Miracle-dz/UniFAR-FTUs huggingface dataset:
Infrared Metasurface Augmented by Deep Learning for Monitoring Dynamics between All Major Classes of Biomolecules

Insights into the fascinating molecular world of biological processes are crucial for understanding diseases, developing diagnostics, and effective therapeutics. These processes are complex as they involve interactions between four major classes of biomolecules, i.e., proteins, nucleic acids, carbohydrates, and lipids, which makes it important to be able to discriminate between all these different biomolecular species. In this work, a deep learning‐augmented, chemically‐specific nanoplasmonic technique that enables such a feat in a label‐free manner to not disrupt native processes is presented. The method uses a highly sensitive multiresonant plasmonic metasurface in a microfluidic device, which enhances infrared absorption across a broadband mid‐IR spectrum and in water, despite its strongly overlapping absorption bands. The real‐time format of the optofluidic method enables the collection of a vast amount of spectrotemporal data, which allows the construction of a deep neural network to discriminate accurately between all major classes of biomolecules. The capabilities of the new method are demonstrated by monitoring of a multistep bioassay containing sucrose‐ and nucleotides‐loaded liposomes interacting with a small, lipid membrane‐perforating peptide. It is envisioned that the presented technology will impact the fields of biology, bioanalytics, and pharmacology from fundamental research and disease diagnostics to drug development.
The Prospective Association of Personality Traits and Successful Aging

We used data (N = 928) from ORANJ BOWL, a six-wave panel of adults (aged 50–74 at baseline) to address the association between personality and successful aging at two points in time, 8 years apart. Regressions examined the associations between Wave 2 neuroticism, extraversion, openness, agreeableness, and conscientiousness and Wave 3 subjective success, functional ability, pain, and chronic conditions. Models tested personality traits independently and then simultaneously, with interactions. Confirmatory analyses used Waves 5/6 data. All traits but openness were individually associated with successful aging at both time points. When testing traits simultaneously, only neuroticism and extraversion were consistently associated with subjective success, with an interaction at Waves 2/3. Neuroticism (Waves 2/3) and conscientiousness (Waves 5/6) were associated with functional ability. Neuroticism was associated with pain (Waves 2/3). Personality was not associated with chronic conditions. These analyses set up future work examining relationships between change in personality and change in successful aging.
Bone Mineralization in a Murine Model of Inflammatory Bowel Disease

Reduced bone mass is a common complication of human inflammatory bowel disease, however, the mechanisms that contribute to osteopenia are not completely understood. Cytokines are up regulated in IBD patients and have been shown to have detrimental effects on osteoblasts. PHEX is expressed predominantly in osteoblasts; disruption of the PHEX gene results in defective bone mineralization and renal phosphate wasting. We hypothesize that PHEX gene expression as well as overall Pi homeostasis are altered in individuals with IBD and therefore, may contribute to alterations in bone mineral density observed in individuals with IBD. In vivo studies: 6-7 week old Balb/C mice were intrarectally instilled with TNBS or 50% ethanol. Animals were treated with or without neutralizing anti-TNFα antibody, dietary curcumin, or systemically with recombinant TNFα. RNA was prepared from bone and gene expression was analyzed by PCR. Kidney and small bowel were harvested from control and TNBS treated animals and embedded in paraffin for immunohistochemical analysis. In vitro studies: Cells were treated with IFNγ, IL1-β, IL-6, or TNFα and RNA was collected for real-time PCR analysis. UMR-106 cells were transfected with Phex promoter constructs. PHEX is down-regulated in mice with chemically induced colitis and in the mice injected with TNFα, this decrease was attenuated by curcumin and TNFα antibody. TNFα decreased endogenous levels of PHEX mRNA, protein, and inhibited spontateous mineralization in UMR-106 cells. This regulation occured at a transcriptional level and it appears that the
Multicentered Gaussian‐based potentials for coarse‐grained polymer simulations: Linking atomistic and mesoscopic scales

