bluuebunny/crossref_metadata_2025 huggingface dataset:
New angles on fast calorimeter shower simulation
Authors: Diefenbacher Sascha , Eren Engin , Gaede Frank , Kasieczka Gregor , Korol Anatolii , Krüger Katja , McKeown Peter , Rustige Lennart
Published: August 2023

The demands placed on computational resources by the simulation requirements of high energy physics experiments motivate the development of novel simulation tools. Machine learning based generative models offer a solution that is both fast and accurate. In this work we extend the Bounded Information Bottleneck Autoencoder (BIB-AE) architecture, designed for the simulation of particle showers in highly granular calorimeters, in two key directions. First, we generalise the model to a multi-parameter conditioning scenario, while retaining a high degree of physics fidelity. In a second step, we perform a detailed study of the effect of applying a state-of-the-art particle flow-based reconstruction procedure to the generated showers. We demonstrate that the performance of the model remains high after reconstruction. These results are an important step towards creating a more general simulation tool, where maintaining physics performance after reconstruction is the ultimate target.
Wet etching of gold on graphene for high-quality resist-free graphene surfaces
Authors: Kunc J , Shestopalov M , Jo J , Park K
Published: August 2023

Wet etching of gold on graphene is challenging due to the weak adhesion of the resist mask to graphene. We report an operating procedure for alkali ion-free wet etching of gold on graphene using a mixture of hydrochloric and nitric acids (aqua regia) with a high lateral resolution down to 100 nm. We investigate the role of positive and negative resists, electron beam lithography (EBL) dose, hard-bake, oxygen etching, aging, and sensitivity to the etch parameters, such as the freshness of dilute aqua regia, etch time, and the order of etched samples. The negative-tone resist provides the best results. The over-dosed EBL exposure can enhance the resist adhesion, as hard-bake below the glass-transition temperature and well-defined wet etch of the resist-residua-free gold surface. We also present a cleaning procedure to avoid bubble formation after the hard bake. Our results demonstrate that wet etching of gold on graphene using aqua regia is a viable method for achieving high-quality resist-free graphene surfaces. This method has potential applications in graphene nanoelectronics and nanophotonics, where high-quality graphene surfaces are essential for device performance.
Less favourable food consumption ratings in the Five-Color Nutri-Score are associated with incident frailty in older adults
Authors: Rey-García Jimena , Donat-Vargas Carolina , Sandoval-Insausti Helena , Banegas José R , Dominguez Ligia J , Rodríguez-Artalejo Fernando , Guallar-Castillón Pilar
Published: August 2023

Background

The Nutri-Score front-of-package labelling classifies food products according to their nutritional quality, so healthier food choices are easier when shopping. This study prospectively assesses the association of a diet rated according to the Nutri-Score system and incident frailty in community-dwelling older adults.

Methods

Cohort study with 1,875 individuals aged ≥60 recruited during 2008–2010 in Spain. At baseline, food consumption was assessed using a validated dietary history. Food was categorised into five Nutri-Score labels (A/green—best quality; B, C, D, E/red—worst quality) utilising an algorithm established in 2017 and currently in use. For each participant, a Five-Color Nutri-Score Dietary Index (5-CNS DI) in grams per day per kilogram was calculated. The 5-CNS DI sums up the grams per day of food consumed times their corresponding nutritional quality value (from A rated as 1 to E rated as 5) and divided by weight in kilograms. From baseline to December 2012, incident frailty was ascertained based on Fried’s criteria. Statistical analyses were performed with logistic regression adjusted for main confounders.

Results

After a mean follow-up of 3.5 years, 136 cases of frailty were identified. The multivariable-adjusted odds ratios (95% confidence interval) of incident frailty across increasing quartiles of the 5-CNS DI were 1, 1.51 (0.86–2.68), 1.56 (0.82–2.98) and 2.32 (1.12–4.79); P-trend = 0.033. The risk of frailty increased by 28% (3–58%) with a 10-unit increment in this dietary index. Similar results were found with the Nutri-Score algorithm modified in 2022.

Conclusions

consumption of a diet with less favourable Nutri-Score ratings doubles the risk of frailty among community-dwelling older adults.
Associations Between Executive Functioning, Behavioral Functioning, and Adaptive Functioning Difficulties in Wiedemann–Steiner Syndrome
Authors: Ng Rowena , Bjornsson Hans Tomas , Fahrner Jill A , Harris Jacqueline
Published: August 2023

Objectives

Wiedemann–Steiner syndrome (WSS) is a neurogenetic disorder caused by heterozygous variants in KMT2A. Recent investigations suggest increased anxiety and behavior regulation challenges among those with WSS although the neurobehavioral phenotype remains largely unknown. This study aims to examine the pattern of and associations between executive functioning (EF) and behavior functioning among those with WSS.

Method

This study involved utilizing caregiver-report inventories (Behavior Rating Inventory of Executive Function 2nd Edition, BRIEF-2; Adaptive Behavior Assessment 3rd Edition, ABAS-3; Strengths and Difficulties Questionnaire, SDQ) to assess day-to-day behavior functioning among those with WSS (N = 24; mean age = 10.68 years, SD = 3.19). Frequency of clinical elevations in daily difficulties in EF, adaptive behaviors, and behavior regulation were reported. Correlations and hierarchical linear regressions were used to determine the relationships between EF with behavior and adaptive functioning.

