bluuebunny/crossref_metadata_2025_split huggingface dataset:
The non-ribosomal peptide synthetase-independent siderophore (NIS) rhizobactin produced by
Caballeronia mineralivorans
PML1(12) confers the ability to weather minerals
Authors: Blanco Nouche Cintia , Paris Cédric , Dhalleine Tiphaine , Oger Philippe , Turpault Marie-Pierre , Uroz Stéphane 
Published: October 2023

ABSTRACT

To mobilize nutrients entrapped into minerals and rocks, heterotrophic bacteria living in nutrient-poor environments have developed different mechanisms based mainly on acidolysis and chelation. However, the genetic bases of these mechanisms remain unidentified. To fill this gap, we considered the model strain
Caballeronia mineralivorans
PML1(12) known to be effective at weathering. Based on its transcriptomics and proteomics responses in Fe-depleted conditions, we pointed a cluster of genes differentially expressed and putatively involved in the production of siderophores. In this study, we report the characterization of this gene region coding for the production of a non-ribosomal peptide synthetase-independent siderophore (NIS). Targeted mutagenesis associated with functional assays and liquid chromatography coupled to high-resolution tandem mass spectrometry demonstrated the production of a single siderophore, identified as rhizobactin. This siderophore represents the first NIS containing malic acid in its structure. The evidence for the implication of rhizobactin in mineral weathering was demonstrated during a hematite dissolution assay. This study provides the first demonstration of the synthesis of a NIS in the genus
Caballeronia
and its involvement in mineral weathering. Our conclusions reinforce the idea that strain PML1(12) is particularly well adapted to nutrient-poor environments.

IMPORTANCE

This work deciphers the molecular and genetic bases used by strain PML1(12) of
Caballeronia mineralivorans
to mobilize iron and weather minerals. Through the combination of bioinformatics, chemical, and phylogenetic analyses, we characterized the siderophore produced by strain PML1(12) and the related genes. This siderophore was identified as rhizobactin and classified as a non-ribosomal peptide synthetase-independent siderophore (NIS). Contrary to the previously identified NIS synthetases that form siderophores containing citric acid, α-ketoglutarate, or succinic acid, our analyses revealed that rhizobactin contains malic acid in its structure, representing, therefore, the first identified NIS with such an acid and probably a new NIS category. Last, this work demonstrates for the first time the effectiveness at weathering minerals of a siderophore of the NIS family. Our findings offer relevant information for different fields of research, such as environmental genomics, microbiology, chemistry, and soil sciences.
Phenomic and transcriptomic analyses reveal the sequential synthesis of Fe
3
O
4
nanoparticles in
Acidithiobacillus ferrooxidans
BYM
Authors: Yang Jiani , Zhang Shuang , Zhang Yu , Zhao Dan , Liu Tao , Sun Xindi , Yan Lei 
Published: October 2023

ABSTRACT

Understanding the molecular mechanism of magnetite (Fe
3
O
4
) nanoparticle synthesis in
Acidithiobacillus ferrooxidans
BYM is particularly important for the commercial development of biogenic Fe
3
O
4
nanoparticles. The phenomic parameters such as intracellular iron content and number and size of Fe
3
O
4
nanoparticles were significantly affected by different treatment conditions, i.e., FeSO
4
·7H
2
O concentrations (0, 40, and 80 g/L), growth times (12, 36, and 50 h), and magnetic field intensities (0.05, 3.5, and 15 mT) (
P
< 0.01). Transcriptome analysis revealed that 2,164, 1,587, and 1,061 differentially expressed genes (DEGs) were accordingly detected, and 24 significant expression profiles were identified in
A. ferrooxidans
BYM under the three treatment conditions. The construction of gene regulatory networks for Fe
3
O
4
nanoparticle synthesis indicated that DEGs mainly enrich ion transport, oxidation-reduction process, membrane structure, signal transduction, and quorum sensing. The four modules were found to be significantly associated with Fe
3
O
4
nanoparticle phenomic parameters using a weighted gene co-expression network. Ten hub genes significantly correlated with Fe
3
O
4
nanoparticle phenomic parameters (
P
< 0.01) were finally selected from 24 eigengenes related to iron metabolism screened from these models. On the basis of the previous research results and the present study findings, we provide a hypothetical molecular model for Fe
3
O
4
nanoparticle synthesis mediated by these hub genes in
A. ferrooxidans
BYM comprising membrane formation, iron uptake and transport, iron redox, and crystal maturity. Our results will enable in-depth studies of Fe
3
O
4
nanoparticle synthesis in non-magnetotactic magnetosome-producing bacteria.

