bluuebunny/crossref_metadata_2025 huggingface dataset:
A temporal analysis of the consequences of the drought regime on the water footprint of agriculture in the Guadalupe Valley, Mexico
Authors: Novoa Vanessa , Rojas Carolina , Rojas Octavio , Ahumada-Rudolph Ramón , Moreno-Santoyo Rebeca
Published: March 2024

Changes in water availability have a substantial impact on the sustainability and maintenance of agriculture, with water footprint (WF) being a robust methodology to assess these transformations. The Guadalupe Valley is one of the places with the highest agricultural production in Mexico. Despite its semi-arid climatic conditions, it provides high-quality crops that are well-positioned in the world. The historical trend of rainfall and temperatures between 1987 and 2017 was analyzed to identify climatic patterns in the territory. Through the calculations of the water footprint of Grapevine and Olive crops, the sensitivity of the crops to recurrent water deficit and their adaptation in their yields to drought episodes was identified. The reduction in precipitation and occurrence of extreme temperatures have contributed significantly towards augmenting crop evapotranspiration and, consequently, intensifying crop irrigation demands. As a result, there has been an apparent increase in the consumption of WFagricultural since 2007. Thus, the period of highest WFagricultural consumption was 2014 (Extremely dry), as opposed to 2011 (Very wet). In particular, the lowest WFgreen consumptions were observed in extremely dry years, that is, > 20% of the WFagricultural intensifying drought events. Therefore, these periods were compensated with higher uses of WFblue and WFgray, which are inversely correlated with precipitation, where vine crops consume 73% more WFagricultural compared to olive plantations, showing greater interannual variability. These results contribute to analyzing the temporal evolution of water consumption for agriculture, providing a basis for rational water use strategies.
Investigating the spatiotemporal associations between meteorological conditions and air pollution in the federal state Baden-Württemberg (Germany)
Authors: Hoffmann Leona , Gilardi Lorenza , Schmitz Marie-Therese , Erbertseder Thilo , Bittner Michael , Wüst Sabine , Schmid Matthias , Rittweger Jörn
Published: March 2024

When analyzing health data in relation to environmental stressors, it is crucial to identify which variables to include in the statistical model to exclude dependencies among the variables. Four meteorological parameters: temperature, ultraviolet radiation, precipitation, and vapor pressure and four outdoor air pollution parameters: ozone ($$\text{O}_3$$

O
3

), nitrogen dioxide ($$\text{NO}_2$$

NO
2

), particulate matter ($$PM_{2.5}$$

P

M

2.5

, $$PM_{10}$$

P

M
10

) were studied on a daily basis for Baden-Württemberg (Germany). This federal state covers urban and rural compartments including mountainous and river areas. A temporal and spatial analysis of the internal relationships was performed among the variables using (a) cross-correlations, both on the grand ensemble of data as well as within subsets, and (b) the Local Indications of Spatial Association (LISA) method. Meteorological and air pollution variables were strongly correlated within and among themselves in time and space. We found a strong interaction between nitrogen dioxide and ozone, with correlation coefficients varying over time. The coefficients ranged from negative correlations in January (−0.84), April (−0.47), and October (−0.54) to a positive correlation in July (0.45). The cross-correlation plot showed a noticeable change in the correlation direction for $$\text{O}_3$$

O
3

and $$\text{NO}_2$$

NO
2

. Spatially, $$\text{NO}_2$$

NO
2

, $$PM_{2.5}$$

P

M

2.5

, and $$PM_{10}$$

P

M
10

concentrations were significantly higher in urban than rural regions. For $$\text{O}_3$$

O
3

, this effect was reversed. A LISA analysis confirmed distinct hot and cold spots of environmental stressors. This work examined and quantified the spatio-temporal relationship between air pollution and meteorological conditions and recommended which variables to prioritize for future health impact analyses. The results found are in line with the underlying physico-chemical atmospheric processes. It also identified postal code areas with dominant environmental stressors for further studies.
Initial response and 12-month outcomes after commencing dexamethasone or vascular endothelial growth factor inhibitors for retinal vein occlusion in the FRB registry
Authors: Garay-Aramburu Gonzaga , Hunt Adrian , Arruabarrena Carolina , Mehta Hemal , Invernizzi Alessandro , Gabrielle Pierre-Henry , Guillaumie Tremeur , Wolff Benjamin , Gillies Mark C. , Zarranz-Ventura Javier
Published: March 2024

To compare baseline characteristics, initial response and 12-month efficacy and safety outcomes in eyes with branch and central retinal vein occlusion (BRVO and CRVO) treated with dexamethasone implants (DEX) or anti-vascular endothelial growth factor (anti-VEGF) we performed a multi-centre, retrospective and observational study using Fight Retinal Blindness! Registry. Of 725 eligible eyes, 10% received DEX initially with very frequent adjunctive anti-VEGF (BRVO-DEX 49%, CRVO-DEX 60%). The primary outcome of mean adjusted change in VA at 12 months with DEX and anti-VEGF initiated groups were not statistically significantly different (BRVO: DEX + 6.7, anti-VEGF + 10.6 letters; CRVO: DEX + 2.8, anti-VEGF + 6.8 letters). DEX initiated eyes had fewer injections and visits than anti-VEGF initiated eyes. The BRVO-DEX eyes had greater initial mean changes in VA and central subfield thickness (CST) and achieved inactivity sooner than BRVO-anti-VEGF eyes. The mean CST after the first three months was above 350 μm in all but the BRVO-anti-VEGF group, suggesting undertreatment. In routine care DEX is uncommonly used when available as initial treatment of BRVO and CRVO requiring supplemental anti-VEGF within the first year. The 12-month outcomes were similar, but DEX initiated eyes had fewer injections and visits but more episodes of raised IOP Vs those starting anti-VEGF.
Autophagy as a new player in the regulation of clock neurons physiology of Drosophila melanogaster
Authors: Szypulski Kornel , Tyszka Aleksandra , Pyza Elzbieta , Damulewicz Milena
Published: March 2024

