Miracle-dz/UniFAR-FTUs huggingface dataset:
The impact of network biology in pharmacology and toxicology

With the need to investigate alternative approaches and emerging technologies in order to increase drug efficacy and reduce adverse drug effects, network biology offers a novel way of approaching drug discovery by considering the effect of a molecule and protein's function in a global physiological environment. By studying drug action across multiple scales of complexity, from molecular to cellular and tissue level, network-based computational methods have the potential to improve our understanding of the impact of chemicals in human health. In this review we present the available large-scale databases and tools that allow integration and analysis of such information for understanding the properties of small molecules in the context of cellular networks. With the recent advances in the omics area, global integrative approaches are necessary to cope with the massive amounts of data, and biomedical researchers are urged to implement new types of analyses that can lead to new therapeutic interventions with increased safety and efficacy compared with existing medications.
Mouse hematopoietic stem cell identification and analysis

Hematopoietic stem cells (HSCs) remain by far the most well‐characterized adult stem cell population both in terms of markers for purification and assays to assess functional potential. However, despite over 40 years of research, working with HSCs in the mouse remains difficult because of the relative abundance (or lack thereof) of these cells in the bone marrow. The frequency of HSCs in bone marrow is about 0.01% of total nucleated cells and ∼5,000 can be isolated from an individual mouse depending on the age, sex, and strain of mice as well as purification scheme utilized. This prohibits the study of processes in HSCs, which require large amounts of starting material. Adding to the challenge is the continual reporting of new markers for HSC purification, which makes it difficult for the uninitiated in the field to know which purification strategies yield the highest proportion of long‐term, multilineage HSCs. This report will review different hematopoietic stem and progenitor purification strategies and compare flow cytometry profiles for HSC sorting and analysis on different instruments. We will also discuss methods for rapid flow cytometric analysis of peripheral blood cell types, and novel strategies for working with rare cell populations such as HSCs in the analysis of cell cycle status by BrdU, Ki‐67, and Pyronin Y staining. The purpose of this review is to provide insight into some of the recent experimental and technical advances in mouse hematopoietic stem cell biology. © 2008 International Society for Advancement of Cytometry
Vibrational spectroscopy—A powerful tool for the rapid identification of microbial cells at the single‐cell level

Rapid microbial detection and identification with a high grade of sensitivity and selectivity is a great and challenging issue in many fields, primarily in clinical diagnosis, pharmaceutical, or food processing technology. The tedious and time‐consuming processes of current microbiological approaches call for faster ideally on‐line identification techniques. The vibrational spectroscopic techniques IR absorption and Raman spectroscopy are noninvasive methods yielding molecular fingerprint information; thus, allowing for a fast and reliable analysis of complex biological systems such as bacterial or yeast cells. In this short review, we discuss recent vibrational spectroscopic advances in microbial identification of yeast and bacterial cells for bulk environment and single‐cell analysis. IR absorption spectroscopy enables a bulk analysis whereas micro‐Raman‐spectroscopy with excitation in the near infrared or visible range has the potential for the analysis of single bacterial and yeast cells. The inherently weak Raman signal can be increased up to several orders of magnitude by applying Raman signal enhancement methods such as UV‐resonance Raman spectroscopy with excitation in the deep UV region, surface enhanced Raman scattering, or tip‐enhanced Raman scattering. © 2008 International Society for Advancement of Cytometry
Stromal vascular progenitors in adult human adipose tissue