IMPORTANCE

As the most important non-magnetotactic magnetosome-producing bacteria,
Acidithiobacillus ferrooxidans
only requires very mild conditions to produce Fe
3
O
4
nanoparticles, thus conferring greater flexibility and potential application in biomagnetic nanoparticle production. However, the available information cannot explain the mechanism of Fe
3
O
4
nanoparticle formation in
A. ferrooxidans
. In this study, we applied phenomic and transcriptomic analyses to reveal this mechanism. We found that different treatment condition factors notably affect the phenomic data of Fe
3
O
4
nanoparticle in
A. ferrooxidans
. Using transcriptomic analyses, the gene network controlling/regulating Fe
3
O
4
nanoparticle biogenesis in
A. ferrooxidans
was proposed, excavating the candidate hub genes for Fe
3
O
4
nanoparticle formation in
A. ferrooxidans
. Based on this information, a sequential model for Fe
3
O
4
nanoparticle synthesis in
A. ferrooxidans
was hypothesized. It lays the groundwork for further clarifying the feature of Fe
3
O
4
nanoparticle synthesis.
Variability of index of absorbance difference (IAD) to indicate fruit maturity at harvest for major apple cultivars in Ontario
Authors: Mostofi Younes , DeEll Jennifer R. 
Published: October 2023

The overall objective of this study was to evaluate the index of absorbance difference ( IAD) of four major apple cultivars in Ontario (‘Honeycrisp’, ‘Ambrosia’, ‘Gala’, and ‘McIntosh’) during the harvest window over multiple seasons (≥4 years), as well as its relationship with fruit firmness, internal ethylene concentration, and starch index values. IAD values differed among the four cultivars, with ‘McIntosh’ having the highest IAD (1.03–1.33) overall and ‘Gala’ having the lowest (0.19–0.56). Principal component analysis showed that the cultivars were separated into distinct groups. ‘Honeycrisp’ was clustered with starch and ethylene, while ‘Gala’ and ‘McIntosh’ were mainly clustered with firmness and IAD, respectively. Variable correlations between IAD and other maturity indices were found over the years. The negative relationship between IAD and ethylene for ‘Gala’ showed variability with R2 ranging from 0.008 in 2012 to 0.47 in 2018. The correlation between IAD and starch for ‘Gala’ was very strong ( rs = −0.82****) in 2018, whereas it was not significant in any year for ‘McIntosh’. Overall, IAD may relate to harvest maturity, but it did not correlate closely or consistently with other maturity indices, varied greatly year to year, and was cultivar dependent. IAD measures are not consistently related to fruit maturity every year, making reliability difficult to attain.
MAGNETOHYDRODYNAMIC TERNARY HYBRID NANOFLUID FLOW OVER A STRETCHING SURFACE SUBJECT TO THERMAL CONVECTIVE AND ZERO MASS FLUX CONDITIONS
Authors: ABAS SYED ARSHAD , ULLAH HAKEEM , ISLAM SAEED , FIZA MEHREEN 
Published: October 2023

Nanoparticles have the capability to augment the thermal conductivity of nanofluids. For the transmission of heat, the material’s low thermal conductivity is the key problem. Therefore, to increase the thermal conductivity, researchers mixed different nanoparticles in the base fluids. In this field of study, utilizing three different particles is the most recent strategy to form a ternary hybrid nanofluid that gives us better results in terms of heat transfer. The interaction of three different kinds of nanoparticles, i.e. copper, alumina and silver, is considered with water serving as the base fluid to form a ternary hybrid nanofluid. The paper explores the behavior of ternary hybrid nanofluids on heat and mass transportation phenomena of the two-dimensional magnetohydrodynamic (MHD) micropolar flow across a porous extending surface with zero mass flux and convective conditions. The Brownian motion, thermal radiation, heat source and sink, and joule heating are taken into consideration in the temperature equation. The chemical reaction is incorporated into the concentration equation. Appropriate similarity transformations are used to transform the system of partial differential equations (PDEs) to a coupled system of ordinary differential equations (ODEs). The homotopy analysis method (HAM) is used to solve the system of the flow equations. The effects of the nanoparticle’s volume fractions and other different physical parameters on the surface drag force, Nusselt number, velocities, microrotation, temperature and concentration profiles are scrutinized through figures and tables. The outcomes of the present investigation show that the heat transfer rate is augmented with the increasing value of thermophoresis parameter. The magnetic field has augmented temperature while the opposite result is seen in velocity and microrotation profiles. With the escalating values of thermophoresis parameter, the concentration and temperature of ternary hybrid nanofluids are boosted while the increasing Brownian and chemical reaction parameters have decreased the concentration profile. The surface friction coefficient exhibited by the ternary hybrid nanofluid is higher than hybrid and conventional nanofluids.
Targeting Transcriptional Regulation with a CDK9 Inhibitor Suppresses Growth of Endocrine- and Palbociclib-Resistant ER+ Breast Cancers
Authors: Soosainathan Arany , Iravani Marjan , El-Botty Rania , Alexander John , Sourd Laura , Morisset Ludivine , Painsec Pierre , Orha Rebecca , Nikitorowicz-Buniak Joanna , Pancholi Sunil , Haider Syed , Dowsett Mitch , Marangoni Elisabetta , Martin Lesley-Ann , Isacke Clare M. 
Published: October 2023

