Miracle-dz/UniFAR-FTUs huggingface dataset:
Computational Study of Photodegradation Process and Conversion Products of the Antidepressant Citalopram in Water

Citalopram (CIT) is a commonly prescribed medication for depression. However, the photodegradation mechanism of CIT has not yet been fully analyzed. Therefore, the photodegradation process of CIT in water is studied by density functional theory and time-dependent density functional theory. The calculated results show that during the indirect photodegradation process, the indirect photodegradation of CIT with ·OH occurs via OH-addition and F-substitution. The minimum activation energy of C10 site was 0.4 kcal/mol. All OH-addition and F-substitution reactions are exothermic. The reaction of 1O2 with CIT includes the substitution of 1O2 for F and an addition reaction at the C14 site. The Ea value of this process is 1.7 kcal/mol, which is the lowest activation energy required for the reaction of 1O2 with CIT. C–C/C–N/C–F cleavage is involved in the direct photodegradation process. In the direct photodegradation of CIT, the activation energy of the C7-C16 cleavage reaction was the lowest, which was 12.5 kcal/mol. Analysis of the Ea values found that OH-addition and F-substitution, the substitution of 1O2 for F and addition at the C14 site, as well as the cleavage reactions of C6–F/C7–C16/C17–C18/C18–N/C19–N/C20–N are the main pathways of photodegradation of CIT.
Pueraria montana Population Structure and Genetic Diversity Based on Chloroplast Genome Data

Despite having a generally conserved structure, chloroplast genome data have been helpful for plant population genetics and evolution research. To mine Pueraria montana chloroplast genome variation architecture and phylogeny, we investigated the chloroplast variation architecture of 104 P. montana accessions from across China. P. montana’s chloroplast genome showed high diversity levels, with 1674 variations, including 1118 single nucleotide polymorphisms and 556 indels. The intergenic spacers, psbZ-trnS and ccsA-ndhD, are the two mutation hotspot regions in the P. montana chloroplast genome. Phylogenetic analysis based on the chloroplast genome dataset supported four P. montana clades. P. montana variations were conserved among and within clades, which showed high gene flow levels. Most P. montana clades were estimated to have diverged at 3.82–5.17 million years ago. Moreover, the East Asian summer monsoon and South Asian summer monsoon may have accelerated population divergence. Our results show that chloroplast genome sequences were highly variable and can be used as molecular markers to assess genetic variation and relationships in P. montana.
Impact of Human Papillomavirus Vaccination on Male Disease: A Systematic Review

Human papillomavirus (HPV)-related diseases are highly prevalent in men worldwide, comprising external anogenital condyloma, anal intraepithelial neoplasia (AIN), penile intraepithelial neoplasia (PIN), and anogenital and oropharyngeal cancers. There is exceptionally low vaccine coverage in the male population. Only 4% of men were fully vaccinated, worldwide, as of 2019. The aim of this review is to assess the impact of HPV vaccination on male disease. Three databases (MEDLINE, Web of Science, Scopus) and Clinical Trials.gov were searched. We included thirteen studies, eight randomized controlled trials (RCTs), and five cohorts, comprising a total of 14,239 participants. Regarding anal disease, seven studies reported HPV vaccine efficacy ranging from 91.1% to 93.1% against AIN1, and ranging from 89.6% to 91.7% against AIN2|3 and anal cancer. Five studies showed an efficacy against genital condyloma of 89.9% in HPV-naïve males, varying between 66.7% and 67.2% in intention-to-treat populations. Studies reporting no efficacy have included older participants. These results support vaccination of young men previously infected, beyond HPV-naïve males. The evidence quality was moderate to low for most outcomes, namely genital diseases. RCTs are needed to assess the efficacy of HPV vaccination on male oropharyngeal cancer.
Binding Mechanism of CD47 with SIRPα Variants and Its Antibody: Elucidated by Molecular Dynamics Simulations

