bluuebunny/crossref_metadata_2025_split huggingface dataset:
ScaffoldGVAE: scaffold generation and hopping of drug molecules via a variational autoencoder based on multi-view graph neural networks
Authors: Hu Chao , Li Song , Yang Chenxing , Chen Jun , Xiong Yi , Fan Guisheng , Liu Hao , Hong Liang 
Published: October 2023

AbstractIn recent years, drug design has been revolutionized by the application of deep learning techniques, and molecule generation is a crucial aspect of this transformation. However, most of the current deep learning approaches do not explicitly consider and apply scaffold hopping strategy when performing molecular generation. In this work, we propose ScaffoldGVAE, a variational autoencoder based on multi-view graph neural networks, for scaffold generation and scaffold hopping of drug molecules. The model integrates several important components, such as node-central and edge-central message passing, side-chain embedding, and Gaussian mixture distribution of scaffolds. To assess the efficacy of our model, we conduct a comprehensive evaluation and comparison with baseline models based on seven general generative model evaluation metrics and four scaffold hopping generative model evaluation metrics. The results demonstrate that ScaffoldGVAE can explore the unseen chemical space and generate novel molecules distinct from known compounds. Especially, the scaffold hopped molecules generated by our model are validated by the evaluation of GraphDTA, LeDock, and MM/GBSA. The case study of generating inhibitors of LRRK2 for the treatment of PD further demonstrates the effectiveness of ScaffoldGVAE in generating novel compounds through scaffold hopping. This novel approach can also be applied to other protein targets of various diseases, thereby contributing to the future development of new drugs. Source codes and data are available at https://github.com/ecust-hc/ScaffoldGVAE.
Computing Dirichlet eigenvalues of the Schrödinger operator with a PT-symmetric optical potential
Authors: Nur Cemile 
Published: October 2023

AbstractWe provide estimates for the eigenvalues of non-self-adjoint Sturm–Liouville operators with Dirichlet boundary conditions for a shift of the special potential $4\cos ^{2}x+4iV\sin 2x$
4

cos
2

x
+
4
i
V
sin
2
x
that is a PT-symmetric optical potential, especially when $|c|=|\sqrt{1-4V^{2}}|<2$
|
c
|
=
|

1
−
4

V
2

|
<
2
or correspondingly $0\leq V<\sqrt {5}/2$
0
≤
V
<

5

/
2
. We obtain some useful equations for calculating Dirichlet eigenvalues also for $|c|\geq 2$
|
c
|
≥
2
or equally $V\geq \sqrt{5}/2$
V
≥

5

/
2
. We discuss our results by comparing them with the periodic and antiperiodic eigenvalues of the Schrödinger operator. We even approximate complex eigenvalues by the roots of some polynomials derived from some iteration formulas. Moreover, we give a numerical example with error analysis.
Immunology in COPD and the use of combustible cigarettes and heated tobacco products
Authors: Błach Justyna , Siedliński Mateusz , Sydor Wojciech 
Published: October 2023

AbstractChronic obstructive pulmonary disease (COPD) is one of the most common chronic respiratory diseases, characterised by high morbidity and mortality. COPD is characterised by a progressive decline of lung function caused by chronic inflammatory reactions in the lung tissue due to continual exposure to harmful molecules by inhalation. As prevention plays a very important role in COPD, quitting smoking is the most important factor in reducing the decline in lung function. Unfortunately, many people are unable to break their nicotine addiction. This paper summarises current knowledge about combustible cigarettes (CSs) and alternative tobacco products such as heated tobacco products (HTPs) in COPD. The paper focuses on the immunological aspects of COPD and the influence of tobacco products on lung tissue immunology. There are differences in research results between HTPs and CSs in favour of HTPs. More long-term studies are needed to look at the effects of HTPs, especially in COPD. However, there is no doubt that it would be best for patients to give up their nicotine addiction completely.
Variability and accuracy of multiple saliva pepsin measurements in laryngopharyngeal reflux patients
Authors: Lechien Jerome R. , Bobin Francois 
Published: October 2023