A new analytical form for bond and angle potentials suitable for obtaining mesoscale effective force fields from target distributions is reported. Applications to realistic coarse-grained models of atactic polystyrene and polyamide-6,6 are described. The potential optimization procedure, despite its simplicity, allows the accurate reproduction of the target atomistic distributions. The procedure has been validated for both bond and angle potentials. Nonbonded numerical potentials have been optimized by pressure-corrected iterative Boltzmann inversion. Thus, the proposed coarse-graining strategy consists of hybrid analytical and numerical contributions to the mesoscale polymer force field. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 871–885, 2005
Concurrent brain parcellation and connectivity estimation via co‐clustering of resting state fMRI data: A novel approach

Connectional topography mapping has been gaining widespread attention in human brain imaging studies. However, existing methods might not effectively utilize the information from neuroimaging data, thus hindering the understanding of the underlying connectional organization in the brain and uncovering the optimal clustering number from the data. In this study, we propose a novel method for the automated construction of inherent functional connectivity topography in a data‐driven manner by leveraging the power of co‐clustering‐based on resting state fMRI (rs‐fMRI) data. We propose the co‐clustering‐based method not only for concurrently parcellating two interconnected brain regions of interest (ROIs) under consideration into functionally homogenous subregions, but also for estimating the connectivity between these subregions from the two brain ROIs. In particular, we first model the connectional topography mapping as a co‐clustering‐based bipartite graph partitioning problem for constructing the inherent functional connectivity topography between the two interconnected brain ROIs. We also adopt an objective criterion, that is, silhouette width index measuring clustering quality, for determining the optimal number of clusters. The proposed method has been validated for mapping thalamocortical connectional topography based on rs‐fMRI data of 57 subjects. Validation results have demonstrated that our method identified the optimal solution with five pairs of mutually connected subregions of the thalamocortical system from the rs‐fMRI data, and could yield more meaningful, interpretable, and homogenous connectional topography than existing methods. The proposed method was further validated by the high symmetry of the mapped connectional topography between two hemispheres.
Impact of hospital-acquired acute kidney injury on Covid-19 outcomes in patients with and without chronic kidney disease: a multicenter retrospective cohort study

Background/aim Hospital-acquired acute kidney injury (HA-AKI) may commonly develop in Covid-19 patients and is expected to have higher mortality. There is little comparative data investigating the effect of HA-AKI on mortality of chronic kidney disease (CKD) patients and a control group of general population suffering from Covid-19. Materials and methods HA-AKI development was assessed in a group of stage 3–5 CKD patients and control group without CKD among adult patients hospitalized for Covid-19. The role of AKI development on the outcome (in-hospital mortality and admission to the intensive care unit [ICU]) of patients with and without CKD was compared. Results Among 621 hospitalized patients (age 60 [IQR: 47–73]), women: 44.1%), AKI developed in 32.5% of the patients, as stage 1 in 84.2%, stage 2 in 8.4%, and stage 3 in 7.4%. AKI developed in 48.0 % of CKD patients, whereas it developed in 17.6% of patients without CKD. CKD patients with HA-AKI had the highest mortality rate of 41.1% compared to 14.3% of patients with HA-AKI but no CKD (p < 0.001). However, patients with AKI+non-CKD had similar rates of ICU admission, mechanical ventilation, and death rate to patients with CKD without AKI. Adjusted mortality risks of the AKI+non-CKD group (HR: 9.0, 95% CI: 1.9–44.2) and AKI+CKD group (HR: 7.9, 95% CI: 1.9–33.3) were significantly higher than that of the non-AKI+non-CKD group. Conclusion AKI frequently develops in hospitalized patients due to Covid-19 and is associated with high mortality. HA-AKI has worse outcomes whether it develops in patients with or without CKD, but the worst outcome was seen in AKI+CKD patients.
Development and usability evaluation of VOICES: A digital health tool to identify elder mistreatment

A major barrier for society in overcoming elder mistreatment is an inability to accurately identify victims. There are several barriers to self‐reporting elder mistreatment, including fear of nursing home placement or losing autonomy or a caregiver. Existing strategies to identify elder mistreatment neglect to empower those who experience it with tools for self‐reporting. In this project, we developed and evaluated the usability of VOICES, a self‐administrated digital health tool that screens, educates, and motivates older adults to self‐report elder mistreatment.
Electrocatalytic Hydrogenation and Hydrogenolysis of Aromatic Halides by Raney Nickel in the Presence of Different Surfactants

Abstract Electrocatalytic hydrogenolysis and hydrogenation of 4-halophenols, 4-chloroaniline and chloronitrobenzene have been investigated in aqueous media using different surfactant agents on two kinds of cathodes investigated on, Raney nickel electrode and carbon electrode.
Aggregating multiple expression prediction models improves the power of transcriptome wide association studies.

