Miracle-dz/UniFAR-FTUs huggingface dataset:
NIR Scaffold Bearing Three Handles for Biocompatible Sequential Click Installation of Multiple Functional Arms.

Near-infrared (NIR) probes are ideal for fluorescence labeling and imaging of biological targets in living animals. But the instability of common NIR dyes hampers the construction of NIR probes bearing multiple functional components such as biomolecules for specific targeting and imaging reagents for multi-modality imaging. To overcome these limitations, we designed a novel NIR scaffold bearing two terminal alkyne as clickable handles and a chloride on the heptamethine backbone that allows nucleophilic substitution with an azide to generate the third clickable handle. This unique scaffold allows for facile installation of multiple functional arms for the construction of multi-functional NIR probes. Various biomacromolecules or imaging reagents can be introduced to the NIR scaffold by sequential one-pot click reactions under biocompatible conditions. The pre-clickable handle chloride on the NIR backbone does not interfere with the initial click reactions, it and can be easily transformed into an azide for a following click reaction. Based on this unique NIR scaffold, we developed a highly efficient method to construct diverse NIR probes containing multiple functional biomolecules including peptides, antibodies, nucleic acids, and NIR/PET (Positron Emission Tomography) dual-modality imaging probes bearing tumor-targeting groups. NIR imaging or multi-modality imaging using these probes were performed on live cells or tumor models on living mice.
Evaluation of Resistance to Violence in Intimate Relationships: Initial Development and Validation

This study addresses the need for assessments to support clinical practice and research with survivors/victims of intimate partner violence (IPV). A total of 236 women who stayed in domestic violence shelters in a Northeastern state completed responses to 38 statements defining three categories of resistance to IPV: (a) yielding, (b) withdrawing, and (c) confronting. Content validity was established through interviews with survivors and reviews by a panel of experts. Results of an exploratory factor analysis yielded a three-factor solution. Subscale scores showed satisfactory internal consistency reliability coefficients. Implications for practitioners and researchers are discussed.
SPH Fluid Tactile Rendering for Ultrasonic Mid-Air Haptics

In our daily lives, we interact with fluids by touching them directly with our hands. Fluids produce a pressure field against the surface of our hands, and we experience fluid dynamics over our skin temporally and spatially at varying pressure distributions depending on fluid properties as well as on the interacting hand's poses and motions. To improve the realism of fluid simulation together with user interaction, we propose a real-time fluid tactile rendering technique that computes the pressure field on a virtual hand surface to be delivered to the user's actual hand via ultrasound-based mid-air haptic display. Our haptic rendering algorithm computes the feedback force in two stages: First, the pressure distribution of the rigid-fluid interaction is computed from a real-time Lagrangian fluid simulation, and then a set of focal points that reflects the generated pressure field is extracted by using a hill-climbing method which gives the local extrema of the pressure field of simulation. We implement a real-time smoothed-particle hydrodynamics fluid simulator and the proposed haptic rendering algorithm using adaptive amplitude modulation approach to demonstrate the effectiveness of our method in fluid tactile rendering in various scenarios.
Functional binding of E-selectin to its ligands is enhanced by structural features beyond its lectin domain

Selectins are key to mediating interactions involved in cellular adhesion and migration, underlying processes such as immune responses, metastasis, and transplantation. Selectins are composed of a lectin domain, an epidermal growth factor (EGF)-like domain, multiple short consensus repeats (SCRs), a transmembrane domain, and a cytoplasmic tail. It is well-established that the lectin and EGF domains are required to mediate interactions with ligands; however, the contributions of the other domains in mediating these interactions remain obscure. Using various E-selectin constructs produced in a newly developed silkworm-based expression system and several assays performed under both static and physiological flow conditions, including flow cytometry, glycan array analysis, surface plasmon resonance, and cell-rolling assays, we show here that a reduction in the number of SCR domains is correlated with a decline in functional E-selectin binding to hematopoietic cell E- and/or L-selectin ligand (HCELL) and P-selectin glycoprotein ligand-1 (PSGL-1). Moreover, the binding was significantly improved through E-selectin dimerization and by a substitution (A28H) that mimics an extended conformation of the lectin and EGF domains. Analyses of the association and dissociation rates indicated that the SCR domains, conformational extension, and dimerization collectively contribute to the association rate of E-selectin–ligand binding, whereas just the lectin and EGF domains contribute to the dissociation rate. These findings provide the first evidence of the critical role of the association rate in functional E-selectin–ligand interactions, and they highlight that the SCR domains have an important role that goes beyond the structural extension of the lectin and EGF domains.
Arabidopsis Class II Formins AtFH13 and AtFH14 Can Form Heterodimers but Exhibit Distinct Patterns of Cellular Localization