Axonal terminals of the small ventral lateral neurons (sLNvs), the circadian clock neurons of Drosophila, show daily changes in their arborization complexity, with many branches in the morning and their shrinkage during the night. This complex phenomenon is precisely regulated by several mechanisms. In the present study we describe that one of them is autophagy, a self-degradative process, also involved in changes of cell membrane size and shape. Our results showed that autophagosome formation and processing in PDF-expressing neurons (both sLNv and lLNv) are rhythmic and they have different patterns in the cell bodies and terminals. These rhythmic changes in the autophagy activity seem to be important for neuronal plasticity. We found that autophagosome cargos are different during the day and night, and more proteins involved in membrane remodeling are present in autophagosomes in the morning. In addition, we described for the first time that Atg8-positive vesicles are also present outside the sLNv terminals, which suggests that secretory autophagy might be involved in regulating the clock signaling network. Our data indicate that rhythmic autophagy in clock neurons affect the pacemaker function, through remodeling of terminal membrane and secretion of specific proteins from sLNvs.
Targeting the NTSR2/TrkB oncogenic pathway in chronic lymphocytic leukemia
Authors: Ikhlef Léa , Yassine May , Chandouri Boutaîna , Rivière Léa , Naves Thomas , Dmytruk Natalya , Gachard Nathalie , Jauberteau Marie-Odile , Gallet Paul-François
Published: March 2024

Current therapies that target the B-cell receptor pathway or the inhibition of anti-apoptotic proteins do not prevent the progressive forms of chronic lymphocytic leukemia (CLL), have low long-term efficacy and are subject to therapeutic resistance. Deciphering the mechanisms of leukemic cell survival and searching for new specific targets therefore remain major challenges to improve the management of this disease. It was evidenced that NTSR2 (neurotensin receptor 2), through the recruitment of TRKB (tropomyosin related kinase B), induces survival pathways in leukemic B cells. We have investigated the therapeutic potential of this protein complex as a new target. The binding domain of NTSR2 and TRKB was identified and a peptide targeting the latter was designed. The peptide binds TRKB and efficiently decreases the interaction of the two proteins. It is also effectively internalized by CLL-B cells in which it notably affects Src family kinase signaling and anti-apoptotic proteins levels. It demonstrated a cytotoxic effect both in vitro on the MEC-1 cell line and ex vivo on a cohort of 30 CLL patients. Altogether, these results underline the therapeutic potential of the NTSR2/TRKB protein complex as a target in CLL and open new perspectives for the development of targeted therapies.
A comprehensive analysis and experimental validation of TK1 in uterine corpus endometrial carcinoma
Authors: Sun Yiqing , Zhang Kaiwen , Wang Tianqi , Zhao Shuangshuang , Gao Chao , Xue Fengxia , Wang Yingmei
Published: March 2024

Uterine corpus endometrial carcinoma (UCEC) is becoming a main malignant cancer that threaten to women's health. Thymidine kinase 1 (TK1) is considering to be associated with tumorigenesis and development. Nevertheless, the function of TK1 in UCEC is still unclear. Herein, we analyzed the TK1 expression level in pan-cancer and found that TK1 was upregulated in a variety of cancers including UCEC. Patients of UCEC with high expression of TK1 were related to poor outcome. TK1 was also related to clinical stage, histologic grade and lymph node metastasis. Abnormal expression of TK1 in UCEC was related to promoter methylation while gene mutation was not frequent. TK1 and its associated genes appeared to be prominent in cell cycle and DNA replication, according to GO and KEGG analysis. Analysis of immune infiltration revealed a negative correlation between TK1 and CD8 + T cells, macrophages, and dendritic cells. In vitro experiments, TK1 knockdown resulted in the inhibition of proliferation, migration, invasion and EMT in UCEC cell lines.
Cobalt sulfide flower-like derived from metal organic frameworks on nickel foam as an electrode for fabrication of asymmetric supercapacitors
Authors: Nasiri Farzaneh , Fotouhi Lida , Shahrokhian Saeed , Zirak Mohammad
Published: March 2024

Metal–organic frameworks, as a kind of advanced nanoporous materials with metal centers and organic linkers, have been applied as promising electrode materials in energy storage devices. In this study, we are successfully prepared cobalt sulfide nanosheets (CoS) derived from the metal–organic framework on nickel foam (NF). The prepared electrodes are characterized by scanning electron microscopy, transmission electron microscopy, X-ray diffraction, X-ray photoelectron spectroscopy, energy-dispersive X-ray spectroscopy, Brunauer–Emmett–Teller and Barrett-Joyner-Halenda and electrochemical methods like voltammetry, galvanostatic charge–discharge curve and electrochemical impedance spectroscopy. The CoS/NF electrode demonstrates a high specific capacity of 377.5 mA h g−1 (1359 C g−1) at the current density of 2 A g−1, considerable rate performance and excellent durability (89.4% after 4000 cycles). A hybrid supercapacitor is assembled using CoS/NF as the positive electrode and activated carbon as the negative electrode, it shows a high energy density of 57.4 W h kg−1 at a power density of 405.2 W kg−1. The electrochemical results suggest that the CoS nanosheet arrays would possess excellent potential for applications in energy storage devices.
Conclusiveness, readability and textual characteristics of plain language summaries from medical and non-medical organizations: a cross-sectional study
Authors: Bralić Nensi , Mijatović Antonija , Marušić Ana , Buljan Ivan
Published: March 2024

