Miracle-dz/UniFAR-FTUs huggingface dataset:
Inﬂuence of in vitro manipulation on the stability of methylation patterns in the Snurf/Snrpn -imprinting region in mouse embryonic stem cells

Recent work on embryonic stem (ES) cells showed that stem cell-derived tissues and embryos, cloned from ES cell nuclei, often fail to maintain epigenetic states of imprinted genes. This deregulation is frequently associated with in vitro manipulations and culture conditions which might affect the cells potential to develop into normal fetuses. Usually, epigenetic instability is reported in differentially methylated regions of mostly growth-related imprinted genes. However, little is known about the epigenetic stability of genes that function late in organogenesis. Hence, we set out to investigate the epigenetic stability of neuronal genes and analyzed DNA methylation patterns in the Snurf/Snrpn imprinted cluster in several cultured mouse ES cell lines. We also determined the effects of in vitro stress factors such as consecutive passaging, tryp-sination, mechanical handling, single cell cloning, centrifugation, staurosporine-induced neurogenesis and the insertion of viral (foreign) DNA into the host genome. Intriguingly, none of these in vitro manipulations interfered with the stability of the methylation patterns in the analyzed neuronal genes. These data imply that, in contrast to growth-related genes like Igf2 , H19 , Igf2r or Grb10 , the methylation imprints of the analyzed neuronal genes in the Snurf/Snrpn cluster may be particularly stable in manipulated ES cells.
A Minimum Variance Method for Genome-wide Data-driven Normalization of qRT-PCR Expression Data

Advances in multiplex qRT-PCR have enabled increasingly accurate and robust quantification of RNA, even at lower concentrations, facilitating RNA expression profiling in clinical and environmental samples. Here we describe a data-driven qRT-PCR normalization method, the minimum variance method, and evaluate it on clinically derived Mycobacterium tuberculosis samples with variable transcript detection percentages. For moderate to significant amounts of non-detection (~50%), our minimum variance method consistently produces the lowest false discovery rates compared to commonly used data-driven normalization methods.
Numerical simulation of vortex-induced vibration of a circular cylinder in a spanwise shear flow

Vortex-induced vibration of a circular cylinder with a length-to-diameter ratio of 19.2 in a spanwise shear flow is investigated numerically. The Reynolds numbers based on the velocity at the centre of the cylinder and the mass ratio are 500 and 2, respectively. The responses of the cylinder in shear flows with shear factors of 0.05 and 0.1 are compared with that in the uniform flow. Although the oscillation of the lift force for a stationary cylinder in a sheared flow is very weak, it is found that if the cylinder is allowed to vibrate, the lock-in regime and the maximum response amplitude are comparable with their counterparts for a cylinder in a uniform flow. The maximum response amplitude for a shear factor of 0.05 is found slightly greater than that for a uniform flow. In the lock-in regime, the vortex shedding and the oscillation of the sectional lift coefficient are found to synchronize (have a same frequency) along the cylinder span, leading to strong vibration of the cylinder. The sectional lift .
HUMAN GENETICS ’99 Functional and Structural Brain Abnormalities Associated with a Genetic Disorder of Speech and Language

The number of children diagnosed with developmental disorders, such as dyslexia, autism, specific language impairment, and attention deficit disorder, is increasing, as these disorders become better defined in terms of their behavioral characteristics. In many of these children, there is significant evidence for a genetic etiology. In addition to reports of families with unusually high concentrations of a particular disorder such as language impairment (Arnold 1961; Samples and Lane 1985; Hurst et al. 1990), twin studies (Bishop et al. 1995), and pedigree analyses examining the incidence of such disorders in the relatives of probands (Lewis 1992), there are genetic-linkage investigations identifying loci that cosegregate with these disorders (Grigorenko et al. 1997; Fisher et al. 1998). It is presumed that genetic factors cause developmental cognitive disorders by influencing the development of the brain. These disorders frequently occur in the absence of a frank neurological deficit, and the nature of the underlying abnormalities in brain development is therefore intriguing. The implication of a genetic etiology is that, during neurogenesis, abnormalities may have occurred, affecting brain structure and function. The structural brain abnormalities are likely to be the result of aberrant neuronal or glial proliferation, reflected, respectively, in site-specific neuronal size and number or in degree of myelination. Such abnormalities may be detectable by morphometric analysis of the brain. Several such studies have been reported, in which, typically, postmortem methods or analysis of structural magnetic resonance imaging (MRI) scans have been used. In contrast to single-case postmortem studies, MRI analyses allow larger samples to be investigated in vivo along with suitable control groups.
Endogenous Cell Type-Specific DISC1 Interactomes Reveal Protein Networks Associated to Neurodevelopmental Disorders