Formins are evolutionarily conserved multi-domain proteins participating in the control of both actin and microtubule dynamics. Angiosperm formins form two evolutionarily distinct families, Class I and Class II, with class-specific domain layouts. The model plant Arabidopsis thaliana has 21 formin-encoding loci, including 10 Class II members. In this study, we analyze the subcellular localization of two A. thaliana Class II formins exhibiting typical domain organization, the so far uncharacterized formin AtFH13 (At5g58160) and its distant homolog AtFH14 (At1g31810), previously reported to bind microtubules. Fluorescent protein-tagged full length formins and their individual domains were transiently expressed in Nicotiana benthamiana leaves under the control of a constitutive promoter and their subcellular localization (including co-localization with cytoskeletal structures and the endoplasmic reticulum) was examined using confocal microscopy. While the two formins exhibit distinct and only partially overlapping localization patterns, they both associate with microtubules via the conserved formin homology 2 (FH2) domain and with the periphery of the endoplasmic reticulum, at least in part via the N-terminal PTEN (Phosphatase and Tensin)-like domain. Surprisingly, FH2 domains of AtFH13 and AtFH14 can form heterodimers in the yeast two-hybrid assay—a first case of potentially biologically relevant formin heterodimerization mediated solely by the FH2 domain.
Molecular Mechanisms of Bortezomib Action: Novel Evidence for the miRNA–mRNA Interaction Involvement

Bortezomib is an anti-tumor agent, which inhibits 26S proteasome degrading ubiquitinated proteins. While apoptotic transcription-associated activation in response to bortezomib has been suggested, mechanisms related to its influence on post-transcriptional gene silencing mediated regulation by non-coding RNAs remain not fully elucidated. In the present study, we examined changes in global gene and miRNA expression and analyzed the identified miRNA–mRNA interactions after bortezomib exposure in human neuroblastoma cells to define pathways affected by this agent in this type of cells. Cell viability assays were performed to assess cytotoxicity of bortezomib. Global gene and miRNA expression profiles of neuroblastoma cells after 24-h incubation with bortezomib were determined using genome-wide RNA and miRNA microarray technology. Obtained results were then confirmed by qRT-PCR and Western blot. Further bioinformatical analysis was performed to identify affected biological processes and pathways. In total, 719 genes and 28 miRNAs were downregulated, and 319 genes and 61 miRNAs were upregulated in neuroblastoma cells treated with bortezomib. Possible interactions between dysregulated miRNA/mRNA, which could be linked to bortezomib-induced neurotoxicity, affect neurogenesis, cellular calcium transport, and neuron death. Bortezomib might exert toxic effects on neuroblastoma cells and regulate miRNA–mRNA interactions influencing vital cellular functions. Further studies on the role of specific miRNA–mRNA interactions are needed to elucidate mechanisms of bortezomib action.
Stem Cell-Induced Inflammation in Cholesteatoma Is Inhibited by the TLR4 Antagonist LPS-RS