The intricate complex system of the differentiation 47 (CD47) and the signal-regulatory protein alpha (SIRPα) cluster is a crucial target for cancer immunotherapy. Although the conformational state of the CD47-SIRPα complex has been revealed through crystallographic studies, further characterization is needed to fully understand the binding mechanism and to identify the hot spot residues involved. In this study, molecular dynamics (MD) simulations were carried out for the complexes of CD47 with two SIRPα variants (SIRPαv1, SIRPαv2) and the commercially available anti-CD47 monoclonal antibody (B6H12.2). The calculated binding free energy of CD47-B6H12.2 is lower than that of CD47-SIRPαv1 and CD47-SIRPαv2 in all the three simulations, indicating that CD47-B6H12.2 has a higher binding affinity than the other two complexes. Moreover, the dynamical cross-correlation matrix reveals that the CD47 protein shows more correlated motions when it binds to B6H12.2. Significant effects were observed in the energy and structural analyses of the residues (Glu35, Tyr37, Leu101, Thr102, Arg103) in the C strand and FG region of CD47 when it binds to the SIRPα variants. The critical residues (Leu30, Val33, Gln52, Lys53, Thr67, Arg69, Arg95, and Lys96) were identified in SIRPαv1 and SIRPαv2, which surround the distinctive groove regions formed by the B2C, C’D, DE, and FG loops. Moreover, the crucial groove structures of the SIRPα variants shape into obvious druggable sites. The C’D loops on the binding interfaces undergo notable dynamical changes throughout the simulation. For B6H12.2, the residues Tyr32LC, His92LC, Arg96LC, Tyr32HC, Thr52HC, Ser53HC, Ala101HC, and Gly102HC in its initial half of the light and heavy chains exhibit obvious energetic and structural impacts upon binding with CD47. The elucidation of the binding mechanism of SIRPαv1, SIRPαv2, and B6H12.2 with CD47 could provide novel perspectives for the development of inhibitors targeting CD47-SIRPα.
Study of Oncolytic Virus Preservation and Formulation

In recent years, oncolytic viruses (OVs) have emerged as an effective means of treating cancer. OVs have multiple oncotherapeutic functions including specifically infecting and lysing tumor cells, initiating immune cell death, attacking and destroying tumor angiogenesis and triggering a broad bystander effect. Oncolytic viruses have been used in clinical trials and clinical treatment as drugs for cancer therapy, and as a result, oncolytic viruses are required to have long-term storage stability for clinical use. In the clinical application of oncolytic viruses, formulation design plays a decisive role in the stability of the virus. Therefore, this paper reviews the degradation factors and their degradation mechanisms (pH, thermal stress, freeze–thaw damage, surface adsorption, oxidation, etc.) faced by oncolytic viruses during storage, and it discusses how to rationally add excipients for the degradation mechanisms to achieve the purpose of maintaining the long-term stability of oncolytic viral activity. Finally, the formulation strategies for the long-term formulation stability of oncolytic viruses are discussed in terms of buffers, permeation agents, cryoprotectants, surfactants, free radical scavengers, and bulking agent based on virus degradation mechanisms.
Oxidized Natural Biopolymer for Enhanced Surface, Physical and Mechanical Properties of Glass Ionomer Luting Cement

This laboratory investigation aimed to synthesize and characterize micron-sized Gum Arabic (GA) powder and incorporate it in commercially available GIC luting formulation for enhanced physical and mechanical properties of GIC composite. Oxidation of GA was performed and GA-reinforced GIC in 0.5, 1.0, 2.0, 4.0 & 8.0 wt. % formulations were prepared in disc-shaped using two commercially available GIC luting materials (Medicem and Ketac Cem Radiopaque). While the control groups of both materials were prepared as such. The effect of reinforcement was evaluated in terms of nano hardness, elastic modulus, diametral tensile strength (DTS), compressive strength (CS), water solubility and sorption. Two-way ANOVA and post hoc tests were used to analyze data for statistical significance (p < 0.05). FTIR spectrum confirmed the formation of acid groups in the backbone of polysaccharide chain of GA while XRD peaks confirmed that crystallinity of oxidized GA. The experimental group with 0.5 wt. % GA in GIC enhanced the nano hardness while 0.5 wt. % and 1.0 wt. % GA in GIC increased the elastic modulus compared to the control. The CS of 0.5 wt. % GA in GIC and DTS of 0.5 wt. % and 1.0 wt. % GA in GIC demonstrated elevation. In contrast, the water solubility and sorption of all the experimental groups increased compared to the control groups. The incorporation of lower weight ratios of oxidized GA powder in GIC formulation helps in enhancing the mechanical properties with a slight increase in water solubility and sorption parameters. The addition of micron-sized oxidized GA in GIC formulation is promising and needs further research for improved performance of GIC luting composition.
Chimeric HLA antibody receptor T cells to target HLA‐specific B cells in solid organ transplantation