Objective To study the variability and diagnostic value of multiple salivary pepsin measurements in the detection of laryngopharyngeal reflux (LPR). Methods Patients with LPR symptoms were consecutively recruited from December 2019 to Augustus 2022. Twenty-one asymptomatic individuals completed the study. The diagnostic was confirmed with hypopharyngeal–esophageal impedance-pH monitoring (HEMII-pH). Patients collected three saliva samples during the 24-h testing period. Symptoms and findings were studied with reflux symptom score-12 and reflux sign assessment. Sensitivity, specificity, positive (PPV) and negative (NPV) predictive values of pepsin measurements were calculated considering morning, post-lunch and post-dinner samples. The consistency and relationship between HEMII-pH, pepsin measurements, and clinical features were investigated. Results Morning, post-lunch and post-dinner saliva pepsin concentrations were measured in 42 patients. Pepsin measurements were 64.9%, 59.5%, and 59.0% sensitive for morning, post-lunch and post-dinner collections at cutoff ≥ 16 ng/mL. Considering the highest concentration of the three pepsin saliva collections, the accuracy, sensitivity, specificity and PPV were 70.5%, 73.0%; 66.7% and 78.9%, respectively. Morning pepsin measurements reported higher consistency, sensitivity, and specificity than post-dinner and post-lunch pepsin measurements. Conclusion The collection of several saliva pepsin samples improves the detection rate of LPR. In case of high clinical LPR suspicion and negative pepsin test, a HEMII-pH study could provide further diagnostic information.
Frequency-dependent Q simulation and viscoacoustic reverse time migration based on the fractional Zener model
Authors: Zhang Yabing , Zhu Hejun , Liu Yang , Chen Tongjun 
Published: October 2023

Seismic attenuation is a basic physical property of the earth, which significantly affects the characteristics of seismic wavefields. Accurately simulating wave propagation in the earth is essential to image subsurface structures. Some prevailing methods (e.g., the standard linear solid and fractional Laplacian equation) to describe seismic wave propagation in attenuating media are mainly based on the constant- Q model (CQM), which is valid at room temperature and pressure. However, laboratory measurements suggest that the quality factor Q is a function of frequencies in some regions. To simulate the frequency-dependent Q effect, we derive a viscoacoustic wave equation from the stress-strain relationship of the fractional Zener model (FZM) with variable fractional orders. During the implementation, we separate the real and imaginary parts of the modulus and introduce a low-rank decomposition method to solve the FZM equation. Because the amplitude dissipation and phase dispersion are decoupled, we establish a compensated reverse time migration ( Q-RTM) algorithm to mitigate adverse effects caused by seismic attenuation and improve the quality of seismic migration in frequency-dependent attenuating media. A two-layer model and the BP gas chimney model are used to perform Q-RTM tests. A low-pass filter with a Tukey window function is applied to suppress numerical instability during the compensation. Numerical results demonstrate that our FZM Q-RTM approach can produce high-resolution images with corrected reflector positions and amplitudes. Because the CQM equation ignores the frequency dependence of Q, it may lead to overcompensation in Q-RTM.
Quantum thermodynamics of an
Reissner-Nordström black hole
Authors: Pourhassan Behnam , Sakallı İzzet , Shi Xiaoping , Faizal Mir , Wani Salman Sajad 
Published: October 2023

Abstract
In this paper, we will go beyond equilibrium description to properly investigate the evaporation of a Reissner-Nordström black hole. Thus, we will explicitly apply techniques of non-equilibrium quantum thermodynamics to this black hole. As the non-equilibrium effects would become important at the quantum scale, we will incorporate the quantum gravitational corrections by using an

Reissner-Nordström black hole. We will start by developing a novel

first law. Then we will investigate the quantum gravitational corrections to the Parikh-Wilczek formalism, and introduce Kullback-Leibler divergence to quantify the effects of corrections. Furthermore, we will demonstrate that the non-thermal nature of radiation in the Parikh-Wilczek formalism can be directly related to the average quantum work done on the emitted particles using non-equilibrium quantum thermodynamics. This is because the average quantum work done is a unitary process in non-equilibrium quantum thermodynamics. We will use the Ramsey scheme for emitted particles to calculate this quantum work distribution for the emitted particles.
Increased Levels of Urine Volatile Organic Compounds Are Associated With Diabetes Risk and Impaired Glucose Homeostasis
Authors: Duan Xiaoxia , Chen Zhenhua , Xia Congying , Zhong Rong , Liu Li , Long Lu 
Published: October 2023

Abstract

Context
Volatile organic compounds (VOCs) are pervasive environmental pollutants that have been linked to various adverse health effects. However, the effect of ambient VOCs, whether individually or in mixtures, on diabetes remains uncertain and requires further investigation.

Objective
This study investigates the effects of ambient VOCs exposure, whether single or mixed, on diabetes mellitus and glucose homeostasis in the general population.

