bluuebunny/crossref_metadata_2025 huggingface dataset:
Machine-learning model for predicting oliguria in critically ill patients
Authors: Yamao Yasuo , Oami Takehiko , Yamabe Jun , Takahashi Nozomi , Nakada Taka-aki
Published: January 2024

This retrospective cohort study aimed to develop and evaluate a machine-learning algorithm for predicting oliguria, a sign of acute kidney injury (AKI). To this end, electronic health record data from consecutive patients admitted to the intensive care unit (ICU) between 2010 and 2019 were used and oliguria was defined as a urine output of less than 0.5 mL/kg/h. Furthermore, a light-gradient boosting machine was used for model development. Among the 9,241 patients who participated in the study, the proportions of patients with urine output < 0.5 mL/kg/h for 6 h and with AKI during the ICU stay were 27.4% and 30.2%, respectively. The area under the curve (AUC) values provided by the prediction algorithm for the onset of oliguria at 6 h and 72 h using 28 clinically relevant variables were 0.964 (a 95% confidence interval (CI) of 0.963–0.965) and 0.916 (a 95% CI of 0.914–0.918), respectively. The Shapley additive explanation analysis for predicting oliguria at 6 h identified urine values, severity scores, serum creatinine, oxygen partial pressure, fibrinogen/fibrin degradation products, interleukin-6, and peripheral temperature as important variables. Thus, this study demonstrates that a machine-learning algorithm can accurately predict oliguria onset in ICU patients, suggesting the importance of oliguria in the early diagnosis and optimal management of AKI.
Embayed beach configuration explained by wave sheltering
Authors: Nobre Silva Ana , Taborda Rui , Andrade César
Published: January 2024

Embayed beaches, characterized by their distinctive planform curvature, are a common feature along coastlines worldwide. This study introduces a novel approach to describe bay shape that extends our understanding about the processes that control embayed beach development. The novel approach was thoroughly tested against one-line models and applied to real-world cases covering a wide range of spatial scales, wave climate conditions and geomorphological settings. Here we show that the equilibrium curvature of embayed beaches can be correctly described and explained by considering headland-provided offshore wave sheltering alone, without explicitly accounting for wave shoaling, refraction, diffraction, or longshore transport. This holds true as long as the offshore wave climate is accurately characterized, including complete information regarding the mean and the spread of the incoming wave direction. For narrow-banded dominant swell wave regimes, the inclusion of background wind sea components has been identified as crucial for predicting curvature in the more sheltered embayed domain. The presented model significantly contributes to the understanding of how waves shape embayed beaches.
Blockchain security enhancement: an approach towards hybrid consensus algorithms and machine learning techniques
Authors: Venkatesan K. , Rahayu Syarifah Bahiyah
Published: January 2024

In this paper, we propose hybrid consensus algorithms that combine machine learning (ML) techniques to address the challenges and vulnerabilities in blockchain networks. Consensus Protocols make ensuring agreement among the applicants in the distributed systems difficult. However, existing mechanisms are more vulnerable to cyber-attacks. Previous studies extensively explore the influence of cyber attacks and highlight the necessity for effective preventive measures. This research presents the integration of ML techniques with the proposed hybrid consensus algorithms and advantages over predicting cyber-attacks, anomaly detection, and feature extraction. Our hybrid approaches leverage and optimize the proposed consensus protocols' security, trust, and robustness. However, this research also explores the various ML techniques with hybrid consensus algorithms, such as Delegated Proof of Stake Work (DPoSW), Proof of Stake and Work (PoSW), Proof of CASBFT (PoCASBFT), Delegated Byzantine Proof of Stake (DBPoS) for security enhancement and intelligent decision making in consensus protocols. Here, we also demonstrate the effectiveness of the proposed methodology within the decentralized networks using the ProximaX blockchain platform. This study shows that the proposed research framework is an energy-efficient mechanism that maintains security and adapts to dynamic conditions. It also integrates privacy-enhancing features, robust consensus mechanisms, and ML approaches to detect and prevent security threats. Furthermore, the practical implementation of these ML-based hybrid consensus models faces significant challenges, such as scalability, latency, throughput, resource requirements, and potential adversarial attacks. These challenges must be addressed to ensure the successful implementation of the blockchain network for real-world scenarios.
Determination of optimal mining width for coal mining under the slope by of using numerical simulation
Authors: Zhou Ze , Zhou Jinlian , Lai Long , Xu Mengtang , Xu Youlin
Published: January 2024

The stability of slope is critical important topic in rock mass engineering. In Panzhihua #7 Coal Mine, the coal mining is occurred under the slope, to obtain the optimal mining width, 125 numerical simulations were conducted, and the corresponding FOS was calculated. From the analysis of the numerical simulation results, it can be found that FOS decrease and then increase with increasing of filling length, meanwhile, the FOS is minimum value when the filling length is within the ranges of 10 m and 20 m, which is under the toe of slope. Furthermore, the minimum FOS decrease with increasing of mining width. Considered the stability of the slope and mining economy, the mining width is set to 6m, and the numerical simulation results is applied to the engineering practice. To guarantee the safety of the slope, some monitoring points were distributed on the slope, the displacement from numerical simulation and engineering practice is quite close, indicating the numerical simulation results is reliable, and the mining width is reasonable.
Interaction of a four-level atom with a quantized field in the presence of a nonlinear Kerr medium
Authors: Almalki S. , Berrada K. , Abdel-Khalek S. , Eleuch H.
Published: January 2024

