bluuebunny/crossref_metadata_2025 huggingface dataset:
On the number and size of holes in the growing ball of first-passage percolation
Authors: Damron Michael , Gold Julian , Lam Wai-Kit , Shen Xiao
Published: December 2023

First-passage percolation is a random growth model defined on

Z

d

\mathbb {Z}^d

using i.i.d. nonnegative weights

(

τ
e

)

(\tau _e)

on the edges. Letting

T
(
x
,
y
)

T(x,y)

be the distance between vertices

x
x

and

y
y

induced by the weights, we study the random ball of radius

t
t

centered at the origin,

B

(
t
)
=
{
x
∈

Z

d

:
T
(
0
,
x
)
≤
t
}

\mathbf {B}(t) = \{x \in \mathbb {Z}^d : T(0,x) \leq t\}

. It is known that for all such

τ
e

\tau _e

, the number of vertices (volume) of

B

(
t
)

\mathbf {B}(t)

is at least order

t
d

t^d

, and under mild conditions on

τ
e

\tau _e

, this volume grows like a deterministic constant times

t
d

t^d

. Defining a hole in

B

(
t
)

\mathbf {B}(t)

to be a bounded component of the complement

B

(
t

)
c

\mathbf {B}(t)^c

, we prove that if

τ
e

\tau _e

is not deterministic, then a.s., for all large

t
t

,

B

(
t
)

\mathbf {B}(t)

has at least

c

t

d
−
1

ct^{d-1}

many holes, and the maximal volume of any hole is at least

c
log
⁡
t

c\log t

. Conditionally on the (unproved) uniform curvature assumption, we prove that a.s., for all large

t
t

, the number of holes is at most

(
log
⁡
t

)
C

t

d
−
1

(\log t)^C t^{d-1}

, and for

d
=
2

d=2

, no hole in

B

(
t
)

\mathbf {B}(t)

has volume larger than

(
log
⁡
t

)
C

(\log t)^C

. Without curvature, we show that no hole has volume larger than

C
t
log
⁡
t

Ct \log t

.
Regularity, singularities and ℎ-vector of graded algebras
Authors: Dao Hailong , Ma Linquan , Varbaro Matteo
Published: December 2023

Let

R
R

be a standard graded algebra over a field. We investigate how the singularities of

Spec
⁡
R

\operatorname {Spec} R

or

Proj
⁡
R

\operatorname {Proj} R

affect the

h
h

-vector of

R
R

, which is the coefficient of the numerator of its Hilbert series. The most concrete consequence of our work asserts that if

R
R

satisfies Serre’s condition

(

S
r

)

(S_r)

and has reasonable singularities (Du Bois on the punctured spectrum or

F
F

-pure), then

h
0

h_0

, …,

h
r

≥
0

h_r\geq 0

. Furthermore the multiplicity of

R
R

is at least

h
0

+

h
1

+
⋯
+

h

r
−
1

h_0+h_1+\dots +h_{r-1}

. We also prove that equality in many cases forces

R
R

to be Cohen-Macaulay. The main technical tools are sharp bounds on regularity of certain

Ext
\operatorname {Ext}

modules, which can be viewed as Kodaira-type vanishing statements for Du Bois and

F
F

-pure singularities. Many corollaries are deduced, for instance that nice singularities of small codimension must be Cohen-Macaulay. Our results build on and extend previous work by de Fernex-Ein, Eisenbud-Goto, Huneke-Smith, Murai-Terai and others.
On the discretised 𝐴𝐵𝐶 sum-product problem
Authors: Orponen Tuomas
Published: December 2023

Let

0
>
β
≤
α
>
1

0 > \beta \leq \alpha > 1

and

κ
>
0

\kappa > 0

. I prove that there exists

η
>
0

\eta > 0

such that the following holds for every pair of Borel sets

A
,
B
⊂

R

A,B \subset \mathbb {R}

with

dim

H

⁡
A
=
α

\dim _{\mathrm {H}} A = \alpha

and

dim

H

⁡
B
=
β

\dim _{\mathrm {H}} B = \beta

:
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="dimension Subscript normal upper H Baseline left-brace right-brace colon element-of element-of cR colon less-than-or-equal-to less-than-or-equal-to of dimdimH left-parenthesis right-parenthesis plus plus upper A times times cB plus plus alpha eta less-than-or-equal-to StartFraction alpha minus beta Over 1 minus beta EndFraction plus kappa period">

dim

H

⁡
{
c
∈

R

:

dim

H

⁡
(
A
+
c
B
)
≤
α
+
η
}
≤

α
−
β

1
−
β

+
κ
.

\begin{equation*} \dim _{\mathrm {H}} \{c \in \mathbb {R}: \dim _{\mathrm {H}} (A + cB) \leq \alpha + \eta \} \leq \tfrac {\alpha - \beta }{1 - \beta } + \kappa . \end{equation*}

This extends a result of Bourgain from 2010, which contained the case

α
=
β

\alpha = \beta

. The paper also contains a

δ
\delta

-discretised, and somewhat stronger, version of the estimate above, and new information on the size of long sums of the form

a

1

B
+
…
+

a

n

B

a_{1}B + \ldots + a_{n}B

.
Cooperative polarization of MCAM/CD146 and ERM family proteins in melanoma
Authors: Miller Suzannah G. , Hoh Maria , Ebmeier Christopher C. , Tay Jian Wei , Ahn Natalie G.
Published: December 2023

