Miracle-dz/UniFAR-FTUs huggingface dataset:
A far-red cyanobacteriochrome lineage specific for verdins

Significance Cyanobacteriochrome (CBCR) photoreceptors leverage light-triggered photoisomerization of bound bilin chromophores to regulate gene expression, directional movement, and cell–cell communication in cyanobacteria. CBCRs responding to far-red light provide an emerging class of small reagents for applications in synthetic biology. We have found CBCRs that use 181,182-dihydrobiliverdin or biliverdin chromophore precursors to sense far-red light. This lineage is distinguished from others by exclusion of phycobilins, the normal CBCR chromophores. Owing to the deep penetrance of far-red light in mammalian tissue and availability of biliverdin therein, this lineage of CBCRs holds great potential for developing synthetic biology tools of biomedical interest. Cyanobacteriochromes (CBCRs) are photoswitchable linear tetrapyrrole (bilin)-based light sensors in the phytochrome superfamily with a broad spectral range from the near UV through the far red (330 to 760 nm). The recent discovery of far-red absorbing CBCRs (frCBCRs) has garnered considerable interest from the optogenetic and imaging communities because of the deep penetrance of far-red light into mammalian tissue and the small size of the CBCR protein scaffold. The present studies were undertaken to determine the structural basis for far-red absorption by JSC1_58120g3, a frCBCR from the thermophilic cyanobacterium Leptolyngbya sp. JSC-1 that is a representative member of a phylogenetically distinct class. Unlike most CBCRs that bind phycocyanobilin (PCB), a phycobilin naturally occurring in cyanobacteria and only a few eukaryotic phototrophs, JSC1_58120g3’s far-red absorption arises from incorporation of the PCB biosynthetic intermediate 181,182-dihydrobiliverdin (181,182-DHBV) rather than the more reduced and more abundant PCB. JSC1_58120g3 can also yield a far-red–absorbing adduct with the more widespread linear tetrapyrrole biliverdin IXα (BV), thus circumventing the need to coproduce or supplement optogenetic cell lines with PCB. Using high-resolution X-ray crystal structures of 181,182-DHBV and BV adducts of JSC1_58120g3 along with structure-guided mutagenesis, we have defined residues critical for its verdin-binding preference and far-red absorption. Far-red sensing and verdin incorporation make this frCBCR lineage an attractive template for developing robust optogenetic and imaging reagents for deep tissue applications.
Low-dose radiation treatment enhances systemic antitumor immune responses by overcoming the inhibitory stroma

Background Despite some successes with checkpoint inhibitors for treating cancer, most patients remain refractory to treatment, possibly due to the inhibitory nature of the tumor stroma that impedes the function and entry of effector cells. We devised a new technique of combining immunotherapy with radiotherapy (XRT), more specifically low-dose XRT, to overcome the stroma and maximize systemic outcomes. Methods We bilaterally established 344SQ lung adenocarcinoma tumors in 129Sv/Ev mice. Primary and secondary tumors were irradiated with either high-dose or low-dose of XRT with systemic anti-programmed cell death protein 1 and anti-cytotoxic T-lymphocyte associated protein 4 administration. Survival and tumor growth were monitored for the various groups, and secondary tumors were phenotyped by flow cytometry for immune populations. Tumor growth factor-beta (TGF-β) cytokine levels were assessed locally after low-dose XRT, and specific immune-cell depletion experiments were conducted to identify the major contributors to the observed systemic antitumor effect. Results Through our preclinical and clinical studies, we observed that when tumor burden was high, there was a necessity of combining high-dose XRT to ‘prime’ T cells at the primary tumor site, with low-dose XRT directed to secondary (metastatic) tumors to ‘modulate the stroma’. Low-dose XRT improved the antitumor outcomes of checkpoint inhibitors by favoring M1 macrophage polarization, enhancing natural killer (NK) cell infiltration, and reducing TGF-β levels. Depletion of CD4+ T cells and NK cells abrogated the observed antitumor effect. Conclusion Our data extend the benefits of low-dose XRT to reprogram the tumor environment and improve the infiltration and function of effector immune cells into secondary tumors.
Enhanced oral bioavailability of an etoposide multiple nanoemulsion incorporating a deoxycholic acid derivative–lipid complex