Abstract

The combination of endocrine therapy and CDK4/6 inhibitors such as palbociclib is an effective and well-tolerated treatment for estrogen receptor–positive (ER+) breast cancer, yet many patients relapse with therapy-resistant disease. Determining the mechanisms underlying endocrine therapy resistance is limited by the lack of ability to fully recapitulate inter- and intratumor heterogeneity in vitro and of availability of tumor samples from women with disease progression or relapse. In this study, multiple cell line models of resistant disease were used for both two-dimensional (2D)– and three-dimensional (3D)–based inhibitor screening. The screens confirmed the previously reported role of pro-proliferative pathways, such as PI3K–AKT–mTOR, in endocrine therapy resistance and additionally identified the transcription-associated cyclin-dependent kinase CDK9 as a common hit in ER+ cell lines and patient-derived organoids modeling endocrine therapy–resistant disease in both the palbociclib-sensitive and palbociclib-resistant settings. The CDK9 inhibitor, AZD4573, currently in clinical trials for hematologic malignancies, acted synergistically with palbociclib in these ER+in vitro 2D and 3D models. In addition, in two independent endocrine- and palbociclib-resistance patient-derived xenografts, treatment with AZD4573 in combination with palbociclib and fulvestrant resulted in tumor regression. Tumor transcriptional profiling identified a set of transcriptional and cell-cycle regulators differentially downregulated only in combination-treated tumors. Together, these findings identify a clinically tractable combination strategy for overcoming resistance to endocrine therapy and CDK4/6 inhibitors in breast cancer and provide insight into the potential mechanism of drug efficacy in targeting treatment-resistant disease.

Significance:
Targeting transcription-associated CDK9 synergizes with CDK4/6 inhibitor to drive tumor regression in multiple models of endocrine- and palbociclib-resistant ER+ breast cancer, which could address the challenge of overcoming resistance in patients.
Transport Strategy in Patients With Suspected Acute Large Vessel Occlusion Stroke: TRIAGE-STROKE, a Randomized Clinical Trial
Authors: Behrndtz Anne , Blauenfeldt Rolf A. , Johnsen Søren P. , Valentin Jan B. , Gude Martin F. , Al-Jazi Mohammad Ahmad , von Weitzel-Mudersbach Paul , Modrau Boris , Damgaard Dorte , Hougaard Kristina Dupont , Hjort Niels , Diedrichsen Tove , Poulsen Marika , Schmitz Marie Louise , Fisher Marc , Andersen Grethe , Simonsen Claus Z. , Sandahl Birgitte , Jeppesen Lise , Bay Rikke , Eiskær Kristina , Andersen Malene , Lauridsen Janni , Mette Anne , Sottrup-Jensen Anne-Mette , Jensen Nina , Hansen Maiken , Tørring Margret, Jesper , Ochonske Anna , Stilund Morten , Sirakov Georgi , Bekan Goran , Perampalam Mayoran , Maanaki Zeinaab , Falah Masoud , Mortensen Janne , Due Søren , Degn Niels 
Published: October 2023

BACKGROUND:
When patients with acute ischemic stroke present with suspected large vessel occlusion in the catchment area of a primary stroke center (PSC), the benefit of direct transport to a comprehensive stroke center (CSC) has been suggested. Equipoise remains between transport strategies and the best transport strategy is not well established.

