bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stress combinations and their interactions in plants database: a one‐stop resource on combined stress responses in plants
Authors: Priya Piyush , Patil Mahesh , Pandey Prachi , Singh Anupriya , Babu Vishnu Sudha , Senthil‐Kumar Muthappa 
Published: October 2023

SUMMARYWe have developed a compendium and interactive platform, named Stress Combinations and their Interactions in Plants Database (SCIPDb; http://www.nipgr.ac.in/scipdb.php), which offers information on morpho‐physio‐biochemical (phenome) and molecular (transcriptome and metabolome) responses of plants to different stress combinations. SCIPDb is a plant stress informatics hub for data mining on phenome, transcriptome, trait‐gene ontology, and data‐driven research for advancing mechanistic understanding of combined stress biology. We analyzed global phenome data from 939 studies to delineate the effects of various stress combinations on yield in major crops and found that yield was substantially affected under abiotic–abiotic stresses. Transcriptome datasets from 36 studies hosted in SCIPDb identified novel genes, whose roles have not been earlier established in combined stress. Integretome analysis under combined drought–heat stress pinpointed carbohydrate, amino acid, and energy metabolism pathways as the crucial metabolic, proteomic, and transcriptional components in plant tolerance to combined stress. These examples illustrate the application of SCIPDb in identifying novel genes and pathways involved in combined stress tolerance. Further, we showed the application of this database in identifying novel candidate genes and pathways for combined drought and pathogen stress tolerance. To our knowledge, SCIPDb is the only publicly available platform offering combined stress‐specific omics big data visualization tools, such as an interactive scrollbar, stress matrix, radial tree, global distribution map, meta‐phenome analysis, search, BLAST, transcript expression pattern table, Manhattan plot, and co‐expression network. These tools facilitate a better understanding of the mechanisms underlying plant responses to combined stresses.
Land, property, and territory: Mutual embeddedness as understood by thetongbianphilosophy
Authors: Tang Wing‐Shing , Gupte Rupali , Shetty Prasad , Benjamin Solomon 
Published: October 2023

AbstractThe dominant tone of the literature on land's territorial politics misses conceptual complexities by neglecting historical constructions of land practices. An alternative understanding intertwines social and political elements emphasised in the non‐dualistic, beyond dialectics,tongbianphilosophy. This views everything as consisting of two mutually embedded, opposite poles—different yet without alienation; set in a ceaseless interaction as processes of becoming, continuity and change. The concept of focus–field relationship via a spatial story deciphers complexities between viewing land as territory (LaT) and land as property (LaP). Mobilising this formulation in sites of intensive real estate change (Hong Kong's Sham Shui Po and Mumbai's Malad) reveals subtleties of historical antecedents shaping contemporary forces. Here, complex institutional entanglements reveal both diachronic and synchronic interactions wherein the dynamics of control, shifts in power, growth or decline in time and space co‐join LaT and LaP. Such political complexities question views of land's transformation being contingent on archaic ideas of the Westphalian state and uni‐polar framings of capital moving from the North to the South. Thetongbianphilosophy allows the exploring of ideas of difference without alienation, embracing epistemic and ontological equivalence in theory and fieldwork, and between the North and South—themes seldom taken up in the geographical literature. Finally, the paper proposes a study of land dynamics using the concept of land occupancy via the spatial story approach.
Practising future‐making: Anticipation and translocal politics of Tesla's Gigafactory in Shanghai as assemblage
Authors: Han Xiao , Liu Weidong , Jiang Tianhe 
Published: October 2023