Results

Out of our sample, 63% met clinical levels of executive functioning difficulties on the BRIEF-2, and 75% with Hyperactivity and 54% with Emotional Problems on the SDQ. In addition, 33% were rated >2 SD below the normative mean in overall adaptive functioning on the ABAS-3. Elevated ratings in BRIEF-2 Shift, reflective of challenges with mental flexibility, predicted more Emotional Problems and accounted for 33.5% of its variance. More difficulties in Emotional Control were related to greater adaptive deficits, accounting for 33.3% of its variance.

Conclusions

Those with WSS are at risk for EF deficits, hyperactivity, and emotional dysregulation. EF correlates with adaptive and affective behaviors, highlighting the promise of behavioral interventions to target cognitive flexibility, emotional awareness, and reactivity in this population.
Secreted arabinogalactan protein from salt-adapted tobacco BY-2 cells appears to be glycosylphosphatidyl inositol-anchored and associated with lipophilic moieties
Authors: Nweke Arinze Boniface , Nagasato Daiki , Matsuoka Ken
Published: August 2023

Arabinogalactan proteins (AGPs) are plant extracellular proteoglycans associated with the plasma membrane by a glycosylphosphatidylinositol (GPI) anchor. This moiety is thought to be cleaved by phospholipase for secretion. Salt-adapted tobacco BY-2 cells were reported to secrete large amounts of AGPs into the medium. To investigate this mechanism, we expressed a fusion protein of tobacco sweet potato sporamin and AGP (SPO-AGP) in BY-2 cells and analyzed its fate after salt-adapting the cells. A two-phase separation analysis using Triton X-114 indicated that a significant proportion of SPO-AGP in the medium was recovered in the detergent phase, suggesting that this protein is GPI-anchored. Differential ultracentrifugation and a gradient density fractionation implicated extracellular vesicles or particles with SPO-AGP in the medium. Endogenous AGP secreted from salt-adapted and nontransgenic BY-2 cells behaved similarly to SPO-AGP. These results suggest that a part of the secreted AGPs from salt-adapted tobacco BY-2 cells are GPI-anchored and associated with particles or vesicles.
CMMS-GCL: cross-modality metabolic stability prediction with graph contrastive learning
Authors: Du Bing-Xue , Long Yahui , Li Xiaoli , Wu Min , Shi Jian-Yu
Published: August 2023

Motivation

Metabolic stability plays a crucial role in the early stages of drug discovery and development. Accurately modeling and predicting molecular metabolic stability has great potential for the efficient screening of drug candidates as well as the optimization of lead compounds. Considering wet-lab experiment is time-consuming, laborious, and expensive, in silico prediction of metabolic stability is an alternative choice. However, few computational methods have been developed to address this task. In addition, it remains a significant challenge to explain key functional groups determining metabolic stability.

Results

To address these issues, we develop a novel cross-modality graph contrastive learning model named CMMS-GCL for predicting the metabolic stability of drug candidates. In our framework, we design deep learning methods to extract features for molecules from two modality data, i.e. SMILES sequence and molecule graph. In particular, for the sequence data, we design a multihead attention BiGRU-based encoder to preserve the context of symbols to learn sequence representations of molecules. For the graph data, we propose a graph contrastive learning-based encoder to learn structure representations by effectively capturing the consistencies between local and global structures. We further exploit fully connected neural networks to combine the sequence and structure representations for model training. Extensive experimental results on two datasets demonstrate that our CMMS-GCL consistently outperforms seven state-of-the-art methods. Furthermore, a collection of case studies on sequence data and statistical analyses of the graph structure module strengthens the validation of the interpretability of crucial functional groups recognized by CMMS-GCL. Overall, CMMS-GCL can serve as an effective and interpretable tool for predicting metabolic stability, identifying critical functional groups, and thus facilitating the drug discovery process and lead compound optimization.

Availability and implementation

The code and data underlying this article are freely available at https://github.com/dubingxue/CMMS-GCL.
Comparative Analysis of Practice Research in Australia and the UK: The Shift to Practice-driven Research
Authors: Webber Martin , Joubert Lynette
Published: August 2023

Australia and the UK share many historic connections. These connections have influenced developments in welfare systems, and the bi-directional migration of social work practitioners between Australia and the UK has helped to support the sharing of knowledge in social work education, research and practice. However, developments in practice research in both countries has largely been influenced by local activity rather than cross-national collaboration, though there have been similar growth trajectories. This article uses a comparative case study methodology to analyse the development of practice research in Australia and the UK since the Salisbury Statement on social work practice research. Each case study explores and provides examples of the nature of the relationship between practitioners and academic researchers; how practice questions are generated; how methodologies are selected; how data are collected within social work practice and the impact of practice research on practice in both countries. The comparative analysis provides a unique insight into how local, and often small, projects provide a more significant narrative about the creation of knowledge in social work practice. These insights have the potential to inform and stimulate the development of practice research in other countries which are earlier in the journey towards practice-driven research.
Apremilast for the treatment of papuloerythroderma of Ofuji
Authors: Yin Xufeng , Huang Chen , Feng Yifei , Xia Jiping , Zhang Meihua , Yin Zhiqiang
Published: August 2023

