bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in interactions over ecological time scales influence single-cell growth dynamics in a metabolically coupled marine microbial community
Authors: Daniels Michael , van Vliet Simon , Ackermann Martin 
Published: January 2023

Abstract
Microbial communities thrive in almost all habitats on earth. Within these communities, cells interact through the release and uptake of metabolites. These interactions can have synergistic or antagonistic effects on individual community members. The collective metabolic activity of microbial communities leads to changes in their local environment. As the environment changes over time, the nature of the interactions between cells can change. We currently lack understanding of how such dynamic feedbacks affect the growth dynamics of individual microbes and of the community as a whole. Here we study how interactions mediated by the exchange of metabolites through the environment change over time within a simple marine microbial community. We used a microfluidic-based approach that allows us to disentangle the effect cells have on their environment from how they respond to their environment. We found that the interactions between two species—a degrader of chitin and a cross-feeder that consumes metabolic by-products—changes dynamically over time as cells modify their environment. Cells initially interact positively and then start to compete at later stages of growth. Our results demonstrate that interactions between microorganisms are not static and depend on the state of the environment, emphasizing the importance of disentangling how modifications of the environment affects species interactions. This experimental approach can shed new light on how interspecies interactions scale up to community level processes in natural environments.
Leveraging molecular structure and bioactivity with chemical language models for de novo drug design
Authors: Moret Michael , Pachon Angona Irene , Cotos Leandro , Yan Shen , Atz Kenneth , Brunner Cyrill , Baumgartner Martin , Grisoni Francesca , Schneider Gisbert 
Published: January 2023

AbstractGenerative chemical language models (CLMs) can be used for de novo molecular structure generation by learning from a textual representation of molecules. Here, we show that hybrid CLMs can additionally leverage the bioactivity information available for the training compounds. To computationally design ligands of phosphoinositide 3-kinase gamma (PI3Kγ), a collection of virtual molecules was created with a generative CLM. This virtual compound library was refined using a CLM-based classifier for bioactivity prediction. This second hybrid CLM was pretrained with patented molecular structures and fine-tuned with known PI3Kγ ligands. Several of the computer-generated molecular designs were commercially available, enabling fast prescreening and preliminary experimental validation. A new PI3Kγ ligand with sub-micromolar activity was identified, highlighting the method’s scaffold-hopping potential. Chemical synthesis and biochemical testing of two of the top-ranked de novo designed molecules and their derivatives corroborated the model’s ability to generate PI3Kγ ligands with medium to low nanomolar activity for hit-to-lead expansion. The most potent compounds led to pronounced inhibition of PI3K-dependent Akt phosphorylation in a medulloblastoma cell model, demonstrating efficacy of PI3Kγ ligands in PI3K/Akt pathway repression in human tumor cells. The results positively advocate hybrid CLMs for virtual compound screening and activity-focused molecular design.
In vivo detection of bile duct pre-cancer with endoscopic light scattering spectroscopy
Authors: Pleskow Douglas K. , Sawhney Mandeep S. , Upputuri Paul K. , Berzin Tyler M. , Coughlan Mark F. , Khan Umar , Glyavina Maria , Zhang Xuejun , Chen Liming , Sheil Conor J. , Cohen Jonah M. , Vitkin Edward , Zakharov Yuri N. , Itzkan Irving , Zhang Lei , Qiu Le , Perelman Lev T. 
Published: January 2023

AbstractBile duct cancer is the second most common primary liver cancer, with most diagnoses occurring in the advanced stages. This leads to a poor survival rate, which means a technique capable of reliably detecting pre-cancer in the bile duct is urgently required. Unfortunately, radiological imaging lacks adequate accuracy for distinguishing dysplastic and benign biliary ducts, while endoscopic techniques, which can directly assess the bile duct lining, often suffer from insufficient sampling. Here, we report an endoscopic optical light scattering technique for clinical evaluation of the malignant potential of the bile duct. This technique employs an ultraminiature spatial gating fiber optic probe compatible with cholangioscopes and endoscopic retrograde cholangiopancreatography (ERCP) catheters. The probe allowed us to investigate the internal cellular composition of the bile duct epithelium with light scattering spectroscopy (LSS) and phenotypic properties of the underlying connective tissue with diffuse reflectance spectroscopy (DRS). In a pilot in vivo double-blind prospective study involving 29 patients undergoing routine ERCP procedures, the technique detected malignant transformation with 97% accuracy, showing that biliary duct pre-cancer can be reliably identified in vivo non-invasively.
Subthalamic beta bursts correlate with dopamine-dependent motor symptoms in 106 Parkinson’s patients
Authors: Lofredi Roxanne , Okudzhava Liana , Irmen Friederike , Brücke Christof , Huebl Julius , Krauss Joachim K. , Schneider Gerd-Helge , Faust Katharina , Neumann Wolf-Julian , Kühn Andrea A. 
Published: January 2023

