bluuebunny/crossref_metadata_2025 huggingface dataset:
Docking-based long timescale simulation of cell-size protein systems at atomic resolution
Authors: Vakser Ilya A. , Grudinin Sergei , Jenkins Nathan W. , Kundrotas Petras J. , Deeds Eric J.
Published: June 2022

Computational methodologies are increasingly addressing modeling of the whole cell at the molecular level. Proteins and their interactions are the key component of cellular processes. Techniques for modeling protein interactions, so far, have included protein docking and molecular simulation. The latter approaches account for the dynamics of the interactions, but are relatively slow, if carried out at all-atom resolution, or are significantly coarse-grained. Protein docking algorithms are far more efficient in sampling spatial coordinates. However, they do not account for the kinetics of the association (i.e., they do not involve the time coordinate). Our proof-of-concept study bridges the two modeling approaches, developing an approach that can reach unprecedented simulation timescales at all-atom resolution. The global intermolecular energy landscape of a large system of proteins was mapped by the pairwise Fast Fourier Transform docking and sampled in space and time by Monte Carlo simulations. The simulation protocol was parametrized on existing data and validated on a number of observations from experiments and molecular dynamics simulations. The simulation protocol performed consistently across very different systems of proteins at different protein concentrations. It recapitulated data on the previously observed protein diffusion rates and aggregation. The speed of calculation allows reaching second-long trajectories of protein systems that approach the size of the cells, at atomic resolution.
Dynamic Phaeodactylum tricornutum Exometabolites Shape Surrounding Bacterial Communities
Authors: Brisson Vanessa , Swink Courtney , Kimbrel Jeffrey , Mayali Xavier , Samo Ty , Kosina Suzanne M. , Thelen Michael , Northen Trent R. , Stuart Rhona K.
Published: June 2022

The roles of exometabolites in mediating algal-bacterial interactions and regulating microbial community composition are not well understood. Here, we identified specific exometabolites from the model diatom Phaeodactylum tricornutum affecting abundance of specific bacterial taxa in isolation and in a community setting. We examined the response of a P. tricornutum-adapted enrichment community and found that both algal exudates and algal presence drove similar changes in community composition compared to controls. Using LC-MS/MS, we identified 50 metabolites produced by axenic P. tricornutum and found that different exometabolites accumulated during different algal growth phases. Profiling growth of 12 bacterial isolates representative of the enrichment community uncovered two algal exometabolites (out of 12 tested) which supported growth of a subset of isolates as a primary carbon source. We compared enrichment community response with and without the addition of two contrasting metabolites: 4-hydroxybenzoic acid, which supported isolate growth, and lumichrome, which did not. Exogenous metabolite additions did promote increased abundances of taxa that were able to utilize the metabolite in the isolate study, but also revealed the importance of factors relating to algal presence in regulating community composition. Collectively, this work demonstrates the influence of specific algal exometabolites in driving microbial community composition.
A genomic platform for epidemiological surveillance and vaccine antigen discovery using long-read amplicon sequencing
Authors: Plaza David Fernando , Zerebinski Julia , Broumou Ioanna , Lautenbach Maximilian Julius , Ngasala Billy , Sundling Christopher , Färnert Anna
Published: June 2022

Many vaccine candidate proteins are under strong selective pressure to diversify in terms of antigenicity. We present a sequencing and data analysis platform for epidemiological surveillance and discovery of indel-rich vaccine antigens by long-read circular consensus sequencing (CCS) in multiclonal pathogen isolates. Our platform uses 40 PCR primers to asymmetrically barcode and identify multiclonal infections in pools of up to 384 samples. We validated the method using 235 mock infections combining 10 synthetic variants of the indel-rich gene merozoite surface protein 2 of Plasmodium falciparum at different concentrations and infection complexities, as well as 95 isolates from P. falciparum-infected residents of Nyamisati, Tanzania. We also constructed a fully automated analysis pipeline that streamlines the processing and interpretation of epidemiological and antigenic diversity data from demultiplexed FASTQ files. This platform can be easily adapted to other polymorphic antigens of interest in Plasmodium and other human pathogens.
Fine tuning of CpG spatial distribution with DNA origami for improved therapeutic cancer vaccination
Authors: Zeng Yang C. , Young Olivia J. , Wintersinger Christopher M. , Anastassacos Frances M. , MacDonald James I. , Isinelli Giorgia , Dellacherie Maxence O. , Sobral Miguel , Bai Haiqing , Graveline Amanda R. , Vernet Andyna , Sanchez Melinda , Mulligan Kathleen , Choi Youngjin , Ferrante Thomas C. , Keskin Derin B. , Fell Geoffrey G. , Neuberg Donna , Wu Catherine J. , Mooney David J. , Kwon Ick Chan , Ryu Ju Hee , Shih William M.
Published: June 2022