The in vivo progenitor of culture‐expanded mesenchymal‐like adipose‐derived stem cells (ADSC) remains elusive, owing in part to the complex organization of stromal cells surrounding the small vessels, and the rapidity with which adipose stromal vascular cells adopt a mesenchymal phenotype in vitro. Immunohistostaining of intact adipose tissue was used to identify three markers (CD31, CD34, and CD146), which together unambiguously discriminate histologically distinct inner and outer rings of vessel‐associated stromal cells, as well as capillary and small vessel endothelial cells. These markers were used in multiparameter flow cytometry in conjunction with stem/progenitor markers (CD90 and CD117) to further characterize stromal vascular fraction (SVF) subpopulations. Two mesenchymal and two endothelial populations were isolated by high speed flow cytometric sorting, expanded in short term culture, and tested for adipogenesis. The inner layer of stromal cells in contact with small vessel endothelium (pericytes) was CD146+/α‐SMA+/CD90±/CD34−/CD31−; the outer adventitial stromal ring (designated supra adventitial‐adipose stromal cells, SA‐ASC) was CD146−/α‐SMA−/CD90+/CD34+/CD31−. Capillary endothelial cells were CD31+/CD34+/CD90+ (endothelial progenitor), whereas small vessel endothelium was CD31+/CD34−/CD90− (endothelial mature). Flow cytometry confirmed these expression patterns and revealed a CD146+/CD90+/CD34+/CD31− pericyte subset that may be transitional between pericytes and SA‐ASC. Pericytes had the most potent adipogenic potential, followed by the more numerous SA‐ASC. Endothelial populations had significantly reduced adipogenic potential compared with unsorted expanded SVF cells. In adipose tissue, perivascular stromal cells are organized in two discrete layers, the innermost consisting of CD146+/CD34− pericytes, and the outermost of CD146−/CD34+ SA‐ASC, both of which have adipogenic potential in culture. A CD146+/CD34+ subset detected by flow cytometry at low frequency suggests a population transitional between pericytes and SA‐ASC. © 2009 International Society for Advancement of Cytometry
A Framework for Treating Cumulative Trauma With Art Therapy

Abstract Cumulative trauma is relatively undocumented in art therapy practice, although there is growing evidence that art therapy provides distinct benefits for resolving various traumas. This qualitative study proposes an art therapy treatment framework for cumulative trauma derived from semi-structured interviews with three art therapists and artistic representations of their approaches. Key components of practice include attention to the variability of symptom presentation, treatment approach, essential elements of therapy, and the use of art as a treatment modality. Art therapists attune themselves to their clients’ subjective levels of distress throughout assessment and the course of treatment.
Multiple Sclerosis in Pregnancy

Multiple sclerosis is the most common chronic neurologic disability in young adults in their childbearing ages of 20 to 45. The disease affects more women than men, which prompts discussion of pregnancy-related issues in a woman with multiple sclerosis. Preconceptual counseling to discuss the safety of medications in pregnancy, the antepartum period along with what the patient can expect during birth, and the postpartum period will be discussed.
Out of hospital treatment of acute pulmonary embolism in patients with a low NT‐proBNP level

Summary. Background: Low NT‐proBNP levels are associated with an uncomplicated course in patients with pulmonary embolism (PE). The aim of this multicenter management study was to investigate the safety of home treatment of patients with PE with low (< 500 pg mL−1) NT‐proBNP. Methods and results: Hemodynamically stable outpatients with acute PE and NT‐proBNP level < 500 pg mL−1 were included. Patients were discharged immediately from the emergency room or within a maximum of 24 h after admission. The primary study objective was the absence of mortality during the first 10 days of treatment. Secondary objectives were the incidence of re‐admission due to PE or its treatment and the patient’s satisfaction during the first 10 days of treatment as well as the incidence of serious adverse events during the 3‐month follow‐up period. Of 351 patients, 152 (43%) fulfilled the inclusion criteria and were treated as outpatients. No deaths, major bleedings or recurrent venous thromboembolism occurred in the first 10 days of treatment or in the follow‐up period of 3 months in these patients. Seven patients required readmission in the first 10 days: three because of complaints that could be related to PE and four due to an illness unrelated to PE. The HADS‐A anxiety score did not change significantly between day 0 and day 10. The PSQ‐18 showed a high score for satisfaction with home treatment. Conclusion: Out of hospital treatment is safe in hemodynamically stable patients with PE with low (< 500 pg mL−1) NT‐proBNP levels. Approximately 45% of patients with PE can be treated in an outpatient setting. Patients do not consider out of hospital treatment as inconvenient and have no increase in anxiety scores. Clinical Trial Registration Information: http://clinicaltrials.gov/ct2/show/NCT00455819.
Platelet hyperreactivity and a prothrombotic phenotype in mice with a gain‐of‐function mutation in phospholipase Cγ2

