bluuebunny/crossref_metadata_2025 huggingface dataset:
Topological electrostatics
Authors: Douçot B , Moessner R , Kovrizhin D L
Published: September 2022

We present a theory of optimal topological textures in nonlinear sigma-models with degrees of freedom living in the GrassmannianGr(M,N)manifold. These textures describe skyrmion lattices ofN-component fermions in a quantising magnetic field, relevant to the physics of graphene, bilayer and other multicomponent quantum Hall systems near integer filling factorsν > 1. We derive analytically the optimality condition, minimizing topological charge density fluctuations, for a general Grassmannian sigma modelGr(M,N)on a sphere and a torus, together with counting arguments which show that for any filling factor and number of components there is a critical value of topological chargedcabove which there are no optimal textures. Belowdca solution of the optimality condition on a torus is unique, while in the case of a sphere one has, in general, a continuum of solutions corresponding to new non-Goldstone zero modes, whose degeneracy is not lifted (via a order from disorder mechanism) by any fermion interactions depending only on the distance on a sphere. We supplement our general theoretical considerations with the exact analytical results for the case ofGr(2,4), appropriate for recent experiments in graphene.
Tunable, stable, and reversible n-type doping of MoS2 via thermal treatment in N-methyl-2-pyrrolidone
Authors: Sunwoo Hyeyeon , Choi Woong
Published: September 2022

Here, we report a highly stable and reversible n-type doping of monolayer MoS2 using thermal treatment in N-methyl-2-pyrrolidone (NMP). The Raman and photoluminescence spectroscopic measurements as well as the device performance of the MoS2 transistors suggested a stronger n-type doping effect with increasing time and temperature of the thermal treatment in NMP. Within the given time (5–60 min) and temperature (50 °C–110 °C), the surface treatment in NMP provided an electron concentration from 6 × 1010 to 2 × 1012 cm−2. Owing to the n-type doping effect, the thermal treatment in NMP reduced the contact resistance and enhanced the field-effect mobility of the MoS2 transistors. The n-type doping via thermal treatment in NMP remained effective for more than 12 months in ambient air, and could be completely removed after immersion in isopropanol. These results demonstrate that thermal treatment in NMP can be a facile and effective route to achieve stable and reversible doping of two-dimensional materials including MoS2 for their applications in high-performance electronics and optoelectronics.
Snap-through of graphene nanowrinkles under out-of-plane compression
Authors: Ma Chengpeng , Zhang Yingchao , Jiao Shuping , Liu Mingchao
Published: September 2022

Nanowrinkles (i.e. the buckled nanoribbons) are widely observed in nano-devices assembled by two-dimensional (2D) materials. The existence of nanowrinkles significantly affects the physical (such as mechanical, electrical and thermal) properties of 2D materials, and thus further, impedes the applications of those devices. In this paper, we take the nanowrinkle formed in a monolayer graphene as a model system to study its deformation behaviours, especially the configuration evolution and the snap-through buckling instabilities, when subjected to the out-of-plane compression. By performing molecular dynamics simulation, the graphene nanowrinkles with or without self-adhesion (which are notated as ‘clipped’ state or ‘bump’ state, respectively) are obtained depending on the geometric size and the applied axial compressive pre-strain. The elastica theory is employed to quantify the shape of ‘bump’ nanowrinkles, as well as the critical condition of the transition between ‘clipped’ and ‘bump’ states. By applying out-of-plane compression to the generated graphene nanowrinkle, it flips to an opposite configuration via snap-through buckling. We identify four different buckling modes according to the configuration evolution. An unified phase diagram is constructed to describe those buckling modes. For the cases with negligible van der Waals interaction getting involved in the snap-buckling process, i.e. without self-adhesion, the force–displacement curves for nanowrinkles with same axial pre-strain but different sizes can be scaled to collapse. Moreover, the critical buckling loads can also be scaled and predicted by the extended elastica theory. Otherwise, for the cases with self-adhesion, which corresponds to the greater axial pre-strain, the van der Waals interaction makes the scaling collapse break down. It is expected that the analysis about the snap-through buckling of graphene nanowrinkles reported in this work will advance the understanding of the mechanical behaviours of wrinkled 2D materials and promote the design of functional nanodevices, such as nanomechanical resonators and capacitors.
An effective edge conductivity for reducing staircasing error in induced electric field computation for low-frequency magnetic field dosimetry
Authors: Diao Yinliang , Zhang Lianlong , Shi Dan , Hirata Akimasa
Published: September 2022