METHODS:
We conducted a national investigator-driven, multicenter, randomized, assessor-blinded clinical trial. Patients eligible for intravenous thrombolysis (IVT) who were suspected for large vessel occlusion were randomized 1:1 to admission to the nearest PSC (prioritizing IVT) or direct CSC admission (prioritizing endovascular therapy). The primary outcome was functional improvement at day 90 for all patients with acute ischemic stroke, measured as shift towards a lower score on the modified Rankin Scale score.

RESULTS:

From September 2018 to May 2022, we enrolled 171 patients of whom 104 had acute ischemic stroke. The trial was halted before full recruitment. Baseline characteristics were well balanced. Primary analysis of shift in modified Rankin Scale (ordinal logistic regression) revealed an odds ratio for functional improvement at day 90 of 1.42 (95% CI, 0.72–2.82,
P
=0.31). Onset to groin time for patients with large vessel occlusion was 35 minutes (
P
=0.007) shorter when patients were transported to a CSC first, whereas onset to needle (IVT) was 30 minutes (
P
=0.012) shorter when patients were transported to PSC first. IVT was administered in 67% of patients in the PSC group versus 78% in the CSC group and EVT was performed in 53% versus 63% of the patients, respectively.

CONCLUSIONS:
This trial investigated the benefit of bypassing PSC. We included only IVT-eligible patients presenting <4 hours from onset and with suspected large vessel occlusion. Lack of power prevented the results from showing effect on functional outcome for patients going directly to CSC.

REGISTRATION:

URL:
https://www.clinicaltrials.gov
; Unique identifier: NCT03542188.
Application of a 1H brain MRS benchmark dataset to deep learning for out-of-voxel artifacts
Authors: Gudmundson Aaron T. , Davies-Jenkins Christopher W. , Özdemir İpek , Murali-Manohar Saipavitra , Zöllner Helge J. , Song Yulu , Hupfeld Kathleen E. , Schnitzler Alfons , Oeltzschner Georg , Stark Craig E. L. , Edden Richard A. E. 
Published: October 2023

Abstract
Neural networks are potentially valuable for many of the challenges associated with MRS data. The purpose of this manuscript is to describe the AGNOSTIC dataset, which contains 259,200 synthetic 1H MRS examples for training and testing neural networks. AGNOSTIC was created using 270 basis sets that were simulated across 18 field strengths and 15 echo times. The synthetic examples were produced to resemble in vivo brain data with combinations of metabolite, macromolecule, residual water signals, and noise. To demonstrate the utility, we apply AGNOSTIC to train two Convolutional Neural Networks (CNNs) to address out-of-voxel (OOV) echoes. A Detection Network was trained to identify the point-wise presence of OOV echoes, providing proof of concept for real-time detection. A Prediction Network was trained to reconstruct OOV echoes, allowing subtraction during post-processing. Complex OOV signals were mixed into 85% of synthetic examples to train two separate CNNs for the detection and prediction of OOV signals. AGNOSTIC is available through Dryad, and all Python 3 code is available through GitHub. The Detection network was shown to perform well, identifying 95% of OOV echoes. Traditional modeling of these detected OOV signals was evaluated and may prove to be an effective method during linear-combination modeling. The Prediction Network greatly reduces OOV echoes within FIDs and achieved a median log10 normed-MSE of—1.79, an improvement of almost two orders of magnitude.
Nigerian Maritime
Authors: Obiakor Maximilian Obinna , Obiakor Chukwuebuka Hamilton , Ezendu Ejike , Ezeonyejiaku Chigozie Damian 
Published: October 2023

Abstract
Maritime industry clustering has in recent years gained attention as a tool for strategic global and regional economic competitiveness policies, owing to their co-location synergies and agglomeration economies. The Nigerian maritime sector is known to have a large industry, which comprises shipping and logistics firms, shipyards, ship consultants and a suite of other firms, institutions and associations with maritime functions. However, nothing is known about the structural characteristics and environmental dynamics of this significant cluster. This article, capitalising on a critical and meta-analytic review of studies and conceptual modelling, explores for the first time the Nigerian maritime industry from a cluster perspective, underpinned by the foundational competitiveness of Nigerian microeconomic performance. It further evaluates broadly the quality of the Nigerian business environment, highlighting the challenges and opportunities for strategic foresight in decision-making. Targeted recommendations predicated on cluster-specific characteristics are provided to improve cluster competitiveness.
Group Minds in Ancient Narrative
Authors: Chrysanthou Chrysanthos S. 
Published: October 2023

