bluuebunny/crossref_metadata_2025_split huggingface dataset:
Scoping Review: Differences between the risk factors of indigenous and non-indigenous latin american and caribbean children younger than 5 years old
Authors: Rodriguez Romero Daniel David , Rojas Gómez Ana María , Cuadrado Guzmán Jesús David 
Published: May 2023

AbstractObjectiveTo map the existing literature on the difference in risk factors for undernutrition between indigenous and non-indigenous children younger than 5 years old of Latin America and caribbean.IntroductionCompared to non-indigenous children, Indigenous children have a higher risk for undernutrition, however, there are not systematic or scoping reviews identifying this difference through the risk factors.Inclusion criteriaEvery paper designed to assess directly or indirectly associations between undernutrition and risk factors, also, it must show results where indigenous people had not been aggregated to other races. We excluded every paper that didn’t have a covariate different to ethnicity.MethodsThis scoping review will use the JBI methodology to search several databases, trial registries, and gray literature for both published and unpublished studies related to malnutrition. Two or more independent reviewers will screen titles and abstracts for inclusion criteria, assess full texts, and extract data using a data extraction tool. Results will be presented as a narrative synthesis with key findings, knowledge gaps, and recommendations. A PRISMA-ScR flow diagram will be included in the final report.
HIRA-mediated loading of histone variant H3.3 controls androgen-induced transcription by regulation of AR/BRD4 complex assembly at enhancers
Authors: Morozov Viacheslav M. , Riva Alberto , Sarwar Sadia , Kim WanJu , Li Jianping , Zhou Lei , Licht Jonathan D. , Daaka Yehia , Ishov Alexander M. 
Published: May 2023

AbstractIncorporation of histone variant H3.3 comprises active territories of chromatin. Exploring the function of H3.3 in prostate cancer (PC), we found that knockout (KO) of H3.3 chaperone HIRA suppresses PC growthin vitroand in xenograft settings, deregulates androgen-induced gene expression and alters androgen receptor (AR) binding within enhancers of target genes. H3.3 affects transcription in multiple ways, including activation of p300 by phosphorylated H3.3 at Ser-31 (H3.3S31Ph), which results in H3K27 acetylation (H3K27Ac) at enhancers. In turn, H3K27Ac recruits bromodomain protein BRD4 for enhancer-promoter interaction and transcription activation. We observed that HIRA KO reduces H3.3 incorporation, diminishes H3.3S31Ph and H3K27Ac, modifies recruitment of BRD4. These results suggest that H3.3-enriched enhancer chromatin serves as a platform for H3K27Ac-mediated BRD4 recruitment, which interacts with and retains AR at enhancers, resulting in transcription reprogramming. AR KO reduced levels of H3.3 at enhancers, indicating feedback mechanism. In addition, HIRA KO deregulates glucocorticoid-driven transcription, suggesting a common H3.3/HIRA-dependent mechanism of nuclear receptors function. Expression of HIRA complex proteins is increased in PC compared with normal prostate tissue, especially in high-risk PC groups, and is associated with a negative prognosis. Collectively, our results demonstrate function of HIRA-dependent H3.3 pathway in regulation of nuclear receptors activity.Key points*H3.3 at enhancers promotes acetylation of H3K27Ac and retention of AR/BRD4 complex for transcription regulation*Knockout of H3.3 chaperone HIRA suppresses PC cells growth and deregulates androgen-induced transcription*H3.3/HIRA pathway regulates both AR and GR, suggesting a common HIRA/H3.3 mechanism of nuclear receptors function
Heterologous expression, purification and structural features of nativeDictyostelium discoideumdye-decolorizing peroxidase bound to a natively incorporated heme
Authors: Kalkan Özlem , Kantamneni Sravya , Brings Lea , Han Huijong , Mancuso Adrian P. , Koua Faisal H.M. 
Published: May 2023