Objective. In the low-frequency exposure (<100 kHz), the induced electric field strength is used as a metric for assessment for human protection. Unlike radio-frequency exposure (>MHz), the computational assessment suffers from staircasing error in biological objects. The international guidelines consider additional reduction factor of 3 when setting the limit. Here we propose a new method to reduce the staircasing error in the skin for low-frequency magnetic field dosimetry of voxelized body models. Approach. We have proposed a new method considering the filling ratio of the skin tissue to the air–skin and skin–fat interfaces to determine an effective conductivity for each voxel edge. The proposed method was applied to voxel head models exposed to a uniform magnetic field at 50 Hz. After validation using layered spherical models with several resolutions, anatomical head models are used for further verification. Main results. A comparison of maximum electric field strengths with analytic solutions in two-layer sphere models suggested that the differences in the proposed approach were less than 5.6%, which was smaller than those without the proposal of 26.7%. The distribution of the skin electric field become smoother using the proposed approach, and the staircasing effects were almost unobservable from the field distributions. Significance. The proposed method suggests vital implications for determining induced electric fields in the skin, which is needed to set the limit for human protection from low-frequency electromagnetic fields. The method would be useful when setting the reduction factor and limit in the exposure guidelines and standard.
A new database with annotations of P waves in ECGs with various types of arrhythmias
Authors: Saclova Lucie , Nemcova Andrea , Smisek Radovan , Smital Lukas , Vitek Martin , Ronzhina Marina
Published: September 2022

Objective. The aim of this study is to create a database for the development, evaluation and objective comparison of algorithms for P wave detection in ECG signals. Brno University of Technology ECG Signal Database with Annotations of P-Wave (BUT PDB) is an ECG signal database with marked peaks of P waves annotated by ECG experts. Currently, there are only a few databases of pathological ECG signals with P-wave annotations, and some are incorrect. Approach. The pathological ECG signals used in this work were selected from three existing databases of ECG signals: MIT-BIH Arrhythmia Database, MIT-BIH Supraventricular Arrhythmia Database and Long Term AF Database. The P-wave positions were manually annotated by two ECG experts in all selected signals. Main results. The final BUT PDB composed of selected signals consists of 50 two-minute, two-lead pathological ECG signal records with annotated P waves. Each record also contains a description of the diagnosis (pathology) present in the selected part of the record and information about positions and types of QRS complexes. Significance. The BUT PDB is created for developing new, more accurate and robust methods for P wave detection. These algorithms will be used in medical practice and will help cardiologists to evaluate ECG records, establish diagnoses and save time.
Impact of ActiGraph sampling rate on free-living physical activity measurement in youth
Authors: Clevenger Kimberly A , Brønd Jan C , Mackintosh Kelly A , Pfeiffer Karin A , Montoye Alexander H K , McNarry Melitta A
Published: September 2022

ActiGraph sampling frequencies of more than 30 Hz may result in overestimation of activity counts in both children and adults, but research on free-living individuals has not included the range of sampling frequencies used by researchers. Objective. We compared count- and raw-acceleration-based metrics from free-living children and adolescents across a range of sampling frequencies. Approach. Participants (n = 445; 10–15 years of age) wore an ActiGraph accelerometer for at least one 10 h day. Vector magnitude counts, mean amplitude deviation, monitor-independent movement summary units, and activity intensity classified using six methods (four cut-points, two-regression model, and artificial neural network) were compared between 30 Hz and 60, 80, 90, and 100 Hz sampling frequencies using mean absolute differences, correlations, and equivalence testing. Main results. All outcomes were statistically equivalent, and correlation coefficients were ≥0.970. Absolute differences were largest for the 30 versus 80 and 30 versus 100 Hz count comparisons. For comparisons of 30 with 60, 80, 90, or 100 Hz, mean (and maximum) absolute differences in minutes of moderate-to-vigorous physical activity per day ranged from 0.1 to 0.3 (0.4 to 1.5), 0.3 to 1.3 (1.6 to 8.6), 0.1 to 0.3 (1.1 to 2.5), and 0.3 to 2.5 (1.6 to 14.3) across the six classification methods. Significance. Acceleration-based outcomes are comparable across the full range of sampling rates and therefore recommended for future research. If using counts, we recommend a multiple of 30 Hz because using a 100 Hz sampling rate resulted in large maximum individual differences and epoch-level differences, and increasing differences with activity level.
Bronchodilator effect on regional lung function in pediatric viral lower respiratory tract infections
Authors: Strodthoff Claas , Kähkönen Toni , Bayford Richard H , Becher Tobias , Frerichs Inéz , Kallio Merja
Published: September 2022

Objective. Viral lower respiratory tract infections (LRTI) are the leading cause for acute admission to the intensive care unit in infants and young children. Nebulized bronchodilators are often used when treating the most severe cases. The aim of this study was to investigate the bronchodilator effect on respiratory mechanics during intensive care with electrical impedance tomography (EIT) and to assess the feasibility of EIT in this context. Approach. We continuously monitored the children with chest EIT for up to 72 h in an observational study design. The treatment decisions were done by clinical assessment, as the clinicians were blinded to the EIT information during data collection. In a retrospective analysis, clinical parameters and regional expiratory time constants determined by EIT were used to assess the effects of bronchodilator administration, especially regarding airway resistance. Main results. We included six children from 11 to 27 months of age requiring intensive care due to viral LRTI and receiving bronchodilator agents. Altogether 131 bronchodilator administrations were identified during EIT monitoring. After validation of the exact timing of events and EIT data quality, 77 administrations were included in the final analysis. Fifty-five bronchodilator events occurred during invasive ventilation and 22 during high-flow nasal cannulae treatment. Only 17% of the bronchodilator administrations resulted in a relevant decrease in calculated expiratory time constants. Significance. Continuous monitoring with EIT might help to optimize the treatment of LRTI in pediatric intensive care units. In particular, EIT-based regional expiratory time constants would allow objective assessment of the effects of bronchodilators and other respiratory therapies.
Reference values for triceps surae tissue oxygen saturation by near-infrared spectroscopy
Authors: Faria Valéria C , Oliveira Luciano Fonseca Lemos de , Ferreira Ana Paula , Cunha Tulio E O , Fernandes Juliana S A , Pussieldi Guilherme A , Pereira Danielle A G
Published: September 2022