Multivalent presentation of ligands often enhances receptor activation and downstream signaling. DNA origami offers precise nanoscale spacing of ligands, a potentially useful feature for therapeutic nanoparticles. Here we introduce a “square block” DNA origami platform to explore the importance of spacing of CpG oligonucleotides, which engage Toll-like receptors and thereby act as danger signals for dendritic cells. Throughin vitrocell-culture studies andin vivotumor-treatment models, we demonstrate that square blocks induce Th1 immune polarization when CpG is spaced at 3.5 nm. We observe that this DNA origami vaccine enhances DC activation, antigen cross-presentation, CD8 T cell activation, Th1-polarized CD4 activation and NK cell activation. The vaccine also synergizes effectively with anti-PD-L1 for improved cancer immunotherapy in melanoma and lymphoma models and induces long-term T cell memory. Our results suggest that DNA origami may serve as an advanced vaccine platform for controlling adjuvant spacing and co-delivering antigens.

One Sentence Summary

This study developed a DNA origami-based cancer vaccine (DoriVac) that co-delivers antigen and CpG immune adjuvant with an optimal nanospacing for Th1 immune polarization.
Highly accurate isoform identification for the human transcriptome
Authors: Sommer Markus J. , Cha Sooyoung , Varabyou Ales , Rincon Natalia , Park Sukhwan , Minkin Ilia , Pertea Mihaela , Steinegger Martin , Salzberg Steven L.
Published: June 2022

We explore a new hypothesis in genome annotation, namely whether computationally predicted protein structures can help to identify which of multiple possible gene isoforms represents a functional protein product. Guided by structure predictions, we evaluated over 140,000 isoforms of human protein-coding genes assembled from over 10,000 RNA sequencing experiments across many human tissues. We illustrate our new method with examples where structure provides a guide to function in combination with expression and evolutionary evidence. Additionally, we provide the complete set of structures as a resource to better understand the function of human genes and their isoforms. These results demonstrate the promise of protein structure prediction as a genome annotation tool, allowing us to refine even the most highly-curated catalog of human proteins.

One-Sentence Summary

We describe the use of 3D protein structures on a genome-wide scale to evaluate human protein isoforms for biological functionality.
Elevator-type Mechanism of the Cyanobacterial Bicarbonate Transporter
Authors: Chan Matthew , Alfawaz Yazeed , Paul Arnav , Shukla Diwakar
Published: June 2022

Cyanobacteria are responsible for up to 80% of aquatic carbon dioxide fixation and have evolved specialized carbon concentrating mechanism to increase photosynthetic yield. As such, cyanobacteria are attractive targets for synthetic biology and engineering approaches to address the demands of global energy security, food production, and climate change for an increasing world's population. The bicarbonate transporter BicA is a sodium-dependent, low-affinity, high-flux bicarbonate symporter expressed in the plasma membrane of cyanobacteria. Despite extensive biochemical characterization of BicA, including the resolution of the BicA crystal structure, the dynamic understanding of the bicarbonate transport mechanism remains elusive. To this end, we have collected over 1 ms of all-atom molecular dynamics simulation data of the BicA dimer to elucidate the structural rearrangements involved in the substrate transport process. We further characterized the energetics of the cooperativity between BicA protomers and investigated potential mutations that are shown to decrease the free energy barrier of conformational transitions. In all, our study illuminates a detailed mechanistic understanding of the conformational dynamics of bicarbonate transporters and provide atomistic insights to engineering these transporters for enhanced photosynthetic production.
Stress-relief function of migrasomal autophagosome formed by inhibition of autophagosome/lysosome fusion
Authors: Lee Seon Yong , Choi Sang-Hun , Ahn Hee-Sung , Ko Young-Gyu , Kim Kyunggon , Chi Sung Wook , Kim Hyunggee
Published: June 2022

Glioblastoma (GBM) is more difficult to treat than other intractable adult tumors. Here, we describe the composition and function of migrasomes generated along with GBM cell migration. Proteomic analysis revealed that LC3B-positive autophagosomes were abundant in the migrasomes of GBM cells. An increased number of migrasomes was observed following treatment with chloroquine (CQ) or inhibition of the expression of STX17 and SNAP29, which are involved in autophagosome/lysosome fusion. Although ATG7 ablation, which is involved in LC3B lipidation, did not suppress migrasome formation, it was confirmed that migrasome formation could be diminished by blocking the alternative autophagy pathway through double knockout of ATG7/BECN1. Furthermore, depletion of ITGA5 or TSPAN4 did not relieve endoplasmic reticulum (ER) stress in cells, resulting in cell death. Taken together, our study suggests that increasing the number of autophagosomes, through inhibition of autophagosome/lysosome fusion, generates migrasomes that have the capacity to alleviate cellular stress.

