bluuebunny/crossref_metadata_2025 huggingface dataset:
Understanding extreme precipitation scaling with temperature: insights from multi-spatiotemporal analysis in South Korea
Authors: Yoo Suhyun , Ahn Kuk-Hyun
Published: November 2023

With global warming, the intensification of extreme precipitation events is anticipated to follow an exponential growth pattern aligned with the Clausius–Clapeyron (CC) scaling rate (approximately 7% per degree Celsius). However, the regional-scale response of extreme precipitation shows significant variability, deviating from the expected CC rate. This deviation is likely caused by diverse weather patterns and local fluctuations in thermodynamic influences, resulting in differences across seasons and within the region of interest. In this study, we examine the spatial distribution of scaling relationships between extreme precipitation and temperature in South Korea, considering daily and sub-daily scales, both annually and seasonally. For a thorough analysis, we utilize multiple precipitation accumulation periods, temperatures, and different conditional quantiles. Our results reveal that, at the annual scale, most scaling patterns exhibit a peak-like structure, with significant variations in breakpoints observed across temperature variables and regions. However, the southern area presents a notable exception with a positive scaling pattern, particularly with the dew point temperature. At the seasonal scale, we observe more variability, with notable shifts occurring during the wet season across different temperatures and regions. Lastly, we explore the long-term historical changes in the peak value in extreme precipitation and find significant increases at high quantiles in the southern area of South Korea. It informs that the observed peak like pattern does not impose a potential upper limit for extreme precipitation. Overall, our findings emphasize the need for cautious interpretation of precipitation scaling within specific spatiotemporal contexts, which could provide a solid basis for better understanding future extreme precipitation events in a changing climate.
Can shallow quantum circuits scramble local noise into global white noise?
Authors: Foldager Jonathan , Koczor Bálint
Published: November 2023

Shallow quantum circuits are believed to be the most promising candidates for achieving early practical quantum advantage—this has motivated the development of a broad range of error mitigation techniques whose performance generally improves when the quantum state is well approximated by a global depolarising (white) noise model. While it has been crucial for demonstrating quantum supremacy that random circuits scramble local noise into global white noise—a property that has been proved rigorously—we investigate to what degree practical shallow quantum circuits scramble local noise into global white noise. We define two key metrics as (a) density matrix eigenvalue uniformity and (b) commutator norm that quantifies stability of the dominant eigenvector. While the former determines the distance from white noise, the latter determines the performance of purification based error mitigation. We derive analytical approximate bounds on their scaling and find in most cases they nicely match numerical results. On the other hand, we simulate a broad class of practical quantum circuits and find that white noise is in certain cases a bad approximation posing significant limitations on the performance of some of the simpler error mitigation schemes. On a positive note, we find in all cases that the commutator norm is sufficiently small guaranteeing a very good performance of purification-based error mitigation. Lastly, we identify techniques that may decrease both metrics, such as increasing the dimensionality of the dynamical Lie algebra by gate insertions or randomised compiling.
Duality of O(N) and Sp(N) random tensor models: tensors with symmetries
Authors: Keppler H , Krajewski T , Muller T , Tanasa A
Published: November 2023

In a recent series of papers, a duality between orthogonal and symplectic random tensor models has been proven, first for quartic models and then for models with interactions of arbitrary order. However, the tensor models considered so far in the literature had no symmetry under permutation of the indices. In this paper, we generalize these results for tensors models with interactions of arbitrary order which further have non-trivial symmetry under the permutation of the indices. Totally symmetric and anti-symmetric tensors are thus treated as a particular case of our result.
A clinical proteomics study of exhaled breath condensate and biomarkers for pulmonary embolism
Authors: Gade Inger Lise , Riddersholm Signe Juul , Stilling-Vinther Thomas , Brøndum Rasmus Froberg , Bennike Tue Bjerg , Honoré Bent
Published: November 2023

Pulmonary embolism (PE) can be a diagnostic challenge. Current diagnostic markers for PE are unspecific and new diagnostic tools are needed. The air we exhale is a possible new source for biomarkers which can be tapped into by analysing the exhaled breath condensate (EBC). We analysed the EBC from patients with PE and controls to investigate if the EBC is a useful source for new diagnostic biomarkers of PE. We collected and analysed EBC samples from patients with suspected PE and controls matched on age and sex. Patients in whom PE was ruled out after diagnostic work-up were included in the control group to increase the sensitivity and generalizability of the identified markers. EBC samples were collected using an RTube™. The protein composition of the EBCs were analysed using data dependent label-free quantitative nano liquid chromatography–tandem mass spectrometry. EBC samples from 28 patients with confirmed PE, and 49 controls were analysed. A total of 928 EBC proteins were identified in the 77 EBC samples. As expected, a low protein concentration was determined which resulted in many proteins with unmeasurable levels in several samples. The levels of HSPA5, PEBP1 and SFTPA2 were higher and levels of POF1B, EPPK1, PSMA4, ALDOA, and CFL1 were lower in PE compared with controls. In conclusion, the human EBC contained a variety of endogenous proteins and may be a source for new diagnostic markers of PE and other diseases.
Valorisation of pomegranate processing waste for the synthesis of ZnO nanoparticles: antioxidant and antimicrobial properties against food pathogens
Authors: Leta Tshiamo B , Adeyemi Jerry O , Fawole Olaniyi A
Published: November 2023

