bluuebunny/crossref_metadata_2025 huggingface dataset:
Hyper clustering model for dynamic network intrusion detection
Authors: Alfoudi Ali Saeed , Aziz Mohammad R. , Alyasseri Zaid Abdi Alkareem , Alsaeedi Ali Hakem , Nuiaa Riyadh Rahef , Mohammed Mazin Abed , Abdulkareem Karrar Hameed , Jaber Mustafa Musa
Published: October 2022

Generally, the existing Intrusion Detection Systems (IDS) solutions suffer from low detection accuracy for some attack types compared with the overall detection accuracy of attacks. The data imbalance technically affects the ratio of detection accuracy of low frequent attacks class (e.g. zero‐day attack) compared to attacks with more instances. Therefore, IDS‐based machine learning algorithms potentially suffer from high false‐positive rates. To overcome the limitation of existing solutions, a hyper‐clustering model is proposed for dynamic intrusion detection based on the Density‐Based Spatial Clustering of Applications with Noise (DBSCAN) and cosine similarity. The proposed solution develops the standard DBSCAN by adding a new evolving process based on distance measures between the clusters to overcome the imbalance dataset. Moreover, a new classifier is proposed based on cosine similarity to predict the labelling of abnormal behaviour. The experimental results show that the proposed model outperformed the original DBCAN and the related works. The mean silhouette of the proposed DBSCAN achieves a high score of 0.87 compared to other solutions. Furthermore, the proposed DBSCAN reduces the mean square error from 0.66 to 0.13 and achieves 86.82%, 79.10% and 90.03% in general accuracy on KDDTest+, KDDTest‐21 NSL‐KDD and UNSW‐NB15 benchmark datasets, respectively.
Control of the formation and amplification of pulse bursts in regenerative amplifiers
Authors: Deutschmann‐Olek Andreas , Schrom Katharina , Kugi Andreas
Published: October 2022

This paper presents control strategies to generate bursts of high‐intensity laser pulses with arbitrary envelope from regenerative amplifiers by suitably adjusting the energy of the injected seed pulses. To this end, existing and experimentally validated models are generalized to obtain a dynamical model of the pulse formation and amplification. The resulting model is applicable to standard regenerative amplifiers as well as amplifiers with a detuned cavity specifically designed for the generation of pulse bursts. Utilizing this mathematical model, an optimization‐based algorithm to obtain desired pulse bursts in steady state is presented. Since the quality of these feedforward solutions is limited due to parameter variations and model imprecisions, an adaptation scheme using iterative learning control methods is employed to track the desired burst envelope. Finally, the developed methods are combined with feedback strategies to allow for an operation in unstable regimes and the closed‐loop behaviour is illustrated by simulation scenarios.
Named data network dynamic cache placement strategy based on programmable data plane
Authors: Hou Saifeng , Hu Yuxiang , Tian Le
Published: October 2022

Aiming at the efficiency and implementation of in‐network cache in Named Data Network, an in‐network cache method based on the programmable data plane was proposed. Set the cache port on the programmable data plane, when the cache policy determined that the content needs to be cached, set the output port as the cache port and forward it to the cache unit for caching. According to the different requirements of different contents on Quality of Service, the request contents were classified. And the cache probability of classified contents was calculated based on the content popularity and the cache cooperation information between nodes. The cache threshold was dynamically set according to the state of cache space occupancy and compared with the cache probability to determine whether to cache the contents. Experimental results show that the proposed cache placement strategy can effectively improve the cache hit ratio and reduce the average transmission latency compared with the traditional cache placement strategy.
Selective harmonic elimination pulse width modulation based hybrid multilevel inverter topology with reduced components
Authors: Wasiq Mohammad , Memon Mudasir Ahmed , Shrivastava Prashant , Mekhilef Saad , Seyedmahmoudian Mehdi , Stojcevski Alex , Horan Ben
Published: October 2022

In this paper, a reduced switch count single‐phase hybrid multilevel inverter (MLI) is presented. Level generation unit (LGU) and polarity changing unit (PCU) are the two parts of the presented topology which are connected in series. Other advantages of the proposed topology include the reduced switch count, higher level generation with reduced sources and the possibility of higher‐level generation with lower component counts. A single unit produces an output voltage of 13 levels with the modulation techniques as selective harmonic elimination pulse width modulation (SHEPWM) to improve harmonics. The use of selective harmonic elimination (SHM) is made to improve harmonics. The logical generation unit carries a series connection of multiple switched dc voltage sources with half and full‐bridge configurations. The proposed topology is verified by a hardware bench setup as well as in simulations which are developed in Simulink/MATLAB® environment.
FEM simulation‐based development of a new tunable non‐magnetic RF high voltage capacitor for the new generation of MRI
Authors: Jebri Zaineb , Bord‐Majek Isabelle , Bardet Matthieu , Ousten Yves
Published: October 2022

