bluuebunny/crossref_metadata_2025_split huggingface dataset:
Denoising of Geochemical Data using Deep Learning–Implications for Regional Surveys
Authors: Zhang Steven E. , Bourdeau Julie E. , Nwaila Glen T. , Parsa Mohammad , Ghorbani Yousef 
Published: February 2024

AbstractRegional geochemical surveys generate large amounts of data that can be used for a number of purposes such as to guide mineral exploration. Modern surveys are typically designed to permit quantification of data uncertainty through data quality metrics by using quality assurance and quality control (QA/QC) methods. However, these metrics, such as data accuracy and precision, are obtained through the data generation phase. Consequently, it is unclear how residual uncertainty in geochemical data can be minimized (denoised). This is a limitation to propagating uncertainty through downstream activities, particularly through complex models, which can result from the usage of artificial intelligence-based methods. This study aims to develop a deep learning-based method to examine and quantify uncertainty contained in geochemical survey data. Specifically, we demonstrate that: (1) autoencoders can reduce or modulate geochemical data uncertainty; (2) a reduction in uncertainty is observable in the spatial domain as a decrease of the nugget; and (3) a clear data reconstruction regime of the autoencoder can be identified that is strongly associated with data denoising, as opposed to the removal of useful events in data, such as meaningful geochemical anomalies. Our method to post-hoc denoising of geochemical data using deep learning is simple, clear and consistent, with the amount of denoising guided by highly interpretable metrics and existing frameworks of scientific data quality. Consequently, variably denoised data, as well as the original data, could be fed into a single downstream workflow (e.g., mapping, general data analysis or mineral prospectivity mapping), and the differences in the outcome can be subsequently quantified to propagate data uncertainty.
Novel LMI-Based Boundary Stabilization of Stochastic Delayed Reaction-Diffusion Cohen–Grossberg BAM Neural Networks with Impulsive Effects
Authors: Gokulakrishnan V. , Srinivasan R. , Syed Ali M. , Rajchakit Grienggrai , Priya Bandana 
Published: February 2024

AbstractThe stabilization problem of stochastic delayed reaction-diffusion Cohen–Grossberg BAM neural networks (SDRDCGBAMNNs) with impulsive effects and boundary control is studied in this paper. By using suitable boundary controllers, Lyapunov–Krasovskii functional, linear matrix inequalities and average impulsive interval method, new sufficient criteria are found to ensure that the SDRDCGBAMNNs achieve boundary stabilization in finite-time. Based on these criteria, the effects of impulsive and boundary controllers on finite-time stability are analyzed. Numerical simulations are performed to demonstrate the feasibility of the theoretical results.
Poset Ramsey Number $$R(P,Q_n)$$. II. N-Shaped Poset
Authors: Axenovich Maria , Winter Christian 
Published: February 2024

AbstractGiven partially ordered sets (posets) $$(P, \le _P)$$

(
P
,

≤
P

)

and $$(P', \le _{P'})$$

(

P
′

,

≤

P
′

)

, we say that $$P'$$

P
′

contains a copy of P if for some injective function $$f:P\rightarrow P'$$

f
:
P
→

P
′

and for any $$A, B\in P$$

A
,
B
∈
P

, $$A\le _P B$$

A

≤
P

B

if and only if $$f(A)\le _{P'} f(B)$$

f

(
A
)

≤

P
′

f

(
B
)

. For any posets P and Q, the poset Ramsey number R(P, Q) is the least positive integer N such that no matter how the elements of an N-dimensional Boolean lattice are colored in blue and red, there is either a copy of P with all blue elements or a copy of Q with all red elements. We focus on the poset Ramsey number $$R(P, Q_n)$$

R
(
P
,

Q
n

)

for a fixed poset P and an n-dimensional Boolean lattice $$Q_n$$

Q
n

, as n grows large. It is known that $$n+c_1(P) \le R(P,Q_n) \le c_2(P) n$$

n
+

c
1

(
P
)

≤
R

(
P
,

Q
n

)

≤

c
2

(
P
)

n

, for positive constants $$c_1$$

c
1

and $$c_2$$

c
2

. However, there is no poset P known, for which $$R(P, Q_n)> (1+\epsilon )n$$

R

(
P
,

Q
n

)

>

(
1
+
ϵ
)

n

, for $$\epsilon >0$$

ϵ
>
0

. This paper is devoted to a new method for finding upper bounds on $$R(P, Q_n)$$

