bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete genome sequence of soybean geminivirus A in soybean in Korea
Authors: Bak Sangmin , Kwon Mina , Baek Seungbin , Min Jean Geung , Kang Dong Hyun , Kim Minseok , Lee Hong-Kyu , Lee Su-Heon 
Published: September 2023

ABSTRACT
Soybean geminivirus A (SGVA), a member of the family Geminiviridae, was detected in a survey of early-stage soybean. The complete genome sequence of SGVA isolate Habin was determined, revealing its characteristics and similarity to Korean and Chinese isolates. This study contributes to understanding the impact of SGVA on soybean production.
Controls on upstream-migrating bed forms in sandy submarine channels
Authors: Englert Rebecca G. , Vellinga Age J. , Cartigny Matthieu J.B. , Clare Michael A. , Eggenhuisen Joris T. , Hubbard Stephen M. 
Published: September 2023

Abstract
Submarine channels parallel river channels in their ability to transport sediment. However, in contrast to rivers, sediment transport and bed-form development in submarine channels are less well understood. Many steep (&gt;1°), sandy submarine channels are dominated by upstream-migrating bed forms. The flow conditions required to form these upstream-migrating bed forms remain debated because the interactions between turbidity currents and active bed forms are difficult to measure directly. Consequently, we used a depth-resolved numerical model to test the role of flow parameters that are hypothesized to control the formation of upstream-migrating bed forms in submarine channels. While our modeling results confirmed the importance of previously identified flow parameters (e.g., densiometric Froude number), we found that basal sediment concentration in turbidity currents is the strongest predictor of upstream-migrating bed-form formation. Our model shows how locally steep gradients enable high sediment concentrations (average &gt;5 vol%) in the basal parts of flows, which allow the development of cyclic step instabilities and their associated bed forms. This new insight explains the previously puzzling observation that upstream-migrating bed forms are abundant in proximal, steep, sandy reaches of submarine channels, while their occurrence becomes more intermittent downslope.
Best practice recommendations for body composition considerations in sport to reduce health and performance risks: a critical review, original survey and expert opinion by a subgroup of the IOC consensus on Relative Energy Deficiency in Sport (REDs)
Authors: Mathisen Therese Fostervold , Ackland Timothy , Burke Louise M , Constantini Naama , Haudum Judith , Macnaughton Lindsay S , Meyer Nanna L , Mountjoy Margo , Slater Gary , Sundgot-Borgen Jorunn 
Published: September 2023

BackgroundThe assessment of body composition (BC) in sport raises concern for athlete health, especially where an overfocus on being lighter or leaner increases the risk of Relative Energy Deficiency in Sport (REDs) and disordered eating.MethodsWe undertook a critical review of the effect of BC on performance (29 longitudinal, prospective or intervention studies) and explored current practice related to BC considerations via a follow-up to a 2013 internationally distributed survey.ResultsThe review found that a higher level of body fat was negatively associated with endurance performance, while a gain in muscle mass resulted in performance benefits across sports. BC did not contribute to early talent identification, and no unique cut-off to signify a performance advantage for BC was identified. BC appears to be one of an array of variables impacting performance, and its influence should not be overstated. The survey (125 practitioners, 61 sports and 26 countries) showed subtle changes in BC considerations over time, such as an increased role for sport dietitian/nutrition practitioners as BC measurers (2013: 54%, 2022: 78%); less emphasis on reporting of body fat percentage (2013: 68%, 2022: 46%) and reduced frequency of BC assessment if ≥every fourth week (2013: 18%, 2022: 5%). Respondents remained concerned about a problematic focus on BC (2013: 69%, 2022: 78%). To address these findings, we provide detailed recommendations for BC considerations, including an overview of preferable BC methodology.ConclusionsThe ‘best practice’ guidelines stress the importance of a multidisciplinary athlete health and performance team, and the treatment of BC data as confidential medical information. The guidelines provide a health focus around BC, aiming to reduce the associated burden of disordered eating, problematic low energy availability and REDs.
Methodology for studying Relative Energy Deficiency in Sport (REDs): a narrative review by a subgroup of the International Olympic Committee (IOC) consensus on REDs
Authors: Ackerman Kathryn E , Rogers Margot Anne , Heikura Ida A , Burke Louise M , Stellingwerff Trent , Hackney Anthony C , Verhagen Evert , Schley Stacey , Saville Grace H , Mountjoy Margo , Holtzman Bryan 
Published: September 2023

