT function(s). The ability to replace OGT with variants provides a path to identifying its essential substrates and binding partners.
Agroecological practices for whole-system sustainability
Authors: Hawes Cathy , Iannetta Pietro P.M. , Squire Geoffrey R.
Published: January 2021

Current food production systems are major contributors to the environmental degradation that leads to climate change and biodiversity loss. Levels of production required for future food security cannot be met by further increases in inputs of non-renewable resources. The world’s food crops must therefore be managed in a sustainable way that maintains long-term ecological functioning, including nutrient, carbon and water cycles, soil quality, primary productivity, microbe-plant associations, pest and pathogen regulation, pollination and arable food web resilience. All of these are determined by agronomic practices at local and regional scales, and all are sustained by the abundance, diversity and functional composition of plants, microbes and invertebrates in the farmed ecosystem. Presence of viable populations and communities of these organisms is therefore essential for system resilience. Long-term sustainability must rely more heavily on the internal generation of products and regulatory ecosystem services than on external inputs. Fully closed systems are impossible to achieve in agriculture as the product is removed for human consumption. There is ample evidence, however, that semi-closed, regenerative, systems can harness the ecosystem services provided by functional biodiversity to enhance crop production whilst simultaneously improving environmental quality. Here, agroecological alternatives to intensive farming practices are reviewed, focusing on key functional indicators and whole-system integration of practical management options designed to achieve multiple beneficial outcomes at field and farm scales.
Recent progress in in situ/operando analysis tools for oxygen electrocatalysis
Authors: Yoo Ji Mun , Shin Heejong , Park Subin , Sung Yung-Eun
Published: January 2021

Fuel cell and water electrolyzer technology have been intensively investigated in the last decades toward sustainable and renewable energy conversion systems. For improved device performance and service life, nanostructured electrocatalysts on electrode have been extensively developed based on the principle of structure-activity-stability correlation. However, overall device efficiency is seriously hindered by sluggish oxygen electrocatalysis, including oxygen reduction reaction and oxygen evolution reaction. As a result, tremendous efforts have been made to construct the most active surfaces with robust durability. For knowledge-based approaches toward systematic development of highly functional nanostructures, fundamental principles within oxygen electrocatalysis should be uncovered including reaction intermediate, active site structures, and atomic dissolution from surface. However, conventionalex situcharacterizations only provide a static picture of electrode surfaces without electrocatalysis. On the other hand,in situ/operandoanalyses allow us to directly monitor dynamics on electrode under operating conditions. In this review, we will introduce a set ofin situ/operandoanalytical tools and summarize their contribution to fundamental researches on oxygen electrocatalysis. Taking both precious and non-precious electrocatalyst materials as examples, the most impending issues in oxygen electrocatalysis are covered within situ/operandostudies to highlight the power ofin situ/operandotechniques and encourage further efforts on advanced analytic techniques.
Measuring plasma-generated ·OH and O atoms in liquid using EPR spectroscopy and the non-selectivity of the HTA assay
Authors: Myers B , Ranieri P , Smirnova T , Hewitt P , Peterson D , Herrera Quesada M , Lenker E , Stapelmann K
Published: January 2021

Plasma-generated hydroxyl radicals (·OH) and oxygen atoms (O) produced by the COST reference plasma jet, a micro-scaled atmospheric pressure plasma jet, were investigated using a variety of experimental techniques. Several gas admixtures were studied to distinguish the contributions of the two reactive oxygen species. Large discrepancies between inferred aqueous ·OH densities were noted when using a 2-hydroxyterephthalic acid (HTA) fluorescence assay and electron paramagnetic resonance (EPR) measurements with the spin trap 5,5-dimethyl-1-pyrroline N-oxide—especially when oxygen was present in the feed gas. A series of follow-up experiments including optical emission spectroscopy, H2O2 quantification, and EPR measurements of atomic oxygen using the spin trap 2,2,6,6-tetramethylpiperidine, revealed that the inconsistencies between the measured aqueous ·OH were likely due to the propensity of atomic oxygen to hydroxylate TA in a manner indistinguishable from ·OH. This renders the HTA assay non-selective when both ·OH radicals and atomic oxygen are present, which we report for all three gas admixtures in our experiments. Additionally, considerable degradation of both HTA and the spin adducts measured using EPR spectroscopy was apparent, meaning actual radical densities in the plasma-treated liquid may be considerably higher than implied. Degradation rates compared favorably to previously measured gas phase densities of atomic oxygen in the predecessor of the COST jet and reported degradation of other chemical probes. These results show the prolific role of atomic oxygen in plasma-induced liquid chemistry and caution against diagnostic techniques that are unable to account for it.
Superconductivity in topological insulator β-PdBi2 under pressure
Authors: Suzuki Ai , Taguchi Tomoya , Li Huan , Wang Yanan , Ishii Hirofumi , Liao Yen-Fa , Goto Hidenori , Eguchi Ritsuko , Kubozono Yoshihiro
Published: January 2021

