bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimization of moderator materials by NSGA II based on macroscopic cross-sections: applications in accelerator neutron sources
Authors: Ge Yulin , Zhong Yao , Yuan Nan , Sun Yanbing , Yang Zhen , Ma Wei , Zou Liping , Murata Isao , Lu Liang
Published: August 2023

In recent years, genetic algorithms have been applied in
nuclear technology design, which have been shown to produce
optimized results more efficiently than traditional enumeration
methods. This advancement in optimization techniques is particularly
useful in the field of nuclear technology design, where complexity
is high and decision-making time is critical. It can be used to
optimize moderator materials for ANS to find composite materials
that provide high neutron beam quality. At present, the direct
combination of Monte Carlo method and genetic algorithm requires a
lot of computing resources and time. And the weights of different
optimization objectives are controversial. Thus, we propose a
two-step method based on NSGA II, which uses macroscopic section as
the intermediate parameters for optimization. It can greatly reduce
the time of genetic algorithm optimization. The method is applied to
the PAFA project of Sun Yat-sen University, the computational speed
has been increased by 50 times based on a 50-generation
optimization. And the results of the genetic algorithm show that the
neutron beam obtained by using composite materials as moderator is
30.8% better than that obtained by using only MgF2 as
moderator. The two-step genetic algorithm optimization has shown its
great potential in the optimization problem of moderator materials.
Data-driven plasma modelling: surrogate collisional radiative models of fluorocarbon plasmas from deep generative autoencoders
Authors: Daly G A , Fieldsend J E , Hassall G , Tabor G R
Published: August 2023

We have developed a deep generative model that can produce accurate optical emission spectra and colour images of an ICP plasma using only the applied coil power, electrode power, pressure and gas flows as inputs—essentially an empirical surrogate collisional radiative model. An autoencoder was trained on a dataset of 812 500 image/spectra pairs in argon, oxygen, Ar/O2, CF4/O2 and SF6/O2 plasmas in an industrial plasma etch tool, taken across the entire operating space of the tool. The autoencoder learns to encode the input data into a compressed latent representation and then decode it back to a reconstruction of the data. We learn to map the plasma tool’s inputs to the latent space and use the decoder to create a generative model. The model is very fast, taking just over 10 s to generate 10 000 measurements on a single GPU. This type of model can become a building block for a wide range of experiments and simulations. To aid this, we have released the underlying dataset of 812 500 image/spectra pairs used to train the model, the trained models and the model code for the community to accelerate the development and use of this exciting area of deep learning. Anyone can try the model, for free, on Google Colab.
A Psychosocial Model of COVID-19 Vaccination: Antecedent and Concurrent Effects of Demographics, Traits, Political Beliefs, Vaccine Intention, Information Sources, Mandates, and Flu Vaccine History
Authors: Godfrey Olivia , Bogg Tim , Milad Elizabeth
Published: August 2023

Background

To date, research investigating psychosocial correlates of COVID-19 vaccination has been cross-sectional, parochial, and/or reliant upon non-stratified international samples, resulting in difficulty in clarifying the contributions of various vaccination-related influences.

Purpose

The present study tested a novel integration of prospective and concurrent associations of demographic and dispositional tendencies, intervening illness and preventive beliefs, vaccine intention, illness experiences, and concurrent contextual vaccine-related influences with subsequent COVID-19 vaccination.

Methods

The preregistered study used a stratified online U.S. sample (N = 500), with assessments aligned to (a) “15 days to slow the spread” in March 2020, (b) vaccine authorization and major case/mortality surge during December 2020 and January 2021, and (c) the period following full vaccine approval in August 2021 during the third major/case mortality surge during September and October 2021.

Results

Path modeling showed the absence of children in the household and greater education were prospective predictors of vaccination. Trait openness and less conservative political beliefs showed indirect prospective associations with vaccination via stronger intermediating vaccine intention. Contextual vaccine-related influences of vaccine-related information sources, employer mandates, and flu vaccine history also showed direct associations with vaccination. In contrast to expectations, lower conscientiousness showed a direct prospective association with vaccination.

Conclusions

Controlling for interrelations among study variables, the results of the integrative psychosocial model clarified the unique contributions and pathways from antecedent characteristics to vaccination while accounting for vaccine-related contextual influences, providing further direction for refining the timing and content of public health messaging for vaccination.
Deep multi-view contrastive learning for cancer subtype identification
Authors: Chen Wenlan , Wang Hong , Liang Cheng
Published: August 2023