Methods
Urinary concentrations of VOC metabolites were obtained from the National Health and Nutrition Examination Survey. Survey-weighted logistic regression and generalized linear regression were used to explore the associations between individual VOC exposure and diabetes risk and glucose homeostasis indicators, respectively. Weighted quantile sum (WQS) regression models were applied to assess the combined effects of VOC mixtures.

Results
Out of 8468 participants, 1504 had diabetes mellitus. Eight VOC metabolites showed positive associations with diabetes mellitus (OR, 1.15-1.43; all P &lt; .05), insulin resistance (IR) (OR, 1.02-1.06; P &lt; .05), and other glucose homeostasis indicators (β, 0.04-2.32; all P &lt; .05). Mixed VOC models revealed positive correlations between the WQS indices and diabetes risk (OR = 1.52; 95% CI, 1.29-1.81), IR (OR = 1.36; 95% CI, 1.14-1.62), and other glucose homeostasis indicators (β, 0.17-2.22; all P &lt; .05).

Conclusion
Urinary metabolites of ambient VOCs are significantly associated with an increased diabetes risk and impaired glucose homeostasis. Thus, primary prevention policies aimed at reducing ambient VOCs could attenuate diabetes burden.
Gut Microecology May Be Involved in the Pathogenesis of Hashimoto Thyroiditis by Reducing Production of Hydrogen Sulfide
Authors: Zhang Shangqing , Zhao Xue , Wang Xiuli , Jin Hongfang , Chen Lei , Ma Yuanyuan , Chi Yan , Zhang Jixin , Zhang Junqing , Gao Ying 
Published: October 2023

Abstract

Context
Hashimoto thyroiditis (HT) is related to intestinal microbiota alteration, but the causal relationship remains unclear. Hydrogen sulfide (H2S) is a microbiota-derived metabolite. We speculated that abnormal intestinal microbiota might limit H2S production capacity, promoting HT pathogenesis.

Objective
This work aimed to illustrate that the intestinal microbiota plays important roles in HT pathogenesis via microbiota-derived H2S levels.

Methods
We collected feces from HT patients and healthy donors for fecal microbiota transplantation (FMT). Thirty-six female CBA/J mice were randomly assigned to 4 groups: experimental autoimmune thyroiditis (EAT) group, EAT + Healthy group, EAT + HT group, and EAT + HT + H2S group. 16S ribosomal RNA sequencing was performed to examine gut microbiota alterations and the H2S production pathway. Serum TgAb and H2S levels were assayed by enzyme-linked immunosorbent assay and H2S-selective sensors, respectively. T-cell subpopulations in the spleen were detected by flow cytometry.

Results
The gut microbiota was different after FMT among the EAT, EAT + Healthy, and EAT + HT groups. The thyroiditis score assessed by hematoxylin and eosin staining was higher in the EAT + HT group than that in the EAT and EAT + HT + H2S groups. Helper T (Th1) and Th17 cell differentiation ratios were increased in the EAT + HT group compared to the other 3 groups. Serum H2S levels were decreased and the dissimilatory sulfate reduction (DSR) pathway was attenuated in the EAT + HT group compared to the EAT + Healthy group.

Conclusion
H2S alleviated thyroiditis severity and related immune disorders, which were aggravated by the FMT from HT patients. The attenuated DSR pathway in the gut microbiota from HT patients might be involved in thyroiditis pathogenesis.
Development, regeneration and aging: a bizarre love triangle
Authors: Cochella Luisa , Chaker Zayna 
Published: October 2023

ABSTRACT
The Jacques Monod Conference on ‘Growth and regeneration during development and aging’ was organized by Claude Desplan and Allison Bardin in May 2023. The conference took place in Roscoff, France, where participants shared recent conceptual advances under the general motto that developmental processes do not end with embryogenesis. The meeting covered various aspects of how development relates to fitness, regeneration and aging across a refreshing diversity of evolutionarily distant organisms.
Bank Supervision and Corporate Credit Supply
Authors: Ivanov Ivan T. , Wang James Z. 
Published: October 2023