HLA‐sensitized patients on the transplant waiting list harbor antibodies and memory B cells directed against allogeneic HLA molecules, which decreases the chance to receive a compatible donor organ. Current desensitization strategies non‐specifically target circulating antibodies and B cells, warranting the development of therapies that specifically affect HLA‐directed humoral immune responses. We developed Chimeric HLA Antibody Receptor (CHAR) constructs comprising the extracellular part of HLA‐A2 or HLA‐A3 coupled to CD28‐CD3ζ domains. CHAR‐transduced cells expressing reporter constructs encoding T‐cell activation markers, and CHAR‐transduced CD8+ T cells from healthy donors were stimulated with HLA‐specific monoclonal antibody‐coated microbeads, and HLA‐specific B cell hybridomas. CHAR T cell activation was measured by upregulation of T cell activation markers and IFNγ secretion, whereas CHAR T cell killing of B cell hybridomas was assessed in chromium release assays and by IgG ELISpot. HLA‐A2‐ and HLA‐A3‐CHAR expressing cells were specifically activated by HLA‐A2‐ and HLA‐A3‐specific monoclonal antibodies, either soluble or coated on microbeads, as shown by CHAR‐induced transcription factors. HLA‐A2 and HLA‐A3 CHAR T cells efficiently produced IFNγ with exquisite specificity and were capable of specifically lysing hybridoma cells expressing HLA‐A2‐ or HLA‐A3‐specific B‐cell receptors, respectively. Finally, we mutated the α3 domain of the CHAR molecules to minimize any alloreactive T‐cell reactivity against CHAR T cells, while retaining CHAR activity. These data show proof of principle for CHAR T cells to serve as precision immunotherapy to specifically desensitize (highly) sensitized solid organ transplant candidates and to treat antibody‐mediated rejection after solid organ transplantation.
Mentalization, Oxytocin, and Cortisol in the General Population

Although evidence suggests the role of oxytocin and cortisol in social cognition and emotion regulation, it is less known how their peripheral levels are related to social perception (biological motion detection) and mentalization (self-reflection, emotional awareness, and affect regulation) in the general population. We assessed 150 healthy individuals from the general community on a mentalization questionnaire, a scale measuring the intensity of positive and negative emotions, and measured oxytocin and cortisol levels in the saliva. Oxytocin but not cortisol level and biological motion detection predicted mentalization abilities. There was a positive correlation between mentalization and positive emotions and between mentalization and biological motion detection. These results suggest that oxytocin, but not cortisol, plays a role in low-level perceptual and self-reflective aspects of social cognition.
Cutaneous Manifestations, Clinical Characteristics, and Prognosis of Patients With Systemic Sclerosis Sine Scleroderma: Data From the International EUSTAR Database.

Importance Systemic sclerosis (SSc) sine scleroderma (ssSSc) is a subset of SSc defined by the absence of skin fibrosis. Little is known about the natural history and skin manifestations among patients with ssSSc. Objective To characterize the clinical phenotype of patients with ssSSc compared with patients with limited cutaneous SSc (lcSSc) and diffuse cutaneous SSc (dcSSc) within the EUSTAR database. Design, Setting, and Participants This longitudinal observational cohort study based on the international EUSTAR database included all patients fulfilling the classification criteria for SSc assessed by the modified Rodnan Skin score (mRSS) at inclusion and with at least 1 follow-up visit; ssSSc was defined by the absence of skin fibrosis (mRSS = 0 and no sclerodactyly) at all available visits. Data extraction was performed in November 2020, and data analysis was performed from April 2021 to April 2023. Main Outcomes and Measures Main outcomes were survival and skin manifestations (onset of skin fibrosis, digital ulcers, telangiectasias, puffy fingers). Results Among the 4263 patients fulfilling the inclusion criteria, 376 (8.8%) were classified as having ssSSc (mean [SD] age, 55.3 [13.9] years; 345 [91.8%] were female). At last available visit, in comparison with 708 patients with lcSSc and 708 patients with dcSSc with the same disease duration, patients with ssSSc had a lower prevalence of previous or current digital ulcers (28.2% vs 53.1% in lcSSc; P < .001; and 68.3% in dcSSc; P < .001) and puffy fingers (63.8% vs 82.4% in lcSSc; P < .001; and 87.6% in dcSSc; P < .001). By contrast, the prevalence of interstitial lung disease was similar in ssSSc and lcSSc (49.8% and 57.1%; P = .03) but significantly higher in dcSSc (75.0%; P < .001). Skin telangiectasias were associated with diastolic dysfunction in patients with ssSSc (odds ratio, 4.778; 95% CI, 2.060-11.081; P < .001). The only independent factor for the onset of skin fibrosis in ssSSc was the positivity for anti-Scl-70 antibodies (odds ratio, 3.078; 95% CI, 1.227-7.725; P = .02). Survival rate was higher in patients with ssSSc (92.4%) compared with lcSSc (69.4%; P = .06) and dcSSc (55.5%; P < .001) after up to 15 years of follow-up. Conclusions and Relevance Systemic sclerosis sine scleroderma should not be neglected considering the high prevalence of interstitial lung disease (>40%) and SSc renal crisis (almost 3%). Patients with ssSSc had a higher survival than other subsets. Dermatologists should be aware that cutaneous findings in this subgroup may be associated with internal organ dysfunction. In particular, skin telangiectasias in ssSSc were associated with diastolic heart dysfunction.
Study and Optimization of a Micro-Structured Waveguiding and Fluorescent Sol-Gel Architecture

