bluuebunny/crossref_metadata_2025 huggingface dataset:
Uncertainty drives deviations in normative foraging decision strategies
Authors: Kilpatrick Zachary P. , Davidson Jacob D. , El Hady Ahmed
Published: July 2021

Nearly all animals forage to acquire energy for survival through efficient search and resource harvesting. Patch exploitation is a canonical foraging behaviour, but there is a need for more tractable and understandable mathematical models describing how foragers deal with uncertainty. To provide such a treatment, we develop a normative theory of patch foraging decisions, proposing mechanisms by which foraging behaviours emerge in the face of uncertainty. Our model foragers statistically and sequentially infer patch resource yields using Bayesian updating based on their resource encounter history. A decision to leave a patch is triggered when the certainty of the patch type or the estimated yield of the patch falls below a threshold. The time scale over which uncertainty in resource availability persists strongly impacts behavioural variables like patch residence times and decision rules determining patch departures. When patch depletion is slow, as in habitat selection, departures are characterized by a reduction of uncertainty, suggesting that the forager resides in a low-yielding patch. Uncertainty leads patch-exploiting foragers to overharvest (underharvest) patches with initially low (high) resource yields in comparison with predictions of the marginal value theorem. These results extend optimal foraging theory and motivate a variety of behavioural experiments investigating patch foraging behaviour.
Raptor wing morphing with flight speed
Authors: Cheney Jorn A. , Stevenson Jonathan P. J. , Durston Nicholas E. , Maeda Masateru , Song Jialei , Megson-Smith David A. , Windsor Shane P. , Usherwood James R. , Bomphrey Richard J.
Published: July 2021

In gliding flight, birds morph their wings and tails to control their flight trajectory and speed. Using high-resolution videogrammetry, we reconstructed accurate and detailed three-dimensional geometries of gliding flights for three raptors (barn owl,Tyto alba; tawny owl,Strix aluco, and goshawk,Accipiter gentilis). Wing shapes were highly repeatable and shoulder actuation was a key component of reconfiguring the overall planform and controlling angle of attack. The three birds shared common spanwise patterns of wing twist, an inverse relationship between twist and peak camber, and held their wings depressed below their shoulder in an anhedral configuration. With increased speed, all three birds tended to reduce camber throughout the wing, and their wings bent in a saddle-shape pattern. A number of morphing features suggest that the coordinated movements of the wing and tail support efficient flight, and that the tail may act to modulate wing camber through indirect aeroelastic control.
SUMOylation modification-mediated cell death
Authors: Sheng Zenghua , Zhu Jing , Deng Ya-nan , Gao Shan , Liang Shufang
Published: July 2021

SUMOylation dynamically conjugates SUMO molecules to the lysine residue of a substrate protein, which depends on the physiological state of the cell and the attached SUMO isoforms. A prominent role of SUMOylation in molecular pathways is to govern the cellular death process. Herein, we summarize the association between SUMOylation modification events and four types of cellular death processes: apoptosis, autophagy, senescence and pyroptosis. SUMOylation positively or negatively regulates a certain cellular death pattern depending on specific conditions including the attached SUMO isoforms, disease types, substrate proteins and cell context. Moreover, we also discuss the possible role of SUMOylation in ferroptosis and propose a potential role of the SUMOylated GPX4 in the regulation of ferroptosis. Mapping the exact SUMOylation network with cellular death contributes to develop novel SUMOylation-targeting disease therapeutic strategies.
A duplicated
amh
is the master sex-determining gene for
Sebastes
rockfish in the Northwest Pacific
Authors: Song Weihao , Xie Yuheng , Sun Minmin , Li Xuemei , Fitzpatrick Cristín K. , Vaux Felix , O'Malley Kathleen G. , Zhang Quanqi , Qi Jie , He Yan
Published: July 2021

Teleost fish are the most diverse group of vertebrates and provide opportunities to study the evolution of sex determination (SD) systems. Using genomic and functional analyses, we identified a male-specific duplication of
anti-Müllerian hormone
(
amh
) gene as the male master sex-determining (MSD) gene in
Sebastes schlegelii
. By resequencing 10 males and 10 females, we characterized a 5 kb-long fragment in HiC_Scaffold_12 as a male-specific region, which contained an
amh
gene (named
amhy
). We then demonstrated that
amhy
is a duplication of autosomal
amh
that was later translocated to the ancestral Y chromosome.
amha
and
amhy
shared high-nucleotide identity with the most significant difference being two insertions in intron 4 of
amhy
. Furthermore,
amhy
overexpression triggered female-to-male sex reversal in
S. schlegelii
, displaying its fundamental role in driving testis differentiation. We developed a PCR assay which successfully identified sexes in two species of northwest Pacific rockfish related to
S. schlegelii
. However, the PCR assay failed to distinguish the sexes in a separate clade of northeast Pacific rockfish. Our study provides new examples of
amh
as the MSD in fish and sheds light on the convergent evolution of
amh
duplication as the driving force of sex determination in different fish taxa.
DDX21 is a p38-MAPK-sensitive nucleolar protein necessary for mouse preimplantation embryo development and cell-fate specification
Authors: Bora Pablo , Gahurova Lenka , Hauserova Andrea , Stiborova Martina , Collier Rebecca , Potěšil David , Zdráhal Zbyněk , Bruce Alexander W.
Published: July 2021