The WRAMP structure is a protein network associated with tail-end actomyosin contractility, membrane retraction, and directional persistence during cell migration. A marker of WRAMP structures is melanoma cell adhesion molecule (MCAM) which dynamically polarizes to the cell rear. However, factors that mediate MCAM polarization are still unknown. In this study, BioID using MCAM as bait identifies the ERM family proteins, moesin, ezrin, and radixin, as WRAMP structure components. We also present a novel image analysis pipeline, Protein Polarity by Percentile (“3P”), which classifies protein polarization using machine learning and facilitates quantitative analysis. Using 3P, we find that depletion of moesin, and to a lesser extent ezrin, decreases the proportion of cells with polarized MCAM. Furthermore, although copolarized MCAM and ERM proteins show high spatial overlap, 3P identifies subpopulations with ERM proteins closer to the cell periphery. Live-cell imaging confirms that MCAM and ERM protein polarization is tightly coordinated, but ERM proteins enrich at the cell edge first. Finally, deletion of a juxtamembrane segment in MCAM previously shown to promote ERM protein interactions impedes MCAM polarization. Our findings highlight the requirement for ERM proteins in recruitment of MCAM to WRAMP structures and an advanced computational tool to characterize protein polarization.
Diffusion MRI tracks cortical microstructural changes during the early stages of Alzheimer’s disease
Authors: Spotorno Nicola , Strandberg Olof , Stomrud Erik , Janelidze Shorena , Blennow Kaj , Nilsson Markus , van Westen Danielle , Hansson Oskar
Published: December 2023

There is increased interest in developing markers reflecting microstructural changes that could serve as outcome measures in clinical trials. This is especially important after unexpected results in trials evaluating disease-modifying therapies targeting amyloid-β (Aβ), where morphological metrics from MRI showed increased volume loss despite promising clinical treatment effects.

In this study, changes over time in cortical mean diffusivity, derived using diffusion tensor imaging, were investigated in a large cohort (n = 424) of non-demented participants from the Swedish BioFINDER study. Participants were stratified following the Aβ/tau (AT) framework. The results revealed a widespread increase in mean diffusivity over time, including both temporal and parietal cortical regions, in Aβ-positive but still tau-negative individuals. These increases were steeper in Aβ-positive and tau-positive individuals and robust to the inclusion of cortical thickness in the model. A steeper increase in mean diffusivity was also associated with both changes over time in fluid markers reflecting astrocytic activity (i.e. plasma level of glial fibrillary acidic protein and CSF levels of YKL-40) and worsening of cognitive performance (all P < 0.01).

By tracking cortical microstructural changes over time and possibly reflecting variations related to the astrocytic response, cortical mean diffusivity emerges as a promising marker for tracking treatments-induced microstructural changes in clinical trials.
At home adaptive dual target deep brain stimulation in Parkinson’s disease with proportional control
Authors: Schmidt Stephen L , Chowdhury Afsana H , Mitchell Kyle T , Peters Jennifer J , Gao Qitong , Lee Hui-Jie , Genty Katherine , Chow Shein-Chung , Grill Warren M , Pajic Miroslav , Turner Dennis A
Published: December 2023

Continuous deep brain stimulation (cDBS) of the subthalamic nucleus (STN) or globus pallidus is an effective treatment for the motor symptoms of Parkinson’s disease. The relative benefit of one region over the other is of great interest but cannot usually be compared in the same patient. Simultaneous DBS of both regions may synergistically increase the therapeutic benefit. Continuous DBS is limited by a lack of responsiveness to dynamic, fluctuating symptoms intrinsic to the disease. Adaptive DBS (aDBS) adjusts stimulation in response to biomarkers to improve efficacy, side effects, and efficiency. We combined bilateral DBS of both STN and globus pallidus (dual target DBS) in a prospective within-participant, clinical trial in six patients with Parkinson’s disease (n = 6, 55–65 years, n = 2 females).

Dual target cDBS was tested for Parkinson’s disease symptom control annually over 2 years, measured by motor rating scales, on time without dyskinesia, and medication reduction. Random amplitude experiments probed system dynamics to estimate parameters for aDBS. We then implemented proportional-plus-integral aDBS using a novel distributed (off-implant) architecture. In the home setting, we collected tremor and dyskinesia scores as well as individualized β and DBS amplitudes.

Dual target cDBS reduced motor symptoms as measured by Unified Parkinson’s Disease Rating Scale (UPDRS) to a greater degree than either region alone (P < 0.05, linear mixed model) in the cohort. The amplitude of β-oscillations in the STN correlated to the speed of hand grasp movements for five of six participants (P < 0.05, Pearson correlation). Random amplitude experiments provided insight into temporal windowing to avoid stimulation artefacts and demonstrated a correlation between STN β amplitude and DBS amplitude. Proportional plus integral control of aDBS reduced average power, while preserving UPDRS III scores in the clinic (P = 0.28, Wilcoxon signed rank), and tremor and dyskinesia scores during blinded testing at home (n = 3, P > 0.05, Wilcoxon ranked sum). In the home setting, DBS power reductions were slight but significant.

Dual target cDBS may offer an improvement in treatment of motor symptoms of Parkinson’s disease over DBS of either the STN or globus pallidus alone. When combined with proportional plus integral aDBS, stimulation power may be reduced, while preserving the increased benefit of dual target DBS.
Considerations for Expanding Antimicrobial Resistance Surveillance Networks
Authors: Gallagher Patrick , Shaw Alina , Bhandari Amit , Poudyal Nimesh , Holm Marianne , MacWright William R
Published: December 2023