Cancer heterogeneity has posed great challenges in exploring precise therapeutic strategies for cancer treatment. The identification of cancer subtypes aims to detect patients with distinct molecular profiles and thus could provide new clues on effective clinical therapies. While great efforts have been made, it remains challenging to develop powerful computational methods that can efficiently integrate multi-omics datasets for the task. In this paper, we propose a novel self-supervised learning model called Deep Multi-view Contrastive Learning (DMCL) for cancer subtype identification. Specifically, by incorporating the reconstruction loss, contrastive loss and clustering loss into a unified framework, our model simultaneously encodes the sample discriminative information into the extracted feature representations and well preserves the sample cluster structures in the embedded space. Moreover, DMCL is an end-to-end framework where the cancer subtypes could be directly obtained from the model outputs. We compare DMCL with eight alternatives ranging from classic cancer subtype identification methods to recently developed state-of-the-art systems on 10 widely used cancer multi-omics datasets as well as an integrated dataset, and the experimental results validate the superior performance of our method. We further conduct a case study on liver cancer and the analysis results indicate that different subtypes might have different responses to the selected chemotherapeutic drugs.
CoCoNat: a novel method based on deep learning for coiled-coil prediction
Authors: Madeo Giovanni , Savojardo Castrense , Manfredi Matteo , Martelli Pier Luigi , Casadio Rita
Published: August 2023

Motivation

Coiled-coil domains (CCD) are widespread in all organisms and perform several crucial functions. Given their relevance, the computational detection of CCD is very important for protein functional annotation. State-of-the-art prediction methods include the precise identification of CCD boundaries, the annotation of the typical heptad repeat pattern along the coiled-coil helices as well as the prediction of the oligomerization state.

Results

In this article, we describe CoCoNat, a novel method for predicting coiled-coil helix boundaries, residue-level register annotation, and oligomerization state. Our method encodes sequences with the combination of two state-of-the-art protein language models and implements a three-step deep learning procedure concatenated with a Grammatical-Restrained Hidden Conditional Random Field for CCD identification and refinement. A final neural network predicts the oligomerization state. When tested on a blind test set routinely adopted, CoCoNat obtains a performance superior to the current state-of-the-art both for residue-level and segment-level CCD. CoCoNat significantly outperforms the most recent state-of-the-art methods on register annotation and prediction of oligomerization states.

Availability and implementation

CoCoNat web server is available at https://coconat.biocomp.unibo.it. Standalone version is available on GitHub at https://github.com/BolognaBiocomp/coconat.
Kernel interpolation generalizes poorly
Authors: Li Yicheng , Zhang Haobo , Lin Qian
Published: August 2023

One of the most interesting problems in the recent renaissance of the studies in kernel regression might be whether kernel interpolation can generalize well, since it may help us understand the ‘benign overfitting phenomenon’ reported in the literature on deep networks. In this paper, under mild conditions, we show that, for any ε>0, the generalization error of kernel interpolation is lower bounded by Ω(n−ε). In other words, the kernel interpolation generalizes poorly for a large class of kernels. As a direct corollary, we can show that overfitted wide neural networks defined on the sphere generalize poorly.
Postzygotic gain-of-function variants in FGFR2 in two patients with hair follicle naevus
Authors: Cheng Qing , Yang Fang , Xue Ruzeng , Wang Huijun , Lin Zhimiao
Published: August 2023

Hair follicle naevus (HFN) is a rare benign hamartoma that predominantly affects the face and neck. The genetic basis of HFN remains unclear. We report on two cases of HFN caused by pathozygotic gain-of-function variants in FGFR2.
The MLO-down on TDP-43
Authors: Dykstra Megan , Barmada Sami J
Published: August 2023

This scientific commentary refers to ‘Transactive response DNA-binding protein 43 is enriched at the centrosome in human cells’ by Bodin et al. (https://doi.org/10.1093/brain/awad228).
ChatGPT-3.5 and ChatGPT-4 dermatological knowledge level based on the Specialty Certificate Examination in Dermatology
Authors: Lewandowski Miłosz , Łukowicz Paweł , Świetlik Dariusz , Barańska-Rybak Wioletta
Published: August 2023

Background

The global use of artificial intelligence (AI) has the potential to revolutionize the healthcare industry. Despite the fact that AI is becoming more popular, there is still a lack of evidence on its use in dermatology.

Objectives

To determine the capacity of ChatGPT-3.5 and ChatGPT-4 to support dermatology knowledge and clinical decision-making in medical practice.

Methods

Three Specialty Certificate Examination in Dermatology tests, in English and Polish, consisting of 120 single-best-answer, multiple-choice questions each, were used to assess the performance of ChatGPT-3.5 and ChatGPT-4.

Results

ChatGPT-4 exceeded the 60% pass rate in every performed test, with a minimum of 80% and 70% correct answers for the English and Polish versions, respectively. ChatGPT-4 performed significantly better on each exam (P < 0.01), regardless of language, compared with ChatGPT-3.5. Furthermore, ChatGPT-4 answered clinical picture-type questions with an average accuracy of 93.0% and 84.2% for questions in English and Polish, respectively. The difference between the tests in Polish and English were not significant; however, ChatGPT-3.5 and ChatGPT-4 performed better overall in English than in Polish by an average of 8 percentage points for each test. Incorrect ChatGPT answers were highly correlated with a lower difficulty index, denoting questions of higher difficulty in most of the tests (P < 0.05).