Background: Disrupted in schizophrenia 1 (DISC1) has been implicated in a number of psychiatric diseases along with neurodevelopmental phenotypes such as the proliferation and differentiation of neural progenitor cells. While there has been significant effort directed towards understanding the function of DISC1 through the determination of its protein-protein interactions within an in-vitro setting, endogenous interactions involving DISC1 within a cell-type specific setting relevant to neural development remain unclear. Methods: Using CRISPR/Cas9 genome engineering technology, we inserted an endogenous 3×-FLAG tag at the C-terminus of the canonical DISC1 gene in human induced pluripotent stem cells. We further differentiated these cells and used affinity purification in order to determine protein-protein interactions involving DISC1 in iPSC-derived neural progenitor cells and astrocytes. Results: We were able to determine 150 novel cell-type specific proteins present in DISC1 endogenous interactomes. The DISC1 interactomes can be clustered into several sub-complexes that suggest novel DISC1 cell-specific functions. In addition, the DISC1 interactome in iPSC* 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 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. Financial Disclosures interests or potential derived neural progenitor cells associates in a connected network containing proteins found to harbor de-novo mutations in patients affected by schizophrenia and contains a subset of novel interactions that are known to harbor syndromic mutations in neurodevelopmental disorders. Conclusions: Endogenous DISC1 interactomes within iPSC-derived human neural progenitor cells and astrocytes are able to provide context to DISC1 function in a cell-type specific setting relevant to neural development and enables the integration of psychiatric disease risk factors within a set of defined molecular functions.
Degradation of ao32, the heat shock regulator in Escherichia coli, is governed by HfIB

The heat shock response in Escherichia coli is governed by the concentration of the highly unstable a factor or32. The essential protein HflB (FtsH), known to control proteolysis of the phage AcII protein, also governs o.32 deg- radation: an HflB-depleted strain accumulated o732 and induced the heat shock response, and the half-life of c732 increased by a factor up to 12 in mutants with reduced HflB function and decreased by a factor of 1.8 in a strain overex- pressing HflB. The hflB gene is in the ftsJ-hflB operon, one promoter of which is positively regulated by heat shock and &-32. The AcIll protein, which stabilizes &-32 and Acll, appears to inhibit the HflB-governed protease. TheE. coli HflB protein controls the stability of two master regulators, AclI and a32, responsible for the lysis-lysogeny decision of phage A and the heat shock response of the host.
Conducting an Integrative Structural Biology Study

Integrative structure determination is a powerful approach to mapping the structures of biological systems, with implications for our understanding of cellular biology and drug discovery. Here, we provide a Primer to introduce the researcher to the theory and methods of integrative approaches, relying on examples to illustrate the practice and challenges involved. These guidelines are intended to aid the researcher in applying integrative structural methods to systems of their interest and thus take advantage of this rapidly evolving field. need for different approaches.
Thermal Electron Temperature Measurements from the Freja Cold Plasma Analyzer

The Freja Cold Plasma Analyzer (CPA) is a hemispherical electrostatic analyzer which forms 2-D, energy/arrival angle images of low-energy (< 200 eV) particle distribution functions. In addition to its 2-D imaging capability, the CPA is unique in that its sensor head is displaced from the spacecraft on a 2 m boom which allows control of the probe-to-plasma potential, thereby compensating for variations in spacecraft potential. Furthermore, the detector biases can be set to measure either positively or negatively charged particle species. This study emphasizes temperature measurements of the core electron population (∼ 1 eV) which are difficult to make since, among other reasons, they are affected by spacecraft charging and are susceptible to contamination from photoelectrons and finite gyroradius effects. We demonstrate that the CPA sensor does detect the core population by showing that probe-to-plasma potential changes of only a fraction of 1 V cause large changes in the electron flux measured at the detector anode. The relation between detector current and sensor bias comprises a modified Langmuir curve, which in contrast to standard Langmuir measurements results from a single particle species only (electrons) and from particles which are restricted in energy (0-70 eV) and in arrival angle to within ±4° of the detector plane. The modified Langmuir curve can be compared to a standard Langmuir curve formed by measuring current onto the external skin of the sensor, which contains contributions from both electrons and ions at all energies and over a wide angular acceptance. Somewhat surprisingly, the two methods agree fairly well in the sunlit portion of a sample orbit, i.e. in the presence of a background photoelectron population, but differ by up to a factor of two in the dark part of the orbit.
Desensitization of b 2 -adrenoceptor-mediated responses by short-acting b 2 -adrenoceptor agonists in human lung mast cells