Successful navigation of the mouse preimplantation stages of development, during which three distinct blastocyst lineages are derived, represents a prerequisite for continued development. We previously identified a role for p38-mitogen-activated kinases (p38-MAPK) regulating blastocyst inner cell mass (ICM) cell fate, specifically primitive endoderm (PrE) differentiation, that is intimately linked to rRNA precursor processing, polysome formation and protein translation regulation. Here, we develop this work by assaying the role of DEAD-box RNA helicase 21 (DDX21), a known regulator of rRNA processing, in the context of p38-MAPK regulation of preimplantation mouse embryo development. We show nuclear DDX21 protein is robustly expressed from the 16-cell stage, becoming exclusively nucleolar during blastocyst maturation, a localization dependent on active p38-MAPK. siRNA-mediated clonal
Ddx21
knockdown within developing embryos is associated with profound cell-autonomous and non-autonomous proliferation defects and reduced blastocyst volume, by the equivalent peri-implantation blastocyst stage. Moreover, ICM residing
Ddx21
knockdown clones express the EPI marker NANOG but rarely express the PrE differentiation marker GATA4. These data contribute further significance to the emerging importance of lineage-specific translation regulation, as identified for p38-MAPK, during mouse preimplantation development.
Delay-dependent attractivity on a tick population dynamics model incorporating two distinctive time-varying delays
Authors: Huang Chuangxia , Zhang Jian , Cao Jinde
Published: July 2021

In this paper, we aim to investigate the influence of delay on the global attractivity of a tick population dynamics model incorporating two distinctive time-varying delays. By exploiting some differential inequality techniques and with the aid of the fluctuation lemma, we first prove the persistence and positiveness for all solutions of the addressed equation. Consequently, a delay-dependent criterion is derived to assure the global attractivity of the positive equilibrium point. And lastly, some numerical simulations are presented to verify that the obtained results improve and complement some existing ones.
Optimization of a type of elastic metamaterial for broadband wave suppression
Authors: Wu Kun , Hu Haiyan , Wang Lifeng
Published: July 2021

The optimal design is studied for a type of one-dimensional dissipative metamaterial to achieve broadband wave attenuation at low-frequency ranges. The complex dispersion analysis is made on a super-cell consisting of multiple mass-in-mass unit cells. An optimization algorithm based on the sequential quadratic programming method is used to design the wave suppression of target frequencies by coupling multiple separate narrow bandgaps into a broad bandgap. A new objective function is proposed in the optimization process for a continuous bandgap. Then, the continuous frequency range with low-wave transmissibility is optimized to achieve the maximal width of bandgap. The stiffness optimization of super-cell gives the broad bandgap from 10 Hz to 22.9 Hz at low-frequency ranges. In addition, numerical simulations are conducted for a type of dissipative metamaterial composed of a finite number of periodicities. The level of vibration isolation can be tuned by adjusting a critical value in the optimization scheme. The wave suppression in the numerical simulation well coincides with the obtained bandgaps and verifies the optimization results.
Complex macroevolutionary dynamics underly the evolution of the crocodyliform skull
Authors: Felice Ryan N. , Pol Diego , Goswami Anjali
Published: July 2021

All modern crocodyliforms (alligators, crocodiles and the gharial) are semi-aquatic generalist carnivores that are relatively similar in cranial form and function. However, this homogeneity represents just a fraction of the variation that once existed in the clade, which includes extinct herbivorous and marine forms with divergent skull structure and function. Here, we use high-dimensional three-dimensional geometric morphometrics to quantify whole-skull morphology across modern and fossil crocodyliforms to untangle the factors that shaped the macroevolutionary history and relatively low phenotypic variation of this clade through time. Evolutionary modelling demonstrates that the pace of crocodyliform cranial evolution is initially high, particularly in the extinct Notosuchia, but slows near the base of Neosuchia, with a late burst of rapid evolution in crown-group crocodiles. Surprisingly, modern crocodiles, especially Australian, southeast Asian, Indo-Pacific species, have high rates of evolution, despite exhibiting low variation. Thus, extant lineages are not in evolutionary stasis but rather have rapidly fluctuated within a limited region of morphospace, resulting in significant convergence. The structures related to jaw closing and bite force production (e.g. pterygoid flange and quadrate) are highly variable, reinforcing the importance of function in driving phenotypic variation. Together, these findings illustrate that the apparent conservativeness of crocodyliform skulls betrays unappreciated complexity in their macroevolutionary dynamics.
Coordination of movement via complementary interactions of leaders and followers in termite mating pairs
Authors: Mizumoto Nobuaki , Lee Sang-Bin , Valentini Gabriele , Chouvenc Thomas , Pratt Stephen C.
Published: July 2021