AbstractHuman geographers are increasingly concerned with how ‘futures’ are imagined and rendered governable, yet mostly their methods lack the sensitivity to explore the functioning of complex relations between heterogeneous actors across places. The world's electric vehicle (EV) sector is booming, presaging a widely expected decarbonised future, associated with a restructuring of the automobile industry as anticipated by proactive players. This paper interrogates the spatiality and politics of the EV future‐making through disentangling the translocal practices involved in realising Tesla's Gigafactory in Shanghai (TGS) as assemblage. Informed by interviews with industrial insiders and opensource information in Chinese and English, the article finds that, first, TGS's imagined future embodies a multiplicity of interdependent but divergent expectations, the coherence of which underlies the formation and operation of the TGS assemblage by virtue of the concerted actions of its member‐actors. Second, such coherence is conditional as designed by TGS's central planners—namely, Tesla and Chinese government agencies at central and local levels—for their differentiated but overlapping interests. The TGS's imagined future is rendered actionable, enrolling other agents at certain moments, through anticipatory practices of regulatory changes, strategic arrangements interweaving land and financing, firm acquisition and intra‐firm reorganisation linking up places in and outside China, as well as the selection of key suppliers and technological use of critical raw materials. Concluding after a sketch on the TGS's ‘possible futures’ and broader implications, the paper contributes an assemblage‐informed approach to disentangle futuremaking practices and generates timely insights into the ‘future‐oriented’ restructuring of the automobile industry.
Ecological environment value assessment and ecological civilization in the Changjiang River basin
Authors: Ma Zhaoli , Guo Xia 
Published: October 2023

AbstractWith the rapid growth of urbanization and industrialization, the strain on resources and the environment has intensified, resulting in challenges such as soil erosion and biodiversity loss. To address these issues, the development of a circular economy and eco‐cities has become crucial. This article proposes an ecosystem assessment model based on the backpropagation neural network (BPNN) that incorporates environmental carrying capacity and energy regeneration capacity. The model aims to evaluate the ecological service value of wetlands in the Changjiang River basin. The results demonstrate that the proposed model outperforms other comparison methods, exhibiting a high level of accuracy. Furthermore, the simulation outcomes indicate that enhancing eco‐efficiency can enhance the environmental carrying capacity and energy regeneration capacity of the ecosystem, ultimately leading to an overall improvement in ecosystem value.
On Rees algebras of 2‐determinantal ideals
Authors: Ramkumar Ritvik , Sammartano Alessio 
Published: October 2023

AbstractLet be the ideal of minors of a matrix of linear forms with the expected codimension. In this paper, we prove that the Rees algebra of and its special fiber ring are Cohen–Macaulay and Koszul; in particular, they are quadratic algebras. The main novelty in our approach is the analysis of a stratification of the Hilbert scheme of determinantal ideals. We study degenerations of Rees algebras along this stratification, and combine it with certain squarefree Gröbner degenerations.
β-(1→3)-D-glucan- and mannan-guided early termination of antifungal therapy in ICU patients: a randomized controlled study
Authors: Erb Timothy , Mihai Sidonia , Strauß Richard , Herbst Larissa , Castellanos Ixchel , Diesch Katharina , Cipa Franziska , Bihlmaier Karl , Lang Anne-Katharina , Ganslmayer Marion , Willam Carsten , Bremer Frank , Fürst Julia , Beyer Christian , Bogdan Christian , Rath Anca , Held Jürgen 
Published: October 2023

ABSTRACT

Candida
spp. are frequently encountered in specimens from ICUs. However, most of these detections represent colonization. Nevertheless, clinical practice shows that a considerable proportion of these patients will receive antifungal therapy (AT). β-(1→3)-D-glucan (BDG) and mannan are fungal biomarkers with high negative predictive values. We aimed to examine whether biomarker-guided discontinuation of AT can reduce the antifungal consumption. Therefore, we conducted a prospective, randomized intervention study between 1 April 2019 and 31 March 2020. All adult ICU patients with a newly started systemic AT but without fungal infection were eligible for inclusion. Enrolled patients were randomized into an intervention and a control group. In both groups, serum BDG and mannan were determined on days 1 and 2 of AT. If all measurements were negative, AT was discontinued in the intervention group. The primary endpoint was antifungal use. The study was terminated after 12 months. Until this time-point, 41 patients had been included. In the intervention group (
n
= 19), AT was stopped in only two patients because all others showed either positive BDG and/or mannan levels. One of these two patients developed candidemia and AT had to be restarted. There was no significant difference in the primary and secondary endpoints. In summary, the strategy of using two negative BDG and mannan levels to stop AT failed to reduce antifungal consumption in our cohort. Indeed, there will inevitably be patients with invasive candidiasis in whom necessary AT is discontinued. The optimal patient population, biomarker set, and termination criteria are critical to the success of biomarker-based termination strategies.
Two different types of tandem sequences mediate the overexpression of
TinCYP51B
in azole-resistant
Trichophyton indotineae
Authors: Yamada Tsuyoshi , Maeda Mari , Nagai Hiroaki , Salamin Karine , Chang Yun-Tsan , Guenova Emmanuella , Feuermann Marc , Monod Michel 
Published: October 2023

