bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomic analysis of the urothelial cancer landscape
Authors: Dressler Franz F. , Diedrichs Falk , Sabtan Deema , Hinrichs Sofie , Krisp Christoph , Gemoll Timo , Hennig Martin , Mackedanz Paulina , Schlotfeldt Mareile , Voß Hannah , Offermann Anne , Kirfel Jutta , Roesch Marie C. , Struck Julian P. , Kramer Mario W. , Merseburger Axel S. , Gratzke Christian , Schoeb Dominik S. , Miernik Arkadiusz , Schlüter Hartmut , Wetterauer Ulrich , Zubarev Roman , Perner Sven , Wolf Philipp , Végvári Ákos 
Published: May 2024

AbstractUrothelial bladder cancer (UC) has a wide tumor biological spectrum with challenging prognostic stratification and relevant therapy-associated morbidity. Most molecular classifications relate only indirectly to the therapeutically relevant protein level. We improve the pre-analytics of clinical samples for proteome analyses and characterize a cohort of 434 samples with 242 tumors and 192 paired normal mucosae covering the full range of UC. We evaluate sample-wise tumor specificity and rank biomarkers by target relevance. We identify robust proteomic subtypes with prognostic information independent from histopathological groups. In silico drug prediction suggests efficacy of several compounds hitherto not in clinical use. Both in silico and in vitro data indicate predictive value of the proteomic clusters for these drugs. We underline that proteomics is relevant for personalized oncology and provide abundance and tumor specificity data for a large part of the UC proteome (www.cancerproteins.org).
Whole-soil warming leads to substantial soil carbon emission in an alpine grassland
Authors: Chen Ying , Qin Wenkuan , Zhang Qiufang , Wang Xudong , Feng Jiguang , Han Mengguang , Hou Yanhui , Zhao Hongyang , Zhang Zhenhua , He Jin-Sheng , Torn Margaret S. , Zhu Biao 
Published: May 2024

AbstractThe sensitivity of soil organic carbon (SOC) decomposition in seasonally frozen soils, such as alpine ecosystems, to climate warming is a major uncertainty in global carbon cycling. Here we measure soil CO2 emission during four years (2018–2021) from the whole-soil warming experiment (4 °C for the top 1 m) in an alpine grassland ecosystem. We find that whole-soil warming stimulates total and SOC-derived CO2 efflux by 26% and 37%, respectively, but has a minor effect on root-derived CO2 efflux. Moreover, experimental warming only promotes total soil CO2 efflux by 7-8% on average in the meta-analysis across all grasslands or alpine grasslands globally (none of these experiments were whole-soil warming). We show that whole-soil warming has a much stronger effect on soil carbon emission in the alpine grassland ecosystem than what was reported in previous warming experiments, most of which only heat surface soils.
Primate retina trades single-photon detection for high-fidelity contrast encoding
Authors: Kilpeläinen Markku , Westö Johan , Tiihonen Jussi , Laihi Anton , Takeshita Daisuke , Rieke Fred , Ala-Laurila Petri 
Published: May 2024

AbstractHow the spike output of the retina enables human visual perception is not fully understood. Here, we address this at the sensitivity limit of vision by correlating human visual perception with the spike outputs of primate ON and OFF parasol (magnocellular) retinal ganglion cells in tightly matching stimulus conditions. We show that human vision at its ultimate sensitivity limit depends on the spike output of the ON but not the OFF retinal pathway. Consequently, nonlinear signal processing in the retinal ON pathway precludes perceptual detection of single photons in darkness but enables quantal-resolution discrimination of differences in light intensity.
ABA-mediated regulation of rice grain quality and seed dormancy via the NF-YB1-SLRL2-bHLH144 Module
Authors: Wang Jin-Dong , Wang Jing , Huang Li-Chun , Kan Li-Jun , Wang Chu-Xin , Xiong Min , Zhou Peng , Zhou Li-Hui , Chen Chen , Zhao Dong-Sheng , Fan Xiao-Lei , Zhang Chang-Quan , Zhou Yong , Zhang Lin , Liu Qiao-Quan , Li Qian-Feng 
Published: May 2024