In collective animal motion, coordination is often achieved by feedback between leaders and followers. For stable coordination, a leader's signals and a follower's responses are hypothesized to be attuned to each other. However, their roles are difficult to disentangle in species with highly coordinated movements, hiding potential diversity of behavioural mechanisms for collective behaviour. Here, we show that twoCoptotermestermite species achieve a similar level of coordination via distinct sets of complementary leader–follower interactions. Even thoughC. gestroifemales produce less pheromone thanC. formosanus, tandem runs of both species were stable. Heterospecific pairs withC. gestroimales were also stable, but not those withC. formosanusmales. We attributed this to the males' adaptation to the conspecific females;C. gestroimales have a unique capacity to follow females with small amounts of pheromone, whileC. formosanusmales rejectC. gestroifemales as unsuitable but are competitive over females with large amounts of pheromone. An information-theoretic analysis supported this conclusion by detecting information flow from female to male only in stable tandems. Our study highlights cryptic interspecific variation in movement coordination, a source of novelty for the evolution of social interactions.
Development, implementation and impact of a new preprint solicitation process atProceedings B
Authors: Neiman Maurine , Bagley Robin K. , Paczesniak Dorota , Singh-Shepherd Shalene
Published: July 2021

Preprints are manuscripts posted on a public server that do not yet have formal certification of peer review from a scholarly journal. The increasingly prominent online repositories for these preprints provide a means of rapidly making scientific results accessible to all with an Internet connection. We here describe the catalysis and subsequent development of a successful new process to solicit preprints for consideration for publication inProceedings B.We present preliminary comparisons between the focal topics and geographic origin of submitting authors of papers submitted in the traditional (non-solicited) route versus solicited preprints. This analysis suggests that the solicitation process seems to be achieving one of the primary goals of the preprint solicitation endeavour: broadening the scope of the papers featured inProceedings B. We also use an informal survey of the early-career scientists that are or have been involved with the Preprint Editorial Team to find that these scientists view their participation positively with respect to career development and knowledge in their field. The inclusion of early-career researchers from across the world in the preprint solicitation process could also translate into social justice benefits by providing a career-building opportunity and a window into the publishing process for young scientists.
Enorma shizhengliae sp. nov. and Eggerthella guodeyinii sp. nov., two new members of the family Coriobacteriaceae
Authors: Ge Yajun , Yang Jing , Lai Xin-He , Jin Dong , Lu Shan , Zhang Gui , Huang Ying , Luo Xuelian , Zheng Han , Tao Yuanmeihui , Yuan Tingting , Li Lianfeng , Zhang Xiaoyan , Xu Jianguo
Published: July 2021

Four obligatory anaerobic, Gram-stain-positive, non-motile and rod-shaped organisms (HF-1365T, HF-1362, HF-1101T and HF-4214) were isolated from faecal samples of healthy Chinese subjects. Results of 16S rRNA gene sequence analyses showed that these isolates belong to the genera

Enorma

(strains HF-1365T and HF-1362) and

Eggerthella

(strains HF-1101T and HF-4214), closest to

Enorma massiliensis

(both 98.6 %) and

Eggerthella sinensis

(98.0 and 97.8 %), respectively. The whole genome sequences of strains HF-1365T and HF-1101T were 2.3 and 4.2 Mb in size with 61.7 and 66.2 mol% DNA G+C content, respectively. The average nucleotide identity and digital DNA–DNA hybridization values indicated that strains HF-1365T and HF-1101T represent novel species in the genera

Enorma

and

Eggerthella

. Major fatty acid constituents (>10 %) of strains HF-1365T and HF-1362 were C12 : 0 (24.7 and 23.9 %), C14 : 0 (21.9 and 20.6 %) and summed feature 1 (C15 : 1iso H/C13 : 0 3OH; 12.8 and 10.8 %); those of strains HF-1101T and HF-4214 were C18 : 1
 ω9c (32.4 and 33.1 %) and C16 : 0 (13.9 and 14.0 %). Strain HF-1365T had phospholipid, glycolipid, lipid and phosphoglycolipid without any known quinones, while strain HF-1101T had diphosphatidylglycerol as the major polar lipid and MK-7 (80.7 %) as the predominant quinone. On the basis of their phylogenetic and phenotypic characteristics, strains HF-1365T and HF-1101T represent two distinct species, respectively, in the genera

Enorma

and

Eggerthella

, for which the names Enorma shizhengliae sp. nov. (type strain HF-1365T=CGMCC 1.17435T=GDMCC 1.1705T=JCM 33601T) and Eggerthella guodeyinii sp. nov. (type strain HF-1101T=CGMCC 1.17436T=GDMCC 1.1668T=JCM 33773T) are proposed.
Desulfosporosinus metallidurans sp. nov., an acidophilic, metal-resistant sulfate-reducing bacterium from acid mine drainage
Authors: Panova Inna A. , Ikkert Olga , Avakyan Marat R. , Kopitsyn Dmitry S. , Mardanov Andrey V. , Pimenov Nikolai V. , Shcherbakova Viktoria A. , Ravin Nikolai V. , Karnachuk Olga V.
Published: July 2021