Using Radio Frequency (RF) waves, magnetic resonance imaging (MRI) systems can make detailed images of human organs for accurate diagnostic processes and disease detection. The overhaul of certain electronic components has become necessary to keep up with the progress of MRI systems. Among the components responsible for image quality, the adjustable non‐magnetic capacitors, also called trimmers, are of great importance. The purpose of this paper is to suggest a new design of a trimmer using non‐magnetic materials, able to hold a high voltage ( >3 kV) and reach a resonance frequency above 100 MHz. Constructional analysis performed on existing commercial trimmers, combined with the electrical Finite Element Method, were carried out to propose a prototype matching the desired specifications. A dielectric shield surrounding the electrodes was sized to ensure voltage withstand. Moreover, the rotor and the worm‐and‐gear set were joined together to combat the vibrations generated by the MRI system. The present study includes the modelling step of the component by numerical simulation, the manufacturing, the electrical performance characterization, and the mechanical solution for tuning capacitance. The final prototype combines electrical performance corresponding to the required specifications in particular a high breakdown voltage (39.7 kV) and a resonance frequency (130 MHz).
The impact of gender diversity on scientific research teams: a need to broaden and accelerate future research
Authors: Love Hannah B. , Stephens Alyssa , Fosdick Bailey K. , Tofany Elizabeth , Fisher Ellen R.
Published: October 2022

Multiple studies from the literature suggest that a high proportion of women on scientific teams contributes to successful team collaboration, but how the proportion of women impacts team success and why this is the case, is not well understood. One perspective suggests that having a high proportion of women matters because women tend to have greater social sensitivity and promote even turn-taking in meetings. Other studies have found women are more likely to collaborate and are more democratic. Both explanations suggest that women team members fundamentally change team functioning through the way they interact. Yet, most previous studies of gender on scientific teams have relied heavily on bibliometric data, which focuses on the prevalence of women team members rather than how they act and interact throughout the scientific process. In this study, we explore gender diversity in scientific teams using various types of relational data to investigate how women impact team interactions. This study focuses on 12 interdisciplinary university scientific teams that were part of an institutional team science program from 2015 to 2020 aimed at cultivating, integrating, and translating scientific expertise. The program included multiple forms of evaluation, including participant observation, focus groups, interviews, and surveys at multiple time points. Using social network analysis, this article tested five hypotheses about the role of women on university-based scientific teams. The hypotheses were based on three premises previously established in the literature. Our analyses revealed that only one of the five hypotheses regarding gender roles on teams was supported by our data. These findings suggest that scientific teams may create ingroups, when an underrepresented identity is included instead of excluded in the outgroup, for women in academia. This finding does not align with the current paradigm and the research on the impact of gender diversity on teams. Future research to determine if high-functioning scientific teams disrupt rather than reproduce existing hierarchies and gendered patterns of interactions could create an opportunity to accelerate the advancement of knowledge while promoting a just and equitable culture and profession.
Clustering and flocking of repulsive chiral active particles with non-reciprocal couplings
Authors: Kreienkamp Kim L , Klapp Sabine H L
Published: October 2022

Recently, non-reciprocal systems have become a focus of growing interest. Examples occur in soft and active matter, but also in engineered quantum materials and neural (brain) networks. Here, we investigate the impact of non-reciprocity on the collective behavior of a system of (dry) chiral active matter. Specifically, we consider a mixture of ‘circle swimmers’ with steric interactions and non-reciprocal alignment couplings. Based on hydrodynamic equations which we derive from a set of Langevin equations, we explore the interplay of non-reciprocity, finite size, and chirality. We first consider, as a reference, one-species systems with reciprocal couplings. Based on a linear stability analysis and numerical simulations, we here observe three different types of collective behavior, that is, flocking, motility-induced phase separation, and a combination of both. Turning then to a non-reciprocal system, we find that non-reciprocity can turn otherwise stationary instabilities into oscillatory ones, affect the relative orientation of flocks, and, crucially, change the general type of instability. This illustrates the drastic impact of non-reciprocity on the emergent collective dynamics of chiral active matter systems, with potentially far-reaching biological implications.
Honeybees modify flight trajectories in turbulent wind
Authors: Hejazi Bardia , Küchler Christian , Bagheri Gholamhossein , Bodenschatz Eberhard
Published: October 2022

In windy conditions, the air is turbulent. The strong and intermittent velocity variations of turbulence are invisible to flying animals. Nevertheless, flying animals, not much larger than the smallest scales of turbulence, manage to maneuver these highly fluctuating conditions quite well. Here we quantify honeybee flight with time-resolved three-dimensional tracking in calm conditions and controlled turbulent winds. We find that honeybee mean speed and acceleration are only weakly correlated with the strength of turbulence. In flight, honeybees accelerate slowly and decelerate rapidly, i.e., they break suddenly during turns and then accelerate again. While this behavior is observed in both calm and turbulent conditions, it is increasingly dominant under turbulent conditions where short straight trajectories are broken by turns and increased maneuvering. This flight-crash behavior is reminiscent of turbulence itself. Our observations may help the development of flight strategies for miniature flying robotics under turbulent conditions.
Understanding recent tropospheric ozone trends in the context of large internal variability: a new perspective from chemistry-climate model ensembles
Authors: Fiore Arlene M , Hancock Sarah E , Lamarque Jean-François , Correa Gustavo P , Chang Kai-Lan , Ru Muye , Cooper Owen , Gaudel Audrey , Polvani Lorenzo M , Sauvage Bastien , Ziemke Jerry R
Published: October 2022