The topological insulator PdBi2 exhibits two different crystal phases at ambient pressure, i.e., ‘α-PdBi2’ and ‘ -PdBi2’. The pressure dependence of crystal structure and superconductivity of α-PdBi2 has been fully elucidated thus far. However, the physical properties of β-PdBi2 crystals under pressure have not been sufficiently investigated. In this study, we fully investigate the crystal structure and superconductivity of β-PdBi2 under pressure based on synchrotron x-ray diffraction (XRD) patterns. The temperature dependence of β-PdBi2 indicates its superconductivity with a superconducting transition temperature (T
c) as high as 4.10 K, and its crystal structure is tetragonal [space group of I4/mmm (no. 139)]. The XRD patterns at 0–22.0 GPa indicate no structural phase transitions, and the unit cell volume shrinks monotonically with pressure, unlike the behavior of α-PdBi2. Furthermore, α-PdBi2 transformed to β-PdBi2 under pressure. This suggests that β-PdBi2 is stable under pressure. The superconductivity is clearly observed at 0–11.8 GPa, and the value of T
c is almost constant at ∼4.4 K. The temperature dependence of the upper critical field at ambient pressure and 10.7 GPa indicates that the superconductivity is not attributed to a simple s-wave dirty limit but an s-wave clean or p-wave polar model. This is the first systematic study of superconductivity of topological insulator β-PdBi2 under pressure.
Magnetoelastic coupling and critical behavior of some strongly correlated magnetic systems
Authors: Dutta Kishore , Singh Rohit
Published: January 2021

The strongly correlated magnetic systems are attracting continuous attention in current condensed matter research due to their very compelling physics and promising technological applications. Being a host to charge, spin, and lattice degrees of freedom, such materials exhibit a variety of phases, and investigation of their physical behavior near such a phase transition bears an immense possibility. This review summarizes the recent progress in elucidating the role of magnetoelastic coupling on the critical behavior of some technologically important class of strongly correlated magnetic systems such as perovskite magnetites, uranium ferromagnetic superconductors, and multiferroic hexagonal manganites. It begins with encapsulation of various experimental findings and then proceeds toward describing how such experiments motivate theories within the Ginzburg–Landau phenomenological picture in order to capture the physics near a magnetic phase transition of such systems. The theoretical results that are obtained by implementing Wilson’s renormalization-group to nonlocal Ginzburg–Landau model Hamiltonians are also highlighted. A list of possible experimental realizations of the coupled model Hamiltonians elucidates the importance of spin–lattice coupling near a critical point of strongly correlated magnetic systems.
Mn-induced spin glass behavior in metallic Ir3Sn7−x
Mn
x
Authors: Speer Smita , Marshall Madalynn , Chang Hong , Nepal Roshan , Blawat Joanna , Chapai Ramakanta , Gui Xin , Xie Weiwei , Jin Rongying
Published: January 2021

Transition metal stannides are usually semiconductors with a narrow band gap. We report experimental investigation on metallic Ir3Sn7–x
Mn
x
(x = 0 and 0.56). Single crystal x-ray diffraction refinement indicates that Ir3Sn7–x
Mn
x
crystals form a cubic structure (space group Im