Channel waveguides with diffraction gratings at their input and output for light injection and extraction, respectively, constitute the key components for applications in integrated optics and photonics. Here, we report for the first time on such fluorescent micro-structured architecture entirely elaborated on glass by sol-gel processing. This architecture particularly takes advantage of a high-refractive index and transparent titanium oxide-based, sol-gel photoresist that can be imprinted through a single photolithography step. This resist enabled us to photo-imprint the input and output gratings on a photo-imprinted channel waveguide doped with a ruthenium complex fluorophore (Rudpp). In this paper, the elaboration conditions and optical characterizations of derived architectures are presented and discussed with respect to optical simulations. We firstly show how the optimization of a two-step deposition/insolation sol-gel procedure leads to reproducible and uniform grating/waveguide architectures elaborated on rather large dimensions. Then, we show how this reproducibility and uniformity govern the reliability of fluorescence measurements in waveguiding configuration. These measurements demonstrate that: (i) our sol-gel architecture is well adapted to the efficient channel–waveguide/diffraction grating coupling at the Rudpp excitation and emission wavelengths; (ii) it enables an efficient propagation of the emission signal in the core of the waveguide allowing its photo-detection after extraction through the output grating; and (iii) it is affected by very reduced parasitic mechanisms, such as propagation losses and photobleaching features. This work constitutes a promising preliminary step toward the integration of our architecture in a microfluidic platform for further fluorescence measurements in liquid medium and waveguiding configuration.
Phytoplankton-Bacteria Interactions 2.0

There are multiple ways in which phytoplankton and bacteria interact, starting from the fundamental symbiotic associations of direct attachment, through intimate interactions within the phytoplankton phycosphere, to random associations within the water column via the exudation and cycling of dissolved organic carbon (DOC) and other chemical compounds [. ].
Collagen-Derived Dipeptide Pro-Hyp Enhanced ATDC5 Chondrocyte Differentiation under Hypoxic Conditions

Chondrocytes are surrounded by a lower oxygen environment than other well-vascularized tissues with higher oxygenation levels. Prolyl-hydroxyproline (Pro-Hyp), one of the final collagen-derived peptides, has been previously reported to be involved in the early stages of chondrocyte differentiation. However, whether Pro-Hyp can alter chondrocyte differentiation under physiological hypoxic conditions is still unclear. This study aimed to investigate whether Pro-Hyp affects the differentiation of ATDC5 chondrogenic cells under hypoxic conditions. The addition of Pro-Hyp resulted in an approximately 18-fold increase in the glycosaminoglycan staining area compared to the control group under hypoxic conditions. Moreover, Pro-Hyp treatment significantly upregulated the expression of SOX9, Col2a1, Aggrecan, and MMP13 in chondrocytes cultured under hypoxic conditions. These results demonstrate that Pro-Hyp strongly promotes the early differentiation of chondrocytes under physiological hypoxic conditions. Therefore, Pro-Hyp, a bioactive peptide produced during collagen metabolism, may function as a remodeling factor or extracellular matrix remodeling signal that regulates chondrocyte differentiation in hypoxic cartilage.
Transsynaptic Assemblies Link Domains of Presynaptic and Postsynaptic Intracellular Structures across the Synaptic Cleft

