Miracle-dz/UniFAR-FTUs huggingface dataset:
Cell Surface Expression of fMet-Leu-Phe Receptors

We have studied how cytosolic free Ca2" ([Ca2+Ii) changes and phorbol myristate acetate (PMA) exposure affects ligand-independent cell surface expression offMet-Leu-Phe receptors on human neutrophils. Mere incubation primed neutrophils to double their binding of fMet-Leu-Phe. This spontaneous increase of peptide binding was unaffected by changes in the extracellular calcium concentration. However, depression of the [Ca2"1, totally abolished the increased binding of fMet-Leu-Phe. ScatchardPlot analysis revealed that the observed increase of peptide binding was due to an increased number of receptors. Normalization of the [Ca2"1 in cells where it was initially depressed resulted in a slow but progressive increase in fMet-Leu-Phe binding. The rate of receptor recruitment could be enhanced by rapidly increasing the [Ca2J1, by addition of ionomycin. Addition of PMA to cells with near maximal receptor expression led to a marked reduction of fMet-Leu-Phe binding without affecting [Ca2+Ii. These observations suggest the existence of a dual regulatory mechanism for upand down-regulation of fMet-Leu-Phe receptors on the cell surface of human neutrophils.
Plasma Receptor for Advanced Glycation Endproducts Predicts Duration of ICU Stay and Mechanical Ventilation in Patients Following Lung Transplantation

Background—Primary graft dysfunction, formerly termed reperfusion pulmonary edema, is the leading cause of short-term complications after lung transplantation. New evidence shows that alveolar type I epithelial cells play an active role in alveolar fluid transport and are therefore presumed to be critical in the absorption of pulmonary edema. We tested the potential relevance of a novel marker of alveolar type I cell injury, the receptor for advanced glycation end products (RAGE), to short-term outcomes of lung transplantation. Methods—Prospective, observational cohort study of 20 patients undergoing single lung, bilateral lung, or combined heart-lung transplantation. Plasma biomarkers were measured 4 hours after allograft reperfusion. Results—Higher plasma RAGE levels were associated with both a longer duration of mechanical ventilation and longer intensive care unit length of stay, in contrast to markers of alveolar type II cell injury, endothelial injury, and acute inflammation. Specifically, for every doubling in plasma RAGE levels, the duration of mechanical ventilation increased on average by 26 hours, adjusting for Correspondence (and to whom reprint requests should be addressed): Carolyn S. Calfee, M.D, University of California, San Francisco, Pulmonary and Critical Care Division, 505 Parnassus Avenue, San Francisco, CA 94143-0130, Phone: (415) 476-1079, Fax: (415) 502-2126, Email: carolyn.calfee@ucsf.edu. Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. NIH Public Access Author Manuscript J Heart Lung Transplant. Author manuscript; available in PMC 2009 September 10. Published in final edited form as: J Heart Lung Transplant. 2007 July ; 26(7): 675–680. doi:10.1016/j.healun. 2007.04. 002. N IH PA Athor M anscript N IH PA Athor M anscript N IH PA Athor M anscript ischemia time (95% CI 7.4-44.7 hours, p=0.01). Likewise, for every doubling of plasma RAGE levels, intensive care unit length of stay increased on average by 1.8 days, again adjusting for ischemia time (95% CI 0.13-3.45; p=0.04). In contrast, the clinical diagnosis of primary graft dysfunction was not predictive of these short-term outcomes. Conclusions—Higher levels of plasma RAGE measured shortly after reperfusion predicted poor short-term outcomes from lung transplantation. Elevated plasma RAGE levels may have both pathogenetic and prognostic value in patients following lung transplantation.
Three-dimensional Transcranial Microbubble Cavitation Localization by Four Sensors

Cavitation is the fundamental physical mechanism of various focused ultrasound (FUS)-mediated therapies in the brain. Accurately knowing the 3D location of cavitation in real-time can improve the targeting accuracy and avoid off-target tissue damage. Existing techniques for 3D passive transcranial cavitation detection require the use of expensive and complicated hemispherical phased arrays with 128 or 256 elements. The objective of this study was to investigate the feasibility of using four sensors for transcranial 3D localization of cavitation. Differential Corresponding author: Hong Chen. hongchen@wustl.edu. HHS Public Access Author manuscript IEEE Trans Ultrason Ferroelectr Freq Control. Author manuscript; available in PMC 2022 February 02. Published in final edited form as: IEEE Trans Ultrason Ferroelectr Freq Control. 2021 November ; 68(11): 3336–3346. doi:10.1109/ TUFFC.2021. 3091950. A uhor M anscript
Animal Model Cardiac Disease in Transgenic Mice Expressing Human Immunodeficiency Virus-1 Nef in Cells of the Immune System