The sustainable management of food waste is a pressing concern, with fruit waste valorisation emerging as a viable strategy to address this challenge. This study investigated the potential of pomegranate peel waste (PPW) and pomegranate seed waste (PSW) as mediating agents for the biosynthesis of zinc oxide (ZnO) nanoparticles (NPs); ZnO-PPW and ZnO-PSW, respectively, for potential utilization as additives in various polymer matrices for food packaging materials. The resulting physicochemical characteristics were ascertained using Ultraviolet visible spectroscopy (UV–vis), x-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), x-ray diffraction (XRD), Scanning electron microscope (SEM) and Energy Dispersive x-Ray Analysis (EDX). The obtained indexed diffractogram from the XRD analysis for both ZnO-PPW and ZnO-PSW confirmed the wurtzite crystalline structure of ZnO NPs. The observed morphology from the TEM and SEM analysis showed a similar spherical shaped structure, with agglomerations. However, ZnO-PSW, had a smaller size (58 nm) in comparison to ZnO-PPW (59 nm). Total phenolic content (TPC) for ZnO-PPW and ZnO-PSW ranged from 16.87–54.4 μg GAE/g DM, respectively. Also, the estimated minimum inhibitory concentration at 50% (IC50) for both DPPH and ABTS are 2.97 and 2.57 mg ml−1 for ZnO-PPW; and 3.43 and 3.33 mg ml−1 for ZnO-PSW, respectively. Moreover, due to its smaller size, ZnO-PSW demonstrated superior antimicrobial activity against five foodborne microorganisms. These findings suggest that pomegranate waste derived ZnO NPs could be beneficial for developing active food packaging materials.
Chinese rose-derived nanostructure carbon as new anode material for lithium-ion batteries
Authors: Qu Ye , Zhu Xinyu , Qiang Yaochun , Chang Junwei , Pan Jinping
Published: November 2023

Renewable biomass carbon materials are of wide interest for energy storage applications. Using high-temperature pyrolysis, we carbonized Chinese rose for the first time at different temperatures to investigate the performance of lithium-ion batteries (LIBs) of the resulting materials under different temperature conditions. The fluffy folded structure after carbonization exhibits multiple active sites, which helps to improve the electrical conductivity and mitigate the damage to the material structure caused by electrode expansion. The negative electrode made from the 1000 °C carbonized material can provide a high specific capacity of 725 mAh g−1 after 250 cycles at 0.1 A g−1, and maintains a specific capacity of 373 mAh g−1 at a high current density of 1 A g−1, with excellent rate performance. The results show that Chinese rose-derived carbon (CRDC) materials can be naturally green anode materials for next-generation lithium-ion batteries.
Monitoring self-discharge in a dual-ion battery using in situ Raman spectro-electrochemistry
Authors: Hassan Ismail Yussuf , van Ekeren Wessel W A , Kotronia Antonia , Hahlin Maria , Asfaw Habtom D
Published: November 2023

A dual-ion battery employs two graphite electrodes to host cations and anions from the electrolyte. The high potential required to intercalate anions in graphite fully, typically > 5 V versus Li+/Li, triggers electrolyte decomposition and dissolution of the aluminium current collector. Such unwanted reactions significantly aggravate self-discharge, leading to low energy efficiency and shorter cycle life. This study investigates changes in graphite structure during the intercalation of bis(fluorosulfonyl)imide (FSI) anion in 4 M LiFSI in ethyl methyl carbonate (EMC) and evaluates the stability of the associated FSI-intercalated graphite compounds using in situ Raman spectroscopy. The results highlight the critical importance of the duration the GICs remain in contact with the electrolyte, before the acquisition of the Raman spectra. Accordingly, the GICs with high FSI anion content exhibited only short-term stability and lost anions during open-circuit potential relaxation; only dilute GIC phases (stages ≥ IV) were sufficiently stable in the presence of the concentrated electrolyte. Furthermore, the formation of gaseous products during the charge–discharge cycles was verified using a 3-electrode cell with a pressure sensor. Future studies can adopt the experimental strategy developed in this work to assess the efficacy of electrolyte additives in mitigating self-discharge in DIBs.
Minimization of hypersurfaces
Authors: Elsenhans Andreas-Stephan , Stoll Michael
Published: November 2023

Let

F
∈

Z

[

x
0

,
…
,

x
n

]

F \in \mathbb {Z}[x_0, \ldots , x_n]

be homogeneous of degree 

d
d

and assume that

F
F

is not a ‘nullform’, i.e., there is an invariant 

I
I

of forms of degree 

d
d

in

n
+
1

n+1

 variables such that

I
(
F
)
≠
0

I(F) \neq 0

. Equivalently,

F
F

is semistable in the sense of Geometric Invariant Theory. Minimizing 

F
F

at a prime 

p
p

means to produce

T
∈
M
a
t
(
n
+
1
,

Z

)
∩
G
L
(
n
+
1
,

Q

)

T \in Mat(n+1, \mathbb {Z}) \cap GL(n+1, \mathbb {Q})

and

e
∈

Z

≥
0

e \in \mathbb {Z}_{\ge 0}

such that

F
1

=

p

−
e

F
(
[

x
0

,
…
,

x
n

]
⋅
T
)