AbstractPathologically increased beta power has been described as a biomarker for Parkinson’s disease (PD) and related to prolonged bursts of subthalamic beta synchronization. Here, we investigate the association between subthalamic beta dynamics and motor impairment in a cohort of 106 Parkinson’s patients in the ON- and OFF-medication state, using two different methods of beta burst determination. We report a frequency-specific correlation of low beta power and burst duration with motor impairment OFF dopaminergic medication. Furthermore, reduction of power and burst duration correlated significantly with symptom alleviation through dopaminergic medication. Importantly, qualitatively similar results were yielded with two different methods of beta burst definition. Our findings validate the robustness of previous results on pathological changes in subcortical oscillations both in the frequency- as well as in the time-domain in the largest cohort of PD patients to date with important implications for next-generation adaptive deep brain stimulation control algorithms.
Design of a hydroxy channel based on the selectivity of water permeation via ions exclusion
Authors: Ghahari Afsaneh , Raissi Heidar , Farzad Farzaneh , Pasban Samaneh 
Published: January 2023

AbstractThe Artificial water channels (AWCs) encapsulate water wires or clusters, analogous to natural porins, and offer iterative and continuous hydrogen bonding that plays an essential role in their stabilization. During the last few years, significant progress has been made in AWCs characterization and synthesis, and bridging these advancements to practical development remains a unique challenge. In this study, the possibility of high water selectivity and permeability, as well as the stability of the AWCs channel, is examined via classical molecular dynamic (MD) simulations and well-tempered metadynamics (Wt-metaD) simulations. The results of MD simulations demonstrated that AWCs could provide paths for rapid and selective water permeation via the formation of water-wire networks. Moreover, our findings revealed that the AWC is stable during the simulation time and non-bonded interactions, especially hydrogen bonding, have an essential role in forming a stable OH channel for transporting water molecules. However, the obtained water fluxes (L m−2 h−1) using nanofiltration AWC give us a high flux value, 19.08 (L m−2 h−1), 17.96, and 20.2 (L m−2 h−1), for AWC/ NO3−, AWC/Mg2+, and AWC/Ca2+, respectively. Well-tempered metadynamics simulations of water transport in the OH channel also report similar activation energy values and provide molecular-scale details of the mechanism for water entry into these channels. The free energy values for the AWC/water complexes at their global minima are about ~−241.912, ~−223.479, and ~−255.98 kJ mol−1 in systems AWC/NO3−, AWC/Mg2+, and AWC/Ca2+, respectively.
Advancing thermal performance through vortex generators morphing
Authors: Ali Samer , Dbouk Talib , Wang Guanghui , Wang Dingbiao , Drikakis Dimitris 
Published: January 2023

AbstractThe design of rigid vortex generators (RVG) influences the thermal performance of various technologies. We employed Discrete Adjoint-Based Optimization to show the optimal development of vortex generators. Under turbulent flow conditions, different bi-objective functions on the RVG design were examined. Specifically, we aimed at an optimal RVG shape that minimizes the pressure drop and maximizes the local heat transfer in a rectangular channel. We show that an optimal design of an RVG can be obtained using computational fluid dynamics in conjunction with the Pareto Front at a computational cost of the order ~$$O(10^{-1})$$

O
(

10

-
1

)

. We obtained three essential vortex generator shapes based on the RVG morphing technique. Compared to the baseline geometry of a delta winglet pair DWP, the first morphed design reduced the pressure drop by $$39\%$$

39
%

, however, at the expense of a $$21\%$$

21
%

reduction in the Nusselt number. The second vortex generator design enhanced the heat transfer by $$18\%$$

18
%

, however, at the cost of a significant increase in pressure drop of about $$40\%$$

40
%

. The final morphed design achieved the highest thermal performance factor of 1.28, representing a heat transfer enhancement of $$6\%$$

