bluuebunny/crossref_metadata_2025 huggingface dataset:
Numerical study of supersonic boundary-layer modal stability for a slightly rarefied gas using Navier—Stokes approach
Authors: Ou Jihui , Chen Jie
Published: November 2021

In this paper, a systematic study on the supersonic boundary-layer modal stability for a slightly rarefied gas is conducted by considering velocity slip and temperature jump effects in the Navier–Stokes (NS) equations. The effects of slip boundary on the first- and second-mode instability at different conditions are presented in detail. The laminar flow is obtained by solving the NS equations along with no-slip and slip boundary conditions, which shows that the slip boundary causes the boundary layer becoming thinner and the supersonic region near the wall becoming narrower. The perturbation slip boundary conditions at the wall and their influence on the stability are carefully discussed. The tangential momentum accommodation coefficient and the thermal accommodation coefficient are set equal or unequal for a broad range to study the combined or leading effects of velocity slip and temperature jump, respectively. It is found that velocity slip significantly stabilizes the second-mode disturbances while largely destabilizes the first-mode perturbations. On the contrary, the temperature jump apparently enhances the second-mode instability, while it has little influence on the first mode. When velocity slip and temperature jump are both present, the first mode is more destabilized, while a competitive effect acts on the second mode. Additional results show that the neutral stability curves for the second and third modes as well as the synchronization between fast and slow modes are delayed further downstream due to velocity slip. These findings are shown consistently regardless of the wall cooling for both supersonic and hypersonic flows.
Stress hyperuniformity and transient oscillatory-exponential correlation decay as signatures of strength vs fragility in glasses
Authors: Lemaître Anaël
Published: November 2021

We examine and compare the local stress autocorrelation in the inherent states of a fragile and a strong glass: the Kob–Andersen (KA) binary mixture and the Beest–Kramer–Santen model of silica. For both systems, local (domain-averaged) stress fluctuations asymptotically reach the normal inverse-volume decay in the large domain limit; accordingly, the real-space stress autocorrelation presents long-range power law tails. However, in the case of silica, local stress fluctuations display a high degree of hyperuniformity, i.e., their asymptotic (normal) decay is disproportionately smaller than their bond level amplitude. This property causes the asymptotic power law tails of the real-space stress autocorrelation to be swamped, up to very large distances (several nanometers), by an intermediate oscillatory-exponential decay regime. Similar contributions exist in the KA stress autocorrelation, but they never can be considered as dominating the power law decay and fully disappear when stress is coarse-grained beyond one interatomic distance. Our observations document that the relevance of power-law stress correlation may constitute a key discriminating feature between strong and fragile glasses. Meanwhile, they highlight that the notion of local stress in atomistic systems involves by necessity a choice of observation (coarse-graining) scale, the relevant value of which depends, in principle, on both the model and the phenomenon studied.
Hard core lattice gas with third next-nearest neighbor exclusion on triangular lattice: One or two phase transitions?
Authors: Jaleel Asweel Ahmed A. , Mandal Dipanjan , Rajesh R.
Published: November 2021

We obtain the phase diagram of the hard core lattice gas with third nearest neighbor exclusion on the triangular lattice using Monte Carlo simulations that are based on a rejection-free flat histogram algorithm. In a recent paper [Darjani et al., J. Chem. Phys. 151, 104702 (2019)], it was claimed that the lattice gas with third nearest neighbor exclusion undergoes two phase transitions with increasing density with the phase at intermediate densities exhibiting hexatic order with continuously varying exponents. Although a hexatic phase is expected when the exclusion range is large, it has not been seen earlier in hard core lattice gases with short range exclusion. In this paper, by numerically determining the entropies for all densities, we show that there is only a single phase transition in the system between a low-density fluid phase and a high density ordered sublattice phase and that a hexatic phase is absent. The transition is shown to be first order in nature, and the critical parameters are determined accurately.
Chaos and subharmonic bifurcations of a soft Duffing oscillator with a non-smooth periodic perturbation and harmonic excitation
Authors: Zhou Liangqiang , Chen Fangqi
Published: November 2021

Chaotic dynamics and subharmonic bifurcations of a soft Duffing oscillator with a non-smooth periodic perturbation and a harmonic excitation are investigated analytically in this paper. With the Fourier series, the system is expanded to the equivalent smooth system, and chaos arising from heteroclinic intersections is studied with the Melnikov method. The chaotic feature on the system parameters is investigated in detail. Some new interesting dynamic phenomena, such as chaotic bands for some excitation frequencies, are presented. The relationship between the frequency range of chaotic bands and the amplitude of the excitation as well as the damping is obtained analytically. Particularly, for some system parameters satisfying a particular relationship, chaos cannot occur for any excitation amplitudes or frequencies. Subharmonic bifurcations are investigated with a subharmonic Melnikov method. It is analytically proved that the system may undergo chaotic motions through infinite or finite odd order subharmonic bifurcations. Numerical simulations are given to verify the chaos threshold and revolution from subharmonic bifurcations to chaos obtained by analytical methods.
Phototransferred thermoluminescence of BeO: Time-response profiles and mechanisms
Authors: Chithambo M. L. , Kalita J. M.
Published: November 2021