This manuscript holds value for all clinicians who encounter patients with papuloerythroderma of Ofuji, providing new insights into the treatment of this condition coexisting with neoplasms.
DOT1L deletion impairs the development of cortical parvalbumin-expressing interneurons
Authors: Cheffer Arquimedes , Garcia-Miralles Marta , Maier Esther , Akol Ipek , Franz Henriette , Srinivasan Vandana Shree Vedartham , Vogel Tanja
Published: August 2023

The cortical plate (CP) is composed of excitatory and inhibitory neurons, the latter of which originate in the ganglionic eminences. From their origin in the ventral telencephalon, maturing postmitotic interneurons migrate during embryonic development over some distance to reach their final destination in the CP. The histone methyltransferase Disruptor of Telomeric Silencing 1-like (DOT1L) is necessary for proper CP development and layer distribution of glutamatergic neurons. However, its specific role on cortical interneuron development has not yet been explored. Here, we demonstrate that DOT1L affects interneuron development in a cell autonomous manner. Deletion of Dot1l in Nkx2.1-expressing interneuron precursor cells results in an overall reduction and altered distribution of GABAergic interneurons in the CP from postnatal day 0 onwards. We observed an altered proportion of GABAergic interneurons in the cortex, with a significant decrease in parvalbumin-expressing interneurons. Moreover, a decreased number of mitotic cells at the embryonic day E14.5 was observed upon Dot1l deletion. Altogether, our results indicate that reduced numbers of cortical interneurons upon DOT1L deletion result from premature cell cycle exit, but effects on postmitotic differentiation, maturation, and migration are likely at play as well.
Fixation-related fMRI analysis reveals the neural basis of natural reading of unspaced and spaced Chinese sentences
Authors: Zhou Wei , Wang Sile , Yan Ming
Published: August 2023

Although there are many eye-movement studies focusing on natural sentence reading and functional magnetic resonance imaging research on reading with serial visual presentation paradigms, there is a scarcity of investigations into the neural mechanism of natural sentence reading. The present study recruited 33 adults to read unspaced and spaced Chinese sentences with the eye tracking and functional magnetic resonance imaging data recorded simultaneously. By using fixation-related functional magnetic resonance imaging analysis, this study showed that natural reading of Chinese sentences produced activations in ventral visual, dorsal attention, and semantic brain regions, which were modulated by the properties of words such as word length and word frequency. The multivoxel pattern analysis showed that the activity pattern in the left middle temporal gyrus could significantly predict the visual layout categories (i.e. unspaced vs. spaced conditions). Dynamic causal modeling analysis showed that there were bidirectional brain connections between the left middle temporal gyrus and the left inferior occipital cortex in the unspaced Chinese sentence reading but not in the spaced reading. These results provide a neural mechanism for the natural reading of Chinese sentences from the perspective of word segmentation.
Brain network flexibility as a predictor of skilled musical performance
Authors: Uehara Kazumasa , Yasuhara Masaki , Koguchi Junya , Oku Takanori , Shiotani Sachiko , Morise Masanori , Furuya Shinichi
Published: August 2023

Interactions between the body and the environment are dynamically modulated by upcoming sensory information and motor execution. To adapt to this behavioral state-shift, brain activity must also be flexible and possess a large repertoire of brain networks so as to switch them flexibly. Recently, flexible internal brain communications, i.e. brain network flexibility, have come to be recognized as playing a vital role in integrating various sensorimotor information. Therefore, brain network flexibility is one of the key factors that define sensorimotor skill. However, little is known about how flexible communications within the brain characterize the interindividual variation of sensorimotor skill and trial-by-trial variability within individuals. To address this, we recruited skilled musical performers and used a novel approach that combined multichannel-scalp electroencephalography, behavioral measurements of musical performance, and mathematical approaches to extract brain network flexibility. We found that brain network flexibility immediately before initiating the musical performance predicted interindividual differences in the precision of tone timbre when required for feedback control, but not for feedforward control. Furthermore, brain network flexibility in broad cortical regions predicted skilled musical performance. Our results provide novel evidence that brain network flexibility plays an important role in building skilled sensorimotor performance.
The long-term benefits of early intensive therapy in chronic diseases—the legacy effect
Authors: Zoccali Carmine , Mallamaci Francesca , Tripepi Giovanni , Fu Edouard L , Stel Vianda S , Dekker Friedo W , Jager Kitty J
Published: August 2023