Summary statement

This study demonstrates that glioblastoma cells contain autophagosomes within their migrasomes. Under stress conditions, the formation of migrasomes serves as a stress-relief mechanism to alleviate cell death.
Cell-free synthesis and reconstitution of Bax in nanodiscs: comparison between wild-type Bax and a constitutively active mutant
Authors: Eyitayo Akandé Rouchidane , Giraud Marie-France , Daury Laetitia , Lambert Olivier , Gonzalez Cécile , Manon Stéphen
Published: June 2022

Bax is a major player in the mitochondrial pathway of apoptosis, by permeabilizing the Outer Mitochondrial Membrane (OMM) to various apoptogenic factors, including cytochrome c. In order to get further insight into the structure and function of Bax when it is inserted in the OMM, we attempted to reconstitute Bax in nanodiscs. Cell-free protein synthesis in the presence of nanodiscs did not allow to obtain Bax-containing nanodiscs, but it provided a simple way to purify full-length Bax without any tag. Purified wild-type Bax (BaxWT) and a constitutively active mutant (BaxP168A) displayed biochemical properties that were in line with previous characterizations following their expression in yeast and human cells followed by their reconstitution into liposomes. Both Bax variants were then reconstituted in nanodiscs. Size exclusion chromatography, dynamic light scattering and transmission electron microscopy showed that nanodiscs formed with BaxP168A were larger than nanodiscs formed with BaxWT. This was consistent with the hypothesis that BaxP168A was reconstituted in nanodiscs as an active oligomer.
Coming in from the cold: overcoming the hostile immune microenvironment of medulloblastoma
Authors: Eisemann Tanja , Wechsler-Reya Robert J.
Published: June 2022

Medulloblastoma is an aggressive brain tumor that occurs predominantly in children. Despite intensive therapy, many patients die of the disease, and novel therapies are desperately needed. Although immunotherapy has shown promise in many cancers, the low mutational burden, limited infiltration of immune effector cells, and immune-suppressive microenvironment of medulloblastoma have led to the assumption that it is unlikely to respond to immunotherapy. However, emerging evidence is challenging this view. Here we review recent preclinical and clinical studies that have identified mechanisms of immune evasion in medulloblastoma, and highlight possible therapeutic interventions that may give new hope to medulloblastoma patients and their families.
Simultaneous swept anhedral helicopter blade tip shape and control-system design
Authors: Sal Firat
Published: June 2022

Purpose

This paper aims to offer a simultaneous design approach for helicopter having swept anhedral blade tip shape and helicopter flight control system (HFCS) to minimize controller cost.

Design/methodology/approach

By considering previously stated offer, control-oriented models and a stochastic optimization method are applied to minimize controller cost of the HFCS.

Findings

Using simultaneous design approach for helicopters having blade tip swept and blade tip anhedral causes considerably less control effort than the helicopters not benefiting this related design approach.

Practical implications

Simultaneous design approach for helicopters having blade tip swept and blade tip anhedral is applicable to consider fuel economy.

Originality/value

One important novelty of this paper is using simultaneous approach for determining optimum shape of blade tip swept and anhedral. Another considerable novelty of this paper is also using a stochastic optimization method called simultaneous perturbation stochastic approximation for previously mentioned purpose. In this paper, it is also reached that using simultaneous design approach for swept anhedral helicopter blade tip shape and HFCS causes less control effort than the helicopters not using this approach. This leads to less fuel consumption and green environment.
Synthesis cascade estimation for aircraft system identification
Authors: Jianhong Wang , Ramirez-Mendoza Ricardo A.
Published: June 2022

Purpose

The purpose of this paper extends the authors’ previous contributions on aircraft system identification, such as open loop identification or closed loop identification, to cascade system identification. Because the cascade system is one special network system, existing in lots of practical engineers, more unknown systems are needed to identify simultaneously within the statistical environment with the probabilistic noises. Consider this problem of cascade system identification, prediction error method is proposed to identify three unknown systems, which are parameterized by three unknown parameter vectors. Then the cascade system identification is transferred as one parameter identification problem, being solved by the online subgradient descent algorithm. Furthermore, the nonparametric estimation is proposed to consider the general case without any parameterized process. To make up the identification mission, model validation process is given to show the asymptotic interval of the identified parameter. Finally, simulation example confirms the proposed theoretical results.

Design/methodology/approach

Firstly, aircraft system identification is reviewed through the understanding about system identification and advances in control theory, then cascade system identification is introduced to be one special network system. Secondly, for the problem of cascade system identification, prediction error method and online subgradient decent algorithm are combined together to identify the cascade system with the parameterized systems. Thirdly from the point of more general completeness, another way is proposed to identify the nonparametric estimation, then model validation process is added to complete the whole identification mission.

Findings

This cascade system corresponds to one network system, existing in lots of practice, such as aircraft, ship and robot, so it is necessary to identify this cascade system, paving a way for latter network system identification. Parametric and nonparametric estimations are all studied within the statistical environment. Then research on bounded noise is an ongoing work.