F_1 = p^{-e} F([x_0, \ldots , x_n] \cdot T)

has integral coefficients and

v
p

(
I
(

F
1

)
)

v_p(I(F_1))

is minimal among all such 

F
1

F_1

. Following Kollár [Electron. Res. Announc. Amer. Math. Soc. 3 (1997), pp. 17–27], the minimization process can be described in terms of applying weight vectors

w
∈

Z

≥
0

n
+
1

w \in \mathbb {Z}_{\ge 0}^{n+1}

to 

F
F

. We show that for any dimension 

n
n

and degree 

d
d

, there is a complete set of weight vectors consisting of

[
0
,

w
1

,

w
2

,
…
,

w
n

]

[0,w_1,w_2,\dots ,w_n]

with

0
≤

w
1

≤

w
2

≤
⋯
≤

w
n

≤
2
n

d

n
−
1

0 \le w_1 \le w_2 \le \dots \le w_n \le 2 n d^{n-1}

. When

n
=
2

n = 2

, we improve the bound to 

d
d

. This answers a question raised by Kollár. These results are valid in a more general context, replacing

Z

\mathbb {Z}

and 

p
p

by a PID 

R
R

and a prime element of 

R
R

.

Based on this result and a further study of the minimization process in the planar case

n
=
2

n = 2

, we devise an efficient minimization algorithm for ternary forms (equivalently, plane curves) of arbitrary degree 

d
d

. We also describe a similar algorithm that allows to minimize (and reduce) cubic surfaces. These algorithms are available in the computer algebra system Magma.
Inhibition of the chromatin remodeling factor NURF rescued sterility by a clinic variant of NuRD
Authors: Shen Zijie , Guo Zhengyang , Ou Guangshuo , Li Wei
Published: November 2023

The nucleosome remodeling and deacetylase (NuRD) complex is essential for gene expression and cell fate determination, and missense mutations of NuRD caused neurodevelopmental diseases. However, the molecular pathogenesis of clinic NuRD variants is unknown. Here, we introduced a clinic CHD3 (L915F) variant into Caenorhabditis elegans homologue LET-418, impairing germline and vulva development and ultimately causing animal sterility. Our ATAC-seq and RNA-seq analyses revealed that this variant generated an abnormal open chromatin structure and disrupted the expression of developmental genes. Through genetic suppressor screens, we uncovered that intragenic mutations, likely renovating NuRD activity, restored animal viability. We also found that intergenic mutations in nucleosome remodeling factor NURF that counteracts NuRD rescued abnormal chromatin structure, gene expression, and animal sterility. We propose that two antagonistic chromatin-remodeling factors coordinate to establish the proper chromatin status and transcriptome and that inhibiting NURF may provide insights for treatment of NuRD mutation-related diseases.
Altitudinal differences in foraging decisions under predation risk in great tits
Authors: Crouchet Thomas , Heeb Philipp , Chaine Alexis S
Published: November 2023

Foraging decisions under risk of predation are crucial for survival as predation risk can contribute to a reduction of food intake over time leading to a trade-off between starvation and predation. Environmental variation can provoke changes in food accessibility or predation risk that will in turn affect foraging decisions. Specifically, less predictable or harsher environments, such as those found at high elevation, should lead to more risk-prone foraging in order to prevent risk of starvation, but empirical confirmation of this hypothesis is lacking. In the current study, we used video playbacks combined with an automatic feeder to measure continuous foraging choices between control and predator videos by wild great tits originating from high and low elevations and tested under controlled conditions. Great tits discriminated between two conditions representing differences in predation risk and visited the feeder less frequently when a predator was shown. Moreover, we found that birds from low elevation populations were more risk-averse and visited the feeder significantly less when a predator video playback was broadcasted compared with high elevation individuals. This elevation-related contrast was also dependent on the season, body mass, and fat reserves of individuals, and was more marked in females. Furthermore, adults visited the feeder less in the presence of a predator compared with yearlings. These results are consistent with predictions from life-history theory and starvation–predation trade-off hypotheses and could have implications for individual movements and population dynamics in changing environments.
scMHNN: a novel hypergraph neural network for integrative analysis of single-cell epigenomic, transcriptomic and proteomic data
Authors: Li Wei , Xiang Bin , Yang Fan , Rong Yu , Yin Yanbin , Yao Jianhua , Zhang Han
Published: November 2023

Technological advances have now made it possible to simultaneously profile the changes of epigenomic, transcriptomic and proteomic at the single cell level, allowing a more unified view of cellular phenotypes and heterogeneities. However, current computational tools for single-cell multi-omics data integration are mainly tailored for bi-modality data, so new tools are urgently needed to integrate tri-modality data with complex associations. To this end, we develop scMHNN to integrate single-cell multi-omics data based on hypergraph neural network. After modeling the complex data associations among various modalities, scMHNN performs message passing process on the multi-omics hypergraph, which can capture the high-order data relationships and integrate the multiple heterogeneous features. Followingly, scMHNN learns discriminative cell representation via a dual-contrastive loss in self-supervised manner. Based on the pretrained hypergraph encoder, we further introduce the pre-training and fine-tuning paradigm, which allows more accurate cell-type annotation with only a small number of labeled cells as reference. Benchmarking results on real and simulated single-cell tri-modality datasets indicate that scMHNN outperforms other competing methods on both cell clustering and cell-type annotation tasks. In addition, we also demonstrate scMHNN facilitates various downstream tasks, such as cell marker detection and enrichment analysis.
Automated and reproducible cell identification in mass cytometry using neural networks
Authors: Saihi Hajar , Bessant Conrad , Alazawi William
Published: November 2023