AbstractAbscisic acid (ABA) plays a crucial role in promoting plant stress resistance and seed dormancy. However, how ABA regulates rice quality remains unclear. This study identifies a key transcription factor SLR1-like2 (SLRL2), which mediates the ABA-regulated amylose content (AC) of rice. Mechanistically, SLRL2 interacts with NF-YB1 to co-regulate Wx, a determinant of AC and rice quality. In contrast to SLR1, SLRL2 is ABA inducible but insensitive to GA. In addition, SLRL2 exhibits DNA-binding activity and directly regulates the expression of Wx, bHLH144 and MFT2. SLRL2 competes with NF-YC12 for interaction with NF-YB1. NF-YB1 also directly represses SLRL2 transcription. Genetic validation supports that SLRL2 functions downstream of NF-YB1 and bHLH144 in regulating rice AC. Thus, an NF-YB1-SLRL2-bHLH144 regulatory module is successfully revealed. Furthermore, SLRL2 regulates rice dormancy by modulating the expression of MFT2. In conclusion, this study revealed an ABA-responsive regulatory cascade that functions in both rice quality and seed dormancy.
Pixel-wise programmability enables dynamic high-SNR cameras for high-speed microscopy
Authors: Zhang Jie , Newman Jonathan , Wang Zeguan , Qian Yong , Feliciano-Ramos Pedro , Guo Wei , Honda Takato , Chen Zhe Sage , Linghu Changyang , Etienne-Cummings Ralph , Fossum Eric , Boyden Edward , Wilson Matthew 
Published: May 2024

AbstractHigh-speed wide-field fluorescence microscopy has the potential to capture biological processes with exceptional spatiotemporal resolution. However, conventional cameras suffer from low signal-to-noise ratio at high frame rates, limiting their ability to detect faint fluorescent events. Here, we introduce an image sensor where each pixel has individually programmable sampling speed and phase, so that pixels can be arranged to simultaneously sample at high speed with a high signal-to-noise ratio. In high-speed voltage imaging experiments, our image sensor significantly increases the output signal-to-noise ratio compared to a low-noise scientific CMOS camera (~2–3 folds). This signal-to-noise ratio gain enables the detection of weak neuronal action potentials and subthreshold activities missed by the standard scientific CMOS cameras. Our camera with flexible pixel exposure configurations offers versatile sampling strategies to improve signal quality in various experimental conditions.
Acute and post-acute respiratory complications of SARS-CoV-2 infection: population-based cohort study in South Korea and Japan
Authors: Choi Yujin , Kim Hyeon Jin , Park Jaeyu , Lee Myeongcheol , Kim Sunyoung , Koyanagi Ai , Smith Lee , Kim Min Seo , Rahmati Masoud , Lee Hayeon , Kang Jiseung , Yon Dong Keon 
Published: May 2024

AbstractConsidering the significant burden of post-acute COVID-19 conditions among patients infected with SARS-CoV-2, we aimed to identify the risk of acute respiratory complications or post-acute respiratory sequelae. A binational population-based cohort study was conducted to analyze the risk of acute respiratory complications or post-acute respiratory sequelae after SARS-CoV-2 infection. We used a Korean nationwide claim-based cohort (K-COV-N; n = 2,312,748; main cohort) and a Japanese claim-based cohort (JMDC; n = 3,115,606; replication cohort) after multi-to-one propensity score matching. Among 2,312,748 Korean participants (mean age, 47.2 years [SD, 15.6]; 1,109,708 [48.0%] female), 17.1% (394,598/2,312,748) were infected with SARS-CoV-2. The risk of acute respiratory complications or post-acute respiratory sequelae is significantly increased in people with SARS-CoV-2 infection compared to the general population (acute respiratory complications: HR, 8.06 [95% CI, 6.92-9.38]; post-acute respiratory sequelae: 1.68 [1.62-1.75]), and the risk increased with increasing COVID-19 severity. We identified COVID-19 vaccination as an attenuating factor, showing a protective association against acute or post-acute respiratory conditions. Furthermore, while the excess post-acute risk diminished with time following SARS-CoV-2 infection, it persisted beyond 6 months post-infection. The replication cohort showed a similar pattern in the association. Our study comprehensively evaluates respiratory complications in post-COVID-19 conditions, considering attenuating factors such as vaccination status, post-infection duration, COVID-19 severity, and specific respiratory conditions.
Potential decoupling of CO2 and Hg uptake process by global vegetation in the 21st century
Authors: Yuan Tengfei , Huang Shaojian , Zhang Peng , Song Zhengcheng , Ge Jun , Miao Xin , Wang Yujuan , Pang Qiaotong , Peng Dong , Wu Peipei , Shao Junjiong , Zhang Peipei , Wang Yabo , Guo Hongyan , Guo Weidong , Zhang Yanxu 
Published: May 2024