Observational records of meteorological and chemical variables are imprinted by an unknown combination of anthropogenic activity, natural forcings, and internal variability. With a 15-member initial-condition ensemble generated from the CESM2-WACCM6 chemistry-climate model for 1950–2014, we extract signals of anthropogenic (‘forced’) change from the noise of internally arising climate variability on observed tropospheric ozone trends. Positive trends in free tropospheric ozone measured at long-term surface observatories, by commercial aircraft, and retrieved from satellite instruments generally fall within the ensemble range. CESM2-WACCM6 tropospheric ozone trends are also bracketed by those in a larger ensemble constructed from five additional chemistry-climate models. Comparison of the multi-model ensemble with observed tropospheric column ozone trends in the northern tropics implies an underestimate in regional precursor emission growth over recent decades. Positive tropospheric ozone trends clearly emerge from 1950 to 2014, exceeding 0.2 DU yr−1 at 20–40 N in all CESM2-WACCM6 ensemble members. Tropospheric ozone observations are often only available for recent decades, and we show that even a two-decade record length is insufficient to eliminate the role of internal variability, which can produce regional tropospheric ozone trends oppositely signed from ensemble mean (forced) changes. By identifying regions and seasons with strong anthropogenic change signals relative to internal variability, initial-condition ensembles can guide future observing systems seeking to detect anthropogenic change. For example, analysis of the CESM2-WACCM6 ensemble reveals year-round upper tropospheric ozone increases from 1995 to 2014, largest at 30 S–40 N during boreal summer. Lower tropospheric ozone increases most strongly in the winter hemisphere, and internal variability leads to trends of opposite sign (ensemble overlaps zero) north of 40 N during boreal summer. This decoupling of ozone trends in the upper and lower troposphere suggests a growing prominence for tropospheric ozone as a greenhouse gas despite regional efforts to abate warm season ground-level ozone.
LinAliFold and CentroidLinAliFold: fast RNA consensus secondary structure prediction for aligned sequences using beam search methods
Authors: Fukunaga Tsukasa , Hamada Michiaki
Published: October 2022

Motivation

RNA consensus secondary structure prediction from aligned sequences is a powerful approach for improving the secondary structure prediction accuracy. However, because the computational complexities of conventional prediction tools scale with the cube of the alignment lengths, their application to long RNA sequences, such as viral RNAs or long non-coding RNAs, requires significant computational time.

Results

In this study, we developed LinAliFold and CentroidLinAliFold, fast RNA consensus secondary structure prediction tools based on minimum free energy and maximum expected accuracy principles, respectively. We achieved software acceleration using beam search methods that were successfully used for fast secondary structure prediction from a single RNA sequence. Benchmark analyses showed that LinAliFold and CentroidLinAliFold were much faster than the existing methods while preserving the prediction accuracy. As an empirical application, we predicted the consensus secondary structure of coronaviruses with approximately 30 000 nt in 5 and 79 min by LinAliFold and CentroidLinAliFold, respectively. We confirmed that the predicted consensus secondary structure of coronaviruses was consistent with the experimental results.

Availability and implementation

The source codes of LinAliFold and CentroidLinAliFold are freely available at https://github.com/fukunagatsu/LinAliFold-CentroidLinAliFold.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
LaGAT: link-aware graph attention network for drug–drug interaction prediction
Authors: Hong Yue , Luo Pengyu , Jin Shuting , Liu Xiangrong
Published: October 2022

Motivation

Drug–drug interaction (DDI) prediction is a challenging problem in pharmacology and clinical applications. With the increasing availability of large biomedical databases, large-scale biological knowledge graphs containing drug information have been widely used for DDI prediction. However, large knowledge graphs inevitably suffer from data noise problems, which limit the performance and interpretability of models based on the knowledge graph. Recent studies attempt to improve models by introducing inductive bias through an attention mechanism. However, they all only depend on the topology of entity nodes independently to generate fixed attention pathways, without considering the semantic diversity of entity nodes in different drug pair links. This makes it difficult for models to select more meaningful nodes to overcome data quality limitations and make more interpretable predictions.

Results

To address this issue, we propose a Link-aware Graph Attention method for DDI prediction, called LaGAT, which is able to generate different attention pathways for drug entities based on different drug pair links. For a drug pair link, the LaGAT uses the embedding representation of one of the drugs as a query vector to calculate the attention weights, thereby selecting the appropriate topological neighbor nodes to obtain the semantic information of the other drug. We separately conduct experiments on binary and multi-class classification and visualize the attention pathways generated by the model. The results prove that LaGAT can better capture semantic relationships and achieves remarkably superior performance over both the classical and state-of-the-art models on DDI prediction.

Availabilityand implementation

The source code and data are available at https://github.com/Azra3lzz/LaGAT.