ABSTRACT

Trichophyton indotineae
is an emerging dermatophyte that causes severe tinea corporis and tinea cruris. Numerous cases of terbinafine- and azole-recalcitrant
T. indotineae
-related dermatophytosis have been observed in India over the past decade, and cases are now being recorded worldwide. Whole genome sequencing of three azole-resistant strains revealed a variable number of repeats of a 2,404 base pair (bp) sequence encoding
TinCYP51B
in tandem specifically at the
CYP51B
locus position. However, many other resistant strains (itraconazole MIC ≥0.25 µg/mL; voriconazole MIC ≥0.25 µg/mL) did not contain such duplications. Whole-genome sequencing of three of these strains revealed a variable number of 7,374 bp tandem repeat blocks harboring
TinCYP51B
. Consequently, two types of
T. indotineae
azole-resistant strains were found to host
TinCYP51B
in tandem sequences (type I with 2,404 bp
TinCYP51B
blocks and type II with 7,374 bp
TinCYP51B
blocks). Using the CRISPR/Cas9 genome-editing tool, the copy number of
TinCYP51B
within the genome of types I and II strains was brought back to a single copy. The azole susceptibility of these modified strains was similar to that of strains without
TinCYP51B
duplication, showing that azole resistance in
T. indotineae
strains is mediated by one of two types of
TinCYP51B
amplification. Type II strains were prevalent among 32 resistant strains analyzed using a rapid and reliable PCR test.
Transcriptional control of carbohydrate catabolism by the CcpA protein in the ruminal bacterium
Streptococcus bovis
Authors: Zhao Xiujuan , Zhang Ying , He Banglin , Han Yu , Shen Ben , Zang Yu , Wang Hongrong 
Published: October 2023

ABSTRACT

As a potent, pleiotropic regulatory protein in Gram-positive bacteria, catabolite control protein A (CcpA) mediates the transcriptional control of carbohydrate metabolism in
Streptococcus bovis
, a lactate-producing bacterium that plays an essential role in rumen acidosis in dairy cows. Although the rumen uptake of carbohydrates is multi-substrate, the focus of
S. bovis
research thus far has been on the glucose. With the aid of gene deletion, whole-genome sequencing, and transcriptomics, we have unraveled the role of CcpA in carbohydrate metabolism, on the one hand, and acidosis, on the other, and we show that the
S. bovis
strain S1 encodes “Carbohydrate-Active Enzymes” and that
ccpA
deletion slows the organism’s growth rate and modulates the organic acid fermentation pathways toward lower lactate, higher formate, and acetate in the maltose and cellobiose. Furthermore, this study revealed the different regulatory functions of the CcpA protein in rumen metabolism and acidosis.

IMPORTANCE

This study is important as it illustrates the varying regulatory role of the
Streptococcus bovis
catabolite control protein A protein in carbohydrate metabolism and the onset of acidosis in dairy cattle.
Direct prediction of carbapenem resistance in
Pseudomonas aeruginosa
by whole genome sequencing and metagenomic sequencing
Authors: Liu Bing , Gao Jianpeng , Liu Xue Fei , Rao Guanhua , Luo Jiajie , Han Peng , Hu Weiting , Zhang Ze , Zhao Qianqian , Han Lizhong , Jiang Zhi , Zhou Min 
Published: October 2023

ABSTRACT

Carbapenem resistance is a major concern in the management of antibiotic-resistant
Pseudomonas aeruginosa
infections. The direct prediction of carbapenem-resistant phenotype from genotype in
P. aeruginosa
isolates and clinical samples would promote timely antibiotic therapy. The complex carbapenem resistance mechanism and the high prevalence of variant-driven carbapenem resistance in
P. aeruginosa
make it challenging to predict the carbapenem-resistant phenotype through the genotype. In this study, using whole genome sequencing (WGS) data of 1,622
P
.
aeruginosa
isolates followed by machine learning, we screened 16 and 31 key gene features associated with imipenem (IPM) and meropenem (MEM) resistance in
P. aeruginosa
, including oprD(HIGH), and constructed the resistance prediction models. The areas under the curves of the IPM and MEM resistance prediction models were 0.906 and 0.925, respectively. For the direct prediction of carbapenem resistance in
P. aeruginosa
from clinical samples by the key gene features selected and prediction models constructed, 72
P
.
aeruginosa
-positive sputum samples were collected and sequenced by metagenomic sequencing (MGS) based on next-generation sequencing (NGS) or Oxford Nanopore Technology (ONT). The prediction applicability of MGS based on NGS outperformed that of MGS based on ONT. In 72
P
.
aeruginosa
-positive sputum samples, 65.0% (26/40) of IPM-insensitive and 63.2% (24/38) of MEM-insensitive
P. aeruginosa
were directly predicted by NGS-based MGS with positive predictive values of 0.897 and 0.889, respectively. By the direct detection of the key gene features associated with carbapenem resistance of
P. aeruginosa
, the carbapenem resistance of
P. aeruginosa
could be directly predicted from cultured isolates by WGS or from clinical samples by NGS-based MGS, which could assist the timely treatment and surveillance of carbapenem-resistant
P. aeruginosa
.
Characterization of a DsbA family protein reveals its crucial role in oxidative stress tolerance of
Listeria monocytogenes
Authors: Xia Jing , Luo Yaru , Chen Mianmian , Liu Yuqing , Wang Zhe , Deng Simin , Xu Jiali , Han Yue , Sun Jing , Jiang Lingli , Song Houhui , Cheng Changyong 
Published: October 2023

ABSTRACT

Listeria monocytogenes
is a facultative, intracellular foodborne pathogen widely distributed in nature and is responsible for severe invasive infection in humans and animals with a mortality rate as high as 30%.
L. monocytogene
s can adapt to various oxidative stresses since it has evolved oxidative modification and regulation mechanisms. The disulfide bond formation protein (Dsb) is required to catalyze the formation of disulfide bonds to promote oxidative folding or modification of proteins involved in bacterial virulence and survival. However, the functions of Lmo1059, a DsbA family protein of
L. monocytogenes
, remain unknown. In this study, we found that Lmo1059 could efficiently catalyze oxidized glutathione (GSSG) reduction, with the residues Cys36 and Cys39 as the key amino acids for its catalytic activity. Moreover, Lmo1059 plays a critical role in oxidative stress tolerance for
L. monocytogenes
, and Cys36 is the crucial amino acid to participate in this process. When Lmo1059 was deleted, the adhesion and invasion of
L. monocytogenes
were reduced while the cell-to-cell spread was increased, suggesting an intricate role of Lmo1059 during bacterial infection. Altogether, these data indicate that the DsbA family protein Lmo1059 is an important participant in the antioxidant stress system and works in concert with other proteins to help protect
L. monocytogenes
from oxidative stress and establish intracellular infection.