Originality/value

To the best of the authors’ knowledge, research on aircraft system identification only concern on open loop and closed loop system identification, no any identification results about network system identification. This paper considers cascade system identification, being one special case on network system identification, so this paper paves a basic way for latter more advanced system identification and control theory.
A comprehensive examination of psychological capital research using bibliometric, TCCM and content analysis
Authors: Goswami Meghna , Goswami Anil Kumar
Published: June 2022

Purpose

In today's dynamic business environment and crisis and pandemic like situations, psychological capital has become very significant for sustainable competitive advantage. Due to its importance in organizational context, researchers are investigating it from various perspectives, making it a burgeoning research area. Hence, this study aims to review the literature, provide identity in terms of various patterns and trends, and build the intellectual structure (academic structure) of psychological capital research by presenting a big picture. It further provides the theories, characteristics, context and methodologies (TCCM) analysis and potential avenues for possible future research to facilitate the growth of the field.

Design/methodology/approach

This study compiles, evaluates and synthesizes the extant literature of psychological capital, consisting of 954 journal articles collected from Web of Science (WOS) database, using bibliometric techniques, content analysis, and TCCM analysis.

Findings

The study identifies various patterns and trends of psychological capital research and unfolds four major themes, namely psychological capital theoretical concept development, psychological capital relationship building with organizational variables, psychological capital as an underlying mechanism for linkage between organizational variables and psychological capital interventions. It also identifies TCCM outcome and potential avenues for possible future research. The study reveals that psychological capital research area is progressing and has enormous potential to advance in the future.

Research limitations/implications

This study is pivotal to past–future orientation wherein past is being investigated for developing new pathways of psychological capital research. It has used research articles published in the WOS database, and future studies may further enhance the understanding of psychological research using other databases.

Practical implications

In addition to advance a comprehensive understanding of psychological capital research, this study will be a quick reference and notable and profound resource for researchers venturing into this marked research area. Further, it will facilitate to leaders and managers to look into various possible avenues to enhance psychological capital of their subordinates for greater organizational good.

Originality/value

To the best of authors' knowledge, this is first study to advance a comprehensive and systematic understanding of psychological capital by integrating bibliometric, TCCM and content analysis.
Talent management practices on employee performance: a mediating role of employee engagement in institution of higher learning: quantitative analysis
Authors: Abdullahi Mohammed Sani , Adeiza Adams , Abdelfattah Fadi , Fatma Mobin , Fawehinmi Olawole , Aigbogun Osaro
Published: June 2022

Purpose

The purpose of this paper is to investigate the effect of talent management (TM) practices on employee performance (EP) and to explore the mediating role of employee engagement (EE) on the relationship between TM practices and EP in Malaysian private universities (MPUs).

Design/methodology/approach

The paper used both descriptive and quantitative approaches, and the unit of analysis of this research consists of MPUs academic staff. The research sample consists of 314 MPUs academic staff, and a questionnaire was used to collect data from the target respondents, while partial least squares-structural equation modelling was used to evaluate the study hypotheses through bootstrapping approach.

Findings

The research outcome revealed that TM practices that comprise of talent recruitment practice (TRP), training and development practice (T&DP), compensation practice (CP) have a significant effect on EP. Furthermore, EE partially mediates the relationship between T&DP, CP and EP, while EE does not mediate the relationship between TRP and EP in MPUs.

Practical implications

The research suggests that universities management should focus on TM practices as a tool to achieve and maintain EE and positive attitudes (EP) in relation to work.

Originality/value

The research makes substantial contributions to the literature by investigating the effect of TM practices on EP through the role of EE as mediation in MPUs. The research is one of the very few studies undertaken in MPUs. Therefore, the results of this research serve as a guide for the universities management to develop their institutional strategies and policies in a manner in which their employees’ success can be achieved and encouraged.International Journal of Business and Society.
Building a thematic framework of identity research in hospitality organizations: a systematic literature review approach
Authors: Ponting Sandra Sun-Ah , Lee Lindsey
Published: June 2022

Purpose

The purpose of this study is to systematically review and synthesize identity research in the hospitality management literature. A critical revision of identity research in hospitality organizations, built on major identity constructs in the general management literature, is conducted to create thematic frameworks. This framework yields theoretical and practical future hospitality research agendas.

Design/methodology/approach

The current study adopted a systematic literature review approach to analyze and synthesize identity research in hospitality organizations. A total of 55 articles published since 2000 are included in this review.

Findings

Stemming from general management conceptualizations, identity research in hospitality organizations are categorized into four overarching themes. This review also points to research gaps in epistemological conceptualizations, definitional frameworks and methodology.

Originality/value

The study reviews identity research in hospitality organizations, builds an integrative thematic framework of identity research in hospitality and proposes directions for future research.
Sustainable supply chain management performance in post COVID-19 era in an emerging economy: a big data perspective
Authors: Nisar Qasim Ali , Haider Shahbaz , Ameer Irfan , Hussain Muhammad Sajjad , Gill Sonaina Safi , Usama Awan
Published: June 2022

Purpose

Big data analytics capabilities are the driving force and deemed as an operational excellence approach to improving the green supply chain performance in the post COVID-19 situation. Motivated by the COVID-19 epidemic and the problems it poses to the supply chain's long-term viability, this study used dynamic capabilities theory as a foundation to assess the imperative role of big data analytics capabilities (management, talent and technological) toward green supply chain performance.