R
(
P
,

Q
n

)

using a duality between copies of $$Q_n$$

Q
n

and sets of elements that cover them, referred to as blockers. We prove several properties of blockers and their direct relation to the Ramsey numbers. Using these properties we show that $$R(\mathcal {N},Q_n)=n+\Theta (n/\log n)$$

R

(
N
,

Q
n

)

=
n
+
Θ

(
n
/
log
n
)

, for a poset $$\mathcal {N}$$
N
with four elements A, B, C, and D, such that $$A<C$$

A
<
C

, $$B<D$$

B
<
D

, $$B<C$$

B
<
C

, and the remaining pairs of elements are incomparable.
Hazardous impacts of heavy metal pollution on biometric and biochemical composition of pearl oyster Pinctada radiata from five sites along Alexandria coast, with reference to its potential health risk assessment
Authors: Abdel-Mohsen Hala Ahmed , Ismail Mona Mohamed , Moussa Moussa Ragia 
Published: February 2024

AbstractThis study investigated the effect of heavy metals on the pearl oyster Pinctada radiata from 5 sites along the coast of Alexandria, with focus on its ecological health and potential risks to human consumption. Pollution results showed that Abu-Qir had the highest Cu and Cd values. Montaza and Eastern Harbor had the highest Fe and Pb values, respectively. Statistically, differences in metal concentrations among study sites were significant (p < 0.05). Non-carcinogenic risk (TTHQ) of tested metals and carcinogenic ones of Cd and Pb showed “high risk” on human health by consuming pearl oysters. Morphometric measurements and condition indices were studied to assess growth patterns and health in relation to heavy metals exposure. Key findings showed detectable declines in size and condition index in Eastern Harbor, whereas Abu-Qir recorded the highest values. This condition index performance presented Abu-Qir, Mammora, and Miami as ideal locations for spat collection and oyster rearing, potentially enhancing Egyptian pearl farming. Average values of spatial proximate contents of pearl oyster showed that it was rich in proteins (33.07–58.52%) with low fat content (1.39–1.87%) and carbohydrates (9.72–17.63%). Biochemical composition of pearl oyster demonstrated its high nutritional value which supported its promotion as a functional food for human consumption. The calorie content of pearl oyster was less than 2 Kcal, making this species an alternative source of healthy food to reduce obesity. Regression analysis indicated that Cu, Cd, and Pb had significant effect on 2-diphenyl-1-picrylhydrazyl (DPPH) scavenging activity, calories, vitamins, and pigment content of the collected oysters.
Optimum Dimensions for Au Nanoframe Tuning in the Near-Infrared Second Window Range for Biomedical Applications: A Numerical Study
Authors: Alali Fatema Abdullah , Alhindi Khadeeja Bader 
Published: February 2024

Abstract
Au nanoparticles are favored in biomedical applications owing to their low cost and negligible cytotoxicity to biological cells. Nanoframes outshine their solid counterparts because of their porosity, which produces pronounced redshifts in their local surface plasmon resonance (LSPR). This feature enables the utilization of nanoframes in photothermal-based therapy, where LSPR excitation of particles within the near-infrared range (NIR) is essential. LSPR redshift in nanoframes is highly sensitive to their dimensions. A slight difference in the nanoframe dimension can result in substantial redshift, potentially pushing its LSPR beyond or below the required NIR range. We perform a systematic numerical study to investigate the optimum dimensions within a range of 1–100 nm for a spherical frame (SpF) and standard cubic frame (CF) to precisely tune their LSPR within the NIR-II window (1000–1400 nm). Our findings indicate that SpF exhibits a shorter LSPR redshift than CF’s at a certain porosity limit that is related to the geometry of the frame. Moreover, SpF displays higher LSPR sensitivity in the NIR region compared to CF. These insights provide valuable guidance for nanoframe design tailored for photothermal-based biomedical applications.
Choice of Open Access in Elsevier Hybrid Journals
Authors: Asai Sumiko 
Published: February 2024