3

̄

m) with the lattice parameter a = 9.362(4) Å for x = 0 and 9.328(6) Å for x = 0.56. The electrical resistivity shows metallic behavior between 2 K and 300 K with T
2 dependence at T < 30 K for x = 0, reflecting the Fermi-liquid ground state. While Ir3Sn7 exhibits weak diamagnetism, partial substitution of Sn by Mn results in spin glass behavior in Ir3Sn7−x
Mn
x
below T
g ∼ 13 K for x = 0.56. Remarkably, an upturn in the resistivity is observed in x = 0.56 below ∼2T
g, suggesting strong spin fluctuation. This fluctuation is suppressed by the application of magnetic field, which is reflected in the observation of negative magnetoresistance. The unusual properties that emerge due to Mn doping are discussed.
Albumin diffusivity coefficient estimation in imitated porous structure of interstitial space by integration of albumin diffusion model (ADM) to electrical impedance tomography (EIT)
Authors: Dharma Irfan Aditya , Kawashima Daisuke , Baidillah Marlin Ramadhan , Darma Panji Nursetia , Takei Masahiro
Published: January 2021

Albumin diffusivity coefficient

D

I

a

in imitated porous structure of interstitial space has been estimated by means of the integration of albumin diffusion model (ADM) to electrical impedance tomography (EIT) (iADM-EIT) under five different porosity

ϕ

conditions (from

ϕ
1

=

0.922 to

ϕ
5

=

0.990) for transport phenomena quantification. The iADM-EIT was conducted by applying an iterative curve-fitting between spatio-temporal albumin concentration

C

I

a

derived from ADM and spatio-temporal distribution of conductivity difference

Δ

σ

reconstructed by EIT. The essential point of the iADM-EIT is the quantification of experimental

C

I

ex

a

from

Δ

σ

by establishing a constitutive relationship among

C

I

ex

a

,

Δ

σ

, and

ϕ

. ADM is developed based on Fick’s second law implemented in Krogh tissue cylinder. EIT is performed to image the

Δ

σ

caused by increase of

C

I

a

due to albumin diffusion phenomenon from a capillary to the imitated porous structure. The imitated porous structure is manufactured with agarose gel in a dynamic phantom including a capillary. As a result, the relative albumin diffusivity coefficient

D

I

a

/

D

0

a

(

D

0

a

: free diffusivity of albumin coefficient) is increased with the increase of

ϕ

in the range from 0.271 to 0.694, which are correspondent to the literature data with percent average relative error

δ

  = 6.83 ± 2.72%.
Palladium zero-mode waveguides for optical single-molecule detection with nanopores
Authors: Klughammer Nils , Dekker Cees
Published: January 2021

Holes in metal films do not allow the propagation of light if the wavelength is much larger than the hole diameter, establishing such nanopores as so-called zero-mode waveguides (ZMWs). Molecules, on the other hand, can still pass through these holes. We use this to detect individual fluorophore-labelled molecules as they travel through a ZMW and thereby traverse from the dark region to the illuminated side, upon which they emit fluorescent light. This is beneficial both for background suppression and to prevent premature bleaching. We use palladium as a novel metal-film material for ZMWs, which is advantageous compared to conventionally used metals. We demonstrate that it is possible to simultaneously detect translocations of individual free fluorophores of different colours. Labelled DNA and protein biomolecules can also be detected at the single-molecule level with a high signal-to-noise ratio and at high bandwidth, which opens the door to a variety of single-molecule biophysics studies.
Ionizing photon interactions modulate the optical properties of crystals with femtosecond scale temporal resolution
Authors: Tao Li , Coffee Ryan N , Jeong Diana , Levin Craig S
Published: January 2021