Objective. To establish the reference values for peripheral tissue perfusion of the triceps surae muscle assessed by Near-infrared spectroscopy (NIRS) at rest and in progressive effort. Approach. A total of 288 apparently healthy individuals of both sexes were included; between 30 and 79 years of age; nonsmokers; without diagnosis of diabetes mellitus, systemic arterial hypertension, kidney disease, symptoms of angina and intermittent claudication, or any musculoskeletal alteration that would prevent physical exertion; and without diagnosis of Peripheral arterial disease (PAD) or other associated symptoms. All individuals performed anthropometric measurements, physical activity levels, and tissue oxygen saturation (StO2) assessments by NIRS during and after arterial occlusion maneuver and incremental shuttle walking test. The variables obtained by NIRS were presented in percentiles (P) for general comparison between sexes and for comparison between sexes according to age group. The relationship between the NIRS data and other variables was tested. Main results. Considering P50 and p<0.05, men had lower StO2 values, higher deoxygenation and reoxygenation (Tx-reox) rates at rest, and higher Tx-reox during progressive effort. There were correlations (p<0.0001) of body composition with the lowest StO2 and Tx-reox values and of functional capacity with Tx-reox in occlusion and Tx-reox. Significance. The percentiles presented can clinically assist in the diagnosis and monitoring of different health conditions; however, it is important to consider the individual’s sex, body composition, and functional capacity.
Hydrogen peroxide production of underwater nanosecond-pulsed streamer discharges with respect to pulse parameters and associated discharge characteristics
Authors: Rataj Raphael , Werneburg Matthias , Below Harald , Kolb Juergen F
Published: September 2022

Pulsed streamer discharges submerged in water have demonstrated potential in a number of applications. Especially the generation of discharges by short high-voltage pulses in the nanosecond range has been found to offer advantages with respect to efficacies and efficiencies. The exploited plasma chemistry generally relies on the initial production of short-lived species, e.g. hydroxyl radicals. Since the diagnostic of these transient species is not readily possible, a quantification of hydrogen peroxide provides an adequate assessment of underlying reactions. These conceivably depend on the characteristics of the high-voltage pulses, such as pulse duration, pulse amplitude, as well as pulse steepness.

A novel electrochemical flow-injection system was used to relate these parameters to hydrogen peroxide concentrations. Accordingly, the accumulated hydrogen peroxide production for streamer discharges ignited in deionized water was investigated for pulse durations of 100 ns and 300 ns, pulse amplitudes between 54 kV and 64 kV, and pulse rise times from 16 ns to 31 ns. An independent control of the individual pulse parameters was enabled by providing the high-voltage pulses with a Blumlein line. Applied voltage, discharge current, optical light emission and time-integrated images were recorded for each individual discharge to determine dissipated energy, inception statistic, discharge expansion and the lifetime of a discharge.

Pulse steepness did not affect the hydrogen peroxide production rate, but an increase in amplitude of 10 kV for 100 ns pulses nearly doubled the rate to (0.19 ± 0.01) mol l−1 s−1, which was overall the highest determined rate. The energy efficiency did not change with pulse amplitude, but was sensitive to pulse duration. Notably, production rate and efficiency doubled when the pulse duration decreased from 300 ns to 100 ns, resulting in the best peroxide production efficiency of (9.2 ± 0.9) g kWh−1. The detailed analysis revealed that the hydrogen peroxide production rate could be described by the energy dissipation in a representative single streamer. The production efficiency was affected by the corresponding discharge volume, which was comprised by the collective volume of all filaments. Hence, dissipating more energy in a filament resulted in an increased production rate, while increasing the relative volume of the discharge compared to its propagation time increased the energy efficiency.
Effect of electron energy distributions on the electron density in nitrogen inductively coupled plasmas
Authors: Kim Kwan-Yong , Kim Jung Hyung , Chung Chin-Wook , Lee Hyo-Chang
Published: September 2022