We previously reported that a severe acquired immune deficiency syndrome-like disease develops in transgenic (Tg) mice expressing the human immunodeficiency virus-1 in its natural target cells: immature and mature CD4 (cid:2) T cells and cells of the macrophage/ dendritic lineage. Here, we show that these mice also develop cardiac disease, characterized most promi-nently by a focal myocytolysis, occasionally by myocarditis and by deposition of endogenous immunoglobulin on cardiomyocytes. Microfil perfusion demonstrated widespread coronary arteriospasm and echocardiographic analysis revealed depressed cardiac function in Tg mice. A higher (but still modest) level of cardiomyocyte apoptosis was detected in Tg as compared to non-Tg hearts. Tg expression was detected in some of the infiltrating mononuclear cells, but not in cardiomyocytes or in cells of the heart vessels, suggesting a human immunodeficiency virus-1-induced disease process mediated by cells of the immune system. The similarity of the heart disease observed in these Tg mice to that observed in acquired immune deficiency syndrome patients suggests a common pathogenesis. (Am J Pathol 2002, 161:321–335) Infection by human immunodeficiency
MOLECULAR PATHOGENESIS OF GENETIC AND INHERITED DISEASES Activation of PINK1-ParkineMediated Mitophagy Degrades Mitochondrial Quality Control Proteins in Fuchs Endothelial Corneal Dystrophy

opyright a 2019 American Society for Inve ttps://doi.org/10.1016/j.ajpath. 2019.06. 012 Corneal endothelium (CE) is a monolayer of mitochondria-rich cells, critical for maintaining corneal transparency compatible with clear vision. Fuchs endothelial corneal dystrophy (FECD) is a heterogeneous, genetically complex disorder, where oxidative stress plays a key role in the rosette formation during the degenerative loss of CE. Increased mitochondrial fragmentation along with excessive mitophagy activation has been detected in FECD; however, the mechanism of aberrant mitochondrial dynamics in CE cell loss is poorly understood. Here, the role of oxidative stress in mitophagy activation in FECD is investigated. Immunoblotting of FECD ex vivo specimens revealed an accumulation of PINK1 and phospho-Parkin (Ser65) along with loss of total Parkin and total Drp1. Similarly, modeling of rosette formation with menadione (MN), led to phospho-Parkin accumulation in fragmented mitochondria resulting in mitophagy-induced mitochondrial clearance, albeit possibly in a PINK1independent manner. Loss of PINK1, phospho-Drp1, and total Drp1 was prominent after MN-induced oxidative stress, but not after mitochondrial depolarization by carbonyl cyanide m-chlorophenyl hydrazone. Moreover, MN-induced mitophagy led to degradation of Parkin along with sequestration of Drp1 and PINK1 that was rescued by mitophagy inhibition. This study shows that in FECD, intracellular oxidative stress induces Parkin-mediated mitochondrial fragmentation where endogenous Drp1 and PINK1 are sequestered and degraded by mitophagy during degenerative loss of post-mitotic cells of ocular tissue. (Am J Pathol 2019, 189: 2061e2076; https://doi.org/10.1016/j.ajpath.2019.06.012)
Fabrication of MEMS Based Air Quality Sensors

This thesis deals with the fabrication of MEMS air quality sensors for automotive applications. The goal of this project is to design, fabricate and test an integrated sensor that measures three important air quality components inside the automotive cabin, which are temperature, relative humidity and carbon monoxide (CO) concentration. The sensors are fabricated on silicon substrate covered with thermal oxide and LPCVD nitride. Various deposition and etching techniques were utilized to fabricate these sensors including E-beam evaporation, thermal oxide growth, PECVD, LPCVD, RIE, KOH and HF etching. The temperature and humidity sensor use nickel as the sensitive material while the CO sensor was designed to use SnO2 although it was not fabricated to completion. A chamber was created where the temperature and humidity are controlled and the sensors were tested. Curves of sensor resistance vs. temperature and sensor resistance vs. humidity were created and the two sensor’s sensitivity was calculated.
ImmuneModulation of the T Cell Response in Asthma throughWnt10b