Supplementary information

Supplementary data are available at Bioinformatics online.
Defining the extent of gene function using ROC curvature
Authors: Fischer Stephan , Gillis Jesse
Published: October 2022

Motivation

Interactions between proteins help us understand how genes are functionally related and how they contribute to phenotypes. Experiments provide imperfect ‘ground truth’ information about a small subset of potential interactions in a specific biological context, which can then be extended to the whole genome across different contexts, such as conditions, tissues or species, through machine learning methods. However, evaluating the performance of these methods remains a critical challenge. Here, we propose to evaluate the generalizability of gene characterizations through the shape of performance curves.

Results

We identify Functional Equivalence Classes (FECs), subsets of annotated and unannotated genes that jointly drive performance, by assessing the presence of straight lines in ROC curves built from gene-centric prediction tasks, such as function or interaction predictions. FECs are widespread across data types and methods, they can be used to evaluate the extent and context-specificity of functional annotations in a data-driven manner. For example, FECs suggest that B cell markers can be decomposed into shared primary markers (10–50 genes), and tissue-specific secondary markers (100–500 genes). In addition, FECs suggest the existence of functional modules that span a wide range of the genome, with marker sets spanning at most 5% of the genome and data-driven extensions of Gene Ontology sets spanning up to 40% of the genome. Simple to assess visually and statistically, the identification of FECs in performance curves paves the way for novel functional characterization and increased robustness in the definition of functional gene sets.

Availability and implementation

Code for analyses and figures is available at https://github.com/yexilein/pyroc.

Supplementary information

Supplementary data are available at Bioinformatics online.
CRISPRon/off: CRISPR/Cas9 on- and off-target gRNA design
Authors: Anthon Christian , Corsi Giulia Ilaria , Gorodkin Jan
Published: October 2022

The effectiveness of CRISPR/Cas9-mediated genome editing experiments largely depends on the guide RNA (gRNA) used by the CRISPR/Cas9 system for target recognition and cleavage activation. Careful design is necessary to select a gRNA with high editing efficiency at the on-target site and with minimum off-target potential. Here, we present our webserver for gRNA design with a user-friendly graphical interface, which provides interoperability between our on- and off-target prediction tools, CRISPRon and CRISPRoff, for a complete and streamlined gRNA selection.

Availability and implementation

The graphical interface uses the Integrative Genomic Viewer (IGV) JavaScript plugin. The backend tools are implemented in Python and C. The CRISPRon and CRISPRoff webservers and command-line tools are freely available at https://rth.dk/resources/crispr.
Management of fracture risk in CKD—traditional and novel approaches
Authors: Haarhaus Mathias , Aaltonen Louise , Cejka Daniel , Cozzolino Mario , de Jong Renate T , D'Haese Patrick , Evenepoel Pieter , Lafage-Proust Marie-Hélène , Mazzaferro Sandro , McCloskey Eugene , Salam Syazrah , Skou Jørgensen Hanne , Vervloet Marc
Published: October 2022

The coexistence of osteoporosis and chronic kidney disease (CKD) is an evolving healthcare challenge in the face of increasingly aging populations. Globally, accelerating fracture incidence causes disability, impaired quality of life and increased mortality. Consequently, several novel diagnostic and therapeutic tools have been introduced for treatment and prevention of fragility fractures. Despite an especially high fracture risk in CKD, these patients are commonly excluded from interventional trials and clinical guidelines. While management of fracture risk in CKD has been discussed in recent opinion-based reviews and consensus papers in the nephrology literature, many patients with CKD stages 3–5D and osteoporosis are still underdiagnosed and untreated. The current review addresses this potential treatment nihilism by discussing established and novel approaches to diagnosis and prevention of fracture risk in patients with CKD stages 3–5D. Skeletal disorders are common in CKD. A wide variety of underlying pathophysiological processes have been identified, including premature aging, chronic wasting, and disturbances in vitamin D and mineral metabolism, which may impact bone fragility beyond established osteoporosis. We discuss current and emerging concepts of CKD–mineral and bone disorders (CKD-MBD) and integrate management of osteoporosis in CKD with current recommendations for management of CKD-MBD. While many diagnostic and therapeutic approaches to osteoporosis can be applied to patients with CKD, some limitations and caveats need to be considered. Consequently, clinical trials are needed that specifically study fracture prevention strategies in patients with CKD stages 3–5D.
An IoT Privacy-Oriented selective disclosure credential system
Authors: Rasslan Mohamed , Nasreldin Mahmoud M , Aslan Heba K
Published: October 2022