In the past decade, the study of relationships among nutrition, exercise and the effects on health and athletic performance, has substantially increased. The 2014 introduction of Relative Energy Deficiency in Sport (REDs) prompted sports scientists and clinicians to investigate these relationships in more populations and with more outcomes than had been previously pursued in mostly white, adolescent or young adult, female athletes. Much of the existing physiology and concepts, however, are either based on or extrapolated from limited studies, and the comparison of studies is hindered by the lack of standardised protocols. In this review, we have evaluated and outlined current best practice methodologies to study REDs in an attempt to guide future research.This includes an agreement on the definition of key terms, a summary of study designs with appropriate applications, descriptions of best practices for blood collection and assessment and a description of methods used to assess specific REDs sequelae, stratified as eitherPreferred,Used and RecommendedorPotential. Researchers can use the compiled information herein when planning studies to more consistently select the proper tools to investigate their domain of interest. Thus, the goal of this review is to standardise REDs research methods to strengthen future studies and improve REDs prevention, diagnosis and care.
Molecular portraits of patients with intrahepatic cholangiocarcinoma who diverge as rapid progressors or long survivors on chemotherapy
Authors: O'Rourke Colm J , Salati Massimiliano , Rae Colin , Carpino Guido , Leslie Holly , Pea Antonio , Prete Maria G , Bonetti Luca R , Amato Francesco , Montal Robert , Upstill-Goddard Rosie , Nixon Colin , Sanchon-Sanchez Paula , Kunderfranco Paolo , Sia Daniela , Gaudio Eugenio , Overi Diletta , Cascinu Stefano , Hogdall Dan , Pugh Sian , Domingo Enric , Primrose John N , Bridgewater John , Spallanzani Andrea , Gelsomino Fabio , Llovet Josep M , Calvisi Diego F , Boulter Luke , Caputo Francesco , Lleo Ana , Jamieson Nigel B , Luppi Gabriele , Dominici Massimo , Andersen Jesper B , Braconi Chiara 
Published: September 2023

ObjectiveCytotoxic agents are the cornerstone of treatment for patients with advanced intrahepatic cholangiocarcinoma (iCCA), despite heterogeneous benefit. We hypothesised that the pretreatment molecular profiles of diagnostic biopsies can predict patient benefit from chemotherapy and define molecular bases of innate chemoresistance.DesignWe identified a cohort of advanced iCCA patients with comparable baseline characteristics who diverged as extreme outliers on chemotherapy (survival <6 m in rapid progressors, RP; survival >23 m in long survivors, LS). Diagnostic biopsies were characterised by digital pathology, then subjected to whole-transcriptome profiling of bulk and geospatially macrodissected tissue regions. Spatial transcriptomics of tumour-infiltrating myeloid cells was performed using targeted digital spatial profiling (GeoMx). Transcriptome signatures were evaluated in multiple cohorts of resected cancers. Signatures were also characterised using in vitro cell lines, in vivo mouse models and single cell RNA-sequencing data.ResultsPretreatment transcriptome profiles differentiated patients who would become RPs or LSs on chemotherapy. Biologically, this signature originated from altered tumour-myeloid dynamics, implicating tumour-induced immune tolerogenicity with poor response to chemotherapy. The central role of the liver microenviroment was confrmed by the association of the RPLS transcriptome signature with clinical outcome in iCCA but not extrahepatic CCA, and in liver metastasis from colorectal cancer, but not in the matched primary bowel tumours.ConclusionsThe RPLS signature could be a novel metric of chemotherapy outcome in iCCA. Further development and validation of this transcriptomic signature is warranted to develop precision chemotherapy strategies in these settings.
Spirometric patterns in young and middle-aged adults: a 20-year European study
Authors: Carsin Anne-Elie , Garcia-Aymerich Judith , Accordini Simone , Dharmage Shyamali , Leynaert Bénédicte , de las Heras Marti , Casas Lidia , Caviezel Seraina , Demoly Pascal , Forsberg Bertil , Gislason Thorarinn , Corsico Angelo Guido , Janson Christer , Jogi Rain , Martínez-Moratalla Jesús , Nowak Dennis , Gómez Leopoldo Palacios , Pin Isabelle , Probst-Hensch Nicole , Raherison-Semjen Chantal , Squillacioti Giulia , Svanes Cecilie , Torén Kjell , Urrutia Isabel , Huerta Ismael , Anto Josep Maria , Jarvis Debbie , Guerra Stefano 
Published: September 2023