The ‘legacy effect’ refers to the long-term benefits of intensive therapy that are observed long after the end of clinical trials and trial interventions in chronic diseases such as diabetes, hyperlipidaemia and hypertension. It emphasizes the importance of intensive treatment to prevent long-term complications and mortality. In chronic kidney disease (CKD), the legacy effect is evident in various studies. Long-term nephroprotection in diabetes is well documented in major studies in the early stages of diabetes, such as Diabetes Control and Complications Trial-Epidemiology of Diabetes Interventions and Complications (DCCT-EDIC), UK Prospective Diabetes Study (UKPDS) and Intensified Multifactorial Intervention in Patients with Type 2 Diabetes and Microalbuminuria (STENO-2). These studies highlight the importance of intensive glycaemic control in reducing microvascular complications, including nephropathy, in patients with recently diagnosed type 1 and type 2 diabetes. However, the legacy effect is less evident in patients with long-term, established diabetes. In chronic glomerulonephritis, studies on immunoglobulin A nephropathy showed that early immunosuppressive treatment could have long-term beneficial effects on kidney function in children and adults with CKD. The Frequent Hemodialysis (FH) and the EXerCise Introduction To Enhance Performance in Dialysis (EXCITE) trials indicated that frequent haemodialysis and a personalized walking exercise program could improve clinical outcomes and reduce the long-term risk of death and hospitalization. The legacy effect concept underscores the importance of intensive intervention in chronic diseases, including CKD. This concept has significant implications for public health and warrants in-depth basic and clinical research to be better understood and exploited in clinical practice. However, its limitations should be considered when interpreting long-term observational data collected after a clinical trial. Appropriate study designs are necessary to investigate an unbiased legacy effect.
CCIDB: a manually curated cell–cell interaction database with cell context information
Authors: Noh Jin Young , Lee Hae In , Choi Ji-Hye , Cho Seong-Ho , Yi Yoon Hui , Lim Ji Hyun , Myung Eun Been , Shin Ye Ju , Shin Hyo Jin , Woo Hyun Goo
Published: August 2023

Cell–cell interaction (CCI) is a crucial event in the development and function of multicellular organisms. The development of CCI databases is beneficial for researchers who want to analyze single-cell sequencing data or study CCI through molecular experiments. CCIs are known to act differently according to cellular and biological contexts such as cell types, gene mutations or disease status; however, previous CCI databases do not completely provide this contextual information pertaining to CCIs. We constructed a cell-cell interaction database (CCIDB) containing the biological and clinical contexts involved in each interaction. To build a database of cellular and tissue contexts, we collected 38 types of context features, which were categorized into seven categories, including ‘interaction’, ‘cell type’, ‘cofactor’, ‘effector’, ‘phenotype’, ‘pathology’ and ‘reference’. CCIs were manually retrieved from 272 studies published recently (less than 6 years ago). In the current version of CCIDB, 520 CCIs and their 38 context features have been manually collected and curated by biodata engineers. We suggest that CCIDB is a manually curated CCI resource that is highly useful, especially for analyzing context-dependent alterations in CCIs.

Database URL https://ccidb.sysmed.kr/
Testing for sexually transmitted infection: who and where? A data linkage study using population and provider data in the Rotterdam area, the Netherlands
Authors: Twisk Denise E , Meima Abraham , Richardus Jan Hendrik , Götz Hannelore M
Published: August 2023

Background

In the Netherlands, insight into sexually transmitted infection (STI) testing and characteristics of those tested by general practitioners (GPs) and sexual health centres (SHC) is limited. This is partly due to lacking registration of socio-demographics at GPs. We aimed to fill this gap by linking different registers.

Methods

Individual STI testing data of GPs and SHC were linked to population register data (aged ≥15 years, Rotterdam area, 2015–2019). We reported population-specific STI positivity, proportion STI tested, and GP-SHC testing rate comparison using negative binomial generalised additive models. Factors associated with STI testing were determined by the provider using logistic regression analyses with generalised estimating equations.

Results

The proportion of STI tested was 2.8% for all residents and up to 9.8% for younger and defined migrant groups. STI positivity differed greatly by subgroup and provider (3.0–35.3%). Overall, GPs performed 3 times more STI tests than the SHC. The smallest difference in GP-SHC testing rate was for 20–24-year-olds (SHC key group). Younger age, non-western migratory background, lower household income, living more urbanised, and closer to a testing site were associated with STI testing by either GP or SHC. GPs and SHC partly test different groups: GPs test women and lower-educated more often, the SHC men and middle/higher educated.

Conclusions

This study highlights GPs’ important role in STI testing. The GPs’ role in the prevention, diagnosis, and treatment of STIs needs continued support and strengthening. Inter-professional exchange and collaboration between GP and SHC is warranted to reach vulnerable groups.
A multiplexed plant–animal SNP array for selective breeding and species conservation applications
Authors: Montanari Sara , Deng Cecilia , Koot Emily , Bassil Nahla V , Zurn Jason D , Morrison-Whittle Peter , Worthington Margaret L , Aryal Rishi , Ashrafi Hamid , Pradelles Julien , Wellenreuther Maren , Chagné David
Published: August 2023