Conclusions

The dermatology knowledge level of ChatGPT was high, and ChatGPT-4 performed significantly better than ChatGPT-3.5. Although the use of ChatGPT will not replace a doctor’s final decision, physicians should support the development of AI in dermatology to raise the standards of medical care.
Gene expression analyses of TAS1R taste receptors relevant to the treatment of cardiometabolic disease
Authors: Stavrou Mariah R , So Sean Souchiart , Finch Angela M , Ballouz Sara , Smith Nicola J
Published: August 2023

The sweet taste receptor (STR) is a G protein-coupled receptor (GPCR) responsible for mediating cellular responses to sweet stimuli. Early evidence suggests that elements of the STR signaling system are present beyond the tongue in metabolically active tissues, where it may act as an extraoral glucose sensor. This study aimed to delineate expression of the STR in extraoral tissues using publicly available RNA-sequencing repositories. Gene expression data was mined for all genes implicated in the structure and function of the STR, and control genes including highly expressed metabolic genes in relevant tissues, other GPCRs and effector G proteins with physiological roles in metabolism, and other GPCRs with expression exclusively outside the metabolic tissues. Since the physiological role of the STR in extraoral tissues is likely related to glucose sensing, expression was then examined in diseases related to glucose-sensing impairment such as type 2 diabetes. An aggregate co-expression network was then generated to precisely determine co-expression patterns among the STR genes in these tissues. We found that STR gene expression was negligible in human pancreatic and adipose tissues, and low in intestinal tissue. Genes encoding the STR did not show significant co-expression or connectivity with other functional genes in these tissues. In addition, STR expression was higher in mouse pancreatic and adipose tissues, and equivalent to human in intestinal tissue. Our results suggest that STR expression in mice is not representative of expression in humans, and the receptor is unlikely to be a promising extraoral target in human cardiometabolic disease.
High risk of rehospitalization within 1 year following a pulmonary embolism—insights from the Danish nationwide registries from 2000–2020
Authors: Sindet-Pedersen Caroline , El-Chouli Mohamad , Nouhravesh Nina , Lamberts Morten , Christensen Daniel Mølager , Kümler Thomas , Lock Morten , Grove Erik Lerkevang , Holt Anders , Schou Morten , Gislason Gunnar , Butt Jawad Haider , Strange Jarl Emanuel
Published: August 2023

Aim

To identify the absolute risk, causes, and factors associated with rehospitalization within 1 year of discharge with a pulmonary embolism (PE).

Methods and results

Using the Danish nationwide registries, all patients admitted with a first-time PE between 2000 and 2020 and discharged alive were included. Subsequent hospitalizations were categorized and crude cumulative incidences were used to estimate the absolute risk (AR) of any rehospitalization and specific causes of rehospitalizations. Risk factors for rehospitalization were investigated using cause specific Cox regression models.

A total of 55 201 patients were identified. The median age of the study population was 70 years (inter quartile range: 59;79), and the most prevalent comorbidities were cancer (29.3%) and ischemic heart disease (12.7%). The 1-year AR of any rehospitalization after discharge with a PE was 48.6% (95% confidence interval (CI); 48.2%–48.8%). The most common cause for being rehospitalized was due to respiratory disease [1-year AR: 9.5% (95% CI: 9.3%–9.8%)], followed by cardiovascular disease [1-year AR: 6.3% (95% CI: 5.9%–6.5%)], cancer [1-year AR: 6.0% (95% CI: 5.8%–6.4%)], venous thromboembolism [1-year AR: 5.2% (95% CI: 5.0%–5.2%)], and symptom diagnoses [1-year AR: 5.2% (95% CI: 5.0%–5.4%)]. Factors that were associated with an increased risk of rehospitalization were cancer, liver disease, chronic obstructive pulmonary disease, chronic kidney disease, and immobilization.

Conclusion

Patients with PE have a high risk of rehospitalization, with almost half of patients being rehospitalized within 1 year. Identification of high-risk patients may help target interventions aiming at reducing the risk of rehospitalization.
The Null Result Penalty
Authors: Chopra Felix , Haaland Ingar , Roth Christopher , Stegmann Andreas
Published: August 2023

We examine how the evaluation of research studies in economics depends on whether a study yielded a null result. Studies with null results are perceived to be less publishable, of lower quality, less important and less precisely estimated than studies with large and statistically significant results, even when holding constant all other study features, including the sample size and the precision of the estimates. The null result penalty is of similar magnitude among PhD students and journal editors. The penalty is larger when experts predict a large effect and when statistical uncertainty is communicated with p-values rather than standard errors. Our findings highlight the value of a pre-result review.
Effectiveness of adding a defibrillator with cardiac resynchronization therapy in heart failure according to the modified Model for End-stage Liver Disease-Albumin score
Authors: Cheng Sijing , Deng Yu , Huang Hao , Yu Yu , Niu Hongxia , Hua Wei
Published: August 2023