Summary. Background: Agonist‐induced platelet activation involves different signaling pathways leading to the activation of phospholipase C (PLC) β or PLCγ2. Activated PLC produces inositol 1,4,5‐trisphosphate and diacylglycerol, which trigger Ca2+ mobilization and the activation of protein kinase C, respectively. PLCβ is activated downstream of Gq‐coupled receptors for soluble agonists with only short interaction times in flowing blood. In contrast, PLCγ2 becomes activated downstream of receptors that interact with immobilized ligands such as the collagen receptor glycoprotein (GP) VI or activated integrins. Objective and methods: We speculated that PLCγ2 activity might be optimized for sustained but submaximal signaling to control relatively slow platelet responses. To test this hypothesis, we analyzed platelets from mice heterozygous for a gain‐of‐function mutation in the Plcg2 gene (Plcg2Ali5/+). Results: Plcg2Ali5/+ platelets showed enhanced Ca2+ mobilization, integrin activation, granule secretion and phosphatidylserine exposure upon GPVI or C‐type lectin‐like receptor‐2 stimulation. Furthermore, integrin αIIbβ3 outside‐in signaling was markedly enhanced in the mutant platelets, as shown by accelerated spreading on different matrices and faster clot retraction. These defects translated into virtually unlimited thrombus formation on collagen under flow in vitro and a prothrombotic phenotype in vivo. Conclusions: These results demonstrate that the enzymatic activity of PLCγ2 is tightly regulated to ensure efficient but limited platelet activation at sites of vascular injury.
Cytometric assessment of mitochondria using fluorescent probes

Mitochondria are most important organelles in the survival of eukaryotic aerobic cells because they are the primary producers of ATP, regulators of ion homeostasis or redox state, and producers of free radicals. The key role of mitochondria in the generation of primordial ATP for the survival and proliferation of eukaryotic cells has been proven by extensive biochemical studies. In this context, it is crucial to understand the complexity of the mitochondrial compartment and its functionality and to develop experimental tools allowing the assessment of its nature and its function and metabolism. This review covers the role of the mitochondria in the cell, focusing on its structure, the mechanism of the mitochondrial respiratory chain, the maintenance of the transmembrane potential and the production of reactive oxygen species. The main probes used for mitochondrial compartment monitoring are described. In addition, various applications using mitochondrial‐specific probes are detailed to illustrate the potential of flow and image cytometry in the study of the mitochondrial compartment. This review contains a panel of tools to explore mitochondria and to help researchers design experiments, determine the approach to be employed, and interpret their results. © 2011 International Society for Advancement of Cytometry
Erratum of “Investigation of Microencapsulated BSH Active Lactobacillus in the Simulated Human GI Tract”

This is to confirm that there is an error in the article “Investigation of Microencapsulated BSH Active Lactobacillus in the Simulated Human GI Tract” by Martoni et al. Published online December 25, 2007, doi: 10.1155/2007/13684. Figure 5 should be replaced by Figure 5 below. Figure 5 Evaluation of microcapsule integrity and morphological changes during simulated GI transit. (a) Pre-stomach transit (b) Post-stomach transit (60 minutes) (c) Post-stomach (60 minutes) and intestinal (10 hours) transit.Microcapsule size (a) 608 ± .
Thrombin‐activatable fibrinolysis inhibitor is degraded by Salmonella enterica and Yersinia pestis

Summary. Background: Pathogenic bacteria modulate the host coagulation system to evade immune responses or to facilitate dissemination through extravascular tissues. In particular, the important bacterial pathogens Salmonella enterica and Yersinia pestis intervene with the plasminogen/fibrinolytic system. Thrombin‐activatable fibrinolysis inhibitor (TAFI) has anti‐fibrinolytic properties as the active enzyme (TAFIa) removes C‐terminal lysine residues from fibrin, thereby attenuating accelerated plasmin formation. Results: Here, we demonstrate inactivation and cleavage of TAFI by homologous surface proteases, the omptins Pla of Y. pestis and PgtE of S. enterica. We show that omptin‐expressing bacteria decrease TAFI activatability by thrombin‐thrombomodulin and that the anti‐fibrinolytic potential of TAFIa was reduced by recombinant Escherichia coli expressing Pla or PgtE. The functional impairment resulted from C‐terminal cleavage of TAFI by the omptins. Conclusions: Our results indicate that TAFI is degraded directly by the omptins PgtE of S. enterica and Pla of Y. pestis. This may contribute to the ability of PgtE and Pla to damage tissue barriers, such as fibrin, and thereby to enhance spread of S. enterica and Y. pestis during infection.
Complications of Posterior Cruciate Ligament Surgery