6
%

with a moderate increase in pressure drop of about $$13\%$$

13
%

compared to DWP vortex generators. Furthermore, we investigated the effect of introducing different size holes on the mass reduction of vortex generators and their thermal performances. The mass of vortex generators can be reduced by $$9\%$$

9
%

and with an increase of $$7\%$$

7
%

in thermal performance factor concerning the DWP baseline. The findings of this study will lead to highly efficient lightweight heat exchangers.
Spatial integration framework of solar, wind, and hydropower energy potential in Southeast Asia
Authors: Sakti Anjar Dimara , Rohayani Pitri , Izzah Nurusshobah Ainul , Toya Nur Afrizal , Hadi Pradita Octoviandiningrum , Octavianti Thanti , Harjupa Wendi , Caraka Rezzy Eko , Kim Yunho , Avtar Ram , Puttanapong Nattapong , Lin Chao-Hung , Wikantika Ketut 
Published: January 2023

AbstractAmid its massive increase in energy demand, Southeast Asia has pledged to increase its use of renewable energy by up to 23% by 2025. Geospatial technology approaches that integrate statistical data, spatial models, earth observation satellite data, and climate modeling can be used to conduct strategic analyses for understanding the potential and efficiency of renewable energy development. This study aims to create the first spatial model of its kind in Southeast Asia to develop multi-renewable energy from solar, wind, and hydropower, further broken down into residential and agricultural areas. The novelty of this study is the development of a new priority model for renewable energy development resulting from the integration of area suitability analysis and the estimation of the amount of potential energy. Areas with high potential power estimations for the combination of the three types of energy are mostly located in northern Southeast Asia. Areas close to the equator, have a lower potential than the northern countries, except for southern regions. Solar photovoltaic (PV) plant construction is the most area-intensive type of energy generation among the considered energy sources, requiring 143,901,600 ha (61.71%), followed by wind (39,618,300 ha; 16.98%); a combination of solar PV and wind (37,302,500 ha; 16%); hydro (7,665,200 ha; 3.28%); a combination of hydro and solar PV (3,792,500 ha; 1.62%); and a combination of hydro and wind (582,700 ha; 0.25%). This study is timely and important because it will inform policies and regional strategies for transitioning to renewable energy, with consideration of the different characteristics present in Southeast Asia.
Overexpression of the NEK9–EG5 axis is a novel metastatic marker in pathologic stage T3 colon cancer
Authors: Kim Meejeong , Jeong Hui Jeong , Ju Hyun-min , Song Ji-young , Jang Se Jin , Choi Jene 
Published: January 2023

AbstractNEK9 is a key player in the NEK9–EG5 axis for microtubule polymerization, chromosome alignment, and mitosis. In present study, we investigated the altered expression of the NEK9, EG5 and acetyl-α-tubulin as well as common epithelial–mesenchymal transition (EMT) markers (E-cadherin, vimentin, claudin-1, and β-catenin) through the immunohistochemistry analysis of 138 patients with pathologic T3 (pT3) stage colon cancers, and evaluated their metastatic potential. NEK9 expression showed an association with distant metastasis (P = 0.032) and was an independent predictive factor for distant metastasis (HR = 3.365, P < 0.001) by multivariate analysis, which was more significant than either the regional nodal metastasis (HR = 2.496, P = 0.007) or lymphovascular invasion (HR = 2.090, P = 0.153). Positive correlations were observed between NEK9 and EG5 or acetyl-α-tubulin (r = 0.236 and P = 0.007; r = 0.181 and P = 0.038, respectively) and concordant overexpression of the NEK9–EG5 axis was further confirmed in colon cancer cell lines. These findings collectively suggest that the overexpression of the NEK9–EG5 axis is present and associated with distant metastasis in colon cancer. These biomarkers might be useful for predicting metastatic potential among the patients with pT3 colon cancers.
Analysis of critical protein–protein interactions of SARS-CoV-2 capping and proofreading molecular machineries towards designing dual target inhibitory peptides
Authors: Arabi-Jeshvaghani Fatemeh , Javadi‐Zarnaghi Fatemeh , Ganjalikhany Mohamad Reza 
Published: January 2023