Current guidelines lack clear recommendations between the implantation of cardiac resynchronization therapy (CRT) with defibrillator (CRT-D) and CRT with pacemaker (CRT-P). We hypothesized that modified model for end-stage liver disease score including albumin (MELD-Albumin score), could be used to select patients who may not benefit from CRT-D. We consecutively included patients with CRT-P or CRT-D implantation between 2010 and 2022. The primary endpoint was the composite of all-cause mortality or worsening heart failure. We performed multivariable-adjusted Cox proportional hazard regression. We assessed the interaction between the MELD-Albumin score and the effect of adding a defibrillator with CRT.A total of 752 patients were included in this study, with 291 implanted CRT-P. During a median follow-up of 880 days, 205 patients reached the primary endpoint. MELD-Albumin score was significantly associated with the primary endpoint in the CRT-D group [HR 1.16 (1.09–1.24); P < 0.001] but not in the CRT-P group [HR 1.03 (0.95–1.12); P = 0.49]. There was a significant interaction between the MELD-Albumin score and the effect of CRTD (P = 0.013). The optimal cut-off value of the MELD-Albumin score was 12. For patients with MELD-Albumin ≥ 12, CRT-D was associated with a higher occurrence of the primary endpoint [HR 1.99 (1.10–3.58); P = 0.02], whereas not in patients with MELD-Albumin < 12 [HR 1.19 (0.83–1.70); P = 0.35). Our findings suggest that CRT-D is associated with an excess risk of composite clinical endpoints in HF patients with higher MELD-Albumin score.
Converted-wave reverse time migration imaging in subduction zone settings
Authors: Langer Leah , Pollitz Fred F , McGuire Jeffrey J
Published: August 2023

We use a newly developed 2-D elastic reverse time migration (RTM) imaging algorithm based on the Helmholtz decomposition to test approaches for imaging the descending slab in subduction zone regions using local earthquake sources. Our elastic RTM method is designed to reconstruct incident and scattered wavefields at depth, isolate constituent P- and S-wave components via Helmholtz decomposition, and evaluate normalized imaging functions that leverage dominant P and S signals. This method allows us to target particular converted-wave scattering geometries, for example incident S to scattered P, which may be expected to have dominant signals in any given data set. The method is intended to be applied to dense seismic array observations that adequately capture both incident and converted wavefields. We draw a direct connection between our imaging functions and the first-order contrasts in shear wave material properties across seismic discontinuities. Through tests on synthetic data using either S → P or P → S conversions, we find that our technique can successfully recover the structure of a subducting slab using data from a dense wide-angle array of surface stations. We also calculate images with a small-aperture array to test the impact of array geometry on image resolution and interpretability. Our results show that our imaging technique is capable of imaging multiple seismic discontinuities at depth, even with a small number of earthquakes, but that limitations arise when a small aperture array is considered. In this case, the presence of artefacts makes it more difficult to determine the location of seismic discontinuities.
Strategies of youth engagement in health promotion: listening sessions, task force participation, surveys and other strategies
Authors: Ingman Benjamin C , Maras Elly Q , Loecke Carla
Published: August 2023

Youth engagement is often purported as a critical dimension of health promotion for young people, but the strategies used to facilitate this engagement are seldom evaluated or studied. This study explored the strategies used to engage youth in a strategic planning process to develop comprehensive health and wellness plans in 28 US school districts. Participating school districts conducted listening sessions, administered anonymous surveys, included youth on a district task force, and employed other strategies to engage youth. Following this initiative, semi-structured interviews were conducted with representatives from all school districts (n = 34) to enumerate the use of these strategies across districts and understand their perspectives related to the effectiveness and importance of these strategies for engaging youth in health promotion. The most prevalent strategy used by districts was listening sessions (27 districts; 564 youth), followed by including youth on the task force (19 districts; 39 youth), anonymous surveys (18 districts; 1988 youth) and other methods (5 districts). Interviewees clarified the benefits and challenges of each strategy and provided commentary on youth engagement for health promotion. The results stress the importance of building trusting relationships with youth, using multiple strategies to engage youth, and embodying an equity mindset throughout the development and implementation of youth engagement efforts.
Urban–rural differences in perceived environmental opportunities for physical activity: a 2002–2017 time-trend analysis in Europe
Authors: Moreno-Llamas Antonio , García-Mayor Jesús , De la Cruz-Sánchez Ernesto
Published: August 2023

Urban–rural disparities in resources, services and facilities not only impact daily living conditions but also contribute to inequalities in physical activity, which may be associated with variations in basic public resources between urban and rural areas. This study aims to examine the evolution of perceived opportunities for physical activity in European urban and rural environments from 2002 to 2017 and their association with an active lifestyle. Data from four waves (2002, 2005, 2013 and 2017) of cross-sectional Eurobarometer surveys were collected (n = 101 373), and multilevel binomial logistic regressions were conducted. Firstly, the time trend of perceived opportunities for physical activity between urban and rural environments was explored, and secondly, the effect of urban–rural perceived opportunities on achieving an active lifestyle over the years was estimated. The findings revealed that individuals residing in rural settings encountered less opportunities to be physically active. Conversely, urban settings experienced an increase in perceived opportunities. The significance of health promotion through perceived physical activity opportunities lies in the increased likelihood of being physically active, regardless of place of residence or individual socioeconomic factors [in the area: odds ratio (OR) = 1.40, 95% confidence interval (CI) = 1.34–1.47; provided by local sport clubs: OR = 1.29, 95% CI = 1.23–1.35]. Modifying environmental aspects, such as enhancing the quantity, quality and accessibility of physical activity opportunities in both rural and urban areas, may lead to improved physical activity and health promotion, particularly among individuals who are more physically inactive.
In Vitro Comparison of Ulotaront (SEP-363856) and Ralmitaront (RO6889450): Two TAAR1 Agonist Candidate Antipsychotics
Authors: Ågren Richard , Betari Nibal , Saarinen Marcus , Zeberg Hugo , Svenningsson Per , Sahlholm Kristoffer
Published: August 2023