Personal credentials, such as passports and drivers’ licenses, can be implemented electronically using multi-show protocols. In this paper, we introduce an IoT Privacy-Oriented selective disclosure credential system, i.e. based on bilinear pairings and multilinear maps. The proposed system consists of three protocols, which allow users to be in control of their personal credentials. The Credentials Authority (CA) verifies and attests to the users credentials. Once the CA signs these credentials, the users cannot modify any of them. Moreover, the users can mask these credentials in every showing process to protect their identity from being revealed through a collusion between the CA and the verifiers. The proposed system maintains unlinkability between the issuing and showing protocols. Furthermore, it achieves unlinkability in the showing protocol such that the verifier cannot distinguish a user in two different sessions of the showing protocol. The proposed system is novel and practical in terms of introducing a new multi-show credential system that supports selective disclosure (Some credentials can be disclosed and others kept secret during the showing protocol.) The proposed system is the first that utilizes multilinear maps in the identification protocol. Making use of bilinear pairings and multilinear maps are suitable for IoT devices that have limited capabilities in terms of power consumption, key storage, and computing power. The security analysis of the proposed system is discussed using Burrows–Abadi–Needham (BAN) logic.
Genetic and epigenetic interplay allows rapid transgenerational adaptation to metal pollution in zebrafish
Authors: Pierron Fabien , Heroin Débora , Daffe Guillemine , Daramy Flore , Barré Aurélien , Bouchez Olivier , Romero-Ramirez Alicia , Gonzalez Patrice , Nikolski Macha
Published: October 2022

Despite still being a matter of debate, there is growing evidence that pollutant-induced epigenetic changes can be propagated across generations. Whereas such modifications could have long-lasting effects on organisms and even on population, environmentally relevant data from long-term exposure combined with follow-up through multiple generations remain scarce for non-mammalian species. We performed a transgenerational experiment comprising four successive generations of zebrafish. Only fish from the first generation were exposed to an environmentally realistic concentration of cadmium (Cd). Using a whole methylome analysis, we first identified the DNA regions that were differentially methylated in response to Cd exposure and common to fish of the first two generations. Among them, we then focused our investigations on the exon 3 (ex3) of the cep19 gene. We indeed recorded transgenerational growth disorders in Cd-exposed fish, and a mutation in this exon is known to cause morbid obesity in mammals. Its methylation level was thus determined in zebrafish from all the four generations by means of a targeted and base resolution method. We observed a transgenerational inheritance of Cd-induced DNA methylation changes up to the fourth generation. However, these changes were closely associated with genetic variations, mainly a single nucleotide polymorphism. This single nucleotide polymorphism was itself at the origin of the creation or deletion of a methylation site and deeply impacted the methylation level of neighboring methylation sites. Cd-induced epigenetic changes were associated with different mRNA transcripts and an improved condition of Cd fish. Our results emphasize a tight relationship between genetic and epigenetic mechanisms and suggest that their interplay and pre-existing diversity can allow rapid adaptation to anthropogenic environmental changes.
Integrative metabolomics and transcriptomics analyses reveal pivotal regulatory mechanisms of 1-methylcyclopropene in maintaining postharvest storage quality of ‘Fuji’ apples
Authors: Zhang Lingling , Zhang Peiyu , Gao Modi , Zhao Yi , Zhang Chunjiao , Zhu Hongliang
Published: October 2022

In this study, integrative metabolomics and transcriptomics analyses were conducted to investigate the effects of 1-methylcyclopropene (1-MCP) on apple fruit quality during long-term cold storage. The results showed that 1-MCP (1 μL/L) treatment could maintain fruits apparent quality (i.e. external color and firmness), inhibit the increase of rot rate and soluble solids content/titratable acidity ratio, decrease ethylene release, and respiratory intensity during cold storage, and extend shelf life. Moreover, 1-MCP had long-term effects on the accumulation of many qualities related to metabolite and gene expression in fruits. 1-MCP affected genes related to metabolism at the early stage of storage, specifically those of the glycolysis and tricarboxylic acid cycle pathways. Genes related to the degradation of sucrose, starch, and cellulose were inhibited, and some starch and cellulose synthesis genes were up-regulated by 1-MCP. Apart from ethylene synthesis and signal transduction being inhibited by 1-MCP, several enzymes (pectinesterase, pectate lyase, polygalacturonase) were involved in pectin degradation, and degradation products of the cell wall (i.e. d-galacturonic acid and d-glucuronic acid) were also strongly inhibited, further maintaining fruit firmness. Cysteine, as precursor glutathione (GSH) related to plant resistance, up-regulated the synthase gene. However, the expression of genes related to cyanoalanine synthase and amino acid utilization pathways was suppressed by 1-MCP. Collectively, 1-MCP could maintain the postharvest quality of apple fruits.
XROMM Analysis of Feeding Mechanics in Toads: Interactions of the Tongue, Hyoid, and Pectoral Girdle
Authors: Keeffe R M , Blob R W , Blackburn D C , Mayerl C J
Published: October 2022