Abstract
The present article adopts a cognitive approach to examine the representation of group minds in ancient narrative and show the specific purposes to which they are put. Herodian’s History of the Roman Empire, a work that illustrates the social and collective dimension of mental functioning, is chosen as a case study. After a brief exposition of the state of research on collective minds in narratology and literature, the present study first discusses the formation of group minds and their stability or mutability over the course of Herodian’s narrative. The next section explores the internal dynamics of group minds, focusing especially on instances of splitting which helpfully illuminate the problematic nature of the Roman principate after Marcus’ death. The final section draws on contemporary theories of philosophy of mind and the cognitive sciences and examines the way and extent that Herodian’s groups can be considered as ‘intentional agents’. In this regard, it is proposed that Herodian represents an approach to group agency that prefigures modern theory of ‘interpretivism’. Overall, the article suggests a novel way of studying ancient narrative, one that reconciles narratological and cognitive analysis with historical and political considerations by revealing the constitutive role of group minds in various aspects of the ancient social world.
Dawānī (d. 1502) and Dashtakī (d. 1498) on Primary (awwalī) and Familiar (mutaʿāraf) Predication
Authors: El-Rouayheb Khaled 
Published: October 2023

Abstract
The present article explores the motivations that led Jalāl al-Dīn al-Dawānī (d. 1502) to draw the distinction between what he called “primary predication” (ḥaml awwalī) and “familiar predication” (ḥaml mutaʿāraf or ḥaml shāʾiʿ). These motivations include allowing for the predication of particulars, such as “This is Zayd” and accounting for apparently true self-negations, such as “The [concept] particular is not a particular.” The article also explores some criticisms of this distinction by Dawānī’s contemporary and rival Ṣadr al-Dīn al-Dashtakī (d. 1498). Despite these criticisms, Dawānī’s distinction was adopted, adapted, and emphasized by the Safavid scholar Mīr Dāmād (d. 1631). Mīr Dāmād’s influence, in turn, accounts for the prominence given to the distinction in later centuries among Iranian and Indo-Muslim logicians.
Afghanistan
Authors: Rahimi Haroun 
Published: October 2023

Abstract
The Taliban returned to power in Afghanistan in August of 2021 and revived the Islamic Emirate of Afghanistan (IEA) in place of the internationally supported Islamic Republic of Afghanistan (2004–2021). Within one year of its rule, the IEA has overhauled the country’s legal system in areas of administration of justice, human rights, family law, civil law, criminal law, and commercial law. However, the country’s legal system under the Taliban remains chaotic, disuniform, and overwhelmed.
Oman: Recent Developments in the Protection of the Rights of Migrant Workers and of Women
Authors: Kanchana Radhika 
Published: October 2023

Abstract
This survey is a review listing some key legislative and executive measures of the government of Oman in the year 2021–2022, which have relevance to mainly the rights of the migrant workers. Further, and in less detail, this survey also refers to some of the developments pertinent to the rights of women living in Oman. However, more generally these rights are less relevant to women who are not Omani nationals. Oman is a member country of the Gulf Cooperation Council (GCC). The GCC comprises six states in the Arab-Gulf region: Oman, Bahrain, the United Arab Emirates (UAE), Kuwait, Qatar and Saudi Arabia. These oil-producing states have a significant proportion of foreign workforce in the population. Foreign workers work mostly in the private sector and are also residents in the host countries. At 46.5 per cent, Oman has a relatively lower proportion of migrants in its population among the GCC members (UN DESA, 2020). Therefore, a broader spectrum of governments’ measures relating to the issues like labour, entry and residence, and ownership of property or business touch the lives of the foreign/migrant workers or expatriates in the Gulf country. Governments’ initiatives targeting domestic workers are relevant also for women because they comprise the majority in this group. The survey notes that most of the governmental activity in Oman in the past year largely concern new laws or amendments of the existing legislation and regulations linked to labour and residency matters. Some of the more relevant ones that the survey has selected here confirms this. It also marks the period post the pandemic, which had posed considerable economic challenge for the government. Hence, as also some neighbouring Gulf countries, Oman has shown a balance of measures. On the one hand, to revive its economic dynamism and competitiveness by facilitating more ease and benefits to attract and retain foreign labour and investment in the country. On the other hand, with measures such as increased nationalization effort and support expressly favouring the national workforce to boost their more active participation in the labour market. The new labour law declared by the Omani government and its signing of the Maritime Labour Convention are a few notable highlights. The survey has essentially drawn on the government’s documents and announcements as available in English or translated text, in addition to information in the press and other relevant sources.