AbstractTheDictyostelium discoideumdye-decolorizing peroxidase (DdDyP) is a newly discovered peroxidase, which belongs to a unique class of heme peroxidase family that lacks homology to the known members of plant peroxidase superfamily.DdDyP catalyzes the H2O2-dependent oxidation of a wide-spectrum of substrates ranging from polycyclic dyes to lignin biomass, holding promise for potential industrial and biotechnological applications. To study the molecular mechanism ofDdDyP, highly pure and functional protein with a natively incorporated heme is required, however, obtaining a functional DyP-type peroxidase with a natively bound heme is challenging and often requires addition of expensive biosynthesis precursors. Alternatively, a hemein vitroreconstitution approach followed by a chromatographic purification step to remove the excess heme is often used. Here, we show that expressing theDdDyP peroxidase in 2×YT enriched medium at low temperature (20 °C), without adding heme supplement or biosynthetic precursors, allows for a correct native incorporation of heme into the apo-protein, giving rise to a stable protein with a strong Soret peak at 402 nm. Further, we crystallized and determined the native structure ofDdDyP at a resolution of 1.95 Å, which verifies the correct heme binding and its geometry. The structural analysis also reveals a binding of two water molecules at the distal site of heme plane bridging the catalytic residues (Arg239 and Asp149) of the GXXDG motif to the heme-Fe(III) via hydrogen bonds. Our results provide new insights into the geometry of nativeDdDyP active site and its implication on DyP catalysis.
The depletion of TRAIP results in the retention of PCNA on chromatin during mitosis, leads to inhibiting DNA replication initiation
Authors: Shiomi Yasushi , Hayashi Akiyo , Saito Yuichiro , Kanemaki Masato T. , Nishitani Hideo 
Published: May 2023

AbstractLoading PCNA onto chromatin is a pivotal step in DNA replication, cell cycle progression, and genome integrity. Conversely, unloading PCNA from chromatin is equally crucial for maintaining genome stability. Cells deficient in the PCNA unloader ATAD5-RFC exhibit elevated levels of chromatin-bound PCNA during S phase, but still show dissociation of PCNA from chromatin in mitosis. In this study, we found that depletion of TRAIP, an E3 ubiquitin ligase, results in the retention of PCNA on chromatin during mitosis. Although TRAIP-depleted cells with chromatin-bound PCNA during mitosis progressed into the subsequent G1 phase, they displayed reduced levels of Cdt1, a key replication licensing factor, and impaired S phase entry. In addition, TRAIP-depleted cells exhibited delayed S phase progression. These results suggest that TRAIP functions independently of ATAD5-RFC in removing PCNA from chromatin. Furthermore, TRAIP appears to be essential for precise pre-replication complexes (pre-RCs) formation necessary for faithful initiation of DNA replication and S phase progression.
Exploring the potential ofBacillus subtilisas cell factory for food ingredients and special chemicals
Authors: Chen Taichi , Brul Stanley , Hugenholtz Jeroen 
Published: May 2023