The principal use of mass cytometry is to identify distinct cell types and changes in their composition, phenotype and function in different samples and conditions. Combining data from different studies has the potential to increase the power of these discoveries in diverse fields such as immunology, oncology and infection. However, current tools are lacking in scalable, reproducible and automated methods to integrate and study data sets from mass cytometry that often use heterogenous approaches to study similar samples. To address these limitations, we present two novel developments: (1) a pre-trained cell identification model named Immunopred that allows automated identification of immune cells without user-defined prior knowledge of expected cell types and (2) a fully automated cytometry meta-analysis pipeline built around Immunopred. We evaluated this pipeline on six COVID-19 study data sets comprising 270 unique samples and uncovered novel significant phenotypic changes in the wider immune landscape of COVID-19 that were not identified when each study was analyzed individually. Applied widely, our approach will support the discovery of novel findings in research areas where cytometry data sets are available for integration.
MVML-MPI: Multi-View Multi-Label Learning for Metabolic Pathway Inference
Authors: Liu Xiaoyi , Yang Hongpeng , Ai Chengwei , Ding Yijie , Guo Fei , Tang Jijun
Published: November 2023

Development of robust and effective strategies for synthesizing new compounds, drug targeting and constructing GEnome-scale Metabolic models (GEMs) requires a deep understanding of the underlying biological processes. A critical step in achieving this goal is accurately identifying the categories of pathways in which a compound participated. However, current machine learning-based methods often overlook the multifaceted nature of compounds, resulting in inaccurate pathway predictions. Therefore, we present a novel framework on Multi-View Multi-Label Learning for Metabolic Pathway Inference, hereby named MVML-MPI. First, MVML-MPI learns the distinct compound representations in parallel with corresponding compound encoders to fully extract features. Subsequently, we propose an attention-based mechanism that offers a fusion module to complement these multi-view representations. As a result, MVML-MPI accurately represents and effectively captures the complex relationship between compounds and metabolic pathways and distinguishes itself from current machine learning-based methods. In experiments conducted on the Kyoto Encyclopedia of Genes and Genomes pathways dataset, MVML-MPI outperformed state-of-the-art methods, demonstrating the superiority of MVML-MPI and its potential to utilize the field of metabolic pathway design, which can aid in optimizing drug-like compounds and facilitating the development of GEMs. The code and data underlying this article are freely available at https://github.com/guofei-tju/MVML-MPI. Contact:  jtang@cse.sc.edu, guofei@csu.edu.com or wuxi_dyj@csj.uestc.edu.cn
IMOVNN: incomplete multi-omics data integration variational neural networks for gut microbiome disease prediction and biomarker identification
Authors: Hu Mingyi , Zhu Jinlin , Peng Guohao , Lu Wenwei , Wang Hongchao , Xie Zhenping
Published: November 2023

The gut microbiome has been regarded as one of the fundamental determinants regulating human health, and multi-omics data profiling has been increasingly utilized to bolster the deep understanding of this complex system. However, stemming from cost or other constraints, the integration of multi-omics often suffers from incomplete views, which poses a great challenge for the comprehensive analysis. In this work, a novel deep model named Incomplete Multi-Omics Variational Neural Networks (IMOVNN) is proposed for incomplete data integration, disease prediction application and biomarker identification. Benefiting from the information bottleneck and the marginal-to-joint distribution integration mechanism, the IMOVNN can learn the marginal latent representation of each individual omics and the joint latent representation for better disease prediction. Moreover, owing to the feature-selective layer predicated upon the concrete distribution, the model is interpretable and can identify the most relevant features. Experiments on inflammatory bowel disease multi-omics datasets demonstrate that our method outperforms several state-of-the-art methods for disease prediction. In addition, IMOVNN has identified significant biomarkers from multi-omics data sources.
Graphical tools for selecting conditional instrumental sets
Authors: Henckel L , Buttenschoen M , Maathuis M H
Published: November 2023

We consider the efficient estimation of total causal effects in the presence of unmeasured confounding using conditional instrumental sets. Specifically, we consider the two-stage least-squares estimator in the setting of a linear structural equation model with correlated errors that is compatible with a known acyclic directed mixed graph. To set the stage for our results, we characterize the class of linearly valid conditional instrumental sets that yield consistent two-stage least-squares estimators for the target total effect and derive a new asymptotic variance formula for these estimators. Equipped with these results, we provide three graphical tools for selecting more efficient linearly valid conditional instrumental sets: first, a graphical criterion that, for certain pairs of linearly valid conditional instrumental sets, identifies which of the two corresponding estimators has the smaller asymptotic variance second, an algorithm that greedily adds covariates that reduce the asymptotic variance to a given linearly valid conditional instrumental set and, third, a linearly valid conditional instrumental set for which the corresponding estimator has the smallest asymptotic variance that can be ensured with a graphical criterion.
The Impact of COVID-19 on Social Care and Social Work in the UK: A Scoping Review
Authors: Owens Janine , Young Alys , Allen Rosie , Pearson Amelia , Cartney Patricia , Robinson Catherine , McPhillips Rebecca , Davies Sue , Regan Martyn
Published: November 2023

