bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spectroscopic assessment of flavor-related chemical compounds in fresh tea shoots using deep learning
Authors: Denaro Lino Garda , Lin Shu-Yen , Huang Cho-ying 
Published: March 2024

AbstractThis study employs a deep-learning method, Y-Net, to estimate 10 tea flavor-related chemical compounds (TFCC), including gallic acid, caffeine and eight catechin isomers, using fresh tea shoot reflectance and transmittance. The unique aspect of Y-Net lies in its utilization of dual inputs, reflectance and transmittance, which are seamlessly integrated within the Y-Net architecture. This architecture harnesses the power of a convolutional neural network-based residual network to fuse tea shoot spectra effectively. This strategic combination enhances the capacity of the model to discern intricate patterns in the optical characteristics of fresh tea shoots, providing a comprehensive framework for TFCC estimation. In this study, we destructively sampled tea shoots from tea farms in Alishan (Ali-Mountain) in Central Taiwan within the elevation range of 879–1552 m a.s.l. Tea shoot reflectance and transmittance data (n = 2032) within the optical region (400–2500 nm) were measured using a portable spectroradiometer and pre-processed using an algorithm; corresponding TFCC were qualified using the high-performance liquid chromatography analysis. To enhance the robustness and performance of Y-Net, we employed data augmentation techniques for model training. We compared the performances of Y-Net and seven other commonly utilized statistical, machine-/deep-learning models (partial least squared regression, Gaussian process, cubist, random forests and three feedforward neural networks) using root-mean-square error (RMSE). Furthermore, we assessed the prediction accuracies of Y-Net and Y-Net using spectra within the visible and near-infrared (VNIR) regions (for higher energy throughput and low-cost instruments) and reflectance only (for airborne and spaceborne remote sensing applications). The results showed that overall Y-Net (mean RMSE ± standard deviation [SD] = 2.51 ± 2.20 mg g−1) outperformed the other statistical, machine- and deep-learning models (≥ 2.59 ± 2.64 mg g−1), demonstrating its superiority in predicting TFCC. In addition, this original Y-Net also yielded slightly lower mean RMSE (± SD) compared with VNIR (2.76 ± 2.41 mg g−1) and reflectance-only (2.68 ± 2.74 mg g−1) Y-Nets using validation data. This study highlights the feasibility of using spectroscopy and Y-Net to assess minor biochemical components in fresh tea shoots and sheds light on the potential of the proposed approach for effective regional monitoring of tea shoot quality.
Distinct regions within SAP25 recruit O-linked glycosylation, DNA demethylation, and ubiquitin ligase and hydrolase activities to the Sin3/HDAC complex
Authors: Goswami Pratik , Banks Charles A.S. , Thornton Janet , Bengs Bethany , Sardiu Mihaela E. , Florens Laurence , Washburn Michael P. 
Published: March 2024

SummaryEpigenetic control of gene expression is crucial for maintaining gene regulation. Sin3 is an evolutionarily conserved repressor protein complex mainly associated with histone deacetylase (HDAC) activity. A large number of proteins are part of Sin3/HDAC complexes, and the function of most of these members remains poorly understood. SAP25, a previously identified Sin3A associated protein of 25 kDa, has been proposed to participate in regulating gene expression programs involved in the immune response but the exact mechanism of this regulation is unclear. SAP25 is not expressed in HEK293 cells, which hence serve as a natural knockout system to decipher the molecular functions uniquely carried out by this Sin3/HDAC subunit. Using molecular, proteomic, protein engineering, and interaction network approaches, we show that SAP25 interacts with distinct enzymatic and regulatory protein complexes in addition to Sin3/HDAC. While the O-GlcNAc transferase (OGT) and the TET1 /TET2/TET3 methylcytosine dioxygenases have been previously linked to Sin3/HDAC, in HEK293 cells, these interactions were only observed in the affinity purification in which an exogenously expressed SAP25 was the bait. Additional proteins uniquely recovered from the Halo-SAP25 pull-downs included the SCF E3 ubiquitin ligase complex SKP1/FBXO3/CUL1 and the ubiquitin carboxyl-terminal hydrolase 11 (USP11), which have not been previously associated with Sin3/HDAC. Finally, we use mutational analysis to demonstrate that distinct regions of SAP25 participate in its interaction with USP11, OGT/TETs, and SCF(FBXO3).) These results suggest that SAP25 may function as an adaptor protein to coordinate the assembly of different enzymatic complexes to control Sin3/HDAC-mediated gene expression.
Machine Learning Assisted Spectral Fingerprinting for Immune Cell Phenotyping
Authors: Nadeem Aceer , Lyons Sarah , Kindopp Aidan , Jamieson Amanda , Roxbury Daniel 
Published: March 2024