Quantum entanglement and atomic coherence are examined for a system consisting of a four-level atom (FLA) interacted with a nonlinear quantum field. We assume that the FLA-field coupling, Kerr medium and quantified field are all $$f$$
f
-deformed with full nonlinear formalism. We consider N-configuration and cascade (C)-configuration of the FLA. We explore the impact of field deformation and Kerr medium on the dynamics of the quantumness measures when the quantized field is initially prepared in a deformed coherent state without and with Kerr medium effect. Moreover, we examine the statistical properties of the radiation field using the second order correlation function. The results indicate how the considered quantumness measures in the FLA–field system can be manipulated and controlled through the parameters of the quantum model.
The study of the role of purified anti-mouse CD193 (CCR3) antibody in allergic rhinitis mouse animal models
Authors: Bao Youwei , Wu Zhaokun , Zhu Xinhua , Wu Jun , Jiang Yinli , Zhang Ying , Zhu Yu , Liu Zheng , Deng Yi , Liu Wenqiang , Wei Mengyi , Luo Weiming , Xiao Yating
Published: January 2024

The pathogenesis of allergic asthma is similar to that of allergic rhinitis, with inflammation cells producing and releasing inflammatory mediators and cytokines closely related to CCR3.Based on the theory of "one airway, one disease", the use of CCR3 monoclonal antibody may have a similar effect on allergic rhinitis. However, there are few studies on CCR3 monoclonal antibody in allergic rhinitis. Therefore, the aim of this study was to investigate the effective concentration of CCR3 monoclonal antibody, to compare the effects of different methods of administration, and to examine the lung condition of allergic mice to investigate whether antibody treatment protects the lungs. In this study, we constructed a mouse model of allergic rhinitis and intraperitoneally injected different doses of CCR3 monoclonal antibody (5, 10, and 20 uL/mg) to observe its therapeutic effect: observing changes in tissue morphology of nasal mucosa, infiltration of inflammation, and using ELISA to detect changes in relevant inflammatory mediators and cytokines, studying the role of CCR3 mAb in inhibiting CCR3-related actions on the nasal mucosa of allergic rhinitis mice. Furthermore, In addition, the therapeutic effects of intraperitoneal injection (i.p.) and intranasal administration (i.n.) were studied on the basis of effective concentrations.
Vaginal reconstruction by collagen scaffolds loaded with vaginal epithelial and smooth muscle cells in pigs
Authors: Zhao Guangfeng , Dong Yishan , Ye Ziying , Yao Simin , Wang Limin , Zhao Yannan , Chen Bing , Liu Dan , Dai Jianwu , Hu Yali
Published: January 2024

Vaginal epithelial and smooth muscle cells were isolated and expanded successfully. A collagen scaffold loaded with vaginal epithelial cells and smooth muscle cells successfully reconstructed the vagina in a vaginal absence pig model.
Insight into the development and proceedings of Au@Al–CeVO4 catalysts for water splitting: an advanced outlook for hydrogen generation with sunlight
Authors: Jalil Muhammad , Rafiq Khezina , Abid Muhammad Zeeshan , Rafay Muhammad , Rauf Abdul , Jin Rongchao , Hussain Ejaz
Published: January 2024

In this study, we report a promising approach and new catalysts, namely Au@Al–CeVO4 photocatalysts, for sustainable hydrogen production from water splitting.
Incorporation of fucoxanthin into 3D printed Pickering emulsion gels stabilized by salmon by-product protein/pectin complexes
Authors: Zhong Xu , Wang Kuiyou , Chen Zhejin , Fei Siyuan , Li Jiaxuan , Tan Mingqian , Su Wentao
Published: January 2024

Schematic diagram of the preparation process of fucoxanthin-loaded 3D printed Pickering emulsion gels stabilized by salmon by-product protein/pectin complexes.
Physical and chemical parameters determining the formation of gold–sp metal (Al, Ga, In, and Pb) nanoalloys
Authors: Coviello Vito , Forrer Daniel , Canton Patrizia , Amendola Vincenzo
Published: January 2024

Gold–sp metal (Al, Ga, In, and Pb) nanoalloy formation via laser ablation in liquid evidenced that alloying rules are solvent-dependent and can be described with only two parameters in acetone (R2 0.98812) and three parameters in ethanol (R2 0.99393).
Spherical nucleic acids: emerging amplifiers for therapeutic nanoplatforms
Authors: Tao Zhenghao , Zhang Haitao , Wu Shang , Zhang Jiaheng , Cheng Yao , Lei Longtianyang , Qin Yang , Wei Hua , Yu Cui-Yun
Published: January 2024

This review summarizes the amplification effect of SNAs in various combined therapy treatment strategies and highlights the recent advances of SNAs in clinical translation.
In situ supramolecular assembly in water for dual room temperature phosphorescence and multicomponent recognition
Authors: Chen Zhong-Yuan , Xia Qing-Qing , Zhu Yu-Qi , Yu Jia-Lin , Wang Lu , Wang Xing-Huo , Wu Ming-Xue
Published: January 2024