We exploit the quasi-random assignment of federal bank examiners to syndicated loans to study the effect of supervision on corporate lending. Following supervisory rating downgrades, banks decrease credit commitments and downgrade internal risk assessments. Borrowers face larger commitment reductions whenever banks have low ex ante screening and monitoring incentives or whenever examiners’ assessments contain more information than banks’ assessments, suggesting that examinations complement bank monitoring. Although public firms can offset the loss of bank credit by tapping external capital markets, smaller and more opaque private firms draw on internal cash balances instead and reduce investment and sales growth. This paper was accepted by Victoria Ivashina, finance. Supplemental Material: The data files are available at https://doi.org/10.1287/mnsc.2023.4854 .
Research on the interactive perception of color paper-cutting culture rendering based on AR
Authors: Huang Yuchen , Xu Yulei , Yuan Jiangping , Zan Chaoyuan , Xiao Kaida 
Published: October 2023

To address the digital medium preference of the millennial generation, this study utilizes augmented reality (AR) technology for rendering color paper cuttings by developing a mobile terminal based on Unity 3D and 3ds Max to demonstrate digital works scanned by paper-cutting entities. Three subjective scaling experiments are conducted to evaluate the aesthetics, viewership, and impression of four genres of digital color paper cutting. The results show that observers have more preference for warm background with the maximum scaling value at the 7.5 mm/s playback speed and a specific superimposed order. Importantly, current experimental design and interactive evaluation provide a reference for AR display parameters.
Integration of serial self-testing for COVID-19 as part of contact tracing in the Brazilian public health system: A pragmatic trial protocol
Authors: Green Rebecca K. , Manchola Camilo , Gerth-Guyette Emily , Oliveira Silva Michelle , Stephanie Raissa , dos Santos Soares Tainá , Bastos Gottin Luiza , Coelho Milena , Green Kimberly E. , Dias Tavares Costa Alexandre , Batista Pereira Dhélio 
Published: October 2023

The coronavirus disease (COVID-19) pandemic has led to an unprecedented public health crisis. Insufficient testing continues to limit the effectiveness of the global response to the COVID-19 pandemic. Molecular testing methods such as reverse transcriptase polymerase chain reaction (RT-PCR) continue to be highly centralized and are a sub-optimal option for population surveillance. Rapid antigen tests (Ag-RDTs) offer multiple benefits including low costs, high flexibility to conduct tests in a wide variety of settings, and faster return of results. Self-test Ag-RDTs (STs) have gained approval in several markets and offer the possibility to expand testing, reaching at-risk populations. While STs have the potential to assist the COVID-19 response, test result integrity, reporting, and appropriate linkage to care continue to hinder the widespread implementation of self-testing programs. This protocol presents a mixed-methods pragmatic trial (ISRCTN91602092) to better understand the feasibility of self-testing as part of a contact tracing strategy within the Brazilian public health system. Approximately 604 close contacts of 150 index cases testing positive for COVID-19 will be enrolled. Index cases will be randomized for their close contacts to participate in either serial (daily) self-testing over a 10-day follow-up period or a more traditional approach to contact tracing with a professional Ag-RDT at one time point post-exposure. Usability workshops and focus group discussions will also be conducted. This study protocol presents a comprehensive plan to assess the effectiveness, operational feasibility, and stakeholder preferences of a serial self-testing strategy for contact tracing within the Brazilian public health system. Our results will contribute to better understanding of the feasibility of a self-testing strategy within the public sector. Potential risks and limitations are discussed. Our findings will have important implications as governments continue working to mitigate the impact of COVID-19, particularly in the context of where to direct limited resources for testing and healthcare infrastructure.
Registration: This trial is registered at ISCTRN (ISRCTN91602092).
Sympathetic innervation of the supraclavicular brown adipose tissue: A detailed anatomical study
Authors: Mori Shumpei , Beyer Ryan S. , Bernardes de Souza Breno , Sorg Julie M. , Hoover Donald B. , Sacks Harold S. , Fishbein Michael C. , Chang Grace , Peacock Warwick J. , St. John Maie A. , Law James , Symonds Micheal E. , Ajijola Olujimi A. , Shivkumar Kalyanam , Srikanthan Preethi 
Published: October 2023

Background
The supraclavicular fossa is the dominant location for human brown adipose tissue (BAT). Activation of BAT promotes non-shivering thermogenesis by utilization of glucose and free fatty acids and has been the focus of pharmacological and non-pharmacological approaches for modulation in order to improve body weight and glucose homeostasis. Sympathetic neural control of supraclavicular BAT has received much attention, but its innervation has not been extensively investigated in humans.

Methods
Dissection of the cervical region in human cadavers was performed to find the distribution of sympathetic nerve branches to supraclavicular fat pad. Furthermore, proximal segments of the 4th cervical nerve were evaluated histologically to assess its sympathetic components.