AbstractSpectral fingerprinting has emerged as a powerful tool, adept at identifying chemical compounds and deciphering complex interactions within cells and engineered nanomaterials. Using near-infrared (NIR) fluorescence spectral fingerprinting coupled with machine learning techniques, we uncover complex interactions between DNA-functionalized single-walled carbon nanotubes (DNA-SWCNTs) and live macrophage cells, enablingin situphenotype discrimination. Through the use of Raman microscopy, we showcase statistically higher DNA-SWCNT uptake and a significantly lower defect ratio in M1 macrophages as compared to M2 and naïve phenotypes. NIR fluorescence data also indicate that distinctive intra-endosomal environments of these cell types give rise to significant differences in many optical features such as emission peak intensities, center wavelengths, and peak intensity ratios. Such features serve as distinctive markers for identifying different macrophage phenotypes. We further use a support vector machine (SVM) model trained on SWCNT fluorescence data to identify M1 and M2 macrophages, achieving an impressive accuracy of > 95%. Finally, we observe that the stability of DNA-SWCNT complexes, influenced by DNA sequence length, is a crucial consideration for applications such as cell phenotyping or mapping intra-endosomal microenvironments using AI techniques. Our findings suggest that shorter DNA-sequences like GT6give rise to more improved model accuracy (> 87%) due to increased active interactions of SWCNTs with biomolecules in the endosomal microenvironment. Implications of this research extend to the development of nanomaterial-based platforms for cellular identification, holding promise for potential applications in real time monitoring ofin vivocellular differentiation.TOC Graphic
Identification of Druggable Binding Sites and Small Molecules as Modulators of TMC1
Authors: De-la-Torre Pedro , Martínez-García Claudia , Gratias Paul , Mun Matthew , Santana Paula , Akyuz Nurunisa , González Wendy , Indzhykulian Artur A. , Ramírez David 
Published: March 2024

ABSTRACTOur ability to hear and maintain balance relies on the proper functioning of inner ear sensory hair cells, which translate mechanical stimuli into electrical signals via mechano-electrical transducer (MET) channels, composed of TMC1/2 proteins. However, the therapeutic use of ototoxic drugs, such as aminoglycosides and cisplatin, which can enter hair cells through MET channels, often leads to profound auditory and vestibular dysfunction. Despite extensive research on otoprotective compounds targeting MET channels, our understanding of how small-molecule modulators interact with these channels remains limited, hampering the discovery of novel drugs. Here, we propose a structure-based screening approach, integrating 3D-pharmacophore modeling, molecular dynamics simulations of the TMC1+CIB2+TMIE complex, and experimental validation. Our pipeline successfully identified several novel compounds and FDA-approved drugs that reduced dye uptake in cultured cochlear explants, indicating MET-modulation activity. Simulations, molecular docking and free-energy estimations allowed us to identify three potential drug-binding sites within the channel pore, phospholipids, key amino acids involved in modulator interactions, and TMIE as a flexible component of the MET complex. We also identified shared ligand-binding features between TMC and structurally related TMEM16 proteins, providing novel insights into their distinct inhibition. Our pipeline offers a broad application for discovering modulators for mechanosensitive ion channels.
CoupleVAE: coupled variational autoencoders for predicting perturbational single-cell RNA sequencing data
Authors: Wu Yahao , Liu Jing , Liu Songyan , Xiao Yanni , Zhang Shuqin , Li Limin 
Published: March 2024