1 The principal aim of the present study was to determine whether long-term treatment of human lung mast cells (HLMC) with the clinically-relevant b 2 -adrenoceptor agonists, salbutamol and terbutaline, leads to desensitization of b 2 -adrenoceptor-mediated responses in these cells. 2 The non-selective b -adrenoceptor agonist, isoprenaline, and the selective b 2 -adrenoceptor agonists, salbutamol and terbutaline, inhibited the IgE-mediated release of histamine from HLMC. Salbutamol (pD 2 ; 7.7 + 0.3) and terbutaline (pD 2 ; 7.3 + 0.2) were roughly equipotent as inhibitors of histamine release although both agonists were less potent than isoprenaline (pD 2 ; 8.6 + 0.2). 3 Isoprenaline (10 7 5 M ), salbutamol (10 7 5 M ) and terbutaline (10 7 5 M ) enhanced total cell cAMP levels in HLMC over basal by 361 + 90, 150 + 38 and 165 + 35%, respectively. 4 Long-term exposure (24 h) of HLMC to either salbutamol (10 7 7 M ) or terbutaline (10 7 7 M ) led to a subsequent reduction in the e(cid:128)ectiveness of salbutamol and terbutaline (both 10 7 9 – 10 7 4 M ) to inhibit histamine release. However, salbutamol was signiﬁcantly ( P 5 0.05) more e(cid:128)ective than terbutaline at promoting the functional desensitization. 5 Radioligand binding studies, using iodinated cyanopindolol, were performed to determine b 2 - adrenoceptor density in cell membranes after pretreatment (24 h) of cells with either salbutamol (10 7 6 M ) or terbutaline (10 7 6 M ). Both agonists reduced b 2 -adrenoceptor density in membranes to about the same extent ( * 25% reduction) but these changes in receptor density were not statistically signiﬁcant ( P 4 0.05). 6 These data indicate that long-term exposure of mast cells to salbutamol causes greater levels of desensitization to b 2 -adrenoceptor-mediated responses in HLMC than terbutaline. These ﬁndings may have wider clinical signiﬁcance in the context of asthma treatment as compromised mast cell inhibition could result following long-term exposure of mast cells to short-acting bronchodilators. British Journal of Pharmacology binding membrane binding 125 ([ I]-CYP).
Integration of Sex and Gender Minority Standardized Patients into a Workshop on Gender-Inclusive Patient Care: Exploring Medical Student Perspectives

Although coverage of health issues specific to sexual and gender minority (SGM) communities has increased in the undergraduate medical curriculum, teaching about sexual diversity and inclusive care can be improved. The second-year clinical skills course at the authors’ institution includes a sexual history workshop that starts with a 1-hour lecture and is followed by a small group session during which students interview an SGM standardized patient. This article presents results of a postworkshop survey assessing students’ perceived effects of the session and experience with SGM standardized patients, as well as suggestions for the next steps regarding improved curricular inclusion and assessment of these topics. Objectives Sexual and gender minority (SGM) communities experience significant health disparities. Although coverage of health issues specific to these communities has increased in the undergraduate medical curriculum, there is still opportunity for improved teaching about sexual diversity and inclusive care. The goal of this study was to assess students' perceptions of and satisfaction with a half-day workshop focused on sexual history taking and transgender health. Methods The second-year clinical skills course at the Florida International University Herbert Wertheim College of Medicine includes a sexual history workshop that starts with a 1-hour lecture on sexual history taking. This is followed by a faculty-facilitated small group session during which students interview an SGM patient and debrief about this experience. In 2020, for the first time, the standardized patients were members of the SGM community, and the session was on Zoom. Students completed an optional, anonymous postsession survey assessing the workshop. Results Students overwhelmingly believed that the integration of SGM standardized patients into the session helped improve their knowledge, attitudes, and skills related to providing care for this population. They noted that the standardized patient interaction and debriefing were the most beneficial parts of the session. Conclusions Given the positive feedback, future iterations of this session will continue to use the SGM community as standardized patients. In addition, student competency related to SGM patient care will be assessed through observed structured clinical examinations.
Advanced Triage Protocol: The Role of an Automated Lactate Order in Expediting Rapid Identification of Patients at Risk of Sepsis in the Emergency Department