Phototransferred thermoluminescence (PTTL) from BeO is reported. The conventional TL glow curve has five peaks, I–V, at 50, 182, 283, 437, and 535 °C when measured at 1 °C s−1 The dominant one is peak II. Only the first three reappear under phototransfer. Electron traps for peaks IV and V weakly contribute to the PTTL. The PTTL at peak III, supposedly associated with these weak donors, is counterintuitively intense. All PTTL peaks are affected by light-induced fading, thermal quenching, and all but peak II by thermal fading. The activation energy for thermal quenching was found as 0.56±0.02, 0.53±0.05, and 0.94±0.07eV using peaks I, II, and III, respectively. Electronic processes relevant in the PTTL of BeO are discussed. PTTL time-response profiles are analyzed using systems of coupled linear differential equations as well as by theoretical modeling.
Quantum dynamics simulation of intramolecular singlet fission in covalently linked tetracene dimer
Authors: Mardazad Sam , Xu Yihe , Yang Xuexiao , Grundner Martin , Schollwöck Ulrich , Ma Haibo , Paeckel Sebastian
Published: November 2021

In this work, we study singlet fission in tetracene para-dimers, covalently linked by a phenyl group. In contrast to most previous studies, we account for the full quantum dynamics of the combined excitonic and vibrational system. For our simulations, we choose a numerically unbiased representation of the molecule’s wave function, enabling us to compare with experiments, exhibiting good agreement. Having access to the full wave function allows us to study in detail the post-quench dynamics of the excitons. Here, one of our main findings is the identification of a time scale t0 ≈ 35 fs dominated by coherent dynamics. It is within this time scale that the larger fraction of the singlet fission yield is generated. We also report on a reduced number of phononic modes that play a crucial role in the energy transfer between excitonic and vibrational systems. Notably, the oscillation frequency of these modes coincides with the observed electronic coherence time t0. We extend our investigations by also studying the dependency of the dynamics on the excitonic energy levels that, for instance, can be experimentally tuned by means of the solvent polarity. Here, our findings indicate that the singlet fission yield can be doubled, while the electronic coherence time t0 is mainly unaffected.
Electrostatic correlations in electrolytes: Contribution of screening ion interactions to the excess chemical potential
Authors: Gillespie Dirk , Valiskó Mónika , Boda Dezső
Published: November 2021

A new theory for the electrostatic component of the chemical potential for homogeneous electrolytes modeled with the primitive model is developed. This Mean Countershell Approximation (MCSA) is an analytic theory derived by including the interactions between the ions’ screening clouds. At molar concentrations, these contribute substantially to the excess chemical potential but are absent in classical Debye–Hückel and Mean Spherical Approximation (MSA) theories. Simulations show that the MCSA is highly accurate, including at the low dielectric constants of ionic liquids. While sharing a mathematical framework with the MSA, the MCSA has simpler formulas and is qualitatively more accurate when there is ion size asymmetry.
Doubling of invariant curves and chaos in three-dimensional diffeomorphisms
Authors: Gonchenko A. S. , Gonchenko S. V. , Turaev D.
Published: November 2021

This paper gives a review of doubling bifurcations of closed invariant curves. We also discuss the role of the curve-doubling bifurcations in the formation of chaotic dynamics. In particular, we study scenarios of the emergence of discrete Lorenz and Shilnikov attractors in three-dimensional Hénon maps.
Iterative design of a high zT thermoelectric material
Authors: Adekoya Adetoye H. , Zhang Yuhe , Peters Matthew , Male James , Chart Yvonne , Dong Jason , Franks Ryan , Furlong Alexander , Guo Binghao (Evan) , Agne Matthias T. , Olson Gregory , Snyder G. Jeffrey
Published: November 2021

Designing a high efficiency thermoelectric material for thermal to electric energy conversion means simultaneously optimizing multiple properties of the material. Although it might seem straightforward to maximize the electrical power and minimize thermal losses, the convoluted relationship between these properties makes optimization complex, requiring a more sophisticated algorithm. The Accelerated Insertion of Materials (AIM) methodology developed to engineer the mechanical properties of complex multiphase steel alloys provides a framework for optimization that can be applied to engineer the thermal and electrical transport properties of a multiphase thermoelectric material. The AIM methodology can be utilized in creating a high figure of merit (zT) material by considering the effects of each structural parameter, such as grain size and grain boundary properties, precipitate volume fraction, and doping and defect concentration of the matrix phase on the zT of the material using a variety of analytical models. The combination of these models provides a way to accelerate the design of high zT materials.
High-quality epitaxial thin films of topological kagome metal CoSn by magnetron sputtering
Authors: Thapaliya T. R. , Yoo Timothy , Hurtado Parra Sebastian , Arndt Nathan D. , Need R. F. , Kikkawa James M. , Kim Honggyu , Huang S. X.
Published: November 2021

The topological kagome metal CoSn hosts orbital-selective Dirac bands and very flat bands near the Fermi energy that lead to a range of exotic phenomena, such as fractional quantum Hall states. In this work, we report the synthesis of high-quality epitaxial (0001) CoSn films by magnetron sputtering. Comprehensive structural characterizations demonstrate high crystalline quality with low disorder, sharp interfaces, and a smooth surface. Complementary magnetic and transport properties show a paramagnetic, metallic ground state as seen in bulk. Our work creates a synthetic foundation to investigate and utilize rich topological physics in CoSn thin films and heterostructures.
An explicit solution for the design of a target-frequency-customized, piezoelectric-defect-introduced phononic crystal for elastic wave energy harvesting
Authors: Jo Soo-Ho , Youn Byeng D.
Published: November 2021

