bluuebunny/crossref_metadata_2025_split huggingface dataset:
Directed evolution of antimicrobial peptides using multi-objective zeroth-order optimization
Authors: Liu Xianliang , Luo Jiawei , Wang Xinyan , Zhang Yang , Chen Junjie 
Published: December 2024

Abstract
Antimicrobial peptides (AMPs) emerge as a type of promising therapeutic compounds that exhibit broad spectrum antimicrobial activity with high specificity and good tolerability. Natural AMPs usually need further rational design for improving antimicrobial activity and decreasing toxicity to human cells. Although several algorithms have been developed to optimize AMPs with desired properties, they explored the variations of AMPs in a discrete amino acid sequence space, usually suffering from low efficiency, lack diversity, and local optimum. In this work, we propose a novel directed evolution method, named PepZOO, for optimizing multi-properties of AMPs in a continuous representation space guided by multi-objective zeroth-order optimization. PepZOO projects AMPs from a discrete amino acid sequence space into continuous latent representation space by a variational autoencoder. Subsequently, the latent embeddings of prototype AMPs are taken as start points and iteratively updated according to the guidance of multi-objective zeroth-order optimization. Experimental results demonstrate PepZOO outperforms state-of-the-art methods on improving the multi-properties in terms of antimicrobial function, activity, toxicity, and binding affinity to the targets. Molecular docking and molecular dynamics simulations are further employed to validate the effectiveness of our method. Moreover, PepZOO can reveal important motifs which are required to maintain a particular property during the evolution by aligning the evolutionary sequences. PepZOO provides a novel research paradigm that optimizes AMPs by exploring property change instead of exploring sequence mutations, accelerating the discovery of potential therapeutic peptides.
Was the Section française de l’Internationale ouvrière (SFIO) also African? 1945–1960
Authors: Blum Françoise 
Published: December 2024

Abstract
This article looks at relations between Europeans and Africans within the sections of the Section française de l’Internationale ouvrière (SFIO) in sub-Saharan Africa. It is based on documentation and correspondence sent to the Paris Centre, mostly by Europeans, and held at the Office universitaire de recherche socialiste (OURS). There were, however, significant differences between the sections in French West Africa (Ivory Coast and Guinea) and those in French East Africa (Chad, Oubangui-Chari, Congo-Brazzaville) and Cameroon. The relationships of domination inherent in the colonial situation were expressed more or less violently in different places. The way in which Europeans in the African SFIO looked at Africans in the sections was generally racist and unsympathetic, and thus said a great deal about power relations in the colonial world. In the end, these relationships of domination got the better of the sections, whose fate was definitively sealed by the advent of African governments and then independence, despite the short-lived experience of the Mouvement socialiste africain (MSA).
French socialism and Austromarxism: archaeology of a failed transfer (1904–1934)
Authors: Lagedamon Pierre-Henri 
Published: December 2024

Abstract
From the end of the nineteenth century onwards, Austrian socialism was characterized by the development of specific theories and practices, known as Austromarxism, building an original way of constructing socialism. This article looks at the reception in France of these theories and experiments initiated within Austrian social democracy. The Austromarxist path aroused an interest in French socialism that, although limited, was nonetheless recurrent from before the First World War. The inclusion of French socialism, marked by a certain theoretical weakness, in the doctrinal debates that agitated international socialism is essential to understanding its evolution from the end of the nineteenth century onwards. The aim of this contribution is therefore to highlight the development of this Austromarxist reference within French socialism, and the influence it may have had on certain tendencies within the French Socialist Party, particularly during the interwar period marked by various attempts at ideological and political renewal.
Documents hidden behind a wall: an episode in the long-term archival conflict between the Este and the Roman Apostolic Chamber, 1633
Authors: Guidi Andrea 
Published: December 2024

Abstract
This article examines the correspondence between Duke Francesco I d’Este (1629–58) and his agents regarding the documents the papal authorities found in 1633 behind a wall of Ferrara’s castle, following the devolution of the city to the Papal States (1598). This article argues that this correspondence discloses the mentality behind the uses and the notions of archives that guided the protagonists of this story – that is, expectations that reveal reliance on the authority of written records as well as a desperate hope in the power of archives.
hsa_circ_0015388 Reduces Macrophage Derived Reactive Oxygen Species in Crohn’s Disease
Authors: Sugiyama Yuya , Konishi Hiroaki , Dokoshi Tatsuya , Tanaka Hiroki , Kobayashi Yu , Sasaki Takahiro , Yamamoto Koji , Sakatani Aki , Takahashi Keitaro , Ando Katsuyoshi , Ueno Nobuhiro , Kashima Shin , Moriichi Kentaro , Tanabe Hiroki , Okumura Toshikatsu , Fujiya Mikihiro 
Published: December 2024