Abstract In this study, a system for oral delivery of etoposide (ETP) was designed to avoid the problems associated with low and variable bioavailability of a commercially available ETP emulsion comprised of polyethylene glycol, glycerol, and citric acid anhydrous. ETP was complexed with low-molecular-weight methylcellulose (ETP/LMC) and loaded into a water-in-oil-in-water multiple nanoemulsion to formulate an ETP/LMC-nanoemulsion (ELNE). To further enhance the oral bioavailability, an ionic complex formed by anionic lipid 1,2-didecanoyl-sn-glycero-3-phosphate (sodium salt) and cationic N α-deoxycholyl-l-lysyl-methylester was incorporated into ELNE, yielding ELNE#7. As expected, ELNE#7 showed 4.07- and 2.25-fold increases in artificial membrane and Caco-2/HT29-MTX-E12 permeability (Papp ), respectively, resulting in 224% greater oral bioavailability compared with the commercially available ETP emulsion. In contrast, inhibition of clathrin- and caveola-mediated endocytosis, macropinocytosis, and bile acid transporters by chlorpromazine, genistein, amiloride, and actinomycin D in Caco-2/HT-29-MTX-E12 monolayers reduced the Papp by 45.0%, 20.5%, 28.8%, and 31.1%, respectively. These findings suggest that these routes play important roles in enhancing the oral absorption of ELNE#7. In addition, our mechanistic study suggested that P-glycoprotein did not have an inhibitory effect on the permeation of ELNE#7. Notably, ELNE#7 showed significantly enhanced toxicity in LLC and A549 cells compared with ETP-E. These observations support the improved oral absorption of ETP in ELNE#7, suggesting that it is a better alternative than ETP emulsion.
Endoplasmic Reticulum Stress in Hearing Loss

The endoplasmic reticulum (ER) plays important roles in coordinating protein biosynthesis and secretion in the cell. Accumulation of misfolded and/or unfolded proteins in the ER causes ER stress and the so-called unfolded protein response (UPR). The UPR alleviates ER stress through blocking protein synthesis and activating expression of chaperone genes, whereas prolonged UPR could induce cell death. Recent research has showed that ER stress and UPR are involved in hearing loss. Accordingly, animal experiments showed that chemical chaperones or ER stress inducers alleviate environment-related hearing loss, whereas ER stress inhibitor has been used to treat certain types of hereditary deafness. Further investigations are needed to fully understand the detailed mechanisms of how ER stress contributes to the loss of auditory function, which will help us to eventually develop ER-stress-related treatment of various types of deafness.
Menstrual Cycle Patterns and Irregularities in Hired Latinx Child Farmworkers.

PURPOSE This study identifies the menstrual cycle irregularities of Latinx child and adolescent farmworkers. METHODS Child and adolescent farmworkers aged 13-20 years completed questionnaires about menstrual cycle patterns in 2019, and wore silicone passive collection wristbands for pesticide detection in 2018. Menstrual cycle irregularities were determined from the American College of Obstetricians and Gynecologists committee opinion. RESULTS Half of participants experienced any menstrual cycle irregularity; the most frequent irregularities were cycle length (38.6%) and having gone 90 days or more without a menstrual period (20.4%). Pesticides were detected in 92.9% of the wristbands; most participants were exposed to an endocrine disrupting chemical (EDC) pesticide. CONCLUSION Half of Latinx children and adolescents hired farmworkers experience irregular menstrual cycles, and most are exposed to EDCs. Inclusion of occupational and menstrual histories in child and adolescent medical visits is critical.
Utility of entomological indices for predicting transmission of dengue virus: secondary analysis of data from the Camino Verde trial in Mexico and Nicaragua