The effect of the electron energy distribution function (EEDF) on the behavior of the electron density (n
e) is investigated under various gas pressures of nitrogen (N2) in inductively coupled plasma (ICP) operated at low and high input powers. A Langmuir probe is used to measure the EEDFs and electron densities, and the antenna coil current is measured to obtain the absorbed power in the plasma (P
abs). At gas pressures above 2.67 Pa (20 mTorr) and 2500 W, P
abs increases continually with increasing the gas pressure, but the electron density slightly decreases. In this case, the EEDF has a Maxwellian distribution with a high-energy tail. On the other hand, at 300 W, P
abs decreases slightly with increasing gas pressure, but the electron density dramatically decreases, and the EEDF evolves from a bi-Maxwellian to a non-Maxwellian distribution with substantially highly depleted high-energetic part (high-energy tail). To analyze the difference in the behavior of the decrease rate in electron density, the total energy loss per electron–ion pair lost (ε
T) is measured through the probe diagnostics, and the measured electron density is compared with the calculated electron density from the global model. An additional experiment is performed in Ar plasma under the same discharge conditions as N2 plasma to compare the EEDF effect. This study provides experimental evidence that the EEDF has a decisive effect on the behavior of the electron density in plasmas.
Long-term trends of impacts of global gasoline and diesel emissions on ambient PM2.5 and O3 pollution and the related health burden for 2000–2015
Authors: Xiong Ying , Partha Debatosh , Prime Noah , Smith Steven J , Mariscal Noribeth , Salah Halima , Huang Yaoxian
Published: September 2022

Global economic development and urbanization during the past two decades have driven the increases in demand of personal and commercial vehicle fleets, especially in developing countries, which has likely resulted in changes in year-to-year vehicle tailpipe emissions associated with aerosols and trace gases. However, long-term trends of impacts of global gasoline and diesel emissions on air quality and human health are not clear. In this study, we employ the Community Earth System Model in conjunction with the newly developed Community Emissions Data System as anthropogenic emission inventory to quantify the long-term trends of impacts of global gasoline and diesel emissions on ambient air quality and human health for the period of 2000–2015. Global gasoline and diesel emissions contributed to regional increases in annual mean surface PM2.5 (particulate matter with aerodynamic diameters ⩽2.5 μm) concentrations by up to 17.5 and 13.7 µg m−3, and surface ozone (O3) concentrations by up to 7.1 and 7.2 ppbv, respectively, for 2000–2015. However, we also found substantial declines of surface PM2.5 and O3 concentrations over Europe, the US, Canada, and China for the same period, which suggested the co-benefits of air quality and human health from improving gasoline and diesel fuel quality and tightening vehicle emissions standards. Globally, we estimate the mean annual total PM2.5- and O3-induced premature deaths are 139 700–170 700 for gasoline and 205 200–309 300 for diesel, with the corresponding years of life lost of 2.74–3.47 and 4.56–6.52 million years, respectively. Diesel and gasoline emissions create health-effect disparities between the developed and developing countries, which are likely to aggravate afterwards.
Loss of tolerance to multiple environmental stresses due to limitation of structural diversity of complex sphingolipids
Authors: Koga Ayano , Takayama Chihiro , Ishibashi Yohei , Kono Yushi , Matsuzaki Momoko , Tani Motohiro
Published: September 2022

Structural diversity of complex sphingolipids is important for the maintenance of various cellular functions. It is shown that the more the structural variation of complex sphingolipids is limited, the more sensitivity to various environmental stresses tends to increase, which is caused by impaired integrity of plasma membranes and cell walls.
Preprint Highlight: The selective autophagy receptor p62 and the heat shock protein HSP27 facilitate lysophagy via the formation of phase-separated condensates
Authors: Bonet-Ponce Luis
Published: September 2022

Ruptured lysosomes are cleared by lysophagy, a selective form of macroautophagy. Thus lysophagy protects cells against lysosomal cell death, a form of cell death caused by the release of lysosomal proteases to the cytosol from ruptured lysosomes. However, the mechanism underlying this process is still incomplete. Using HeLa cells, rat primary neurons, and human neurons, the authors show that SQSTM1/p62 is a key lysophagy adaptor that forms phase-separated condensates. Mechanistically, p62 oligomerizes but remains in liquid phase to ensure the formation of an autophagosome along the ruptured lysosome. The liquidlike state of p62 is maintained by the small chaperone HSP27. Amyotrophic lateral sclerosis (ALS)-associated mutations in p62 prevent its localization and disrupt lysophagy. These results demonstrate a new role of p62 in lysophagy and implicate lysophagy in the pathobiology of ALS.
Pavlov’s quest
Authors: Todes Daniel P.
Published: September 2022

From 1903 until his death in early 1936, Pavlov attempted experimentally to constrain the psyche within deterministic law. For Pavlov, the conditional reflex and the psyche were two dimensions of what he termed “higher nervous activity.” He sought not to replace psychology with physiology, but to fuse them. His method consisted of three basic steps: First, discover the regularities in the salivation elicited by thousands of experiments on the dynamics of conditional reflexes. Second, build from these patterns a model of the unseen processes in the higher nervous system. Finally, use that model to explain the psychological experiences and personality of experimental animals and, ultimately, humans. He discovered many important facts and relationships of enduring value, but the avalanche of data defeated every attempt at systematization. Continually adding new variables (such as mental illness, experience, and “nervous type”), he extended his explanatory reach at the cost of precision and refutability.
Nervous types
Authors: Todes Daniel P.
Published: September 2022