Dual RTP emission and modulation in water can be easily realised using an efficient, green, and universal water-implemented supramolecular assembly strategy, and the assembly materials showed great potential in multicomponent identification.
Pillar[5]arene-based dually crosslinked supramolecular gel as a sensor for the detection of adiponitrile
Authors: Rodin Maksim , Helle David , Kuckling Dirk
Published: January 2024

An SPR-based dually crosslinked gel sensor for adiponitrile bearing pillar[5]arene responsive sites with a low limit of detection was developed.
Lipid-based nutritional supplement impact on energy intake, appetite, glucose and insulin levels in under-weight pregnant and lactating women with preeclampsia
Authors: Mohammad Nabila Sher , Nazli Rubina , Fatima Sadia , Fozia Fozia , Zafar Hafza , Zafar Mashal , Zafar Zarghuna , Khan Warda , Abulmeaty Mahmoud M.A. , Aldisi Dara , Andrade Laborde Juan E. , Aboul-Soud Mourad A.M.
Published: January 2024

Objective: The objective of the study is to investigate the response of nutritional supplement (LNS-PLW) on appetite score, energy intake, insulin and glucose levels in preeclamptic women.

Design and participiants: Sixty under-weight preeclamptic primigravida were divided into two groups randomly and provided LNS-PLW/placebo in the fasted state. Blood samples were collected at fasting state, after 30 min of supplementation, ‘ad libitum buffet’ breakfast and lunch for glucose and insulin levels.

Results: Total energy intake was higher significantly in the LNS-PLW group, although during breakfast it was significantly reduced. The insulin and glucose concentration was significantly increased after 30 min of supplementation in the LNS-PLW group.

Conclusion: Intake of the LNS-PLW by preeclamptic women had short-term suppression on subsequent meal but improved total energy intake during trial.
The effect of O2 pressure on phase formation and superconductivity properties of Tl-based HTS
Authors: Surmanidze D. L. , Lobzhanidze T. E. , Metskhvarishvili I. R. , Dgebuadze G. N. , Gabunia V. M. , Bendeliani B. G. , Metskhvarishvili M. R. , Jishiashvili D. A.
Published: January 2024

Thallium-based high-temperature superconductors exhibit excellent superconductivity performance (Tc, Jc). Formation of the Tl-based superconducting materials critically depends on the used precursor and synthesis conditions. In the present investigation, we used the in situ polymerization method for synthesizing high-purity and reaction-ability precursors. We find the critical dependence of Tl-based superconductor phase formation on the quantity of applied oxygen pressure. The experimental results showed that the Tl-1223 phase formed at an oxygen gas pressure at 1 to 2 atm, Tl-2223 phase at 3 atm, and Tl-2212 phase at 4 to 8 atm.
Cryovacuum facilities for studying astrophysical ices
Authors: Golikov O. , Yerezhep D. , Akylbayeva A. , Sokolov D. , Korshikov E. , Aldiyarov A.
Published: January 2024

This work introduces a cryovacuum apparatus used to investigate substances under near-space conditions. This device allows one to study the refractive index, infrared spectra, and density of substances that are condensed from the vapor phase onto a cooled substrate at temperatures ranging from 11 K to 300 K. Concurrently, the ultimate pressure of 0.1 nTorr can be obtained in the vacuum chamber. The introduced setup utilizes FTIR spectroscopy with a spectral measurement range of 400–7800 cm−1 and laser interference needed to determine the important physical and optical parameters. Several experiments allow us to stress that the data acquired using this apparatus are quite similar to those obtained by other researchers. Because of the non-directional deposition of substances from the vapor phase, the ice formed closely resembles the ice formed in space. This makes the introduced setup particularly useful. It is possible to use the presented cryovacuum apparatus to interpret data acquired in the course of astrophysical observations, allowing a researcher to determine the properties of space objects.
Blast wave propagation characteristics of moving charge at diminished pressure
Authors: Yuan Yuhong , Huang Yinsheng , Li Rui , Wang Quan
Published: January 2024

The effects of different diminished pressures on moving charge blast wave parameters were investigated by employing the AUTODYN software. Meanwhile, a theoretical calculation model was established to predict the peak overpressure of the moving charge under diminished pressure conditions and was verified by experimental data and numerical simulations. Results indicate that the model can evaluate the blast wave peak overpressure of moving charge at diminished pressure effectively. As the velocity of the moving charge increases, the peak overpressure of the blast wave from the moving charge increases when the azimuth angle is less than 90°, but it decreases when the azimuth angle is greater than 90°. The blast wave peak overpressure of moving charge decreases but the blast wave action range increases as the ambient pressure decreases.
Gastrointestinal helminth parasites of the grey kangaroos, Macropus fuliginosus and M. giganteus
Authors: Beveridge Ian
Published: January 2024