This paper proposes an explicit solution for the design of a target-frequency-customized, one-dimensional phononic crystal (PNC) with a defect for piezoelectric energy harvesting under longitudinal waves. Due to the innate narrow bandwidth nature of the defect modes of a PNC at the target frequency, there is a great need to generate an electromechanically coupled defect band of a piezoelectric-defect-introduced PNC. This work considers the transfer matrix method which has been widely used in analytical approaches. The need for defect bands to be included in a bandgap inspires the use of a quarter-wave stack as a unit cell to match the bandgap's central frequency with the target frequency. In band structure analysis, considering that the electromechanically coupled defect band corresponds to a set of real wavenumbers despite being within the bandgap, several possible solutions for the piezoelectric defect's length are derived in an explicit fashion. Since switching from a short- to an open-circuit condition causes defect bands to slightly increase due to piezoelectric effects, an explicit solution that reflects the piezoelectric defect's electrical characteristics is finally proposed. Finite-element-based numerical validation studies are conducted to study two aspects, specifically parametric studies (i.e., the natural numbers in the solution to the piezoelectric defect's length, the supercell sizes, and the defect locations) and supporting studies (i.e., the electrical boundary conditions and unit cell designs). At the target frequency, it is demonstrated that the proposed PNC design actualizes the formation of one defect band and the representation of the peak output voltage.
Water diffusion in complex systems measured by PGSE NMR using chemical shift selective stimulated echo: Elimination of magnetization exchange effects
Authors: Meikle Thomas , Keizer David W. , Separovic Frances , Yao Shenggen
Published: November 2021

The interpretation of molecular translational diffusion as measured by pulsed gradient spin-echo NMR (PGSE NMR) can be complicated by the presence of chemical exchange and/or dipolar cross-relaxation (including relayed cross-relaxation via spin diffusion). The magnitude of influence depends on the kinetics of exchange and/or dipolar cross-relaxation present within the system as well as the PGSE NMR sequences chosen for measurements. First, we present an exchange induced zero-crossing phenomenon for signal attenuation of water in lipidic cubic phases (formed by a mixture of monoolein and water) in the presence of pulsed gradients observed using a standard STimulated Echo (STE) sequence. This magnetization exchange induced zero-crossing phenomenon, a pseudo-negative diffraction-like feature, resembles that reported previously for restricted diffusion when locally anisotropic pores are polydisperse or randomly oriented. We then demonstrate the elimination of these exchange and/or dipolar cross-relaxation induced effects with the use of a chemical shift selective STE (CHESS-STE) sequence, adapted from the previously reported band-selective short transient STE sequence, along with results obtained from the bipolar pulse pair STE sequence for comparison. The CHESS-STE sequence introduced here represents a generic form of PGSE NMR sequences for obtaining water diffusion coefficients free from the influence of exchange and/or dipolar cross-relaxation in complex systems. It has potential applications in measuring translational diffusion of water in biopolymer mixtures as well as probing the microscopic structure in materials via water restricted diffusion measured by PGSE NMR, particularly when the potential presence of exchange/cross-relaxation is of concern.
Modeling dark- and light-induced crystal structures and single-crystal optical absorption spectra of ruthenium-based complexes that undergo SO2-linkage photoisomerization
Authors: Jain Apoorv , Cole Jacqueline M. , Vázquez-Mayagoitia Álvaro , Sternberg Michael G.
Published: November 2021

A family of coordination complexes of the type [Ru(SO2)(NH3)4X]m+Yn− (m, n = 1 or 2) exhibit optical switching capabilities in their single-crystal states. This striking effect is caused by the light-induced formation of SO2-linkage photoisomers, which are metastable if kept at suitably cool temperatures. We modeled the dark- and light-induced states of these large crystalline complexes via plane-wave (PW)- and molecular-orbital (MO)-based density functional theory (DFT) and time-dependent DFT in order to calculate their structural and optical properties; the calculated results are compared with experimental data. We show that the PW-DFT-based periodic models replicate the structural properties of these complexes more effectively than the MO-DFT-based molecular-fragment models, observing only small deviations in key bond lengths relative to the experimentally derived crystal structures. The periodic models were also found to more effectively simulate trends seen in experimental optical absorption spectra, with optical absorbance and coverage of the visible region increasing with the formation of the photoinduced geometries. The contribution of the metastable photoisomeric species more heavily focuses on the lower-energy end of the spectra. Spectra generated from the molecular-fragment models are limited by the geometry of the fragment used and the number of excited-state roots considered in those calculations. In general, periodic models outperform the molecular-fragment models owing to their ability to better appreciate the periodic phenomena that are present in these crystalline materials as opposed to MO approaches, which are finite methods. We thus demonstrate that PW-DFT-based periodic models should be considered as a more than viable method for simulating the optical and electronic properties of these single-crystal optical switches.
Is the water/Pt(111) interface ordered at room temperature?
Authors: Mikkelsen August E. G. , Schiøtz Jakob , Vegge Tejs , Jacobsen Karsten W.
Published: November 2021