Background Dengue vector entomological indices are widely used to monitor vector density and disease control activities. But the value of these indices as predictors of dengue infection is not established. We used data from the impact assessment of a trial of community mobilization for dengue prevention (Camino Verde) to examine the associations between vector indices and evidence of dengue infection and their value for predicting dengue infection levels. In 150 clusters in Mexico and Nicaragua, two entomological surveys, three months apart, allowed calculation of the mean Container Index, Breteau index, Pupae per Household Index, and Pupae per Container Index across the two surveys. We measured recent dengue virus infection in children, indicated by a doubling of dengue antibodies in paired saliva samples over the three-month period. We examined the associations between each of the vector indices and evidence of dengue infection at household level and at cluster level, accounting for trial intervention status. To examine the predictive value for dengue infection, we constructed receiver operating characteristic (ROC) curves at household and cluster level, considering the four vector indices as continuous variables, and calculated the positive and negative likelihood ratios for different levels of the indices. None of the vector indices was associated with recent dengue infection at household level. The Breteau Index was associated with recent infection at cluster level (Odds ratio 1.36, 95% confidence interval 1.14–1.61). The ROC curve confirmed the weak predictive value for dengue infection of the Breteau Index at cluster level. Other indices showed no predictive value. Conventional vector indices were not useful in predicting dengue infection in Mexico and Nicaragua. The findings are compatible with the idea of sources of infection outside the household which were tackled by community action in the Camino Verde trial.
Data-Driven Insights on the Effects of COVID-19 on Public Interest in Medical Aesthetics: Part II (Active Analysis)

Abstract Background The COVID-19 pandemic significantly affected financial and psychosocial factors that influence plastic surgery demand. Objectives The authors sought to actively assess public interest changes and the reasons underlying these shifts. Methods Using Amazons’ Mechanical Turk, we crowdsourced public opinions regarding aesthetic interventions from April 30 to May 3, 2020. The survey assessed prior experience with and interest in 6 aesthetic interventions before and during the pandemic and reasons for changing interest. United States residents aged 18 years and over who passed the attention check were included. Results We included 704 of 838 total responses. One-half of respondents were female; the median age group was 25 to 34 years. During the pandemic, 21% of respondents had increased and 33% decreased interest in at least one intervention. Non-invasive procedures (7.3%), facial aesthetic surgery (6.6%), and medical-grade skincare (5.9%) elicited the greatest interest increase. Seeing themselves in the mirror more often (43.2%), desire to look better after the crisis (41.8%), and increased time on social media (40.4%) were the top reasons for increased interest. The most common reasons for decreased interest were changing spending priorities (58%), focusing on other health aspects (49.8%), and worrying about infection in medical facilities (46.3%). Almost one-half of respondents considered virtual consultations for interventions of increased interest. Conclusions The COVID-19 pandemic significantly affected interest in medical aesthetics. Offering telemedicine and discussing detailed COVID-19 infection control policies with patients will be critical to address patient needs and concerns. These findings can be used to improve patient outreach, advertisement, and counseling as practices focus on reopening.
Investigation on Hamburg Wheel-Tracking Device Stripping Performance Properties of Recycled Hot-Mix Asphalt Mixtures

Moisture damage in hot mix asphalt pavements is a periodic but persistent problem nowadays, even though laboratory testing is performed to identify different moisture-susceptible mixtures. In this study, a Hamburg Wheel Tracking device (HWTD) was used for rutting tests which were conducted on control and a high percentage of recycled asphalt pavement (RAP), i.e., 30%, 50% and 100% of virgin mixtures, under air dry and water-immersed conditions. Similarly, the extracted bitumen from RAP was tested for binder physical properties. Results showed that the asphalt mixtures containing RAP have less rut depth as compared to the control mix both in air dry and immersion conditions and hence showed better anti-rutting properties and moisture stability. Stripping performance of control and RAP containing mixtures was also checked, concluding that the RAP mixture was greatly dependent on the interaction between the binder (virgin plus aged) and aggregates.
Identification of a Novel de Novo Variant in the SYT2 Gene Causing a Rare Type of Distal Hereditary Motor Neuropathy