AbstractWith the rapid advances in single-cell sequencing technology, it is now feasible to conduct in-depth genetic analysis in individual cells. Study on the dynamics of single cells in response to perturbations is of great significance for understanding the functions and behaviours of living organisms. However, the acquisition of post-perturbation cellular states via biological experiments is frequently cost-prohibitive. Predicting the single-cell perturbation responses poses a critical challenge in the field of computational biology. In this work, we propose a novel deep learning method called coupled variational autoencoders (CoupleVAE), devised to predict the post-perturbation single-cell RNA-Seq data. CoupleVAE is composed of two coupled VAEs connected by a coupler, initially extracting latent features for both controlled and perturbed cells via two encoders, subsequently engaging in mutual translation within the latent space through two nonlinear mappings via a coupler, and ultimately generating controlled and perturbed data by two separate decoders to process the encoded and translated features. CoupleVAE facilitates a more intricate state transformation of single cells within the latent space. Experiments in three real datasets on infection, stimulation and cross-species prediction show that CoupleVAE surpasses the existing comparative models in effectively predicting single-cell RNA-seq data for perturbed cells, achieving superior accuracy.
Conformational switch of a peptide provides a novel strategy to design peptide loaded porous organic polymer for Pyroptosis pathway mediated cancer therapy
Authors: Mishra Snehasis , Sannigrahi Achinta , Ruidas Santu , Chatterjee Sujan , Roy Kamalesh , Misra Deblina , Maity Barun Kumar , Paul Rabindranath , Das Saha Krishna , Bhaumik Asim , Chattopadhyay Krishnananda 
Published: March 2024

AbstractWhile peptide-based drug development is now extensively explored, this strategy does have limitations, which come from their rapid excretion from the body (or shorter half-life in the body), and vulnerability to protease-mediated degradation. To overcome these limitations, here we introduce a novel strategy for the development of a peptide-based anticancer agent using the conformation switch property of a chameleon sequence stretch, which we derived from a mycobacterium secretory protein, MPT63. Then, we loaded this peptide in a new porous organic polymer (PG-DFC-POP) synthesized using phloroglucinol and acresolderivative via condensation reaction for delivering the peptide selectively to the cancer cells. Employing an ensemble and single molecule approaches, we demonstrate that this peptide undergoes a disordered to alpha-helical conformational transition, which is triggered by a low pH environment inside cancer cells. This adopted alpha-helical conformation results in the formation of proteolysis-resistant oligomers, which show efficient membrane pore-forming activity selectively for negatively charged phospholipid which is accumulated in cancer cell membrane. Ourin vitroandin vivoexperimental results demonstrate that the peptide-loaded nanomaterial PG-DFC-POP-PEP 1 exhibits significant cytotoxicity in cancer cells, leading to cell death through the Pyroptosis pathway that is confirmed by monitoring numerous associated events starting from lysosome membrane damage to GSDMD-induced cell membrane demolition. We believe that this novel conformational switch-based drug design strategy has great potential in endogenous environment-responsive cancer therapy and the development of future drug candidates to mitigate cancers.
Shear Stress Promotes Remodeling of Platelet Glycosylation via Upregulation of Platelet Glycosidase Activity: The Ulterior Cause of MCS-Related Thrombocytopenia?
Authors: Roka-Moiia Yana , Lewis Sabrina , Cleveland Estevan , Italiano Joseph E. , Slepian Marvin J. 
Published: March 2024

ABSTRACTObjectiveMechanical circulatory support (MCS) is a mainstay of therapy for advanced and end-stage heart failure. Accompanied by systemic anticoagulation, contemporary MCS has become less thrombogenic, with bleeding complications emerging as a major cause of readmission and 1-year mortality of device-supported patients. Shear-mediated platelet dysfunction (SMPD) and thrombocytopenia of undefined etiology are primary drivers of MCS-related bleeding. Recently, it has been demonstrated that deprivation of platelet surface glycosylation is associated with the decline of hemostatic function, microvesiculation, and premature apoptosis. We tested the hypothesis that shear stress induces remodeling of platelet surface glycosylation via upregulation of glycosidase activity, thus facilitating platelet count decline and intense microvesiculation.Approach and ResultsHuman gel-filtered platelets were exposed to continuous shear stressin vitro. Platelets and platelet-derived microparticles were quantified via flow cytometry using size standard fluorescent nanobeads. Platelet surface glycosylation was evaluated using lectin staining and multicolor flow cytometry; lectin blotting was utilized to verify glycosylation of individual glycoproteins. Platelet neuraminidase, galactosidase, hexosaminidase, and mannosidase activities were quantified using 4-methylumbelliferone-based fluorogenic substrates. We demonstrated that shear stress promotes selective remodeling of platelet glycosylation via downregulation of 2,6-sialylation, terminal galactose, and mannose, while 2,3-sialylation remained largely unchanged. Shear-mediated deglycosylation is partially attenuated by neuraminidase inhibitors DANA and zanamivir, strongly suggesting involvement of platelet neuraminidase in observed phenomena. Platelets exhibited high basal hexosaminidase and mannosidase activities; basal activities of platelet neuraminidase and galactosidase were rather low and were significantly upregulated by shear stress. Shear stress of increased magnitude and duration potentiated an incremental decline of platelet count and immense microvesiculation, both being further exacerbated by neuraminidase.ConclusionsOur data indicate that shear stress accumulation, consistent with supraphysiologic conditions of device-supported circulation, promotes remodeling of platelet glycosylation via selective upregulation of platelet glycosidase activity. Shear-mediated platelet deglycosylation is associated with platelet count drop and increased microvesiculation, thus offering a direct link between deglycosylation and thrombocytopenia observed in device-supported patients.GRAPHICAL ABSTRACT
Engineering an in vitro retinothalamic nerve model
Authors: Amos Giulia , Ihle Stephan J , Clément Blandine F , Duru Jens , Girardin Sophie , Maurer Benedikt , Delipinar Tuğçe , Vörös János , Ruff Tobias 
Published: March 2024