OBJECTIVES: We undertook a process improvement initiative to expedite rapid identification of potential sepsis patients based on triage chief complaint, vital signs, and initial lactate level. DESIGN: Prospective cohort study. SETTING: Seven hundred-bed tertiary care hospital with ≅65,000 patient visits/yr. PATIENTS: Patients presenting to emergency department (ED) triage who met the following criteria: greater than or equal to two of the three systemic inflammatory response syndrome criteria assessable in triage, a chief complaint suggestive of infection, emergency severity index 2 or 3, and ambulatory to ED. INTERVENTIONS: A computer-generated lactate order was created, staff education and resources increased, and point-of-care lactate testing was introduced. MEASUREMENTS AND MAIN RESULTS: Primary endpoints include the following: percent of patients having a lactate level drawn, percent of lactate samples resulting before room placement, and time intervals from triage to lactate blood draw and to lactate result. Secondary endpoints were percentage of patients admitted to the hospital, percentage admitted to the ICU, and in-hospital mortality. Six thousand nine hundred six patients were included: 226 historic controls (HCs) and 6,680 intervention group patients. The mean serum lactate level was 1.77 ± 1.18 mmol/L. The percentage of patients having a lactate resulted increased from 27.4% in the HC period to 79.6%. The percentage of these lactate results available while the patient was still in the waiting room increased from 0.4% during the HC period to 33.7% during Phase 5 (p < 0.0001). In the intervention period, time from triage to lactate result decreased (78.1–63.4 min; p < 0.0001) and time to treatment room decreased (59.3–39.6 min; p < 0.0001). CONCLUSIONS: Implementation of a computerized lactate order using readily available data obtained during ED triage, combined with point-of-care lactate testing, improves time to lactate blood draw and lactate result in patients at risk for severe sepsis. Initial lactate levels correlated with admission to the hospital, admission to the ICU, and in-hospital mortality.
C/EBP (cid:98) , but not C/EBP (cid:97) , is essential for ductal morphogenesis, lobuloalveolar proliferation, and functional differentiation in the mouse mammary gland

The CCAAT/enhancer binding proteins (C/EBPs) are differentially expressed throughout mammary gland development and interact with binding sites within the promoter of a milk protein gene, (cid:98) -casein. The specific roles of C/EBP (cid:98) and C/EBP (cid:97) in mouse mammary gland development and differentiation have been investigated in mice that carry targeted deletions of these genes. C/EBP (cid:98) −/− virgin mice exhibited cystic, enlarged mammary ducts with decreased secondary branching. Transplantation of C/EBP (cid:98) −/− mammary epithelium into the cleared mammary fat pads of nude mice confirmed that this defect in ductal morphogenesis was intrinsic to the epithelium. When treated with estrogen/progesterone (E+P) to simulate pregnancy, C/EBP (cid:98) −/− mammary glands displayed only limited lobuloalveolar development and ductal side branching. Primary mammary epithelial cells obtained from E+P-treated C/EBP (cid:98) −/− mice that were cultured on extracellular matrix gels did not functionally differentiate in response to lactogenic hormones despite their organization into three-dimensional structures. Expression of (cid:98) -casein protein was inhibited 85%–100% and whey acidic protein (WAP) was undetectable. In contrast, no detectable alterations in mammary development or (cid:98) -casein expression were observed in mammary outgrowths derived from newborn C/EBP (cid:97) −/− mammary epithelium transplanted into the cleared mammary fat pads of syngeneic hosts. These results demonstrate that C/EBP (cid:98) , but not C/EBP (cid:97) , is required for ductal morphogenesis, lobuloalveolar development, and functional differentiation of mammary epithelial cells.
On the role of the C-terminus of cx-calcitonin-gene-related peptide (xCGRP) The structure of des-phenylaianinamide37-aCGRP and its interaction with the CGRP receptor