The structure of the water/Pt(111) interface has been a subject of debate over the past decades. Here, we report the results of a room temperature molecular dynamics study based on neural network potentials, which allow us to access long time scale simulations while retaining ab initio accuracy. We find that the water/Pt(111) interface is characterized by a double layer composed of a primary, strongly bound adsorption layer with a coverage of ∼0.15 ML, which is coupled to a secondary, weakly bound adsorption layer with a coverage of ∼0.58 ML. By studying the order of the primary adsorption layer, we find that there is an effective repulsion between the adsorbed water molecules, which gives rise to a dynamically changing, semi-ordered interfacial structure, where the water molecules in the primary adsorption layer are distributed homogeneously across the interface, forming frequent hydrogen bonds to water molecules in the secondary adsorption layer. We further show that these conclusions are beyond the time scales accessible to ab initio molecular dynamics.
Quantification of endophyte
Authors: Abin Nastaran , Rokni Nader , Reza Shafeinia Ali , Hossein Borhan M.
Published: November 2021

Context The fungal endophyte Serendipita indica enhances plant growth and plant resistance to biotic and abiotic stresses. Inoculum concentration greatly impacts the endophyte–plant interaction from mutualism to antagonism. Aims and methods We used both microscopy and qPCR to examine the effect of inoculum concentrations on the extent (%) and density of Brassica napus L. root colonisation by S. indica. B. napus seeds were inoculated with the fungus at five different inoculum concentrations (1–10% w/w basis). Key results Standard curves were constructed using the mean threshold cycle (Ct) and serially diluted gDNA ranging between 4.14 × 102 and 2.65 × 105 colony forming units (CFU). The result indicated a linear relationship between Ct and the log of input DNA. Variation in inoculum concentration significantly affected the root colonisation density by the fungus shown by qPCR. However, the percent root colonisation (PRC) measure was not affected and remained the same across all the treatments. Conclusions Our findings show that the qPCR assay developed will determine the colonisation density whereas PRC gives a measure of the incidence of infected roots. Also, we suggest that the optimum quantity of inoculum is a key factor for a successful interaction that impacts the plant–S. indica interaction. Implications To our knowledge, this is the first study that quantitative qPCR has been used to investigate the correlation between inoculum quantities and the corresponding density of root colonisation in S. indica.
Revision of the genus Plexaurella Kölliker, 1865 (Anthozoa: Octocorallia) and resurrection of Plexaurellidae Verrill, 1912 new rank
Authors: Cordeiro R. T. S. , McFadden C. S. , Sanchez J. A. , Pérez C. D.
Published: November 2021

The current knowledge on the diversity of the genus Plexaurella is based on a series of dated revisions, often with no examination of types. Although being common octocorals in western Atlantic reefs, there is no consensus on an exact number of valid species. Furthermore, phylogenetic reconstructions do not support the current classification of Plexaurella within the family Plexauridae. Thus, this study reviews the genus based on examination of available types and assesses monophyly using mitochondrial (COI+igr, mtMutS) and nuclear (28S) markers, mostly from available molecular data. Until now, up to six species were considered valid. Our results show that the group is composed of at least seven previously described species: P. dichotoma, P. nutans, P. grisea, P. teres, P. grandiflora, P. regia and P. obesa; and one new species: Plexaurella rastrera sp. nov. An illustrated key to the valid species and a list of all available names are provided and the current classification of the genus is discussed. Based on congruent phylogenetic reconstructions and genetic distances, we propose the elevation of the former plexaurid subfamily Plexaurellinae to family level. Finally, based on examination of types, we propose the synonymy between Pseudoplexaura crucis and Plexaurella tenuis under Pseudoplexaura tenuis new comb.
A molecular phylogeny of the circum-Antarctic Opiliones family Neopilionidae
Authors: Giribet Gonzalo , Sheridan Kate , Baker Caitlin M. , Painting Christina J. , Holwell Gregory I. , Sirvid Phil J. , Hormiga Gustavo
Published: November 2021

The Opiliones family Neopilionidae is restricted to the terranes of the former temperate Gondwana: South America, Africa, Australia, New Caledonia and New Zealand. Despite decades of morphological study of this unique fauna, it has been difficult reconciling the classic species of the group (some described over a century ago) with recent cladistic morphological work and previous molecular work. Here we attempted to investigate the pattern and timing of diversification of Neopilionidae by sampling across the distribution range of the family and sequencing three markers commonly used in Sanger-based approaches (18S rRNA, 28S rRNA and cytochrome-c oxidase subunit I). We recovered a well-supported and stable clade including Ballarra (an Australian ballarrine) and the Enantiobuninae from South America, Australia, New Caledonia and New Zealand, but excluding Vibone (a ballarrine from South Africa). We further found a division between West and East Gondwana, with the South American Thrasychirus/Thrasychiroides always being sister group to an Australian–Zealandian (i.e. Australia + New Zealand + New Caledonia) clade. Resolution of the Australian–Zealandian taxa was analysis-dependent, but some analyses found Martensopsalis, from New Caledonia, as the sister group to an Australian–New Zealand clade. Likewise, the species from New Zealand formed a clade in some analyses, but Mangatangi often came out as a separate lineage from the remaining species. However, the Australian taxa never constituted a monophyletic group, with Ballarra always segregating from the remaining Australian species, which in turn constituted 1–3 clades, depending on the analysis. Our results identify several generic inconsistencies, including the possibility of Thrasychiroides nested within Thrasychirus, Forsteropsalis being paraphyletic with respect to Pantopsalis, and multiple lineages of Megalopsalis in Australia. In addition, the New Zealand Megalopsalis need generic reassignment: Megalopsalis triascuta will require its own genus and M. turneri is here transferred to Forsteropsalis, as Forsteropsalis turneri (Marples, 1944), comb. nov.
Network-based forecasting of climate phenomena
Authors: Ludescher Josef , Martin Maria , Boers Niklas , Bunde Armin , Ciemer Catrin , Fan Jingfang , Havlin Shlomo , Kretschmer Marlene , Kurths Jürgen , Runge Jakob , Stolbova Veronika , Surovyatkina Elena , Schellnhuber Hans Joachim
Published: November 2021