This cross-sectional study compared plain language summaries (PLSs) from medical and non-medical organizations regarding conclusiveness, readability and textual characteristics. All Cochrane (medical PLSs, n = 8638) and Campbell Collaboration and International Initiative for Impact Evaluation (non-medical PLSs, n = 163) PLSs of latest versions of systematic reviews published until 10 November 2022 were analysed. PLSs were classified into three conclusiveness categories (conclusive, inconclusive and unclear) using a machine learning tool for medical PLSs and by two experts for non-medical PLSs. A higher proportion of non-medical PLSs were conclusive (17.79% vs 8.40%, P < 0.0001), they had higher readability (median number of years of education needed to read the text with ease 15.23 (interquartile range (IQR) 14.35 to 15.96) vs 15.51 (IQR 14.31 to 16.77), P = 0.010), used more words (median 603 (IQR 539.50 to 658.50) vs 345 (IQR 202 to 476), P < 0.001). Language analysis showed that medical PLSs scored higher for disgust and fear, and non-medical PLSs scored higher for positive emotions. The reason for the observed differences between medical and non-medical fields may be attributed to the differences in publication methodologies or disciplinary differences. This approach to analysing PLSs is crucial for enhancing the overall quality of PLSs and knowledge translation to the general public.
The association between platelet-related parameters and nonalcoholic fatty liver disease in a metabolically healthy nonobese population
Authors: Choe Eun Kyung , Kang Hae Yeon
Published: March 2024

Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disease characterized by subclinical inflammation and is related to obesity and metabolic syndrome (MS), but it is also frequently observed in nonobese populations. We aimed to evaluate the relationship between the white blood cell count-to-mean platelet volume ratio (WBC/MPV), platelet-to-lymphocyte count ratio (PLR) and lymphocyte-monocyte ratio (LMR) in association with NAFLD, considering the presence of obesity and MS. Additionally, we aimed to investigate whether these parameters exhibited similar correlations in metabolic dysfunction-associated steatotic liver disease (MASLD) as observed in NAFLD. This cross-sectional study included subjects who underwent a comprehensive health evaluation, including blood tests and abdominal ultrasonography. Subgroup analyses were conducted based on obesity and MS. Out of a total 5929 subjects (3271 males, mean age 49.7 ± 10.6 years), 2253 (38.0%) had NAFLD. WBC/MPV was significantly higher, and PLR was significantly lower in subjects with NAFLD. In the analysis restricted to the nonobese (BMI < 25 kg/m2) population without MS, both WBC/MPV and PLR were independently associated with NAFLD: WBC/MPV (adjusted OR 3.366; 95% CI 2.238–5.066) and PLR (adjusted OR 0.997; 95% CI 0.996–0.999). When assessing the risk of NAFLD based on the WBC/MPV and PLR quartiles, the adjusted OR and 95% CI for the lowest quartile compared to the highest were 2.055 (95% CI 1.626–2.602) for WBC/MPV and 0.660 (95% CI 0.523–0.832) for PLR in the nonobese, metabolically healthy group. The levels of WBC/MPV and PLR were independently associated with NAFLD. Furthermore, in MASLD, an association with WBC/MPV, PLR and LMR was identified, similar to the results observed in NAFLD, even after adjusting for confounding variables. In conclusion, the present study demonstrated a significant association between NAFLD and platelet-related parameters, especially in nonobese, metabolically healthy subjects.
Mapping the seamless hourly surface visibility in China: a real-time retrieval framework using a machine-learning-based stacked ensemble model
Authors: Zhang Xutao , Gui Ke , Zeng Zhaoliang , Fei Ye , Li Lei , Zheng Yu , Peng Yue , Liu Yurun , Shang Nanxuan , Zhao Hengheng , Yao Wenrui , Wang Hong , Wang Zhili , Wang Yaqiang , Che Huizheng , Zhang Xiaoye
Published: March 2024

Surface visibility (SV), a key indicator of atmospheric transparency, is used widely in the fields of environmental monitoring, transportation, and aviation. However, the sparse distribution and limited number of SV monitoring sites make it difficult to fulfill the urgent need for spatiotemporally seamless fine-scale monitoring. Here, we developed the operational real-time SV retrieval (RT-SVR) framework for China that incorporates information from multiple data sources, including Chinese Land Data Assimilation System meteorological data, in situ observations, and other ancillary data. Seamless hourly SV data with 6.25-km spatial resolution are available in real time via the operational RT-SVR model, which was built using a two-layer stacked ensemble approach that combines multiple machine learning algorithms and a deep learning module. Sample-based cross-validation of the RT-SVR model on approximately 41.3 million data pairs revealed strong robustness and high accuracy, with a Pearson correlation coefficient (R) value of 0.95 and a root mean square error (RMSE) of 3.17 km. An additional hindcast-validation experiment, performed with continuous observations obtained over one year (approximately 20.8 million data pairs), demonstrated the powerful generalization capabilities of the RT-SVR model, albeit with slight degradation in performance (R = 0.85, RMSE = 5.28 km). The seamless hourly SV data with real-time update capability enable tracking of the generation, development, and dissipation of various low-SV events (e.g., fog, haze, and dust storms) in China. The developed framework might also prove useful for quantitative retrieval of aerosol-related parameters (e.g., PM2.5, PM10, and aerosol optical depth).
Proteogenomic analysis of enriched HGSOC tumor epithelium identifies prognostic signatures and therapeutic vulnerabilities
Authors: Bateman Nicholas W. , Abulez Tamara , Soltis Anthony R. , McPherson Andrew , Choi Seongmin , Garsed Dale W. , Pandey Ahwan , Tian Chunqiao , Hood Brian L. , Conrads Kelly A. , Teng Pang-ning , Oliver Julie , Gist Glenn , Mitchell Dave , Litzi Tracy J. , Tarney Christopher M. , Crothers Barbara A. , Mhawech-Fauceglia Paulette , Dalgard Clifton L. , Wilkerson Matthew D. , Pierobon Mariaelena , Petricoin Emanuel F. , Yan Chunhua , Meerzaman Daoud , Bodelon Clara , Wentzensen Nicolas , Lee Jerry S. H. ,   The APOLLO Research Network, Makohon-Moore Sasha C. , Barakat Waleed , Zhang Xijun , Hunt Allison , Ao Wei , Lytle-Gabbin Stacey L. , Casablanca Yovanni , Hamilton Chad A. , Newell Miranda , Wells Justin , Sukumar Gauthaman , Bacikova Dagmar , Freyman John , Cohn David E. , Berchuck Andrew , Havrilesky Laura , Duska Linda , Odunsi Adekunle , Sood Anil , Brenton James , Sala Evis , Annunziata Christina , Dorigo Oliver , Nelson Brad , Cochrane Dawn R. , Moore Kathleen , Baldelli Elisa , Chen Qing-rong , Hu Ying , Fereday Sian , Traficante Nadia , DeFazio Anna , Goode Ellen L. , Huntsman David G. , Shah Sohrab , Shriver Craig D. , Phippen Neil T. , Darcy Kathleen M. , Bowtell David D. L. , Conrads Thomas P. , Maxwell G. Larry
Published: March 2024