The helminth parasites of Macropus fuliginosus and Macropus giganteus are reported based on examination of a total of 285 animals extending, for the first time, across the entire geographical range of both species and including, where possible, data from previous regional studies. A total of 64 species of helminths was found including 42 species of strongyloid nematodes in the stomach, seven species of trichostrongyloid nematodes in the pylorus and small intestine and seven species of nematodes in the terminal ileum and large intestine, one species of spirurid nematode in the stomach and six species of cestodes and one species of trematode. Forty-three species were encountered in both M. fuliginosus and M. giganteus. The helminth communities of the two kangaroo species exhibited a similarity of 85.4% based on all helminth species encountered or 91.4% if only the species specific to grey kangaroos were considered. Interchange of helminths between the two species of kangaroos revealed several different patterns with instances both of transfer and lack of transfer in areas of host sympatry as well as transfers beyond the zone of sympatry. The findings are discussed in relationship to the phylogeography of the host species.
Magnetism and metallicity in moiré transition metal dichalcogenides
Authors: Tscheppe Patrick , Zang Jiawei , Klett Marcel , Karakuzu Seher , Celarier Armelle , Cheng Zhengqian , Marianetti Chris A. , Maier Thomas A. , Ferrero Michel , Millis Andrew J. , Schäfer Thomas
Published: January 2024

The ability to control the properties of twisted bilayer transition metal dichalcogenides in situ makes them an ideal platform for investigating the interplay of strong correlations and geometric frustration. Of particular interest are the low energy scales, which make it possible to experimentally access both temperature and magnetic fields that are of the order of the bandwidth or the correlation scale. In this manuscript, we analyze the moiré Hubbard model, believed to describe the low energy physics of an important subclass of the twisted bilayer compounds. We establish its magnetic and the metal–insulator phase diagram for the full range of magnetic fields up to the fully spin-polarized state. We find a rich phase diagram including fully and partially polarized insulating and metallic phases of which we determine the interplay of magnetic order, Zeeman-field, and metallicity, and make connection to recent experiments.
Directional constructions in Matukar Panau
Authors: Davey Kira , Barth Danielle
Published: January 2024

The Oceanic language Matukar Panau has three equivalent morphosyntactic strategies for describing the direction of the event represented by a verb, with a system of ten directional morphemes that can appear in each construction. This variation is explored using a corpus from Matukar Panau and analysed quantitatively with Bayesian regression analyses to assess what factors influence the choice of directional construction. Variables pertaining to the lexical verb and the directional morphemes are found to be the most important factors affecting the variation in the directional system. Sociolinguistic factors are shown to play a less significant role. The findings have implications for the grammaticalization of directional elements, as well as the typology of directional constructions in Oceanic languages.
Self-repeat as a multimodal retraction practice
Authors: Shor Leon , Marmorstein Michal
Published: January 2024

The paper focuses on a particular practice of self-repeat through which participants retract their prior formulations, and explores its multimodal design and use in the dynamic construction of meaning in Hebrew conversation. Drawing on interactional approaches to language and embodied action, we show that the practice of self-repeat is used to retract a formulation judged by its producer as being inadequate and ill-calibrated in the given interactional context. This function is supported by the multimodal configuration in which the lexical repeat is cast, which involves a stable prosodic component and a variable embodied component. Through its prosodic and embodied design, the repeat is contextualized as a noticeable display of accountability for having made an ill-suited choice of words. While the self-repeat alone is sufficient in proposing a problem of calibration, it can also be followed by a lexical replacement, which makes explicit the adjusted or recalibrated term. The self-repeat practice shows how participants engage in semantic work through online and situated revision of their formulations. This exposed process of meaning construction reveals their understanding of the constitutive link between the conceptual and the normative orders as practiced in actual conversation.
Westward shift of tropical cyclogenesis over the southern Indian Ocean
Authors: Cao Xi , Watanabe Masahiro , Wu Renguang , Wu Liang , Deng Difei , Ha Yao , Xu Mengchen , Yuan Meng , Dai Yifeng , Du Zhencai
Published: January 2024

Tropical cyclones (TCs), commonly called cyclones in the southern Indian Ocean (SIO), represent one of the most devastating disasters in the oceanfront regions of Africa. The present study explores the long-term tendency of annual mean TC genesis location in the SIO. A notable westward shift is detected in the SIO TC genesis longitude since 1979, which is linked to an increase in the TC genesis frequency in the southwestern SIO and a decrease in the TC genesis frequency in the northeastern SIO. The dipole trend pattern of the TC genesis frequency in the SIO is intimately linked to the weakening of the westerly vertical wind shear over the western SIO and the strengthening of the easterly vertical wind shear over the eastern SIO, resulting from a reduced meridional temperature gradient. The weakened meridional temperature gradient is attributed to the enhanced warming of the subtropical troposphere that is a response of atmospheric temperature to global warming. Our study implies a potential increase in the risks faced by coastal and island countries in eastern Africa.
Infinite affine, hyperbolic and Lorentzian Weyl groups with their associated Calogero models
Authors: Correa Francisco , Fring Andreas , Quintana Octavio
Published: January 2024

We propose generalizations of Calogero models that exhibit invariance with respect to the infinite Weyl groups of affine, hyperbolic, and Lorentzian types. Our approach involves deriving closed analytic formulas for the action of the associated Coxeter elements of infinite order acting on arbitrary roots within their respective root spaces. These formulas are then utilized in formulating the new type of Calogero models.
From braces to pre-Lie rings
Authors: Shalev Aner , Smoktunowicz Agata
Published: January 2024

Let

A
A

be a brace of cardinality

p

n

p^{n}

where

p
>
n
+
1

p>n+1

is prime and let

a
n
n
(

p

2

)

ann (p^{2})

be the set of elements of additive order at most

p

2

p^{2}

in this brace. We construct a pre-Lie ring related to the brace

A

/

a
n
n
(

p

2

)

A/ann(p^{2})

.