BackgroundUnderstanding the natural history of abnormal spirometric patterns at different stages of life is critical to identify and optimise preventive strategies. We aimed to describe characteristics and risk factors of restrictive and obstructive spirometric patterns occurring before 40 years (young onset) and between 40 and 61 years (mid-adult onset).MethodsWe used data from the population-based cohort of the European Community Respiratory Health Survey (ECRHS). Prebronchodilator forced expiratory volume in one second (FEV1) and forced vital capacity (FVC) were assessed longitudinally at baseline (ECRHS1, 1993–1994) and again 20 years later (ECRHS3, 2010–2013). Spirometry patterns were defined as: restrictive if FEV1/FVC≥LLN and FVC<10th percentile, obstructive if FEV1/FVC<LLN or normal otherwise. Five spirometry patterns were derived depending on whether participants never developed restrictive/obstructive (normal), developed restrictive/obstructive at baseline (young onset) or at last follow-up (mid-adult onset). The characteristics and risk factors associated with these patterns were described and assessed using multilevel multinomial logistic regression analysis adjusting for age, sex, sample (random or symptomatic) and centre.ResultsAmong 3502 participants (mean age=30.4 (SD 5.4) at ECRHS1, 50.4 (SD 5.4) at ECRHS3), 2293 (65%) had a normal, 371 (11%) a young restrictive, 301 (9%) a young obstructive, 187 (5%) a mid-adult onset restrictive and 350 (10%) a mid-adult onset obstructive spirometric pattern. Being lean/underweight in childhood and young adult life was associated with the occurrence of the young spirometric restrictive pattern (relative risk ratio (RRR)=1.61 95% CI=1.21 to 2.14, and RRR=2.43 95% CI=1.80 to 3.29; respectively), so were respiratory infections before 5 years (RRR=1.48, 95% CI=1.05 to 2.08). The main determinants for young obstructive, mid-adult restrictive and mid-adult obstructive patterns were asthma, obesity and smoking, respectively.ConclusionSpirometric patterns with onset in young and mid-adult life were associated with distinct characteristics and risk factors.
Core outcome set for pulmonary rehabilitation of patients with COPD: results of a modified Delphi survey
Authors: Souto-Miranda Sara , Saraiva Isabel , Spruit Martijn A , Marques Alda 
Published: September 2023

IntroductionThere is high heterogeneity of outcomes and measures reported in pulmonary rehabilitation (PR) trials of people with chronic obstructive pulmonary disease (COPD). This hinders study comparability and benchmarking of PR. We have developed a core outcome set (COS) to overcome these challenges.MethodsThis study was informed by a systematic review and two qualitative studies and had patient involvement since its inception. A two-round Delphi survey was available in seven languages. Outcomes (n=63) scored 7–9 (crucial) by ≥70% of the participants and 1–3 (not that important) by ≤15% of participants from both groups in the Likert scale were automatically included in the COS, while outcomes that were considered crucial by only one of the groups were further discussed by the authors in a meeting.ResultsA total of 299 people (n=229 healthcare professionals/researchers/policy-makers; n=70 people with COPD and informal caregivers) participated in the survey (83% retention), which covered 29 countries/five continents. After the second round, six outcomes were included and three were added in the meeting. The final COS contains dyspnoea, fatigue, functional exercise capacity, health-related quality of life, health behaviours/lifestyle, knowledge about the disease, lower limb muscle function, personal goals and problematic activities of daily living.ConclusionA COS for PR of people with COPD is now available and can be used by different stakeholders to improve consistency and comparability of studies, benchmark PR and improve the quality of care provided. Future research should establish the core measures and investigate the uptake of this COS.
Topological classes of higher-dimensional black holes in massive gravity
Authors: Chen Deyou , He Yucheng , Tao Jun 
Published: September 2023

AbstractIn this paper, we study topological numbers for five-, six- and seven-dimensional anti-de Sitter black holes in the ghost-free massive gravity. We find that when the black holes are charged, they have the same topological number. The topological numbers for the uncharged black holes are 0 or 1, and the specific values are determined by the values of the black holes’ parameters. Since k and $$c_ 0^2c_2 m^2 $$

c
0
2

c
2

m
2

appear together in the generalized free energy in the form of $$k +c_ 0^2c_2 m^2 $$

k
+

c
0
2

c
2

m
2

, where k characterizes the horizon curvature and $$c_2 m^2 $$

c
2

m
2

is the coefficient of the second term of massive potential associated with the graviton mass, this result is applicable to the black holes with the spherical, Ricci flat or hyperbolic horizons. This work shows that the parameters of the ghost-free massive gravity play an important role in topological classes of black holes.
SUSY partners and S-matrix poles of the one-dimensional Rosen–Morse II potential
Authors: San Millán Carlos , Gadella Manuel , Kuru Şengül , Negro Javier 
Published: September 2023