Design/methodology/approach

This study was quantitative and cross-sectional. Data were collected from 374 executives through a survey questionnaire method by applying an appropriate random sampling technique. The authors employed PLS-SEM to analyze the data.

Findings

The findings revealed that big data analytics capabilities play a significant role in boosting up sustainable supply chain performance. It was found that big data analytics capabilities significantly contributed to supply chain risk management and innovative green product development that ultimately enhanced innovation and learning performance. Moreover, innovation and green learning performance has a significant and positive relationship with sustainable supply chain performance. In the post COVID-19 situation, organizations can enhance their sustainable supply chain performance by giving extra attention to big data analytics capabilities and supply chain risk and innovativeness.

Originality/value

The paper specifically emphasizes on the factors that result in the sustainability in supply chain integrated with the big data analytics. Additionally, it offers the boundary condition for gaining the sustainable supply chain management.
The retailer’s trade-in activity under the manufacturer’s upgrading strategy
Authors: Yang Feng , Wu Xiang , Shan Feifei
Published: June 2022

Purpose

This paper aims to study the impact of manufacturer’s upgrading strategy of durable products on the retailer’s decision on trade-in program and her decision on the secondary market.

Design/methodology/approach

This paper develops a channel that consists of a manufacturer and a retailer, where the manufacturer releases an upgraded product, and the retailer introduces a trade-in program for consumers, simultaneously, decides whether to enter the secondary market. These approaches are modeled through Stackelberg game.

Findings

This paper reveals that the optimal conditions for manufacturer to release upgraded products and retailer to resell used products in the secondary market, and it reveals that under what conditions it is profitable for retailer to enter the secondary market under product upgrade levels.

Practical implications

If the manufacturer’s upgrade level is low, it is profitable for the retailer to enter the secondary market. However, if the manufacturer’s upgrade level is high, it is unprofitable for the retailer to enter the secondary market.

Originality/value

In this paper, the active secondary market, upgrading of new products, consumer market segmentation and especially, the upgrade degree of new products as a function of consumer demand are considered simultaneously.
Impact of industry competitive intensity on brand performance: mediating role of market orientation and organizational learning
Authors: Talari Mohammad , Khoshroo Mina
Published: June 2022

Purpose

The purpose of this paper is to investigate the effect of industry competitive intensity (ICI) on brand performance with the mediating role of market orientation and organizational learning using theoretical and experimental materials in fast-moving consumer goods (FMCGs) firms.

Design/methodology/approach

To test the research hypotheses, a model was designed and tested on 124 chief executive officers from 30 FMCG firms active in both food and chemical industries using structural equation modeling and partial least squares methodology.

Findings

The research findings showed that ICI has significant effect on market orientation and organizational learning. It also has significant effect on the firm’s brand performance through developing the market orientation capability as a mediating variable, but the development of organizational learning capability (as a mediating variable) is not effective in the relationship between ICI and brand performance.

Originality/value

Since the early 1990s, addressing intraorganizational capabilities and resources has been a major topic of strategic and marketing research. In this regard, many theoretical and experimental contents have been presented so far. However, little research has simultaneously addressed the industrial environment and the development of competitive capabilities. A manager’s understanding of the competition rate of an industry has the potential to influence the development of organizational capabilities through strategic responsiveness to his/her perception of the environment. This study attempts to show that managers and firms that consider their industrial environment to be volatile must develop their learning capabilities and market orientation, leading to superior brand performance.
Physical manufacturing: from the multidisciplinary perspective
Authors: Liu F.C. , Wang P.Y. , Li M. , Li L. , Yue Z.F.
Published: June 2022

Purpose

In order to promote the development of modern manufacturing towards high-precision, high-quality intelligence and precision, this paper puts forward the concept of physical manufacturing and conducts a more in-depth theoretical discussion on its basic connotation and characteristics, based on which the application of physical manufacturing in cutting and autoclave curing molding of composite material is briefly introduced.

Design/methodology/approach

As a brand-new manufacturing concept, physical manufacturing determines the optimal process parameters according to multidisciplinary simulations, which emphasizes the physical characteristics about long life and high reliability of the processed products, and makes intelligent adjustment of process parameters according to the changes in the environment and equipment status during manufacturing.

Findings

The concept of physical manufacturing has pioneering significance for the basic research and development of advanced manufacturing technology, which helps to further improve production efficiency, reduce production costs and improve product quality.

Originality/value

The concept of physical manufacturing was first proposed, which emphasizes the analysis, reasoning, perception, and deduction during the manufacturing process, to achieve high-quality processing of products.
Competitive consequences determined by phenotypic but not genetic distance: A study with asexual water flea genotypes
Authors: Tian Xiaofei , Ohtsuki Hajime , Urabe Jotaro
Published: June 2022

How evolutionary relatedness influences the strength of competitive interactions among genetically isolated populations has been a long‐standing interest in ecology. Darwin's ‘Competition‐Relatedness Hypothesis (CRH)’ states that, since closely related species should compete more strongly, they are less likely to coexist, while Herbert's ‘Bimodal Competition Hypothesis (BCH)’ predicts that competitive exclusion is less likely to occur when the competing species are genetically close or distant.