Prior to the COVID pandemic, staffing levels, staff turnover and vacancies in adult social care and social work within the UK were a major concern, with staff experiencing high workloads, burnout, stress and poor morale. The paucity of published evidence in a rapidly evolving contemporary situation indicated the suitability of a scoping review. Systematic searching produced evidence published between 1 December 2019 and 9 May 2023. Out of ninety-seven articles retrieved, the final analysis included thirty nine articles. To report the review findings clearly and accessibly, the analysis used the Patterns, Advances, Gaps, Evidence for practice and Research recommendations framework. Abundant evidence emerged on psychological distress and the impact of COVID-19 on the working environment for social care and social workers, but a paucity of psychosocial resilience, supporting social care managers, Personal Assistants and moral injury. Social care needs and the statutory duties of social work are likely to become even more intense. The COVID pandemic magnified a chronic lack of funding, staffing, support and regard for adult social care, with no future planning compared to the NHS. This legacy and backlogs of social care assessment and service delivery are of concern despite the proposed actions of the Adult Social Care Reform Act in England.
Vascular cutaneous manifestations of COVID-19 and RNA viral pathogens: a systematic review
Authors: Karch Jamie L , Okorie Chiamaka L , Maymone Mayra B C , Laughter Melissa , Vashi Neelam A
Published: November 2023

Background

COVID-19, the widely recognized and highly contagious respiratory tract infection, has had a substantial impact on the field of dermatology since its emergence in 2019. SARS-CoV-2, the causative virus of COVID-19, is classified as an RNA virus. Various skin-related symptoms have been reported in patients with COVID-19, most notably the distinctive purple–red acral rash resembling chilblain lesions, commonly referred to as ‘COVID toe’; similarly, skin-related symptoms have been observed in connection with other RNA viruses.

Objectives

To explore the relationship between RNA viruses and their associated vascular cutaneous manifestations vs. those observed in patients infected with SARS-CoV-2.

Methods

A systematic literature review was conducted using PubMed and medical subject heading terms related to RNA viruses and related skin manifestations.

Results

In total, 3994 patients diagnosed with COVID-19 presenting with skin rashes were included. Chilblain-like lesions were most frequently observed (30.2%), followed by erythematous maculopapular/morbilliform rashes (9.1%) and urticarial rashes (4.7%). Of 8362 patients diagnosed with RNA viruses, more than half of the skin findings reported were erythematous/maculopapular/morbilliform rashes (52.3%), followed by unspecified (11.3%) and purpuric rashes (10.6%).

Conclusions

When comparing RNA viral infections with COVID-19 infection, we observed similarities in the reported skin manifestations and their presumed pathways, with many implicated in the proinflammatory response. Owing to the wide range of cutaneous symptoms associated with RNA viruses and our currently limited understanding of the underlying mechanisms, additional research is warranted to investigate the pathology behind viral-induced skin lesions.
Notes on the data quality of bibliographic records from the MEDLINE database
Authors: Bramley Robin , Howe Stephen , Marmanis Haralambos
Published: November 2023

The US National Library of Medicine has created and maintained the PubMed® database, a collection of over 33.8 million records that contain citations and abstracts from the biomedical and life sciences literature. This database is an important resource for researchers and information service providers alike. As part of our work related to the creation of an author graph for coronaviruses, we encountered several data quality issues with records from a curated subset of the PubMed database called MEDLINE. We provide a data quality assessment for records selected from the MEDLINE database and report on several issues ranging from parsing issues (e.g. character encodings and schema definition weaknesses) to low scores for identifiers against several data quality metrics (e.g. completeness, validity and uniqueness).

Database URL  https://pubmed.ncbi.nlm.nih.gov
OncoCTMiner: streamlining precision oncology trial matching via molecular profile analysis
Authors: Xu Quan , Liu Yueyue , Sun Dawei , Huang Xiaoqian , Li Feihong , Zhai JinCheng , Li Yang , Zhou Qiming , Qian Niansong , Niu Beifang
Published: November 2023

By establishing omics sequencing of patient tumors as a crucial element in cancer treatment, the extensive implementation of precision oncology necessitates effective and prompt execution of clinical studies for approving molecular-targeted therapies. However, the substantial volume of patient sequencing data, combined with strict clinical trial criteria, increasingly complicates the process of matching patients to precision oncology studies. To streamline enrollment in these studies, we developed OncoCTMiner, an automated pre-screening platform for molecular cancer clinical trials. Through manual tagging of eligibility criteria for 2227 oncology trials, we identified key bio-concepts such as cancer types, genes, alterations, drugs, biomarkers and therapies. Utilizing this manually annotated corpus along with open-source biomedical natural language processing tools, we trained multiple named entity recognition models specifically designed for precision oncology trials. These models analyzed 460 952 clinical trials, revealing 8.15 million precision medicine concepts, 9.32 million entity-criteria-trial triplets and a comprehensive precision oncology eligibility criteria database. Most significantly, we developed a patient-trial matching system based on cancer patients’ clinical and genetic profiles, which can seamlessly integrate with the omics data analysis platform. This system expedites the pre-screening process for potentially suitable precision oncology trials, offering patients swifter access to promising treatment options.