AbstractAmong the list of one-dimensional solvable Hamiltonians, we find the Hamiltonian with the Rosen–Morse II potential. The first objective is to analyse the scattering matrix corresponding to this potential. We show that it includes a series of poles corresponding to the types of redundant poles or anti-bound poles. In some cases, there are even bound states and this depends on the values of given parameters. Then, we perform different supersymmetric transformations on the original Hamiltonian using either the ground state (for those situations where there are bound states) wave functions, or other solutions that come from anti-bound states or redundant states. We study the properties of these transformations.
Balanced Allocations with the Choice of Noise
Authors: Los Dimitrios , Sauerwald Thomas 
Published: September 2023

We consider the allocation of
m
balls (jobs) into
n
bins (servers). In the standard
Two-Choice
process, at each step
t
=1,2,... ,m we first sample
two
randomly chosen bins, compare their two loads and then place a ball in the least loaded bin. It is well-known that for any
m
⩾
n
, this results in a gap (difference between the maximum and average load) of log
2
log
n
+ Θ (1) (with high probability).

In this work, we consider
Two-Choice
in different settings with noisy load comparisons. One key setting involves an adaptive adversary whose power is limited by some threshold

\(g \in \mathbb {N}\)

. In each step, such adversary can determine the result of any load comparison between two bins whose loads differ by at most
g
, while if the load difference is greater than
g
, the comparison is correct.

For this adversarial setting, we first prove that for any
m
⩾
n
the gap is

\(\mathcal {O}(g+\log n)\)

with high probability. Then through a refined analysis we prove that if
g
⩽ log
n
, then for any
m
⩾
n
the gap is

\(\mathcal {O}(\frac{g}{\log g} \cdot \log \log n)\)

. For constant values of
g
, this generalizes the heavily loaded analysis of [
19
,
61
] for the
Two-Choice
process, and establishes that asymptotically the same gap bound holds even if load comparisons among “similarly loaded” bins are wrong. Finally, we complement these upper bounds with tight lower bounds, which establish an interesting phase transition on how the parameter
g
impacts the gap.

The analysis also applies to settings with outdated and delayed information. For example, for the setting of [
18
] where balls are allocated in consecutive batches of size

\(b = n\)

, we present an improved and tight gap bound of

\(\Theta (\frac{\log n}{\log \log n})\)

. This bound also extends for a range of values of
b
and applies to a relaxed setting where the reported load of a bin can be any load value from the last
b
steps.
Spatial and Temporal Mapping of Breast Cancer Lung Metastases Identify TREM2 Macrophages as Regulators of the Metastatic Boundary
Authors: Yofe Ido , Shami Tamar , Cohen Noam , Landsberger Tomer , Sheban Fadi , Stoler-Barak Liat , Yalin Adam , Phan Truong San , Li Baoguo , Monteran Lea , Scharff Ye'ela , Giladi Amir , Elbaz Miriam , David Eyal , Gurevich-Shapiro Anna , Gur Chamutal , Shulman Ziv , Erez Neta , Amit Ido 
Published: September 2023

Abstract

Cancer mortality primarily stems from metastatic recurrence, emphasizing the urgent need for developing effective metastasis-targeted immunotherapies. To better understand the cellular and molecular events shaping metastatic niches, we used a spontaneous breast cancer lung metastasis model to create a single-cell atlas spanning different metastatic stages and regions. We found that premetastatic lungs are infiltrated by inflammatory neutrophils and monocytes, followed by the accumulation of suppressive macrophages with the emergence of metastases. Spatial profiling revealed that metastasis-associated immune cells were present in the metastasis core, with the exception of TREM2+ regulatory macrophages uniquely enriched at the metastatic invasive margin, consistent across both murine models and human patient samples. These regulatory macrophages (Mreg) contribute to the formation of an immune-suppressive niche, cloaking tumor cells from immune surveillance. Our study provides a compendium of immune cell dynamics across metastatic stages and niches, informing the development of metastasis-targeting immunotherapies.