To test these hypotheses, we experimentally examined the difference in the competitive ability and life tables of fecundity and survivorship among four different genotypes of asexualDaphniacf.pulexthat diverged from a single ancestral genotype.

The experiments showed that the competitive consequences differed depending on the pairing of the competing genotypes, and that the degree of the competitive exclusion was lower when the competing genotypes were genetically closer to each other. These results partially supported the BCH but not the CRH at all. More importantly, the degree of competitive exclusion was better predicted by the phenotypic rather than genetic distances between the competing genotypes.

The life table experiments revealed that competitively inferior genotypes had higher early reproduction rates, but survival rates decreased with age and thus body size, probably a result of selection by predation pressures found in nature.

These results indicate that competitive superiority is highly dependent on selection pressures that given organisms have been evolutionally subjected to, and, that genetic similarity is not necessarily an appropriate measure for predicting the completive exclusion on an ecological time‐scale. To predict competitive relationships among the organisms, it is essential to comprehend their phenotypic differences rather than simply knowing their genetic or phylogenetic relationships.

Read the freePlain Language Summaryfor this article on the Journal blog.
Water Storage Decisions and Consumptive Use May Constrain Ecosystem Management under Severe Sustained Drought
Authors: Bruckerhoff Lindsey A. , Wheeler Kevin , Dibble Kimberly L. , Mihalevich Bryce A. , Neilson Bethany T. , Wang Jian , Yackulic Charles B. , Schmidt John C.
Published: June 2022

Drought has impacted the Colorado River basin for the past 20 years and is predicted to continue. In response, decisions about how much water should be stored in large reservoirs and how much water can be consumptively used will be necessary. These decisions have the potential to limit riverine ecosystem management options through the effect water‐supply decisions have on reservoir elevations. We used projected hydrology and river temperatures to compare the outcome of combinations of water storage scenarios and consumptive use limits on metrics associated with ecosystem management of the Colorado River in Grand Canyon. Ecosystem management metrics included the ability to implement designer flows, temperature suitability for fishes, and fragmentation. We compared current water management operations to prioritizing storage in either Lake Mead or Lake Powell combined with three levels of consumptive use. Projected reservoir levels limited environmental flow delivery and increased fragmentation regardless of where water was stored if consumptive use was not limited. Warmer river temperatures associated with low reservoir levels are likely, creating suitable conditions for non‐native species of concern, such as smallmouth bass. Water storage decisions provided variability and management flexibility, but water storage was less important when less water was available, highlighting the importance of keeping water in the system to provide flexibility for achieving ecosystem goals.
Impact of dysphagia and its severity on long‐term survival and swallowing function outcomes in patients with idiopathic inflammatory myopathies other than inclusion body myositis
Authors: Ohmura Shin‐ichiro , Tamechika Shin‐ya , Miyamoto Toshiaki , Kunieda Kenjiro , Naniwa Taio
Published: June 2022

Objective

To investigate the impact of dysphagia on long‐term survival and swallowing function outcomes in patients with idiopathic inflammatory myopathy other than inclusion body myositis.

Methods

We retrospectively evaluated consecutive patients with idiopathic inflammatory myopathy other than inclusion body myositis to investigate the impact of dysphagia and its severity assessed using the Food Intake LEVEL Scale on survival and swallowing function outcomes. Time‐to‐event analyses were used, including Kaplan‐Meier curves with log‐rank (trend) test, cumulative incidence with Gray’s test, and Cox proportional hazards models.

Results

Of the 254 patients, 26 were dysphagic, including eight severe (Food Intake LEVEL Scale [FILS] score 2, 3) and six most severe (FILS score 1) cases; 210 were non‐dysphagic, and 18 were indeterminate cases. During the 5 years after myositis diagnosis, 15 (57.7%) dysphagic and 31 (14.8%) non‐dysphagic patients died, and dysphagic patients had significantly shorter survival. However, multivariate analysis showed that shorter survival was significantly associated with baseline age‐adjusted Charlson Comorbidity Index (hazard ratio [HR] 1.57, 95% confidence interval [CI] 1.36‐1.82]), but not with dysphagia (HR 1.46, 95% CI 0.69‐3.10). Dysphagia severity was significantly associated with delayed recovery of dysphagia. In 20 non‐severe or severe dysphagic cases, 19 restored swallowing function within 1 year. The most severe cases had a significantly higher cumulative probability of death before recovery from dysphagia than severe cases.