We performed a deep proteogenomic analysis of bulk tumor and laser microdissection enriched tumor cell populations from high-grade serous ovarian cancer (HGSOC) tissue specimens spanning a broad spectrum of purity. We identified patients with longer progression-free survival had increased immune-related signatures and validated proteins correlating with tumor-infiltrating lymphocytes in 65 tumors from an independent cohort of HGSOC patients, as well as with overall survival in an additional 126 HGSOC patient cohort. We identified that homologous recombination deficient (HRD) tumors are enriched in pathways associated with metabolism and oxidative phosphorylation that we validated in independent patient cohorts. We further identified that polycomb complex protein BMI-1 is elevated in HR proficient (HRP) tumors, that elevated BMI-1 correlates with poor overall survival in HRP but not HRD HGSOC patients, and that HRP HGSOC cells are uniquely sensitive to BMI-1 inhibition.
MoS2 decorated carbon fiber yarn hybrids for the development of freestanding flexible supercapacitors
Authors: Carvalho José Tiago , Correia Afonso , Cordeiro Neusmar J. A. , Coelho João , Lourenço Sidney A. , Fortunato Elvira , Martins Rodrigo , Pereira Luís
Published: March 2024

Academic and industrial efforts have focused on developing energy storage devices for wearable and portable electronics using low-cost, scalable, and sustainable materials and approaches. In this work, commercially available stretch-broken carbon fiber yarns (SBCFYs) were hybridized with mixed phases of 1 T and 2H MoS2 nanosheets via conventional and microwave-assisted heating (CAH, MAH) without the use of binders to fabricate symmetric freestanding 1D fiber-shaped supercapacitors (FSCs). Electrochemical characterization performed in a three-electrode configuration showed promising results with specific capacitance values of 184.41 and 180.02 F·g−1, at 1 mV·s−1 for CAH and MAH, respectively. Furthermore, after performing 3000 CV cycles at 100 mV·s−1, the capacitance retention was 79.5% and 95.7%, respectively. Using these results as a reference, symmetric 1D FSCs were fabricated by pairing hybridized SBCFYs with MoS2 by MAH. The devices exhibited specific capacitances of approximately 58.60 ± 3.06 F·g−1 at 1 mV·s−1 and 54.81 ± 7.34 F·g−1 at 0.2 A·g−1 with the highest power density achieved being 15.17 W·g−1 and energy density of 5.06×10–4 Wh·g−1. In addition, five 1D FSCs were hand-stitched and connected in series onto a cotton fabric. These supercapacitors could power a temperature and humidity sensor for up to six minutes, demonstrating the practicality and versatility of the prepared 1D FSCs for powering future electronic systems.
Characterising user engagement with mHealth for chronic disease self-management and impact on machine learning performance
Authors: Duckworth Christopher , Cliffe Bethany , Pickering Brian , Ainsworth Ben , Blythin Alison , Kirk Adam , Wilkinson Thomas M. A. , Boniface Michael J.
Published: March 2024

Mobile Health (mHealth) has the potential to be transformative in the management of chronic conditions. Machine learning can leverage self-reported data collected with apps to predict periods of increased health risk, alert users, and signpost interventions. Despite this, mHealth must balance the treatment burden of frequent self-reporting and predictive performance and safety. Here we report how user engagement with a widely used and clinically validated mHealth app, myCOPD (designed for the self-management of Chronic Obstructive Pulmonary Disease), directly impacts the performance of a machine learning model predicting an acute worsening of condition (i.e., exacerbations). We classify how users typically engage with myCOPD, finding that 60.3% of users engage frequently, however, less frequent users can show transitional engagement (18.4%), becoming more engaged immediately ( < 21 days) before exacerbating. Machine learning performed better for users who engaged the most, however, this performance decrease can be mostly offset for less frequent users who engage more near exacerbation. We conduct interviews and focus groups with myCOPD users, highlighting digital diaries and disease acuity as key factors for engagement. Users of mHealth can feel overburdened when self-reporting data necessary for predictive modelling and confidence of recognising exacerbations is a significant barrier to accurate self-reported data. We demonstrate that users of mHealth should be encouraged to engage when they notice changes to their condition (rather than clinically defined symptoms) to achieve data that is still predictive for machine learning, while reducing the likelihood of disengagement through desensitisation.
Performance polyamides built on a sustainable carbohydrate core
Authors: Manker Lorenz P. , Hedou Maxime A. , Broggi Clement , Jones Marie J. , Kortsen Kristoffer , Puvanenthiran Kalaiyarasi , Kupper Yildiz , Frauenrath Holger , Marechal François , Michaud Veronique , Marti Roger , Shaver Michael P. , Luterbacher Jeremy S.
Published: March 2024