Capturing Data on Antimicrobial Resistance Patterns and Trends in Use in Regions of Asia (CAPTURA) gained insight into the range of national antimicrobial resistance (AMR) stakeholders' long-term visions for AMR surveillance networks. As national AMR networks mature, stakeholders often contemplate adding laboratories to the network to achieve greater representativeness, boost data quantity, or meet other goals. Therefore, stakeholders should carefully select laboratories for expansion based on their goals and several practical criteria. Based on CAPTURA experience, the key criteria a national network may consider when expanding its AMR surveillance network include location, laboratory ownership, access to linked clinical and prescription databases, logistical ease, a laboratory's collaborative spirit, laboratory practices and equipment, laboratory staffing and quality assessments, laboratory methods and specimen types, data cleanliness and completeness, and the quantity of AMR data.
Evaluating Quality Management and Diagnostics Microbiology Performance Within an International External Quality Assessment (EQA) Program Serving National One Health Sector Reference Laboratories Across Asia: Experience Amid the Coronavirus Disease 2019 (COVID-19) Pandemic
Authors: Abegaz Freshwork Ayalew , dos Santos Patrícia Teixeira , Mogeni Ondari D , Guarnacci Tobin , Poudyal Nimesh , Hong Jinhui , Kwon Soo Young , Braae Rikke , Prathan Rangsiya , Tongkum Taradon Luang , Kamjumpho Watcharaporn , Chuanchuen Rungtip , Marks Florian , Hendriksen Rene S , Holm Marianne
Published: December 2023

Background

Strengthening external quality assessment (EQA) services across the One Health sector supports implementation of effective antimicrobial resistance (AMR) control strategies. Here we describe and compare 2 different approaches for conducting virtual laboratory follow-up assessments within an EQA program to evaluate quality management system (QMS) and procedures for pathogen identification and antimicrobial susceptibility testing (AST).

Methods

During the coronavirus disease 2019 (COVID-19) pandemic in 2021 and 2022, 2 laboratory assessment approaches were introduced: virtual-based and survey-based methodologies. The evaluation of 2 underperforming Animal Health laboratories through a virtual-based approach occurred between May and August 2021. This evaluation encompassed the utilization of 3 online meetings and document reviews, performed subsequent to the execution of EQA procedures. Within a distinct group of laboratories, the survey-based assessment was implemented from December 2021 to February 2022, also following EQA procedures. This phase encompassed the dissemination of an online survey to 31 participating laboratories, alongside a sole online consultation meeting involving 4 specific underperforming laboratories.

Results

The virtual-based assessment post-EQA aimed to identify gaps and areas for improvement in the laboratory's practices for pathogen identification and AST. This approach was, however, time-intensive, and, hence, only 2 laboratories were assessed. In addition, limited interactions in virtual platforms compromised the assessment quality. The survey-based post-EQA assessment enabled evaluation of 31 laboratories. Despite limitations for in-depth analysis of each procedure, gaps in QMS across multiple laboratories were identified and tailored laboratory-specific recommendations were provided.

Conclusions

Reliable internet and plans for efficient time management, post-EQA virtual laboratory follow-up assessments are an effective alternative when conducting onsite evaluation is infeasible as observed during the COVID-19 pandemic, although the successful implementation of remediation plans will likely require in person assessments. We advocate application of hybrid approaches (both onsite and virtual) for targeted capacity building of AMR procedures with the ability to implement and oversee the process.
Effective Stakeholder Engagement for Collation, Analysis and Expansion of Antimicrobial Resistance (AMR) Data: A CAPTURA Experience
Authors: Poudyal Nimesh , Holm Marianne , Joh Hea Sun , Gautam Sanjay , Sujan Mohammad Julhas , Kwon Soo Young , Sahikh Affan , Shaw Alina , Gallagher Partick , Prifti Kristi , Cho Alyssa , Chi Kyu-young Kevin , Aboushady Ahmed Taha , MacWright William R , Stelling John , Marks Florian
Published: December 2023

Background

An effective implementation of antimicrobial resistance (AMR) surveillance projects requires sustainable and multidisciplinary engagement with stakeholders from various backgrounds, interests and aims. The “Capturing Data on Antimicrobial resistance Patterns and Trends in Use in Regions of Asia” (CAPTURA) project, funded by the Fleming Fund, initially targeted 12 countries in South Asia (SA) and Southeast Asia (SEA) to “expand the volume of historical and current data on AMR and antimicrobial usage” and support local agencies through capacity building activities.

Methods

In this article, we focus on early stakeholder engagement activities and present overall statistics on AMR data collated from 72 laboratories across seven countries. This included 2.3 million records of antimicrobial susceptibility testing (AST) data, which were curated, analyzed, and shared back to the facilities for informed decision making.

Results

Approximately 98% of the data collated by CAPTURA originated from laboratories based in SA countries. Furthermore, country-wide data were analyzed to identify commonly reported pathogens in each country, followed by descriptions of AST practices and multidrug-resistant (MDR) pathogens. Overall, we found meager adherence to standard guidelines to perform and record AST results, and a significant number of MDR pathogens were reported.

Conclusions

We conclude that close collaboration with the existing national mechanisms for identifying AMR data sources was crucial for the project's success. Although we show a vast retrospective dataset on AMR is available for data sharing in Asia, there remain critical gaps in data generation/management practice and analysis capacity for AMR data at most facilities.
Breast cancer risk association with postmenopausal hormone therapy: Health Insurance Database in South Korea–based cohort study
Authors: Yuk Jin-Sung , Kim Taeran , Cho Hyunjin , Gwak Geumhee
Published: December 2023

Context

Although many physicians have been concerned that the menopausal hormones used currently in clinical practice may affect the risk of breast cancer, there are currently few informative updated studies about the associations between menopausal hormone therapy (MHT) and the risk of breast cancer.

Objective

This study aims to evaluate the association between the risk of breast cancer and MHT using the National Health Insurance Database in South Korea (HISK) cohort between 2002 and 2019 retrospectively.