Network theory, as emerging from complex systems science, can provide critical predictive power for mitigating the global warming crisis and other societal challenges. Here we discuss the main differences of this approach to classical numerical modeling and highlight several cases where the network approach substantially improved the prediction of high-impact phenomena: 1) El Niño events, 2) droughts in the central Amazon, 3) extreme rainfall in the eastern Central Andes, 4) the Indian summer monsoon, and 5) extreme stratospheric polar vortex states that influence the occurrence of wintertime cold spells in northern Eurasia. In this perspective, we argue that network-based approaches can gainfully complement numerical modeling.
Maternal cannabis use is associated with suppression of immune gene networks in placenta and increased anxiety phenotypes in offspring
Authors: Rompala Gregory , Nomura Yoko , Hurd Yasmin L.
Published: November 2021

Significance

Cannabis use is becoming more prevalent, including during developmentally sensitive periods such as pregnancy. Here we find that maternal cannabis use is associated with increased cortisol, anxiety, aggression, and hyperactivity in young children. This corresponded with widespread reductions in immune-related gene expression in the placenta which correlated with anxiety and hyperactivity. Future studies are needed to examine the effects of cannabis on immune function during pregnancy as a potential regulatory mechanism shaping neurobehavioral development.
Genome-wide association study reveals genetic variants associated with HIV-1C infection in a Botswana study population
Authors: Shevchenko Andrey K. , Zhernakova Daria V. , Malov Sergey V. , Komissarov Alexey , Kolchanova Sofia M. , Tamazian Gaik , Antonik Alexey , Cherkasov Nikolay , Kliver Sergey , Turenko Anastasiia , Rotkevich Mikhail , Evsyukov Igor , Vlahov David , Thami Prisca K. , Gaseitsiwe Simani , Novitsky Vladimir , Essex Myron , O’Brien Stephen J.
Published: November 2021

Significance

The search for genetic variants associated with resistance or susceptibility to HIV/AIDS already yielded insights that allowed developing therapeutics that contribute to dramatic reduction in AIDS-related comorbidities. Unfortunately, nearly all studies focused on European-descent populations, even though most infections happen in Africa. In this genome-wide association study we explored the genetic background of several hundred individuals from Botswana in search of associations with HIV infection. We discovered several genetic variant associations in genes implicated in HIV/AIDS pathogenesis. We also confirmed several associations reported in previous research. This study provides valuable data on the influence of human genetic variation on HIV-1C infection and pathogenesis in southern Africa, a region with the world’s largest number of HIV-1 infections.
Plant height heterosis is quantitatively associated with expression levels of plastid ribosomal proteins
Authors: Birdseye Devon , de Boer Laura A. , Bai Hua , Zhou Peng , Shen Zhouxin , Schmelz Eric A. , Springer Nathan M. , Briggs Steven P.
Published: November 2021

Significance

Heterosis (hybrid vigor) boosts the productivity and resilience of crops and livestock above the levels of both parents, yet its underlying mechanisms remain unknown. We analyzed expression patterns of proteins in maize hybrids and their inbred parents. Differences in several molecular machines and biochemical pathways were found and quantitatively assessed using a panel of 15 hybrids. Seedling leaf chloroplast ribosomal proteins were able to quantitatively infer levels of adult plant heterosis. Expression levels of biosynthetic enzymes for the stress hormone ethylene were reduced in hybrids, as was previously reported for the dicot
Arabidopsis
. Mutation of these genes in a maize inbred caused the proteome to resemble a hybrid. Repression of ethylene biosynthesis may be a conserved component of heterosis physiology.
Staphylococcal ClpXP protease targets the cellular antioxidant system to eliminate fitness-compromised cells in stationary phase
Authors: Alqarzaee Abdulelah A. , Chaudhari Sujata S. , Islam Mohammad Mazharul , Kumar Vikas , Zimmerman Matthew C. , Saha Rajib , Bayles Kenneth W. , Frees Dorte , Thomas Vinai C.
Published: November 2021

Significance

Bacterial populations that transition to stationary phase can efficiently maintain their competitive fitness potential even when subject to various stressors that damage cellular macromolecules. However, the mechanism remains unclear. Here, we show that stationary phase staphylococci that harbor damaged proteins in their cytoplasm undergo a regulated form of cell death to maintain the competitive fitness potential of the bacterial population. The activation of cell death is achieved by the down-regulation or degradation of cellular antioxidant proteins by the ATP-dependent ClpXP protease, which usually functions to maintain protein quality control in cells.
Hugin
+
neurons provide a link between sleep homeostat and circadian clock neurons
Authors: Schwarz Jessica E. , King Anna N. , Hsu Cynthia T. , Barber Annika F. , Sehgal Amita
Published: November 2021