A novel, spore-forming, acidophilic and metal-resistant sulfate-reducing bacterium, strain OLT, was isolated from a microbial mat in a tailing dam at a gold ore mining site. Cells were slightly curved immotile rods, 0.5 µm in diameter and 2.0–3.0 µm long. Cells were stained Gram-negative, despite the Gram-positive cell structure revealed by electron microscopy of ultrathin layers. OLT grew at pH 4.0–7.0 with an optimum at 5.5. OLT utilised H2, lactate, pyruvate, malate, formate, propionate, ethanol, glycerol, glucose, fructose, sucrose, peptone and tryptone as electron donors for sulfate reduction. Sulfate, sulfite, thiosulfate, nitrate and fumarate were used as electron acceptors in the presence of lactate. Elemental sulfur, iron (III), and arsenate did not serve as electron acceptors. The major cellular fatty acids were C16:1ω7c (39.0 %) and C16 : 0 (12.1 %). The draft genome of OLT was 5.29 Mb in size and contained 4909 protein-coding genes. The 16S rRNA gene sequence placed OLT within the phylum

Firmicutes

, class

Clostridia

, family

Peptococcaceae

, genus Desulfosporosinus. Desulfosporosinus nitroreducens 59.4BT was the closest relative with 97.6 % sequence similarity. On the basis of phenotypic and phylogenetic characteristics, strain OLT represents a novel species within the genus

Desulfosporosinus

, for which we propose the name Desulfosporosinus metallidurans sp. nov. with the type strain OLT (=DSM 104464T=VKM В−3021T).
Discerning the role of a functional arsenic-resistance cassette in the evolution and adaptation of a rice pathogen
Authors: Kaur Amandeep , Rana Rekha , Saroha Tanu , Patil Prabhu B.
Published: July 2021

Arsenic is highly toxic element to all forms of life and is a major environmental contaminant. Understanding acquisition, detoxification and adaptation mechanisms in bacteria that are associated with the host in arsenic-rich conditions can provide novel insights into the evolutionary dynamics of host–microbe–environment interactions. In the present study, we have investigated an arsenic-resistance mechanism acquired during the evolution of a particular lineage in the population of

Xanthomonas oryzae

pv. oryzae, which is a serious plant pathogen infecting rice. Our study revealed the horizontal acquisition of a novel chromosomal 12 kb ars cassette in

X. oryzae

pv. oryzae IXO1088 that confers high resistance to arsenate/arsenite. The ars cassette comprises several genes that constitute an operon induced in the presence of arsenate/arsenite. Transfer of the cloned ars cassette to

X. oryzae

pv. oryzae BXO512, which lacks the cassette, confers an arsenic-resistance phenotype. Furthermore, the transcriptional response of

X. oryzae

pv. oryzae IXO1088 under arsenate/arsenite exposure was analysed using RNA sequencing. Arsenic detoxification and efflux, oxidative stress, iron acquisition/storage, and damage repair are the main cellular responses to arsenic exposure. Our investigation has provided insights into the existence of a novel detoxification and adaptation mechanism within the

X. oryzae

pv. oryzae population to deal with high-arsenic conditions outside the rice plant.
Learning cell communication from spatial graphs of cells
Authors: Fischer David S. , Schaar Anna C. , Theis Fabian J.
Published: July 2021

Tissue niches are sources of cellular variation and key to understanding both single-cell and tissue phenotypes. The interaction of a cell with its niche can be described through cell communication events. These events cannot be directly observed in molecular profiling assays of single cells and have to be inferred. However, computational models of cell communication and variance attribution defined on data from dissociated tissues suffer from multiple limitations with respect to their ability to define and to identify communication events. We address these limitations using spatial molecular profiling data with node-centric expression modeling (NCEM), a computational method based on graph neural networks which reconciles variance attribution and communication modeling in a single model of tissue niches. We use these models in varying complexity across spatial assays, such as immunohistochemistry and MERFISH, and biological systems to demonstrate that the statistical cell–cell dependencies discovered by NCEM are plausible signatures of known molecular processes underlying cell communication. We identify principles of tissue organisation as cell communication events across multiple datasets using interpretation mechanisms. In the primary motor cortex, we found gene expression variation that is due to niche composition variation across cortical depth. Using the same approach, we also identified niche-dependent cell state variation in CD8 T cells from inflamed colon and colorectal cancer. Finally, we show that NCEMs can be extended to mixed models of explicit cell communication events and latent intrinsic sources of variation in conditional variational autoencoders to yield holistic models of cellular variation in spatial molecular profiling data. Altogether, this graphical model of cellular niches is a step towards understanding emergent tissue phenotypes.
SurvBenchmark: comprehensive benchmarking study of survival analysis methods using both omics data and clinical data
Authors: Zhang Yunwei , Wong Germaine , Mann Graham , Muller Samuel , Yang Jean Y.H.
Published: July 2021

Survival analysis is a branch of statistics that deals with both, the tracking of time and of the survival status simultaneously as the dependent response. Current comparisons of survival model performance mostly center on clinical data with classic statistical survival models, with prediction accuracy often serving as the sole metric of model performance. Moreover, survival analysis approaches for censored omics data have not been thoroughly investigated. The common approach is to binarise the survival time and perform a classification analysis.