AbstractBackgroundBacillus subtilishas been established as model microorganism for fundamental research in the laboratory on protein production/secretion and sporulation and as model bacterium for controlling spoilage in the food industry. It has also been used for production of (commercial) enzymes and several secondary metabolites such as vitamins. However, this doesn’t fully reflect the potential ofB. subtilisas a cell-factory. Here, various strains ofB. subtilis, including food-grade, spore-deficient strains and industrially used strains, were compared for their growth and metabolic potential. Industry-relevant parameters were analyzed for all strains under various aeration regimes, under anaerobic conditions, in various nutritious and nutrient-limited cultivation media, with and without organic nitrogen sources, and with and without sugar.ResultsPractical experiments were conducted to compare industrial relevant properties like growth rates, intracellular components and extracellular metabolite profile of differentB. subtilisstrains. Based on growth flexibility in different media, we found that some strains like NCIB3610 and DSM1092 are adapted to inorganic or organic nitrogen source utilization, which is highly relevant when considering a biorefinery approach using various cheap and abundant waste/sidestreams. Secondly, spore-deficient strains such as 3NA, 168S and PY79S, showed advantages in microbial protein and acetolactate pathway expression, which is associated with applications in food industry for protein supplement and diacetyl production. Lastly, WB800 and PY79S exhibited potential for fermentative production of Dipicolinic acid, 2,3-Butanediol and Lactic acid that could serve as precursors for biopolymers.ConclusionThis study demonstrates the broad potential for more extensive industrial use ofBacillus subtilisin the (bio-based) chemical industry for use of sidestreams, in the personal care industry, in the food industry for food additive production, and in the bio-sustainable industry for biofuel and bio-degradable plastic precursors production. In addition, selecting differentB. subtilisstrains for specific purposes makes full use of the diversity of this species and increases the potential ofB. subtilisin its contribution to the bio-based economy.
Nutrient-driven dedifferentiation of enteroendocrine cells promotes adaptive intestinal growth
Authors: Nagai Hiroki , Nagai Luis Augusto Eijy , Tasaki Sohei , Nakato Ryuichiro , Umetsu Daiki , Kuranaga Erina , Miura Masayuki , Nakajima Yu-ichiro 
Published: May 2023

SUMMARYPost-developmental organ resizing improves organismal fitness under constantly changing nutrient environments. Although stem cell abundance is a fundamental determinant of adaptive resizing, our understanding of its underlying mechanisms remains primarily limited to the regulation of stem cell division. Here we demonstrate that nutrient fluctuation induces dedifferentiation in theDrosophilaadult midgut to drive adaptive intestinal growth. From lineage tracing and single-cell RNA-sequencing, we identify a subpopulation of enteroendocrine cells (EEs) that convert into functional intestinal stem cells (ISCs) in response to dietary glucose and amino acids by activating the JAK-STAT pathway. Genetic ablation of EE-derived ISCs severely impairs ISC expansion and midgut growth despite the retention of resident ISCs, andin silicomodeling further indicates that EE dedifferentiation enables efficient increase in the midgut cell number while maintaining epithelial cell composition. Our findings uncover a physiologically-induced dedifferentiation that ensures ISC expansion during adaptive organ growth in concert with nutrient conditions.
The effects of prior exposure to prism lenses onde novomotor skill learning
Authors: Lang-Hodge Annmarie M. , Cooke Dylan F. , Marigold Daniel S. 
Published: May 2023

ABSTRACTMotor learning involves plasticity in a network of brain areas across the cortex and cerebellum. Such traces of learning have the potential to affect subsequent learning of other tasks. In some cases, prior learning can interfere with subsequent learning, but it may be possible to potentiate learning of one task with a prior task if they are sufficiently different. Because prism adaptation involves extensive neuroplasticity, we reasoned that the elevated excitability of neurons could increase their readiness to undergo structural changes, and in turn, create an optimal state for learning a subsequent task. We tested this idea, selecting two different forms of learning tasks, asking whether exposure to a sensorimotor adaptation task can improve subsequentde novomotor skill learning. Participants first learned a new visuomotor mapping induced by prism glasses in which prism strength varied trial-to-trial. Immediately after and the next day, we tested participants on a mirror tracing task, a form ofde novoskill learning. Prism-trained and control participants both learned the mirror tracing task, with similar reductions in error and increases in distance traced. Both groups also showed evidence of offline performance gains between the end of day 1 and the start of day 2. However, we did not detect differences between groups. Overall, our results do not support the idea that prism adaptation learning can potentiate subsequentde novolearning. We discuss factors that may have contributed to this result.
Cell behaviors underlyingMyxococcus xanthusaggregate dispersal
Authors: Murphy Patrick , Comstock Jessica , Khan Trosporsha , Zhang Jiangguo , Welch Roy , Igoshin Oleg 
Published: May 2023