AbstractIn recent years, the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as the cause of the coronavirus disease (COVID-19) global pandemic, and its variants, especially those with higher transmissibility and substantial immune evasion, have highlighted the imperative for developing novel therapeutics as sustainable solutions other than vaccination to combat coronaviruses (CoVs). Beside receptor recognition and virus entry, members of the SARS-CoV-2 replication/transcription complex are promising targets for designing antivirals. Here, the interacting residues that mediate protein–protein interactions (PPIs) of nsp10 with nsp16 and nsp14 were comprehensively analyzed, and the key residues’ interaction maps, interaction energies, structural networks, and dynamics were investigated. Nsp10 stimulates both nsp14’s exoribonuclease (ExoN) and nsp16’s 2′O-methyltransferase (2′O-MTase). Nsp14 ExoN is an RNA proofreading enzyme that supports replication fidelity. Nsp16 2′O-MTase is responsible for the completion of RNA capping to ensure efficient replication and translation and escape from the host cell’s innate immune system. The results of the PPIs analysis proposed crucial information with implications for designing SARS-CoV-2 antiviral drugs. Based on the predicted shared protein–protein interfaces of the nsp16-nsp10 and nsp14-nsp10 interactions, a set of dual-target peptide inhibitors was designed. The designed peptides were evaluated by molecular docking, peptide–protein interaction analysis, and free energy calculations, and then further optimized by in silico saturation mutagenesis. Based on the predicted evolutionary conservation of the interacted target residues among CoVs, the designed peptides have the potential to be developed as dual target pan-coronavirus inhibitors.
IL-1β neutralization prevents diastolic dysfunction development, but lacks hepatoprotective effect in an aged mouse model of NASH
Authors: Kucsera Dániel , Tóth Viktória E. , Sayour Nabil V. , Kovács Tamás , Gergely Tamás G. , Ruppert Mihály , Radovits Tamás , Fábián Alexandra , Kovács Attila , Merkely Béla , Ferdinandy Péter , Varga Zoltán V. 
Published: January 2023

AbstractInterleukin-1β (IL-1β) is a key mediator of non-alcoholic steatohepatitis (NASH), a chronic liver disease, and of systemic inflammation-driven aging. IL-1β contributes to cardio-metabolic decline, and may promote hepatic oncogenic transformation. Therefore, IL-1β is a potential therapeutic target in these pathologies. We aimed to investigate the hepatic and cardiac effects of an IL-1β targeting monoclonal antibody in an aged mouse model of NASH. 24 months old male C57Bl/6J mice were fed with control or choline deficient (CDAA) diet and were treated with isotype control or anti-IL-1β Mab for 8 weeks. Cardiac functions were assessed by conventional—and 2D speckle tracking echocardiography. Liver samples were analyzed by immunohistochemistry and qRT-PCR. Echocardiography revealed improved cardiac diastolic function in anti-IL-1β treated mice with NASH. Marked hepatic fibrosis developed in CDAA-fed group, but IL-1β inhibition affected fibrosis only at transcriptomic level. Hepatic inflammation was not affected by the IL-1β inhibitor. PCNA staining revealed intensive hepatocyte proliferation in CDAA-fed animals, which was not influenced by neutralization of IL-1β. IL-1β inhibition increased hepatic expression of Pd-1 and Ctla4, while Pd-l1 expression increased in NASH. In conclusion, IL-1β inhibition improved cardiac diastolic function, but did not ameliorate features of NASH; moreover, even promoted hepatic immune checkpoint expression, with concomitant NASH-related hepatocellular proliferation.
How the volatile organic compounds emitted by corpse plant change through flowering
Authors: Kang Lili , Kaur Jasmeen , Winkeler Kelsey , Kubiak Daniella , Hill Jane E. 
Published: January 2023

AbstractThe corpse plant (Amorphophallus titanum) is so named because it produces a pungent, foul odor when flowering. Little is known about how the emitted volatiles change throughout the two-day flowering period. In this study, the comprehensive monitoring of the presence and change in volatile molecules during the female and the male flowering phases of A. titanum was conducted, and the plant temperature was monitored. A total of 422 volatile features were detected over the entire sampling period, of which 118 features were statistically significantly different between the pre-flowering and both flowering phases, and an additional 304 features were found present throughout the flowering period. A total of 45 molecules could be assigned putative names. The volatile profile of A. titanum changes over the two-day flowering period, with the S-containing molecules and aldehydes dominant in the female flowering phase, and the alcohols and hydrocarbons dominant in the male flowering phase. The two-dimensional gas chromatography time-of-flight mass spectrometry (GC × GC-TOFMS) enabled us to identify 32 new molecules produced by A. titanum. Each of these molecules alone, and in combination, likely contribute to the different odors emitted during the flowering phase of A. titanum.
Association of preexisting psychiatric disorders with post-COVID-19 prevalence: a cross-sectional study
Authors: Kataoka Mayumi , Hazumi Megumi , Usuda Kentaro , Okazaki Emi , Nishi Daisuke 
Published: January 2023