In the case of strongly nilpotent braces of nilpotency index

k
>
p

k>p

the brace

A

/

a
n
n
(

p

2

)

A/ann(p^{2})

can be recovered by applying the construction of the group of flows to the resulting pre-Lie ring. We do not know whether or not our construction is related to the group of flows when applied to braces which are not right nilpotent.
Investigating the effect of host plant identity on instar number in fall webworm, a common generalist herbivore
Authors: Tanino-Springsteen Mykaela M , Vyas Dhaval K , Mitchell Audrey , Durso Catherine , Murphy Shannon M
Published: January 2024

For herbivorous insects with a broad diet breadth, host plant identity can influence larval development by either accelerating or delaying growth. For some species of Lepidoptera, the number of larval instars varies depending on the host plant’s identity. Fall webworm (Hyphantria cunea, Drury) is a polyphagous herbivore that feeds on over 450 host plants worldwide. Of the 2 morphotypes (red- and black-head) of fall webworm, the number of instars for the red-head fall webworms has not been characterized. Given its broad diet breadth, fall webworm developmental stages may vary with plant identity. We investigated whether host plant identity affected the number of instars observed during red-head fall webworm development. We measured the head capsules of over 6,000 fall webworm larvae reared on 6 different plants commonly eaten by fall webworms in Colorado. We modeled head capsule widths as Gaussian mixture models, with a Gaussian distribution that corresponded to each instar. We show that our red-head fall webworms varied in number of instars depending on the identity of their host plant upon which they fed. We found that red-head fall webworm exhibited 7 instars on 5 of the host plants and 8 instars on 1 host plant that we studied. Our results for the number of instars for red-head fall webworm are consistent with reports of the number of instars for black-head fall webworm. Our research provides insight into the influence of host plant identity on fall webworm development, which can be used to advance lab and field research of this species.
Signatures of Co-evolution and Co-regulation in the CYP3A and CYP4F Genes in Humans
Authors: Richard-St-Hilaire Alex , Gamache Isabel , Pelletier Justin , Grenier Jean-Christophe , Poujol Raphaël , Hussin Julie G
Published: January 2024

Cytochromes P450 (CYP450) are hemoproteins generally involved in the detoxification of the body of xenobiotic molecules. They participate in the metabolism of many drugs and genetic polymorphisms in humans have been found to impact drug responses and metabolic functions. In this study, we investigate the genetic diversity of CYP450 genes. We found that two clusters, CYP3A and CYP4F, are notably differentiated across human populations with evidence for selective pressures acting on both clusters: we found signals of recent positive selection in CYP3A and CYP4F genes and signals of balancing selection in CYP4F genes. Furthermore, an extensive amount of unusual linkage disequilibrium is detected in this latter cluster, indicating co-evolution signatures among CYP4F genes. Several of the selective signals uncovered co-localize with expression quantitative trait loci (eQTL), which could suggest epistasis acting on co-regulation in these gene families. In particular, we detected a potential co-regulation event between CYP3A5 and CYP3A43, a gene whose function remains poorly characterized. We further identified a causal relationship between CYP3A5 expression and reticulocyte count through Mendelian randomization analyses, potentially involving a regulatory region displaying a selective signal specific to African populations. Our findings linking natural selection and gene expression in CYP3A and CYP4F subfamilies are of importance in understanding population differences in metabolism of nutrients and drugs.
Computational reproducibility of Jupyter notebooks from biomedical publications
Authors: Samuel Sheeba , Mietchen Daniel
Published: January 2024

Background

Jupyter notebooks facilitate the bundling of executable code with its documentation and output in one interactive environment, and they represent a popular mechanism to document and share computational workflows, including for research publications. The reproducibility of computational aspects of research is a key component of scientific reproducibility but has not yet been assessed at scale for Jupyter notebooks associated with biomedical publications.

Approach

We address computational reproducibility at 2 levels: (i) using fully automated workflows, we analyzed the computational reproducibility of Jupyter notebooks associated with publications indexed in the biomedical literature repository PubMed Central. We identified such notebooks by mining the article’s full text, trying to locate them on GitHub, and attempting to rerun them in an environment as close to the original as possible. We documented reproduction success and exceptions and explored relationships between notebook reproducibility and variables related to the notebooks or publications. (ii) This study represents a reproducibility attempt in and of itself, using essentially the same methodology twice on PubMed Central over the course of 2 years, during which the corpus of Jupyter notebooks from articles indexed in PubMed Central has grown in a highly dynamic fashion.

Results

Out of 27,271 Jupyter notebooks from 2,660 GitHub repositories associated with 3,467 publications, 22,578 notebooks were written in Python, including 15,817 that had their dependencies declared in standard requirement files and that we attempted to rerun automatically. For 10,388 of these, all declared dependencies could be installed successfully, and we reran them to assess reproducibility. Of these, 1,203 notebooks ran through without any errors, including 879 that produced results identical to those reported in the original notebook and 324 for which our results differed from the originally reported ones. Running the other notebooks resulted in exceptions.