Cholesteatoma is a severe non-cancerous lesion of the middle ear characterized by massive inflammation, tissue destruction, and an abnormal growth of keratinized squamous epithelium. We recently demonstrated the presence of pathogenic stem cells within cholesteatoma tissue, unfortunately their potential roles in regulating disease-specific chronic inflammation remain poorly understood. In the presented study, we utilized our established human in vitro cholesteatoma stem cell model for treatments with lipopolysaccharides (LPS), tumor necrosis factor α (TNFα), and the TLR4-antagonist LPS from R. sphaeroides (LPS-RS) followed by qPCR, western blot, and immunocytochemistry. Middle ear cholesteatoma stem cells (ME-CSCs) showed a significantly increased expression of TLR4 accompanied by a significantly enhanced LPS-dependent pro-inflammatory gene expression pattern of TNFα, IL-1α, IL-1ß, IL-6, and IL-8 compared to non-pathogenic control cells. LPS-dependent pro-inflammatory gene expression in ME-CSCs was driven by an enhanced activity of NF-κB p65 leading to a TNFα-mediated feed-forward-loop of pro-inflammatory NF-κB target gene expression. Functional inactivation of TLR4 via the TLR4-antagonist LPS-RS blocked chronic inflammation in ME-CSCs, resulting in a nearly complete loss of IL-1ß, IL-6, and TNFα expression. In summary, we determined that ME-CSCs mediate the inflammatory environment of cholesteatoma via TLR4-mediated NF-κB-signaling, suggesting a distinct role of ME-CSCs as drivers of cholesteatoma progression and TLR4 on ME-CSCs as a therapeutic target.
Ultradeep Microbial Communities at 4.4 km within Crystalline Bedrock: Implications for Habitability in a Planetary Context

The deep bedrock surroundings are an analog for extraterrestrial habitats for life. In this study, we investigated microbial life within anoxic ultradeep boreholes in Precambrian bedrock, including the adaptation to environmental conditions and lifestyle of these organisms. Samples were collected from Pyhäsalmi mine environment in central Finland and from geothermal drilling wells in Otaniemi, Espoo, in southern Finland. Microbial communities inhabiting the up to 4.4 km deep bedrock were characterized with phylogenetic marker gene (16S rRNA genes and fungal ITS region) amplicon and DNA and cDNA metagenomic sequencing. Functional marker genes (dsrB, mcrA, narG) were quantified with qPCR. Results showed that although crystalline bedrock provides very limited substrates for life, the microbial communities are diverse. Gammaproteobacterial phylotypes were most dominant in both studied sites. Alkanindiges -affiliating OTU was dominating in Pyhäsalmi fluids, while different depths of Otaniemi samples were dominated by Pseudomonas. One of the most common OTUs detected from Otaniemi could only be classified to phylum level, highlighting the uncharacterized nature of the deep biosphere in bedrock. Chemoheterotrophy, fermentation and nitrogen cycling are potentially significant metabolisms in these ultradeep environments. To conclude, this study provides information on microbial ecology of low biomass, carbon-depleted and energy-deprived deep subsurface environment. This information is useful in the prospect of finding life in other planetary bodies.
Bioinformatics and Computational Tools for Next-Generation Sequencing Analysis in Clinical Genetics

Clinical genetics has an important role in the healthcare system to provide a definitive diagnosis for many rare syndromes. It also can have an influence over genetics prevention, disease prognosis and assisting the selection of the best options of care/treatment for patients. Next-generation sequencing (NGS) has transformed clinical genetics making possible to analyze hundreds of genes at an unprecedented speed and at a lower price when comparing to conventional Sanger sequencing. Despite the growing literature concerning NGS in a clinical setting, this review aims to fill the gap that exists among (bio)informaticians, molecular geneticists and clinicians, by presenting a general overview of the NGS technology and workflow. First, we will review the current NGS platforms, focusing on the two main platforms Illumina and Ion Torrent, and discussing the major strong points and weaknesses intrinsic to each platform. Next, the NGS analytical bioinformatic pipelines are dissected, giving some emphasis to the algorithms commonly used to generate process data and to analyze sequence variants. Finally, the main challenges around NGS bioinformatics are placed in perspective for future developments. Even with the huge achievements made in NGS technology and bioinformatics, further improvements in bioinformatic algorithms are still required to deal with complex and genetically heterogeneous disorders.
Preparation and Characterization of Surface Heat Sintered Nanohydroxyapatite and Nanowhitlockite Embedded Poly (Lactic-co-glycolic Acid) Microsphere Bone Graft Scaffolds: In Vitro and in Vivo Studies