AbstractOpen access articles in hybrid journals have recently increased despite high article processing charges. This study investigated the impacts of grants and transformative agreements on authors’ choice of open and non-open access articles by comparing two article types. The samples were hybrid journals launched independently by Elsevier. The results revealed that the authors who received more grants in countries with transformative agreements were more likely to choose open access articles. By contrast, authors in developing countries were likely to publish non-open access articles. These findings imply that authors’ choices depend on the funding systems and open access policies in individual countries. Consequently, open access may become a barrier to the dissemination of work for researchers who have financial difficulty choosing open access, although it enables everyone to access articles free of charge.
Designing incentive systems for participation in digital ecosystems—An integrated framework
Authors: Mihale-Wilson Cristina , Carl K. Valerie 
Published: February 2024

AbstractDigital ecosystems are a highly relevant phenomenon in contemporary practice, offering unprecedented value creation opportunities for both companies and consumers. However, the success of these ecosystems hinges on their ability to establish the appropriate incentive systems that attract and engage diverse actors. Following the notion that setting “the right” incentives is essential for forming and growing digital ecosystems, this article presents an integrated framework that supports scholars and practitioners in identifying and orchestrating incentives into powerful incentive systems that encourage active participation and engagement. This framework emphasizes the importance of understanding how individuals and groups are motivated to engage in the ecosystem to incentivize them effectively. To demonstrate its applicability and value, we show its application in the context of an emergent digital ecosystem within the Smart Living domain.
Pharmacokinetic and safety analysis of biosimilar adalimumab in healthy volunteers in Bangladesh
Authors: Kulsum Umme , Azad Kasrina , Washif Mubasshir , Hossain Mohabbat , Sultana Nishat , Hossain Ismail , Ahmed Faez , Rahman Ridwanur , Muktadir Abdul , Muktadir Hasneen , Karim Mahbubul , Rahman Mohammad Mizanur , Hossain Md Shawkat , Monim Syed Abdul , Pandey Alex S. , Qadri Firdausi , Kawser Zannat 
Published: February 2024

Abstract
Aims
Advixa is a monoclonal antibody manufactured as a biosimilar to adalimumab (Humira, Abbvie Inc.). The key objectives of this study were to use a healthy population group to assess pharmacokinetics (PK) and safety similarity between Advixa and Humira in healthy participants and to quantify the effects on adalimumab PK and safety to assess the impact of treatment with Advixa.

Methods
A group of healthy participants selected by screening aged between 18 and 45 years. According to the randomization table, each participant was given Adalimumab (Advixa or Humira) in the inpatient facilities in a hospital and observed for 72 h. Several blood samples were collected from the participants at different time points up to day 64 to measure their Pharmacokinetics and biosimilarity. The study was registered at clinicaltrial.gov retrospectively.

Results
The serum concentration–time profiles for PK and safety were compared in this randomized, double-blinded study between Humira and Advixa. A review of the data for biosimilarity confirmed that these products are similar to each other regarding healthy participants. 90% confidence interval of the relative mean Cmax, AUC0-t, and AUCo-inf of the Advixa and Humira were found within the acceptance criteria. No differences in safety profiles were observed in these studies.

Conclusion
PK and safety are similar between Advixa and Humira in participants with healthy status demonstrated in this clinical trial (NCT05172817; Registration Date/Initial Release Date: 28/09/2021). Adalimumab PK was also similar to treatment with Humira and Advixa.
DeepMCGCN: Multi-channel Deep Graph Neural Networks
Authors: Meng Lei , Ye Zhonglin , Yang Yanlin , Zhao Haixing 
Published: February 2024

AbstractGraph neural networks (GNNs) have shown powerful capabilities in modeling and representing graph structural data across various graph learning tasks as an emerging deep learning approach. However, most existing GNNs focus on single-relational graphs and fail to fully utilize the rich and diverse relational information present in real-world graph data. In addition, deeper GNNs tend to suffer from overfitting and oversmoothing issues, leading to degraded model performance. To deeply excavate the multi-relational features in graph data and strengthen the modeling and representation abilities of GNNs, this paper proposes a multi-channel deep graph convolutional neural network method called DeepMCGCN. It constructs multiple relational subgraphs and adopts multiple GCN channels to learn the characteristics of different relational subgraphs separately. Cross-channel connections are utilized to obtain interactions between different relational subgraphs, which can learn node embeddings richer and more discriminative than single-channel GNNs. Meanwhile, it alleviates overfitting issues of deep models by optimizing convolution functions and adding residual connections between and within channels. The DeepMCGCN method is evaluated on three real-world datasets, and the experimental results show that its node classification performance outperforms that of single-channel GCN and other benchmark models, which improves the modeling and representation capabilities of the model.
Genetic mutation patterns among glioblastoma patients in the Taiwanese population – insights from a single institution retrospective study
Authors: Huang Yu-Fen , Chiao Ming-Tsang , Hsiao Tzu-Hung , Zhan Yong-Xiang , Chen Tse-Yu , Lee Chung-Hsin , Liu Szu-Yuan , Liao Chih-Hsiang , Cheng Wen-Yu , Yen Chun-Ming , Lai Chih-Ming , Chen Jun-Peng , Shen Chiung-Chyi , Yang Meng-Yin 
Published: February 2024