Background

Trace amine-associated receptor-1 (TAAR1) agonists have been proposed as potential antipsychotics, with ulotaront and ralmitaront having reached clinical trials. While ulotaront demonstrated efficacy in a recent Phase II trial, a corresponding study studies of ralmitaront failed to show efficacy as a monotherapy or as an adjunct to atypical antipsychotics. In addition to TAAR1 agonism, ulotaront is a partial agonist at the serotonin 1A receptor (5-HT1AR). However, little is known about ralmitaront.

Methods

We compared ulotaront and ralmitaront at TAAR1, 5-HT1AR, and dopamine D2 using luciferase complementation-based G protein recruitment, cAMP accumulation, and G protein–coupled inward rectifier potassium channel activation assays.

Results

Ralmitaront showed lower efficacy at TAAR1 in G protein recruitment, cAMP accumulation, and GIRK activation assays. Moreover, ralmitaront lacked detectable activity at 5-HT1AR and dopamine D2.

Conclusions

Compared with ulotaront, ralmitaront shows lower efficacy and slower kinetics at TAAR1 and lacks efficacy at 5-HT1AR. These data may be relevant to understanding differences in clinical profiles of these 2 compounds.
Elevated preoperative plasma D-dimer level was an independent prognostic factor for patients with PDAC after curative resection: a retrospective analysis
Authors: Zhifei Li , Yuexiang Liang , Shaofei Chang , Shuo Li , Hongwei Wang , Chuntao Gao
Published: August 2023

Objective

In this study, the relationship between preoperative plasma D-dimer level and overall survival and recurrence free survival were evaluated in patients with curative resection of pancreatic ductal adenocarcinoma.

Methods

Preoperative plasma D-dimer level of 573 patients with pancreatic ductal adenocarcinoma were collected. The univariate and multivariate Cox hazard models were used to identify independent variables associated with overall survival and recurrence free survival in this study. The Kaplan–Meier method was used to evaluate overall survival and recurrence free survival, and the differences between survival curves were analyzed using the Log-rank test. Continuous variables were presented as $\overline{x}\pm s$, parametric analysis was performed using t-test. Categorical variables were analyzed by means of the chi-square or Fisher’s exact test.

Results

Based on the analysis for the whole study, the results showed that patients in the elevated plasma D-dimer levels had a tendency to have an elder mean age (58.69 ± 8.32 years vs. 63.05 ± 8.44 years, P < 0.001), larger tumour size ≥4 cm (P = 0.006), advanced T stage (P = 0.024), N stage (P = 0.041), Tumor, Node and Metastasis (TNM) stage (P = 0.029) and postoperative complications (P = 0.042) was more likely occurred. Besides, according to the results of Cox multivariate analysis, elevated preoperative plasma D-dimer level was an independent prognostic factor not only for overall survival (Hazard Ratio (HR):1.430, 95% Confidence Interval (CI) (1.163–1.759), P = 0.001) but also for recurrence free survival (HR:1.236, 95% CI (1.018–1.500), P = 0.032).

Conclusion

In our study, the elevated preoperative plasma D-dimer level may act as an independent prognostic factor for overall survival and recurrence free survival in patients with pancreatic ductal adenocarcinoma after curative resection. Pancreatic ductal adenocarcinoma patients with elevated preoperative plasma D-dimer level had a worse prognosis than those with normal plasma D-dimer level; and the elevated preoperative plasma D-dimer level may imply heavy tumour burden and provide supplementary information regarding disease status.
Evaluating the roughness dynamics of kefir biofilms grown on Amazon cupuaçu juice: a monofractal and multifractal approach
Authors: Matos Robert S , Pinto Erveton P , Pires Marcelo A , Ramos Glenda Q , Ţălu Ştefan , Lima Lucas S , da Fonseca Filho Henrique D
Published: August 2023

We conducted a comprehensive analysis of the surface microtexture of kefir biofilms grown on Theobroma grandiflorum Shum (cupuaçu) juice using atomic force microscopy. Our goal was to investigate the unique monofractal and multifractal spatial patterns of these biofilms to complement the existing limited literature. The biofilms were prepared dispersing four different concentrations of kefir grains in cupuaçu juice. Our morphological analysis showed that the surface of the obtained biofilms is essentially formed by the presence of cupuaçu fibers and microorganisms like lactobacilli and yeast. The topographic height-based parameter analysis reveals that there is a dependence between surface roughness and the concentration of kefir grains used. The strongly anisotropic well-centralized topographical height distribution of the biofilms also exhibited a quasi-symmetrical and platykurtic pattern. The biofilms exhibit comparable levels of spatial complexity, surface percolation and surface homogeneity, which can be attributed to their similar topographic uniformity. This aspect was further supported by the presence of similar multifractality in the biofilms, suggesting that despite their varying topographic roughness, their vertical growth dynamics follow a similar pattern. Our findings demonstrate that the surface roughness of kefir biofilms cultivated on cupuaçu juice is influenced by the concentration of kefir grains in the precursor solution. However, this dependence follows a consistent pattern across different concentrations.