In this work, we continue our study of a new method for the detection of ionizing radiation with the potential for a dramatic improvement in coincidence time resolution (CTR) for time-of-flight positron emission tomography (ToF-PET) using the modulation of a material’s optical properties instead of the scintillation mechanism. Our previous work has shown that for non-scintillation materials such as bismuth silicon oxide (BSO) and cadmium telluride (CdTe), their refractive index can be modulated by annihilation photon interactions. The ultrafast nature of this process however remains unexplored. The ionizing radiation-induced charge carriers alter the local band structure in these materials, thus changing the complex refractive index. This mechanism is routinely used at the linac coherent light source (LCLS) facility of the SLAC National Accelerator Laboratory to measure x-ray pulse arrival times with femtosecond scale resolution for photon energies between 0.5 and 10 keV. The method described here follows that example by using a frequency chirped visible continuum pulse to provide a monotonic wavelength-to-time mapping by which one can measure the time-dependent refractive index modulation. In addition, we describe an interference-based measurement setup that allows for significantly improved sensitivity while preserving a timing precision of approximately 10 fs (σ) when measuring the arrival time of below 10 keV x-ray pulses with yttrium aluminum garnet (YAG) crystal. The method is presented in the context of ToF-PET application with further discussions on the potential CTR achievable if a similar detection concept is adopted for detecting 511 keV photons. Semi-empirical analysis indicates that the predicted CTR achievable is on the order of 1 ps (FWHM).
Electric field and turbulence in global Braginskii simulations across the ASDEX Upgrade edge and scrape-off layer
Authors: Zholobenko W , Body T , Manz P , Stegmeir A , Zhu B , Griener M , Conway G D , Coster D , Jenko F
Published: January 2021

Turbulence simulations in diverted geometry across the edge and scrape-off layer (SOL) of ASDEX Upgrade are performed with the GRILLIX code (Stegmeir et al 2019 Phys. Plasmas
26 052517). The underlying global (full-f) drift-reduced Braginskii model allows to concurrently study the self-consistent dynamics of the turbulence and the background as well as the evolution of toroidal and zonal flows. Different contributions to the radial electric field are identified. The dominant contribution on closed flux surfaces comes from the ion pressure gradient, due to the diamagnetic drift in the curved magnetic field. Large deviations can be induced, in particular, by the polarization particle flux, leading to zonal flows. The latter are driven by small-scale eddies, but do not exhibit much impact on the overall transport which is driven by ballooning modes at larger scales. Ion viscosity is found to be important in damping poloidal rotation through adjusting of the parallel velocity profile, but not via direct vorticity damping. The zonal flow drive peaks at the separatrix, where a strong shear layer forms due to the sheath-induced counter-propagating SOL flow, allowing for the formation of a transport barrier. The temperature profile across the separatrix is determined by the competition between cross-field transport and outflow in the SOL, the latter being largely controlled by the parallel heat conductivity.
ASCOT simulations of 14 MeV neutron rates in W7-X: effect of magnetic configuration
Authors: Kontula J , Koschinsky J P , Äkäslompolo S , Kurki-Suonio T
Published: January 2021

Neutron production rates in fusion devices are determined not only by the kinetic profiles but also the fast ion slowing-down distributions. In this work, we investigate the effect of magnetic configuration on neutron production rates in future deuterium plasmas in the Wendelstein 7-X stellarator. The neutral beam injection, beam and triton slowing-down distributions, and the fusion reactivity are simulated with the ASCOT suite of codes. The results indicate that the magnetic configuration has only a small effect on the production of 2.45 MeV neutrons from thermonuclear and beam-target fusion. The 14.1 MeV neutron production rates were found to be between 1.49 × 1012 and

1.67
×

10

12

 

s

−
1

, which is estimated to be sufficient for a time-resolved detection using a scintillating fiber detector, although only in high-performance discharges.
Enhancing teleportation of a single-qubit state by the unitary transformation in arbitrary decoherence rate
Authors: Chen Zun-Yi , Xu Jin-Rong , Yu Jiangying , Hou Kui
Published: January 2021

The proposal of the quantum teleportation(QT) is to transfer an unknown quantum state from one place to another through local operations and classical communication. However, the efficiency of standard QT will be significantly reduced due to the influence of the inevitable noise in environments. In this work, we propose two schemes to improve the efficiency of the QT protocol when quantum channel is subjected to bit-flip or phase-flip noise. We find that the so-called more entanglement means low efficiency in the performance of the standard teleportation protocol, and the optimal fidelity is obtained only by using the appropriate unitary operation. Specially, we show that the optimal averaged fidelity to our schemes is always more than the best classically achievable fidelity 2/3. We also provide a physical explanation of the obtained conclusions and our results will be helpful for improving quantum communication with real implementation.
Guided assembly of cancer ellipsoid on suspended hydrogel microfibers estimates multi-cellular traction force
Authors: Lee Cheng-Tai , Gill Elisabeth L , Wang Wenyu , Gerigk Magda , Terentjev Eugene M , Shery Huang Yan Yan
Published: January 2021