Synopsis

During feeding in many terrestrial vertebrates, the tongue acts in concert with the hyoid and pectoral girdle. In frogs, these three elements are interconnected by musculature. While the feeding mechanics of the anuran tongue are well-studied, little is known of how the motions of the tongue relate to the movements of the skeleton or how buccal structures move following closure of the mouth. Although features such as the pectoral girdle and hyoid are not externally visible in frogs, their motions can be tracked in X-ray video. We used XROMM (X-ray Reconstruction of Moving Morphology) techniques to track the 3D movements of the tongue, hyoid apparatus, pectoral girdle, skull, and jaw during the feeding cycle of the cane toad, Rhinella marina. We show how the movements of these elements are integrated during tongue protrusion and prey capture, as well as during prey transport, swallowing, and recovery. Our findings suggest that the hyoid apparatus is important both for prey manipulation and swallowing. The tongue consistently stretches posterior to the skull during swallowing, often more than it stretches during protrusion to reach the prey. Feeding kinematics are similar between individuals, and the kinematics of unsuccessful strikes generally resemble those of successful strikes. Our data also provide a new perspective on the potential role of the pectoral girdle, an element with a predominant locomotor function, during feeding events. This work raises new questions about the evolution of feeding in frogs, as well as how the diversity of pectoral and buccal anatomy observed across anurans may influence feeding kinematics.
Investigating the immunomodulatory activities of omadacycline
Authors: Bryant Amy E , Stevens Dennis L
Published: October 2022

Background

Apart from their antimicrobial activities, some antibiotics have immunomodulatory effects on host cells, particularly monocytes. Because hyperactivation of the pro-inflammatory cytokine response contributes to acute lung injury in patients with bacterial pneumonia and other lung diseases, antimicrobial agents with immunomodulatory activity can reduce cytokine-mediated tissue injury and improve outcomes.

Objectives

Omadacycline has been recently FDA-approved for community-acquired bacterial pneumonia and acute bacterial skin and skin-structure infections. The present study investigated omadacycline’s ability to modulate LPS-induced production of pro-inflammatory cytokines (TNF-α, IL-1β), acute-phase reactants (IL-6) and anti-inflammatory cytokines (IL-4, IL-10) by human monocytes in vitro.

Methods

Isolated human monocytes from healthy consenting adults were cultured in RPMI with 1% pooled human serum. Cells were pre-exposed to omadacycline (0.5–64 μg/mL), minocycline (25, 50 or 25 μg/mL) or azithromycin (20, 40 or 80 μg/mL) for 2 h, followed by stimulation with Escherichia coli LPS for 24 h. Cytokines elaborated in the culture supernatant were quantitated by multiplex immunoassay.

Results

Omadacycline dose-dependently suppressed LPS-induced production of all cytokines tested. Only high-dose minocycline (100 μg/mL) modestly suppressed TNF-α whereas minocycline significantly increased LPS-induced IL-1β production. Lower concentrations of minocycline were also stimulatory for IFN-γ, IL-6 and IL-4. Except for suppression of IL-6, azithromycin was largely without effect.

Conclusions

Omadacycline has unique and broad immunomodulatory properties. Such activity supports its use in settings where hyperactivation of the immune response contributes to tissue injury and poor outcomes, especially at sites where pro-inflammatory M-type 1 macrophages dominate the cellular immune response.
In vivo pharmacokinetics and pharmacodynamics of ceftibuten/ledaborbactam, a novel oral β-lactam/β-lactamase inhibitor combination
Authors: Fratoni Andrew J , Avery Lindsay M , Nicolau David P , Asempa Tomefa E
Published: October 2022

Objectives

Oral β-lactam treatment options for MDR Enterobacterales are lacking. Ledaborbactam (formerly VNRX-5236) is a novel orally bioavailable β-lactamase inhibitor that restores ceftibuten activity against Ambler Class A-, C- and D-producing Enterobacterales. We assessed the ledaborbactam exposure needed to produce bacteriostasis against ceftibuten-resistant Enterobacterales in the presence of humanized ceftibuten exposures in the neutropenic murine thigh infection model.

Methods

Twelve ceftibuten-resistant clinical isolates (six Klebsiella pneumoniae, five Escherichia coli and one Enterobacter cloacae) were utilized. Ceftibuten/ledaborbactam MICs ranged from 0.12 to 2 mg/L (ledaborbactam fixed at 4 mg/L). A ceftibuten murine dosing regimen mimicking ceftibuten 600 mg q12h human exposure was developed and administered alone and in combination with escalating exposures of ledaborbactam. The log10 cfu/thigh change at 24 h relative to 0 h controls was plotted against ledaborbactam fAUC0–24/MIC and the Hill equation was used to determine exposures associated with bacteriostasis.

Results

The mean ± SD 0 h bacterial burden was 5.96 ± 0.24 log10 cfu/thigh. Robust growth (3.12 ± 0.93 log10 cfu/thigh) was achieved in untreated control mice. Growth of 2.51 ± 1.09 log10 cfu/thigh was observed after administration of humanized ceftibuten monotherapy. Individual isolate exposure–response relationships were strong (mean ± SD R2 = 0.82 ± 0.15). The median ledaborbactam fAUC0–24/MIC associated with stasis was 3.59 among individual isolates and 6.92 in the composite model.