Reliable and high-throughput genotyping platforms are of immense importance for identifying and dissecting genomic regions controlling important phenotypes, supporting selection processes in breeding programs, and managing wild populations and germplasm collections. Amongst available genotyping tools, single nucleotide polymorphism arrays have been shown to be comparatively easy to use and generate highly accurate genotypic data. Single-species arrays are the most commonly used type so far; however, some multi-species arrays have been developed for closely related species that share single nucleotide polymorphism markers, exploiting inter-species cross-amplification. In this study, the suitability of a multiplexed plant–animal single nucleotide polymorphism array, including both closely and distantly related species, was explored. The performance of the single nucleotide polymorphism array across species for diverse applications, ranging from intra-species diversity assessments to parentage analysis, was assessed. Moreover, the value of genotyping pooled DNA of distantly related species on the single nucleotide polymorphism array as a technique to further reduce costs was evaluated. Single nucleotide polymorphism performance was generally high, and species-specific single nucleotide polymorphisms proved suitable for diverse applications. The multi-species single nucleotide polymorphism array approach reported here could be transferred to other species to achieve cost savings resulting from the increased throughput when several projects use the same array, and the pooling technique adds another highly promising advancement to additionally decrease genotyping costs by half.
An expanded GCaMP reporter toolkit for functional imaging in Caenorhabditis elegans
Authors: Ding Jimmy , Peng Lucinda , Moon Sihoon , Lee Hyun Jee , Patel Dhaval S , Lu Hang
Published: August 2023

In living organisms, changes in calcium flux are integral to many different cellular functions and are especially critical for the activity of neurons and myocytes. Genetically encoded calcium indicators (GECIs) have been popular tools for reporting changes in calcium levels in vivo. In particular, GCaMPs, derived from GFP, are the most widely used GECIs and have become an invaluable toolkit for neurophysiological studies. Recently, new variants of GCaMP, which offer a greater variety of temporal dynamics and improved brightness, have been developed. However, these variants are not readily available to the Caenorhabditis elegans research community. This work reports a set of GCaMP6 and jGCaMP7 reporters optimized for C. elegans studies. Our toolkit provides reporters with improved dynamic range, varied kinetics, and targeted subcellular localizations. Besides optimized routine uses, this set of reporters is also well suited for studies requiring fast imaging speeds and low magnification or low-cost platforms.
Leveraging osteoclast genetic regulatory data to identify genes with a role in osteoarthritis
Authors: Mullin Benjamin H , Zhu Kun , Brown Suzanne J , Mullin Shelby , Dudbridge Frank , Pavlos Nathan J , Richards J Brent , Grundberg Elin , Bell Jordana T , Zeggini Eleftheria , Walsh John P , Xu Jiake , Wilson Scott G
Published: August 2023

There has been a growing interest in the role of the subchondral bone and its resident osteoclasts in the progression of osteoarthritis (OA). A recent genome-wide association study (GWAS) identified 100 independent association signals for OA traits. Most of these signals are led by noncoding variants, suggesting that genetic regulatory effects may drive many of the associations. We have generated a unique human osteoclast-like cell-specific expression quantitative trait locus (eQTL) resource for studying the genetics of bone disease. Considering the potential role of osteoclasts in the pathogenesis of OA, we performed an integrative analysis of this dataset with the recently published OA GWAS results. Summary data-based Mendelian randomization (SMR) and colocalization analyses identified 38 genes with a potential role in OA, including some that have been implicated in Mendelian diseases with joint/skeletal abnormalities, such as BICRA, EIF6, CHST3, and FBN2. Several OA GWAS signals demonstrated colocalization with more than one eQTL peak, including at 19q13.32 (hip OA with BCAM, PRKD2, and BICRA eQTL). We also identified a number of eQTL signals colocalizing with more than one OA trait, including FAM53A, GCAT, HMGN1, MGAT4A, RRP7BP, and TRIOBP. An SMR analysis identified 3 loci with evidence of pleiotropic effects on OA-risk and gene expression: LINC01481, CPNE1, and EIF6. Both CPNE1 and EIF6 are located at 20q11.22, a locus harboring 2 other strong OA candidate genes, GDF5 and UQCC1, suggesting the presence of an OA-risk gene cluster. In summary, we have used our osteoclast-specific eQTL dataset to identify genes potentially involved with the pathogenesis of OA.
Association of Kidney Function With Dementia and Structural Brain Differences: A Large Population-Based Cohort Study
Authors: Wang Shuqi , Wang Jiao , Guo Jie , Dove Abigail , Xu Hong , Qi Xiuying , Xu Weili
Published: August 2023

Background

The association between kidney function and dementia risk and the mechanisms underlying this relationship remain unclear.

Methods

Within the UK Biobank, 191 970 dementia-free participants aged ≥60 (mean age: 64.1 ± 2.9 years) were followed for 16 years to detect incident dementia. Serum creatinine and Cystatin C were measured at baseline to calculate estimated glomerular filtration rate (eGFR, mL/min/1.73 m2). Kidney function was categorized as normal (eGFR ≥ 90), mildly impaired (60 ≤ eGFR < 90), or moderately to severely impaired (eGFR < 60). Dementia was assessed based on self-reported medical history and medical records. During the follow-up, a subsample of 12 637 participants underwent brain MRI scans. Volumes of total brain, gray matter, white matter, hippocampus, and white matter hyperintensities were assessed.

Results

Over the follow-up, 5 327 (2.8%) participants developed dementia. Compared to normal kidney function, there was an increased risk of dementia with moderate to severely impaired kidney function (hazard ratio = 1.53, 95% confidence interval [CI]: 1.32–1.76) but not mildly impaired kidney function. In Laplace regression, dementia onset among people with moderate to severely impaired kidney function occurred 1.53 (95% CI: 0.98–2.08) years earlier than those with normal kidney function. Moderate to severely impaired kidney function was related to significantly lower gray matter volume (β = −0.11, 95% CI: −0.19 to −0.03), but not to other brain magnetic resonance imaging measures.