Sustainably producing plastics with performance properties across a variety of materials chemistries is a major challenge—especially considering that most performance materials use aromatic precursors that are still difficult to source sustainably. Here we demonstrate catalyst-free, melt polymerization of dimethyl glyoxylate xylose, a stabilized carbohydrate that can be synthesized from agricultural waste with 97% atom efficiency, into amorphous polyamides with performances comparable to fossil-based semi-aromatic alternatives. Despite the presence of a carbohydrate core, these materials retain their thermomechanical properties through multiple rounds of high-shear mechanical recycling and could be chemically recycled. Techno-economic and life-cycle analyses suggest selling prices close to those of nylon 66 with a reduction of global warming potential of up to 75%. This work illustrates the versatility of a carbohydrate moiety to impart performance that can compete with that of semi-aromatic polymers across two important materials chemistries.
Endothelial SMAD1/5 signaling couples angiogenesis to osteogenesis in juvenile bone
Authors: Lang Annemarie , Benn Andreas , Collins Joseph M. , Wolter Angelique , Balcaen Tim , Kerckhofs Greet , Zwijsen An , Boerckel Joel D.
Published: March 2024

Skeletal development depends on coordinated angiogenesis and osteogenesis. Bone morphogenetic proteins direct bone formation in part by activating SMAD1/5 signaling in osteoblasts. However, the role of SMAD1/5 in skeletal endothelium is unknown. Here, we found that endothelial cell-conditional SMAD1/5 depletion in juvenile mice caused metaphyseal and diaphyseal hypervascularity, resulting in altered trabecular and cortical bone formation. SMAD1/5 depletion induced excessive sprouting and disrupting the morphology of the metaphyseal vessels, with impaired anastomotic loop formation at the chondro-osseous junction. Endothelial SMAD1/5 depletion impaired growth plate resorption and, upon long-term depletion, abrogated osteoprogenitor recruitment to the primary spongiosa. Finally, in the diaphysis, endothelial SMAD1/5 activity was necessary to maintain the sinusoidal phenotype, with SMAD1/5 depletion inducing formation of large vascular loops and elevated vascular permeability. Together, endothelial SMAD1/5 activity sustains skeletal vascular morphogenesis and function and coordinates growth plate remodeling and osteoprogenitor recruitment dynamics in juvenile mouse bone.
OrgaSegment: deep-learning based organoid segmentation to quantify CFTR dependent fluid secretion
Authors: Lefferts Juliet W. , Kroes Suzanne , Smith Matthew B. , Niemöller Paul J. , Nieuwenhuijze Natascha D. A. , Sonneveld van Kooten Heleen N. , van der Ent Cornelis K. , Beekman Jeffrey M. , van Beuningen Sam F. B.
Published: March 2024

Epithelial ion and fluid transport studies in patient-derived organoids (PDOs) are increasingly being used for preclinical studies, drug development and precision medicine applications. Epithelial fluid transport properties in PDOs can be measured through visual changes in organoid (lumen) size. Such organoid phenotypes have been highly instrumental for the studying of diseases, including cystic fibrosis (CF), which is characterized by genetic mutations of the CF transmembrane conductance regulator (CFTR) ion channel. Here we present OrgaSegment, a MASK-RCNN based deep-learning segmentation model allowing for the segmentation of individual intestinal PDO structures from bright-field images. OrgaSegment recognizes spherical structures in addition to the oddly-shaped organoids that are a hallmark of CF organoids and can be used in organoid swelling assays, including the new drug-induced swelling assay that we show here. OrgaSegment enabled easy quantification of organoid swelling and could discriminate between organoids with different CFTR mutations, as well as measure responses to CFTR modulating drugs. The easy-to-apply label-free segmentation tool can help to study CFTR-based fluid secretion and possibly other epithelial ion transport mechanisms in organoids.
Cell-particles interaction – selective uptake and transport of microdiamonds
Authors: Ebrahimi Armin M. , Gawlik Wojciech , Wojciechowski Adam M. , Rajfur Zenon
Published: March 2024

Diamond particles have recently emerged as novel agents in cellular studies because of their superb biocompatibility. Their unique characteristics, including small size and the presence of fluorescent color centers, stimulate many important applications. However, the mechanism of interaction between cells and diamond particles—uptake, transport, and final localization within cells—is not yet fully understood. Herein, we show a novel, to the best of our knowledge, cell behavior wherein cells actively target and uptake diamond particles rather than latex beads from their surroundings, followed by their active transport within cells. Furthermore, we demonstrate that myosin-X is involved in cell-particle interaction, while myosin-II does not participate in particle uptake and transport. These results can have important implications for drug delivery and improve sensing methods that use diamond particles.
Mapping of facial and vocal processing in common marmosets with ultra-high field fMRI
Authors: Dureux Audrey , Zanini Alessandro , Everling Stefan
Published: March 2024