AbstractThis study utilized Next-Generation Sequencing (NGS) to explore genetic determinants of survival duration in Glioblastoma Multiforme (GBM) patients. We categorized 30 primary GBM patients into two groups based on their survival periods: extended survival (over two years, N = 17) and abbreviated survival (under two years, N = 13). For identifying pathogenic or likely pathogenic variants, we leveraged the ClinVar database. The cohort, aged 23 to 66 (median: 53), included 17 patients in Group A (survival >2 years, 10 males, 7 females), and 13 patients in Group B (survival <2 years, 8 males, 5 females), with a 60% to 40% male-to-female ratio. Identified mutations included CHEK2 (c.1477 G > A, p.E493K), IDH1 (c.395 G > A, p.R132H), and TP53 mutations. Non-coding regions exhibited variants in the TERT promoter (c.-146C > T, c.-124C > T) and TP53 RNA splicing site (c.376-2 A > C, c.376-2 A > G). While Group A had more mutations, statistical significance wasn’t reached, likely due to sample size. Notably, TP53, and ATR displayed a trend toward significance. Surprisingly, TP53 mutations were more prevalent in Group A, contradicting Western findings on poorer GBM prognosis. In Taiwanese GBM patients, bevacizumab usage is linked to improved survival rates, affirming its safety and effectiveness. EGFR mutations are infrequent, suggesting potential distinctions in carcinogenic pathways. Further research on EGFR mutations and amplifications is essential for refining therapeutic approaches. TP53 mutations are associated with enhanced survival, but their functional implications necessitate detailed exploration. This study pioneers genetic analysis in Taiwanese GBM patients using NGS, advancing our understanding of their genetic landscape.
The Dimorphos ejecta plume properties revealed by LICIACube
Authors: Dotto E. , Deshapriya J. D. P. , Gai I. , Hasselmann P. H. , Mazzotta Epifani E. , Poggiali G. , Rossi A. , Zanotti G. , Zinzi A. , Bertini I. , Brucato J. R. , Dall’Ora M. , Della Corte V. , Ivanovski S. L. , Lucchetti A. , Pajola M. , Amoroso M. , Barnouin O. , Campo Bagatin A. , Capannolo A. , Caporali S. , Ceresoli M. , Chabot N. L. , Cheng A. F. , Cremonese G. , Fahnestock E. G. , Farnham T. L. , Ferrari F. , Gomez Casajus L. , Gramigna E. , Hirabayashi M. , Ieva S. , Impresario G. , Jutzi M. , Lasagni Manghi R. , Lavagna M. , Li J.-Y. , Lombardo M. , Modenini D. , Palumbo P. , Perna D. , Pirrotta S. , Raducan S. D. , Richardson D. C. , Rivkin A. S. , Stickle A. M. , Sunshine J. M. , Tortora P. , Tusberti F. , Zannoni M. 
Published: February 2024

AbstractThe Double Asteroid Redirection Test (DART) had an impact with Dimorphos (a satellite of the asteroid Didymos) on 26 September 20221. Ground-based observations showed that the Didymos system brightened by a factor of 8.3 after the impact because of ejecta, returning to the pre-impact brightness 23.7 days afterwards2. Hubble Space Telescope observations made from 15 minutes after impact to 18.5 days after, with a spatial resolution of 2.1 kilometres per pixel, showed a complex evolution of the ejecta3, consistent with other asteroid impact events. The momentum enhancement factor, determined using the measured binary period change4, ranges between 2.2 and 4.9, depending on the assumptions about the mass and density of Dimorphos5. Here we report observations from the LUKE and LEIA instruments on the LICIACube cube satellite, which was deployed 15 days in advance of the impact of DART. Data were taken from 71 seconds before the impact until 320 seconds afterwards. The ejecta plume was a cone with an aperture angle of 140 ± 4 degrees. The inner region of the plume was blue, becoming redder with increasing distance from Dimorphos. The ejecta plume exhibited a complex and inhomogeneous structure, characterized by filaments, dust grains and single or clustered boulders. The ejecta velocities ranged from a few tens of metres per second to about 500 metres per second.
Incomplete transcripts dominate the Mycobacterium tuberculosis transcriptome
Authors: Ju Xiangwu , Li Shuqi , Froom Ruby , Wang Ling , Lilic Mirjana , Delbeau Madeleine , Campbell Elizabeth A. , Rock Jeremy M. , Liu Shixin 
Published: February 2024