Objective: To report the first de novo missense mutation in the SYT2 gene causing distal hereditary motor neuropathy. Methods: Genetic testing was carried out, including clinical exome sequencing for the proband and Sanger sequencing for the proband and his parents. We described the clinical and electrophysiological features found in the patient. Results: We reported a proband with a new de novo missense mutation, c.917C>T (p.Ser306Leu), in the C2B domain of SYT2. The clinical presentation was similar to that of phenotypes described in previous studies. A notable feature in our study was normal electrophysiological testing results of the patient. Conclusions: In this study we reinforced the association between SYT2 mutations and distal hereditary motor neuropathy. We also described the clinical presentation of the patient carrying this pathogenic variant and provided unusual results of electrophysiological testing. The results showed that a diagnosis of SYT2-associated neuropathy should be based on the similarity of clinical manifestations, rather than the results of electrophysiological testing.
In the Model Host Caenorhabditis elegans, Sphingosine-1-Phosphate-Mediated Signaling Increases Immunity toward Human Opportunistic Bacteria

Sphingosine-1-phophate (S1P) is a sphingolipid-derived signaling molecule that controls diverse cellular functions including cell growth, homeostasis, and stress responses. In a variety of metazoans, cytosolic S1P is transported into the extracellular space where it activates S1P receptors in a concentration-dependent manner. In the free-living nematode Caenorhabditis elegans, the spin-2 gene, which encodes a S1P transporter, is activated during Gram-positive or Gram-negative bacterial infection of the intestine. However, the role during infection of spin-2 and three additional genes in the C. elegans genome encoding other putative S1P transporters has not been elucidated. Here, we report an evolutionally conserved function for S1P and a non-canonical role for S1P transporters in the C. elegans immune response to bacterial pathogens. We found that mutations in the sphingosine kinase gene (sphk-1) or in the S1P transporter genes spin-2 or spin-3 decreased nematode survival after infection with Pseudomonas aeruginosa or Enterococcus faecalis. In contrast to spin-2 and spin-3, mutating spin-1 leads to an increase in resistance to P. aeruginosa. Consistent with these results, when wild-type C. elegans were supplemented with extracellular S1P, we found an increase in their lifespan when challenged with P. aeruginosa and E. faecalis. In comparison, spin-2 and spin-3 mutations suppressed the ability of S1P to rescue the worms from pathogen-mediated killing, whereas the spin-1 mutation had no effect on the immune-enhancing activity of S1P. S1P demonstrated no antimicrobial activity toward P. aeruginosa and Escherichia coli and only minimal activity against E. faecalis MMH594 (40 µM). These data suggest that spin-2 and spin-3, on the one hand, and spin-1, on the other hand, transport S1P across cellular membranes in opposite directions. Finally, the immune modulatory effect of S1P was diminished in C. elegans sek-1 and pmk-1 mutants, suggesting that the immunomodulatory effects of S1P are mediated by the p38 MAPK signaling pathway.
OrderRex clinical user testing: a randomized trial of recommender system decision support on simulated cases

Abstract Objective To assess usability and usefulness of a machine learning-based order recommender system applied to simulated clinical cases. Materials and Methods 43 physicians entered orders for 5 simulated clinical cases using a clinical order entry interface with or without access to a previously developed automated order recommender system. Cases were randomly allocated to the recommender system in a 3:2 ratio. A panel of clinicians scored whether the orders placed were clinically appropriate. Our primary outcome included the difference in clinical appropriateness scores. Secondary outcomes included total number of orders, case time, and survey responses. Results Clinical appropriateness scores per order were comparable for cases randomized to the order recommender system (mean difference -0.11 order per score, 95% CI: [-0.41, 0.20]). Physicians using the recommender placed more orders (median 16 vs 15 orders, incidence rate ratio 1.09, 95%CI: [1.01-1.17]). Case times were comparable with the recommender system. Order suggestions generated from the recommender system were more likely to match physician needs than standard manual search options. Physicians used recommender suggestions in 98% of available cases. Approximately 95% of participants agreed the system would be useful for their workflows. Discussion User testing with a simulated electronic medical record interface can assess the value of machine learning and clinical decision support tools for clinician usability and acceptance before live deployments. Conclusions Clinicians can use and accept machine learned clinical order recommendations integrated into an electronic order entry interface in a simulated setting. The clinical appropriateness of orders entered was comparable even when supported by automated recommendations.
Simulation of whole mammalian kidneys using complex networks