Transcriptome-wide association study (TWAS) is an important integrative method for identifying genes that are causally associated with phenotypes. A key step of TWAS involves the construction of expression prediction models for every gene in turn using its cis-SNPs as predictors. Different TWAS methods rely on different models for gene expression prediction and each such model makes a distinct modeling assumption that is often suitable for a particular genetic architecture underlying expression. However, the genetic architectures underlying gene expression vary across genes throughout the transcriptome. Consequently, different TWAS methods may be beneficial in detecting genes with distinct genetic architectures. Here, we develop a new method, HMAT, which aggregates TWAS association evidence obtained across multiple gene expression prediction models by leveraging the harmonic mean p value combination strategy. Because each expression prediction model is suited to capture a particular genetic architecture, aggregating TWAS associations across prediction models as in HMAT improves accurate expression prediction and enables subsequent powerful TWAS analysis across the transcriptome. A key feature of HMAT is its ability to accommodate the correlations among different TWAS test statistics and produce calibrated p values after aggregation. Through numerical simulations, we illustrated the advantage of HMAT over commonly used TWAS methods as well as ad-hoc p value combination rules such as Fisher's method. We also applied HMAT to analyze summary statistics of nine common diseases. In the real data applications, HMAT was on average 30.6% more powerful compared to the next best method, detecting many new disease-associated genes that were otherwise not identified by existing TWAS approaches. In conclusion, HMAT represents a flexible and powerful TWAS method that enjoys robust performance across a range of genetic architectures underlying gene expression.
Development of a fluorescence-linked immunosorbent assay for detection of avermectins using a fluorescent single-domain antibody

A fluorescent single-domain antibody (fluobody), consisting of a single-chain variable fragment antibody (scFv) and a green fluorescent protein extracted from aequorea coerulescens (AcGFP), was produced and used to develop a rapid and sensitive fluorescence-linked immunosorbent assay (FLISA) for the detection of avermectins (AVMs). The scFv gene was prepared by cloning VH and VL genes from a hybridoma cell line (2C11) and then fused to the C-terminus of AcGFP (fluobody) with a flexible peptide linker (Gly4Ser)2 between the two domains. After expression and purification, the functional fluobody was used to develop a one-step FLISA protocol for the determination of AVMs in milk samples. The 50% inhibition concentration (IC50) value and the limit of detection (LOD) of the optimized immunoassay for abamectin (ABM) were 2.13 and 1.07 ng mL−1, respectively. Cross-reactivity studies showed that the fluobody exhibited high affinity for the other four AVMs. The recoveries from the spiked milk samples ranged between 86.8 and 125.0%, with relative standard deviation lower than 10.2%. Moreover, the developed FLISA was applied to field samples, followed by confirmation with liquid chromatography-fluorescence detection (LC-FLD) analysis. The consistency of results between the immunoassay and instrumental techniques in detecting the presence of AVMs near the detection limit of the FLISA indicated that the newly developed method is suitable for rapid screening of AVM contamination in food samples prior to chromatographic analysis.
SETD7 mediates the vascular invasion in articular cartilage and chondrocytes apoptosis in osteoarthriis