In the context of using bone graft materials to restore and improve the function of damaged bone tissues, macroporous biodegradable composite bone graft scaffolds have osteoinductive properties that allow them to provide a suitable environment for bone regeneration. Hydroxyapatite (HAP) and whitlockite (WLKT) are the two major components of hard tissues such as bone and teeth. Because of their biocompatibility and osteoinductivity, we synthesized HAP (nHAP) and WLKT nanoparticles (nWLKT) by using the chemical precipitation method. The nanoparticles were separately incorporated within poly (lactic-co-glycolic acid) (PLGA) microspheres. Following this, the composite microspheres were converted to macroporous bone grafts with sufficient mechanical strength in pin or screw shape through surface sintering. We characterized physico-chemical and mechanical properties of the nanoparticles and composites. The biocompatibility of the grafts was further tested through in vitro cell adhesion and proliferation studies using rabbit bone marrow stem cells. The ability to promote osteogenic differentiation was tested through alkaline phosphate activity and immunofluorescence staining of bone marker proteins. For in vivo study, the bone pins were implanted in tibia bone defects in rabbits to compare the bone regeneration ability though H&E, Masson’s trichrome and immunohistochemical staining. The results revealed similar physico-chemical characteristics and cellular response of PLGA/nHAP and PLGA/nWLKT scaffolds but the latter is associated with higher osteogenic potential towards BMSCs, pointing out the possibility to use this ceramic nanoparticle to prepare a sintered composite microsphere scaffold for potential bone grafts and tissue engineered implants.
Meta-Analysis of Dilated Cardiomyopathy Using Cardiac RNA-Seq Transcriptomic Datasets

Dilated cardiomyopathy (DCM) is one of the most common causes of heart failure. Several studies have used RNA-sequencing (RNA-seq) to profile differentially expressed genes (DEGs) associated with DCM. In this study, we aimed to profile gene expression signatures and identify novel genes associated with DCM through a quantitative meta-analysis of three publicly available RNA-seq studies using human left ventricle tissues from 41 DCM cases and 21 control samples. Our meta-analysis identified 789 DEGs including 581 downregulated and 208 upregulated genes. Several DCM-related genes previously reported, including MYH6, CKM, NKX2–5 and ATP2A2, were among the top 50 DEGs. Our meta-analysis also identified 39 new DEGs that were not detected using those individual RNA-seq datasets. Some of those genes, including PTH1R, ADAM15 and S100A4, confirmed previous reports of associations with cardiovascular functions. Using DEGs from this meta-analysis, the Ingenuity Pathway Analysis (IPA) identified five activated toxicity pathways, including failure of heart as the most significant pathway. Among the upstream regulators, SMARCA4 was downregulated and prioritized by IPA as the top affected upstream regulator for several DCM-related genes. To our knowledge, this study is the first to perform a transcriptomic meta-analysis for clinical DCM using RNA-seq datasets. Overall, our meta-analysis successfully identified a core set of genes associated with DCM.
Specific components of a complex depression care program can affect staff outcomes differently: post-hoc analyses of a stepped-wedge cluster-randomized trial in nursing homes

ABSTRACT Objective: The Act in case of Depression program showed effects on the quality of life and depression in nursing home (NH) residents. We aimed to explore the effects of this complex multidisciplinary program on job satisfaction, job demands, and autonomy in nursing home staff. Design: Four data points from a stepped-wedge cluster-randomized trial on patient outcomes were used for secondary analyses on staff outcomes. Setting: Sixteen dementia special care and 17 somatic care units in Dutch NHs. Participants were 717 (90.1%) care staff or trainees, 34 (4.3%) paramedical staff, and 45 (5.7%) other staff members. Intervention describes procedures for nursing staff, activity therapists, psychologists, and physicians. It contains evidence-based pathways for depression assessment, treatment, and monitoring treatment results. Results: Mixed models for intention-to-treat analyses showed no significant changes in job demands, job satisfaction, or autonomy. Models corrected for the ratio of unit residents who received, when indicated, a specific program component revealed reduced job demands and improved job satisfaction and autonomy when treatment procedures were used. A better use of assessment procedures was associated with increased job demands, while conducting monitoring procedures was associated with increased job demands and decreased autonomy. Conclusions: Components of complex care programs may affect the staff outcomes in opposite directions and, taken together, produce a zero-sum or a statistically insignificant effect. While implementing treatment protocols affecting patients directly can also improve job outcomes such as satisfaction and autonomy and decrease job demands, it is possible that other procedures of complex programs may have unfavorable effects on job outcomes. It is important to account for specific components of complex interventions when evaluating intervention effects.
Effect of Toll‐like receptor 4 on depressive‐like behaviors induced by chronic social defeat stress