Here, we develop a benchmarking framework, SurvBenchmark, that evaluates a diverse collection of survival models for both clinical and omics datasets. SurvBenchmark not only focuses on classical approaches such as the Cox model, but it also evaluates state-of-art machine learning survival models. All approaches were assessed using multiple performance metrics, these include model predictability, stability, flexibility and computational issues. Our systematic comparison framework with over 320 comparisons (20 methods over 16 datasets) shows that the performances of survival models vary in practice over real-world datasets and over the choice of the evaluation metric. In particular, we highlight that using multiple performance metrics is critical in providing a balanced assessment of various models. The results in our study will provide practical guidelines for translational scientists and clinicians, as well as define possible areas of investigation in both survival technique and benchmarking strategies.

Contact

jean.yang@sydney.edu.au
Collaborations and deceptions in strategic interactions revealed by hyperscanning fMRI
Authors: Shen Siao-Shan , Cheng Jen-Tang , Hsu Yi-Ren , Chen Der-Yow , Weng Ming-Hung , Kung Chun-Chia
Published: July 2021

Despite its ubiquity, deceiving as a social phenomenon is scarcely addressed with fMRI, partly due to the spontaneity and individual differences in cheating, and the contextual variability that fosters lying. In this hyperscanning fMRI study, the participant pairs (n=33) from Taipei and Tainan joined an opening-treasure-chest (OTC) game, where the dyads took alternative turns as senders (to inform) and receivers (to decide) for guessing the right chest. The cooperation condition was achieved by, upon successful guessing, splitting the $200NTD trial reward, thereby promoting mutual trust. The competition condition, in contrast, was done by, also upon winning, the latter receivers taking all the $150NTD reward, thereby encouraging strategic interactions. One key fMRI finding was the negative correlations between the connectivity of the right temporo-parietal junction (rTPJ), known as the theory-of-mind function, and amygdala, parahippocampal gyrus, and rostral anterior cingulate (rACC), to senders’ behavioral lying rates. Furthermore, the Multi-Voxel Pattern Analysis (MVPA) over multiple searchlight-identified Region-Of-Interests (ROIs), in classifying either the “truthful vs. lying in $150” or the “truthful in $200 vs. truthful in $150” conditions achieved 61% and 84.5% accuracy, respectively, reflecting the idiosyncratic brain networks involved in distinguishing the social trust vs. deceptions in the dyadic interactions.
Parallel Framework for Inferring Genome Scale Gene Regulatory Networks
Authors: Sebastian Softya , Roy Swarup
Published: July 2021

Genome-scale network inference is essential to understand comprehensive interaction patterns. Current methods are limited to the reconstruction of small to moderate-size networks. The most obvious alternative is to propose a novel method or alter existing methods that may leverage parallel computing paradigms. Very few attempts also have been made to re-engineer existing methods by executing selective iterative steps concurrently. We propose a generic framework in this paper that leverages parallel computing without re-engineering the original methods. The proposed framework uses state-of-the-art methods as a black box to infer sub-networks of the segmented data matrix. A simple merger was designed based on preferential attachment to generate the global network by merging the sub-networks.

Fifteen (15) inference methods were considered for experimentation. Qualitative and speedup analysis was carried out using DREAM challenge networks. The proposed framework was implemented on all the 15 inference methods using large expression matrices. The results were auspicious as we could infer large networks in reasonable time without compromising the qualitative aspects of the original (serial) algorithm.

CLR, the top performer, was then used to infer the network from the expression profiles of an Alzheimer’s disease (AD) affected mouse model consisting of 45,101 genes. We have also highlighted few hub genes from the network that are functionally related to various diseases.
Improved Interpretability of Brain-Behavior CCA with Domain-driven Dimension Reduction
Authors: Liu Zhangdaihong , Whitaker Kirstie J. , Smith Stephen M. , Nichols Thomas E.
Published: July 2021

Canonical Correlation Analysis (CCA) has been widely applied to study correlations between neuroimaging data and behavioral data. Practical use of CCA typically requires dimensionality reduction with, for example, Principal Components Analysis (PCA), however, this can result in CCA results that are difficult to interpret. In this paper, we introduce a Domain-driven Dimension Reduction (DDR) method, reducing the dimensionality of the original datasets combining human knowledge of the structure of the variables studied. We apply the method to the Human Connectome Project S1200 release and compare standard PCA across all variables with DDR applied to individual classes of variables, finding that DDR-CCA results are more stable and interpretable, allowing the contribution of each class of variable to be better understood. By carefully designing the analysis pipeline and cross-validating the results, we offer more insights on the interpretation of CCA applied to brain-behaviour data.
Artemisinin acts by inhibiting Plasmodium falciparum Ddi1, a retropepsin, resulting into the accumulation of ubiquitinated proteins
Authors: Onchieku Noah Machuki , Kumari Sonam , Pandey Rajan , Sharma Vaibhav , Kumar Mohit , Deshmukh Arunaditya , Kaur Inderjeet , Mohmmed Asif , Gupta Dinesh , Kiboi Daniel , Gaur Naseem , Malhotra Pawan
Published: July 2021