The pathological characteristics of osteoarthritis are cartilage matrix degradation, chondrocytes apoptosis, and low‐grade inflammation of the joint. Recent studies have shown that blood vessels grow from the subchondral bone to the articular cartilage. However, the relationship among inflammation, angiogenesis, and chondrocyte apoptosis is still unclear. We found that chondrocytes could secrete chemokines and VEGF to promote the migration of vascular endothelial cells in response to TNF‐α stimulation. The invasion of blood vessels leads to increased oxygen tension in the local environment, which increased the expression of SETD7 in chondrocytes by activating the JAK‐STAT5 pathway. The bond of phosphorylated STAT5 and the specific locus in the promoter of SETD7 directly increased the transcription of SETD7. On the one hand, SETD7‐regulated chemokine expression by forming a positive loop; on the other hand, SETD7‐mediated chondrocyte apoptosis by inhibiting the nuclear localization of HIF‐1α. In this study, we discovered a novel function of chondrocytes as mediators of inflammation and angiogenesis. Our study demonstrates that SETD7 is a potential molecular target to prevent OA development and progression.
Reducing Risky Drug Use Behaviors by Enrolling Syringe Exchange Registrants in Methadone Maintenance

Abstract Background Referral of syringe exchange registrants with opioid use disorder to agonist treatment provides a pathway to further reduce drug use risk behaviors. Objective: This study evaluates the drug use risk reduction benefits of enrolling syringe exchange registrants in methadone maintenance, and the impact of continued illicit drug use on risk reduction. Method: Baltimore Needle Exchange Program (BNEP) registrants (n = 210) participated in a parent study evaluating treatment initiation strategies for methadone maintenance and were followed for six months. The Risk Assessment Battery (RAB; Metzger, 1993) was administered monthly to evaluate drug use risks; urinalysis testing was conducted weekly. Results: Treatment enrollment reduced drug use risk behaviors, and longer treatment episodes resulted in additional, though modest, risk reduction. Use of opioids or cocaine in treatment diminished risk-reduction benefits, though drug use risks declined over time and remained well below baseline levels. Conclusions: These findings demonstrate that methadone maintenance enhances the well-known risk-reduction benefits of syringe exchange participation. Improving coordination between syringe exchanges and treatment facilities may enhance the public health.
Effect of nanoclays on the dyeability of polypropylene nanocomposite fibres

using a melt spinning technique and relationships between the structure and properties of the nanopolypropylene fibres are discussed. Experiments carried out using transmission electron microscopy showed that the chemical structure of the organic modifier and the interlayer spacing of the clay induced different dispersions of the clay, thus improving accessibility of the nano fibre. It is known that nanoclays are effective and efficient sorbents for dyes. Therefore, the dyeing behaviour of the nano polypropylene fibres with two distinct acid dyes and a disperse dye was studied and the build-up of dyes, measured as colour yield, reported. The best results were obtained when the clay was well dispersed in nanopolypropylene fibres; that is, when maleated polypropylene was added as a compatibiliser and when disperse dye was used. Good wash fastness was then obtained.
Longevity of resin-bonded fixed partial dentures made of metal alloys: A review of the literature.

PURPOSE In this review, we evaluate the survival rate of resin-bonded fixed partial dentures (RBFPDs) made of metal alloys. METHODS An electronic search of English peer-reviewed dental literature on PubMed was conducted to identify all publications reporting on RBFPDs made of metal alloys until March 2019. The searched keywords were: bridge OR fixed partial denture OR fixed prosthesis OR fixed prostheses AND resin bonded AND metal OR alloy AND survival OR longevity (RBFPD was not included). Furthermore, the "Related Articles" feature of PubMed was used to identify further references of interest during the primary search. A definitive list of articles was screened to extract qualitative data after the application of the inclusion and exclusion criteria, and the results were analyzed. RESULTS Overall, 977 publications were found through an electronic and manual search, out of which 130 articles were selected after screening based on title and abstract. A total of 52 publications passed the second review phase after assessment for eligibility, from which 24 studies were excluded after full-text screening. Finally, a total of 28 studies were selected. CONCLUSIONS The survival rate of RBFPDs differed greatly depending on the type of metal alloy, adhesion system, and observation period assessed, e.g. the 10-year survival rate ranged from 18 % to 88 %. The wide range of survival rates of the RBFPDs reported indicates that though RBFPD is a reliable prosthesis, it is prone to failure if some processes are not completed.
Fabrication and Characterization of Regenerated Cellulose Films Using Different Ionic Liquids