Pavlov’s dogs were recognizable individuals who lived for years in the lab, displaying distinctive personalities that became an integral part of lab culture, a factor in the interpretation of experiments, and the theme of a central line of investigation on “nervous types.” Individual dogs responded differently to identical experiments. Coworkers were also familiar with their different personalities. Pavlov viewed dogs as simple people and people as complex dogs. He and his coworkers routinely described their canine collaborators as weak, strong, obtuse, intelligent, cowardly, or heroic. Research on nervous types attempted to explain physiologically the dogs’ varied responses to conditional reflex experiments and to relate this to their personalities. The dynamics of this research are evident from experiments with four dogs in the 1920s: Milord and Postrel (who Pavlov compared to Freud’s “Anna O.”), Avgust (who revealed the physiology of cowardice), and Garsik (who helped resolve a mystery about Pavlov’s biography).
Behavioral choices in negotiation
Authors: Menkel-Meadow Carrie
Published: September 2022

This chapter describes the strategies (plans) and tactics (individual behavioral choices) which can be used in the different frameworks and models of negotiation. Different choices are presented in a chronological order of most negotiations—planning, research, preparation, first offers, introductions, agenda setting, solution planning, settings, information gathering, use of principles, persuasion, arguments, questioning, development of packages/proposals, brainstorming, bargaining, movement, moves and turns, language uses, agreement confirmation, drafting, execution, enforcement, dispute resolution and evaluation, legal issues in agreements in different contexts.
Challenges to reaching negotiated agreements
Authors: Menkel-Meadow Carrie
Published: September 2022

This chapter reviews documented social, cognitive, and psychological barriers to human negotiation and communication, including human error in information processing and attributions made about others and self. These include such distortions in our thinking as giving too much attention to what goes first (primacy or anchoring), what is most vivid or recent or available to us. We make choices based on our own preferences for gain or loss (and assume others share our preferences); we reason with statistical fallacies, we devalue what others with whom we disagree say, we have social biases that prevent us from accurately processing information and hearing what others say and want, all of which impede our ability to reach mutually rewarding solutions to negotiated problems. We are often overconfident about our own goals and abilities, and we underestimate and devalue others, all while often seeking to confirm what we already think, rather than attempting to learn new things. This chapter explores ways we can correct for these biases in order to improve our own information processing and ability to see better solutions to negotiation problems, both through better cognition and information processing and more attention to others (e.g. with use of greater empathy and the use of mediation processes).
Music and Technology: A Very Short Introduction
Authors: Katz Mark
Published: September 2022

This Very Short Introduction takes an expansive and inclusive approach meant to broaden and challenge traditional views of music and technology. In its most common use, “music technology” tends to evoke images of twentieth and twenty-first century electronic devices: synthesizers, recording equipment, music notation software, and the like. This volume, however, treats all tools used to create, store, reproduce, and transmit music—new or old, electronic or not—as technologies worthy of investigation. All musical instruments can be considered technologies. The modern piano, for example, is a marvel of keys, hammers, strings, pedals, dampers, and jacks; just the sound-producing mechanism, or action, on a piano has dozens of parts. In this broad view, technology in music encompasses instruments, whether acoustic, electric, or electronic; engraving and printing; sound recording and playback; broadcasting; software; and much more. This volume challenges the view that technology is unnatural, something external to music. It was sometimes said in the early twentieth century that so-called mechanical music (especially player pianos and phonographs) was a menace to “real” music; alternatively, technology can be freighted with utopian hopes and desires. Positive or negative, these views assume that technology is something that acts upon music. By contrast, this volume characterizes technology as an integral part of all musical activity and portrays traditional instruments and electronic machines as equally technological.
Bodies and senses
Authors: Katz Mark
Published: September 2022

Starting from the premise that our bodies are the primary and constant mediators of the music we experience, this chapter investigates how technology mediates the relationship between music and the human body. Often technologies offer a compromise: in providing new ways to experience music, they limit access to some of our senses. Radio, recordings, and streaming audio, for example, expand our access to music while removing or reducing the visual element of musical listening. Other technologies are designed to enhance our embodied experience of music, whether by providing visual elements or engaging with our sense of touch through what is known as vibrotactile feedback. Case studies explore music that is made but not seen, musical haptics, 18th- and 19th-century musical androids, Vocaloids, and musical holograms.
Predicting cell line-specific synergistic drug combinations through a relational graph convolutional network with attention mechanism
Authors: Zhang Peng , Tu Shikui , Zhang Wen , Xu Lei
Published: September 2022