Significance

This manuscript identifies a mechanism by which sleep can sometimes occur at the wrong circadian time of day. Sleep is regulated by two processes, the circadian system, which confers 24-h rhythms on sleep, and the homeostatic system, which ensures an organism sleeps sufficiently. Sleep occurs at night because of circadian timing cues and also homeostatic sleep drive triggered by prolonged daytime wakefulness. However, the homeostatic system can sometimes override the circadian system; for instance, following a night of sleep deprivation. We identify a mechanism by which the homeostatic system suppresses circadian signals, allowing sleep to occur against the circadian clock. We find connections between homeostatic and circadian circuits and show that homeostatic sleep drive decreases circadian neuronal activity.
Structure of the ATP synthase from
Mycobacterium smegmatis
provides targets for treating tuberculosis
Authors: Montgomery Martin G. , Petri Jessica , Spikes Tobias E. , Walker John E.
Published: November 2021

The structure has been determined by electron cryomicroscopy of the adenosine triphosphate (ATP) synthase from
Mycobacterium smegmatis
. This analysis confirms features in a prior description of the structure of the enzyme, but it also describes other highly significant attributes not recognized before that are crucial for understanding the mechanism and regulation of the mycobacterial enzyme. First, we resolved not only the three main states in the catalytic cycle described before but also eight substates that portray structural and mechanistic changes occurring during a 360° catalytic cycle. Second, a mechanism of auto-inhibition of ATP hydrolysis involves not only the engagement of the C-terminal region of an α-subunit in a loop in the γ-subunit, as proposed before, but also a “fail-safe” mechanism involving the b′-subunit in the peripheral stalk that enhances engagement. A third unreported characteristic is that the fused bδ-subunit contains a duplicated domain in its N-terminal region where the two copies of the domain participate in similar modes of attachment of the two of three N-terminal regions of the α-subunits. The auto-inhibitory plus the associated “fail-safe” mechanisms and the modes of attachment of the α-subunits provide targets for development of innovative antitubercular drugs. The structure also provides support for an observation made in the bovine ATP synthase that the transmembrane proton-motive force that provides the energy to drive the rotary mechanism is delivered directly and tangentially to the rotor via a Grotthuss water chain in a polar L-shaped tunnel.
On the influence of ENSO complexity on Pan-Pacific coastal wave extremes
Authors: Boucharel Julien , Almar Rafael , Kestenare Elodie , Jin Fei-Fei
Published: November 2021

Significance

This study demonstrates how the main wave regimes in the Pacific, in particular related to tropical and extratropical storm activity, are activated by different El Niño/Southern Oscillation (ENSO) teleconnections patterns. By combining these robust relationships with the latest theoretical advances in ENSO research, a mathematical model of wave energy modulation is derived. It allows a better representation of wave extremes over a range of time scales wider than previously possible with the previous baseline understanding of ENSO’s influence on coastal impacts. This paves the way for unprecedented seasonal to monthly forecasts of coastal hazards around the densely populated Pacific basin.
The tension between global GHG emissions of animal source foods, sustainability, and food security in Latin America and the Caribbean
Authors: Gutiérrez-Gómez Constanza , Inostroza Rodrigo Arias , José Luis Riveros
Published: November 2021

The livestock sector faces an important challenge in the medium and long term since it must satisfy an increasing demand for animal products as a result of the increase in population and the world economy but safeguarding natural resources and at the same time minimizing the environmental contamination, especially the greenhouse gas (GHG) emissions attributed to livestock husbandry. For Latin America and the Caribbean (LAC), this becomes more relevant given the importance of the sector for the food security of rural communities, particularly for small-scale producers. In this manuscript, we address the main challenges of LAC in this context, from a global perspective that includes the demographic, economic, cultural, and environmental effects. The biggest global challenge for the LAC livestock sector for the coming decades is how to satisfy the growing human demand for animal protein in a sustainable way maintaining the food security of their communities. The efforts to achieve these goals require focusing on improving the efficiency of both animal husbandry and production systems. Therefore, it is necessary to implement technologies of sustainable intensification and it is urgent that those who make political decisions become aware of these issues.
Milk lactose, specific gravity and mineral of etawa dairy goat fed with palm kernel cake based concentrate, tithonia (Tithonia diversifolia), sweet potato leaves (Ipomoea batatas L) and gamal (Gliricidia sepium)
Authors: Arief  , Jamarun N , Satria B , Pazla R
Published: November 2021