ABSTRACTUnderstanding the retinogeniculate pathwayin vitrocan offer insights into its development and potential for future therapeutic applications. This study presents a Polydimethylsiloxane-based two-chamber system with axon guidance channels, designed to replicate unidirectional retinogeniculate signal transmissionin vitro. The system enables the formation of up to 20 identical functional retinothalamic networks on a single transparent microelectrode array. Using embryonic rat retinas, we developed a model where retinal spheroids innervate thalamic targets through up to 6 mm long microfluidic channels. We found that network integrity depends on channel length, with 0.5-2 mm channels maintaining over 90 % morphological and 40 % functional integrity. A reduced network integrity was recorded in longer channels. The results indicate a notable reduction in forward spike propagation in channels longer than 4 mm. Additionally, spike conduction fidelity decreased with increasing channel length. Yet, stimulation-induced thalamic target activity remained unaffected by channel length. Finally, we assessed the impact of stimulation frequency and channel length on the sustainability of the thalamic target spheroid response. The study found that a sustained thalamic calcium response could be elicited with stimulation frequencies up to 31 Hz, with higher frequencies leading to transient responses. In conclusion, this study shows how channel length affects retina to brain network formation and signal transmissionin vitro.
Addressing technical pitfalls in pursuit of molecular factors that mediate immunoglobulin gene regulation
Authors: Engelbrecht Eric , Rodriguez Oscar L. , Watson Corey T. 
Published: March 2024

AbstractThe expressed antibody repertoire is a critical determinant of immune-related phenotypes. Antibody-encoding transcripts are distinct from other expressed genes because they are transcribed from somatically rearranged gene segments. Human antibodies are composed of two identical heavy and light chain polypeptides derived from genes in the immunoglobulin heavy chain (IGH) locus and one of two light chain loci. The combinatorial diversity that results from antibody gene rearrangement and the pairing of different heavy and light chains contributes to the immense diversity of the baseline antibody repertoire. During rearrangement, antibody gene selection is mediated by factors that influence chromatin architecture, promoter/enhancer activity, and V(D)J recombination. Interindividual variation in the composition of the antibody repertoire associates with germline variation in IGH, implicating polymorphism in antibody gene regulation. Determining how IGH variants directly mediate gene regulation will require integration of these variants with other functional genomic datasets. Here, we argue that standard approaches using short reads have limited utility for characterizing regulatory regions in IGH at haplotype-resolution. Using simulated and ChIP-seq reads, we define features of IGH that limit use of short reads and a single reference genome, namely 1) the highly duplicated nature of DNA sequence in IGH and 2) structural polymorphisms that are frequent in the population. We demonstrate that personalized diploid references enhance performance of short-read data for characterizing mappable portions of the locus, while also showing that long-read profiling tools will ultimately be needed to fully resolve functional impacts of IGH germline variation on expressed antibody repertoires.
Antigenicity assessment of SARS-CoV-2 saltation variant BA.2.87.1
Authors: Yang Sijie , Yu Yuanling , Jian Fanchong , Yisimayi Ayijiang , Song Weiliang , Liu Jingyi , Wang Peng , Xu Yanli , Wang Jing , Niu Xiao , Yu Lingling , Wang Yao , Shao Fei , Jin Ronghua , Wang Youchun , Cao Yunlong 
Published: March 2024