AbstractMercury (Hg), a potent neurotoxin posing risks to human health, is cycled through vegetation uptake, which is susceptible to climate change impacts. However, the extent and pattern of these impacts are largely unknown, obstructing predictions of Hg’s fate in terrestrial ecosystems. Here, we evaluate the effects of climate change on vegetation elemental Hg [Hg(0)] uptake using a state-of-the-art global terrestrial Hg model (CLM5-Hg) that incorporates plant physiology. In a business-as-usual scenario, the terrestrial Hg(0) sink is predicted to decrease by 1870 Mg yr−1 in 2100, that is ~60% lower than the present-day condition. We find a potential decoupling between the trends of CO2 assimilation and Hg(0) uptake process by vegetation in the 21st century, caused by the decreased stomatal conductance with increasing CO2. This implies a substantial influx of Hg into aquatic ecosystems, posing an elevated threat that warrants consideration during the evaluation of the effectiveness of the Minamata Convention.
Targeting neddylation and sumoylation in chemoresistant triple negative breast cancer
Authors: Powell Reid T. , Rinkenbaugh Amanda L. , Guo Lei , Cai Shirong , Shao Jiansu , Zhou Xinhui , Zhang Xiaomei , Jeter-Jones Sabrina , Fu Chunxiao , Qi Yuan , Baameur Hancock Faiza , White Jason B. , Stephan Clifford , Davies Peter J. , Moulder Stacy , Symmans W. Fraser , Chang Jeffrey T. , Piwnica-Worms Helen 
Published: May 2024

AbstractTriple negative breast cancer (TNBC) accounts for 15–20% of breast cancer cases in the United States. Systemic neoadjuvant chemotherapy (NACT), with or without immunotherapy, is the current standard of care for patients with early-stage TNBC. However, up to 70% of TNBC patients have significant residual disease once NACT is completed, which is associated with a high risk of developing recurrence within two to three years of surgical resection. To identify targetable vulnerabilities in chemoresistant TNBC, we generated longitudinal patient-derived xenograft (PDX) models from TNBC tumors before and after patients received NACT. We then compiled transcriptomes and drug response profiles for all models. Transcriptomic analysis identified the enrichment of aberrant protein homeostasis pathways in models from post-NACT tumors relative to pre-NACT tumors. This observation correlated with increased sensitivity in vitro to inhibitors targeting the proteasome, heat shock proteins, and neddylation pathways. Pevonedistat, a drug annotated as a NEDD8-activating enzyme (NAE) inhibitor, was prioritized for validation in vivo and demonstrated efficacy as a single agent in multiple PDX models of TNBC. Pharmacotranscriptomic analysis identified a pathway-level correlation between pevonedistat activity and post-translational modification (PTM) machinery, particularly involving neddylation and sumoylation targets. Elevated levels of both NEDD8 and SUMO1 were observed in models exhibiting a favorable response to pevonedistat compared to those with a less favorable response in vivo. Moreover, a correlation emerged between the expression of neddylation-regulated pathways and tumor response to pevonedistat, indicating that targeting these PTM pathways may prove effective in combating chemoresistant TNBC.
Perinatal thymic-derived CD8αβ-expressing γδ T cells are innate IFN-γ producers that expand in IL-7R–STAT5B-driven neoplasms
Authors: Sumaria Nital , Fiala Gina J. , Inácio Daniel , Curado-Avelar Marta , Cachucho Ana , Pinheiro Rúben , Wiesheu Robert , Kimura Shunsuke , Courtois Lucien , Blankenhaus Birte , Darrigues Julie , Suske Tobias , Almeida Afonso R. M. , Minguet Susana , Asnafi Vahid , Lhermitte Ludovic , Mullighan Charles G. , Coffelt Seth B. , Moriggl Richard , Barata João T. , Pennington Daniel J. , Silva-Santos Bruno 
Published: May 2024

AbstractThe contribution of γδ T cells to immune responses is associated with rapid secretion of interferon-γ (IFN-γ). Here, we show a perinatal thymic wave of innate IFN-γ-producing γδ T cells that express CD8αβ heterodimers and expand in preclinical models of infection and cancer. Optimal CD8αβ+ γδ T cell development is directed by low T cell receptor signaling and through provision of interleukin (IL)-4 and IL-7. This population is pathologically relevant as overactive, or constitutive, IL-7R–STAT5B signaling promotes a supraphysiological accumulation of CD8αβ+ γδ T cells in the thymus and peripheral lymphoid organs in two mouse models of T cell neoplasia. Likewise, CD8αβ+ γδ T cells define a distinct subset of human T cell acute lymphoblastic leukemia pediatric patients. This work characterizes the normal and malignant development of CD8αβ+ γδ T cells that are enriched in early life and contribute to innate IFN-γ responses to infection and cancer.
In silico-designed antimicrobial peptide targeting MRSA and E. coli with antibacterial and antibiofilm actions
Authors: Madni Hafsa , Mohamed Hana A. , Abdelrahman Hana Adel Mohamed , dos Santos-Silva Carlos André , Benko-Iseppon Ana Maria , Khatir Zenaba , Eltai Nahla O. , Mohamed Nura A. , Crovella Sergio 
Published: May 2024