Database URL  https://oncoctminer.chosenmedinfo.com
Bacterial communities of the threatened Western Pond Turtle may be impacted by land use
Authors: White Alison , Giannetto Madison , Mulla Lubna , Del Rosario Amber , Lim Tammy , Culver Edward , Timmer Matthew , Bushell Jessie , Lambert Max R , Hernández-Gómez Obed
Published: November 2023

As semi-aquatic species that use both terrestrial and aquatic habitats, freshwater turtles and their microbial communities are especially sensitive to the impacts of habitat disturbance. In this study, we use 16S rRNA amplicon sequencing to characterize the shell and cloacal bacterial communities of turtles in the San Francisco Bay Area. We captured western pond turtles (Actinemys/Emys marmorata) across eight sites located in urban and rural environments, along with invasive red-eared sliders (Trachemys scripta elegans). We assessed differences in western pond turtle bacterial communities diversity/composition between shell and cloacal samples and evaluated how alpha/beta diversity metrics were influenced by habitat quality. We found phylum-level bacterial taxonomic turnover in the bacterial communities of western pond turtles relative to the host tissue substrate samples. Our findings indicate that location identity elicits a high degree of lower-level (i.e. species/genus) bacterial taxonomic turnover. Further, we found that samples originating from good quality habitat had poorer shell bacterial communities but more diverse cloacal ones. The shell bacterial communities of red-eared sliders overlapped with those western pond turtles suggesting the existence of microbial dispersal between these two species. Our results add to our current understanding of turtle symbiont microbial ecology by establishing patterns of bacterial symbiont variation in an urban to rural gradient.
Internet-Based Conversational Engagement Randomized Controlled Clinical Trial (I-CONECT) Among Socially Isolated Adults 75+ Years Old With Normal Cognition or Mild Cognitive Impairment: Topline Results
Authors: Dodge Hiroko H , Yu Kexin , Wu Chao-Yi , Pruitt Patrick J , Asgari Meysam , Kaye Jeffrey A , Hampstead Benjamin M , Struble Laura , Potempa Kathleen , Lichtenberg Peter , Croff Raina , Albin Roger L , Silbert Lisa C ,   the I-CONECT Team, Alfaro Elena , McDonald Mattie , Lindsey Jacob , Scavone Colton , Sheridan Nita , Nguyen Khoa , Ellis Alexis , Weisberg Louis , Moore Deborah , Peacock Brandy , Heller Brennan , Thornall Carissa , Ruhf Sandy , Ziemer-McGinn Mary , Custodio Farah , Farrell Diane , Lynch Aimee , Banker Dillon , Reyes Gracia , Rabe Kathryn , Seeton Laura , Pedroza Jessica , Forystek David , May Nicolas , Reader Jonathan , Bhaumik Arijit K
Published: November 2023

Background and Objectives

Social isolation is a risk factor for cognitive decline and dementia. We conducted a randomized controlled clinical trial (RCT) of enhanced social interactions, hypothesizing that conversational interactions can stimulate brain functions among socially isolated older adults without dementia. We report topline results of this multisite RCT (Internet-based conversational engagement clinical trial [I-CONECT]; NCT02871921).

Research Design and Methods

The experimental group received cognitively stimulating semistructured conversations with trained interviewers via internet/webcam 4 times per week for 6 months (induction) and twice per week for an additional 6 months (maintenance). The experimental and control groups both received weekly 10 minutes telephone check-ins. Protocol modifications were required due to the coronavirus disease 2019 pandemic.

Results

A total of 186 participants were randomized. After the induction period, the experimental group had higher global cognitive test scores (Montreal Cognitive Assessment [primary outcome]; 1.75 points [p = .03]) compared with the control group. After induction, experimental group participants with normal cognition had higher language-based executive function (semantic fluency test [secondary outcome]; 2.56 points [p = .03]). At the end of the maintenance period, the experimental group of mild cognitive impairment subjects had higher encoding function (Craft Story immediate recall test [secondary outcome]; 2.19 points [p = .04]). Measure of emotional well-being improved in both control and experimental groups. Resting-state functional magnetic resonance imaging showed that the experimental group had increased connectivity within the dorsal attention network relative to the control group (p = .02), but the sample size was limited.

Discussion and Implications

Providing frequent stimulating conversational interactions via the internet could be an effective home-based dementia risk-reduction strategy against social isolation and cognitive decline.