Asthma is a chronic inflammatory disease, which is characterized by activation of CD4 T helper 2 cells orchestrating an allergic airway response. Whereas the role of Wnt family members in regulating T cell maintenance and maturation is established, their contribution to T cell activation in allergic asthma is not known. We hypothesized that Wnt10b plays a role in the modulation of the allergic airway response and affectsT cell activation andpolarization.Using an in vivohousedust mite asthma model, Wnt10b-deficient (Wnt10b) mice were allergen-sensitized and inflammation, as well as T cell activation, was studied in vivo and in vitro. Wnt10b mice exhibited an augmented inflammatory phenotype with an increase in eosinophils in the bronchoalveolar lavage and IL-4 and IL-13 in the lungs when compared with wild-type mice. In vitro studies confirmed an increased T helper type 2 polarization and increased T cell activation of Wnt10b cells. Accordingly, the percentage of naive T cells was elevated by the addition of recombinant Wnt10b protein. Finally, Wnt10b mice exhibited an increase in the percentage of effector T cells in the lungs after house dust mite sensitization, which indicated a heightened activation state, measured by an increased percentage of CD69CD11a cells. These findings suggest that Wnt10b plays an important role in regulating asthmatic airway inflammation through modification of the T cell response and is a prospective target in the disease process.
Edmonton Symptom Assessment Scale Time Duration of Self-Completion Versus Assisted Completion in Patients with Advanced Cancer: A Randomized Comparison

Introduction. To compare the time duration of selfcompletion (SC) of the Edmonton Symptom Assessment Scale (ESAS) by patients with advanced cancer (ACPs) versus assisted completion (AC) with a health care professional. Materials and Methods. In this randomized comparison of ACPs seen in initial consultation at the outpatient Supportive Care Center at MD Anderson, ACPs who have never completed the ESAS at MD Anderson were allocated (1:1) to either SC of the ESAS form versus AC by a nurse. Time of completion was measured by the nurse using a stopwatch. Patients completed the Rapid Estimate of Adult Literacy in Medicine (REALM) test prior to administration of the ESAS. In the SC group, the nurse reviewed the responses to verify that the reported ESAS scores were correct. Results. A total of 126 ACPs were enrolled (69 patients to AC and 57 to SC). Seventy-one patients were female, median age was 60 years, and median REALM score was 65. Median (interquartile range) time (in seconds) of SC was significantly less than AC (73 [42.9–89.1] vs. 109 [79.5–136.7], p < .0001). With nurse review time included, median time of SC increased to 117 seconds, which was not significantly different from AC (p = .28). Lower literacy (REALM) score and shortness of breath were significantly associated with increased completion time (p = .007). Conclusion. Regular use of ESAS will have minimal impact on clinical time, as it can be completed in about 1 minute and provides a concise yet comprehensive and multidimensional perspective of symptoms that affect quality of life of patients with cancer. The Oncologist 2021;26:165–171 Implications for Practice: Because the Edmonton Symptom Assessment Scale can be completed in less than 2 minutes, hopefully the routine use of this simple yet comprehensive and multidimensional symptom assessment tool will be used at all medical visits in all patients with cancer so that the timely management of symptoms affecting patients’ lives and treatment courses can occur, further enhancing personalized cancer care.
Commercially Sexually Exploited Young Women’s Healthcare Needs, Access, and Utilization Patterns: “Work Around What I Need”

PURPOSE: We sought to understand the perspectives of commercially sexually exploited (CSE) young women regarding their healthcare needs, access, and utilization patterns. METHODS: Twenty-one CSE young women participated in this mixed-methods study. Data collection included brief surveys measuring healthcare utilization, followed by in-depth, semistructured interviews to gain insight into CSE young women’s healthcare needs, barriers and facilitators to healthcare, utilization patterns, and recommendations for improving care. Data analysis techniques included descriptive statistics for the quantitative survey data and thematic analysis for the qualitative interviews. Corresponding author: Mikaela Kelly, mikaelakelly@mednet.ucla. edu, phone: (310) 825-7952, fax, UCLA Semel Neuropsychiatric Institute, 760 Westwood Plaza, Room A8-228, Los Angeles, CA United States, 90024. Abrams@luskin.ucla. edu. Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process erwrors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. HHS Public Access Author manuscript Womens Health Issues. Author manuscript; available in PMC 2020 July 01. Published in final edited form as: Womens Health Issues. 2019 ; 29(4): 315–324. doi:10.1016/j.whi. 2019.02. 002. A uhor M anscript
Original Contribution Association Between Midpregnancy Polyunsaturated Fatty Acid Levels and Offspring Autism Spectrum Disorder in a California Population-Based Case-Control Study