Methods

Postmenopausal women over 40 years of age from 2003 to 2011 were selected as the subject population, and their follow-up data were collected until 2019. We analyzed the risk and mortality of breast cancer according to the type of MHT received, namely, tibolone, combined estrogen plus progestin by manufacturer (CEPM), oral estrogen, combined estrogen plus progestin by physician (CEPP), or topical estrogen.

Results

The risk of breast cancer increased in the CEPM group [hazard ratio (HR) 1.439, 95% CI 1.374-1.507, P-value < .001] in comparison with the non-MHT group. However, no significant associations were found between the use of tibolone, oral estrogen, CEPP, or topical estrogen and breast cancer risk in comparison with the non-MHT group (HR 0.968, 95% CI 0.925-1.012; HR 1.002, 95% CI 0.929-1.081; HR 0.929, 95% CI 0.75-1.15; HR 1.139, 95% CI 0.809-1.603). The mortality rate from breast cancer is lower in the MHT group in comparison with the non-MHT group, indicating that significant associations were found for tibolone, CEPM, and oral estrogen (HR 0.504, 95% CI 0.432-0.588; HR 0.429, 95% CI 0.352-0.522; HR 0.453 95% CI 0.349-0.588, P-value < .001).

Conclusions

This study suggests that the risk of breast cancer is increased by drugs in the CEPM group but not by tibolone, oral estrogen, CEPP, or topical estrogen. The mortality rate from breast cancer is lower with MHT (tibolone, CEPM, oral estrogen) than without MHT.
Oral anticoagulation after atrial fibrillation catheter ablation: benefits and risks
Authors: Kanaoka Koshiro , Nishida Taku , Iwanaga Yoshitaka , Nakai Michikazu , Tonegawa-Kuji Reina , Nishioka Yuichi , Myojin Tomoya , Okada Katsuki , Noda Tatsuya , Kusano Kengo , Miyamoto Yoshihiro , Saito Yoshihiko , Imamura Tomoaki
Published: December 2023

Background and Aims

Few recent large-scale studies have evaluated the risks and benefits of continuing oral anticoagulant (OAC) therapy after catheter ablation (CA) for atrial fibrillation (AF). This study evaluated the status of continuation of OAC therapy and the association between continuation of OAC therapy and thromboembolic and bleeding events according to the CHADS2 score.

Methods

This retrospective study included data from the Japanese nationwide administrative claims database of patients who underwent CA for AF between April 2014 and March 2021. Patients without AF recurrence assessed by administrative data of the treatment modalities were divided into two groups according to continuation of OAC therapy 6 months after the index CA. The primary outcomes were thromboembolism and major bleeding after a landmark period of 6 months. After inverse probability of treatment weighting analysis, the association between OAC continuation and outcomes was determined according to the CHADS2 score.

Results

Among 231 374 patients included, 69.7%, 21.6%, and 8.7% had CHADS2 scores of ≤1, 2, and ≥3, respectively. Of these, 71% continued OAC therapy at 6 months. The OAC continuation rate was higher in the high CHADS2 score group than that in the low CHADS2 score group. Among all patients, 2451 patients (0.55 per 100 person-years) had thromboembolism and 2367 (0.53 per 100 person-years) had major bleeding. In the CHADS2 score ≤1 group, the hazard ratio of the continued OAC group was 0.86 [95% confidence interval (CI): 0.74–1.01, P = .06] for thromboembolism and was 1.51 (95% CI: 1.27–1.80, P < .001) for major bleeding. In the CHADS2 score ≥3 group, the hazard ratio of the continued OAC group was 0.61 (95% CI: 0.46–0.82, P = .001) for thromboembolism and was 1.05 (95% CI: 0.71–1.56, P = 0.81) for major bleeding.

Conclusions

This observational study suggests that the benefits and risks of continuing OAC therapy after CA for AF differ based on the patient’s CHADS2 score. The risk of major bleeding due to OAC continuation seems to outweigh the risk reduction of thromboembolism in patients with lower thromboembolic risk.
Spatio-temporal variability in slab temperature within dynamic 3-D subduction models
Authors: Turino Valeria , Holt Adam F
Published: December 2023

Spatio-temporal variability in arc geochemistry and the conditions recorded by exhumed rocks suggest subduction zone thermal structure evolves in time and along-strike. Although much effort has been dedicated to studying subduction zone thermal structure, we lack an understanding of spatio-temporal temperature variability during time-dependent subduction. We model 3-D, dynamic subduction and examine the time evolution of the along-strike temperature difference of the slab’s upper surface (‘slab-top’) at the centre relative to the edge of the subduction zone. We examine this slab-top temperature variability for subduction systems of different widths and with different plate mobilities (i.e. fixed versus free subducting and overriding plates). In all of our models, the main control on slab-top temperature is convergence rate; either by simply controlling the rate of slab sinking or via the effect it has on the decoupling depth (DD). In the early stages of subduction, more rapid convergence at the plate centre produces a cooler slab relative to warmer slab edges. For mature subduction, this flips; a shallower DD at the slab centre produces warmer temperatures with respect to the edge. Importantly, our maximum along-strike temperature changes are reduced (≤50 °C) relative to previous kinematically driven modelling studies, due to a reduced role for slab-top heating via toroidal flow. Our dynamic subduction models, therefore, point towards a strong time dependence in the sense of along-strike temperature variation, but with relatively low absolute values in geometrically simple subduction zones.
Ketamine or ECT? What Have We Learned From the KetECT and ELEKT-D Trials?
Authors: Ekstrand Joakim , Takamiya Akihiro , Nordenskjold Axel , Kirov George , Sienaert Pascal , Kellner Charles H , Movahed Rad Pouya
Published: December 2023