Identifying synergistic drug combinations (SDCs) is a great challenge due to the combinatorial complexity and the fact that SDC is cell line specific. The existing computational methods either did not consider the cell line specificity of SDC, or did not perform well by building model for each cell line independently. In this paper, we present a novel encoder-decoder network named SDCNet for predicting cell line-specific SDCs. SDCNet learns common patterns across different cell lines as well as cell line-specific features in one model for drug combinations. This is realized by considering the SDC graphs of different cell lines as a relational graph, and constructing a relational graph convolutional network (R-GCN) as the encoder to learn and fuse the deep representations of drugs for different cell lines. An attention mechanism is devised to integrate the drug features from different layers of the R-GCN according to their relative importance so that representation learning is further enhanced. The common patterns are exploited through partial parameter sharing in cell line-specific decoders, which not only reconstruct the known SDCs but also predict new ones for each cell line. Experiments on various datasets demonstrate that SDCNet is superior to state-of-the-art methods and is also robust when generalized to new cell lines that are different from the training ones. Finally, the case study again confirms the effectiveness of our method in predicting novel reliable cell line-specific SDCs.
Computational modelling in health and disease: highlights of the 6th annual SysMod meeting
Authors: Niarakis Anna , Thakar Juilee , Barberis Matteo , Rodríguez Martínez María , Helikar Tomáš , Birtwistle Marc , Chaouiya Claudine , Calzone Laurence , Dräger Andreas
Published: September 2022

The Community of Special Interest (COSI) in Computational Modelling of Biological Systems (SysMod) brings together interdisciplinary scientists interested in combining data-driven computational modelling, multi-scale mechanistic frameworks, large-scale -omics data and bioinformatics. SysMod’s main activity is an annual meeting at the Intelligent Systems for Molecular Biology (ISMB) conference, a meeting for computer scientists, biologists, mathematicians, engineers and computational and systems biologists. The 2021 SysMod meeting was conducted virtually due to the ongoing COVID-19 pandemic (coronavirus disease 2019). During the 2-day meeting, the development of computational tools, approaches and predictive models was discussed, along with their application to biological systems, emphasizing disease mechanisms. This report summarizes the meeting.

Availability and implementation

All resources and further information are freely accessible at https://sysmod.info.
Changes in cortical endoplasmic reticulum clusters in the fertilized mouse oocyte
Authors: Wang Huizhen , Christenson Lane K , Kinsey William H
Published: September 2022

Oocytes from many invertebrate and vertebrate species exhibit unique endoplasmic reticulum (ER) specializations (cortical ER clusters), which are thought to be essential for egg activation. In examination of cortical ER clusters, we observed that they were tethered to previously unreported fenestrae within the cortical actin layer. Furthermore, studies demonstrated that sperm preferentially bind to the plasma membrane overlying the fenestrae, establishing close proximity to underlying ER clusters. Moreover, following sperm–oocyte fusion, cortical ER clusters undergo a previously unrecognized global change in volume and shape that persists through sperm incorporation, before dispersing at the pronuclear stage. These changes did not occur in oocytes from females mated with Izumo1 −/− males. In addition to these global changes, highly localized ER modifications were noted at the sperm binding site as cortical ER clusters surround the sperm head during incorporation, then form a diffuse cloud surrounding the decondensing sperm nucleus. This study provides the first evidence that cortical ER clusters interact with the fertilizing sperm, indirectly through a previous unknown lattice work of actin fenestrae, and then directly during sperm incorporation. These observations raise the possibility that oocyte ER cluster–sperm interactions provide a competitive advantage to the oocyte, which may not occur during assisted reproductive technologies such as intracytoplasmic sperm injection.
Anti-SARS-CoV-2 and anticoagulant properties of Pentacta pygmaea fucosylated chondroitin sulfate depend on high molecular weight structures
Authors: Dwivedi Rohini , Sharma Poonam , Eilts Friederike , Zhang Fuming , Linhardt Robert J , Tandon Ritesh , Pomin Vitor H
Published: September 2022

Fucosylated chondroitin sulfate (FucCS) is a unique marine glycosaminoglycan that exhibits diverse biological functions, including antiviral and anticoagulant activity. In previous work, the FucCS derived from Pentacta pygmaea (PpFucCS) showed moderate anticoagulant effect but high inhibitory activity against the Wuhan strain of severe acute respiratory syndrome coronavirus (SARS-CoV-2). In this study, we perform free-radical depolymerization of PpFucCS by the copper-based Fenton method to generate low molecular weight (MW) oligosaccharides. PpFucCS oligosaccharides were structurally analyzed by 1H nuclear magnetic resonance spectroscopy and were used to conduct structure–activity relationship studies regarding their effects against SARS-CoV-2 and clotting. Anticoagulant properties were measured by activated partial thromboplastin time, protease (factors Xa and IIa) inhibition by serine protease inhibitors (antithrombin [AT] and heparin cofactor II [HCII]), and competitive surface plasmon resonance (SPR) assay using AT, HCII, and IIa. Anti-SARS-CoV-2 properties were measured by the concentration-response inhibitory curves of HEK-293T-human angiotensin-converting enzyme-2 cells infected with a baculovirus pseudotyped SARS-CoV-2 Delta variant spike (S)-protein and competitive SPR assays using multiple S-proteins (Wuhan, N501Y [Alpha], K417T/E484K/N501Y [Gamma], L542R [Delta], and Omicron [BA.2 subvariant]). Cytotoxicity of native PpFucCS and oligosaccharides was also assessed. The PpFucCS-derived oligosaccharide fraction of the highest MW showed great anti-SARS-CoV-2 Delta activity and reduced anticoagulant properties. Results have indicated no cytotoxicity and MW dependency on both anti-SARS-CoV-2 and anticoagulant effects of PpFucCS, as both actions were reduced accordingly to the MW decrease of PpFucCS. Our results demonstrate that the high-MW structures of PpFucCS is a key structural element to achieve the maximal anti-SARS-CoV-2 and anticoagulant effects.
The Unintended Consequences of Information Provision: The World Health Organization and Border Restrictions during COVID-19
Authors: Worsnop Catherine Z , Grépin Karen A , Lee Kelley , Marion Summer
Published: September 2022