Primate communication relies on multimodal cues, such as vision and audition, to facilitate the exchange of intentions, enable social interactions, avoid predators, and foster group cohesion during daily activities. Understanding the integration of facial and vocal signals is pivotal to comprehend social interaction. In this study, we acquire whole-brain ultra-high field (9.4 T) fMRI data from awake marmosets (Callithrix jacchus) to explore brain responses to unimodal and combined facial and vocal stimuli. Our findings reveal that the multisensory condition not only intensifies activations in the occipito-temporal face patches and auditory voice patches but also engages a more extensive network that includes additional parietal, prefrontal and cingulate areas, compared to the summed responses of the unimodal conditions. By uncovering the neural network underlying multisensory audiovisual integration in marmosets, this study highlights the efficiency and adaptability of the marmoset brain in processing facial and vocal social signals, providing significant insights into primate social communication.
Carbocationoids, a concept for controlling highly reactive cationic species
Authors: Fujita Hikaru , Shimada Daichi , Kudo Jotaro , Kosha Kazuyuki , Kakuyama Satoshi , Terasaki Hiromitsu , Kunishima Munetaka
Published: March 2024

Carbocations, which are positively charged highly electrophilic intermediates, are efficacious for the direct alkylation of low-reactive nucleophiles. The utilization of carbocations in SN1 reactions relies on the activation of their precursors in the presence of a nucleophile. However, undesirable interactions between the nucleophile and the leaving group activator limit the scope of acceptable nucleophiles. Here we report a strategy to conduct SN1 reactions involving unstable carbocations in an alternative stepwise procedure, which was demonstrated by the benzylation of various neutral nucleophiles. In the first step, carbocations were accumulated in a nucleophile-free solution in the form of carbocationoids utilizing the coordinative stabilization of triazinediones. Subsequently, the addition of these solutions in the second step enabled room-temperature alkylation without the need for acidic additives. This methodology overcomes the inherent challenges of carbocations in SN1 reactions.
Statics and dynamics of non-Hermitian many-body localization
Authors: Mák József , Bhaseen M. J. , Pal Arijeet
Published: March 2024

Many-body localized phases retain memory of their initial conditions in disordered interacting systems with unitary dynamics. The stability of the localized phase due to the breakdown of unitarity is of relevance to experiment in the presence of dissipation. Here we investigate the impact of non-Hermitian perturbations on many-body localization. We focus on the interacting Hatano-Nelson model which breaks unitarity via asymmetric hopping. We explore the phase diagram for the mid-spectrum eigenstates as a function of the interaction strength and the non-Hermiticity. In contrast to the non-interacting case, our findings are consistent with a two-step approach to the localized regime. We also study the dynamics of the particle imbalance. We show that the distribution of relaxation time scales differs qualitatively between the localized and ergodic phases. Our findings suggest the possibility of an intermediate dynamical regime in disordered open systems.
Quasiprobability fluctuation theorem behind the spread of quantum information
Authors: Zhang Kun , Wang Jin
Published: March 2024

Information spreads in time. For example, correlations dissipate when the correlated system locally couples to a third party, such as the environment. This simple but important fact forms the known quantum data-processing inequality. Here we theoretically uncover the quantum fluctuation theorem behind the quantum informational inequality. The fluctuation theorem quantitatively predicts the statistics of the underlying stochastic quantum process. To fully capture the quantum nature, the fluctuation theorem established here is extended to the quasiprobability regime. We also experimentally apply an interference-based method to measure the amplitudes composing the quasiprobability and verify our established fluctuation theorem by the IBM quantum computer.
Interstitial fluid-based wearable biosensors for minimally invasive healthcare and biomedical applications
Authors: Wu Zixiong , Qiao Zheng , Chen Shuwen , Fan Shicheng , Liu Yuanchao , Qi Jiaming , Lim Chwee Teck
Published: March 2024

Interstitial fluid (ISF), a biological fluid rich in diverse biomarkers and analytes and similar to blood composition, has garnered significant attention as a valuable source of clinically relevant information. Consequently, ISF-based wearable biosensors are emerging as powerful tools for non-invasive and minimally invasive disease diagnosis, personalized medicine, and other healthcare and biomedical applications. This review provides a comprehensive overview of recent advancements in ISF-based biosensors, with a particular focus on wearable ISF sensors. We first offer insights into ISF biomarkers and sampling techniques and discuss recent ISF sensing strategies that encompass materials, fabrication methods, and sensing mechanisms. Then, we present a comprehensive overview of their applications. Finally, we address the challenges faced in this field and offer a forward-looking perspective on promising future directions.
Strain-mediated phase crossover in Ruddlesden–Popper nickelates
Authors: Cui Ting , Choi Songhee , Lin Ting , Liu Chen , Wang Gang , Wang Ningning , Chen Shengru , Hong Haitao , Rong Dongke , Wang Qianying , Jin Qiao , Wang Jia-Ou , Gu Lin , Ge Chen , Wang Can , Cheng Jin-Guang , Zhang Qinghua , Si Liang , Jin Kui-juan , Guo Er-Jia
Published: March 2024

Recent progress on the signatures of pressure-induced high-temperature superconductivity in Ruddlesden–Popper (RP) nickelates (Lan+1NinO3n+1) has attracted growing interest in both theoretical calculations and experimental efforts. The fabrication of high-quality single-crystalline RP nickelate thin films is critical for possible reducing the superconducting transition pressure and advancing applications in microelectronics in the future. In this study, we report the observations of an active phase transition in RP nickelate films induced by misfit strain. We found that RP nickelate films favor the perovskite structure (n = ∞) under tensile strains, while compressive strains stabilize the La3Ni2O7 (n = 2) phase. The selection of distinct phases is governed by the strain dependent formation energy and electronic configuration. In compressively strained La3Ni2O7, we experimentally determined the eg splitting energy is ~0.2 eV and electrons prefer to occupy in-plane orbitals. First-principles calculations unveil a robust coupling between strain effects and the valence state of Ni ions in RP nickelates, suggesting a dual driving force for the inevitable phase co-existence transition in RP nickelates. Our work underscores the sensitivity of RP nickelate formation to epitaxial strain, presenting a significant challenge in fabricating pure-phase RP nickelate films. Therefore, special attention to stacking defects and grain boundaries between different RP phases is essential when discussing the pressure-induced superconductivity in RP nickelates.
Unravelling the complex causal effects of substance use behaviours on common diseases
Authors: Xue Angli , Zhu Zhihong , Wang Huanwei , Jiang Longda , Visscher Peter M. , Zeng Jian , Yang Jian
Published: March 2024

Background

Substance use behaviours (SUB) including smoking, alcohol consumption, and coffee intake are associated with many health outcomes. However, whether the health effects of SUB are causal remains controversial, especially for alcohol consumption and coffee intake.