AbstractAntibiotic resistance is a paramount global health issue, with numerous bacterial strains continually fortifying their resistance against diverse antibiotics. This surge in resistance levels primarily stems from the overuse and misuse of antibiotics in human, animal, and environmental contexts. In this study, we advocate for exploring alternative molecules exhibiting antibacterial properties to counteract the escalating antibiotic resistance. We identified a synthetic antimicrobial peptide (AMP) by using computational search in AMP public databases and further engineering through molecular docking and dynamics. Microbiological evaluation, cytotoxicity, genotoycity, and hemolysis experiments were then performed. The designed AMP underwent rigorous testing for antibacterial and antibiofilm activities against Methicillin-Resistant Staphylococcus aureus (MRSA) and Escherichia coli (E. coli), representing gram-positive and gram-negative bacteria, respectively. Subsequently, the safety profile of the AMP was assessed in vitro using human fibroblast cells and a human blood sample. The selected AMP demonstrated robust antibacterial and antibiofilm efficacy against MRSA and E. coli, with an added assurance of non-cytotoxicity and non-genotoxicity towards human fibroblasts. Also, the AMP did not demonstrate any hemolytic activity. Our findings emphasize the considerable promise of the AMP as a viable alternative antibacterial agent, showcasing its potential to combat antibiotic resistance effectively.
The chemical profiles and cytotoxicity of gaharu bouya oil from Borneo’s Gonystylus bancanus wood
Authors: Oktavianawati Ika , Santoso Mardi , Fatmawati Sri 
Published: May 2024

AbstractGaharu bouya oil obtained from distillation of the woods from Gonystylus genus has attracted essential oil industry interest. However, the information about gaharu bouya essential oil profile is limited. The presence of Gonystylus species is also critically endangered on the IUCN Red List. Therefore, exploring the -omics profiles of Gonystylus bancanus, a native plant from Borneo Island, is important for Indonesia to conserve the population. This research investigated the metabolite profiling of G. bancanus oil, especially the volatile components of its essential oils. Distillations were performed in two technical ways: hydrodistillation on a laboratory scale and steam distillation on an industrial scale. According to LC–MS and GC–MS profiles, both essential oils displayed similar chemical compositions. This article also discusses the similarity of the chemical contents of gaharu bouya oil and agarwood oil from the gaharu superior type (Aquilaria) to support the value of the oil. This research also investigated the cytotoxicity of gaharu bouya oil against three cell lines: HeLa, MCF-7, and HT-29.
Balance function in critical illness survivors and evaluation of psychometric properties of the Mini-BESTest
Authors: Egger Marion , Finsterhölzl Melanie , Buetikofer Alisa , Wippenbeck Franziska , Müller Friedemann , Jahn Klaus , Bergmann Jeannine 
Published: May 2024

AbstractCritical illness survivors commonly face impairments, such as intensive care unit-acquired weakness (ICUAW) which is characterized by muscle weakness and sensory deficits. Despite these symptoms indicating potential balance deficits, systematic investigations and validated assessments are lacking. Therefore, we aimed to assess balance function using the Mini-BESTest, evaluate its psychometric properties, and identify associated variables. Balance was assessed post-ICU discharge (V1) and at discharge from inpatient neurorehabilitation (V2) in patients with ≥ 5 days of invasive ventilation. Mini-BESTest measurement characteristics were evaluated in an ambulatory subgroup. A multiple linear regression was conducted. The prospective cohort study comprised 250 patients (34% female, 62 ± 14 years, median ICU stay 55 days). Median Mini-BESTest scores improved significantly from V1 (5 (IQR 0–15)) to V2 (18.5 (10–23)) with a large effect size. Excellent inter-rater and test–retest reliabilities of the Mini-BESTest were observed (ICC = 0.981/0.950). Validity was demonstrated by a very high correlation with the Berg Balance Scale (ρ = 0.90). No floor or ceiling effects were detected. Muscle strength, cognitive function, cerebral disease, critical illness polyneuropathy/myopathy, and depression were significantly associated with balance. Despite significant improvements during the rehabilitation period, balance disorders were prevalent in critical illness survivors. Ongoing therapy is recommended. Due to its excellent psychometric properties, the Mini-BESTest is suitable for use in critical illness survivors.Registration: The study was registered at the German Clinical Trials Register (DRKS00021753, date of registration: 2020-09-03).
Comparing researchers’ degree of dichotomous thinking using frequentist versus Bayesian null hypothesis testing
Authors: Muradchanian Jasmine , Hoekstra Rink , Kiers Henk , Fife Dustin , van Ravenzwaaij Don 
Published: May 2024