1. Two recent clinical trials, KetECT and ELEKT-D, compared the effectiveness of ketamine and electroconvulsive therapy (ECT) for major depressive disorder. Notably, these trials reported marked differences in ECT's clinical outcomes of, with remission rates of 63% for KetECT and a strikingly lower rate of 22% for ELEKT-D, while the remission rates for ketamine were 46% and 38%, respectively. Considering that the primary objective of both trials was to compare the standard treatment (ECT) with an experimental intervention (ketamine), it is crucial to highlight the pronounced disparities in ECT’s clinical outcomes. This article offers a comprehensive comparison of these trials while also exploring how patient characteristics, treatment protocols, and study designs may contribute to such pronounced outcome discrepancies. These differences highlight the heterogeneous nature of depression and underscore the need for personalized treatments. These studies also provide valuable insights into identifying the most suitable candidates for ketamine and ECT.
Biofilm Formation by Nontypeable Haemophilus Influenzae and Resistance to Complement-Mediated Clearance
Authors: Belkacem Nouria , Deghmane Ala-Eddine , Taha Muhamed-Kheir
Published: December 2023

Biofilm formation has been suggested to be associated with phenotype changes compared with the planktonic form. We screened 1092 Haemophilus influenzae isolates for their genetic relationships and then selected 29 isolates from different genotypes and phenotypes and tested their ability to form biofilm. Our data showed a higher capacity of nontypable isolates, particularly isolates from respiratory and genital infections to form biofilm, compared with typable isolates. This ability to form biofilm was also correlated with reduced deposition of the complement component C3b on biofilm-involved bacteria. These data suggest that the biofilm formation contributes to the virulence of nontypable H. influenzae.
Mental health and neglected tropical diseases – the neglected dimension of burden: identifying the challenges and understanding the burden
Authors: Molyneux David H
Published: December 2023

Mental health co-morbidity and the Neglected Tropical Diseases (NTDs) has been highlighted as a major component of the ill health. The impact of mental illness is considered to be significantly underestimated in the calculations of the overall Disability-Adjusted Life Years (DALYs). This commentary discusses the DALY burden of anxiety, depression and associated stigma of NTDs. The economic losses incurred as a result of mental health conditions is assessed, and the impact on caregivers and families. It recommends that mental health care is incorporated into NTDs programme planning and implementation. Priority research is the estimation of the NTD burden of depressive and anxiety disorders and neuropsychiatric conditions of NTDs and an evaluation of the economic costs of mental illness derived from NTDs causation.
Lipopeptide culture filtrates from Bacillus spp. provide effective protection to wheat against the foliar pathogen Zymoseptoria tritici
Authors: El Arbi Amel , Arnauld Ségolène , Chataigné Gabrielle , Lecouturier Didier , Bricout Alexandre , Gharsallah Néji , Jacques Philippe , Siah Ali , Rochex Alice
Published: December 2023

Aims

Biocontrol products based on microorganisms and natural substances are promising alternatives to chemical pesticides that could contribute to develop a more sustainable agriculture. Here, we investigated the potential of cell-free culture filtrates (CFCFs) from two strains of the Bacillus subtilis group to inhibit Zymoseptoria tritici, a major fungal pathogen of wheat.

Methods and results

Foliar application of CFCFs from Bacillus velezensis GA1 and Bacillus sp. III1 on wheat seedlings in a greenhouse strongly reduced Z. tritici disease severity (>90%). In vitro bioassays showed that CFCFs completely inhibited the spore germination and fungal growth (100%). In planta cytological investigations revealed a significant impact of the treatments on both spore germination (∼40% inhibition) and fungal growth of Z. tritici (>80% inhibition). High Performance Liquid Chromatography (HPLC) analysis showed that the Bacillus strains displayed different lipopeptide profiles. The CFCF obtained from Bacillus GA1 contained 90 mg l−1 of iturin A + surfactins + fengycins and the CFCF obtained from Bacillus sp. III1 contained 25 mg l−1 of mojavensin A (iturin family) + surfactins + fengycins.

Conclusions

Strains of the B. subtilis group producing different iturins could provide several CFCF-based solutions for the biocontrol of Z. tritici.
Thoracic SMARCA4-deficient undifferentiated tumor: current knowledge and future perspectives
Authors: Shinno Yuki , Ohe Yuichiro ,   the Lung Cancer Study Group of the Japan Clinical Oncology Group (JCOG)
Published: December 2023

Thoracic SMARCA4-deficient undifferentiated tumor is a newly recognized disease entity characterized as a high-grade malignant neoplasm with an undifferentiated or rhabdoid phenotype. The tumor was initially identified as a subtype of thoracic sarcoma with SMARCA4 loss, but further investigation resulted in its classification as a subtype of epithelial malignancies in the current World Health Organization classification. SMARCA4-deficient undifferentiated tumor is highly aggressive and has a poor prognosis. Because of its rarity, an optimal treatment strategy has not yet been identified. In this review, we summarize the literature on SMARCA4-deficient undifferentiated tumor in terms of its clinical characteristics, diagnosis, treatment strategy and future perspectives.
Human CD34+/dim neutrophil-committed progenitors do not differentiate into neutrophil-like CXCR1+CD14+CD16− monocytes in vitro
Authors: Signoretto Ilaria , Calzetti Federica , Gasperini Sara , Bianchetto-Aguilera Francisco , Gardiman Elisa , Finotti Giulia , Tecchio Cristina , Tamassia Nicola , Cassatella Marco A
Published: December 2023