Methods

In this study, we assess 11 commonly used Mendelian Randomization (MR) methods by simulation and apply them to investigate the causal relationship between 7 SUB traits and health outcomes. We also combine stratified regression, genetic correlation, and MR analyses to investigate the dosage-dependent effects.

Results

We show that smoking initiation has widespread risk effects on common diseases such as asthma, type 2 diabetes, and peripheral vascular disease. Alcohol consumption shows risk effects specifically on cardiovascular diseases, dyslipidemia, and hypertensive diseases. We find evidence of dosage-dependent effects of coffee and tea intake on common diseases (e.g., cardiovascular disease and osteoarthritis). We observe that the minor allele effect of rs4410790 (the top signal for tea intake level) is negative on heavy tea intake $$({\hat{b}}_{GWAS}=-0.091,s.e.=0.007,P=4.90\times {10}^{-35})$$

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but positive on moderate tea intake $$({\hat{b}}_{GWAS}=0.034,s.e.=0.006,P=3.40\times {10}^{-8})$$

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, compared to the non-tea-drinkers.

Conclusion

Our study reveals the complexity of the health effects of SUB and informs design for future studies aiming to dissect the causal relationships between behavioural traits and complex diseases.
The BulkECexplorer compiles endothelial bulk transcriptomes to predict functional versus leaky transcription
Authors: Brash James T. , Diez-Pinel Guillermo , Colletto Chiara , Castellan Raphael F. P. , Fantin Alessandro , Ruhrberg Christiana
Published: March 2024

Transcriptomic data can be mined to understand the molecular activity of cell types. Yet, functional genes may remain undetected in RNA sequencing (RNA-seq) experiments for technical reasons, such as insufficient read depth or gene dropout. Conversely, RNA-seq experiments may detect lowly expressed mRNAs thought to be biologically irrelevant products of leaky transcription. To represent a cell type’s functional transcriptome more accurately, we propose compiling many bulk RNA-seq datasets into a compendium and applying established classification models to predict whether detected transcripts are likely products of active or leaky transcription. Here, we present the BulkECexplorer (bulk RNA-seq endothelial cell explorer) compendium of 240 bulk RNA-seq datasets from five vascular endothelial cell subtypes. This resource reports transcript counts for genes of interest and predicts whether detected transcripts are likely the products of active or leaky gene expression. Beyond its usefulness for vascular biology research, this resource provides a blueprint for developing analogous tools for other cell types.
Basal–epithelial subpopulations underlie and predict chemotherapy resistance in triple-negative breast cancer
Authors: Inayatullah Mohammed , Mahesh Arun , Turnbull Arran K , Dixon J Michael , Natrajan Rachael , Tiwari Vijay K
Published: March 2024

Triple-negative breast cancer (TNBC) is the most aggressive breast cancer subtype, characterized by extensive intratumoral heterogeneity, high metastasis, and chemoresistance, leading to poor clinical outcomes. Despite progress, the mechanistic basis of these aggressive behaviors remains poorly understood. Using single-cell and spatial transcriptome analysis, here we discovered basal epithelial subpopulations located within the stroma that exhibit chemoresistance characteristics. The subpopulations are defined by distinct signature genes that show a frequent gain in copy number and exhibit an activated epithelial-to-mesenchymal transition program. A subset of these genes can accurately predict chemotherapy response and are associated with poor prognosis. Interestingly, among these genes, elevated ITGB1 participates in enhancing intercellular signaling while ACTN1 confers a survival advantage to foster chemoresistance. Furthermore, by subjecting the transcriptional signatures to drug repurposing analysis, we find that chemoresistant tumors may benefit from distinct inhibitors in treatment-naive versus post-NAC patients. These findings shed light on the mechanistic basis of chemoresistance while providing the best-in-class biomarker to predict chemotherapy response and alternate therapeutic avenues for improved management of TNBC patients resistant to chemotherapy.
Enhanced ROS scavenging and tissue adhesive abilities in injectable hydrogels by protein modification with oligoethyleneimine
Authors: Palai Debabrata , Ohta Miho , Cetnar Iga , Taguchi Tetsushi , Nishiguchi Akihiro
Published: March 2024

Tissue adhesive using polyamine-modified gelatin and crosslinker, exhibit scavenging ability of reactive oxygen species and high tissue adhesive strength, shows potential for immunomodulatory hydrogel design, advancing minimally invasive surgery.
Leveraging machine learning models for peptide–protein interaction prediction
Authors: Yin Song , Mi Xuenan , Shukla Diwakar
Published: March 2024

A timeline showcasing the progress of machine learning and deep learning methods for peptide–protein interaction predictions.
Molecularly imprinted nanoparticles reveal regulatory scaffolding features in Pyk2 tyrosine kinase
Authors: Zanela Tania M. Palhano , Zangiabadi Milad , Zhao Yan , Underbakke Eric S.
Published: March 2024

We employ peptide-binding molecularly imprinted nanoparticles (MINPs) to probe the regulatory conformations and scaffolding interactions governing Pyk2 kinase activation.
Additive engineering with 2,8-dibromo-dibenzothiophene-S,S-dioxide enabled tin-based perovskite solar cells with 14.98% power conversion efficiency
Authors: Zhou Xianyong , Peng Wenbo , Liu Zhixin , Zhang Yong , Zhang Luozheng , Zhang Meiqing , Liu Chang , Yan Lei , Wang Xingzhu , Xu Baomin
Published: March 2024