Abstract

Background
Crohn’s disease (CD) is a refractory inflammatory bowel disease with an unclear etiology. CircularRNA (circRNA) has been highlighted as a novel class of functional noncoding RNAs associated with the pathogenesis of various diseases. However, the functions of circRNA in CD remain unclear.

Methods
Biopsies were obtained from noninflammatory sites in the terminal ileum of the CD group (n = 4) and non-CD group (n = 4) and analyzed for circRNA expression using RNA sequencing. The significantly altered circRNAs were validated in the CD group (n = 45) and non-CD group (n = 15) using quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR). Transcriptome analysis was conducted using circRNA-downregulated macrophage-like THP-1 cells. Reactive oxygen species (ROS) levels, cytokine mRNA expression, phagocytosis, and migration were evaluated in circRNA-downregulated THP-1 cells.

Results
CircularRNA sequencing analysis revealed significant differences in 31 circRNAs between the CD group and non-CD group. Quantitative reverse transcriptase-polymerase chain reaction analysis for each circRNA demonstrated significant upregulation of hsa_circ_0015388 in the CD group. Hsa_circ_0015388 was expressed in THP-1 cells, but not in HCEC-1CT and Caco-2/bbe. Transcriptome analysis in THP-1 cells transfected with scramble or hsa_circ_0015388 siRNA (small interfering RNA) showed a significant alteration in innate immune response related pathway. Reactive oxygen species production was significantly increased in the hsa_circ_0015388 downregulated THP-1 cells. Reactive oxygen species induction in the hsa_circ_0015388 knocked down THP-1 was diminished by the inhibition of TNFSF10.

Conclusion
A comprehensive analysis of circRNA expression revealed that 31 circRNAs were dysregulated in the CD group. Hsa_circ_0015388 is expressed in macrophages and negatively regulates ROS function inhibiting the TNFSF10 pathway. This study first revealed that hsa_circ_0015388 plays a role in the pathogenesis of CD by suppressing ROS production in macrophages.
Revealing the adaptation strategies of pelagic fleets in the Bay of Biscay by combining fishery data and fishers’ knowledge
Authors: Lahellec Gabriel , Daurès Fabienne , Lehuta Sigrid 
Published: December 2024

Abstract
The French pelagic fishery in the Bay of Biscay is currently facing new challenges. To anticipate and support future adaptations of fishers’ strategies, we proposed to scrutinize fishers’ past behaviours and determine the driving factors of their adaptations using a combination of quantitative and qualitative analysis. Annual strategies deployed by the pelagic fleet between 2010 and 2018 were identified through fishing data. Individual sequences of strategies used by vessels then served as a basis for the definition of a new fleet segmentation, revealing behavioural patterns and bridges between strategies. Fishers from two segments were then interviewed to identify the factors underlying their decisions at four different time scales. Fishers surveyed felt in control of both long-term (pluri-annual) and short-term (daily) decisions. Social aspects and personal preferences were found to be preponderant at these time scales. On the contrary, seasonal and annual activities were perceived as being dictated by market opportunities and ecological cycles. We showed that fishers were forced toward a greater dependence on sardine by regulatory constraints and the lack of opportunities on other species. Our study draws perspective by combining historical fishery data analysis with fisher’s experiential knowledge to understand fishing behaviours.
A signal-processing tool adapted to the periodic biphasic phenomena: the Dynalet transform
Authors: Demongeot Jacques , Minonzio Jean-Gabriel 
Published: December 2024

Abstract
The linear functional analysis, historically founded by Fourier and Legendre (Fourier’s supervisor), has provided an original vision of the mathematical transformations between functional vector spaces. Fourier, and later Laplace and Wavelet transforms, respectively, defined using the simple and damped pendulum have been successfully applied in numerous applications in Physics and engineering problems. However, the classical pendulum basis may not be the most appropriate in several problems, such as biological ones, where the modelling approach is not linked to the pendulum. Efficient functional transforms can be proposed by analyzing the links between the physical or biological problem and the orthogonal (or not) basis used to express a linear combination of elementary functions approximating the observed signals. In this study, an extension of the Fourier point of view called Dynalet transform is described. The approach provides robust approximated results in the case of relaxation signals of periodic biphasic organs in human physiology.
Schistosomiasis treatment in young children: a welcome step towards deployment of the paediatric praziquantel formulation
Authors: Stothard J Russell 
Published: December 2024

Abstract
It is an awkward fact that effective public health control of schistosomiasis in Africa has yet to deliver a fully comprehensive intervention for appropriate anthelmintic treatment of those preschool-age children and infants with active infection(s) and/or insidious disease. Over the last decade, despite the steady progress of the Pediatric Praziquantel Consortium in developing a monoenantiomeric oral dispersible tablet, future challenges remain in securing its deployment and implementation at scale. This commentary provides a forward-looking critique for the international community, reminding us of this unfortunate treatment gap, and seeks to encourage commensurate action on ameliorating this overlooked medical inequity.
Arsenic modifies the microbial community assembly of soil–root habitats in Pteris vittata
Authors: Lin Jiahui , Dai Zhongmin , Lei Mei , Qi Qian , Zhou Weijun , Ma Lena Q , Dahlgren Randy A , Xu Jianming 
Published: December 2024

Abstract
Pteris vittata, renowned for its ability to hyperaccumulate arsenic, presents a promising solution to the escalating issue of global soil arsenic contamination. This fern cultivates a unique underground microbial community to enhance its environmental adaptability. However, our understanding of the assembly process and the long-term ecological impacts of this community remains limited, hindering the development of effective soil remediation strategies. This study addresses this gap by investigating soil–root habitats from three geographically diverse fields comprising a gradient of arsenic contamination, complemented by a time-scale greenhouse experiment. Field investigations reveal that arsenic stress influences community assembly dynamics in the rhizosphere by enhancing processes of homogeneous selection. Greenhouse experiments further reveal that arsenic exposure alters the assembly trajectory of rhizosphere communities by promoting key microbial modules. Specifically, arsenic exposure increases the enrichment of a core taxon (i.e. Rhizobiaceae) in the rhizosphere, both in field and greenhouse settings, boosting their abundance from undetectable levels to 0.02% in the soil after phytoremediation. Notably, arsenic exposure also promotes a pathogenic group (i.e. Spirochaetaceae) in the rhizosphere, increasing their abundance from undetectable levels to 0.1% in the greenhouse. This raise concerns that warrant further investigation in future phytoremediation studies. Overall, this study elucidates the assembly dynamics of the soil microbiome following the introduction of a remediation plant and emphasizes the often-overlooked impacts on soil microbial community following phytoremediation. By probing the ecological impacts of remediation plants, this work advances a more nuanced understanding of the complex ecological implications inherent in phytoremediation processes.
Soil microbial carbon use efficiency differs between mycorrhizal trees: insights from substrate stoichiometry and microbial networks
Authors: Yu Jing , Yang Jingyi , Qu Lingrui , Huang Xiaoyi , Liu Yue , Jiang Ping , Wang Chao 
Published: December 2024

Abstract
The role of mycorrhizal associations in controlling forest soil carbon storage remains under debate. This uncertainty is potentially due to an incomplete understanding of their influence on the free-living soil microbiome and its functions. In this study, rhizosphere and non-rhizosphere soils were collected from eight arbuscular mycorrhizal (AM) and seven ectomycorrhizal (ECM) tree species in a temperate forest. We employed high-throughput sequencing and 18O-H2O labeling to analyze the soil microbial community and carbon use efficiency (CUE), respectively. We find microbial respiration rates are higher in rhizosphere than that in non-rhizosphere soils for ECM trees, whereas microbial growth rates show no significant differences. Consequently, microbial CUE is lower in rhizosphere compared to non-rhizosphere soils for ECM trees. In addition, we find that non-rhizosphere soils from ECM trees exhibited higher CUE compared to those from AM trees. Furthermore, we observe that bacterial–fungal co-occurrence networks in ECM soils exhibit greater complexity relative to AM ones. Using random forest and structural equation modeling analyses, we find that microbial stoichiometric carbon/nitrogen imbalance and network complexity are key predictors of soil microbial CUE for AM and ECM trees, respectively. Our findings shed new light on the pivotal role of mycorrhizal associations in shaping free-living microbial communities and their metabolic characteristics in the studied soils. These insights are critical for predicting soil carbon sequestration in response to shifts in ECM and AM species within temperate forest under climate change.
Targeting senescent cells for the treatment of age-associated diseases
Authors: Suda Masayoshi , Tchkonia Tamar , Kirkland James L , Minamino Tohru 
Published: December 2024