Significance:
Temporal and spatial single-cell analysis of metastasis stages revealed new players in modulating immune surveillance and suppression. Our study highlights distinct populations of TREM2 macrophages as modulators of the microenvironment in metastasis, and as the key immune determinant defining metastatic niches, pointing to myeloid checkpoints to improve therapeutic strategies.
This article is featured in Selected Articles from This Issue, p. 2489
DNA2 Nuclease Inhibition Confers Synthetic Lethality in Cancers with Mutant p53 and Synergizes with PARP Inhibitors
Authors: Folly-Kossi Helena , Graves Joshua D. , Garan Lidija A. Wilhelms , Lin Fang-Tsyr , Lin Weei-Chin 
Published: September 2023

Abstract

The tumor suppressor p53 promotes tumor-suppressive activities including cell-cycle inhibition, apoptosis, senescence, autophagy, and DNA repair. However, somatic mutations in the TP53 gene are one of the most common alterations in human cancers. We previously showed that mutant p53 (mutp53) can bind TopBP1, an ATR activator, to attenuate its ATR-activating function. A partially defective ATR function caused by mutp53 makes cancer cells more vulnerable to inhibitors of other TopBP1-independent ATR activators, such as DNA2. DNA2 plays a role in homologous recombination (HR) repair by resecting DNA ends in double-strand breaks and preparing them for invasion of homologous duplex. Here we identify a new DNA2 inhibitor, namely d16, and show that d16 exhibits anticancer activities and overcomes chemotherapy resistance in mutp53-bearing cancers. Similar to DNA2 depletion, d16 treatment results in cell-cycle arrest mainly at S-phase. Moreover, reexpression of mutp53 in a p53-null cancer cell line makes cells more vulnerable to d16-mediated inhibition of ATR activity. As d16 also inhibits HR, a combination of d16 and PARP inhibitors displays synergistic induction of cell death. DNA2 is often overexpressed in cancer, particularly in cancer cells harboring mutp53. Overexpression of DNA2 is associated with poor outcome in ovarian cancer. Overall, our results provide a rationale to target DNA2 as a new synthetic lethality approach in mutp53-bearing cancers, and further extend the benefit of PARP inhibitors beyond BRCA-mutated cancers.

Significance:
This study identifies a new DNA2 inhibitor as a synthetic lethal targeted therapy for mutp53-harboring cancers, and provides a new therapeutic strategy by combining DNA2 inhibitors with PARP inhibitors for these cancers.
Contribution of Lipoprotein(a) to Polygenic Risk Prediction of Coronary Artery Disease: A Prospective UK Biobank Analysis
Authors: Manikpurage Hasanga D. , Paulin Audrey , Girard Arnaud , Eslami Aida , Mathieu Patrick , Thériault Sébastien , Arsenault Benoit J. 
Published: September 2023

Background:
Lp(a) (lipoprotein[a]) is a highly atherogenic lipoprotein subfraction that may contribute to polygenic risk of coronary artery disease (CAD), but the extent of this contribution is unknown. Our objective was to estimate the contribution of Lp(a) to polygenic risk of CAD and to evaluate the respective contributions of Lp(a) and a CAD polygenic risk score (PRS) to CAD.

Methods:
A total of 372 385 UK Biobank participants of European ancestry free of CAD at baseline were included. Plasma Lp(a) levels were measured and a CAD-PRS was calculated using the LDpred2 algorithm. Over the median follow-up of 12.6 years, 13 538 participants had incident CAD (myocardial infarction, coronary artery bypass grafting, or coronary angioplasty).

Results:

The
LPA
region contribution to the CAD-PRS-mediated CAD risk was modest (7.2% [95% CI, 6.1–8.3]). Lp(a) levels significantly increased the predictive performance of a CAD-PRS including age and sex in Cox regression (C statistic 0.751 versus 0.746, difference, 0.005 [95% CI, 0.004–0.006]). Compared with participants in the bottom CAD-PRS quintile with Lp(a) levels <25 nmol/L (CAD event rate, 1.4%), the hazard ratio for incident CAD in participants in the top CAD-PRS quintile with Lp(a) levels ≥125 nmol/L was 5.45 (95% CI, 4.93–6.03;
P
=9.35×10
-242
, CAD event rate 6.6%).

Conclusions:
Compared with individuals with a low genetic risk of CAD (low CAD-PRS and low Lp[a] levels), those with a high genetic risk (high CAD-PRS and high Lp[a] levels) had a 5-fold higher CAD risk. These results highlight a substantial contribution of genetic risk factors to CAD and that accurate estimation of genetic risk of CAD may need to consider blood levels of Lp(a).