Conclusions

We zoom in on common problems and practices, highlight trends, and discuss potential improvements to Jupyter-related workflows associated with biomedical publications.
4. Mary Wollstonecraft
Authors: Spruce Emma
Published: January 2024

Critiquing the Canon: Political Theory draws upon critical scholarship to bring together diverse ways of thinking about and critiquing key thinkers from the canon of political theory. Each chapter is dedicated to a particular thinker and their work, and encourages students to explore the limitations of the canon and ask important questions about whose views might be marginalized, ignored, or sidelined in the construction of ‘canonical’ thought. Pedagogical features include author tutorial videos and end-of-chapter questions to prompt students to develop their own voice and challenge dominant ideas.
Phenotyping, genetics, and “-omics” approaches to unravel and introgress enhanced resistance against apple scab (Venturia inaequalis) in apple cultivars (Malus × domestica)
Authors: Švara Anže , De Storme Nico , Carpentier Sebastien , Keulemans Wannes , De Coninck Barbara
Published: January 2024

Apple scab disease, caused by the fungus Venturia inaequalis, endangers commercial apple production globally. It is predominantly managed by frequent fungicide sprays that can harm the environment and promote the development of fungicide-resistant strains. Cultivation of scab-resistant cultivars harboring diverse qualitative Rvi resistance loci and quantitative trait loci associated with scab resistance could reduce the chemical footprint. A comprehensive understanding of the host–pathogen interaction is, however, needed to efficiently breed cultivars with enhanced resistance against a variety of pathogenic strains. Breeding efforts should not only encompass pyramiding of Rvi loci and their corresponding resistance alleles that directly or indirectly recognize pathogen effectors, but should also integrate genes that contribute to effective downstream defense mechanisms. This review provides an overview of the phenotypic and genetic aspects of apple scab resistance, and currently known corresponding defense mechanisms. Implementation of recent “-omics” approaches has provided insights into the complex network of physiological, molecular, and signaling processes that occur before and upon scab infection, thereby revealing the importance of both constitutive and induced defense mechanisms. Based on the current knowledge, we outline advances toward more efficient introgression of enhanced scab resistance into novel apple cultivars by conventional breeding or genetic modification techniques. However, additional studies integrating different “-omics” approaches combined with functional studies will be necessary to unravel effective defense mechanisms as well as key regulatory genes underpinning scab resistance in apple. This crucial information will set the stage for successful knowledge-based breeding for enhanced scab resistance.
Assessing the feasibility, safety, and nutritional quality of using wild-caught pest flies in animal feed
Authors: Van Nest Kortnee , Swistek Sabrina E , Olmstead Morgan L , De La Mota-Peynado Alina , Ewing Robert D , Brabec Daniel , Mitzel Dana , Oppert Brenda , Cohnstaedt Lee W , Shults Phillip
Published: January 2024

Studies have investigated the potential of using farmed insects in animal feeds; however, little research has been done using wild-caught insects for this purpose. Concerns about inadequate quantities collected, environmental impacts, and the spread of pathogens contribute to the preferred utilization of farmed insects. Nevertheless, by harvesting certain pest species from intensified agricultural operations, producers could provide their animals with affordable and sustainable protein sources while also reducing pest populations. This study explores the possibility of collecting large quantities of pest flies from livestock operations and analyzes the flies’ nutritional content, potential pathogen load, and various disinfection methods. Using a newly designed mass collection-trapping device, we collected 5 kg of biomass over 13 wk, primarily house flies, from a poultry facility. While a substantial number of pests were removed from the environment, there was no reduction in the fly population. Short-read sequencing was used to compare the bacterial communities carried by flies from differing source populations, and the bacterial species present in the fly samples varied based on farm type and collection time. Drying and milling the wild-caught flies as well as applying an additional heat treatment significantly reduced the number of culturable bacteria present in or on the flies, though their pathogenicity remains unknown. Importantly, these disinfection methods did not affect the nutritional value of the processed flies. Further research is necessary to fully assess the safety and viability of integrating wild-caught insects into livestock feed; however, these data show promising results in favor of such a system.
Lipofibromatosis arising in a right labiocrural fold in a 14-month-old female: a case report study with a 3-year follow-up
Authors: Zvizdic Zlatan , Milisic Emir , Bilalovic Nurija , Ibisevic Nermina , Bukvic Melika , Vranic Semir
Published: January 2024

Lipofibromatosis (LF) is a rare benign fibrofatty tumor of infancy and childhood with a predilection for distal extremities, poor margination, and a high local recurrence rate. We report a toddler who presented with an LF involving her right labiocrural fold. Imaging showed a soft tissue mass extending through the right labiocrural fold with possible infiltration into the underlying muscles. The mass was excised entirely, preserving adjacent structures. The histopathologic report revealed the mass to be LF. A 3-year follow-up revealed no disease recurrence. No other cases of LF in this localization have been presented in the literature. Despite its rarity, LF should be considered in diagnosing soft tissue neoplasms in children. Accurate diagnosis and proper surgical management with complete resection are essential to reduce the postoperative recurrence risk.
The internal structure of medieval Latin legendaries: a computational analysis
Authors: de Valeriola Sébastien , Dubuisson Bastien
Published: January 2024