Reduced sensitivity of the human malaria parasite, Plasmodium falciparum, to Artemisinin and its derivatives (ARTs) threatens the global efforts towards eliminating malaria. ARTs have been shown to cause ubiquitous cellular and genetic insults, which results in the activation of the unfolded protein response (UPR) pathways. The UPR restores protein homeostasis, which otherwise would be toxic to cellular survival. Here, we interrogated the role of DNA-damage inducible protein 1 (PfDdi1), a unique proteasome-interacting retropepsin in mediating the actions of the ARTs. We demonstrate that PfDdi1 is an active A2 family protease that hydrolyzes ubiquitinated substrates. We further show that treatment with ARTs lead to the accumulation of ubiquitinated proteins in the parasites and blocks the destruction of the ubiquitinated substrates by PfDdi1. Besides, whereas the PfDdi1 is predominantly localised in the cytoplasm, exposure of the parasites to ARTs leads to DNA fragmentation and increased recruitment of the PfDdi1 into the nucleus. Furthermore, Ddi1 knock-out Saccharomyces cerevisiae cells are more suceptible to ARTs and the PfDdI1 protein robustly restores the corresponding functions in the knock-out cells. Together, these results show that ARTs act by inducing DNA and protein damage, and impairing the damage recovery by inhibiting the activity of PfDdi1, an essential ubiquitin-proteasome retropepsin.
Human engineered skeletal muscle of hypaxial origin from pluripotent stem cells with advanced function and regenerative capacity
Authors: Shahriyari Mina , Islam Md Rezaul , Sakib M. Sadman , Rika Anastasia , Krüger Dennis , Kaurani Lalit , Anandakumar Harithaa , Shomroni Orr , Schmidt Matthias , Salinas Gabriela , Unger Andreas , Linke Wolfgang A. , Zschüntzsch Jana , Schmidt Jens , Fischer André , Zimmermann Wolfram-Hubertus , Tiburcy Malte
Published: July 2021

Human pluripotent stem cell derived muscle models show great potential for translational research. Here, we describe developmentally inspired methods for derivation of skeletal muscle cells and their utility in three-dimensional skeletal muscle organoid formation as well as skeletal muscle tissue engineering. Key steps include the directed differentiation of human pluripotent stem cells to embryonic muscle progenitors of hypaxial origin followed by primary and secondary fetal myogenesis into hypaxial muscle with development of a satellite cell pool and evidence for innervation in vitro. Skeletal muscle organoids faithfully recapitulate all steps of embryonic myogenesis in 3D Tissue engineered muscle exhibits organotypic maturation and function, advanced by thyroid hormone. Regenerative competence was demonstrated in a cardiotoxin injury model with evidence of satellite cell activation as underlying mechanism. Collectively, we introduce a hypaxial muscle model with canonical properties of bona fide skeletal muscle in vivo to study muscle development, maturation, disease, and repair.
Electrocorticography based monitoring of anaesthetic depth in mice
Authors: Schmidt Dominik , English Gwendolyn , Gent Thomas , Yanik Mehmet Fatih , von der Behrens Wolfger
Published: July 2021

To improve animal welfare and data quality and reproducibility during research conducted under anaesthesia, anaesthetic depth in laboratory animals must be precisely monitored and controlled. While a variety of methods have been developed to estimate the depth of anaesthesia in humans, such tools for monitoring anaesthetic depth in laboratory animals remain limited. Here we propose an epidural electrocorticogram-based monitoring system that accurately tracks the depth of anesthesia in mice receiving inhalable isoflurane anaesthesia. Several features of the electrocorticogram signals exhibit robust modulation by the concentration of the administered anesthetic, notably, corticocortical coherence serves as an excellent indicator of anaesthetic depth. We developed a gradient boosting regressor framework that utilizes the extracted features to accurately estimate the depth of anaesthesia. Our method for feature extraction and estimation is conducted with a latency of only ten seconds, establishing a system for the real-time tracking of anaesthetic depth in mice.
Flight-tone mediated circadian control of audibility in mating swarms of Anopheles mosquitoes
Authors: Somers Jason , Georgiades Marcos , Su Matthew P , Bagi Judit , Andrés Marta , Mills Gordon , Ntabaliba Watson , Moore Sarah J , Spaccapelo Roberta , Albert Joerg T
Published: July 2021

Mating swarms of malaria mosquitoes form every day at sunset throughout the tropical world, they typically last less than 30 minutes. Activity patterns must thus be highly synchronized between the sexes. Moreover, males must be able to identify the few sporadically entering females by detecting the females’ faint flight tones. We here show that the Anopheles circadian clock ensures a tight synchrony of male and female activity and –importantly – also retunes the males’ acoustic detection system: by lifting their own flight tones at dusk, males actively enhance the audibility of females. The reported phenomenon of ‘harmonic convergence’ is a random by-product of the mosquitoes’ flight tone variance. Intriguingly, flight tones of individual mosquitoes occupy narrow –partly non-overlapping-frequency ranges, suggesting that the audibility of individual females varies across males.