The advent of recent cutting-edge technologies has allowed the discovery and characterization of novel progenitors of human neutrophils, including SSCloCD66b+CD15+CD11b−CD49dhiproNeu1s, SSChiCD66b+CD15+CD11b−CD49dintproNeus2s, CD66b+CD15+CD11b+CD49d+CD101−preNeus, and Lin−CD66b+CD117+CD71+eNePs. In this research field, we recently identified CD66b−CD38+CD64dimCD115−, CD34+, and CD34dim/− cells exclusively committed to the neutrophil lineage (which we renamed as CD34+ and CD34dim/− neutrophil-committed progenitors), representing the earliest neutrophil precursors identifiable and sorted by flow cytometry. Moreover, based on their differential CD34 and CD45RA expression, we could identify 4 populations of neutrophil-committed progenitors: CD34+CD45RA−/NCP1s, CD34+CD45RA+/NCP2s, CD34dim/−CD45RA+/NCP3s, and CD34dim/−CD45RA−/NCP4s. This said, a very recent study by Ikeda and coworkers (PMID: 36862552) reported that neutrophil precursors, termed either neutrophil progenitors or “early neutrophil-committed progenitors,” would generate immunosuppressive neutrophil-like CXCR1+CD14+CD16− monocytes. Hence, presuming that neutrophil progenitors/“early neutrophil-committed progenitors” correspond to neutrophil-committed progenitors, the selective neutrophil commitment that we attributed to neutrophil-committed progenitors is contradicted by Ikeda and coworkers’ article. In this study, by performing a more analytical reevaluation at the phenotypic and molecular levels of the cells generated by neutrophil-committed progenitors 2 and 4 (selected as representatives of neutrophil-committed progenitors), we categorically exclude that neutrophil-committed progenitors generate neutrophil-like CXCR1+CD14+CD16− monocytes. Rather, we provide substantial evidence indicating that the cells generated by neutrophil progenitors/“early neutrophil-committed progenitors” are neutrophilic cells at a different stage of maturation, displaying moderate levels of CD14, instead of neutrophil-like CXCR1+CD14+CD16− monocytes, as pointed by Ikeda and coworkers. Hence, the conclusion that neutrophil progenitors/“early neutrophil-committed progenitors” aberrantly differentiate into neutrophil-like monocytes derives, in our opinion, from data misinterpretation.
Teaching and knowledge: uneasy bedfellows
Authors: Fisher Andrew , Tallant Jonathan
Published: December 2023

In this paper we explore the connection between the act of teaching and the imparting of knowledge. Our overarching aim is to demonstrate that the connection between them is less tight than one might suppose. Our stepping off point is a recent paper by David Bakhurst who (on one reading, at least) takes a strong view, opposed to our own. On our reading, Bakhurst argues that there is a tight conceptual connection between teaching and the imparting of knowledge. We argue that this is not the case; the connection does not hold. We then consider several ways we might weaken the alleged conceptual connection between teaching and knowledge, finally considering two ways of severing the conceptual connection altogether, whilst at the same time allowing that much teaching does indeed lead to the imparting of knowledge. We argue that such views are to be preferred.
Effect of overexpression of partial TDH1 and TDH2/3 gene sequences in a starter strain of industrial bioethanol fermentation on the Brettanomyces bruxellensis contaminant growth
Authors: Branco Patrícia , Carvalho Luísa , Prista Catarina , Albergaria Helena
Published: December 2023

Selected Saccharomyces cerevisiae strains, such as the commercial Ethanol-Red (ER) strain, are used as starters in the bioethanol industry. Yet, bioethanol fermentations are prone to microbial contaminations, mainly by Brettanomyces bruxellensis and lactic acid bacteria. Chemicals, such as sulphuric acid and antibiotics, are commonly used to combat those contaminations, but they have negative environmental impacts. Recently, ER strain was found to secrete antimicrobial peptides (AMPs) active against B. bruxellensis. Therefore, the partial TDH1 and TDH2/3 genes sequences that codify those AMPs were inserted into the pSR41k plasmid and cloned in ER strains. The relative expression levels (plasmidic/genomic) of those sequences in the respective modified ER strains were quantified by real-time quantitative polimerase chain reaction (RT-qPCR), confirming their overexpression. The effect of the modified strains on B. bruxellensis (Bb) growth was then evaluated during synthetic must (SM) and carob syrup (CS) fermentations, co-inoculated with 105 cells ml−1 of ER and Bb in SM and with 106 of ER and 5 × 103 cells ml−1 of Bb in CS. Results showed that modified ER strains exerted a much higher inhibitory effect against B. bruxellensis (72-fold in SM and 10-fold in CS) than the non-modified ER strain. In those fermentations, 90–100 g l−1 of ethanol was produced in 3–6 days.
EPOCHS IX. When cosmic dawn breaks: evidence for evolved stellar populations in 7 < z < 12 galaxies from PEARLS GTO and public NIRCam imaging
Authors: Trussler James A A , Conselice Christopher J , Adams Nathan , Austin Duncan , Ferreira Leonardo , Harvey Tom , Li Qiong , Vijayan Aswin P , Wilkins Stephen M , Windhorst Rogier A , Bhatawdekar Rachana , Cheng Cheng , Coe Dan , Cohen Seth H , Driver Simon P , Frye Brenda , Grogin Norman A , Hathi Nimish , Jansen Rolf A , Koekemoer Anton , Marshall Madeline A , Nonino Mario , Ortiz Rafael , Pirzkal Nor , Robotham Aaron , Ryan Russell E , D’Silva Jordan C J , Summers Jake , Tompkins Scott , Willmer Christopher N A , Yan Haojing
Published: December 2023