Since the middle of the 17th century, scholars have been systematically describing numerous medieval manuscripts preserved in libraries and religious institutions that contain hagiographic texts, that is texts recounting the lives of saints. In this article, we apply quantitative tools to the resulting database to consider these codices from a new point of view. As such, we study their internal organization, that is the order in which their texts are arranged. We first present a visualization tool that allows to grasp this structure at a glance. Then, we describe a model to automatically classify manuscripts according to their internal organization, based on a constrained spline regression. The results of this classification task make it possible to identify the manuscripts that have a particular internal organization, called per circulum anni (following the course of the year), and thus to study their properties. Furthermore, they open the possibility to obtain clues regarding the origin of some codices and potential kinship links between them.
Constructing a digital system of historical geographic information from the perspective of digital humanities: a case study of the historical geographic information database of Tibetan Buddhist monasteries
Authors: Chen Danying , Zhao Yaolong , Chao Zihao , Li Yuchen , Fang Subin
Published: January 2024

Digital techniques are critical in the digital age. Research in various disciplines requires the use of digital technology. Extracting and digitizing information from text, particularly historical geographical information, is the most fundamental operation of digital humanities. However, digitizing historical geographical information is a challenging work. This article proposes a framework for constructing a digital system of historical geographic information. The feasibility of the digital system was verified in a case study of Tibetan Buddhist monasteries in Tibetan inhabited areas of China. The results demonstrate that the digital system proposed in this study can be used as a guide for digitizing historical geographic information of Tibetan Buddhist monasteries from the perspective of digital humanities. This study provides a useful reference for the digitalization of historical geographic information in the digital humanities discipline.
Should Human Immunodeficiency Virus Testing Be Replaced With Combined Blood-Borne Virus Testing?
Authors: Orkin Chloe
Published: January 2024

Standalone HIV testing is a missed opportunity- a recent systematic review showed eight cases of viral hepatitis would be missed for each new HIV diagnosis. The review builds on a decade of research demonstrating the additional benefit of BBV testing.
Safety and Immune Responses Following Anti-PD-1 Monoclonal Antibody Infusions in Healthy Persons With Human Immunodeficiency Virus on Antiretroviral Therapy
Authors: Gay Cynthia L , Bosch Ronald J , McKhann Ashley , Cha Raymond , Morse Gene D , Wimbish Chanelle L , Campbell Danielle M , Moseley Kendall F , Hendrickx Steven , Messer Michael , Benson Constance A , Overton Edgar T , Paccaly Anne , Jankovic Vladimir , Miller Elizabeth , Tressler Randall , Li Jonathan Z , Kuritzkes Daniel R , Macatangay Bernard J C , Eron Joseph J , Hardy W David ,   for the A5370 Team, Tipton Amanda , Pedersen Susan , Jarocki Bernadette , Anderson Scott , Purdue Lynette , Whitson Kyle , Zabih Sara , Jennings Cheryl , Lankford-Turner Pamela , Mehta Patrick , Uldrick Thomas
Published: January 2024

Background

T cells in people with human immunodeficiency virus (HIV) demonstrate an exhausted phenotype, and HIV-specific CD4+ T cells expressing programmed cell death 1 (PD-1) are enriched for latent HIV, making antibody to PD-1 a potential strategy to target the latent reservoir.

Methods

This was a phase 1/2, randomized (4:1), double-blind, placebo-controlled study in adults with suppressed HIV on antiretroviral therapy with CD4+ counts ≥350 cells/μL who received 2 infusions of cemiplimab versus placebo. The primary outcome was safety, defined as any grade 3 or higher adverse event (AE) or any immune-related AE (irAE). Changes in HIV-1–specific polyfunctional CD4+ and CD8+ T-cell responses were evaluated.

Results

Five men were enrolled (median CD4+ count, 911 cells/μL; median age, 51 years); 2 received 1 dose of cemiplimab, 2 received 2 doses, and 1 received placebo. One participant had a probable irAE (thyroiditis, grade 2); another had a possible irAE (hepatitis, grade 3), both after a single low-dose (0.3 mg/kg) infusion. The Safety Monitoring Committee recommended no further enrollment or infusions. All 4 cemiplimab recipients were followed for 48 weeks. No other cemiplimab-related serious AEs, irAEs, or grade 3 or higher AEs occurred. One 2-dose recipient of cemiplimab had a 6.2-fold increase in polyfunctional, Gag-specific CD8+ T-cell frequency with supportive increases in plasma HIV RNA and decreases in total HIV DNA.

Conclusions

One of 4 participants exhibited increased HIV-1-specific T-cell responses and transiently increased HIV-1 expression following 2 cemiplimab infusions. The occurrence of irAEs after a single, low dose may limit translating the promising therapeutic results of cemiplimab for cancer to immunotherapeutic and latency reversal strategies for HIV.

Clinical Trials Registration. NCT03787095.
Making the EHR Work for You—Modifications of an Electronic Health Record System to Improve Tracking and Management of Patients Receiving Outpatient Parenteral Antibiotic Therapy
Authors: Munsiff Sonal S , Burgoyne Colleen , Dobson Erica , Yamshchikov Alexandra
Published: January 2024

Background

Managing the complex needs of outpatient parenteral antibiotic therapy (OPAT) patients is challenging and time-consuming. We describe development of multimodal interventions to facilitate patient management within an Epic® (Epic Systems Corporation)-based electronic health record (EHR) platform.