Conclusion

The poor survival of dysphagic myositis patients was largely confounded by advanced age and comorbid malignancies. However, patients with the most severe dysphagia had a significantly worse swallowing function and survival prognosis than those with milder dysphagia.
Improving the predictability and interpretability of co‐occurrence modelling through feature‐based joint species distribution ensembles
Authors: Powell‐Romero Francisca , Fountain‐Jones Nicholas M. , Norberg Anna , Clark Nicholas J.
Published: June 2022

Species Distribution Models (SDMs) are vital tools for predicting species occurrences and are used in many practical tasks including conservation and biodiversity management. However, the expanding minefield of SDM methodologies makes it difficult to select the most reliable method for large co‐occurrence datasets, particularly when time constraints make designing a bespoke model challenging. To facilitate model selection for practical out‐of‐sample prediction, we consider three major challenges: (a) the difficulty of incorporating multiple functional forms for species associations; (b) the limited knowledge on how characteristics of co‐occurrence data impact model performance; and (c) whether individual model predictions could be combined to obtain optimised community predictions without the need for bespoke models.

To address these gaps, we propose an ensemble method that uses descriptive features of binary co‐occurrence datasets to predict model weightings for a set of candidate SDMs. We demonstrate how this method may be applied through a simple case study that uses five independent Joint Species Distribution Models (JSDMs) and Stacked Species Distribution Models (SSDMs) to predict out‐of‐sample observations for a diversity of co‐occurrence datasets. Moreover, we introduce a novel SSDM that offers the potential to include multiple functional forms for each species while delivering robust community predictions.

Our case study highlights two major findings. First, the ability for the feature‐based ensemble to offer more robust species co‐occurrence predictions compared to other candidate SDMs while providing insights into the data features that impact model performance. Second, the competitiveness of the novel SSDM method for forecasting species co‐occurrences, even when using a simple univariate generalised linear model (GLM) as the base model prior to stacking.

We conclude that feature‐based ensembles can provide ecologists with a useful tool for generating species distribution predictions in a way that is reliable and informative. Moreover, the flexibility of the ensemble and the novel SSDM method both offer exciting prospects for incorporating a diversity of functional forms while prioritising out‐of‐sample prediction.
Modeling reciprocal relations between emotion dysregulation and alcohol use using dynamic structural equation modeling: A micro‐longitudinal study
Authors: Weiss Nicole H. , Brick Leslie A. , Forkus Shannon R. , Goldstein Silvi C. , Thomas Emmanuel D. , Schick Melissa R. , Barnett Nancy P. , Contractor Ateka A. , Sullivan Tami P.
Published: June 2022

Background

Research examining emotion dysregulation and alcohol use has increased exponentially over the past decade. However, these studies have been limited by their use of cross‐sectional designs and narrow definitions of emotion dysregulation. To address these significant gaps in the extant literature, this study utilized state‐of‐the‐art methodology (i.e., experience sampling) and statistics (i.e., dynamic structural equation modeling) to examine potential reciprocal associations between negative and positive emotion dysregulation and alcohol use at the momentary level.

Methods

Participants were 145 community women (mean age = 40.56, 40.3% white) experiencing intimate partner violence (IPV) and using substances. Surveys assessing negative and positive emotion dysregulation and alcohol use (i.e., number of standard drinks) were administered three times a day for 30 days using phone‐based interactive voice recording.

Results

Significant contemporaneous effects indicated that negative and positive emotion dysregulation both co‐occurred with alcohol use. However, levels of negative and positive emotion dysregulation did not predict later alcohol use, nor did alcohol use predict later levels of negative or positive emotion dysregulation. There was significant variability among participants in cross‐lagged effects.

Conclusions

Findings showed that negative and positive emotion dysregulation co‐occurred with alcohol use and that there was significant interindividual variability in the cross‐lagged associations between negative and positive emotion dysregulation and alcohol use. Research using idiographic approaches may identify women experiencing IPV for whom negative and positive emotion dysregulation drive alcohol use and alcohol use drives negative and positive emotion dysregulation.
Paeonol ameliorates diabetic erectile dysfunction by inhibiting HMGB1/RAGE/NF‐kB pathway
Authors: Sun Taotao , Xu Wenchao , Wang Jiaxin , Song Jingyu , Wang Tao , Wang Shaogang , Liu Kang , Liu Jihong
Published: June 2022

Background

The management of diabetes mellitus‐induced erectile dysfunction (DMED) is progressively becoming tricky due to the surge in the number of patients and the poor efficiency of phosphodiesterase type 5 inhibitors in DMED. Paeonol (Pae), as a traditional Chinese medicine, has been more and more widely used in the treatment of diabetic complications. However, whether Pae could be a potential therapeutic drug of DMED needs to be further evaluated.

Objectives

To investigate the pharmacological effect and possible mechanism of Pae in the treatment of DMED.