A growing body of evidence suggests that stress is an important factor in depression, and pro‐inflammatory cytokines contribute to the occurrence and development of depression in both animal models and human patients. Toll‐like receptor 4 (TLR4) has been shown to be a key innate immune pattern recognition receptor involved in the regulation of stress responses and inflammation. However, the exact effects of TLR4 on depressive‐like behaviors induced by chronic social defeat stress (CSDS) are not known.
Evaluation of inactivated Bordetella pertussis as a delivery system for the immunization of mice with Pneumococcal Surface Antigen A

Pneumococcal Surface Protein A (PspA) has been successfully tested as vaccine candidate against Streptococcus pneumoniae infections. Vaccines able to induce PspA-specific antibodies and Th1 cytokines usually provide protection in mice. We have shown that the whole cell pertussis vaccine (wP) or components from acellular pertussis vaccines, such as Pertussis Toxin or Filamentous Hemagglutinin (FHA), are good adjuvants to PspA, suggesting that combined pertussis-PspA vaccines would be interesting strategies against the two infections. Here, we evaluated the potential of wP as a delivery vector to PspA. Bordetella pertussis strains producing a PspA from clade 4 (PspA4Pro) fused to the N-terminal region of FHA (Fha44) were constructed and inactivated with formaldehyde for the production of wPPspA4Pro. Subcutaneous immunization of mice with wPPspA4Pro induced low levels of anti-PspA4 IgG, even after 3 doses, and did not protect against a lethal pneumococcal challenge. Prime-boost strategies using wPPspA4Pro and PspA4Pro showed that there was no advantage in using the wPPspA4Pro vaccine. Immunization of mice with purified PspA4Pro induced higher levels of antibodies and protection against pneumococcal infection than the prime-boost strategies. Finally, purified Fha44:PspA4Pro induced high levels of anti-PspA4Pro IgG, but no protection, suggesting that the antibodies induced by the fusion protein were not directed to protective epitopes.
Switchable Wettability of Poly(NIPAAm-co-HEMA-co-NMA) Coated PET Fabric for Moisture Management

In this study, we synthesized a random poly[(N-isopropylacrylamide)-co-(2-hydroxyethylmethacrylate)-co-(N-methylolacrylamide)] [poly(NIPAAm-co-HEMA-co-NMA)] copolymer through free-radical polymerization. The NIPAAm, HEMA and NMA moieties were framed to provide thermoresponsiveness, water absorption and retention control, and chemical cross-linking to achieve stability in aqueous medium, respectively. The copolymer showed a significant change in optical transmittance with a variation in temperature due to the change in volume (i.e., hydrophilic/hydrophobic) between 25 °C and 40 °C, attributed to the lower critical solution temperature property of the NIPAAm moiety. The copolymers were wire-bar-coated onto polyethylene terephthalate (PET) fabric. Variation in the water contact angle affirmed the switchable wettability due to the change in temperature. We tested the coated fabrics for moisture absorption and release at different temperatures. The results at 20 °C and 37 °C indicated that the P2 copolymer had the highest moisture absorption and release capability. Therefore, the copolymers with tailored properties can be used as smart textiles for activity specific clothing.
The gathering firestorm in southern Amazonia

Amazon wildfires could emit 17.0 Pg of CO2 by 2050, and avoiding new deforestation could cut associated net emissions by half. Wildfires, exacerbated by extreme weather events and land use, threaten to change the Amazon from a net carbon sink to a net carbon source. Here, we develop and apply a coupled ecosystem-fire model to quantify how greenhouse gas–driven drying and warming would affect wildfires and associated CO2 emissions in the southern Brazilian Amazon. Regional climate projections suggest that Amazon fire regimes will intensify under both low- and high-emission scenarios. Our results indicate that projected climatic changes will double the area burned by wildfires, affecting up to 16% of the region’s forests by 2050. Although these fires could emit as much as 17.0 Pg of CO2 equivalent to the atmosphere, avoiding new deforestation could cut total net fire emissions in half and help prevent fires from escaping into protected areas and indigenous lands. Aggressive efforts to eliminate ignition sources and suppress wildfires will be critical to conserve southern Amazon forests.