Methods

During 2016–2018, a multidisciplinary team created several modifications in our local EHR to improve gaps in OPAT care, including shared note templates, shared patient lists, automatically triggered notifications, and comprehensive order sets. A SmartForm was created, allowing collection of discrete, self-contained extractable data about each OPAT episode. We reviewed OPAT episodes from January 2019 through December 2022.

Results

The multimodal EHR interventions culminated in the creation of a patient report, the “OPAT Monitoring View” collating OPAT-relevant data from multiple sections of the chart onto 1 screen display. This view is accessible both within the patient chart and from multiple list-based, in-basket, and snapshot-anchored preview functions in the EHR. Implementation of the EHR bundle facilitated management of 3402 OPAT episodes from 2019 to 2022 (850 episodes/year), about 50% higher than anticipated based on 540 OPAT courses in 2016. The OPAT EHR bundle allowed efficient (<3 hours) multidisciplinary rounds for management of 130–145 patients each week, streamlining of care transitions, and increasing staff satisfaction.

Conclusions

Bundled multimodal modifications to the local EHR increased patient care efficiency and staff satisfaction and facilitated data collection to support a large OPAT program. These modifications apply commonly available EHR functionalities to OPAT care and could be adapted to other settings with different EHR platforms.
We Shape Our Tools and Then Our Tools Shape Us: OPAT and the EHR
Authors: Rivera Christina G
Published: January 2024

A commentary on Canterino et al. (2024) and Munsiff et al. (2024), articles where clinicians from two large OPAT programs
Incidence, Correlates, and Prognostic Significance of Mixed Response in Advanced Non-small Cell Lung Cancer
Authors: Gerber David E , Wang Yating , Ramalingam Suresh S , Bhalla Sheena , Sun Zhuoxin , Borghaei Hossein , Brahmer Julie R , Schiller Joan H
Published: January 2024

Background

Mixed response (MR), a scenario featuring discordant tumor changes, has been reported primarily with targeted therapies or immunotherapy. We determined the incidence and prognostic significance of MR in advanced non–small cell lung cancer (NSCLC) treated with cytotoxic chemotherapy.

Patients and Methods

We analyzed patient-level data from ECOG-ACRIN E5508 (carboplatin-paclitaxel + bevacizumab induction followed by randomization to maintenance therapy regimens). For patients with at least 2 target lesions and available measurements after cycle 2, we characterized response as homogeneous response (HR, similar behavior of all lesions), MR (similar behavior but >30% difference in magnitude of best and least responding lesions), or true mixed response (TMR, best and least responding lesions showing different behavior: ≥10% growth versus ≥10% shrinkage). We compared category characteristics using Mann-Whitney U and Chi-square tests, and overall survival (OS) using log-rank test and Cox models.

Results

Among 965 evaluable patients, HR occurred in 609 patients (63%), MR in 208 (22%), and TMR in 148 (15%). Median OS was 13.6 months for HR, 12.0 months for MR, and 7.6 months for TMR (P < .001). Compared to HR, TMR had inferior OS among stable disease cases (HR 1.62; 95% CI, 1.23-2.12; P < .001) and a trend toward inferior OS among progressive disease cases (HR 1.39; 95% CI, 0.83-2.33; P = .2). In multivariate analysis, TMR was associated with worse OS (HR 1.48; 95% CI, 1.22-1.79; P < .001).

Conclusion

True mixed response occurs in a substantial minority of lung cancer cases treated with chemotherapy and independently confers poor prognosis.
Clinical research progress of novel antituberculosis drugs on multidrug-resistant tuberculosis
Authors: Zhong Xinxin , Lin Ao , Luo Jian , Li Yeqin , Chen Jinlan , Ning Chao , Cao Fu
Published: January 2024

Multidrug-resistant tuberculosis (MDR-TB) has become a critical challenge to public health, and the prevention and treatment of MDR-TB are of great significance in reducing the global burden of tuberculosis. How to improve the effectiveness and safety of chemotherapy for MDR-TB is a pressing issue that needs to be addressed in tuberculosis control efforts. This article provides a comprehensive review of the clinical application of new antituberculosis drugs in MDR-TB, aiming to provide a scientific basis for the prevention and treatment strategy of MDR-TB.
TOPLESS Corepressors as an Emerging Hub of Plant Pathogen Effectors
Authors: Khan Mamoona , Djamei Armin
Published: January 2024

Transcriptional corepressors form an ancient and essential layer of gene expression control in eukaryotes. TOPLESS and TOPLESS-RELATED (TPL/TPR) proteins constitute a conserved family of Groucho (Gro)/thymidine uptake 1 (Tup1)-type transcriptional corepressors and control diverse growth, developmental, and stress signaling responses in plants. Because of their central and versatile regulatory roles, they act as a signaling hub to integrate various input signaling pathways in the transcriptional responses. Recently, increasing pieces of evidence indicate the roles of TPL/TPR family proteins in the modulation of plant immunity. This is supported by studies on effectors of distantly related pathogens that target TPL/TPR proteins in planta. In this short review, we will summarize the latest findings concerning pathogens targeting plant TPL/TPR proteins to manipulate plant signaling responses for the successful invasion of their hosts.

[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .