bluuebunny/crossref_metadata_2025 huggingface dataset:
Imaging and multi-omics datasets converge to define different neural progenitor origins for ATRT-SHH subgroups
Authors: Lobón-Iglesias María-Jesús , Andrianteranagna Mamy , Han Zhi-Yan , Chauvin Céline , Masliah-Planchon Julien , Manriquez Valeria , Tauziede-Espariat Arnault , Turczynski Sandrina , Bouarich-Bourimi Rachida , Frah Magali , Dufour Christelle , Blauwblomme Thomas , Cardoen Liesbeth , Pierron Gaelle , Maillot Laetitia , Guillemot Delphine , Reynaud Stéphanie , Bourneix Christine , Pouponnot Célio , Surdez Didier , Bohec Mylene , Baulande Sylvain , Delattre Olivier , Piaggio Eliane , Ayrault Olivier , Waterfall Joshua J. , Servant Nicolas , Beccaria Kevin , Dangouloff-Ros Volodia , Bourdeaut Franck
Published: October 2023

Atypical teratoid rhabdoid tumors (ATRT) are divided into MYC, TYR and SHH subgroups, suggesting diverse lineages of origin. Here, we investigate the imaging of human ATRT at diagnosis and the precise anatomic origin of brain tumors in the Rosa26-CreERT2::Smarcb1flox/flox model. This cross-species analysis points to an extra-cerebral origin for MYC tumors. Additionally, we clearly distinguish SHH ATRT emerging from the cerebellar anterior lobe (CAL) from those emerging from the basal ganglia (BG) and intra-ventricular (IV) regions. Molecular characteristics point to the midbrain-hindbrain boundary as the origin of CAL SHH ATRT, and to the ganglionic eminence as the origin of BG/IV SHH ATRT. Single-cell RNA sequencing on SHH ATRT supports these hypotheses. Trajectory analyses suggest that SMARCB1 loss induces a de-differentiation process mediated by repressors of the neuronal program such as REST, ID and the NOTCH pathway.
Single virus fingerprinting by widefield interferometric defocus-enhanced mid-infrared photothermal microscopy
Authors: Xia Qing , Guo Zhongyue , Zong Haonan , Seitz Scott , Yurdakul Celalettin , Ünlü M. Selim , Wang Le , Connor John H. , Cheng Ji-Xin
Published: October 2023

Clinical identification and fundamental study of viruses rely on the detection of viral proteins or viral nucleic acids. Yet, amplification-based and antigen-based methods are not able to provide precise compositional information of individual virions due to small particle size and low-abundance chemical contents (e.g., ~ 5000 proteins in a vesicular stomatitis virus). Here, we report a widefield interferometric defocus-enhanced mid-infrared photothermal (WIDE-MIP) microscope for high-throughput fingerprinting of single viruses. With the identification of feature absorption peaks, WIDE-MIP reveals the contents of viral proteins and nucleic acids in single DNA vaccinia viruses and RNA vesicular stomatitis viruses. Different nucleic acid signatures of thymine and uracil residue vibrations are obtained to differentiate DNA and RNA viruses. WIDE-MIP imaging further reveals an enriched β sheet components in DNA varicella-zoster virus proteins. Together, these advances open a new avenue for compositional analysis of viral vectors and elucidating protein function in an assembled virion.
TRIM21 mediates the synergistic effect of Olaparib and Sorafenib by degrading BRCA1 through ubiquitination in TNBC
Authors: Huang Ning , Li Peng , Sun Xiaolin , Tong Li , Dong Xinyi , Zhang Xuemei , Duan Jifeng , Sheng Xia , Xin Hong
Published: October 2023

Triple-negative breast cancer (TNBC) is a heterogeneous and aggressive type of breast cancer with a poor prognosis and a high recurrence rate. Chemotherapy is still the mainstay of treatment for cancer patients without a genetic BRCA mutation, despite the approval of Olaparib, an inhibitor of the poly (ADP-ribose) polymerase (PARP) enzyme. Tripartite motif containing-21 (TRIM21) is one of the TRIM family members that has been investigated in various types of cancer. Here, we found that a low TRIM21 expression level was correlated with poor overall survival of TNBC patients. Knockout of TRIM21 promoted the proliferation of TNBC cells in vivo and in vitro, as well as migratory and invasive capabilities in vitro. Importantly, breast cancer susceptibility gene 1 (BRCA1) was identified as a ubiquitination substrate of TRIM21. It was confirmed that BRCA1 was upregulated after Olaparib treatment, which may explain the relative resistance of BRCA1-proficient TNBC cells to Olaparib. Moreover, Sorafenib, a standard treatment for hepatocellular carcinoma, increased the sensitivity of TNBC cells to Olaparib by promoting TRIM21-mediated ubiquitination degradation of BRCA1. Thus, a synergic effect of Olaparib and Sorafenib was found in vitro and in vivo. This combined treatment also aggravated DNA damage, cell cycle arrest, and apoptosis of TNBC cells. In summary, the findings verified the synergistic effect of Olaparib and Sorafenib and revealed TRIM21 as a potential target for TNBC therapy.
Systematic review and meta-analysis of the factors affecting waning of post-vaccination neutralizing antibody responses against SARS-CoV-2
Authors: Jacobsen Henning , Sitaras Ioannis , Katzmarzyk Maeva , Cobos Jiménez Viviana , Naughton Robert , Higdon Melissa M. , Deloria Knoll Maria
Published: October 2023

Mass COVID-19 vaccination and continued introduction of new SARS-CoV-2 variants increased prevalence of hybrid immunity at various stages of waning protection. We systematically reviewed waning of post-vaccination neutralizing antibody titers in different immunological settings to investigate differences. We searched published and pre-print studies providing post-vaccination neutralizing antibody responses against the Index strain or Omicron BA.1. We used random effects meta-regression to estimate fold-reduction from months 1 to 6 post last dose by primary vs booster regimen and infection-naïve vs hybrid-immune cohorts. Among 26 eligible studies, 65 cohorts (range 3–21 per stratum) were identified. Month-1 titers varied widely across studies within each cohort and by vaccine platform, number of doses and number of prior infections. In infection-naïve cohorts, the Index strain waned 5.1-fold (95%CI: 3.4–7.8; n = 19 cohorts) post-primary regimen and 3.8-fold (95%CI: 2.4–5.9; n = 21) post-booster from months 1 to 6, and against Omicron BA.1 waned 5.9-fold (95%CI: 3.8–9.0; n = 16) post-booster; Omicron BA.1 titers post-primary were too low to assess. In hybrid-immune, post-primary cohorts, titers waned 3.7-fold (95%CI: 1.7–7.9; n = 8) against the Index strain and 5.0-fold (95%CI: 1.1–21.8; n = 6) against Omicron BA.1; post-booster studies of hybrid-immune cohorts were too few (n = 3 cohorts each strain) to assess. Waning was similar across vaccination regimen and prior-infection status strata but was faster for Omicron BA.1 than Index strains, therefore, more recent sub-variants should be monitored. Wide differences in peak titers by vaccine platform and prior infection status mean titers drop to non-protective levels sooner in some instances, which may affect policy.
The NOAA NCEI marine microplastics database
Authors: Nyadjro Ebenezer S. , Webster Jennifer A. B. , Boyer Tim P. , Cebrian Just , Collazo Leonard , Kaltenberger Gunnar , Larsen Kirsten , Lau Yee H. , Mickle Paul , Toft Tiffany , Wang Zhankun
Published: October 2023

Microplastics (<5 mm) pollution is a growing problem affecting coastal communities, marine ecosystems, aquatic life, and human health. The widespread occurrence of marine microplastics, and the need to curb its threats, require expansive, and continuous monitoring. While microplastic research has increased in recent years and generated significant volumes of data, there is a lack of a robust, open access, and long-term aggregation of this data. The National Oceanic and Atmospheric Administration (NOAA) National Centers for Environmental Information (NCEI) now provides a global open access to marine microplastics data on an easily discoverable and accessible GIS web map and data portal (https://www.ncei.noaa.gov/products/microplastics). The objective of this data portal is to develop a repository where microplastics data are aggregated, archived, and served in a user friendly, consistent, and reliable manner. This work contributes to NCEI’s efforts towards data standardization, integration, harmonization, and interoperability among national and international collaborators for monitoring global marine microplastics. This paper describes the NOAA NCEI global marine microplastics database, its creation, quality control procedures, and future directions.
Effects of oxytocin on the hair growth ability of dermal papilla cells
Authors: Kageyama Tatsuto , Seo Jieun , Yan Lei , Fukuda Junji
Published: October 2023

Oxytocin (OXT) is a neuropeptide hormone termed “love hormone” produced and released during childbirth and lactation. It is also produced in response to skin stimulation (e.g., during hugging and massaging) and music therapy. The effects of OXT on various organs have been revealed in recent years; however, the relationship between hair follicles and OXT remains unclear. In this study, we examined the effects of OXT on dermal papilla (DP) cells that control hair growth by secreting growth/regression signals. Gene expression analysis revealed that DP signature markers were significantly upregulated in DP cells treated with OXT. In addition, we tested the hair growth-promoting effects of OXT using in vitro hair follicle organoids. OXT promoted the growth of hair peg-like sprouting by upregulating the expression of growth-promoting factors, including genes encoding vascular endothelial growth factor A (VEGFA). This study highlights the positive effects of OXT in hair follicles and may assist in the development of new treatments for alopecia.
Expression of TNFR1, VEGFA, CD147 and MCT1 as early biomarkers of diabetes complications and the impact of aging on this profile
Authors: Raimundo Joyce Regina Santos , da Costa Aguiar Alves Beatriz , Encinas Jéssica Freitas Araujo , Siqueira Andressa Moreira , de Gois Katharyna Cardoso , Perez Matheus Moreira , Petri Giuliana , dos Santos José Francisco Ramos , Fonseca Fernando Luiz Affonso , da Veiga Glaucia Luciano
Published: October 2023

Hyperglycemia leads to microvascular lesions in various tissues. In diabetic nephropathy—DN, alterations in usual markers reflect an already installed disease. The study of new biomarkers for the early detection of diabetic complications can bring new prevention perspectives. Rats were divided into diabetic adult—DMA—or elderly—DME and control sham adult—CSA—or control sham elderly—CSE. Blood and urine samples were collected for biochemical analysis. Bulbar region, cardiac, hepatic and renal tissues were collected for target gene expression studies. As result, DMA showed decreased TNFR1, MCT1 and CD147 expression in the bulbar region, TNFR1 in the heart, VEGFA and CD147 in the kidney and TNFR1 in blood. Positive correlations were found between TNFR1 and MCT1 in the bulbar region and HbA1c and plasma creatinine, respectively. DME showed positive correlation in the bulbar region between TNFR1 and glycemia, in addition to negative correlations between CD147 in the heart versus glycemia and urea. We concluded that the initial hyperglycemic stimulus already promotes changes in the expression of genes involved in the inflammatory and metabolic pathways, and aging alters this profile. These changes prior to the onset of diseases such as DN, show that they have potential for early biomarkers studies.
In silico design and cell-based evaluation of two dual anti breast cancer compounds targeting Bcl-2 and GPER
Authors: Morelos-Garnica Loreley-A. , Guzmán-Velázquez Sonia , Padilla-Martínez Itzia-I. , García-Sánchez José-R. , Bello Martiniano , Bakalara Norbert , Méndez-Luna David , Correa-Basurto José
Published: October 2023

According to WHO statistics, breast cancer (BC) disease represents about 2.3 million diagnosed and 685,000 deaths globally. Regarding histological classification of BC, the Estrogen (ER) and Progesterone (PR) receptors negative-expression cancer, named Triple-Negative BC (TNBC), represents the most aggressive type of this disease, making it a challenge for drug discovery. In this context, our research group, applying a well-established Virtual Screening (VS) protocol, in addition to docking and molecular dynamics simulations studies, yielded two ligands identified as 6 and 37 which were chemically synthesized and evaluated on MCF-7 and MDA-MB-231 cancer cell lines. Strikingly, 37 assayed on MDA-MB-231 (a TNBC cell model) depicted an outstanding value of 18.66 μM much lower than 65.67 μM yielded by Gossypol Bcl-2 inhibitor whose main disadvantage is to produce multiple toxic effects. Highlighted above, enforce the premise of the computational tools to find new therapeutic options against the most aggressive forms of breast cancer, as the results herein showed.
Photophysiologically active green, red, and brown macroalgae living in the Arctic Polar Night
Authors: Summers Natalie , Fragoso Glaucia M. , Johnsen Geir
Published: October 2023

Arctic macroalgae species have developed different growth strategies to survive extreme seasonal changes in irradiance in polar regions. We compared photophysiological parameters such as the light saturation parameter (Ek) and pigment composition of green, red, and brown macroalgae collected in January (Polar Night) and October 2020 (end of the light season). Macroalgae in January appeared healthier (morphologically) and had longer lamina (new growth) than those in October. EK values for red, and brown algae were higher with lower maximum quantum yield of PS II fluorescence (Fv/Fm) in January versus October. Furthermore, in January, new tissues in kelp species had higher EK than the older tissue. Higher EK and lower Fv/Fm during the Polar Night indicates that the photosynthetic apparatus is active but slow. Furthermore, we discuss Chlorophyll (Chl) a emission spectra under blue and green excitation light to determine the ratio of Chl a in photosystem II (PS II) vs photosystem I (PS I). Absorbance spectra of P. palmata was used to interpret the emission spectra. The observed spectral shifts in the absorbance and reflectance spectra of different macroalgae is discussed. Photophysiological methods provide health information complementary to future mapping and monitoring of macroalgae. These results reveal that macroalgae grow new tissue in darkness.
Effect of morpholine, and 4-methylmorpholine on urethane formation: a computational study
Authors: Waleed Hadeer Q. , Hadjadj Rachid , Viskolcz Béla , Fiser Béla
Published: October 2023

A theoretical study of urethane formation through the reaction of phenyl isocyanate and butan-1-ol was carried out, without and in the presence of morpholine, and 4-methylmorpholine catalysts. The reaction with and without catalysts was studied at BHandHLYP/6-31G(d) and G3MP2BHandHLYP levels of theories. The reaction mechanism in the presence of catalysts differs significantly from the catalyst-free case and includes seven steps. The catalyst-free system was investigated along with the catalytic process, the geometries were optimized, and the corresponding thermodynamic properties were calculated. Calculated reactant complexes were compared with crystal structures of morpholine, and 4-methylmorpholine complexed with diols found in the literature. The structures were strikingly similar and thus, the validity of the proposed and studied general organocatalytic reaction mechanism was partially verified. Meanwhile, an irregularity in the energy profile occurred due to the zwitterionic nature of an intermediate. To handle the irregularity, a correction was implemented which handles the appearance of a zwitterionic structure and the corresponding energetic properties. The results showed that morpholine is less effective catalyst compared to 4-methylmorpholine, which can be associated with the difference in their PA (1523.95 and 963.07 kJ/mol, respectively). The current results prove the important role of amine catalysts in urethane synthesis which can be applied in polyurethane catalyst design and development.
Hypofibrinogenemia is an independent predictor of hemophagocytic lymphohistiocytosis in children with sepsis
Authors: Luo Xin , Zhou Chentao , Ji Cunwei , Lu Chunmin , Luo Yasha , Chen Zhenhui , Zhong Tianhua , Ye Ruoting , Zeng Liwei , Luo Mingyong
Published: October 2023

Hemophagocytic lymphohistiocytosis (HLH) is a potentially life-threatening condition in children with sepsis. We herein aimed to identify clinical and laboratory predictors of HLH in children with sepsis. We conducted a retrospective study of 568 children with sepsis admitted to Guangdong Women and Children Hospital from January 2019 to June 2022. HLH, while rare (6.34%), proved to be a highly fatal complication (37.14%) in children with sepsis. Children with HLH had higher levels of aspartate aminotransferase, lactate dehydrogenase, triglycerides, and ferritin than children without HLH; conversely, they displayed decreased levels of neutrophils, hemoglobin, platelets, fibrinogen, and albumin. Additionally, the HLH group showed higher rates of prolonged fever (> 10 days), hepatomegaly, and splenomegaly than the non-HLH group. Our retrospective analysis identified hypofibrinogenemia (OR = 0.440, P = 0.024) as an independent predictor for the development of HLH in patients with sepsis. The optimal cutoff value for fibrinogen was found to be < 2.43 g/L. The area under the curve for diagnosing HLH was 0.80 (95% confidence interval: 0.73–0.87, P < 0.0001), with a sensitivity of 72.41% and specificity of 76.27%. Thus, hypofibrinogenemia emerges as a potentially valuable predictor for HLH in children with sepsis.
Transfer learning for accurate fetal organ classification from ultrasound images: a potential tool for maternal healthcare providers
Authors: Ghabri Haifa , Alqahtani Mohammed S. , Ben Othman Soufiene , Al-Rasheed Amal , Abbas Mohamed , Almubarak Hassan Ali , Sakli Hedi , Abdelkarim Mohamed Naceur
Published: October 2023

Ultrasound imaging is commonly used to aid in fetal development. It has the advantage of being real-time, low-cost, non-invasive, and easy to use. However, fetal organ detection is a challenging task for obstetricians, it depends on several factors, such as the position of the fetus, the habitus of the mother, and the imaging technique. In addition, image interpretation must be performed by a trained healthcare professional who can take into account all relevant clinical factors. Artificial intelligence is playing an increasingly important role in medical imaging and can help solve many of the challenges associated with fetal organ classification. In this paper, we propose a deep-learning model for automating fetal organ classification from ultrasound images. We trained and tested the model on a dataset of fetal ultrasound images, including two datasets from different regions, and recorded them with different machines to ensure the effective detection of fetal organs. We performed a training process on a labeled dataset with annotations for fetal organs such as the brain, abdomen, femur, and thorax, as well as the maternal cervical part. The model was trained to detect these organs from fetal ultrasound images using a deep convolutional neural network architecture. Following the training process, the model, DenseNet169, was assessed on a separate test dataset. The results were promising, with an accuracy of 99.84%, which is an impressive result. The F1 score was 99.84% and the AUC was 98.95%. Our study showed that the proposed model outperformed traditional methods that relied on the manual interpretation of ultrasound images by experienced clinicians. In addition, it also outperformed other deep learning-based methods that used different network architectures and training strategies. This study may contribute to the development of more accessible and effective maternal health services around the world and improve the health status of mothers and their newborns worldwide.
Establishment of a novel indicator of pyroptosis regulated gene transcription level and its application in pan-cancer
Authors: Xu Jin-Zhou , Xia Qi-Dong , Sun Jian-Xuan , Liu Chen-Qian , Lu Jun-Lin , Xu Meng-Yao , An Ye , Xun Yang , Liu Zheng , Hu Jia , Li Cong , Wang Shao-Gang
Published: October 2023

Pyroptosis is a type of programmed cell death and plays a dual role in distinct cancers. It is elusive to evaluate the activation level of pyroptosis and to appraise the involvement of pyroptosis in the occurrence and development of diverse tumors. Accordingly, we herein established an indicator to evaluate pyroptosis related gene transcription levels based on the expression level of genes involved in pyroptosis and tried to elaborated on the association between pyroptosis and tumors across diverse tumor types. We found that pyroptosis related gene transcription levels could predict the prognosis of patients, which could act as either a favorable or a dreadful factor in diverse cancers. According to signaling pathway analyses we observed that pyroptosis played a significant role in immune regulation and tumorigenesis and had strong links with other forms of cell death. We also performed analysis on the crosstalk between pyroptosis and immune status and further investigated the predictive potential of pyroptosis level for the efficacy of immunotherapy. Lastly, we manifested that pyroptosis status could serve as a biomarker to the efficacy of chemotherapy across various cancers. In summary, this study established a quantitative indicator to evaluate pyroptosis related gene transcription levels, systematically explored the role of pyroptosis in pan-cancer. These results could provide potential research directions targeting pyroptosis, and highlighted that pyroptosis may be used to develop a novel strategy for the treatment of cancer.
Primate-specific isoform of Nedd4-1 regulates substrate binding via Ser/Thr phosphorylation and 14-3-3 binding
Authors: Kefalas George , Rotin Daniela
Published: October 2023

Nedd4 (Nedd4-1) is an E3 ubiquitin ligase involved in crucial biological processes such as growth factor receptor signaling. While canonical Nedd4-1 comprises a C2-WW(4)-HECT domain architecture, alternative splicing produces non-canonical isoforms that are poorly characterized. Here we characterized Nedd4-1(NE), a primate-specific isoform of Nedd4-1 that contains a large N-terminal Extension (NE) that replaces most of the C2 domain. We show that Nedd4-1(NE) mRNA is ubiquitously expressed in human tissues and cell lines. Moreover, we found that Nedd4-1(NE) is more active than the canonical Nedd4-1 isoform, likely due to the absence of a C2 domain-mediated autoinhibitory mechanism. Additionally, we identified two Thr/Ser phosphoresidues in the NE region that act as binding sites for 14-3-3 proteins, and show that phosphorylation on these sites reduces substrate binding. Finally, we show that the NE region can act as a binding site for the RPB2 subunit of RNA polymerase II, a unique substrate of Nedd4-1(NE) but not the canonical Nedd4-1. Taken together, our results demonstrate that alternative splicing of the ubiquitin ligase Nedd4-1 can produce isoforms that differ in their catalytic activity, binding partners and substrates, and mechanisms of regulation.
Rapid improvements and subsequent effects in major depressive disorder patients with somatic pain using rTMS combined with sertraline
Authors: Sun Yuanfeng , Lei Fei , Zou Ke , Zheng Zhong
Published: October 2023

This study aims to explore changes in depression and pain for major depressive disorder (MDD) patients with somatic pain after repetitive transcranial magnetic stimulation (rTMS) using the event-related potentials (ERPs) technique. Eighty MDD patients with somatic pain were randomly assigned to drug therapy (DT) and combined therapy (CT) groups. CT group underwent intermittent theta burst stimulation over the left dorsolateral prefrontal cortex (DLPFC) with 800 pulses and 1 Hz over the right DLPFC with 800 pulses, 5 times a week for 3 weeks. All patients were given sertraline at 50–100 mg per day. All subjects were evaluated at baseline and at weeks three and six of therapy using the Hamilton Rating Scale for Depression (HAMD), Hamilton Anxiety Scale (HAMA), and Numerical Rating Scales (NRS), and the latency and amplitude of P300 and mismatch negativity (MMN) were measured. There were no significant differences in all indices between groups at baseline. At 3 weeks, HAMD subscale scores of Cognitive Impairment and NRS scores were significantly lower in the CT group than in the DT group. At 6 weeks, NRS and HAMD total scores in the CT group decreased significantly in the CT group compared with the DT group, especially for anxiety and pain, and the MMN and P300 latencies and P300 amplitude showed greater improvements. Our findings highlight that rTMS in combination with antidepressants is a rapid method of symptom improvement in patients with somatic pain with MDD and is helpful for cognitive impairment and anxiety.
Effects of skin moisturization on various aspects of touch showing differences with age and skin site
Authors: Dione Mariama , Watkins Roger Holmes , Aimonetti Jean-Marc , Jourdain Roland , Ackerley Rochelle
Published: October 2023

The human body is encompassed by a thin layer of tissue, the skin, which is heterogenous and highly specialized to protect the body and encode interactions with the external world. There is a fundamental scientific drive to understand its function, coupled with the need to preserve skin as we age, which impacts on our physiological and psychological well-being. In the present study, we aimed to define differences in touch perception between age groups and with skin cream application. We investigated touch on the finger, the forearm and cheek in younger (20–28 years, n = 22) and older (65–75 years, n = 22) females. We measured skin hydration, touch detection, finger spatial discrimination, forearm tactile pleasantness together with electrodermal activity, and perceptual ratings about cream use, skin dryness, and cosmetic habits. Glabrous finger skin became drier and touch performance was impaired with age, but these aspects were preserved in hairy skin. Skin moisturization immediately increased hydration levels, but did not significantly change touch perception. We also found that touch appreciation increased with age. We conclude that reduced finger capacity may impact self-evaluation of the skin and that long-term skin care strategies should focus on hydrating the hand to preserve touch capacities.
A novel bidirectional LSTM deep learning approach for COVID-19 forecasting
Authors: Aung Nway Nway , Pang Junxiong , Chua Matthew Chin Heng , Tan Hui Xing
Published: October 2023

COVID-19 has resulted in significant morbidity and mortality globally. We develop a model that uses data from thirty days before a fixed time point to forecast the daily number of new COVID-19 cases fourteen days later in the early stages of the pandemic. Various time-dependent factors including the number of daily confirmed cases, reproduction number, policy measures, mobility and flight numbers were collected. A deep-learning model using Bidirectional Long-Short Term Memory (Bi-LSTM) architecture was trained on data from 22nd Jan 2020 to 8 Jan 2021 to forecast the new daily number of COVID-19 cases 14 days in advance across 190 countries, from 9 to 31 Jan 2021. A second model with fewer variables but similar architecture was developed. Results were summarised by mean absolute error (MAE), root mean squared error (RMSE), mean absolute percentage error (MAPE), and total absolute percentage error and compared against results from a classical ARIMA model. Median MAE was 157 daily cases (IQR: 26–666) under the first model, and 150 (IQR: 26–716) under the second. Countries with more accurate forecasts had more daily cases and experienced more waves of COVID-19 infections. Among countries with over 10,000 cases over the prediction period, median total absolute percentage error was 33% (IQR: 18–59%) and 34% (IQR: 16–66%) for the first and second models respectively. Both models had comparable median total absolute percentage errors but lower maximum total absolute percentage errors as compared to the classical ARIMA model. A deep-learning approach using Bi-LSTM architecture and open-source data was validated on 190 countries to forecast the daily number of cases in the early stages of the COVID-19 outbreak. Fewer variables could potentially be used without impacting prediction accuracy.
Identifying prognostic genes related PANoptosis in lung adenocarcinoma and developing prediction model based on bioinformatics analysis
Authors: Zhang Chi , Xia Jiangnan , Liu Xiujuan , Li Zexing , Gao Tangke , Zhou Tian , Hu Kaiwen
Published: October 2023

Cell death-related genes indicate prognosis in cancer patients. PANoptosis is a newly observed form of cell death that researchers have linked to cancer cell death and antitumor immunity. Even so, its significance in lung adenocarcinomas (LUADs) has yet to be elucidated. We extracted and analyzed data on mRNA gene expression and clinical information from public databases in a systematic manner. These data were utilized to construct a reliable risk prediction model for six regulators of PANoptosis. The Gene Expression Omnibus (GEO) database validated six genes with risk characteristics. The prognosis of LUAD patients could be accurately estimated by the six-gene-based model: NLR family CARD domain-containing protein 4 (NLRC4), FAS-associated death domain protein (FADD), Tumor necrosis factor receptor type 1-associated DEATH domain protein (TRADD), Receptor-interacting serine/threonine-protein kinase 1 (RIPK1), Proline-serine-threonine phosphatase-interacting protein 2 (PSTPIP2), and Mixed lineage kinase domain-like protein (MLKL). Group of higher risk and Cluster 2 indicated a poor prognosis as well as the reduced expression of immune infiltrate molecules and human leukocyte antigen. Distinct expression of PANoptosis-related genes (PRGs) in lung cancer cells was verified using quantitative reverse transcription polymerase chain reaction (qRT-PCR). Furthermore, we evaluated the relationship between PRGs and somatic mutations, tumor immune dysfunction exclusion, tumor stemness indices, and immune infiltration. Using the risk signature, we conducted analyses including nomogram construction, stratification, prediction of small-molecule drug response, somatic mutations, and chemotherapeutic response.
Artificial intelligence-driven shimming for parallel high field nuclear magnetic resonance
Authors: Becker Moritz , Cheng Yen-Tse , Voigt Achim , Chenakkara Ajmal , He Mengjia , Lehmkuhl Sören , Jouda Mazin , Korvink Jan G.
Published: October 2023

Rapid drug development requires a high throughput screening technology. NMR could benefit from parallel detection but is hampered by technical obstacles. Detection sites must be magnetically shimmed to ppb uniformity, which for parallel detection is precluded by commercial shimming technology. Here we show that, by centering a separate shim system over each detector and employing deep learning to cope with overlapping non-orthogonal shimming fields, parallel detectors can be rapidly calibrated. Our implementation also reports the smallest NMR stripline detectors to date, based on an origami technique, facilitating further upscaling in the number of detection sites within the magnet bore.
Synthetic MRI in breast cancer: differentiating benign from malignant lesions and predicting immunohistochemical expression status
Authors: Li Xiaojun , Fan Zhichang , Jiang Hongnan , Niu Jinliang , Bian Wenjin , Wang Chen , Wang Ying , Zhang Runmei , Zhang Hui
Published: October 2023

To evaluate and compare the performance of synthetic magnetic resonance imaging (SyMRI) in classifying benign and malignant breast lesions and predicting the expression status of immunohistochemistry (IHC) markers. We retrospectively analysed 121 patients with breast lesions who underwent dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) and SyMRI before surgery in our hospital. DCE-MRI was used to assess the lesions, and then regions of interest (ROIs) were outlined on SyMRI (before and after enhancement), and apparent diffusion coefficient (ADC) maps to obtain quantitative values. After being grouped according to benign and malignant status, the malignant lesions were divided into high and low expression groups according to the expression status of IHC markers. Logistic regression was used to analyse the differences in independent variables between groups. The performance of the modalities in classification and prediction was evaluated by receiver operating characteristic (ROC) curves. In total, 57 of 121 lesions were benign, the other 64 were malignant, and 56 malignant lesions performed immunohistochemical staining. Quantitative values from proton density-weighted imaging prior to an injection of the contrast agent (PD-Pre) and T2-weighted imaging (T2WI) after the injection (T2-Gd), as well as its standard deviation (SD of T2-Gd), were valuable SyMRI parameters for the classification of benign and malignant breast lesions, but the performance of SyMRI (area under the curve, AUC = 0.716) was not as good as that of ADC values (AUC = 0.853). However, ADC values could not predict the expression status of breast cancer markers, for which SyMRI had excellent performance. The AUCs of androgen receptor (AR), estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER-2), p53 and Ki-67 were 0.687, 0.890, 0.852, 0.746, 0.813 and 0.774, respectively. SyMRI had certain value in distinguishing between benign and malignant breast lesions, and ADC values were still the ideal method. However, to predict the expression status of IHC markers, SyMRI had an incomparable value compared with ADC values.
Application of anti-inflammatory treatment in two different ovine Acute Respiratory Distress Syndrome injury models: a preclinical randomized intervention study
Authors: Wildi Karin , Livingstone Samantha , Ainola Carmen , Colombo Sebastiano Maria , Heinsar Silver , Sato Noriko , Sato Kei , Bouquet Mahé , Wilson Emily , Abbate Gabriella , Passmore Margaret , Hyslop Kieran , Liu Keibun , Wang Xiaomeng , Palmieri Chiara , See Hoe Louise E. , Jung Jae-Seung , Ki Katrina , Mueller Christian , Laffey John , Pelosi Paolo , Li Bassi Gianluigi , Suen Jacky , Fraser John
Published: October 2023

Whilst the presence of 2 subphenotypes among the heterogenous Acute Respiratory Distress Syndrome (ARDS) population is becoming clinically accepted, subphenotype-specific treatment efficacy has yet to be prospectively tested. We investigated anti-inflammatory treatment in different ARDS models in sheep, previously shown similarities to human ARDS subphenotypes, in a preclinical, randomized, blinded study. Thirty anesthetized sheep were studied up to 48 h and randomized into: (a) OA: oleic acid (n = 15) and (b) OA-LPS: oleic acid and subsequent lipopolysaccharide (n = 15) to achieve a PaO2/FiO2 ratio of < 150 mmHg. Then, animals were randomly allocated to receive treatment with methylprednisolone or erythromycin or none. Assessed outcomes were oxygenation, pulmonary mechanics, hemodynamics and survival. All animals reached ARDS. Treatment with methylprednisolone, but not erythromycin, provided the highest therapeutic benefit in Ph2 animals, leading to a significant increase in PaO2/FiO2 ratio by reducing pulmonary edema, dead space ventilation and shunt fraction. Animals treated with methylprednisolone displayed a higher survival up to 48 h than all others. In animals treated with erythromycin, there was no treatment benefit regarding assessed physiological parameters and survival in both phenotypes. Treatment with methylprednisolone improves oxygenation and survival, more so in ovine phenotype 2 which resembles the human hyperinflammatory subphenotype.
Burnout dynamic among Ukrainian academic staff during the war
Authors: Tsybuliak Natalia , Suchikova Yana , Shevchenko Liudmyla , Popova Anastasia , Kovachev Serhii , Hurenko Olha
Published: October 2023

This study examined burnout dynamics among Ukrainian academic staff during the full-scale war. A cross-sectional study was conducted twice: the first wave in July 2022 and the second in January 2023. To assess the burnout syndrome as the final outcome, the self-reported Maslach Burnout Inventory-Human Services adapted for socioeconomic professions by Vodopyanova was used and correlated with different characteristics. The results showed a significant positive trend in emotional exhaustion among Ukrainian academic staff, with females being more sensitive to war-related factors. The results demonstrate that prolonged stressful situations associated with the ongoing war and constant changes in professional conditions lead to significant depersonalization dynamics among academic staff of both sexes. For male academic staff, factors such as age and academic position become less significant for depersonalization. However, university relocation and migration processes were significant factors affecting female academic staff’s' perception of effectiveness and accomplishment in their professional activities. The alarming dynamic of burnout levels detected among Ukrainian academic staff urges the national and institutional levels to take prompt actions to enhance the academic staff’s mental health in the workplace for preserving not only the quality of higher education, but also human capital in war times for postwar recovery in Ukraine.
Long-term outcomes of endoscopic resection for duodenal neuroendocrine tumors
Authors: Yi Kiyoun , Kim Gwang Ha , Kim Su Jin , Choi Cheol Woong , Lee Moon Won , Lee Bong Eun , Song Geun Am
Published: October 2023

Duodenal neuroendocrine tumors (d-NETs) ≤ 10 mm in size, confined to the submucosal layer, without lymph node or distant metastasis, can be treated safely and effectively by endoscopic management. However, most results are based on limited data and short follow-up outcomes. Herein, we aimed to evaluate the short-term and long-term outcomes of endoscopic resection for d-NETs. We retrospectively analyzed 63 patients with 68 d-NETs who had undergone endoscopic resection at two hospitals between January 2009 and December 2021. En-bloc resection, endoscopically complete resection, and histopathologically complete resection rates were evaluated as short-term outcomes. Furthermore, long-term outcomes were analyzed in 46 patients with 50 d-NETs with a follow-up period of > 1 year. The overall en-bloc, endoscopically complete, and histopathologically complete resection rates were 92.6% (63/68), 100% (68/68), and 69.1% (47/68), respectively. Tumor size (> 5 mm) was the only predictive factor for histopathologically incomplete resection (p = 0.015). The procedure-related bleeding and perforation rates were 0% and 5.9%, respectively. No recurrences were observed in patients with histopathologically complete resection and those with histopathologically incomplete resection at a median follow-up period of 48 months (range 12–132 months). Endoscopic resection for d-NETs ≤ 10 mm in size, limited to the submucosal layer, and without lymph node or distant metastasis provides favorable long-term outcomes when endoscopically complete resection is achieved.
Solubility and stability enhancement of ethanol in diesel fuel by using tri-n-butyl phosphate as a new surfactant for CI engine
Authors: El-Sheekh Mostafa M. , El-Nagar Aya A. , ElKelawy Medhat , Bastawissi Hagar Alm-Eldin
Published: October 2023

Nowadays, researchers are very interested in improving the stability and solubility of blending diesel fuel with a high percentage of ethanol. As a result, the goal of this paper was to find a way to use the surfactant of Tri-n-butyl phosphate (TBP) substance to blend ethanol with diesel fuel to a level of 40%. Diesel fuel is mixed with ethanol in volumetric proportions of 10%, 20%, 30%, and 40%, as well as a tiny amount of TBP from 1 to 4%. The prepared blends were the subject of an experiment evaluation by fueling a direct injection diesel engine. This engine is a water-cooled, commercial diesel engine, single cylinder, and four-stroke with 12 kW maximum power. The four blends were evaluated as clean fuel mixtures of 10% ethanol/90% diesel/1% TBP, 20% ethanol/80% diesel/2% TBP, 30% ethanol/70% diesel/3% TBP, and 40% ethanol/60% diesel/4% TBP. As the starting fuel, we used 100% diesel to compare the results. The engine’s output and emissions have been measured at various engine loads and constant speeds of 1500 rpm. According to the data gathered, even when the percentage of ethanol was increased to 40%, neither the base fuel nor the engine BTE changed significantly. The engine exhaust gas temperature was found to decrease slightly when the proportion of ethanol was increased. When bioethanol is increased to 40% of the base volume, it causes an increase in the combustion of unburned hydrocarbons and CO emissions. However, when the percentage of ethanol was increased from 100% diesel to the base fuel to 40%, CO2 emissions decreased, and O2 emissions slightly increased.
Understanding the combining ability of nutritional, agronomic and industrial traits in soybean F2 progenies
Authors: das Chagas Paulo Henrique Menezes , Teodoro Larissa Pereira Ribeiro , Santana Dthenifer Cordeiro , Filho Marcelo Carvalho Minhoto Teixeira , Coradi Paulo Carteri , Torres Francisco Eduardo , Bhering Leonardo Lopes , Teodoro Paulo Eduardo
Published: October 2023

Obtaining soybean genotypes that combine better nutrient uptake, higher oil and protein levels in the grains, and high grain yield is one of the major challenges for current breeding programs. To avoid the development of unpromising populations, selecting parents for crossbreeding is a crucial step in the breeding pipeline. Therefore, our objective was to estimate the combining ability of soybean cultivars based on the F2 generation, aiming to identify superior segregating parents and populations for agronomic, nutritional and industrial traits. Field experiments were carried out in two locations in the 2020/2021 crop season. Leaf contents of the following nutrients were evaluated: phosphorus, potassium, calcium, magnesium, sulfur, copper, iron, manganese, and zinc. Agronomic traits assessed were days to maturity (DM) and grain yield (GY), while the industrial traits protein, oil, fiber and ash contents were also measured in the populations studied. There was a significant genotype × environment (G × A) interaction for all nutritional traits, except for P content, DM and all industrial traits. The parent G3 and the segregating populations P20 and P27 can be used aiming to obtain higher nutritional efficiency in new soybean cultivars. The segregating populations P11 and P26 show higher potential for selecting soybean genotypes that combine earliness and higher grain yield. The parent G5 and segregant population P6 are promising for selection seeking improvement of industrial traits in soybean.
Multicentric pilot study to standardize clinical whole exome sequencing (WES) for cancer patients
Authors: Menzel Michael , Ossowski Stephan , Kral Sebastian , Metzger Patrick , Horak Peter , Marienfeld Ralf , Boerries Melanie , Wolter Steffen , Ball Markus , Neumann Olaf , Armeanu-Ebinger Sorin , Schroeder Christopher , Matysiak Uta , Goldschmid Hannah , Schipperges Vincent , Fürstberger Axel , Allgäuer Michael , Eberhardt Timo , Niewöhner Jakob , Blaumeiser Andreas , Ploeger Carolin , Haack Tobias Bernd , Tay Timothy Kwang Yong , Kelemen Olga , Pauli Thomas , Kirchner Martina , Kluck Klaus , Ott Alexander , Renner Marcus , Admard Jakob , Gschwind Axel , Lassmann Silke , Kestler Hans , Fend Falko , Illert Anna Lena , Werner Martin , Möller Peter , Seufferlein Thomas Theodor Werner , Malek Nisar , Schirmacher Peter , Fröhling Stefan , Kazdal Daniel , Budczies Jan , Stenzinger Albrecht
Published: October 2023

A growing number of druggable targets and national initiatives for precision oncology necessitate broad genomic profiling for many cancer patients. Whole exome sequencing (WES) offers unbiased analysis of the entire coding sequence, segmentation-based detection of copy number alterations (CNAs), and accurate determination of complex biomarkers including tumor mutational burden (TMB), homologous recombination repair deficiency (HRD), and microsatellite instability (MSI). To assess the inter-institution variability of clinical WES, we performed a comparative pilot study between German Centers of Personalized Medicine (ZPMs) from five participating institutions. Tumor and matched normal DNA from 30 patients were analyzed using custom sequencing protocols and bioinformatic pipelines. Calling of somatic variants was highly concordant with a positive percentage agreement (PPA) between 91 and 95% and a positive predictive value (PPV) between 82 and 95% compared with a three-institution consensus and full agreement for 16 of 17 druggable targets. Explanations for deviations included low VAF or coverage, differing annotations, and different filter protocols. CNAs showed overall agreement in 76% for the genomic sequence with high wet-lab variability. Complex biomarkers correlated strongly between institutions (HRD: 0.79–1, TMB: 0.97–0.99) and all institutions agreed on microsatellite instability. This study will contribute to the development of quality control frameworks for comprehensive genomic profiling and sheds light onto parameters that require stringent standardization.
On-surface synthesis of nitrogen-doped nanographene with an [18]annulene pore on Ag(111)
Authors: Sun Kewei , Li Donglin , Kaihara Takahito , Minakata Satoshi , Takeda Youhei , Kawai Shigeki
Published: October 2023

On-surface synthesis is of importance to fabricate low dimensional carbon-based nanomaterials with atomic precision. Here, we synthesize nitrogen-doped nanographene with an [18]annulene pore and its dimer through sequential reactions of debromination, aryl–aryl coupling, cyclodehydrogenation and C–N coupling on Ag(111) from 3,12-dibromo-7,8-diaza[5]helicene. The inner structures of the products were characterized with scanning tunneling microscopy with a CO terminated tip at low temperature. Furthermore, the first four unoccupied electronic states of the nanographene were investigated with a combination of scanning tunneling spectroscopy and theoretical calculations. Except for the LUMO + 2 state observed at +1.3 V, the electronic states at 500 mV, 750 mV and 1.9 V were attributed to the superatom molecular orbitals at the [18]annulene pore, which were significantly shifted towards the Fermi level due to the hybridization with the confined surface state.
Hierarchical 2D honeycomb-like network from barium-seamed nanocapsules
Authors: Sikligar Kanishka , Kelley Steven P. , Baker Gary A. , Atwood Jerry L.
Published: October 2023

We report on a two-dimensional hexagonal “honeycomb” network comprising barium-seamed metal–organic nanocapsules involving a hexameric assembly of pyrogallol[4]arene ligands.
MoC@NC cocatalyst-modified ZnIn2S4 with strong 2D/2D hetero-interface interaction for efficient H2 evolution
Authors: Chen Lu , Wang Deling , Huang Renkun , Liang Ruowen , Zhang Linzhu , Ying Shaoming , Yan Guiyang
Published: October 2023

The MoC@NC/ZnIn2S4 photocatalyst exhibits a remarkable photocatalytic hydrogen production rate of 45.4 μmol h−1, which is 8.3 times higher than that of pristine ZnIn2S4. Its apparent quantum efficiency is 51.5% at 420 nm.
Probing site-selective doping and charge compensating defects in KMgF3: insights from a hybrid DFT study
Authors: Modak Pampa , Modak Brindaban , Arya A.
Published: October 2023

The present study explored that Eu prefers the Mg site over K in the absence of any defects, while it prefers both sites in the presence of lattice vacancy defects. All these factors contribute to the observed optical activity.
Cooperativity between H-bonds and tetrel bonds. Transformation of a noncovalent C⋯N tetrel bond to a covalent bond
Authors: Wang Xin , Li Qingzhong , Scheiner Steve
Published: October 2023

Both a long noncovalent C⋯N tetrel bond and a short covalent C–N bond between imidazole and F2CO represent minima of comparable energy, when the cooperativity of a H-bond is introduced into the system.