Abstract
Cellular senescence, which entails cellular dysfunction and inflammatory factor release—the senescence-associated secretory phenotype (SASP)—is a key contributor to multiple disorders, diseases and the geriatric syndromes. Targeting senescent cells using senolytics has emerged as a promising therapeutic strategy for these conditions. Among senolytics, the combination of dasatinib and quercetin (D + Q) was the earliest and one of the most successful so far. D + Q delays, prevents, alleviates or treats multiple senescence-associated diseases and disorders with improvements in healthspan across various pre-clinical models. While early senolytic therapies have demonstrated promise, ongoing research is crucial to refine them and address such challenges as off-target effects. Recent advances in senolytics include new drugs and therapies that target senescent cells more effectively. The identification of senescence-associated antigens—cell surface molecules on senescent cells—pointed to another promising means for developing novel therapies and identifying biomarkers of senescent cell abundance.
Interaction mapping between nucleoporins in the fission yeast Schizosaccharomyces pombe using mass-spectrometry
Authors: Asakawa Haruhiko , Nagao Koji , Fukagawa Tatsuo , Obuse Chikashi , Hiraoka Yasushi , Haraguchi Tokuko 
Published: December 2024

Abstract
Nuclear pore complexes (NPCs) act as gateways across the nuclear envelope for molecular transport between the nucleus and the cytoplasm in eukaryotes. NPCs consist of several subcomplexes formed by multiple copies of approximately 30 different proteins known as nucleoporins (Nups). In the fission yeast Schizosaccharomyces pombe, the NPC structure is unique, particularly in its outer ring subcomplexes, where the cytoplasmic and nucleoplasmic outer rings are composed of distinct sets of proteins. However, it remains unclear how this unique outer ring structure in S. pombe is supported by interactions between subcomplexes or individual Nups. In this study, we investigated protein–protein interactions between S. pombe Nups using mass spectrometry and identified Nups that interact with each subcomplex or a specific Nup. The cytoplasmic outer ring Nups bind to both the cytoplasmic filament Nups and the inner ring Nups, while the nucleoplasmic outer ring Nups bind to the nuclear basket Nups in addition to the inner ring Nups. Among the inner ring Nups, Nup155 interacts with most of the cytoplasmic and nucleoplasmic outer ring Nups, suggesting that Nup155 may serve as a hub supporting the uniquely asymmetric outer ring structure of the S. pombe NPC.
Hospital function-associated deaths among patients with cancer: a comprehensive national study using death records in Japan
Authors: Takahashi Richi , Nakazawa Yoko , Etoh Norihito , Kizawa Yoshiyuki , Miyashita Mitsunori , Hamano Jun 
Published: December 2024

Abstract

Background
In Japan, about 70%–80% of cancer deaths occur in hospitals. The actual number of cancer patients who die in hospitals where palliative care is available is not clear. This study aimed to examine whether hospitals where cancer patients died offered palliative care.

Methods
Patients aged ≥20 who died of cancer in 2018 were included. We used the Japanese death records and publicly available data on hospital functions. Cancer death numbers and hospitals were summarized according to hospital function and age group. Logistic regression analysis was performed to examine the death influence in patients with cancer in designated cancer hospitals.

Results
The study included 302 511 patients, and 168 835 patients (55.8%) died in hospitals with palliative care. In hospitals without palliative care, those with 100–199 and 200–499 beds had more deaths than hospitals not in these ranges of beds. Their median number of deaths per year was 17 and 26, respectively. Categorized by the death numbers per hospital without palliative care, hospitals with 20–49 cancer deaths were common. In the designated cancer hospitals, younger patients aged 20–29 had a higher odds ratio (OR) for death (4.28) than those aged 70–79. Blood cancer had a higher OR (2.36) than colorectal and rectal cancer.