Abstract
A large amount of scientific literature in social and behavioural sciences bases their conclusions on one or more hypothesis tests. As such, it is important to obtain more knowledge about how researchers in social and behavioural sciences interpret quantities that result from hypothesis test metrics, such as p-values and Bayes factors. In the present study, we explored the relationship between obtained statistical evidence and the degree of belief or confidence that there is a positive effect in the population of interest. In particular, we were interested in the existence of a so-called cliff effect: A qualitative drop in the degree of belief that there is a positive effect around certain threshold values of statistical evidence (e.g., at p = 0.05). We compared this relationship for p-values to the relationship for corresponding degrees of evidence quantified through Bayes factors, and we examined whether this relationship was affected by two different modes of presentation (in one mode the functional form of the relationship across values was implicit to the participant, whereas in the other mode it was explicit). We found evidence for a higher proportion of cliff effects in p-value conditions than in BF conditions (N = 139), but we did not get a clear indication whether presentation mode had an effect on the proportion of cliff effects.

Protocol registration
The stage 1 protocol for this Registered Report was accepted in principle on 2 June 2023. The protocol, as accepted by the journal, can be found at: https://doi.org/10.17605/OSF.IO/5CW6P.
FOXP3 splice variant expression in males and females in healthy populations and in kidney transplant recipients
Authors: Saleh Qais W. , Mohammadnejad Afsaneh , Tepel Martin 
Published: May 2024

AbstractThe forkhead box P3 (FOXP3) transcript is essential for tolerance of alloantigens. Here, we describe the expression of FOXP3 mRNA variants in healthy females and males, and in kidney transplant recipients (KTR). We measured FOXP3 in peripheral blood mononuclear cells from healthy kidney donors (N = 101), and in blood from KTRs (N = 248) before and after transplantation. FOXP3 was measured with quantitative polymerase chain reaction, and differentiated between pre-mature mRNA FOXP3, Total mature FOXP3, FOXP3 in which exon two is spliced, and full length FOXP3. We found similar levels of FOXP3 in healthy female and male kidney donors. We confirmed this result in a publicly available cohort (N = 33) of healthy individuals (GSE97475). Homogenously, female and male KTR FOXP3 levels were similar pre-transplantation, one day post-transplantation and 29 days post-transplantation. This may suggest that kidney transplantation and related immunosuppressive treatments do not influence FOXP3 expression differently in females and males. Finally, fold difference analysis revealed that KTRs express lower levels of mature FOXP3 and higher levels of pre-mature FOXP3 mRNA pre-transplant compared to healthy individuals. This finding may suggest higher pre-mRNA synthesis, lower pre-mRNA degradation, lower spliceosome efficiency or higher degradation of mature FOXP3 mRNA in kidney transplant candidates.
The development strategies of amateur table tennis matches in China based on the SWOT-AHP model: a case study in Shanghai
Authors: Yi Qing , Liu Zuhong , Liu Xutao , Wang Yidan , Li Rongzhi 
Published: May 2024

AbstractGiven the significance of amateur sports matches in health promotion and city culture construction. It is essential to systematically analyze the organizational mode of city amateur matches and propose development strategies. This study aimed to investigate the sustainable development strategies for city amateur matches in China. This study adopted a hybrid model of combined SWOT and the AHP analysis, using the Shanghai City Amateur Table Tennis Matches (ATTM) as a case study. Results showed that 20 factors of the SWOT analysis were included, and the ranking of weights of the SWOT group are Strengths, Opportunities, Weaknesses and Threats, respectively, and the strategic vector (θ, ρ) are (74.21°, 0.5861). ATTM should adopt the S–O pioneering strategy and leverages its advantages and opportunities to promote further development. The findings indicate that ATTM with advanced organizational mode, has good internal strengths and external opportunities, which can enlighten the development of amateur table tennis matches for other regions and countries. Future research should apply the hybrid model to a broader range of events and conduct comparative analyses across countries and regions.