Graphical Abstract
Genomic alterations affecting tumor-infiltrating lymphocytes and PD-L1 expression patterns in triple-negative breast cancer
Authors: Wang Han , Ding Xiao-Hong , Liu Cheng-Lin , Xiao Yi , Shui Ruo-Hong , Li Yan-Ping , Chen Chen , Yang Wen-Tao , Liu Suling , Chen Ce-Shi , Shao Zhi-Ming , Jiang Yi-Zhou
Published: August 2023

Background

Tumor-infiltrating lymphocytes (TILs) and programmed cell death 1 ligand 1 (PD-L1) remain imperfect in predicting clinical outcomes of triple-negative breast cancer because outcomes do not always correlate with the expression of these biomarkers. Genomic and transcriptomic alterations that may contribute to the expression of these biomarkers remain incompletely uncovered.

Methods

We evaluated PD-L1 immunohistochemistry scores (SP142 and 28-8 assays) and TILs in our triple-negative breast cancer multiomics dataset and 2 immunotherapy clinical trial cohorts. Then, we analyzed genomic and transcriptomic alterations correlated with TILs, PD-L1 expression, and patient outcomes.

Results

Despite TILs serving as a decent predictor for triple-negative breast cancer clinical outcomes, exceptions remained. Our study revealed that several genomic alterations were correlated with unexpected events. In particular, PD-L1 expression may cause a paradoxical relationship between TILs and prognosis in certain patients. Consequently, we classified triple-negative breast cancers into 4 groups based on PD-L1 and TIL levels. The TIL-negative PD-L1–positive and TIL-positive PD-L1–negative groups were not typical “hot” tumors; both were associated with worse prognoses and lower immunotherapy efficacy than TIL-positive PD-L1–positive tumors. Copy number variation of PD-L1 and oncogenic signaling activation were correlated with PD-L1 expression in the TIL-negative PD-L1–positive group, whereas GSK3B-induced degradation may cause undetectable PD-L1 expression in the TIL-positive PD-L1–negative group. These factors have the potential to affect the predictive function of both PD-L1 and TILs.

Conclusions

Several genomic and transcriptomic alterations may cause paradoxical effects among TILs, PD-L1 expression, and prognosis in triple-negative breast cancer. Investigating and targeting these factors will advance precision immunotherapy for patients with this disease.
Crosstalk between ABA and ethylene in regulating stomatal behavior in tomato under high CO2 and progressive soil drying
Authors: Liang Kehao , Chen Xuefei , Liu Fulai
Published: August 2023

Increasing atmospheric CO2 concentrations accompanied by intensifying drought markedly impact plant growth and physiology. This study aimed to explore the role of abscisic acid (ABA) in mediating the response of stomata to elevated CO2 (e[CO2]) and drought. Tomato plants with different endogenous ABA concentrations [Ailsa Craig (AC), the ABA-deficient mutant flacca, and ABA-overproducing transgenic tomato SP5] were grown in ambient (a[CO2], 400 μmol mol–1) and elevated (e[CO2],800 μmol mol–1) CO2 environments and subjected to progressive soil drying. Compared with a[CO2] plants, e[CO2] plants had significantly lower stomatal conductance in AC and SP5 but not in flacca. Under drought, e[CO2] plants had better water status and higher water use efficiency. e[CO2] promoted the accumulation of ABA in leaves of plants subjected to drought, which coincided with the up-regulation of ABA biosynthetic genes and down-regulation of ABA metabolic genes. Although the increase of ABA induced by drought in flacca was much less than in AC and SP5, flacca accumulated large amounts of ethylene, suggesting that in plants with ABA deficiency, ethylene might play a compensatory role in inducing stomatal closure during soil drying. Collectively, these findings improve our understanding of plant performance in a future drier and higher-CO2 environment.
Emotions: functions and significance for attitudes, behaviour, and communication
Authors: Dennison James
Published: August 2023

Emotions are regularly cited as vital components of effective strategic communication. However, there is relatively little guidance about how emotions should be used. Eliciting emotions is key to persuasion because attitudes have a cognitive and emotive component, with predictable physiological outcomes that make messages more resonant and impactful on behaviour, supporting policy objectives. This article shows that communicators—in the field of migration and beyond—should choose their campaign’s emotional frame according to their desired physiological and behavioural reaction. This article applies the emotion schema of Plutchik to offer 32 separate emotions and their theorised physiological reactions, examples of stimuli, and behavioural societal effects. Furthermore, emotional outcomes can be altered via narratives, frames, personal-based messages, facial expressions and body language, aesthetics, ordering (‘emotional flow’), intensities, and combinations. Finally, the limits of emotion-based communication—not least the ‘appeal to emotion’ logical fallacy—and how to overcome those limits—grounding emotion-based communication in facts, values, identities, and efficacy—are considered. Emotion-based communication in the field of migration, although widely used, is largely untested so communicators should test different approaches but also can take lessons from fields such as corporate, health, and climate change communication.
Standing Tall: Do Height-Based Accountability Incentives Predict Artificial Increases in Measured Height Among Sailors in the U.S. Military?
Authors: Heissel Jennifer A , Healy Olivia J , Burke Ollieanna , Lopez Cristina
Published: August 2023