Three-dimensional (3D) multi-cellular aggregates hold important applications in tissue engineering and in vitro biological modeling. Probing the intrinsic forces generated during the aggregation process, could open up new possibilities in advancing the discovery of tissue mechanics-based biomarkers. We use individually suspended, and tethered gelatin hydrogel microfibers to guide multicellular aggregation of brain cancer cells (glioblastoma cell line, U87), forming characteristic cancer ‘ellipsoids’. Over a culture period of up to 13 days, U87 aggregates evolve from a flexible cell string with cell coverage following the relaxed and curly fiber contour; to a distinct ellipsoid-on-string morphology, where the fiber segment connecting the ellipsoid poles become taut. Fluorescence imaging revealed the fiber segment embedded within the ellipsoidal aggregate to exhibit a morphological transition analogous to filament buckling under a compressive force. By treating the multicellular aggregate as an effective elastic medium where the microfiber is embedded, we applied a filament post-buckling theory to model the fiber morphology, deducing the apparent elasticity of the cancer ellipsoid medium, as well as the collective traction force inherent in the aggregation process.
Edge effect and interface confinement modulated strain distribution and interface adhesion energy in graphene/Si system
Authors: Huang Ying-Di , Xie Jia-Ting , Hu Su-Mei , He Yan
Published: January 2021

In order to clarify the edge and interface effect on the adhesion energy between graphene (Gr) and its substrate, a theoretical model is proposed to study the interaction and strain distribution of Gr/Si system in terms of continuum medium mechanics and nanothermodynamics. We find that the interface separation and adhesion energy are determined by the thickness of Gr and substrate. The disturbed interaction and redistributed strain in the Gr/Si system induced by the effect of surface and interface can make the interface adhesion energy decrease with increasing thickness of Gr and diminishing thickness of Si. Moreover, our results show that the smaller area of Gr is more likely to adhere to the substrate since the edge effect improves the active energy and strain energy. Our predictions can be expected to be a guide for designing high performance of Gr-based electronic devices.
Three-dimensional cytoplasmic calcium propagation with boundaries
Authors: Jiang Han-Yu , He Jun
Published: January 2021

Ca2+ plays an important role in cell signal transduction. Its intracellular propagation is the most basic process of Ca2+ signaling, such as calcium wave and double messenger system. In this work, with both numerical simulation and mean field ansatz, the three-dimensional probability distribution of Ca2+, which is read out by phosphorylation, is studied in two scenarios with boundaries. The coverage of distribution of Ca2+ is found at an order of magnitude of μm, which is consistent with experimental observed calcium spike and wave. Our results suggest that the double messenger system may occur in the ER-PM junction to acquire great efficiency. The buffer effect of kinase is also discussed by calculating the average position of phosphorylations and free Ca2+. The results are helpful to understand the mechanism of Ca2+ signaling.
Fast-ion pressure dominating the mass dependence of the core heat transport in ASDEX Upgrade H-modes
Authors: Schneider P.A. , Bonanomi N. , Angioni C. , Weiland M. , Cavedon M. , David P. , Fischer R. , Hennequin P. , Hobirk J. , Kappatou A. , Kurzan B. , McDermott R.M. , Plank U. , Pütterich T. , Ryter F. , Willensdorfer M. , the ASDEX Upgrade Team  , and the EUROfusion MST1 Team
Published: January 2021