Why do some international agreements fail to achieve their goals? Rather than states’ engaging in cheap talk, evasion, or shallow commitments, the World Health Organization's (WHO) International Health Regulations (IHR)—the agreement governing states’ and WHO's response to global health emergencies—point to the unintended consequences of information provision. The IHR have a dual goal of providing public health protection from health threats while minimizing unnecessary interference in international traffic. As such, during major outbreaks WHO provides information about spread and severity, as well as guidance about how states should respond, primarily regarding border policies. During COVID-19, border restrictions such as entry restrictions, flight suspensions, and border closures have been commonplace even though WHO recommended against such policies when it declared the outbreak a public health emergency in January 2020. Building on findings from the 2014 Ebola outbreak, we argue that without raising the cost of disregarding (or the benefits of following) recommendations against border restrictions, information from WHO about outbreak spread and severity leads states to impose border restrictions inconsistent with WHO's guidance. Using new data from COVID-19, we show that WHO's public health emergency declaration and pandemic announcement are associated with increases in the number of states imposing border restrictions.
23 Sustainable Livestock Breeding with a Focus on Heat Stress
Authors: Misztal Ignacy
Published: September 2022

The genetic selection is a form of optimization. Traits in explicit or implicit selection index are improved, while other traits change according to genetic correlations among the traits. After long selection, usually production traits improve while fitness traits deteriorate. At the gene level, it seems that genes associated with positive effects on major traits tend to fixation, and remaining genes with large effect exhibit pleiotropy. While selection for fitness traits is moderately successful because of small heritability, constantly improving management counterbalances the deterioration of fitness traits. Treating the selection as an optimization raises a question about selection limits, particular with feed conversion. Latest experiences suggest that eventually strong selection for residual feed intake reduces fertility and increases late mortality. The environment changes, with climate change having a profound effect. The industry faces a choice of either breeding for new conditions or devising new managemental modifications. The choice depends on species as the environment can be more easily improved for animals in confinement or raised in intensive conditions (pigs, broilers, dairy cattle), but less for animals on pasture (beef cattle and sheep). The choice depends on financials and speed. An interesting example of such a trade-off is in dairy industry approach to mitigate heat stress, which results in plummeting fertility, decreased milk yield, and premature culling leading to insufficient replacements. To counter these challenges, a methodology for genetic evaluation for heat tolerance was developed and applied to US national data for Holsteins. Instead of genetics, the industry implemented managemental modifications: improved cooling devices, timed AI increased fertility, and the use of sexed semen. In pigs and chicken, that the response to stress is less in nucleus and stronger in commercial environment, and selection for commercial performance is paramount. In summary, mitigations of stress involve a combination of genetic and environmental factors.
68 Nutritional Importance of Animal-Sourced Foods in a Healthy Diet
Authors: Davis Teresa A
Published: September 2022

Animal-sourced foods are nutrient-dense foods that provide substantial amounts of high-quality protein, amino acids, vitamins, and minerals that are challenging to obtain solely through the consumption of plant-based foods. Numerous studies have documented that animal-sourced foods provide crucial nutrients that support the growth and development of children, maintenance of muscle mass in adults, and mitigation of sarcopenia in the elderly. Animal-sourced foods also can play an important role in weight management, prevention of anemia, and promotion of muscle mass and strength in exercising individuals. Although some epidemiological or observational studies have raised concerns that animal-sourced foods may increase the risk for chronic diseases, including cardiovascular disease and cancer, other epidemiological and clinical studies do not support these assertions. The 2020-2025 Dietary Guidelines for Americans, published by the United States Department of Agriculture and Department of Health and Human Services, support the role of animal-sourced foods in the diet at every stage of life. Lean meat is a high-quality protein source that is nutrient dense and low in calories and thus, plays an important role in a healthy diet.
74 Automation, Machine Learning and Computer Vision as Decision Support: Taking What Animal Agricultural Does Well Into the Future
Authors: McClain Scott
Published: September 2022