Conclusions

Impaired kidney function is associated with about 50% increased risk of dementia and anticipates dementia onset by more than 1.5 years. Brain neurodegeneration may underlie the kidney function–dementia association.
Validation of the Pittsburgh Performance Fatigability Index in the Study of Muscle, Mobility and Aging
Authors: Qiao Yujia (Susanna) , Harezlak Jaroslaw , Cawthon Peggy M , Cummings Steven R , Forman Daniel E , Goodpaster Bret H , Hawkins Marquis , Moored Kyle D , Nicklas Barbara J , Toledo Frederico G S , Toto Pamela E , Santanasto Adam J , Strotmeyer Elsa S , Newman Anne B , Glynn Nancy W
Published: August 2023

Background

The Pittsburgh Performance Fatigability Index (PPFI) quantifies the percent decline in cadence using accelerometry during standardized walking tasks. Although PPFI has shown strong correlations with physical performance, the developmental sample was relatively homogenous and small, necessitating further validation.

Methods

Participants from the Study of Muscle, Mobility and Aging (N = 805, age = 76.4 ± 5.0 years, 58% women, 85% White) wore an ActiGraph GT9X on the nondominant wrist during usual-paced 400 m walk. Tri-axial accelerations were analyzed to compute PPFI (higher score = greater fatigability). To evaluate construct and discriminant validity, Spearman correlations (rs) between PPFI and gait speed, Short Physical Performance Battery (SPPB), chair stand speed, leg peak power, VO2peak, perceived fatigability, and mood were examined. Sex-specific PPFI cut-points that optimally discriminated gait speed using classification and regression tree were then generated. Their discriminate power in relation to aforementioned physical performance were further evaluated.

Results

Median PPFI score was 1.4% (25th–75th percentile range: 0%–21.7%), higher among women than men (p < .001). PPFI score was moderate-to-strongly correlated with gait speed (rs = −0.75), SPPB score (rs = −0.38), chair stand speed (rs = −0.36), leg peak power (rs = −0.34) and VO2peak (rs = −0.40), and less strongly with perceived fatigability (rs = 0.28–0.29), all p < .001. PPFI score was not correlated with mood (|rs| < 0.08). Sex-specific PPFI cut-points (no performance fatigability: PPFI = 0%; mild performance fatigability: 0% < PPFI < 3.5% [women], 0% < PPFI < 5.4% [men]; moderate-to-severe performance fatigability: PPFI ≥ 3.5% [women], PPFI ≥ 5.4% [men]) discriminated physical performance (all p < .001), adjusted for demographics and smoking status.

Conclusion

Our work underscores the utility of PPFI as a valid measure to quantify performance fatigability in future longitudinal epidemiologic studies and clinical/pharmaceutical trials.
Scanned information exposure and support for tobacco regulations among US youth and young adult tobacco product users and non-users
Authors: Kim Kwanho
Published: August 2023

The influences of information exposure on youth and young adults’ (YYA) support for smoking/vaping regulations have been understudied. This study examines (i) the relationships between routine exposure to (i.e. scanning) anti-smoking/pro-vaping information and YYA support for anti-smoking/vaping regulations and (ii) whether these relationships differ across YYA users and non-users of tobacco products. We analyzed the data from a nationally representative two-wave rolling cross-sectional survey of YYA in the United States, collected from 2014 to 2017 (baseline n = 10 642; follow-up n = 4001). Less than 5% of the participants ever scanned pro-smoking and anti-vaping information. Scanning anti-smoking information had significant positive relationships with support for all anti-smoking policies cross-sectionally, and this pattern was longitudinally significant in two anti-smoking policy contexts. Scanning pro-vaping information had significant negative associations with support for anti-vaping policies cross-sectionally, but not longitudinally. The lagged positive relationships between scanning anti-smoking information and support for anti-smoking regulations were stronger among YYA smokers than among YYA non-smokers, whereas evidence from adult data suggested the opposite pattern. The findings suggest that scanning information can affect YYA support for tobacco regulations. Future efforts are required to investigate mechanisms underlying the influences of scanned information on YYA support for tobacco regulations.
The transcription factor CsS40 negatively regulates TCS1 expression and caffeine biosynthesis in connection to leaf senescence in Camellia sinensis
Authors: Yao Xinzhuan , Chen Hufang , Ai Antao , Wang Fen , Lian Shanshan , Tang Hu , Jiang Yihe , Jiao Yujie , He Yumei , Li Tong , Lu Litang
Published: August 2023