H-mode plasmas in ASDEX Upgrade (AUG) using different hydrogen isotopes are analysed with respect to their core transport properties. The experimental results are discussed and we present gyrokinetic simulations which are able to reproduce the experimental observations. A novel strategy allows us to disentangle core and pedestal physics by mitigating the isotopic dependence of pedestal properties while keeping the heat and particle sources the same. Matched pedestal profiles are obtained between hydrogen (H) and deuterium (D) plasmas when increasing the triangularity in H plasmas with respect to D plasmas. In the core of these plasmas little isotopic dependence is observed when the fast-ion content is low W
fast/W
th < 1/3. Quasi-linear modelling with TGLF reproduces the experimental trends under these conditions. For larger fast-ion fractions an isotope dependence is observed in the core heat transport. This is related to a difference in fast-ion stabilization of turbulent transport. The fast-ion pressure in H and D plasmas is different due to the mass dependence in the fast-ion slowing down time as well as to operational restrictions when heating with H neutral beam injection (H-NBI) or D-NBI. Typically, W
fast,H < 1/2W
fast,D for comparable NBI heating powers in AUG. The gyrokinetic analysis shows that linear growth rates of ITG modes do not show a pure gyro-Bohm mass dependence, but follow the experimentally observed mass dependence when taking collisions, EM-effects and fast ions into account. Non-linear gyrokinetic simulations reproduce the experimental heat fluxes for different isotopes when fast ions are included. This highlights the role of the fast-ion pressure as a key element to explain the observed differences in the core of H and D plasmas.
Ballistic propagation of a local impact in the one-dimensional XY model
Authors: Yoshinaga Atsuki
Published: January 2021

Light-cone-like propagation of information is a universal phenomenon of nonequilibrium dynamics of integrable spin systems. In this paper, we investigate propagation of a local impact in the one-dimensional XY model with the anisotropy γ in a magnetic field h by calculating the magnetization profile. Applying a local and instantaneous unitary operation to the ground state, which we refer to as the local-impact protocol, we numerically observe various types of light-cone-like propagation in the parameter region 0 ⩽ γ ⩽ 1 and 0 ⩽ h ⩽ 2 of the model. By combining numerical integration with an asymptotic analysis, we find the following: (i) for |h| ⩾ |1 − γ
2| except for the case on the line h = 1 with

0
<
γ
<

3

/
2

, a wave front propagates with the maximum group velocity of quasiparticles, except for the case γ = 1 and 0 < h < 1, in which there is no clear wave front; (ii) for |h| < |1 − γ
2| as well as on the line h = 1 with

0
<
γ
<

3

/
2

, a second wave front appears owing to multiple local extrema of the group velocity; (iii) for |h| = |1 − γ
2|, edges of the second wave front collapses at the origin, and as a result, the magnetization profile exhibits a ridge at the impacted site. Furthermore, we find by an asymptotic analysis that the height of the wave front decays in a power law in time t with various exponents depending on the model parameters: the wave fronts exhibit a power-law decay t
−2/3 except for the line h = 1, on which the decay can be given by either ∼t
−3/5 or ∼t
−1; the ridge at the impacted site for |h| = |1 − γ
2| shows the decay t
−1/2 as opposed to the decay t
−1 in other cases.
Stationary properties of a non-Markovian Brownian gyrator
Authors: Nascimento Eduardo dos S , Morgado Welles A M
Published: January 2021

We investigate the stochastic behavior of a non-Markovian version of an elementary Brownian gyrator. The model is defined by overdamped Langevin-like dynamics with a two-dimensional harmonic potential that presents distinct principal axes and is coupled to heat baths at different temperatures. The thermal noises are assumed to be Gaussian, and are related to friction forces through a dissipation memory kernel. The stationary states present rotational motion with non-trivial average torques due to harmonic, friction and fluctuating thermal forces. However, the Markovian limit of the system exhibits a zero average torque produced by fluctuating thermal forces. For the case of stochastic torque exerted by harmonic force, the cumulant-generating function is calculated exactly. We also study the average heat fluxes in the steady-state regime, where a memory-dependent behavior is observed.
The open XXZ chain at Δ = −1/2 and the boundary quantum Knizhnik–Zamolodchikov equations
Authors: Hagendorf Christian , Liénardy Jean
Published: January 2021

The open XXZ spin chain with the anisotropy parameter

Δ
=
−

1

2

and diagonal boundary magnetic fields that depend on a parameter x is studied. For real x > 0, the exact finite-size ground-state eigenvalue of the spin-chain Hamiltonian is explicitly computed. In a suitable normalisation, the ground-state components are characterised as polynomials in x with integer coefficients. Linear sum rules and special components of this eigenvector are explicitly computed in terms of determinant formulas. These results follow from the construction of a contour-integral solution to the boundary quantum Knizhnik–Zamolodchikov equations associated with the R-matrix and diagonal K-matrices of the six-vertex model. A relation between this solution and a weighted enumeration of totally-symmetric alternating sign matrices is conjectured.
Backward bifurcation arises from the smoking transmission model considering media campaign
Authors: Fatimah M. , Aldila D. , Handari B. D.
Published: January 2021