This study aims to evaluate the milk lactose, specific gravity, and mineral of Etawa Crossbreed Dairy Goat (ECDG) fed with palm kernel cake-based concentrate (PKCC), tithonia (Tithonia diversifolia), sweet potato leaves, (Ipomoea batatas L.), and Gamal (Gliricidia sepium) as a source of roughage. The design of the experiment used was a completely randomized design (CRD) with four treatment rations and four replications. Treatment formulations are as follow A). 100% basal ration (BR); B). 50% BR + 50% Concentrate Based Palm Kernel Cake (CPKC) + tithonia; C). 50% BR+ % CPKCC + sweet potato leaves; D).50% BR + 50% CPKC + Gamal (Gliricidia sepium). The ratio of concentrate and roughage is 50:50. The concentrate ratio consists of 30% palm kernel cake, 40% tofu waste, 20% rice bran, 9 % corn, and 1% mineral. The parameters were milk lactose, specific gravity, and mineral of milk. Data were analysed by Analysis of Varian (ANOVA) and DMRT (Duncans Multiple Range Test) according to Steel and Torrie (2002). The results showed that the treatment had no significant effect (P> 0.05) on lactose, specific gravity, and mineral of milk. From this study, it can be concluded that the use of PKC, titonia, sweet potato, and gamal can replace basal ration without affecting the quality of milk (lactose, specific grafity and mineral)
Enhancing performance of Murrah Buffalo through improved probiotic feed management in Kapau Village, Agam Regency
Authors: Roza E , Aritonang S N , Yellita Y , Susanty H , Rizqan  , Adha D A
Published: November 2021

This study aims to improve the production performance of Murrah buffalo which covers average weight gain, feed consumption, and feed conversion by increasing probiotic feed. The research was conducted on the herd of Murrah buffalo at Kelok Rambai, Kapau Village, West Sumatera, Indonesia. Fifteen Murrah buffaloes with three to five years of age were used in the research. There were three treatments conducted including P1 = basal feed + probiotics; P2 = P1 + concentrate (cassava leaf pellet); and P3 = P1 + commercial concentrate (pellet). All three treatments were also given 7 cc/head/month of probiotics. The results of the study with probiotic feeding on Murrah buffalo showed the average feed consumption of P2 (36.55), P3 (35.99), P1 (35.74) and daily weight gain (DWG) P2 (1.09 kg/head/day), P3 (0.91 kg/head/day), P1 (0.55 kg/head/day) did not show a significant difference, while in feed conversion, P2 (0.68 ), P1 (0.46), P3 (0. 31) it showed a significant difference (p>0.05). This study concludes that the provision of basal ration plus cassava leaf pellets showed significant results on feed conversion in Murrah buffalo but did not show significant differences in feed consumption and DWG. However, it showed a substantial enough average of P2 that could be used as a feed supplement in Murrah buffalo.
Variation of prolactin and β-Lactoglobulin genes in the Indonesian FH Cattle
Authors: Agung P P , Wulandari A S , Putra W P B , Destianty T R , Muzaki F K , Hillary S , Wijayanti G E , Gunawan M , Kaiin E M
Published: November 2021

Prolactin is a polypeptide hormone, encoded by the prolactin (PRL) gene, synthesized and secreted by anterior pituitary, and affecting milk yield and composition. β-Lactoglobulin (BLG) is the major whey proteinin the milk of ruminants. This study was conducted to identify the PRL and LGB genes polymorphism in the Indonesian FH cattle. A total of 139 individual cattle blood samples from West Java were used to obtain DNA samples through the DNA extraction process. Identification of the PRL and LGB genes was performed using PCR-RFLP method with RsaI (PRL gene) and HaeIII (BLG gene) restriction enzymes. The PRL gene was amplified using forward primer 5’-ccaaatccactgaattatgctt-3’ and reverse primer 5’-acagaaatcacctctctcattca-3’. The BLG gene was amplified using forward primer 5’-tgtgctggacaccgactacaaaaag-3’ and reverse primer 5’-gctcccggtatatgaccaccctct-3’. The PRL and BLG genes in the Indonesia FH cattle were polymorphic based on the PCR-RFLP analysis but the heterozygosity value was low. There were two alleles (G and A) and three genotypes (GG, GA, and AA) identified in the PRL gene of the Indonesian FH cattle with genotype frequencies were 0.914, 0.079, and 0,007 for GG, GA, and AA genotypes respectively. There were two genotypes (CC and CG) identified in the BLG gene with genotype frequencies were 0.91 (CC), and 0.09 (CG). Information about the PRL and BLG genes polymorphism in this study can be considered for further study to analyse its association with milk yield trait.
Use of body measurements to predict live body weight of Simmental bull in Lembang Artificial Insemination Center, West Java
Authors: Shoimah U S , Dakhlan A , Sulastri  , Hamdani M D I
Published: November 2021

This research aimed to evaluate the use of body measurements (chest girth (CG), body length (BL), and shoulder height (SH)) to predict live body weight (BW) of Simmental bulls in Lembang Artificial Insemination Center, West Java. This research was carried out in December 2019 using a survey method of which all Simmental bulls aged 1—12 years were used in this study. Data were analyzed using simple and multiple correlations and regression models using the R program. Pearson correlation analysis was used to analyze correlation between BW and body measurements, while to find the fittest and more parsimonious regression model we used determination coefficient (R2) and stepwise regression analysis as criteria of selection. The results showed that the average of BW, CG, BL, and SH were 814.54 ± 144.18 kg, 215.72 ± 16.50 cm, 170.13 ± 17.09 cm, and 142.79 ± 11.01 cm, respectively. The results of this study also indicated that CG, BL, and SH positively and significantly correlated with BW, with correlation value of 0.90, 0.85, and 0.79, respectively. Combination of CG, BL, and SH produced the highest correlations value (r = 0.92) with the fittest regression model for predicting BW, namely BW=-888.64 + 4.21*CG + 2.83*BL + 2.20*SH, with R2 of 0.86.
Protease-activated receptor 2 expression in the mammary gland tissues in correlation with mastitis severity in goats
Authors: Sukiman M Z , Chai M H , Sharifuddin N S , Shamin A , Ariffin S M Z , Ghazali M F
Published: November 2021