Modelling of kidney physiology can contribute to understanding of kidney function by formalising existing knowledge into mathematical equations and computational procedures. Modelling in this way can suggest further research or stimulate theoretical development. The quantitative description provided by the model can then be used to make predictions and identify further areas for experimental or theoretical research, which can then be carried out, focusing on areas where the model and reality are different, creating an iterative process of improved understanding. Better understanding of organ function can contribute to the prevention and treatment of disease, as well as to efforts to engineer artificial organs. Existing research in the area of kidney modelling generally falls into one of three categories: • Morphological and anatomical models that describe the form and structure of the kidney • Tubule and nephron physiological models that describe the function of small internal parts of the kidney • Whole kidney physiological models that describe aggregate function but without any internal detail There is little overlap or connection between these categories of kidney models as they currently exist. This thesis brings together these three types of kidney models by computer generating an anatomical model using data from rat kidneys, simulating dynamics and interactions using the resulting whole rat kidney model with explicit representation of each nephron, and comparing the simulation results against physiological data from rats. This thesis also describes methods for simulation and analysis of the physiological model using high performance computer hardware. In unifying the three types of models above, this thesis makes the following contributions: • Development of methods for automated construction of anatomical models of arteries, nephrons and capillaries based on rat kidneys. These methods produce a combined network and three-dimensional euclidean space model of kidney anatomy. • Extension of complex network kidney models to include modelling of blood flow in an arterial network and modelling of vascular coupling communication between nephrons using the same arterial network. • Development of methods for simulation of kidney models on high performance computer hardware, and storage and analysis of the resulting data. The methods used include multithreaded parallel computation and GPU hardware acceleration.
Differential Gene Expression Changes in Human Primary Dental Pulp Cells Treated with Biodentine and TheraCal LC Compared to MTA

This study aimed to analyze the effects of pulp capping materials on gene expression changes in primary tooth-derived dental pulp cells using next-generation sequencing. Dental pulp cells were extracted and treated with mineral trioxide aggregate (MTA), Biodentine (BD), or TheraCal LC (TC). Cell viability assays were performed. Total RNA was extracted and analyzed through mRNA sequencing. Bioinformatic analysis of differential gene expression in dental pulp cells exposed to BD or TC versus MTA was performed. MTA, BD, and TC exposure had no significant effect on pulp cell viability (p > 0.05). Gene sets associated with inflammatory response (p = 2.94 × 10−5) and tumor necrosis factor alpha (TNF-α) signaling via the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) pathway (p = 2.94 × 10−5) were enriched in all materials. In BD-treated cells, Wnt/β-catenin signaling (p = 3.15 × 10−4) gene sets were enriched, whereas enrichment of interferon gamma (IFN-γ) response (p = 3 × 10−3) was observed in TC-treated cells. In gene plot analysis, marked increases in receptor activator of nuclear factor kappa-Β ligand (RANKL) expression were seen in TC-treated cells over time. Despite the similar cell viabilities exhibited among MTA-, BD-, and TC-treated cells, patterns of gene networks differed, suggesting that diverse functional gene differences may be associated with treatment using these materials.
Reliability of T-WSI to Evaluate Neighborhoods Walkability and Its Changes over Time

More walkable neighborhoods are linked to increased physical activity. The Walking Suitability Index of the territory (T-WSI) is an easy method to evaluate walkability on the basis of direct observation. T-WSI provides 12 indicators divided into 4 categories (practicability, safety, urbanity, pleasantness); the weighted analysis of these indicators gives an overall score of the actual usability of the neighborhood. The aim of the study is to evaluate the ability of T-WSI’ indicators to measure, in a reliable way, any street’s walkability variations occurred over time. The investigation was performed in 2018 in nine urban neighborhoods of Rieti city. Cronbach’s α is used to evaluate internal consistency of T-WSI; Intraclass Correlation Coefficient (ICC) is used to evaluate the reproducibility of measurements (or ratings) made by different investigators. Cronbach’s α is 0.89 (± 0.02); ICC is also good (ICC = 0.89; 95% CI: 0.84–0.92). The results of the 2018 investigation are also compared with those collected in 2016 in the same districts. The results show that T-WSI is a reliable and easy to use tool, useful to measure the effectiveness of the interventions already realized at local level, but it could also contribute to making decisions to develop regeneration projects.