Introduction

The objective of this study was to investigate the changes in men’s and women’s measured height in response to weight gain above standards for the U.S. Navy and to quantify associated distortions in body mass index (BMI). We expected that some servicemembers would manipulate their measured height to comply with service standards.

Materials and Methods

The study was a retrospective observational study. The data were housed in the Person-Event Data Environment, an individual-level administrative registry from the United States Department of Defense. All participants were active-duty U.S. Navy sailors aged 21–50 during the years 2010–2019. The main outcomes were height and weight as recorded during twice-yearly physical fitness assessments and BMI calculated as: height in pounds × 703/(height in inches)2. We assessed whether weight gain above standards was associated with an increase in height at the subsequent height–weight assessment.

Results

Among the 489,020 sailors, individuals were nearly 1.5 times as likely to measure taller when they gained weight that put them above military height–weight standards as compared to those who continued to remain within standards. Men were more often out of standards and therefore their measured height increased during subsequent assessments more often than women. Increases in height depressed measures of BMI slightly.

Conclusions

Among U.S. sailors, taller height was correlated with surpassing height-based weight limits, where taller individuals were allowed to weigh more and still meet professional weight standards. Results underscore that current height–weight accountability standards may distort behavior, leading servicemembers to manipulate measurements rather than improve job-relevant fitness. Instead, greater reliance on fitness-based measures of health, such as fitness tests, may hold promise for upholding servicemember readiness. Our results highlight that when stakes are attached to a measure, individuals may work to raise their performance using strategies that are misaligned with the policy intent.
CAFE-AMR: a computational MHD solar physics simulation tool that uses AMR
Authors: Ochoa-Armenta Ricardo , Guzmán Francisco S
Published: August 2023

The study of our Sun holds significant importance in space weather research, encompassing a diverse range of phenomena characterized by distinct temporal and spatial scales. To address these complexities, we developed CAFE-AMR, an implementation of an adaptive mesh refinement (AMR) strategy coupled with a magnetohydrodynamics (MHD) equation solver, aiming to tackle solar-physics-related problems. CAFE-AMR employs standard fluid dynamics methods, including finite-volume discretization, HLL and Roe class flux formulas, linear order reconstructors, second-order Runge–Kutta, and corner transport upwind time stepping. In this paper, we present the core structure of CAFE-AMR, discuss and evaluate mesh refinement criteria strategies, and conduct various tests, including simulations of idealized solar wind models, relevant for space weather applications.
The accretion/ejection link in the neutron star X-ray binary 4U 1820-30 I: a boundary layer-jet coupling?
Authors: Marino A , Russell T D , Del Santo M , Beri A , Sanna A , Coti Zelati F , Degenaar N , Altamirano D , Ambrosi E , Anitra A , Carotenuto F , D’Aì A , Di Salvo T , Manca A , Motta S E , Pinto C , Pintore F , Rea N , van den Eijnden J
Published: August 2023

The accretion flow/jet correlation in neutron star (NS) low-mass X-ray binaries (LMXBs) is far less understood when compared to black hole (BH) LMXBs. In this paper we will present the results of a dense multiwavelength observational campaign on the NS LMXB 4U 1820-30, including X-ray (NICER, NuSTAR, and AstroSat) and quasi-simultaneous radio (ATCA) observations in 2022. 4U 1820-30 shows a peculiar 170 d super-orbital accretion modulation, during which the system evolves between ‘modes’ of high and low X-ray flux. During our monitoring, the source did not show any transition to a full hard state. X-ray spectra were well described using a disc blackbody, a Comptonization spectrum along with a Fe K emission line at ∼6.6 keV. Our results show that the observed X-ray flux modulation is almost entirely produced by changes in the size of the region providing seed photons for the Comptonization spectrum. This region is large (∼15 km) in the high mode and likely coincides with the whole boundary layer, while it shrinks significantly (≲10 km) in low mode. The electron temperature of the corona and the observed rms variability in the hard X-rays also exhibit a slight increase in low mode. As the source moves from high to low mode, the radio emission due to the jet becomes ∼5 fainter. These radio changes appear not to be strongly connected to the hard-to-soft transitions as in BH systems, while they seem to be connected mostly to variations observed in the boundary layer.
Observational constraints on the origin of the elements – VI. Origin and evolution of neutron-capture elements as probed by the Gaia-ESO survey
Authors: Lian Jianhui , Storm Nicholas , Guiglion Guillaume , Serenelli Aldo , Cote Benoit , Karakas Amanda I , Boardman Nicholas , Bergemann Maria
Published: August 2023