AbstractThe soil bacteriumMyxococcus xanthusis a model organism with a set of diverse behaviors. These behaviors include the starvation-induced multicellular development program, in which cells move collectively to assemble multicellular aggregates. After initial aggregates have formed, some will disperse, with smaller aggregates having a higher chance of dispersal. Initial aggregation is driven by two changes in cell behavior: cells slow down inside of aggregates and bias their motion by reversing direction less frequently when moving towards aggregates.However, the cell behaviors that drive dispersal are unknown. Here we use fluorescent microscopy to quantify changes in cell behavior after initial aggregates have formed. We observe that after initial aggregate formation, cells adjust the bias in reversal timings by initiating reversals more rapidly when approaching unstable aggregates. Using agent-based modeling, we then show dispersal is predominantly generated by this change in bias, which is strong enough to overcome slowdown inside aggregates. Notably, the change in reversal bias is correlated with the nearest aggregate’s size, connecting cellular activity to previously observed correlations between aggregate size and fate. To determine if this connection is consistent across strains, we analyze a secondM. xanthusstrain with reduced levels of dispersal. We find that far fewer cells near smaller aggregates modified their bias. This implies that aggregate dispersal is under genetic control, providing a foundation for further investigations into the role it plays in the life cycle ofM. xanthus.ImportanceUnderstanding the processes behind bacterial biofilm formation, maintenance, and dispersal is essential for addressing their effects on health and ecology. Within these multicellular communities, various cues can trigger differentiation into distinct cell types, allowing cells to adapt to their specific local environment. The soil bacteriumMyxococcus xanthusforms biofilms in response to starvation, marked by cells aggregating into mounds. Some aggregates persist as spore-filled fruiting bodies, while others disperse after initial formation for unknown reasons. Here, we use a combination of cell tracking analysis and computational simulations to identify behaviors at the cellular level that contribute to aggregate dispersal. Our results suggest that cells in aggregates actively determine whether to disperse or persist and undergo a transition to sporulation based on a self-produced cue related to the aggregate’s size. Identifying these cues is an important step in understanding and potentially manipulating bacterial cell-fate decisions.
Jumbo phages are active against extensively-drug-resistant eyedrop-associatedPseudomonas aeruginosainfections
Authors: Cobián Güemes Ana Georgina , Ghatbale Pooja , Blanc Alisha N. , Morgan Chase J. , Garcia Andrew , Leonard Jesse , Huang Lina , Kovalick Grace , Proost Marissa , Chiu Megan , Kuo Peiting , Oh Joseph , Karthikeyan Smruthi , Knight Rob , Pogliano Joe , Schooley Robert T. , Pride David T. 
Published: May 2023

ABSTRACTAntibiotic resistant bacteria present an emerging challenge to human health as the pressure instituted on the microbial world through the liberal use of antibiotics has resulted in their emergence across the globe. Those bacteria that acquire mobile genetic elements such as plasmids are especially concerning because those plasmids may be shared readily with other microbes that then can also become antibiotic resistant. Serious infections have recently been related to contamination of preservative-free eyedrops with extensively drug resistant (XDR) isolates ofPseudomonas aeruginosa, already resulting in three deaths. These drug-resistant isolates cannot be managed with most conventional antibiotics. We sought to identify alternatives to conventional antibiotics for lysis of these XDR isolates, and identified multiple bacteriophages (viruses that attack bacteria) that killed them efficiently. We found both jumbo phages (>200kb in genome size) and non-jumbo phages that were active against these isolates, the former killing more efficiently. Jumbo phages effectively killed the 3 separate XDRP. aeruginosaisolates both on solid and liquid medium. Given the ongoing nature of the XDRP. aeruginosaeyedrop outbreak, the identification of phages active against them provides physicians with several novel potential alternatives for treatment.
Separating abusive from efficient related-party transactions: evidence from India
Authors: Saurabh Kinshuk 
Published: May 2023