Mastitis is a common disease in small ruminant industry. The present study aimed to determine the presence of protease activated receptor-2 (PAR2) mRNA expression in the mammary gland of mastitis challenged goats. 30 clinically healthy mix breed lactating goats were divided into three groups, consisting of Staphylococcus aureus (Group 1), methicillin-resistant S. aureus (Group 2) and sterile phosphate-buffered saline (Control) groups. The data regarding physical condition of udder and clinical parameters of goats were recorded while milk samples and mammary gland tissues were collected at 24 and 48 hours post infection. Somatic cell count (SCC) was measured by direct microscopic method. The presence of PAR2 mRNA in the mammary gland tissue samples was detected by real-time PCR. Goats from group 1 developed mild to moderate clinical signs while Group 2 exhibited moderate to severe clinical signs. SCC was higher in both challenged groups than control group. PAR2 mRNA expression was detected in all mammary gland samples from Group 1 and Group 2. The gene expression was significantly highly in mammary gland tissue with severe clinical signs. The finding of PAR2 expression in caprine mammary gland is novel and important, suggesting serine proteases involved the development of mastitis in goat.
Pesisir cattle superovulation with various dosage of Follicle Stimulating Hormone (FSH) on embrio production
Authors: Afriani T , Purwati E , Hellyward J , Jaswandi  , Mundana M , Rastosari Adisti , Farhana A
Published: November 2021

This study aimed to determine the use of various doses of FSH hormone, the number of lutheum corpus and the number and quality of embryos produced in the superovulation program in Pesisir cattle. The experimental design was Analysis of Variance (Anova) in a completely randomized design. The research material used 16 cows from Pesisir cattle that had been synchronized with estrous with CIDR implants for 13 days and were injected with the PGF2α hormone after the release of CIDR, then scheduled AI was performed. The dose of FSH hormone was 16 ml, 17 ml, 18 ml and 19 ml, each treatment consisting of 4 replications. The injection of the FSH hormone was carried out for 3 days at a decreased dose. Collection of donor embryos was carried out on days 6 to 8 after the scheduled AI. The parameters observed included superovulation response, number of corpus luteum, number of embryos and quality of embryos. The results showed that the response of Pesisir cattle superovulation was 81.25%. The average number of CL obtained was 13.75 and embryos for Pesisir cattle was 11.25. The results also showed that the quality of the embryos obtained were grade A 19, grade B 18, grade C 7, grade D 1. It can be concluded that the use of various doses of FSH hormone at doses of 16 mg, 17 ml, 18 ml and 19 ml had shown a superovulatory response. The 17 ml dose of FSH hormone showed a large number of embryos and had the best embryo quality.
Physical characteristics and organoleptic of chicken crepes
Authors: Bulang K K A D , Susilo A , Al Awwaly K U
Published: November 2021

Crepes are one of the fast-food snacks from France. Crepes are round pancakes that are folded like a fan and thin. It can be added using chicken meat. This study aimed to determine the physical characteristics and organoleptic of chicken crepes substituted with mocap flour with bamboo shoots. This study used a completely randomized design with six treatments and three replications. There were P0 (rice flour, maize flour, and mocap flour 4.5%, without using bamboo shoot flour); P1 (2.5% mocap flour and 2% bamboo shoot flour); P2 (2% mocap flour and 2.5% bamboo shoot flour); P3 (1.5% mocap flour and 3% bamboo shoot flour); P4 (2% mocap flour and 2.5 percent bamboo shoot flour), P5 (1% mocap flour and 3.5 percent bamboo shoot flour). The data obtained were analyzed using ANOVA and continued using the Duncan Multiple Rate test if there was a significant or very significant difference (P˂0.05). The study concluded that the best treatment was on chicken crapes with P1 treatment (2.5% mocap flour and 2% bamboo shoot flour) from the water content test, Water Holding Capacity (WHC), pick up, hygroscopic and organoleptic. The results of the research on chicken crepes did not affect Water Holding Capacity (WHC) and pick-up values obtained (P> 0.05), while the water content and hygroscopic had a significant effect on chicken crepes with a significance value of 0.001 (P˂ 0.05). The organoleptic test results on chicken crapes significantly affected the texture (P˂0.05). Meanwhile, chicken crepes had no significant effect on color, taste, and aroma (P>0.05).
Effect of washing treatment on quality characteristics of burger made from spent laying duck meat
Authors: Md Fauzi N F , Huda N , Zzaman W
Published: November 2021

Experiment was carried out to investigate the influence number of washing treatment (without, single and double washing) on the quality characteristics and acceptability of duck burger made from spent laying Khaki Campbell duck meat. The chemical composition of burger at different number of washing treatment was varied in terms of moisture content, fats and protein content. The number washing cycles treatment were found to increase moisture content and reduce fat and protein content significantly. Increase number of washing treatment showed significantly higher (p <0.05) lightness (L*), hardness, diameter shrinkage and cooking loss. As for sensory evaluation, there was no significantly difference (p >0.05) within the sample and control (chicken burger). The spent laying duck Khaki Campbell produced using different number of washing treatment may have a possible use as raw material in restructured meat products such as burger.