AbstractThe recent emergence of a SARS-CoV-2 saltation variant, BA.2.87.1, which features 65 spike mutations relative to BA.2, has attracted worldwide attention. In this study, we elucidate the antigenic characteristics and immune evasion capability of BA.2.87.1. Our findings reveal that BA.2.87.1 is more susceptible to XBB-induced humoral immunity compared to JN.1. Notably, BA.2.87.1 lacks critical escaping mutations in the receptor binding domain (RBD) thus allowing various classes of neutralizing antibodies (NAbs) that were escaped by XBB or BA.2.86 subvariants to neutralize BA.2.87.1, although the deletions in the N-terminal domain (NTD), specifically 15-23del and 136-146del, compensate for the resistance to humoral immunity. Interestingly, several neutralizing antibody drugs have been found to restore their efficacy against BA.2.87.1, including SA58, REGN-10933 and COV2-2196. Hence, our results suggest that BA.2.87.1 may not become widespread until it acquires multiple RBD mutations to achieve sufficient immune evasion comparable to that of JN.1.
Rapid Degradation of the Human ACE2 Receptor Upon Binding and Internalization of SARS-Cov-2-Spike-RBD Protein
Authors: Feinstein Paul 
Published: March 2024

AbstractIt is widely accepted that the SARS-CoV-2 betacoronavirus infects humans through binding the human Angiotensin Receptor 2 (ACE2) that lines the nasal cavity and lungs, followed by import into a cell utilizing the Transmembrane Protease, Serine 2 (TMPRSS2) cofactor. ACE2 binding is mediated by an approximately 200-residue portion of the SARS-CoV-2 extracellular spike protein, the receptor binding domain (RBD). Robust interactions are shown using a novel cell-based assay between an RBD membrane tethered-GFP fusion protein and the membrane bound ACE2-Cherry fusion protein. Several observations were not predicted including, quick and sustained interactions leading to internalization of RBD fusion protein into the ACE2 cells and rapid downregulation of the ACE2-Cherry fluorescence. Targeted mutation in the RBD disulfide Loop 4 led to a loss of internalization for several variants tested. However, a secreted RBD did not cause ACE2 downregulation of ACE2-Cherry fluorescence. Thus, the membrane associated form of RBD found on the viral coat may have long-term system wide consequences on ACE2 expressing cells.
JAK-STAT pathway activation compromises nephrocyte function in aDrosophilahigh-fat diet model of chronic kidney disease
Authors: Zhao Yunpo , Duan Jianli , van de Leemput Joyce , Han Zhe 
Published: March 2024

ABSTRACTChronic kidney disease is a major healthy issue and is gaining prevalence. Using aDrosophilamodel for chronic kidney disease we show that a high-fat diet (HFD) disrupts the slit diaphragm filtration structure in nephrocytes, the fly functional equivalent of mammalian podocytes. The structural disruption resulted in reduced filtration function in the affected nephrocytes. We demonstrate that a HFD activates the JAK-STAT pathway in nephrocytes, which has previously been linked to diabetic kidney disease. JAK-STAT activation was initiated by increased expression and release of the adipokine, Upd2, from the fat body. This leptin-like hormone is a known ligand of JAK-STAT. Both genetic and pharmacological inhibition of JAK-STAT restored nephrocyte HFD-associated dysfunction. Altogether, our study reveals the importance of the JAK-STAT signaling pathway in the adipose tissue−nephrocyte axis and its contribution to HFD-associated nephropathy. These findings open new avenues for intervention in treating diabetic nephropathy and chronic kidney disease.HIGHLIGHTSHigh-fat diet (HFD) disrupt nephrocyte slit diaphragm structure and filtrationHFD releases fat body adipokine, Upd2, which activates JAK-STAT in nephrocytesGenetic/pharmacological inhibition of JAK-STAT reverses HFD nephrocyte dysfunctionJAK-STAT signaling mediates adipose-nephrocyte axis in HFD-associated nephropathyIMPACT STATEMENTUsing aDrosophilamodel for chronic kidney disease, Zhao et al. show that a high-fat diet induces excretion of a leptin-like JAK-STAT ligand from the fat body. Thus, driving the adipose-nephrocyte (podocyte equivalent) axis through activated JAK-STAT signaling. These findings link obesity to kidney disease, implicating new avenues for therapeutics.