Conclusion
Our findings suggest that outreach of palliative care to hospitals with 100–199 or 200–499 beds and 20–49 deaths lacking palliative care could effectively improve end-of-life cancer care.
Practice Variability in Uptake and Implementation of New U.S. DHHS Guidelines for Feeding of HIV-Exposed Infants
Authors: Rozen Eisenberg Ilan , Campbell Jeffrey I , Clarke Diana , Cooper Ellen R , Pelton Stephen I , Vuppula Sharon S 
Published: December 2024

Abstract
New U.S. guidelines support shared decision-making regarding breastfeeding for mothers living with HIV and their neonates. We surveyed Pediatric Infectious Diseases Society members about the implementation of these guidelines. We found heterogeneity in uptake, variability in clinical practice, and concerns about implementation. Future research should address these policy-practice gaps.
Quantification of beam size impact on intensity-modulated proton therapy with robust optimization in head and neck cancer—comparison with intensity-modulated radiation therapy
Authors: Baba Hiromi , Hotta Kenji , Takahashi Ryo , Motegi Kana , Sugama Yuya , Sakae Takeji , Tachibana Hidenobu 
Published: December 2024

Abstract
We assessed the effect of beam size on plan robustness for intensity-modulated proton therapy (IMPT) of head and neck cancer (HNC) and compared the plan quality including robustness with that of intensity-modulated radiation therapy (IMRT). IMPT plans were generated for six HNC patients using six beam sizes (air-sigma 3–17 mm at isocenter for a 70–230 MeV) and two optimization methods for planning target volume-based non-robust optimization (NRO) and clinical target volume (CTV)-based robust optimization (RO). Worst-case dosimetric parameters and plan robustness for CTV and organs-at-risk (OARs) were assessed under different scenarios, assuming a ± 1–5 mm setup error and a ± 3% range error. Statistical comparisons of NRO-IMPT, RO-IMPT and IMRT plans were performed. In regard to CTV-D99%, RO-IMPT with smaller beam size was more robust than RO-IMPT with larger beam sizes, whereas NRO-IMPT showed the opposite (P &lt; 0.05). There was no significant difference in the robustness of the CTV-D99% and CTV-D95% between RO-IMPT and IMRT. The worst-case CTV coverage of IMRT (±5 mm/3%) for all patients was 96.0% ± 1.4% (D99%) and 97.9% ± 0.3% (D95%). For four out of six patients, the worst-case CTV-D95% for RO-IMPT (±1–5 mm/3%) were higher than those for IMRT. Compared with IMRT, RO-IMPT with smaller beam sizes achieved lower worst-case doses to OARs. In HNC treatment, utilizing smaller beam sizes in RO-IMPT improves plan robustness compared to larger beam sizes, achieving comparable target robustness and lower worst-case OARs doses compared to IMRT.
Comparison of single- and multi-isocenter planning with Dynamic WaveArc for multiple brain metastases
Authors: Terabe Mitsuaki , Kamomae Takeshi , Taniguchi Yuki , Ichikawa Hajime , Yamada Takehiro , Miyachi Takayuki , Miyauchi Risei , Ito Junji , Ishihara Shunichi 
Published: December 2024

Abstract
Dynamic WaveArc (DWA) is a technique used for continuous, non-coplanar volumetric-modulated arc therapy on the Vero4DRT platform. This study aimed to evaluate the application of single-isocenter DWA (SI-DWA) for treating multiple brain metastases by comparing dose distribution and irradiation time with multi-isocenter DWA (MI-DWA) through retrospective treatment planning. Treatment plans were developed for SI-DWA and MI-DWA in 14 cases with 3–5 brain metastases. Parameters assessed included target dose indices, such as conformity index (CI) of the planning target volume (PTV), volumes of normal brain excluding gross tumor volumes (GTVs) receiving a single dose equivalent of 14 Gy (V14), V30%, V20%, V10%, volumes of normal brain, including GTVs receiving a single dose equivalent of 12 Gy (V12), D2% for other organs at risk, and beam-on time. SI-DWA showed inferior CI, V14, and V12 values for lesions with PTV volumes &lt;1 cc, whereas it performed equivalently to MI-DWA for lesions with PTV volumes ≥1 cc. SI-DWA resulted in higher volumes of normal brain receiving low doses compared to MI-DWA. SI-DWA exhibited significantly shorter beam-on times than MI-DWA. In conclusion, SI-DWA is an effective method for treating multiple brain metastases with PTV volumes ≥1 cc, offering an index of radiation-induced brain necrosis comparable with MI-DWA while allowing for shorter irradiation times.