bluuebunny/crossref_metadata_2025_split huggingface dataset:
Soybean-mediated suppression of BjaI/BjaR
1
quorum sensing in
Bradyrhizobium diazoefficiens
impacts symbiotic nitrogen fixation
Authors: Han Fang , Li Huiquan , Lyu Ermeng , Zhang Qianqian , Gai Haoyu , Xu Yunfang , Bai Xuemei , He Xueqian , Khan Abdul Qadir , Li Xiaolin , Xie Fang , Li Fengmin , Fang Xiangwen , Wei Min 
Published: January 2024

ABSTRACT

The acyl-homoserine lactones (AHLs)-mediated LuxI/LuxR quorum sensing (QS) system orchestrates diverse bacterial behaviors in response to changes in population density. The role of the BjaI/BjaR
1
QS system in
Bradyrhizobium diazoefficiens
USDA 110, which shares homology with LuxI/LuxR, remains elusive during symbiotic interaction with soybean. Here this genetic system in wild-type (WT) bacteria residing inside nodules exhibited significantly reduced activity compared to free-living cells, potentially attributed to soybean-mediated suppression. The deletion mutant strain ΔbjaR
1
showed significantly enhanced nodulation induction and nitrogen fixation ability. Nevertheless, its ultimate symbiotic outcome (plant dry weight) in soybeans was compromised. Furthermore, comparative analysis of the transcriptome, proteome, and promoter activity revealed that the inactivation of BjaR
1
systematically activated and inhibited genomic modules associated with nodulation and nitrogen metabolism. The former appeared to be linked to a significant decrease in the expression of NodD2, a key cell-density-dependent repressor of nodulation genes, while the latter conferred bacterial growth and nitrogen fixation insensitivity to environmental nitrogen. In addition, BjaR
1
exerted a positive influence on the transcription of multiple genes involved in a so-called central intermediate metabolism within the nodule. In conclusion, our findings highlight the crucial role of the BjaI/BjaR
1
QS circuit in positively regulating bacterial nitrogen metabolism and emphasize the significance of the soybean-mediated suppression of this genetic system for promoting efficient symbiotic nitrogen fixation by
B. diazoefficiens
.

IMPORTANCE
The present study demonstrates, for the first time, that the BjaI/BjaR1 QS system of Bradyrhizobium diazoefficiens has a significant impact on its nodulation and nitrogen fixation capability in soybean by positively regulating NodD2 expression and bacterial nitrogen metabolism. Moreover, it provides novel insights into the importance of suppressing the activity of this QS circuit by the soybean host plant in establishing an efficient mutual relationship between the two symbiotic partners. This research expands our understanding of legumes’ role in modulating symbiotic nitrogen fixation through rhizobial QS-mediated metabolic functioning, thereby deepening our comprehension of symbiotic coevolution theory. In addition, these findings may hold great promise for developing quorum quenching technology in agriculture.
Response of Soil Microorganisms and Phenolic to Pseudostelariae heterophylla Cultivation in Different Soil Types
Authors: Liu Yingying , Wu Dan , Kan Yongjun , Zhao Li , Jiang Chang , Pang Wensheng , Hu Juan , Zhou Meilan 
Published: January 2024

Abstract
Pseudostellaria heterophylla of the Caryophyllaceae family is an important medicinal herb in traditional Chinese medicine, but it encounters continuous cropping obstacle during cultivation. This study aimed to study the differences in the response of Pseudostellaria heterophylla cultivation to soil microorganisms and phenolic substances in different types of soil (Loamy soil and Clayey soil). The analysis of soil metabolites using HPLC-ESI-Q/TOF-MS and HPLC-DAD techniques revealed that the content of various phenolic components in the rhizosphere soil increased significantly after Pseudostellaria heterophylla cultivation. Pseudostellaria heterophylla cultivation in yellow soil could increase the abundance of Proteobacteria, Ascomycota, and Thermoplasmatota, while in brown soil, the abundance of Ascomycota significantly decreased. In addition, Pseudostellaria heterophylla cultivation could increase the α-diversity of bacteria and fungi in yellow soil, while reducing the α-diversity of archaea, and the impact on diversity in brown soil was relatively small. Correlation analysis showed that phenolic compounds were more likely to regulate the genera Bradyrhizobium, Calcarisporiella, Boothiomyces and Methanocella. Pseudostellaria heterophylla may regulate rhizosphere microbial diversity and community structure by secreting phenolic. However, in different types of soil environments, the response mechanism of soil microorganisms to Pseudostellaria heterophylla planting might vary. Our study provides new insights that the variability in the response of different soil types to Pseudostelariae heterophylla cultivation should be taken into account when developing strategies for reducing continuous cropping obstacles in medicinal plants.
One-year effectiveness of high-load compared with low-load strengthening exercise on self-reported function in patients with hypermobile shoulders: a secondary analysis from a randomised controlled trial
Authors: Liaghat Behnam , Juul-Kristensen Birgit , Faber Daniel A , Christensen Emil O , Søgaard Karen , Skou Søren T , Søndergaard Jens , Juhl Carsten B 
Published: January 2024

ObjectivesTo investigate the long-term effectiveness of high-load versus low-load strengthening exercise on self-reported function in patients with hypermobility spectrum disorder (HSD) and shoulder symptoms.MethodsA secondary analysis of a superiority, parallel-group, randomised trial (balanced block randomisation 1:1, electronic concealment) including adult patients (n=100) from primary care with HSD and shoulder pain and/or instability ≥3 months. Patients received 16 weeks of shoulder exercises (three sessions/week): HEAVY (n=50, full-range, high-load, supervised twice/week) or LIGHT (n=50, neutral/mid-range, low-load, supervised three times in total). The 1-year between-group difference in change in self-reported function was measured using the Western Ontario Shoulder Instability Index (WOSI, scale 0–2100, 0=best). Secondary outcomes were self-reported measures including changes in shoulder-related symptoms, function, emotions and lifestyle, quality of life, patient-perceived effect, treatment utility and adverse events. A blinded analyst conducted the analyses using linear mixed model repeated measurements analysis.ResultsOne-year data were available in 86 out of 100 participants (79% women, mean age 37.8 years) (LIGHT 84%, HEAVY 88%). The mean WOSI score between-group difference favoured HEAVY (−92.9, 95% CI −257.4 to 71.5, p=0.268) but was not statistically significant. The secondary outcomes were mostly inconclusive, but patients in HEAVY had larger improvement in the WOSI emotions subdomain (−36.3; 95% CI −65.4 to −7.3, p=0.014). Patient-perceived effect favoured HEAVY anchored in WOSI-emotions (55% vs 31%, p=0.027) and WOSI-lifestyle (50% vs 29%, p=0.042).ConclusionHigh-load shoulder strengthening exercise was not superior to low-load strengthening exercise in improving self-reported function at 1 year. High-load strengthening exercise may be more effective in improving patient emotions about shoulder pain and function, but more robust data are needed to support these findings.Trial registration numberNCT03869307.
Short-duration selective decontamination of the digestive tract infection control does not contribute to increased antimicrobial resistance burden in a pilot cluster randomised trial (the ARCTIC Study)
Authors: Kean Iain Robert Louis , Clark John A , Zhang Zhenguang , Daubney Esther , White Deborah , Ferrando-Vivas Paloma , Milla Gema , Cuthbertson Brian , Pappachan John , Klein Nigel , Mouncey Paul , Rowan Kathy , Myburgh John , Gouliouris Theodore , Baker Stephen , Parkhill Julian , Pathan Nazima , ARCTIC research team  
Published: January 2024

ObjectiveSelective decontamination of the digestive tract (SDD) is a well-studied but hotly contested medical intervention of enhanced infection control. Here, we aim to characterise the changes to the microbiome and antimicrobial resistance (AMR) gene profiles in critically ill children treated with SDD-enhanced infection control compared with conventional infection control.DesignWe conducted shotgun metagenomic microbiome and resistome analysis on serial oropharyngeal and faecal samples collected from critically ill, mechanically ventilated patients in a pilot multicentre cluster randomised trial of SDD. The microbiome and AMR profiles were compared for longitudinal and intergroup changes. Of consented patients, faecal microbiome baseline samples were obtained in 89 critically ill children. Additionally, samples collected during and after critical illness were collected in 17 children treated with SDD-enhanced infection control and 19 children who received standard care.ResultsSDD affected the alpha and beta diversity of critically ill children to a greater degree than standard care. At cessation of treatment, the microbiome of SDD patients was dominated by Actinomycetota, specificallyBifidobacterium,at the end of mechanical ventilation. Altered gut microbiota was evident in a subset of SDD-treated children who returned late longitudinal samples compared with children receiving standard care. Clinically relevant AMR gene burden was unaffected by the administration of SDD-enhanced infection control compared with standard care. SDD did not affect the composition of the oral microbiome compared with standard treatment.ConclusionShort interventions of SDD caused a shift in the microbiome but not of the AMR gene pool in critically ill children at the end mechanical ventilation, compared with standard antimicrobial therapy.
Seroconversion in syphilis screening without positive confirmatory tests points at early infection
Authors: Nieuwenburg Silvia Achia , Jongen Vita Willemijn , Schim van der Loeff Maarten , de Vries Henry , van Dam Alje 
Published: January 2024

IntroductionThe chemiluminescence immunoassay (CLIA) is a widely used screening test for syphilis. A CLIA seroconversion in the absence of a positive line immunoassay (LIA) or rapid plasma reagin (RPR) could indicate either an early incubating syphilis or a false positive result. We aimed to evaluate the diagnostic value of such seroconversions.MethodsWe retrospectively analysed data of clients visiting the Centre for Sexual Health Amsterdam between July 2013 and August 2021 with a positive CLIA and a negative RPR and negative or indeterminate LIA (at time To), and a preceding visit (T−1) with a negative CLIA <6 months of To(‘unconfirmed CLIA seroconversion’). If available, data of follow-up visits (T1) <2 months of Towere also included. A syphilis diagnosis was confirmed if darkfield microscopy or PCR forTreponema pallidumwas positive at T0or T1, or if RPR and/or LIA were positive at T1.ResultsWe included data of 107 clients with unconfirmed CLIA seroconversion. The value of CLIA seroconversion could not be established in 13 (12.1%) clients. In the remaining 94 clients, the unconfirmed CLIA seroconversion was confirmed as early syphilis in 72 (76.6%) clients and probable syphilis in 6 (6.4%) clients. In 16 (17.0%) clients, the unconfirmed CLIA seroconversion was regarded as a false positive reaction of whom 4 (5.3%) clients had a seroreversion of the CLIA at T1.ConclusionThe majority of unconfirmed CLIA seroconversions represented early syphilis infections. Therefore, additionalT. pallidumPCR, a follow-up consultation or early treatment is recommended.
The jelly report: Forecasting jellyfish using email and social media
Authors: Record Nicholas R. , Tupper Benjamin , Pershing Andrew J. 
Published: January 2024

Abstract
Ecosystem forecasting has potential societal value, for industry, recreation, and human health applications to name a few. The complexities of ecological systems, the expenses associated with monitoring them, and the suddenness at which forecasts become needed often make forecasts impractical. We tested a novel rapid spin-up daily forecasting system for jellyfish — Cyanea capillata (lion’s mane jellyfish), Aurelia aurita (moon jellyfish), and Staurostoma mertensii (whitecross jellyfish) — in the Gulf of Maine. The system blended satellite data with citizen reports collected via email and social media. The forecasting system took 1–3 weeks of tuning before performance plateaued, after which forecast performance was consistently high. Good model performance did not always correspond with good forecast performance, and predictor variables whose contribution improved model performance in some cases had the opposite effect on forecast performance. An adaptive learning mode provided a very modest improvement in performance. In a test of forecast range, forecast performance decreased significantly at a forecast range of around 1 week. Overall, the approach appeared to be a promising avenue toward rapid spin-up of forecasts for undermonitored systems.
Factors that influence measurements of sweet cherry (Prunus avium) flower bud cold hardiness obtained using differential thermal analysis
Authors: Houghton Elizabeth , Hannam Kirsten , Neilsen Denise , Nelson Louise M. 
Published: January 2024

Differential thermal analysis (DTA) is a technique commonly used to evaluate the cold hardiness of plant organs that supercool as a means for cold survival. The aim of this study was to evaluate the effect of different pretest bud storage conditions, cooling rates, and bud excision techniques on dormant sweet cherry flower bud low temperature exotherms (LTEs) measured using DTA. Furthermore, this study compared cold hardiness estimates made using DTA and controlled freezing tests. We determined that buds stored at warmer temperatures (12.5 °C and room temperature) for 2–6 h prior to DTA or transported to the lab in a moist environment underwent biologically relevant changes in their apparent sensitivity to cold, as indicated by LTEs produced at warmer temperatures. The DTA cooling rate also significantly affected LTEs, with faster cooling resulting in the production of LTEs at warmer temperatures. Overall, LTEs were comparable among buds with varying amounts of plant material remaining attached to the bud base. It is important to note that the region directly subtending the primordia was always left intact on the buds being compared. This study demonstrated that overall, DTA and controlled freezing tests resulted in comparable measures of cold hardiness. The findings presented in this study are pertinent to researchers interested in conducting cold hardiness measurements in sweet cherry and highlight that consistency in DTA pretest conditions and bud preparation are required to achieve reliable LTE results that can be compared among studies.
Electromagnetic extension of Buchdahl bound in f(R, T) gravity
Authors: Bhattacharya Soumik , Sharma Ranjan , Maharaj Sunil D. 
Published: January 2024

AbstractWe develop a static charged stellar model in f(R, T) gravity where the modification is assumed to be linear in T which is the trace of the energy momentum tensor. The exterior spacetime of the charged object is described by the Reissner–Nordström metric. The interior solution is obtained by invoking the Buchdahl–Vaidya–Tikekar ansatz, for the metric potential $$g_{rr}$$

g

rr

, which has a clear geometric interpretation. A detailed physical analysis of the model clearly shows distinct physical features of the resulting stellar configuration under such a modification. We find the maximum compactness bound for such a class of compact stars which is a generalization of the Buchdahl bound for a charged sphere described in f(R, T) gravity. Our result shows physical behaviour that is distinct from general relativity.
The effective potential in Fermi gauges beyond the standard model
Authors: Zuk Jonathan , Balázs Csaba , Papaefstathiou Andreas , White Graham 
Published: January 2024

AbstractWe derive the field-dependent masses in Fermi gauges for arbitrary scalar extensions of the Standard Model. These masses can be used to construct the effective potential for various models of new physics. We release a flexible notebook () which performs these calculations and renders large-scale phenomenological studies of various models possible. Motivated by the debate on the importance of gauge dependence, we show that, even in relatively simple models, there exist points where the global minimum is discontinuous in the gauge parameter. Such points require some care in discovering, indicating that a gauge-dependent treatment might still give reasonable results when examining the global features of a model.
Black hole surrounded by the pseudo-isothermal dark matter halo
Authors: Yang Yi , Liu Dong , Övgün Ali , Lambiase Gaetano , Long Zheng-Wen 
Published: January 2024

AbstractIn this paper, we obtain a new spherically symmetric black hole surrounded by the pseudo-isothermal dark matter halo. Furthermore, to explore the effects of the pseudo-isothermal halo profile on a rotating black hole at the M87 galactic center, we derive a rotating black hole solution encompassed by the pseudo-isothermal halo by using the Newman-Janis method. Our investigation focuses on the impact of the pseudo-isothermal halo on the black hole event horizon, time-like and null orbits, as well as the black hole shadow. We find that as the spin parameter a increases, the interval between the inner event horizon and the outer event horizon of the rotating black hole surrounded by the pseudo-isothermal halo in M87 diminishes. This leads to the formation of an extreme black hole. The presence of dark matter, however, has minimal effect on the event horizon. Moreover, in the M87 as the spin parameter a increases, the black hole shadow deviates increasingly from a standard circle, with larger spin parameters causing more pronounced distortion relative to the standard circle. Surprisingly, we observe that the dark matter density has very little influence on the shadow of the black hole surrounded by the pseudo-isothermal halo in the M87. This study contributes to a deeper understanding of black hole structures and the role of dark matter in the universe.
Width Helps and Hinders Splitting Flows
Authors: Cáceres Manuel , Cairo Massimo , Grigorjew Andreas , Khan Shahbaz , Mumey Brendan , Rizzi Romeo , Tomescu Alexandru I. , Williams Lucia 
Published: January 2024

Minimum flow decomposition (MFD) is the NP-hard problem of finding a smallest decomposition of a network flow/circulation
X
on a directed graph
G
into weighted source-to-sink paths whose weighted sum equals
X
. We show that, for acyclic graphs, considering the
width
of the graph (the minimum number of paths needed to cover all of its edges) yields advances in our understanding of its approximability. For the version of the problem that uses only non-negative weights, we identify and characterise a new class of
width-stable
graphs, for which a popular heuristic is a
O
(log
Val
(
X
))-approximation (
Val
(
X
) being the total flow of
X
), and strengthen its worst-case approximation ratio from

\(\Omega (\sqrt {m})\)

to Ω (
m
/log
m
) for sparse graphs, where
m
is the number of edges in the graph. We also study a new problem on graphs with cycles, Minimum Cost Circulation Decomposition (MCCD), and show that it generalises MFD through a simple reduction. For the version allowing also negative weights, we give a (⌈ log ‖ X ‖ ⌉ +1)-approximation (‖
X
‖ being the maximum absolute value of
X
on any edge) using a power-of-two approach, combined with parity fixing arguments and a decomposition of unitary circulations (‖
X
‖ ≤ 1), using a generalised notion of width for this problem. Finally, we disprove a conjecture about the linear independence of minimum (non-negative) flow decompositions posed by Kloster et al. [
2018
], but show that its useful implication (polynomial-time assignments of weights to a given set of paths to decompose a flow) holds for the negative version.
Clinical and Genomic Predictors of Adverse Events in Newly Diagnosed Glioblastoma
Authors: Lim-Fat Mary Jane , Iorgulescu J. Bryan , Rahman Rifaquat , Bhave Varun , Muzikansky Alona , Woodward Eleanor , Whorral Sydney , Allen Marie , Touat Mehdi , Li Xiaomei , Xy Gongwen , Patel Jay , Gerstner Elizabeth R. , Kalpathy-Cramer Jayashree , Youssef Gilbert , Chukwueke Ugonma , McFaline-Figueroa J. Ricardo , Nayak Lakshmi , Lee Eudocia Q. , Reardon David A. , Beroukhim Rameen , Huang Raymond Y. , Bi Wenya Linda , Ligon Keith L. , Wen Patrick Y. 
Published: January 2024

Abstract

Purpose:
Adverse clinical events cause significant morbidity in patients with GBM (GBM). We examined whether genomic alterations were associated with AE (AE) in patients with GBM.

Experimental Design:
We identified adults with histologically confirmed IDH-wild-type GBM with targeted next-generation sequencing (OncoPanel) at Dana Farber Cancer Institute from 2013 to 2019. Seizure at presentation, lymphopenia, thromboembolic events, pseudoprogression, and early progression (within 6 months of diagnosis) were identified as AE. The biologic function of genetic variants was categorized as loss-of-function (LoF), no change in function, or gain-of-function (GoF) using a somatic tumor mutation knowledge base (OncoKB) and consensus protein function predictions. Associations between functional genomic alterations and AE were examined using univariate logistic regressions and multivariable regressions adjusted for additional clinical predictors.

Results:
Our study included 470 patients diagnosed with GBM who met the study criteria. We focused on 105 genes that had sequencing data available for ≥ 90% of the patients and were altered in ≥10% of the cohort. Following false-discovery rate (FDR) correction and multivariable adjustment, the TP53, RB1, IGF1R, and DIS3 LoF alterations were associated with lower odds of seizures, while EGFR, SMARCA4, GNA11, BRD4, and TCF3 GoF and SETD2 LoF alterations were associated with higher odds of seizures. For all other AE of interest, no significant associations were found with genomic alterations following FDR correction.

Conclusions:
Genomic biomarkers based on functional variant analysis of a routine clinical panel may help identify AE in GBM, particularly seizures. Identifying these risk factors could improve the management of patients through better supportive care and consideration of prophylactic therapies.