The presence of evolved stars in high-redshift galaxies can place valuable indirect constraints on the onset of star formation in the Universe. Thus, we use PEARLS GTO (Prime Extragalactic Areas for Reionization and Lensing Science Guaranteed Time Observations) and public NIRCam (Near Infrared Camera) photometric data to search for Balmer-break candidate galaxies at 7 < z < 12. We find that our Balmer-break candidates at z ∼ 10.5 tend to be older (115 Myr), have lower inferred [O iii] + Hβ equivalent widths (120 Å), have lower specific star formation rates (6 Gyr−1) and redder UV slopes (β = −1.8) than our control sample of galaxies. However, these trends all become less strong at z ∼ 8, where the F444W filter now probes the strong rest-frame optical emission lines, thus providing additional constraints on the current star formation activity of these galaxies. Indeed, the bursty nature of epoch of reionization galaxies can lead to a disconnect between their current spectral energy distribution (SED) profiles and their more extended star formation histories. We discuss how strong emission lines, the cumulative effect of weak emission lines, dusty continua, and active galactic nuclei can all contribute to the photometric excess seen in the rest-frame optical, thus mimicking the signature of a Balmer break. Additional medium-band imaging will thus be essential to more robustly identify Balmer-break galaxies. However, the Balmer break alone cannot serve as a definitive proxy for the stellar age of galaxies, being complexly dependent on the star formation history. Ultimately, deep Near Infrared Spectrograph (NIRSpec) continuum spectroscopy and Mid-Infrared Instrument (MIRI) imaging will provide the strongest indirect constraints on the formation era of the first galaxies in the Universe, thereby revealing when cosmic dawn breaks.
Diagnostic diagrams for ram pressure stripped candidates
Authors: Krabbe A C , Hernandez-Jimenez J A , Mendes de Oliveira C , Jaffe Y L , Oliveira C B , Cardoso N M , Smith Castelli A V , Dors O L , Cortesi A , Crossett J P
Published: December 2023

This paper presents a method for finding ram pressure stripped (RPS) galaxy candidates by performing a morphological analysis of galaxy images obtained from the Legacy survey. We consider a sample of about 600 galaxies located in different environments such as groups and clusters, tidally interacting pairs and the field. The sample includes 160 RPS previously classified in the literature into classes from J1 to J5, based on the increasing level of disturbances. Our morphological analysis was done using the astromorphlib software followed by the inspection of diagnostic diagrams involving combinations of different parameters like the asymmetry (A), concentration (C), Sérsic index (n), and bulge strength parameters $F(G,\, M_{20})$. We found that some of those diagrams display a distinct region in which galaxies classified as J3, J4, and J5 decouples from isolated galaxies. We call this region as the morphological transition zone and we also found that tidally interacting galaxies in pairs are predominant within this zone. Nevertheless, after visually inspecting the objects in the morphological transition zone to discard obvious contaminants, we ended up with 33 bona fide new RPS candidates in the studied nearby groups and clusters (Hydra, Fornax, and CLoGS sample), of which one-third show clear evidence of unwinding arms. Future works may potentially further increase significantly the samples of known RPS using such method.
The mass range of hot subdwarf B stars from MESA simulations
Authors: Arancibia-Rojas Eduardo , Zorotovic Monica , Vučković Maja , Bobrick Alexey , Vos Joris , Piraino-Cerda Franco
Published: December 2023

Hot subdwarf B (sdB) stars are helium core burning stars that have lost almost their entire hydrogen envelope due to binary interaction. Their assumed canonical mass of ${M_{\mathrm{sdB}}}\sim 0.47$ M⊙ has recently been debated given a broad range found both from observations as well as from the simulations. Here, we revise and refine the mass range for sdBs derived two decades ago with the Eggleton code, using the stellar evolution code mesa, and discuss the effects of metallicity and the inclusion of core overshooting during the main sequence. We find an excellent agreement for low-mass progenitors, up to ∼2.0 M⊙. For stars more massive than ∼2.5 M⊙, we obtain a wider range of sdB masses compared to the simulations from the literature. Our mesa models for the lower metallicity predict, on average, slightly more massive sdBs. Finally, we show the results for the sdB lifetime as a function of sdB mass and discuss the effect this might have in the comparison between simulations and observational samples. This study paves the way for reproducing the observed Galactic mass distribution of sdB binaries.
An investigation of the state changes of PSR J2021+4026 and the Vela pulsar
Authors: Wang H-H , Takata J , Lin L C-C , Tam P-H T
Published: December 2023

We report on long-term evolution of gamma-ray flux and spin-down rate of two bright gamma-ray pulsars, PSR J2021+4026 and Vela (PSR J0835−4510). PSR J2021+4026 shows repeated state changes in gamma-ray flux and spin-down rate. We report two new state changes, a first one from a low gamma-ray flux to a high flux that occurred around MJD 58910, and a second one from high to low flux that occurred around MJD 59510. We find that the flux changes associated with these two state changes are smaller than those determined in the previous events, and the waiting time of the new state change from the high gamma-ray flux to low gamma-ray flux is significantly shorter than previous events. Since the waiting time-scale of the quasi-periodic state changes of PSR J2021+4026 is similar to the waiting time-scale of the glitch events of the Vela pulsar, we search for the state change of the gamma-ray emission of the Vela pulsar to investigate the possibility that the glitching process is the trigger of the state change of PSR J2021+4026. For the Vela pulsar, the flux of the radio pulses briefly decreased around the 2016 glitch, suggesting that the glitch may have affected the structure of the magnetosphere. Nevertheless, we could not find any significant change of the gamma-ray emission properties using 15 yr of Fermi-LAT data. Overall, it seems inconclusive that a glitch-like process similar to that occurred to the Vela pulsar triggers the structure change of the global magnetosphere and causes state changes of PSR J2021+4026. Further and deep investigations to clarify the mechanism of the mode change for PSR J2021+4026 are required.
Ionized X-ray winds in the radio galaxy Mrk 6
Authors: Kayanoki Taishu , Mao Junjie , Fukazawa Yasushi
Published: December 2023