The chemical synapse is a complex machine separated into three parts: presynaptic, postsynaptic, and cleft. Super-resolution light microscopy has revealed alignment of presynaptic vesicle release machinery and postsynaptic neurotransmitter-receptors and scaffolding components in synapse spanning nanocolumns. Cryo-electron tomography confirmed that postsynaptic glutamate receptor-like structures align with presynaptic structures in proximity to synaptic vesicles into transsynaptic assemblies. In our electron tomographic renderings, nearly all transcleft structures visibly connect to intracellular structures through transmembrane structures to form transsynaptic assemblies, potentially providing a structural basis for transsynaptic alignment. Here, we describe the patterns of composition, distribution, and interactions of all assemblies spanning the synapse by producing three-dimensional renderings of all visibly connected structures in excitatory and inhibitory synapses in dissociated rat hippocampal neuronal cultures of both sexes prepared by high-pressure freezing and freeze-substitution. The majority of transcleft structures connect to material in both presynaptic and postsynaptic compartments. We found several instances of assemblies connecting to both synaptic vesicles and postsynaptic density scaffolding. Each excitatory synaptic vesicle within 30 nm of the active zone contacts one or more assembly. Further, intracellular structures were often shared between assemblies, entangling them to form larger complexes or association domains, often in small clusters of vesicles. Our findings suggest that transsynaptic assemblies physically connect the three compartments, allow for coordinated molecular organization, and may combine to form specialized functional association domains, resembling the light-level nanocolumns. SIGNIFICANCE STATEMENT A recent tomographic study uncovered that receptor-like cleft structures align across the synapse. These aligned structures were designated as transsynaptic assemblies and demonstrate the coordinated organization of synaptic transmission molecules between compartments. Our present tomographic study expands on the definition of transsynaptic assemblies by analyzing the three-dimensional distribution and connectivity of all cleft-spanning structures and their connected intracellular structures. While one-to-one component alignment occurs across the synapse, we find that many assemblies share components, leading to a complex entanglement of assemblies, typically around clusters of synaptic vesicles. Transsynaptic assemblies appear to form domains which may be the structural basis for alignment of molecular nanodomains into synapse spanning nanocolumns described by super-resolution light microscopy.
Homotypic SCOTIN assemblies form ER‐endosome membrane contacts and regulate endosome dynamics

The ER regulates the spatiotemporal organization of endolysosomal systems by membrane contact. In addition to tethering via heterotypic interactions on both organelles, we present a novel ER‐endosome tethering mechanism mediated by homotypic interactions. The single‐pass transmembrane protein SCOTIN is detected in the membrane of the ER and endosomes. In SCOTIN‐knockout (KO) cells, the ER‐late endosome contacts are reduced, and the perinuclear positioning of endosomes is disturbed. The cytosolic proline‐rich domain (PRD) of SCOTIN forms homotypic assemblies in vitro and is necessary for ER‐endosome membrane tethering in cells. A region of 28 amino acids spanning 150–177 within the SCOTIN PRD is essential to elicit membrane tethering and endosomal dynamics, as verified by reconstitution in SCOTIN‐KO cells. The assembly of SCOTIN (PRD) is sufficient to mediate membrane tethering, as purified SCOTIN (PRD), but not SCOTIN (PRDΔ150‐177), brings two different liposomes closer in vitro. Using organelle‐specific targeting of a chimeric PRD domain shows that only the presence on both organellar membranes enables the ER‐endosome membrane contact, indicating that the assembly of SCOTIN on heterologous membranes mediates organelle tethering.
Study on band selection algorithms of hyperspectral image data

Based on the characteristic of the HRS image data, the method of dimensionality reduction was discussed.And then some key algorithms such as joint entropy,optimal index factor,auto-subspace partition,adaptive band selection,band index and optimal band index were analyzed.In addition,the effectivity,shortage and complexity between different algorithms were discussed and compared.According to the shortage of band index,the new band selection method which named optimal band index(OBI) was proposed.At last,the feasibility of proposed methods was proved by experiment results.