One Sentence Summary

Male mosquitoes sharpen their hearing at sunset.
In vivoevidence thatSORL1, encoding the endosomal recycling receptor SORLA, can function as a causal gene in Alzheimer’s Disease
Authors: Andersen Olav M. , Bøgh Nikolaj , Landau Anne M. , Pløen Gro Grunnet , Jensen Anne Mette G. , Monti Giulia , Ulhøi Benedicte Parm , Nyengaard Jens Randel , Jacobsen Kirsten Rosenmay , Jørgensen Margarita Melnikova , Holm Ida E. , Kristensen Marianne L. , Hansen Esben Søvsø Szocska , Teunissen Charlotte E. , Breidenbach Laura , Droescher Mathias , Liu Ying , Pedersen Hanne Skovsgaard , Callesen Henrik , Luo Yonglun , Bolund Lars , Brooks David J. , Laustsen Christoffer , Small Scott A. , Mikkelsen Lars F. , Sørensen Charlotte B.
Published: July 2021

The few established causal genes in Alzheimer’s disease (AD), mutations inAPPandPSENs,have been functionally characterized using biomarkers, capturing anin vivoprofile reflecting the disease’s initial preclinical phase.SORL1, a gene encoding the endosome recycling receptor SORLA, epidemiologically behaves as a causal gene when truncating mutations lead to partial loss of protein function. Here, in an effort to test whetherSORL1can indeed function as an AD causal gene, we used CRISPR-Cas9-based gene editing to develop a novel model ofSORL1haploinsufficiency in Göttingen Minipigs taking advantage of porcine models for biomarker investigations.SORL1haploinsufficiency in young minipigs was found to phenocopy the preclinicalin vivoprofile of AD observed with other causal genes, resulting in spinal fluid abnormalities in Aβ and tau, with no evident neurodegeneration or amyloid plaque formation. These studies provide functional support thatSORL1is a bona fide causal gene in AD, and when taken together with recent insight on other AD-causal genes, support the idea that dysfunctional endosomal recycling is a dominant pathogenic pathway in the disease.
Di-μ-nitrato-bis(μ-octaethyl pyrophosphoramide)bis[aquadinitratocalcium(II)]
Authors: Micallef Duncan , Baisch Ulrich
Published: July 2021

The title compound, di-μ-nitrato-κ3
O,O′:O;O:O,O′-bis(μ-octaethyl pyrophosphoramide-κ2
O:O′)bis[aquabis(nitrato-κ2
O,O′)calcium(II)], [Ca2(NO3)4(C16H40N4O3P2)2(H2O)2] was obtained as a side product during the work up of the synthesis of octaethyl pyrophosphoramide and represents the first structurally characterized complex of this ligand. The compound crystallizes in the monoclinic space group P21/n and the asymmetric unit contains one pyrophosphoramide molecule and one Ca2+ ion coordinated to two nitrate ions and one water molecule. The complex exists as a dimer with a centre of inversion located between two eight-coordinate calcium(II) centres, which are bridged by two nitrate ions and two octaethyl pyrophosphoramide ligands. Each Ca2+ cation is also coordinated to a further nitrate anion, acting as a bidentate ligand, and a water molecule. The complexes stack parallel to the a axis and are held in place by a network of intermolecular O—H...O hydrogen bonds also running parallel to a.
N,N′-Dicyclohexyl-N-(phthaloylglycyl)urea
Authors: Bernès Sylvain , Hernández-Linares María Guadalupe
Published: July 2021

The molecular structure of the title compound {systematic name: 1,3-dicyclohexyl-1-[2-(1,3-dioxo-2,3-dihydro-1H-isoindol-2-yl)acetyl]urea}, C23H29N3O4, derived from N,N′-dicyclohexylurea, shows that the tertiary N atom substituted by a cyclohexyl and phthaloylglycyl groups adopts a perfectly planar geometry (bond-angle sum = 360.0°). In the same way as for N,N′-dicyclohexylurea, the extended structure of the title compound features N—H...O hydrogen bonds, which generate chains of molecules running in the [001] direction.
The effect of political connections on firm performance: evidence from Egypt
Authors: Eissa Aref M. , Eliwa Yasser
Published: July 2021

Purpose

This paper examines the effect of political connections (PCs) on firms' profitability and market value in the Egyptian market after the uprising of 2013.

Design/methodology/approach

An empirical study is conducted based on 284 firm-year observations for non-financial listed firms on the EGX100 during the period of 2014–2017. To test the study’s hypothesis, two independent samplet-test, Pearson correlation analysis and ordinary least square (OLS) regressions are conducted.

Findings

The results suggest that PCs are common across all industries in Egypt, the PCs through top officers do not improve firm's profitability; however, it has a positive effect on firms' market value. Further, PCs through business owners improve neither profitability nor the market value. Finally, the results suggest that PCs through government ownership have a positive effect on both firms' profitability and market value.

Practical implications

The study’s finding encourages policymakers and regulators in emerging markets, e.g. Egypt, to develop stricter laws, policies and regulatory initiatives to restrain the potential conflict of interest in the politically connected firms.

Originality/value

To the best of the authors' knowledge, this study is one of the first to examine the relationship between PCs and both firms’ profitability and market value in Egypt.
Emerging union–management partnership in Chilean firms: particularities and limitations
Authors: Gutiérrez Crocco Francisca , Martin Caballero Angel
Published: July 2021

Purpose

The article explains why some Chilean companies have implemented a partnership strategy with trade unions, in a national context broadly described as unfavorable to such approach. Moreover, it discusses the shape and limits of this strategy.