PurposeThe aim of this study is to understand a family firm's choice of related-party transaction (RPT) types and analyze their value impacts to separate the abusive from benign RPTs.Design/methodology/approachIt uses a 10-year panel of BSE-listed 378 family (and 200 non-family) firms. The fixed effects, logit and difference-in-difference (DID) models help examine value effects, propensity and persistence of harmful RPTs.FindingsLoans/guarantees (irrespective of counterparties) destroy firm value. Capital asset RPTs decrease the firm value but enhance value when undertaken with holding parties. Operating RPTs increase firm value and profitability. They improve asset utilization and reduce discretionary expenses (especially when made with controlled entities). Family firms have larger loans/guarantees and capital asset volumes but have smaller operating RPTs than non-family firms. They are less likely to undertake loans/guarantees (and even operating RPTs) and more capital RPTs vis-à-vis non-family firms. Family firms persist with dubious loans/guarantees but hold back beneficial operating RPTs, despite RPTs being in investor cross-hairs amid the Satyam scam.Research limitations/implicationsRent extractability and counterparty incentives supplement each other. (1) The higher extractability of related-party loans and guarantees (RPLGs) dominates the lower extraction incentives of controlled parties. (2) Holding parties' bringing assets, providing a growth engine and adding value dominate their higher extraction incentives (3) The big gains to the operational efficiency come from operating RPTs with controlled parties, generally operating companies in the family house. (4) Dubious RPTs seem more integral to family firms' choices than non-family firms. (5) Counterparty incentives behind the divergent use of RPTs deserve more research attention. Future studies can give more attention to how family characteristics affect divergent motives behind RPTs.Practical implicationsFirst, the study does not single out family firms for dubious use of all RPTs. Second, investors, auditors or creditors must pay close attention to RPLGs as a special expropriation mechanism. Third, operating RPTs (and capital RPTs with holding parties) benefit family firms. However, solid procedural safeguards are necessary. Overall, results may help clarify the dilemma Indian regulators face in balancing the abusive and business sides of RPTs.Originality/valueThe study fills the gap by arguing why some RPTs may be dubious or benign and then shows how RPTs' misuse depends on counterparty types. It shows operating RPTs enhance operating efficiencies on several dimensions and that benefits may vary with counterparty types. It also presents the first evidence that family firms favor dubious RPTs more and efficient RPTs less than non-family firms.
Relational governance in the ITO: the role of self-determination theory and the mediating effect of control perceived
Authors: Braga de Oliveira Friaes Ligiane Cristina , Poleto Thiago , Negreiros Clemente Thárcylla Rebecca , Ramos Camila Carvalho , de Carvalho Victor Diogho Heuer , Nepomuceno Thyago Celso Cavalcante 
Published: May 2023

PurposeResearchers in the field recognize the importance of the relationship between contractor and contractee in the process of information technology (IT) outsourcing. However, little is known about the impact of the manager's profile in this process. Thus, the objective of this research was to analyze the impact of the perception of competence, autonomy and relationship of public managers on relational governance (RG), as well as, to identify the effect of perceived control in this relationship.Design/methodology/approachThis study uses a quantitative approach to investigate the impact of the behavioral characteristics of IT managers from the self-determination theory (SDT). The data were collected in Brazilian public institutions active in the areas of education, finance, statistics and technology, and the hypotheses were identified and evaluated using the technique of partial least squares structural equation modeling (PLS-SEM).FindingsThe results identified that managers' self-determination is related to the perception of control, which, consequently, impacts the RG by providing feelings of competence and autonomy capable of building a beneficial relationship with the IT provider.Practical implicationsThis study promotes the understanding that upper management needs to support the autonomy of managers to increase their levels of intrinsic motivation when managing supplier deliveries.Originality/valueThe application of SDT to the IT outsourcing context provides new insights into the mediation of perceived control by explaining the relationship between managers' expectations and motivations as an important driver for RG.