Clinical Trials Registration Number

NCT02871921
A periodic table of monosaccharides
Authors: Cummings Richard D
Published: November 2023

It is important to recognize the great diversity of monosaccharides commonly encountered in animals, plants, and microbes, as well as to organize them in a visually interesting style that also emphasizes their similarities and relatedness. This article discusses the nature of building blocks, monosaccharides, and monosaccharide derivatives—terms commonly used in discussing “glycomolecules” found in nature. To aid in awareness of monosaccharide diversity, here is presented a Periodic Table of Monosaccharides. The rationale is given for construction of the Table and the selection of 103 monosaccharides, which is largely based on those presented in the KEGG and SNFG websites of monosaccharides, and includes room to enlarge as new discoveries are made. The Table should have educational value and is intended to capture the attention and foster imagination of those not very familiar with glycosciences, and encourage researchers to delve deeper into this fascinating area.
Deciphering the Neighborhood Atlas Area Deprivation Index: the consequences of not standardizing
Authors: Petterson Stephen
Published: November 2023

The Area Deprivation Index (ADI) is a widely used measure recently selected for several federal payment models that adjusts payments based on where beneficiaries live. A recent debate in Health Affairs focuses on seemingly implausible ADI rankings in major cities and across New York. At the root of the issue is the importance of standardization of measures prior to calculating index scores. Neighborhood Atlas researchers are implicitly arguing that their choice to not standardize is of little consequence. Using the same data and methods as the Neighborhood Atlas, this paper focuses on this choice by calculating and comparing standardized and unstandardized ADI scores. The calculated unstandardized ADI nearly perfectly matches the Neighborhood Atlas ADI (r > 0.9999), whereas the correlation with a standardized version is much lower (r = 0.7245). The main finding is that, without standardization, the ADI is reducible to a weighted average of just 2 measures—income and home values—certainly not the advertised multidimensional measure. Federal programs that have incorporated the ADI risk poorly allocating scarce resources meant to reduce health inequities.
Rescuing the liberal international order: crisis, resilience and EU security policy
Authors: Bargués Pol , Joseph Jonathan , Juncos Ana E
Published: November 2023

This article reflects on how European Union (EU) narratives of the crisis of the liberal international order (LIO) have reshaped its resilience approach and its foreign and security policy more broadly. Drawing on qualitative textual analysis, we trace the evolution of the EU's resilience approach over time and the way it has been shaped by crisis narratives. While the idea of resilience was introduced in EU foreign policy to foster the resilience of crisis-affected societies from the bottom up, the perception of an increasingly contested world first led to a reinterpretation of resilience in pragmatic ways, with values and interests combined selectively to protect the rules-based international order. More recently, on the grounds of a worsening crisis of the LIO, resilience has taken a defensive turn, adopting a more geopolitical stance to strengthen the EU's own resilience and that of the LIO. We argue that EU crisis narratives about the LIO thus serve to sustain and to rescue it. Furthermore, we conclude that the defensive reinterpretation of resilience is eroding the normative character of EU foreign and security policy. It also challenges the persistence of the LIO in the long term.
Authoritarian middle powers and the liberal order: Turkey's contestation of the EU
Authors: Aydın-Düzgit Senem
Published: November 2023

The conventional expectation that middle powers support the liberal international order (LIO) is now increasingly being questioned. This article seeks to explore why and how emerging authoritarian middle powers contest the LIO through a study of Turkey's contestation of the EU. By conceptualizing contestations of the LIO as claims to global justice, the article examines the justice claims that underlie Turkey's contestation; with regard to discourse, it does so through a qualitative content analysis of President Erdoğan's speeches, and with regard to practice, through a survey of Turkey's contestatory foreign policy practices. The article shows that middle powers can discursively attack the legitimacy of the LIO by underlining its constituents' failures in upholding their moral duties towards citizens extending beyond their borders (impartiality) and to those who suffer from structural inequalities in the international order (mutual recognition). It demonstrates that their contestatory practices, however, are made with a view to pursue the sovereign interests of the state, with minimal regard for impartiality and mutual recognition. The article unpacks this inconsistency and finds that authoritarian middle powers' contestation of the LIO is mainly driven by concerns for regime security, where the centrality of an issue area to the government's survival prospects is the key factor which determines whether contestation will occur.
Global justice and EU climate policy in a contested liberal international order
Authors: Diez Thomas , von Lucke Franziskus
Published: November 2023

Following the failure of the Conference of the Parties (COP15) in 2009 in Copenhagen, the European Union has significantly altered its negotiation strategy in the global climate regime. It moved from an emphasis on ‘leadership by example’ and an insistence on top-down, binding targets within a framework of strong global governance institutions (impartiality in global justice terms) towards a strategy of shared leadership, increased dialogue (mutual recognition) and acceptance of more voluntary instruments (non-domination). This article traces this shift through an examination of EU policy documents and makes sense of it by reference to learning effects of an EU with solidarist ambitions in a pluralist international society, and the changing power distribution and contestations of the post-Cold War liberal order on the global level. Furthermore, it assesses the consequences of the shift for international society (especially concerning different ‘solidarisms’) and global climate justice. We argue that while a changed EU approach has been vital to maintaining the EU's status as a relevant actor and to secure the Paris Agreement, too much emphasis on the pluralist dimension and non-domination may also hinder effective global solutions to climate change. It is therefore vital that the EU continues its solidarist ambitions by pushing for rigorous measures of accountability, but also by alleviating structural domination in the climate regime and particularly by better recognizing and including civil society actors from the global South.
European public opinion: united in supporting Ukraine, divided on the future of NATO
Authors: Thomson Catarina , Mader Matthias , Münchow Felix , Reifler Jason , Schoen Harald
Published: November 2023

• How strong is public support for Ukraine in Europe? Given reports that Russian President Vladimir Putin may be ‘playing for time’ in the hopes that weary publics will demand an end to supporting Ukraine, this is an important question.