The demand for substitution of fossil-based materials by renewable bio-based materials is increasing with the fossil resources reduction and its negative impacts on the environment. In this study, environmentally friendly regenerated cellulose films were successfully prepared using 1-allyl-3-methylimidazolium chloride (AmimCl), 1-butyl-3-methylimidazolium chloride (BmimCl), 1-ethyl-3-methylimidazolium chloride (EmimCl), and 1-ethyl-3-methylimidazolium acetate (EmimAc) as solvents, respectively. The results of morphology from scanning electron microscopy (SEM) and atomic force microscopy (AFM) showed that all the cellulose films possessed smooth, highly uniform, and dense surface. The solid-state cross-polarization/magic angle spinning (CP/MAS) 13C NMR spectra and X-ray diffraction (XRD) corroborated that the transition from cellulose I to II had occurred after preparation. Moreover, it was shown that the ionic liquid EmimAc possessed much stronger dissolubility for cellulose as compared with other ionic liquids and the cellulose film regenerated from EmimCl exhibited the most excellent tensile strength (119 Mpa). The notable properties of regenerated cellulose films are promising for applications in transparent biodegradable packaging and agricultural purpose as a substitute for PP and PE.
Structural basis for noradrenergic regulation of neural circuits in the mouse olfactory bulb

Olfactory input is processed in the glomerulus of the main olfactory bulb (OB) and relayed to higher centers in the brain by projection neurons. Conversely, centrifugal inputs from other brain regions project to the OB. We have previously analyzed centrifugal inputs into the OB from several brain regions using single‐neuron labeling. In this study, we analyzed the centrifugal noradrenergic (NA) fibers derived from the locus coeruleus (LC), because their projection pathways and synaptic connections in the OB have not been clarified in detail. We analyzed the NA centrifugal projections by single‐neuron labeling and immunoelectron microscopy. Individual NA neurons labeled by viral infection were three‐dimensionally traced using Neurolucida software to visualize the projection pathway from the LC to the OB. Also, centrifugal NA fibers were visualized using an antibody for noradrenaline transporter (NET). NET immunoreactive (‐ir) fibers contained many varicosities and synaptic vesicles. Furthermore, electron tomography demonstrated that NET‐ir fibers formed asymmetrical synapses of varied morphology. Although these synapses were present at varicosities, the density of synapses was relatively low throughout the OB. The maximal density of synapses was found in the external plexiform layer; about 17% of all observed varicosities contained synapses. These results strongly suggest that NA‐containing fibers in the OB release NA from both varicosities and synapses to influence the activities of OB neurons. The present study provides a morphological basis for olfactory modulation by centrifugal NA fibers derived from the LC.
Did COVID-19 change the interventions provided by oncology social workers in the epicenter of the pandemic? A natural experiment

Abstract Background: Throughout history, the field of medical social work has been shaped by epidemics and pandemics. As COVID-19 rapidly overwhelmed the healthcare system in 2020, oncology departments found that space, staff, and funds were reallocated to address patient needs during the pandemic. Traditional outpatient services were required to operate with reduced resources, with special attention to additional measures to protect workers and patients from exposure to the virus. Little is known about how these changes affected the nature of the practice of oncology social work. Methods: We compared data on OSW interventions for three months (March-May) 2019 to the same period in 2020. Mount Sinai Downtown Cancer Center’s Department of Social Work routinely collects data on services provided by social workers using a validated instrument. As NYC became the epicenter of the COVID-19 in March 2020, the comparison of these time periods creates a natural experiment to examine whether and how the presence of the virus impacted the services provided by OSWs. Findings: There was little difference in the number of encounters that took place between the two time periods (2186 encounters in 2019 and 2084 encounters in 2020); however, there were notable differences in the types of interventions. While interventions involving supportive counseling decreased in 2020, we identified a significant increase specific to bereavement counseling. Conclusion: The study shows a remarkable consistency in the volume and types of services provided by OSWs, in spite of the radical increase in stressors they experienced during the height of the COVID-19 pandemic. These findings suggest that the OSWs did not allow these stressors to interfere with their work with patients. This study demonstrates how routine use of an instrument to measure OSW interventions can be used to examine services provided over time and to evaluate potential influences of external factors.