Caffeine is considered as one of the most important bioactive components in the popular plant beverages tea, cacao, and coffee, but as a wide-spread plant secondary metabolite its biosynthetic regulation at transcription level remains largely unclear. Here, we report a novel transcription factor Camellia sinensis Senescnece 40 (CsS40) as a caffeine biosynthesis regulator, which was discovered during screening a yeast expression library constructed from tea leaf cDNAs for activation of tea caffeine synthase (TCS1) promoter. Besides multiple hits of the non-self-activation CsS40 clones that bound to and activated TCS1 promoter in yeast-one-hybrid assays, a split-luciferase complementation assay demonstrated that CsS40 acts as a transcription factor to activate the CsTCS1 gene and EMSA assay also demonstrated that CsS40 bound to the TCS1 gene promoter. Consistently, immunofluorescence data indicated that CsS40-GFP fusion was localized in the nuclei of tobacco epidermal cells. The expression pattern of CsS40 in ‘Fuding Dabai’ developing leaves was opposite to that of TCS1; and knockdown and overexpression of CsS40 in tea leaf calli significantly increased and decreased TCS1 expression levels, respectively. The expression levels of CsS40 were also negatively correlated to caffeine accumulation in developing leaves and transgenic calli of ‘Fuding Dabai’. Furthermore, overexpression of CsS40 reduced the accumulation of xanthine and hypoxanthine in tobacco plants, meanwhile, increased their susceptibility to aging. CsS40 expression in tea leaves was also induced by senescence-promoting hormones and environmental factors. Taken together, we showed that a novel senescence-related factor CsS40 negatively regulates TCS1 and represses caffeine accumulation in tea cultivar ‘Fuding Dabai’. The study provides new insights into caffeine biosynthesis regulation by a plant-specific senescence regulator in tea plants in connection to leaf senescence and hormone signaling.
Spatio-temporal species distribution models reveal dynamic indicators for ecosystem-based fisheries management
Authors: Badger J J , Large S I , Thorson J T
Published: August 2023

Many economic sectors rely on marine ecosystem services, and holistic management is necessary to evaluate trade-offs between sectors and facilitate sustainable use. Integrated ecosystem assessments (IEA) integrate system components so that managers can evaluate pathways to achieve desired goals. Indicators are a central element of IEAs and capture the status and trend of individual components and should be sensitive to changes in the system; however, most indicators are aggregated over space and time as annual values, potentially leading to incomplete or inaccurate inferences about system change. Here, we demonstrate the utility of spatially and temporally explicit ecological indicators by fitting multivariate spatio-temporal models to survey data from the northeast US Shelf Ecosystem, encompassing three distinct ecoregions: Georges Bank, Gulf of Maine, and mid-Atlantic Bight. We evaluate three case studies to explore how these models can help assess ecosystem performance relative to management objectives, such as to: (1) identify dominant modes of variation in zooplankton communities; (2) quantify components of system stability; and (3) assess the density-dependent condition of groundfish over time. Collectively, these three examples demonstrate multiple interesting processes, but particularly highlight the rapid zooplankton changes and associated changes in benthivore condition and stability in the Gulf of Maine. Attributing changes in ecosystem indicators to localized processes is difficult using conventional “regionally aggregated” indicators, so this example highlights the benefits of spatio-temporal methods for integrated ecosystem analysis in this and other regions.
A Dual-Process Model of Xunzi’s Philosophy of Music
Authors: Kim Hannah H
Published: August 2023

Music, alongside ritual, plays an important role in Confucian moral education. Among all the Confucians, Xunzi gives music the most radical ability to transform people, and this is striking given his pessimistic view of human nature. Though he set the standard for Chinese aesthetics for millennia, there is no systematic account that brings together Xunzi’s various commitments: that only music from virtuous previous dynasties are morally conducive, that music can bring about lasting character change, that even those uninterested in moral cultivation can benefit from music, and that the junzi (“gentleman”) and the xiaoren (“petty man”) derive joy in different ways while listening to music. In this article, I explain why currently existing accounts cannot capture all the commitments, and I turn to analytic aesthetics to provide a new Dual-Process Model of Xunzi’s philosophy of music. Jenefer Robinson’s discussions of “the Jazzercise effect” and emotional misattribution will be key in the new account.
Serratia endocarditis: antimicrobial management strategies and clinical outcomes
Authors: Shah Sunish , McCrary Madeline , Schranz Asher J , Clarke Lloyd , Davis Matthew W , Marx Ashley , Slain Douglas , Stoner Bobbi Jo , Topal Jeffrey , Shields Ryan K
Published: August 2023

Objectives

The incidence of Serratia endocarditis is increasing, yet optimal treatment has not been defined. Our objective was to investigate the outcomes of patients with Serratia endocarditis by treatment strategy.

Methods

We reviewed adult patients with definitive Serratia endocarditis at two independent health systems between July 2001 and April 2023. Combination therapy was defined as receipt of ≥2 in vitro active agents for ≥72 h.

Results

Seventy-five patients were included; 64% (48/75) were male and 85% (64/75) were people who inject drugs. Compared with monotherapy, receipt of combination therapy was associated with lower rates of microbiological failure (0% versus 15%, P = 0.026) and 90 day all-cause mortality (11% versus 31%, P = 0.049). Antimicrobial discontinuation due to an adverse event was more common among patients receiving combination therapy compared with monotherapy (36% versus 8%, P = 0.058).