In this paper, we present and analyze a smoking cessation model with intervention from media campaigns. In our model, we consider potential smokers choosing not to smoke because of media campaign interventions. From the mathematical analysis, we obtain a threshold value of the model, called the basic reproduction number, which is the threshold condition for the smoking-free and endemic equilibrium stability. Next, it is shown that two endemic equilibrium may exist when the threshold basic reproduction number less than unity, and a unique endemic equilibrium exists if the threshold basic reproduction number exceeds unity. Using the center-manifold theory, we show that a backward bifurcation may occur when the value of the basic reproduction number equal to unity. This result implies that the classical epidemiological requirement of making basic reproduction number less than unity is no longer sufficient, although necessary, for effectively controlling the spread of smoking in a population. The numerical simulation was conducted for several scenarios to support and visualize our analytical results.
Applications of cuckoo search and ant lion optimization for analyzing protein-protein interaction through regularized Markov clustering on coronavirus
Authors: Rizki A , Bustamam A , Sarwinda D
Published: January 2021

All living viruses have important structures such as protein. Proteins can interact with each other forming large networks of Protein-Protein Interaction (PPI). In order to facilitate the study of these PPI networks, there needs to be clustering analysis of the PPI. In this research, we use PPI network datasets from SARS-CoV-2 and humans. The interactions of the PPI network will then be formed into graphs. Regularized Markov Clustering (RMCL) is used to perform graph clustering. RMCL consists of three main steps which are regularization, inflation, and pruning. The RMCL algorithm is a variant of Markov Clustering (MCL). However, the inflation parameter in RMCL must be inputted manually by the user to obtain the best results. To solve the limitations of RMCL, we developed a new method by combining each Cuckoo Search (CS) and Ant Lion Optimization (ALO) with the original RMCL algorithm. The optimizers are used to optimize the inflation parameter in RMCL. CS and ALO are a part of swarm intelligence which is inspired by the behaviour of cuckoo birds and antlions in nature. The results show that the interactions formed from CS-RMCL vary from 1401 to 1402. It is more stable than the interactions formed from ALO-RMCL which ranges from 1408 to 3641. The difference between the best elite in each iteration of ALO-RMCL is very influential to the interaction compared to the best nest from the CS-RMCL.
Enhanced proliferation and angiogenic phenotype of endothelial cells via negatively-charged alginate and chondroitin sulfate microsphere hydrogels
Authors: Xiong Xiong , Xiao Wen , Zhou Sijie , Cui Rongwei , Xu Hockin H K , Qu Shuxin
Published: January 2021

Sodium alginate-based hydrogel was the one of the most used polymers for cell delivery. However, the adsorption of extracellular matrix and proteins was inhibited due to the formation of a hydrated surface layer of these hydrogels. In this study, a novel cell delivery system, negatively-charged alginate and chondroitin sulfate microsphere hydrogel (nCACSMH), was fabricated with excellent permeability and biocompatibility in the action of a high voltage direct-current electric field. Negative charge was introduced to the surface of nCACSMH to obtain the expanded network and enhanced permeability. Additionally, the increasing content of chondroitin sulfate in nCACSMH could give rise to the charge density and its asymmetric structure, thus the uneven, plicate and expanded surface of nCACSMH which was favorable to cell proliferation was developed. Moreover, chondroitin sulfate was released with the degradation of nCACSMH, which played a crucial role in maintaining the normal physiological functions of cells. Thus the proliferation of human umbilical vein endothelial cells (HUVECs) was further accelerated and the angiogenesis related genes expression in endothelial cells was continuously and dramatically up-regulated. After 4 d, the proliferation and viability of HUVECs were significantly improved, the cells were distributed evenly in nCACSMH. The novel nCACSMH has the potential to be used as cell delivery, three-dimensional (3D) cell cultures for cell therapy, 3D bioprinting, high-throughput screening for drugs, and disease model for regeneration and constructing of tissue engineering.