Methods

Intraperitoneal streptozotocin injection and an apomorphine test were used to construct the model of DMED. Seventeen DMED rats were divided into two groups: DMED group (n = 8) and DMED+Pae group (Pae; 100 mg/kg/d; oral administration; n = 9). In addition, there were still 10 normal age‐matched male rats as control group. Four weeks later, the cavernous nerve electric stimulation was carried out to measure the erectile response. Moreover, the corpus cavernosum smooth muscle cells (CCSMCs) were primarily isolated and exposed to high glucose (HG) stimulation, Pae treatment and glycyrrhizin (GL; the selective inhibitor of HMGB1). After an incubation for 1 week, the CCSMCs were harvested for detection.

Results

The impairment of erectile function was observed in DMED rats compared with control samples, accompanied by the upregulation of HMGB1/RAGE/NF‐κB Pathway. The lower nitric oxide and cGMP level and the higher level of inflammation, fibrosis, and apoptosis were also observed in DMED rats. It showed contrast that Pae treatment could improve the erectile function, as well as histologic alteration and related molecular changes. In addition, Pae could downregulate the HMGB1/RAGE/NF‐κB pathway to regulate the apoptosis and inflammation levels of CCSMCs in high‐glucose conditions, which is similar to the results of GL treatment.

Conclusion

Pae alleviated ED in DMED rats, likely by inhibiting HMGB1/RAGE/NF‐κB Pathway, inflammatory, apoptosis, and fibrotic activity, and moderating endothelial dysfunction. Our study provide evidence for a potential new therapy for DMED.
Diphallia: literature review and proposed surgical classification system
Authors: Kendrick Dylan John , Kimble Roy Mark
Published: June 2022

Background

Diphallia occurs once in 5–6 million births, with no two patients presenting with the same anatomical variation. Here we discuss a review of diphallia case reports, as well as present a new surgical classification system based on the soft tissue composition of the two phalluses, the anatomy of the urethra present within the most normal phallus and the bladder configuration.

Methods

Eighty‐seven diphallia case reports were collected and analysed, excluding those presented in animals and articles that were non‐English, with the results compiled to provide an in‐depth reference of the specific anatomy found in diphallia patients and the associated abnormalities.

Results

Our proposed classification system was then applied to each patient and the most common configuration base on our classification system presented, along with commonly seen associated anomalies.

Conclusion

The reviewed cases represent a subset of the most unique diphallia patients; thus, several cases may be left unreported. Future reports can then be categorized, aiding as a reference, and potentially building on the classification, should the patient not fit into a specific group, leading to an expansion of the classification system.
Mapping promoting factors and mechanisms of resilience for performance improvement: The role of strategic human resource management systems and psychological empowerment
Authors: Zhai Xiaoxuan , Zhu Cherrie Jiuhua , Zhang Mingqiong Mike
Published: June 2022

Based on broaden‐and‐build theory of positive emotions, this study posits that strategic human resource management (SHRM) systems enrich positive emotions associated with psychological empowerment and resilience and in turn, broaden employees' momentary thought‐action repertoires. People with such positive psychological emotions build enduring personal resources to buffer the negative impacts of adversity and produce better performance outcomes. An integrative model is developed and examined through a two‐stage structural equation modelling method of meta‐analysis based on data involving 60,637 individuals in 87 independent datasets from 79 primary studies published up to September 2020. Empirical evidence suggests that psychological empowerment and resilience both independently and collectively mediate the relationship between SHRM systems and performance outcomes. This study makes an innovative attempt to incorporate theories of positive psychology into SHRM research, throwing fresh light on the promoting factors (i.e., SHRM) and psychological mechanisms (i.e., psychological empowerment) antecedent to employee resilience leading to desired performance outcomes. This study has practical implications for managers in relation to the importance of cultivating a psychologically empowered and resilient workforce, especially in difficult times such as those during the recent COVID‐19 pandemic.
Longitudinal genetic analysis of semen production traits in Holstein bulls according to a random regression animal models on age
Authors: Fujimoto Ikuko , Hanamure Takeshi , Baba Toshimi , Kawakami Junpei , Hagiya Koichi
Published: June 2022

Here we used random regression animal models (RRAMs) to investigate genetic change over age in the semen volume (VOL) and sperm concentration (CON) of Holstein bulls. We used 35,294 collection records from 1284 Holstein bulls and their 4166 pedigree records. The models included year and month of collection, collection place, collection method, and number of collections attempted for each day and month of age (second‐order regressions) as fixed effects; technician as a random effect; and additive genetic and permanent environment as random regressions (first‐order regressions). We examined two RRAMs with homogeneous and heterogeneous residual variances (RRAM1 and RRAM2, respectively). By using RRAM1, heritability for VOL and CON increased from 0.08 to 0.61 and 0.18 to 0.57, respectively, between 10 and 126 months of age. By using RRAM2, heritability for VOL increased from 0.11 to 0.28 between 10 and 24 months of age for young bulls and increased from 0.08 to 0.48 between 25 and 126 months of age for mature bulls; heritability for CON ranged from 0.18 to 0.19 for young bulls and increased from 0.10 to 0.48 for mature bulls. Posterior genetic correlations between young ages and older ages were strongly positive for VOLs but weak for CONs.