Conclusions

In the largest series of Serratia endocarditis to date, combination antibiotic treatment was associated with improved outcomes. However, larger, prospective studies are warranted.
A model of evaluative opinion to encourage greater transparency and justification of interpretation in postmortem forensic toxicology
Authors: Maskell Peter D , Elliott Simon , Desharnais Brigitte , Findell Martin , Jackson Graham
Published: August 2023

Over the past decades, the calls to improve the robustness of interpretation in forensic science have increased in magnitude. Forensic toxicology has seen limited progress in this regard. In this work, we propose a transparent interpretive pathway for use in postmortem forensic toxicology cases. This process allows the selection of the interpretive methodology based on the amount of previous information that is available for the drug(s) in question. One approach is an assessment of various pharmacological and circumstantial considerations resulting in a toxicological significance score (TSS), which is particularly useful in situations where limited information about a drug is available. When there is a robust amount of case data available, then a probabilistic approach, through the evaluation of likelihood ratios by the forensic toxicologist and of prior probabilities by the fact finder, is utilized. This methodology provides a transparent means of making an interpretive decision on the role of a drug in the cause of death. This will allow the field of forensic toxicology to take a step forward in using best practice in evaluative reporting, a tool already used by many other forensic science disciplines.
Parameter interpretations of wave dispersion and attenuation in rock physics based on deep neural network
Authors: Wang Bochen , Liu Jiawei , Guo Zhenwei
Published: August 2023

Acoustic wave features, including velocity dispersion and attenuation, induced by fluid flow in porous media have attracted significant attention in reservoir exploration. To enhance the quantitative understanding of these features, various wave propagation mechanisms have been developed. It has been discovered that wave dispersion and attenuation are associated with multiple reservoir parameters, each with different sensitivity. It is difficult to distinguish the effects of individual physical parameters on acoustic features by traditional wave equations. Considering the ability of deep neural networks (DNNs) in establishing the relationships between two datasets, a fully connected DNN has been employed as a surrogate rock physics model, and the Shapley additive explanations model (SHAP) based on this DNN has been introduced to evaluate the contributions of different parameters. In this study, the classic White model is used to generate datasets for training the DNN. Datasets include seven parameters (bulk modulus, shear modulus, and density of the solid matrix, frequency, porosity, fluid saturation, and permeability), along with velocity dispersion and attenuation. By embedding SHAP into the trained DNN, the presented ShaRock algorithm allows for a clear quantification of the contributions of various reservoir parameters to acoustic features. Furthermore, we analyze the underlying interactions between two parameters by using their combined quantified contributions to the features. The application of this proposed algorithm, which is based on wave propagation mechanisms, demonstrates its potential in providing valuable insights for parameter inversions in hydrocarbon exploration.
Micro-seismic monitoring using sparse planar array and a weak signal enhancement method
Authors: Yang Xiaohui , Lin Zhengliang , Yang Xinchao , Chen Zhanguo , Si Wenpeng
Published: August 2023

Traditional ground micro-seismic monitoring is performed by laying long survey lines. This is expensive and difficult to implement in complex mountainous areas and deep marine shale gas reservoirs in China. To address these challenges, this study proposes a ground micro-seismic monitoring method using a sparse planar array that offers greater flexibility in implementation. This study presents a weak signal enhancement method based on a broadband-array adaptive beamforming algorithm to improve the signal-to-noise ratio (SNR) of micro-seismic data collected by sparse planar arrays and to suppress coherent noise. The proposed method involves establishing a signal model for a broadband planar array, estimating the direction of arrival (DOA) of broadband signals using a grid search method, and setting constraint conditions and objective functions based on the DOA results. The optimal weight vector is then calculated by solving the objective function to obtain the desired signal and suppress noise. This study demonstrates that the proposed method effectively improved the SNR and suppressed coherent noise in synthetic and real data. It also highlights the effectiveness of the sparse planar array as a ground micro-seismic monitoring method and the adaptive broadband beamforming method as a practical weak signal enhancement technology.
Adoption of Amyelois transitella (navel orangeworm) monitoring and management practices across California tree nut crops
Authors: Gordon Phoebe E , Goodrich Brittney K , Wilson Houston
Published: August 2023

In California, the most significant insect pest of almonds and pistachios is the navel orangeworm, Amyelois transitella (Walker) and is a pest of walnuts. This pest attacks the nuts and infestation is associated with aflatoxin contamination. While there are multiple integrated pest management (IPM) practices available, anecdotal evidence suggests that not all tools are equally utilized. To understand current industry practices and barriers to adoption, the authors surveyed tree nut growers and industry professionals across 7 University of California Cooperative Extension meetings in California’s Central Valley. Findings indicate that as managed acres decreased, participants were less likely to report using as many IPM tools, and pest control advisers reported higher use of multiple practices compared to orchard owners and managers. Key barriers to adoption varied by practice and included high economic costs, low labor availability, environmental conditions, and/or timing constraints. Many respondents were skeptical of the efficacy of mating disruption, a relatively new strategy compared to other IPM tools. Finally, a cluster analysis identified thirteen aggregate grower profiles. Groups primarily differed in their use of monitoring practices, although some groups were also less likely to use sanitation or pesticides. Two groups were distinguished as “early adopters” through their use of mating disruption and/or ovibait traps. These findings document variability in adoption of IPM practices for A. transitella in tree nuts. Identification of the primary barriers and constraints for specific grower groups will inform research and extension efforts to further promote adoption of key IPM strategies.