Commercial protein production involves ever more reliance on monitoring operations due to needs around disease intervention, animal loss, and optimized nutrition. With poultry flock and cattle herd sizes in the thousands, as two examples, early alert systems that forewarn of the need to make adjustments for optimized health are critical. There are never enough eyes and ears to alert to all the impactful changes that affect animal health and production output. Discussed here are examples of analytic data science where the extensive history of agriculture data collection and experience can be married with statistics and analytic data modeling. The goals include making the data available; providing easy access to modern analytic tools; and visual access to trusted analytic decision points on modern devices.
400 Improving Heat Stress Resilience to Reduce the Negative Effects of pre- and Postnatal Heat Stress in Swine
Authors: Johnson Jay S , Brito Luiz Fernando F , Maltecca Christian , Tiezzi Francesco
Published: September 2022

Heat stress will become a more substantial issue for swine production as global temperatures continue to rise. Efforts have been made to mitigate the negative impacts of heat stress through advances in genetic selection, nutrition, precision technology, and management practices. However, heat stress is still a limiting factor to swine production that must be addressed. A key aspect to mitigating heat stress-related production losses in swine may be developing better management approaches and genetic selection techniques to improve heat stress resilience. This is especially true for heat stress sensitive populations such as gestating and lactating sows. Gestating and lactating sows are considered heat stress sensitive due to greater metabolic heat production resulting from fetal growth and milk production, respectively. Additionally, swine offspring are adversely affected by in utero heat stress, which imprints long-term negative phenotypes that reduce health and productivity regardless of environmental conditions. To address these concerns, swine producers have implemented a variety of cooling and management strategies to mitigate heat stress. However, the recommended or perceived heat stress temperature thresholds for implementation may not accurately reflect the thermal requirements of modern swine with current genetics or at variable gestation stages leading to ineffective use. As such, a re-evaluation of heat stress thresholds for modern swine is warranted. Additionally, genetic selection for productivity traits (e.g., litter sizes and lean growth) has increased metabolic heat production resulting in increased heat stress sensitivity. Therefore, the ability to perform large-scale measures of and implement heat stress tolerance traits within breeding populations may be advantageous for producers to improve heat stress resilience within their herds. Taken together, as heat stress becomes a greater issue for the swine industry, it will become increasingly important to develop sustainable approaches that improve swine heat stress resilience while maintaining or improving producer profitability.
150 Effects of Annual and Perennial Forage Systems on Forage Biomass and Quality, Grazing Animal Performance, and Enteric Methane Emissions
Authors: Wasden Megan , Ribeiro Gabriel O , Damiran Daalkhaijav , Biligetu Bill , Larson Kathy A , Lardner Bart
Published: September 2022

The effects of perennial and annual forage systems on forage biomass and quality, grazing animal performance, and enteric methane emissions were evaluated over two summer grazing seasons in 2020 and 2021. Forage systems (treatments) included (1) AC Success hybrid bromegrass (Bromus riparius Rehm. × Bromus inermis Leyss.) + PS30006 alfalfa (Medicago sativa L.) (HBG-ALF), (2) AC Armada meadow bromegrass (Bromus riparius Rehm.) + AAC Mountainview sainfoin (Onobrychis viciifolia Scop.) (MBG-SF), (3) AC Hazlet fall rye (Secale cereale L.) + Frosty berseem clover (Trifolium alexandrinum L.) (FR-CLOV) and (4) Winfred forage brassica (Brassica oleracea L.× Brassica rapa L.) + Gorilla forage brassica (Brassica napus L.) + 4010 pea (Pisum sativum L.) + CDC Austenson barley (Hordeum vulgare L.) (BAR-PEA-BRASS). Yearling beef steers (n=156, body weight = 364 ± 14 kg) were randomly allocated to 1 of 4 replicated (n=3) forage systems for an average of 54 d grazing period each year. Dry matter yield (DMY) was greatest (P=0.006) for HBG-ALF (3036 kg/ha) and lowest for FR-CLOV (993 kg/ha) (P=0.005). Dry matter yield of BAR-PEA-BRASS (2123 kg/ha) and MBG-SF (1950 kg/ha) was similar (P=0.57). Total digestible nutrients (TDN) of BAR-PEA-BRASS (63.0%) and FR-CLOV (62.0%) was greater (P=0.001) than HBG-ALF (53.8%) and MBG-SF (54.7%). Crude protein (CP) was greatest (P=0.001) in FR-CLOV (13%). Crude protein of BAR-PEA-BRASS (9.6%) was greater (P=0.003) than HBG-ALF (6.6%) and MBG-SF (5.3%). Steer performance was greatest (P=0.03) on HBG-ALF (124 kg/ha). Steer performance on FR-CLOV (82 kg/ha), MBG-SF (76 kg/ha) and BAR-PEA-BRASS (74 kg/ha) was similar (P=0.92). Enteric methane emissions from beef steers did not differ between forage treatments (P=0.08). In summary, HBG-ALF forage system provided greater DMY, and grazing animal performance compared to the other forage systems, however TDN and CP content was lower than other forage systems and enteric methane emissions did not differ among treatments.