AbstractMycobacterium tuberculosis (Mtb) is a bacterial pathogen that causes tuberculosis (TB), an infectious disease that is responsible for major health and economic costs worldwide1. Mtb encounters diverse environments during its life cycle and responds to these changes largely by reprogramming its transcriptional output2. However, the mechanisms of Mtb transcription and how they are regulated remain poorly understood. Here we use a sequencing method that simultaneously determines both termini of individual RNA molecules in bacterial cells3 to profile the Mtb transcriptome at high resolution. Unexpectedly, we find that most Mtb transcripts are incomplete, with their 5′ ends aligned at transcription start sites and 3′ ends located 200–500 nucleotides downstream. We show that these short RNAs are mainly associated with paused RNA polymerases (RNAPs) rather than being products of premature termination. We further show that the high propensity of Mtb RNAP to pause early in transcription relies on the binding of the σ-factor. Finally, we show that a translating ribosome promotes transcription elongation, revealing a potential role for transcription–translation coupling in controlling Mtb gene expression. In sum, our findings depict a mycobacterial transcriptome that prominently features incomplete transcripts resulting from RNAP pausing. We propose that the pausing phase constitutes an important transcriptional checkpoint in Mtb that allows the bacterium to adapt to environmental changes and could be exploited for TB therapeutics.
Analysing the influence of ground granulated blast furnace slag and steel fibre on RC beams flexural behaviour
Authors: Murthy A. Ramachandra , Prasanna P. K. , Nipun G. , Srinivasu K. , Gandla Kumaraswamy , Khan Afzal Husain , Sabi Ehab 
Published: February 2024

AbstractThis study examines the effect of Ground Granulated Blast Furnace Slag (GGBS) and steel fibers on the flexural behaviour of RC beams under monotonic loading. Various percentages of GGBS were used to substitute cement, namely 0%, 20%, 40%, 60%, and 80% and fibers were added to the concrete mix as 0%, 0.5%, 1%, and 1.5% of the volume of concrete. The load–deflection behaviour of GGBS-incorporated RC beams with fibers was compared with the control RC beam. Beams were tested under load control for 28 days and 180 days. The ultimate load of the GGBS-incorporated RC beam up to 40% cement replacement was found to higher than that of the control beam. The strength of concrete is reduced by 28% and 19% when cement was partially replaced by 80% of GGBS at 28 and 180 days, respectively, compared to control concrete without fibres. Further, the analytical load–deflection response of GGBS-incorporated RC beams was determined by using several codes of practice, namely, ACI 318-11(2011), CSA A23.3-04 (2004), EC-04 (2004), and IS 456 (2000). The Codal provisions were primarily based on the effective moment of inertia, Young’s modulus, and modulus of rupture, stiffness, and cracking. Average load–deflection plots obtained from experiments were compared with the computed load–deflection of analytical studies. It was found that the analytically predicted load–deflection behaviour is comparable with the corresponding average experimental load–deflection response. Moment curvature relations were also developed for RC beams.
Bashing irreproducibility with shournal
Authors: Kirchner Tycho , Riege Konstantin , Hoffmann Steve 
Published: February 2024

AbstractArguably, the most important tool for many computational scientists is the Linux shell. Processing steps carried out there are critical for a large number of analyses. While the manual documentation of the work is time-consuming and error-prone, existing tools do not integrate well into the shell or suffer from a large overhead. Here, we present shournal, which integrates tightly into the shell and automatically records all shell commands along with their associated file events. Thus, for all files, it can later be told how they were generated and processed. Additionally, it allows the creation of detailed reports for whole project folders. shournal retrieves its data directly from the Linux kernel and allows the monitoring of whole process trees with low overhead.