AbstractEvidence demonstrating the association of preexisting psychiatric disorders with post-COVID-19 is limited. We aim to investigate the association using larger sample sizes and more extended postinfection periods than previous studies. A total of 6015 (response rate = 77.5%) COVID-19 survivors were surveyed using a self-administered questionnaire from July to September 2021. Poisson regression analysis with robust error variance was performed to estimate post-COVID-19 prevalence ratios (PRs) with or without preexisting psychiatric disorders. Participants with preexisting psychiatric disorders numbered 1067 (17.7%), and with post-COVID-19 were 2149 (35.7%). Post-COVID-19 PR with preexisting psychiatric disorders was 1.09 (95% CI 1.02–1.18, p = 0.013). The interaction between preexisting psychiatric disorders and postinfection periods was significant (p for interaction < 0.001). The subgroup analysis showed that those with preexisting psychiatric disorders might be at greater prolonged risk of post-COVID-19 than those without the disorders. These findings suggested that preexisting psychiatric disorders were associated with an increased post-COVID-19 risk, and post-COVID-19 with preexisting psychiatric disorders might prolong even if time passes.
Nonlinear EHD instability of two viscoelastic fluids under the influence of mass and heat transfer
Authors: Moatimid Galal M. , Zekry Marwa H. , Ibrahim Doaa A. 
Published: January 2023

AbstractThis study attempts to provide an approach to studying the nonlinear stability of a vertical cylindrical interface between two Oldroyd-B prototypes. An unchanged axial electric field influences the system, and porous medium, and the effects of heat and mass transfer (MHT) are considered. Hsieh's modulation and the viscous potential flow (VPT) are used to abbreviate the mathematical analysis. The viscoelastic Oldroyd-B model significant role in geothermal, engineering and industrial enhancement motivated us to carry out this in-depth investigation. The methodology of the nonlinear technique depends mainly on solving the linear equations of motion and applying the appropriate nonlinear boundary conditions. Numerous non-dimensional physical numbers are exposed using a non-dimensional technique. The stability conditions are theoretically achieved and numerically verified. As a limiting case, the linear dispersion equation is accomplished, and a set of stability diagrams is reachable. Together with the nonlinear stability method, a Ginzburg–Landau equation is derived. Subsequently, both theoretical and numerical methods are used to achieve the nonlinear stability criteria. Furthermore, a precise perturbed approach for surface deflection is achieved theoretically and numerically using the Homotopy perturbation method and the extended frequency conception. Along with the linear approach, it is found that the structure becomes unstable by the Laplace, Reynolds, Weber, and elasticity quantities as well as the linear MHT parameter. Furthermore, the stability zones are enhanced in the nonlinear instability approach.
Hypersaline Lake Urmia: a potential hotspot for microbial genomic variation
Authors: Kheiri Roohollah , Mehrshad Maliheh , Pourbabaee Ahmad Ali , Ventosa Antonio , Amoozegar Mohammad Ali 
Published: January 2023

AbstractLake Urmia located in Iran is a hypersaline environment with a salinity of about 27% (w/v). Metagenomic analyses of water samples collected from six locations in the lake exhibited a microbial community dominated by representatives of the family Haloferacaceae (69.8%), mainly those affiliated to only two genera, Haloquadratum (59.3%) and Halonotius (9.1%). Similar to other hypersaline lakes, the bacterial community was dominated by Salinibacter ruber (23.3%). Genomic variation analysis by inspecting single nucleotide variations (SNVs) and insertions/deletions (INDELs) exhibited a high level of SNVs and insertions, most likely through transformation for abundant taxa in the Lake Urmia community. We suggest that the extreme conditions of Lake Urmia and specifically its high ionic concentrations could potentially increase the SNVs and insertions, which can consequently hamper the assembly and genome reconstruction from metagenomic reads of Lake Urmia.