Conclusions

Ledaborbactam fAUC0–24/MIC exposures for stasis were quantified with a ceftibuten human-simulated regimen against β-lactamase-producing Enterobacterales. This study supports the continued development of oral ceftibuten/ledaborbactam etzadroxil (formerly ceftibuten/VNRX-7145).
16 An Overview of the AVMA Working Group on the Psychological Impacts of Humane Endings and Related Guidance Documents
Authors: Kollias Nathaniel S
Published: October 2022

The psychological impacts of humane endings on veterinarians, animal health and production personnel, and support staff are a growing concern within the veterinary community. The COVID-19 pandemic has further highlighted the need for resources, understanding, and compassion for our colleagues involved in the care and wellbeing of animals. Whether humane endings activities are related to euthanasia of individual animals, slaughter of animals for human consumption, or rare emergency situations warranting depopulation of a large group of animals, the veterinarian plays an important role in these determinations. The AVMA has led and continues to lead in providing guidance on humane endings including their three documents: AVMA Guidelines for the Euthanasia of Animals, AVMA Guidelines for the Humane Slaughter of Animals, and AVMA Guidelines for the Depopulation of Animals. Recently, the AVMA formed a working group on the psychological impacts of humane endings to address the needs of veterinarians and other animal health professionals. This working group has reviewed the existing literature to lay the foundation and rationale for improved preparation, development of mental health resources, and to offer recommendations on pragmatic ways to support and prepare veterinary professionals impacted by depopulation events. While there are mental health challenges shared by those involved in euthanasia, slaughter, and depopulation, there are some stressors specific to depopulation, and it is those that this group is addressing first.
45 Imaging and Phenotyping Technologies for Poultry Welfare Evaluation
Authors: Chai Lilong
Published: October 2022

United States is currently the world’s largest broiler producer and the second largest egg producer (e.g., poultry and eggs had a sale value of $40 billion in 2021), but poultry and egg productions are facing grand challenges of animal welfare concerns, food safety issues, and environmental impacts. The rapid growth rate of broilers is associated with welfare concerns such as leg issues and lameness. Broilers with lameness suffer behavior restrictions, physical discomforts, and impingement of fundamental freedoms. Those welfare concerns have triggered the attention of the general public and the food industry to improve broiler well-being, and well-being evaluation. Animal welfare evaluation is currently performed manually by farm workers daily or occasionally in the poultry houses, which is time consuming, labor intensive, and subject to human errors. This task calls for the design of an automated system that can monitor poultry welfare automatically. Sensing technologies, such as ultra-wideband, radio frequency identification, accelerometer, and computer vision-based monitoring, have been and are being adapted and tested for livestock and poultry farming systems to aide well-being evaluation. Computer vision-based phenotyping technologies have been tested efficient in monitoring large animals such as cattle and pigs. However, it is technically challenging to monitor smaller animals such as broiler and layer chickens. Researchers at the University of Georgia are developing specific imaging and phenotyping technologies (e.g., deep learning models) for monitoring/tracking floor distribution patterns of broiler chickens and individual birds’ moving in different zones of feeding, drinking, and resting. The imaging technologies have also been applied to monitor laying hen’s behaviors of perching, pecking, and floor egg laying in the cage-free houses. Those imaging and phenotyping technologies will be further innovated for developing integrative sensing systems to evaluate poultry welfare indicators in commercial broiler and cage-free layer houses.
267 AQualitative Exploration of Barriers and Recommendations from Women Leaders in Science and Agriculture
Authors: Owens Casey M , Harlin Julie F , Alvarado Christine
Published: October 2022

The purpose of the study was to conduct a qualitative exploration of barriers and recommendations from women leaders in science and agriculture. This study used a voluntary sample descriptive survey design that included 8 demographic, 11 importance/satisfaction, 7 negative/positive attribution, 11 barrier, and two open-ended questions. Responses were collected over a one-week period using social networking sites for women leaders in science and agriculture resulting in 60 respondents. The average respondents were all women in leadership roles in science and agriculture, 44years old, married, with no children, making between $60-120,000 per year, who were also highly educated with a Masters or Doctoral degree and traveled more than two-three times per month. This study focused on responses of the two open-ended questions. Comments to the questions: “If there was one piece of advice you could go back and give yourself when you began your career, what would you share?” and “Please let us know if there was something else you wanted to share related to women in leadership roles in science and agriculture” resulted in 72 individual responses analyzed using the constant comparative method. Peer debriefings and inter-coder reliability were used to ensure trustworthiness and credibility. The qualitative analysis resulted in the following emerging themes: Having it all, Personal Development and Education, Personal Advocacy, and Networking. Though the results of this study are limited to this group of respondents, it is an important step in understanding the nuanced issues women face in leadership roles. One participant summed it up by stating: “The "take this opportunity now because it might never happen again" advice Iwas given for my career, Iused too much... and sometimes…the opportunities DO happen again... your life doesn't though, and at the end of the day, it's your family and health that stick.”
5 Effect of Species and Maturity on Winter Hardy Small Grain Silage Yield and Quality
Authors: Sartin Abigail , Calus Kallie , Hall Alyssa , Grabau Morgan , Redfearn Daren , Drewnoski Mary E
Published: October 2022