• In February 2023, we conducted a survey of public attitudes in ten major European countries: France, Germany, the United Kingdom, Estonia, Hungary, Poland, Finland, Sweden, Italy and Spain.

• Our findings suggest that Europeans are (almost) unanimous in blaming Russia for the war and strongly in favour of standing by Ukraine in its war effort.

• Only minorities of respondents are of the opinion that Ukraine should be urged to accept territorial losses that could help end the war, or that economic sanctions against Russia should be lifted. Even in countries where support for Ukraine is lower (Hungary and Italy), or among more sceptical groups, we typically find a majority or plurality on Ukraine's side (or, at worst, we find only a small majority are pro-Russia).

• Regarding NATO, there is no widespread appetite for increasing its presence in eastern Europe (except in Poland and Estonia), and even less support for Ukraine joining the alliance. At least in the eyes of the public, fighting a war in Ukraine is perceived as a goal in itself that does not necessarily elicit broader changes to existing security alliances like NATO.

• Looking ahead, if the gap between the expectations audiences had for the Ukrainian counter-offensive and what it actually delivers is too great, we would expect public support for Ukraine in the conflict to weaken overall.

• If governments wish to keep support levels high, we recommend targeting communications to reach groups we have found to be less supportive. This could include utilizing non-traditional media platforms to reach younger audiences, or members of populist right-wing groups.
Independent relevance of adiposity measures to coronary heart disease risk among 0.5 million adults in UK Biobank
Authors: Trichia Eirini , Malden Debbie E , Jin Danyao , Wright Neil , Taylor Hannah , Karpe Fredrik , Sherliker Paul , Murgia Federico , Hopewell Jemma C , Lacey Ben , Emberson Jonathan , Bennett Derrick , Lewington Sarah
Published: November 2023

Background

Evidence on body fat distribution shows opposing effects of waist circumference (WC) and hip circumference (HC) for coronary heart disease (CHD). We aimed to investigate the causality and the shape of such associations.

Methods

UK Biobank is a prospective cohort study of 0.5 million adults aged 40–69 years recruited between 2006 and 2010. Adjusted hazard ratios (HRs) for the associations of measured and genetically predicted body mass index (BMI), WC, HC and waist-to-hip ratio with incident CHD were obtained from Cox models. Mendelian randomization (MR) was used to assess causality. The analysis included 456 495 participants (26 225 first-ever CHD events) without prior CHD.

Results

All measures of adiposity demonstrated strong, positive and approximately log-linear associations with CHD risk over a median follow-up of 12.7 years. For HC, however, the association became inverse given the BMI and WC (HR per usual SD 0.95, 95% CI 0.93–0.97). Associations for BMI and WC remained independently positive after adjustment for other adiposity measures and were similar (1.14, 1.13–1.16 and 1.18, 1.15–1.20, respectively), with WC displaying stronger associations among women. Blood pressure, plasma lipids and dysglycaemia accounted for much of the observed excess risk. MR results were generally consistent with the observational, implying causality.

Conclusions

Body fat distribution measures displayed similar associations with CHD risk as BMI except for HC, which was inversely associated with CHD risk (given WC and BMI). These findings suggest that different measures of body fat distribution likely influence CHD risk through both overlapping and independent mechanisms.
Barriers and facilitators experienced in delivering alcohol screening and brief interventions in community pharmacy: a qualitative evidence synthesis
Authors: Smith Alexander , Buchanan Ryan , Parkes Julie , Stone Helen , Tan Qian Yue , Ibrahim Kinda
Published: November 2023

Background

Following increases in deaths due to alcohol during the COVID-19 pandemic, there have been renewed calls to increase resources in alcohol screening and brief intervention (SBI). Research has shown that community pharmacy could be a promising setting for SBI. This review aimed to investigate the barriers and facilitators to SBI delivery in community pharmacy to inform its further development.

Methods

A systematic search of four databases (MEDLINE, EMBASE, CINAHL, and PsycINFO) was conducted in October 2021 to identify relevant published qualitative or mixed-method studies. Relevant qualitative data were extracted from the included studies and a framework synthesis was performed using the Capability–Opportunity–Motivation–Behaviour (COM-B) model.

Results

Two thousand two hundred and ten articles were screened and nine studies were included in the review (seven in the United Kingdom and two in Australia). Identified barriers and facilitators to delivering SBI corresponded to all components of the COM-B model. Facilitators included non-confrontational communication skills, aligning SBI with existing pharmacy services and pharmacist role legitimacy. Barriers included multiple demands on staff time, a lack of staff experience with screening tools, and staff concerns of causing offence. Using the Behaviour Change Wheel (BCW), we propose five elements of a pharmacy SBI to address identified barriers.

Conclusions

Research into SBI in community pharmacy is limited in comparison to other healthcare settings and this review provides an understanding of the barriers and facilitators to the delivery of SBI in community pharmacy from a behavioural perspective. Through the use of COM-B and BCW, our findings could inform the development of future pharmacy-based SBI.