Most heavy elements beyond the iron peak are synthesized via neutron capture processes. The nature of the astrophysical sites of neutron capture processes is still very unclear. In this work, we explore the observational constraints of the chemical abundances of s-process and r-process elements on the sites of neutron-capture processes by applying Galactic chemical evolution (GCE) models to the data from Gaia-ESO large spectroscopic stellar survey. For the r-process, the [Eu/Fe]–[Fe/H] distribution suggests a short delay time of the site that produces Eu. Other independent observations (e.g. NS–NS binaries), however, suggest a significant fraction of long delayed (>1 Gyr) neutron star mergers (NSM). When assuming NSM as the only r-process sites, these two observational constraints are inconsistent at above 1σ level. Including short delayed r-process sites like magnetorotational supernova can resolve this inconsistency. For the s-process, we find a weak metallicity dependence of the [Ba/Y] ratio, which traces the s-process efficiency. Our GCE model with up-to-date yields of AGB stars qualitatively reproduces this metallicity dependence, but the model predicts a much higher [Ba/Y] ratio compared to the data. This mismatch suggests that the s-process efficiency of low-mass AGB stars in the current AGB nucleosynthesis models could be overestimated.
Primordial power spectrum in light of JWST observations of high redshift galaxies
Authors: Parashari Priyank , Laha Ranjan
Published: August 2023

Early data releases of JWST have revealed several high redshift massive galaxy candidates by photometry, and some of them have been confirmed spectroscopically. We study their implications on the primordial power spectrum. In the first part, we use the CEERS photometric survey data, along with respective spectroscopic updates, to compute the cumulative comoving stellar mass density. We find that a very high star formation efficiency (unlikely in various theoretical scenarios) is required to explain these observations within Lambda cold dark matter (ΛCDM) cosmology. We show that the tension can be eased if the primordial power spectrum has a blue tilt. In the second part, we study spectroscopically confirmed galaxies reported in the JADES survey to investigate their implications on a red-tilted primordial power spectrum. We estimate the star formation efficiency from an earlier observation at similar redshift by Spitzer, and find that the star formation efficiency is an order of magnitude smaller than required to explain the CEERS photometric observations mentioned earlier. Using the estimated star formation efficiency, we find the strongest constraints on the red tilt of the power spectrum over some scales. Our study shows that JWST will be an excellent probe of the power spectrum and can lead to novel discoveries.
4U 1626−67 returns to spin-down: timing features toe the line
Authors: Sharma Rahul , Jain Chetana , Paul Biswajit
Published: August 2023

We present a comprehensive analysis of X-ray pulsar  4U 1626−67 during its current spin-down (2SD) state, following a recent torque reversal. Since its discovery, this ultra-compact binary has experienced multiple torque states, transitioning from spin-up (1SU) during 1977–1990 to spin-down (1SD) during 1990–2008, and again spin-up (2SU) until 2023. From  Nuclear Spectroscopic Telescope ARray observation of May 2023, we have investigated the timing and spectral properties of this pulsar during its 2SD phase, while also comparing them with previous spin-up-down states. For energies up to 8 keV, a distinct bi-horned pulse profile was observed during the spin-up phase, while several substructures emerged during spin-down. Beyond 8 keV, a broad asymmetric peak was consistently observed across all torque states. The pulse fraction during the 2SD phase was higher than that during 2SU phase. A prominent ∼46.8 mHz quasi-periodic oscillation has been exclusively detected during the spin-down phase. The broad-band spectrum during the 2SD phase is described by empirical Negative and Positive power-law with Exponential cutoff model, cyclotron absorption feature and its first harmonic. The spectrum during 2SU phase requires an additional blackbody component and asymmetry in the cyclotron absorption line. A significant flux drop by a factor of ∼3 in the 2SD was observed.
IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data
Authors: Peres Ayelet , Lees William D , Rodriguez Oscar L , Lee Noah Y , Polak Pazit , Hope Ronen , Kedmi Meirav , Collins Andrew M , Ohlin Mats , Kleinstein Steven H , Watson Corey T , Yaari Gur
Published: August 2023

In adaptive immune receptor repertoire analysis, determining the germline variable (V) allele associated with each T- and B-cell receptor sequence is a crucial step. This process is highly impacted by allele annotations. Aligning sequences, assigning them to specific germline alleles, and inferring individual genotypes are challenging when the repertoire is highly mutated, or sequence reads do not cover the whole V region. Here, we propose an alternative naming scheme for the V alleles, as well as a novel method to infer individual genotypes. We demonstrate the strengths of the two by comparing their outcomes to other genotype inference methods. We validate the genotype approach with independent genomic long-read data. The naming scheme is compatible with current annotation tools and pipelines. Analysis results can be converted from the proposed naming scheme to the nomenclature determined by the International Union of Immunological Societies (IUIS). Both the naming scheme and the genotype procedure are implemented in a freely available R package (PIgLET https://bitbucket.org/yaarilab/piglet). To allow researchers to further explore the approach on real data and to adapt it for their uses, we also created an interactive website (https://yaarilab.github.io/IGHV_reference_book).