Polyunsaturated fatty acids (PUFAs) are critical for brain development and have been linked with neurodevelopmental outcomes. We conducted a population-based case-control study in California to examine the association between PUFAs measured in midpregnancy serum samples and autism spectrum disorder (ASD) in offspring. ASD cases (n = 499) were identified through the California Department of Developmental Services and matched to live-birth population controls (n = 502) on birth month, year (2010 or 2011), and sex. Logistic regression models were used to examine crude and adjusted associations. In secondary analyses, we examined ASD with and without co-occurring intellectual disability (ID; n = 67 and n = 432, respectively) and effect modification by sex and ethnicity. No clear patterns emerged, though there was a modest inverse association with the top quartile of linoleic acid level (highest quartile vs. lowest: adjusted odds ratio = 0.74, 95% confidence interval: 0.49, 1.11; P for trend = 0.10). Lower levels of total and ω-3 PUFAs were associated with ASD with ID (lowest decile of total PUFAs vs. deciles 4–7: adjusted odds ratio = 2.78, 95% confidence interval: 1.13, 6.82) but not ASD without ID. We did not observe evidence of effect modification by the factors examined. These findings do not suggest a strong association between midpregnancy PUFA levels and ASD. In further work, researchers should consider associations with ASD with ID and in other time windows.
Photothermally tunable Fabry-Pérot fiber interferometer for photoacoustic mesoscopy

An optical fiber based Fabry-Pérot interferometer whose resonant wavelength can be dynamically tuned was designed and realized for photoacoustic mesoscopy. The optical path length (OPL) of the Fabry-Pérot cavity can be modulated by a photothermal heating process, which was achieved by adjusting the power of a 650 nm heating laser. The optical heating process can effectively change the thickness and refractive index of the polymer spacer of the sensor cavity. The robustness of the sensor can be greatly improved by proper packaging. The interferometer was interrogated by a relatively cheap wavelength-fixed 1550 nm laser for broadband and sensitive ultrasound detection, eliminating the requirement for an expensive tunable interrogation laser. The sensing module was then integrated into a photoacoustic mesoscopic imaging system. Two phantom imaging experiments and an ex vivo imaging experiment demonstrated the capability of such a miniature sensor. The interferometer has an acoustic detection bandwidth of up to 30 MHz and a noise equivalent pressure of 40 mPa/Hz1/2 (i.e., 220 Pa over the full detection bandwidth). The new tuning mechanism and the batch-production compatibility of the sensor holds promises for commercialization and parallelized detection. © 2020 Optical Society of America under the terms of the OSA Open Access Publishing Agreement
Indirect Role of Ca in the Assembly of Extracellular Matrix Proteins

We have investigated through molecular dynamics the binding properties at the interface between the C-type lectin subdomain (CLD) of aggrecan and the fibronectin type III domains (FnIII) of tenasin, in particular the mechanistically unknown, but essential role of Ca in the binding. The binding between the CLD and FnIII is critical in cross-linking aggrecan, hyaluronan, and tenascin to form extended protein networks found in tissues such as cartilage. None of the structurally resolved Ca ions in the complex of the CLD and FnIII is directly bridging the two proteins. However, one of the Ca ions (Ca2) is found to play the role of maintaining the structure of the L4 loop at the CLD binding surface, thus facilitating a high affinity binding between the CLD and FnIII. Removal of this Ca ion causes a drastic structural change in the L4 loop, which presumably hinders the binding of the CLD to the FnIII. The other bound Ca ions (Ca1 and Ca3) have no significant effect on the structure of the CLD binding surface, and thus are not expected to affect the binding. Our results might also suggest that the role of Ca2 in maintaining the structure of the L4 loop is most important during the binding process. Once the complex is formed, the dependence of the complex on the structuring role of Ca2 is reduced. In response to tensile force, the CLD and FnIII separate by breaking first the electrostatic interactions at the interface, followed by the hydrophobic ones. The sequence of the unbinding events and the maximum force required to separate the two proteins are independent of the presence of the Ca ions, underlying the indirect role of Ca in the binding.
Identification of SNPs Associated with Periodontal Disease in Head and Neck Cancer Irradiation Patients by Exome Sequencing