Design/methodology/approach

The argument draws on a case study conducted between 2016 and 2018 in three large companies. Human resources managers, line managers and union officers were interviewed in each of these companies, and internal and administrative documentation were analyzed.

Findings

The article demonstrates that the management’s partnership strategy in the studied companies has emerged to contain the union revitalization. Additionally, it suggests this strategy has not favored trust-based relationships that guarantee long-term mutual gains for employees and companies. The article identifies some factors that explain this situation: the regulation, the economic uncertainty and the absence of a pluralist management perspective.

Originality/value

The article has the value of providing empirical evidence on union–management partnership, a topic that has gained strategic importance for large Chilean companies but remains unexplored in the mainstream the human resources management literature. The article also contributes to underscore the theoretical relevance of political and cultural variables in explaining management strategies and their results.
Making of an innovative economy: a study of diversity of Chinese enterprise innovation
Authors: Salike Nimesh , Huang Yanghua , Yin Zhifeng , Zeng Douglas Zhihua
Published: July 2021

Purpose

This research examines the effects of firm ownership and size on innovation capability using data from the World Bank China Enterprise Survey (WBCES), which provides directly measurable innovation-related variables. Key consideration is given to the role and innovation capability of state-owned enterprises (SOEs) compared with domestic and foreign private enterprises in the Chinese economy.

Design/methodology/approach

In its quest for technological self-reliance and a new developmental path, China is focusing on its enterprise innovation capability.

Findings

The findings suggest that SOEs and domestic private enterprises are similar in terms of innovation participation but differ in terms of innovation diversification, which implies ownership-specific innovative advantages. In general, the authors find that SOEs are more innovative with respect to processes innovation but less so with respect to product, management and promotion innovations. Foreign-owned enterprises are superior in all types of innovation except product innovation.

Research limitations/implications

The authors also find that size is an important determinant of innovation capability, with the effect varying depending on location and industry. Moreover, the joint effect of firm ownership and size on innovation declines with increasing size. These findings provide new insights into the evaluation of China's major policies.

Originality/value

This research examines the effects of ownership and size on enterprise innovation capability, using the WBCES (2013) data, which include direct measurable innovation related variables.
Challenges of network interaction in managing sustainable development projects in developing countries: case of an international consulting company
Authors: Dziubaniuk Olga , Ivanova-Gongne Maria , Berdysheva Ekaterina
Published: July 2021

Purpose

This study aims to explore the challenges and complexities of interaction in international stakeholder networks within the context of projects focused on the implementation of sustainable development goals (SDGs). In particular, it examines the challenges faced by stakeholders in a network from a developed country during interaction in the context of a developing country.

Design/methodology/approach

Using a qualitative approach, this study analyses interview data collected from the key managers of an international consulting company in charge of a water supply and sanitation project in Nepal. The primary data is triangulated with secondary data, such as project reports and related academic articles.

Findings

This study illustrates how interaction in international stakeholder networks affects and is interrelated with SDGs, as well as how aiming to achieve one specific goal can stimulate the implementation of other sustainable goals. Further, this research shows how project managers from a developed country had to adapt to the specifics of the developing country context and how their sustainability project influenced the well-being of local communities by improving environmental and social sustainability.

Research limitations/implications

The research suggests that challenges in stakeholder interaction may arise because of differences in process management methods used by the international stakeholders involved in the project and country-context specifics, such as corruption, imperfect national regulations, cultural specifics, effects of climate change, etc.

Originality/value

The paper contributes to the literature on international multi-stakeholder interaction between actors from developed and developing countries. Furthermore, it adds to the literature on stakeholder networking by highlighting the importance of engaging in a dialogue with local communities during the conceptualisation stages of both sustainability and SDG implementation because of diverging worldviews and practices.
Application of lattice Boltzmann method to curved boundaries for simulating nanofluid flow in an L-Shape enclosure
Authors: Naseri Nia Shayan , Rabiei Faranak , Rashidi M.M.
Published: July 2021

Purpose

This paper aims to use the Lattice Boltzmann method (LBM) to numerically simulate the natural convection heat transfer of Cu-water nanofluid in an L-shaped enclosure with curved boundaries.

Design/methodology/approach

LBM on three different models of curved L-shape cavity using staircase approach is applied to perform a comparative investigation for the effects of curved boundary on fluid flow and heat transfer. The staircase approximation is a straightforward and efficient approach to simulating curved boundaries in LBM.

Findings

The effect of curved boundary on natural convection in different parameter ranges of Rayleigh number and nanoparticle volume fraction is investigated. The curved L-shape results are also compared to the rectangular L-shape results that were also achieved in this study. The curved boundary LBM simulation is also validated with existing studies, which shows great accuracy in this study. The results show that the top curved boundary in curved L-shape models causes a notable increase in the Nusselt number values.

Originality/value

Based on existing literature, there is a lack of comparative studies which would specifically examine the effects of curved boundaries on natural convection in closed cavities. Particularly, the application of curved boundaries to an L-shape cavity has not been examined. In this study, curved boundaries are applied to the sharp corners of the bending section in the L-shape and the results of the curved L-shape models are compared to the simple rectangular L-shape model. Hence, a comparative evaluation is performed for the effect of curved boundaries on fluid flow in the L-shape enclosure.