BrDS doping can effectively inhibit the oxidation of Sn2+ and passivate grain boundary defects and point defects in tin-based perovskite films. As a result, the device achieved a PCE of 14.98% with a certified efficiency of 14.36%.
Uniform trehalose nanogels for glucagon stabilization
Authors: Puente Ellie G. , Sivasankaran Rajalakshmi P. , Vinciguerra Daniele , Yang Jane , Lower Haillie-Ann C. , Hevener Andrea L. , Maynard Heather D.
Published: March 2024

Uniform trehalose nanogels improve stability and solubility of glucagon in aqueous solution, particularly useful for long term storage at cold temperatures. Additionally, the glucagon nanogels were nontoxic, nonhemolytic, and efficacious in vitro.
Harnessing osteoimmunity to treat peri-implant inflammatory osteolysis
Authors: Chen Zijun , Wang Yuxi , Yang Rui , Liu Xiangdong , Zhang Guanhua , Lu Qun , Ma Wei , Song Yingliang
Published: March 2024

Osteoimmunity is an interactive schema by which organisms maintain bone homeostasis.
Entanglement of cation ordering and manipulation of the magnetic properties through a temperature-controlled topotactic interface reaction in nanocomposite perovskite oxides
Authors: Bhattacharya Sudipa , Das Radhamadhab , Chowdhury Shreyashi , Supin K. K. , Vasundhara M. , Sahu Jyoti Ranjan , Bhunia Trilochan , Gayen Arup , Lebedev Oleg I. , Seikh Md. Motin
Published: March 2024

Schematic view of cation ordering across the interface of the grain boundary of two different perovskites via controlled thermal treatment. Such ordering is sensitive to the magnetic property.
Waste plastic derived nitrogen-doped reduced graphene oxide decorated core–shell nano-structured metal catalyst (WpNrGO-Pd–Ru) for a proton exchange membrane fuel cell
Authors: Dhali Sunil , Karakoti Manoj , Tatrari Gaurav , Pandey Sandeep , Rawat Kundan Singh , Tewari Chetna , Bhushan Boddepalli Santhi , Jung Yong Chae , Srivastava Anurag , Sahoo Nanda Gopal
Published: March 2024

Graphical representation of the WpNrGO_Pd_Ru nano-structured metal catalyst.
Ultrasmall Mn-doped iron oxide nanoparticles with dual hepatobiliary and renal clearances for T1 MR liver imaging
Authors: Lee Sanghoon , Byun Arim , Jo Juhee , Suh Jong-Min , Yoo Jeasang , Lim Mi Hee , Kim Ji-wook , Shin Tae-Hyun , Choi Jin-sil
Published: March 2024

Ultrasmall Mn-doped iron oxide nanoparticles (UMIOs) offer sequential blood vessel and liver imaging, optimal T1 effects, hepatocyte uptake, and dual excretion pathways, improving imaging efficacy and safety compared to conventional agents.
Sources of biases in the in vitro testing of nanomaterials: the role of the biomolecular corona
Authors: Castagnola Valentina , Tomati Valeria , Boselli Luca , Braccia Clarissa , Decherchi Sergio , Pompa Pier Paolo , Pedemonte Nicoletta , Benfenati Fabio , Armirotti Andrea
Published: March 2024

A comparative journey into biomolecular corona features involving proteomics, lipidomics, high throughput in vitro screening, and molecular feature analysis to investigate the in vivo/in vitro bias for nanomaterials testing in biology.
Synthesis and biological evaluation of novel hybrid compounds bearing pyrazine and 1,2,4-triazole analogues as potent antitubercular agents
Authors: Naik Shivakumar , Puttachari Dinesha , A. L. Vanishree , D. Udayakumar , Shetty Varsha Prakash , Prabhu Chaitra , Deekshit Vijaya Kumar
Published: March 2024

In this study, we synthesized a series of hybrid compounds (T1–T18) containing pyrazine and 1,2,4-triazole moiety and assessed their effectiveness against mycobacterium tuberculosis.
An hourglass-shaped nickel-based polyoxometalate crystalline material as a highly efficient bifunctional electrocatalyst for the oxygen evolution reaction and detection of H2O2
Authors: Li Yajie , Zhu Na , Su Zhixuan , Hu Xiaoli , Dou Zhiyu , Su Zhongmin
Published: March 2024

A novel P4Mo6-based POMOFs (CUST-576) was synthesized as a pre-catalyst in the OER reaction, and NiOOH, Ni(OH)2 obtained by in situ reconstruction was used as the main active site with good electrocatalytic OER and H2O2 detection performance.
Decarboxylative 1,3-dipolar cycloadditions of l-proline
Authors: Doraghi Fatemeh , Serajian Azam , Karimian Somaye , Ghanbarlou Mehdi , Moradkhani Fatemeh , Larijani Bagher , Mahdavi Mohammad
Published: March 2024

l-Proline is widely used in 1,3-dipolar cycloaddition reactions. Azomethine ylide derived from decarboxylative condensation of l-proline and 1,2-dicarbonyl compounds can directly react with various dipolarophiles through 1,3-dipolar cycloaddition.
Strategies to improve the performance of polyetheretherketone (PEEK) as orthopedic implants: from surface modification to addition of bioactive materials
Authors: Huang Huagui , Liu Xin , Wang Jinzuo , Suo Moran , Zhang Jing , Sun Tianze , Wang Honghua , Liu Chengde , Li Zhonghai
Published: March 2024

Various modification strategies have been used to improve the physicochemical and biological properties of PEEK as orthopedic implants.