Objective—Periodontal disease (PD) is a common oral complication in head and neck cancer (HNC) patients who undergo radiation therapy (RT). Our objective was to identify candidate single nucleotide polymorphisms (SNPs) associated with PD in radiation treated HNC patients. Study Design—DNA was extracted from HNC patients’ saliva (n=69) pre-RT. A clinical attachment loss (CAL) increment of >0.2mm over 24 months post-RT was used to define PD progression. Following exome sequencing, SNPs associated with post-RT PD progression were identified by logistic regression and homozygosity analysis. STRING, DAVID, GeneCodis, and Ensembl Variant Effect predictor webtools were used for functional analysis. Results—Of the 48 HNC patients with post-RT PD progression, 24 had no tooth ≥5mm pocket depth pre-RT, whereas for 21 HNC patients without progression, 11 had PD initially. A total of 330 SNPs (249 genes) with over-represented homozygous genotype (98.5% variant allele) were found associated with post-RT PD. Sixty of these corresponded to PD-related pathways including previously identified genes. For HNC patients with post-RT PD progression, SNPs were found in genes (n=10) different from those without progression (n=7). Conclusion—Collagen genes SNPs were identified, potentially defining susceptibility to PD in HNC patients, which may be investigated to characterize PD drug targets. Corresponding Author and Co-Corresponding Author: Jean-Luc Charles Mougeot, PhD, Department of Oral Medicine, Carolinas Medical Center-Atrium Health, Charlotte, NC 28232-2861, USA, PO Box 32861, Phone: 704-355-8132, Fax: 704-355-5301, jeanluc.mougeot@atriumhealth.org; Farah Bahrani Mougeot, PhD, Department of Oral Medicine, Carolinas Medical Center-Atrium Health, Charlotte, NC 28232-2861, USA, PO Box 32861, Phone: 704-355-4279, Fax: 704-355-5301, farah.mougeot@atriumhealth.org. AUTHORS’ CONTRIBUTIONS FBM and JLM conceived the study, directed the overall statistical and systems biology analysis, participated in interpretation of the data and contributed to revisions of the manuscript. VT drafted the manuscript and performed all bioinformatics analyses in close collaboration with JW (bioinformatics mentor at UNC-Charlotte, NC). RVL and MTB contributed to the conception of the study, clinical interpretation and revisions of the manuscript. Disclosures: Authors have no conflict of interest. HHS Public Access Author manuscript Oral Surg Oral Med Oral Pathol Oral Radiol. Author manuscript; available in PMC 2021 June 25. Published in final edited form as: Oral Surg Oral Med Oral Pathol Oral Radiol. 2020 July ; 130(1): 32–42.e4. doi:10.1016/ j.oooo. 2020.02. 013. A uhor M anscript
Study Design Retaining Hispanics: Lessons From the Hispanic Community Health Study/ Study of Latinos

We aimed to examine the retention of Hispanics/Latinos participating in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), a prospective cohort study of 16,415 adults in 4 US cities who were enrolled between 2008 and 2011. We summarized retention strategies and examined contact, response, and participation rates over 5 years of annual follow-up interviews. We then evaluated motivations for participation and satisfaction with retention efforts among participants who completed a second in-person interview approximately 6 years after their baseline interview. Finally, we conducted logistic regression analyses estimating associations of demographic, health, and interview characteristics at study visit 1 (baseline) with participation, high motivation, and high satisfaction at visit 2. Across 5 years, the HCHS/SOL maintained contact, response, and participation rates over 80%. The most difficult Hispanic/Latino populations to retain included young, single, US-born males with less than a high school education. At visit 2, we found high rates of motivation and satisfaction. HCHS/SOL participants primarily sought to help their community and learn more about their health. High rates of retention of Hispanics/Latinos can be facilitated through the employment of bilingual/bicultural staff and the development of culturally tailored retention materials.