Winter-hardy small grains offer an opportunity to improve soil health as a cover crop, and they can also be used as a forage source for cattle. Winter-hardy small grains differ in the time needed to reach various maturity stages. Species selection may also impact yield and nutritive value. A two-year study was conducted in eastern Nebraska to determine the effect of species and maturity on yield and nutritive value of winter-hardy small grains used for silage. Three species were evaluated; cereal rye, winter wheat, and winter triticale at four stages of maturity: boot, anthesis, milk, and soft dough. The experimental design was a randomized complete block design with four blocks per year. Small grain species were considered whole plots with maturity at harvest considered sub-plot. Each year, the small grain species were randomly assigned within each block. Within each plot, maturity was randomly assigned to one quarter of each plot. Dry matter (DM) forage yield, crude protein (CP), digestible organic matter (DOM), and nutrient yield per hectare were measured and analyzed using the mixed procedure of SAS. Forage yield increased for all species (P < 0.01) with maturity, except for wheat, where there was a decrease at soft dough. Forage yield of cereal rye and triticale did not differ (P>0.05), except at soft dough where triticale was greater (P < 0.01) than cereal rye. Forage yield of triticale and cereal rye yield was greater (P£0.05) than wheat at anthesis and soft dough. Crude protein (% DM) decreased (P < 0.01) with maturity across all species. Among species, CP for cereal rye was greater (P£0.01) than triticale at boot, anthesis, and soft dough, but not different (P³0.10) from wheat at boot, milk, and soft dough. At boot, anthesis, and milk stages, CP of triticale was not different (P³0.07) than wheat, but triticale was lower than wheat (P < 0.01) at soft dough. The DOM (% DM) decreased (P < 0.01) with maturity, except at soft dough. The DOM of cereal rye and wheat did not differ (P > 0.05), but both were greater (P < 0.01) than triticale. Cereal rye and triticale had greater (P £ 0.05) nutrient yields than wheat in terms of energy (DOM) and CP. There was no difference for CP yield across stages (P = 0.10), but there was an effect of maturity on DOM yield. The DOM yield increased from boot to anthesis, (P = 0.05), anthesis and milk did not differ (P = 0.08) and increased (P < 0.01) again at soft dough. This suggests that planting either cereal rye or triticale resulted in the greatest nutrient yield per acre. Harvest at anthesis had increased yield compared to boot with minimal loss in nutritive value; for maximizing energy yield per acre, harvesting at soft dough was the best option.
9 Strategically Supplementing Yearling Cattle on Cool Season Pasture: Implications for Cattle Performance and Return to Management
Authors: Wheeler Kaylee E , Wilke Karla , Drewnoski Mary E , Parsons Jay , Dustin Dean
Published: October 2022

The cattle industry and its associated markets are inherently volatile, leading producers to search for more economically sustainable production practices. Supplementation with high protein feed increases yearling gain. However, strategically supplementing in the latter half of the grazing season, as forage quality declines, could provide a more economical increase in gain and return to management. Therefore, a three-year experiment was conducted at the High Plains Agriculture Laboratory, in Sidney, NE. The effects of strategically supplementing dry distillers grains (DDG) on yearling cattle performance and return to management were compared among a variety of economic conditions. Yearlings (313±46 kg) were stocked at 4.3 ha/animal on crested wheatgrass pastures for an average of 112 days beginning in mid-May. They were supplemented either throughout the entire period (FULL), only during the latter part (STRAT), or not at all (CONT) (n = 4 reps/treatment in years 1 and 2, 3 reps/treatment in year 3). Supplemented yearlings received 1.59 kg of DDGs 6 days/week. On average, CP (%DM) of crested wheatgrass declined from 10.2 (May) to 6.8 (September), while IVDMD (%DM) declined from 51 (May) to 37 (September). There were no significant (P > 0.53) experimental year and treatment effects for cattle performance. However, there was an effect (P < 0.01) of treatment and year on ADG and final body weight. On average, non-supplemented yearlings had an average daily gain (ADG) of 0.68 kg/d. Providing supplement increased ADG by 0.23 kg/d (P < 0.01). Performance did not differ (P < 0.01) between STRAT and FULL, despite STRAT receiving nearly half (54%) the amount of supplement. Cattle and DDG prices from the previous decade (2012–2021) were applied to experimental data to create various potential marketing scenarios. Return to management was calculated as the return to labor costs for providing supplement. On average, FULL returned $14.96 more and STRAT returned $32.21 more per yearling than CONT. Within economic year, return of STRAT was greater (P ≤ 0.05) than CONT in all years except 2012, 2019 and 2021. Return of FULL was greater (P ≤ 0.05) than CONT in all years except 2012, 2018, 2019, and 2021. Numerically, STRAT was always greater than CONT and FULL. Higher DDG prices coupled with lower live cattle prices caused less return in those years. Breakeven DDG costs for STRAT averaged $530/909 kg and ranged from $268/909 kg to $822/909 kg. Applying a $0.30/yearling/day labor cost, the average breakeven for this strategy declines to $345/909 kg of DDG. These results suggest that strategically supplementing DDG as forage quality of crested wheatgrass declines in the summer will provide similar yearling performance to supplementing throughout the entire grazing season. Strategic supplementation also appears to have a high likelihood increasing return to management.