Active galactic nucleus (AGN) outflows including jets and ionized winds have been key phenomena such as jet collimation and AGN feedback to the host galaxy in astrophysics. Radio galaxies, a type of AGN with misaligned jets, have provided valuable insights into the properties and relationships of these outflows. However, several aspects regarding AGN outflows remain unclarified, such as the relationship between jets and ultrafast outflows (UFOs) and the differences between the properties of radio-loud AGN disc winds and radio-quiet AGN ionized winds. To clarify these aspects, radio galaxies containing UFOs and warm absorbers (WAs) must be studied. Currently, both UFOs and WAs have been reported in only two radio galaxies, 3C 390.3 and 4C +74.26. To enhance our understanding of the connection between the jets and ionized winds, we conducted a study on Mrk 6, a potential candidate for the third case of a radio galaxy displaying these characteristics. Using X-ray spectra obtained from XMM–Newton, we performed photoionization modelling using the spex code. The best-fitting model analysis results revealed the presence of a UFO component with a relatively low ionization parameter (Fe xix/xviii lines blueshifted by $-34700^{+400}_{-200}~{\rm km~s^{-1}}$) and a WA component with an outflow velocity of −7600 ± 200 km s−1. To further confirm the nature of the UFO and WA in Mrk 6, we simulated the X-ray imagining and spectroscopy mission spectra.
ExoMol line lists – LII. Line lists for the methylidyne cation (CH+)
Authors: Pearce Oliver , Yurchenko Sergei N , Tennyson Jonathan
Published: December 2023

Comprehensive and accurate rovibronic line lists for the X 1Σ+ and A 1Π states of 12C1H+ and 13C1H+ which should be applicable up to temperatures of 5000 K are presented. Available empirical potential energy curves and high-level ab initio dipole and transition dipole moment curves are used with the program level to compute rovibronic energy levels and Einstein A coefficients. Λ-doubling is incorporated into the energy levels and A-coefficients involving the A 1Π state using an empirical method. For 12C1H+, line positions are improved by using both laboratory and astronomical observational spectra as input to the MARVEL (Measured Active Rotational-Vibrational Energy Levels) procedure. The 12C1H+ line list contains 1505 states and 34 194 transitions over the frequency range of 0–33 010 cm−1 (λ > 300 nm). Comparisons with observed astronomical and laboratory spectra give very good agreement. The PYT CH+ line lists and partition functions are available from the ExoMol database at www.exomol.com.
A benchmark white dwarf–ultracool dwarf wide field binary
Authors: Ferreira Thiago , Saito Roberto K , Minniti Dante , Mejías Andrea , Caceres Claudio , Alonso-García Javier , Beamín Juan Carlos , Smith Leigh C , Gomez Matías , Lucas Philip W , Ivanov Valentin D
Published: December 2023

We present the discovery and multiwavelength characterization of VVV J1438-6158 AB, a new field wide-binary system consisting of a $4.6^{+5.5}_{-2.4}~{\rm Gyr}$ and $T_{\rm eff} = 9500\pm 125~\mathrm{ K}$ DA white dwarf (WD) and a $T_{\rm eff} = 2400\pm 50~\mathrm{ K}$ M8 ultracool dwarf (UCD). The projected separation of the system is $a = 1236.73~{\rm au}$ ($\sim 13.8\, \mathrm{ arcsec}$), and although along the line of sight towards the Scorpius–Centaurus stellar association, VVV J1438-6158 AB is likely to be a field star, from a kinematic 6D probabilistic analysis. We estimated the physical and dynamical parameters of both components via interpolations with theoretical models and evolutionary tracks, which allowed us to retrieve a mass of $0.62\pm 0.18~\mathrm{ M}_\odot$ for the WD, and a mass of $98.5\pm 6.2~\mathrm{ M}_{\rm Jup}$ ($\sim 0.094\pm 0.006~\mathrm{ M}_\odot$) for the UCD. The radii of the two components were also estimated at $0.01309\pm 0.0003~\mathrm{ R}_{\odot }$ and $1.22\pm 0.05~\mathrm{ R}_{\rm Jup}$, respectively. VVV J1438-6158 AB stands out as a benchmark system for comprehending the evolution of WDs and low-mass companions given its status as one of the most widely separated WD+UCD systems known to date, which likely indicates that both components may have evolved independently of each other, and also being characterized by a large-mass ratio ($q = 0.15\pm 0.04$), which likely indicates a formation pathway similar to that of stellar binary systems.
The first white dwarf debris disc observed by JWST
Authors: Swan Andrew , Farihi Jay , Su Kate Y L , Desch Steven J
Published: December 2023

This letter reports the first JWST spectroscopy of a white dwarf debris disc, giving a preliminary assessment of the salient features, and recommendations for future observations. The polluted and dusty star WD 0145+234 experienced a major collisional event in its circumstellar disc in 2018, accompanied by an infrared outburst, and subsequently a gradual decrease in thermal emission. Time-series NIRSpec observations demonstrate that the circumstellar disc is returning to a quiescent state with a T ≈ 1000 K infrared excess similar to the bulk of known dusty white dwarfs. MIRI spectroscopy reveals a 9–12 $\mu$m solid-state emission feature consistent with silicate minerals as seen in debris discs observed with Spitzer. The strength and morphology of the silicate feature appear unchanged relative to the continuum in spectra taken over a year apart, consistent with steady-state collisional evolution of the circumstellar debris. A tentative emission feature around 7 $\mu$m may be due to carbonates, and if confirmed would indicate aqueous alteration in the parent body.