Results
Nerve branches terminating in supraclavicular fat pad were identified in all dissections, including those from the 3rd and 4th cervical nerves and from the cervical sympathetic plexus. Histology of the proximal segments of the 4th cervical nerves confirmed tyrosine hydroxylase positive thin nerve fibers in all fascicles with either a scattered or clustered distribution pattern. The scattered pattern was more predominant than the clustered pattern (80% vs. 20%) across cadavers. These sympathetic nerve fibers occupied only 2.48% of the nerve cross sectional area on average.

Conclusions
Human sympathetic nerves use multiple pathways to innervate the supraclavicular fat pad. The present finding serves as a framework for future clinical approaches to activate human BAT in the supraclavicular region.
Lifestyle parameters of Japanese agricultural and non-agricultural workers aged 60 years or older and less than 60 years: A cross-sectional observational study
Authors: Kinoshita Fumie , Yoshida Kei , Fujitani Masaya , Imai Yuta , Kobayashi Yumiko , Ito Tomoya , Okumura Yuto , Sato Hiroyuki , Mikami Tatsuya , Jung Songee , Hirakawa Akihiro , Nakatochi Masahiro 
Published: October 2023

Objectives
Improving the lifestyle of occupational workers is essential for extending healthy life expectancy. We investigated various lifestyle-related items in a rural Japanese population and compared them between agricultural and non-agricultural workers.

Methods
This cross-sectional study was conducted as a part of the “Iwaki Health Promotion Project.” Lifestyle-related items such as sleep, work hours, nutrition, health-related quality of life, and proportion of time spent performing each daily activity were compared between agricultural and non-agricultural workers in the ≥60 years (n = 251) and <60 years (n = 560) age groups.

Results
Agricultural workers had significantly lower Pittsburgh Sleep Quality Index total scores than non-agricultural workers in the <60 years group. The proportion of participants with more than 5 weekly working days was high among agricultural workers in both groups. Additionally, the proportion of people who worked more than 8 h per day was high among agricultural workers in both age groups. Energy intake per day was high among agricultural workers in the <60 years group. In both age groups, agricultural workers slept and woke up approximately 40 min earlier than did non-agricultural workers.

Conclusions
Agricultural workers have better sleep habits but work longer than non-agricultural workers, with some differences in energy intake and proportion of time spent on each daily activity. These differences should be considered when planning lifestyle intervention programs for agricultural workers.
Association between pertussis vaccination in infancy and childhood asthma: A population-based record linkage cohort study
Authors: Pérez Chacón Gladymar , Fathima Parveen , Jones Mark , Estcourt Marie J. , Gidding Heather F. , Moore Hannah C. , Richmond Peter C. , Snelling Tom 
Published: October 2023

BackgroundAsthma is among the commonest noncommunicable diseases of childhood and often occurs with other atopic comorbidities. A previous case-control study found evidence that compared to children who received acellular pertussis (aP) vaccines in early infancy, children who received one or more doses of whole-cell pertussis (wP) vaccine had lower risk of developing IgE-mediated food allergy. We hypothesized that wP vaccination in early infancy might protect against atopic asthma in childhood.MethodsRetrospective record-linkage cohort study of children between 5 and < 15 years old and born between January 1997, and December 1999, in the Australian states of Western Australia (WA) and New South Wales (NSW), receiving wP versus aP vaccine as the first pertussis vaccine dose. The main outcome and measures were first and recurrent hospitalizations for asthma; hazard ratios (HRs) and 95% confidence intervals (CIs) were computed by means of Cox and Andersen and Gill models.Results274,405 children aged between 5 and < 15 years old (78.4% NSW-born) received a first dose of either wP (67.8%) or aP vaccine before 4 months old. During the follow-up period, there were 5,905 hospitalizations for asthma among 3,955 children. The incidence rate for first hospitalization was 1.5 (95% CI 1.4–1.5) per 1,000 child-years among children receiving wP vaccine as a first dose, and 1.5 (95% CI 1.4–1.6) among those vaccinated with aP vaccine as a first dose. The adjusted HRs for those who received wP vaccine versus aP vaccine as the first dose were 1.02 (95% CI 0.94–1.12) for first hospitalizations and 1.07 (95% CI 0.95–1.2) for recurrent hospitalizations for asthma.ConclusionsWe found no convincing evidence of a clinically relevant association between receipt of wP versus aP vaccines in early infancy and hospital presentations for asthma in childhood.