a-Calcitonin-gene-related peptide (aCGRP) lacking its C-terminal phenylalaninamide residue was found not to bind to its receptor as did full-length (amidated) aCGRP. Investigation of the structure of these peptides by c.d. and n.m. r. revealed no significant difference, so it seemed that the effect of deleting
Galectin-3 Levels and Outcomes after Myocardial Infarction: A Community Study

BACKGROUND: Galectin-3 (Gal-3) is implicated in cardiac fibrosis but its association with adverse outcomes after myocardial infarction (MI) is unknown. OBJECTIVES: To examine the prognostic value of Gal-3 in a community cohort of incident MI. METHODS: A population-based incidence MI cohort was prospectively assembled in Olmsted County, MN, between 2002 and 2012. Gal-3 levels were measured at the time of MI. Patients were followed for heart failure (HF) and death. RESULTS: We enrolled 1342 patients (mean age 67.1 years, 61.3% male, 78.8% non-ST-elevation MI). Patients with elevated Gal-3 were older and had more comorbidities. Over a mean follow-up of 5.4 years, 484 patients (36.1%) died and 368 (27.4%) developed HF. After adjustment for age, sex, comorbidities and troponin, patients with Gal-3 values in tertiles 2 and 3 had a 1.3-fold (95% CI, 0.9–1.7) and a 2.4-fold (95% CI, 1.8–3.2) increased risk of death, respectively (P trend <0.001) compared with patients with Gal-3 values in tertile 1. Patients with Gal-3 values in tertiles 2 and 3 had a higher risk of HF with hazard ratios of 1.4 (95% CI, 1.0–2.0) and 2.3 (95% CI, 1.6–3.2), respectively (P trend <0.001). With further adjustment for soluble suppression of tumorigenicity-2 (sST2), elevated Gal-3 remained associated with increased risk of death and HF. The increased risk of HF did not differ by HF type and was independent of the occurrence of recurrent MI. CONCLUSIONS: Gal-3 is an independent predictor of mortality and HF post MI. These findings suggest a role for measuring Gal-3 levels for risk stratification post MI. ABSTRACT The present study evaluates the prognostic value of galectin-3 (Gal-3) measured at the time of incident myocardial infarction (MI) in a large contemporary community cohort. This is the first population-based study to examine the association between Gal-3 levels and long-term outcomes after MI demonstrating that Gal-3 is a strong predictor of mortality and heart failure post MI independently of other known prognostic factors and biomarkers, including troponin and soluble suppression of tumoriegenicity-2 (sST2). These findings support the use of Gal-3 as a biomarker for risk stratification in patients with MI.
Vascular Biology, Atherosclerosis and Endothelium Biology (cid:1) 5 (cid:2) 1 Integrin Blockade Inhibits Lymphangiogenesis in Airway Inflammation

The integrin (cid:1) 5 (cid:2) 1 has been previously implicated in tumor angiogenesis, but its role in the remodeling of both blood vessels and lymphatics during inflammation is at an early stage of understanding. We examined this issue using a selective, small-molecule inhibitor of (cid:1) 5 (cid:2) 1 integrin, 2-aroylamino-3-{4-[(pyri-din-2-ylaminomethyl)heterocyclyl]phenyl}propionic acid (JSM8757), in a model of sustained airway inflammation in mice with Mycoplasma pulmonis infection, which is known to be accompanied by robust blood vessel remodeling and lymphangiogenesis. The inhibitor significantly decreased the proliferation of lymphatic endothelial cells in culture and the number of lymphatic sprouts and new lymphatics in airways of mice infected for 2 weeks but did not reduce remodeling of blood vessels in the same airways. In inflamed airways, (cid:1) 5 integrin immunoreactivity was present on lymphatic sprouts, but not on collecting lymphatics or blood vessels, and was not found on any lymphatics of normal airways. Macrophages, potential targets of the inhibitor, did not have (cid:1) 5 integrin