IMPORTANCE

The adaption and tolerance to various environmental stresses are the fundamental factors for the widespread existence of
Listeria monocytogenes
. Anti-oxidative stress is the critical mechanism for the survival and pathogenesis of
L. monocytogenes
. The thioredoxin (Trx) and glutaredoxin (Grx) systems are known to contribute to the anti-oxidative stress of
L. monocytogenes
, but whether the Dsb system has similar roles remains unknown. This study demonstrated that the DsbA family protein Lmo1059 of
L. monocytogenes
participates in bacterial oxidative stress tolerance, with Cys36 as the key amino acid of its catalytic activity and anti-oxidative stress ability. It is worth noting that Lmo1059 was involved in the invading and cell-to-cell spread of
L. monocytogenes
. This study lays a foundation for further understanding the specific mechanisms of oxidative cysteine repair and antioxidant stress regulation of
L. monocytogenes
, which contributes to an in-depth understanding of the environmental adaptation mechanisms for foodborne bacterial pathogens.
Potential for England’s statutory school entry assessment to identify special educational needs and reveal structural inequalities: a population-based study
Authors: Wood Megan L , Gunning Lydia , Relins Sam , Sohal Kuldeep , Wright John , Mon-Williams Mark , Atkinson Amy L 
Published: October 2023

ObjectiveTo investigate at a population level whether England’s universal assessment of ‘school readiness’ is associated with later identification of special educational needs (SEN). Also, whether ethnic differences exist in SEN identification (white British versus ethnic minority) and whether this varies as a function of school readiness.MethodAnalysis included 53 229 individuals aged 5–12 years from the Connected Bradford Database (2012/2013–2019/2020). Logistic regression analyses examined: (1) whether reaching a ‘good level of development’ on England’s ‘school readiness’ assessment was associated with later SEN identification; and (2) whether interactions exist between school readiness and ethnicity.Results32 515 of 53 229 children reached a good level of development, of which 3036 (9.3%) were identified as having SEN. In contrast, 10 171 of 20 714 (49.1%) of children who did not reach a good level of development were later identified as having SEN. Children not reaching a good level of development had increased odds of being later identified as having SEN after controlling for covariates (OR: 8.50, 95% CI: 8.10 to 8.91). In children who did not reach a good level of development, white British children had higher odds of being identified as having SEN compared with ethnic minority peers (OR: 1.22, 95% CI: 1.11 to 1.34). No ethnic differences of having SEN were observed in children reaching a good level of development (OR: 1.04, 95% CI: 0.93 to 1.16).ConclusionsSchool readiness assessments are associated with later SEN identification. Structural inequalities may exist in SEN identification in children not entering formal education ‘school ready’. Such assessments could facilitate earlier identification of SEN and reduce structural inequalities in its identification.
Prolonged use of closed-loop inspired oxygen support in preterm infants: a randomised controlled trial
Authors: Schouten Tim M R , Abu-Hanna Ameen , van Kaam Anton H , van den Heuvel Maria E N , Bachman Thomas E , van Leuteren Ruud W , Hutten G Jeroen , Onland Wes 
Published: October 2023

ObjectiveThis randomised study in preterm infants on non-invasive respiratory support investigated the effectiveness of automated oxygen control (A-FiO2) in keeping the oxygen saturation (SpO2) within a target range (TR) during a 28-day period compared with manual titration (M-FiO2).DesignA single-centre randomised control trial.SettingA level III neonatal intensive care unit.PatientsPreterm infants (<28 weeks’ gestation) on non-invasive respiratory support.InterventionsA-FiO2versus M-FiO2control.MethodsMain outcomes were the proportion of time spent and median area of episodes in the TR, hyperoxaemia, hypoxaemia and the trend over 28 days using a linear random intercept model.Results23 preterm infants (median gestation 25.7 weeks; birth weight 820 g) were randomised. Compared with M-FiO2, the time spent within TR was higher in the A-FiO2group (68.7% vs 48.0%, p<0.001). Infants in the A-FiO2group spent less time in hyperoxaemia (13.8% vs 37.7%, p<0.001), but no difference was found in hypoxaemia. The time-based analyses showed that the A-FiO2efficacy may differ over time, especially for hypoxaemia. Compared with the M-FiO2group, the A-FiO2group had a larger intercept but with an inversed slope for the daily median area below the TR (intercept 70.1 vs 36.3; estimate/day −0.70 vs 0.69, p<0.001).ConclusionA-FiO2control was superior to manual control in keeping preterm infants on non-invasive respiratory support in a prespecified TR over a period of 28 days. This improvement may come at the expense of increased time below the TR in the first days after initiating A-FiO2control.Trial registration numberNTR6731.