In addition to standard risks associated with all orthopedic surgical procedures, posterior cruciate ligament (PCL) reconstruction poses some relatively unique potential complications. These complications arise from a combination of several factors: the relative infrequency of PCL injuries, the lack of knowledge and experience in treating them, the proximity of neurovascular structures to the PCL, and the technically demanding nature of reconstructive procedures. This article discusses the anatomy, pathogenesis, and prevention of intraoperative and postoperative complications of PCL surgery including neurovascular injury, osteonecrosis, fracture, motion loss, and persistent laxity.
NIST/ISAC standardization study: Variability in assignment of intensity values to fluorescence standard beads and in cross calibration of standard beads to hard dyed beads

Results from a standardization study cosponsored by the International Society for Advancement of Cytometry (ISAC) and the US National Institute of Standards and Technology (NIST) are reported. The study evaluated the variability of assigning intensity values to fluorophore standard beads by bead manufacturers and the variability of cross calibrating the standard beads to stained polymer beads (hard‐dyed beads) using different flow cytometers. Hard dyed beads are generally not spectrally matched to the fluorophores used to stain cells, and spectral response varies among flow cytometers. Thus if hard dyed beads are used as fluorescence calibrators, one expects calibration for specific fluorophores (e.g., FITC or PE) to vary among different instruments. Using standard beads surface‐stained with specific fluorophores (FITC, PE, APC, and Pacific Blue™), the study compared the measured intensity of fluorophore standard beads to that of hard dyed beads through cross calibration on 133 different flow cytometers. Using robust CV as a measure of variability, the variation of cross calibrated values was typically 20% or more for a particular hard dyed bead in a specific detection channel. The variation across different instrument models was often greater than the variation within a particular instrument model. As a separate part of the study, NIST and four bead manufacturers used a NIST supplied protocol and calibrated fluorophore solution standards to assign intensity values to the fluorophore beads. Values assigned to the reference beads by different groups varied by orders of magnitude in most cases, reflecting differences in instrumentation used to perform the calibration. The study concluded that the use of any spectrally unmatched hard dyed bead as a general fluorescence calibrator must be verified and characterized for every particular instrument model. Close interaction between bead manufacturers and NIST is recommended to have reliable and uniformly assigned fluorescence standard beads. © 2012 International Society for Advancement of Cytometry
Optimized protocol for the isolation of spleen‐resident murine neutrophils

Neutrophils are an important cellular component of the innate immune system that provides immediate protection to the host from infection. Neutrophil infiltration into inflamed peripheral tissues during infection is beneficial for immunity through phagocytosis of microbes, the release of antimicrobial factors, and secretion of proinflammatory cytokines. Recent reports further suggest that spleen‐infiltrating neutrophils play a role in the adaptive immune response by providing survival signals to B cells. However, neutrophils may have detrimental effects on immunity in inflammatory diseases where their recruitment to lymphoid tissues and activation occur abnormally. To determine the contribution of neutrophils that reside in secondary lymphoid tissues to adaptive immunity, direct evaluation of the functional properties of tissue‐resident neutrophils is required. We have developed a modified magnetic bead isolation approach for purifying neutrophils from inflamed spleens of autoimmune‐prone mice by negative selection. Using this approach, we yielded neutrophils with greater than 90% purity without compromising cell viability. Equally important, the isolation procedure had little effect on the activation of neutrophils and did not impair phagocytic function. Thus, isolation of spleen‐resident neutrophils by this optimized approach could be useful for interrogating the functional role of murine neutrophils in normal and abnormal immune responses. © 2012 International Society for Advancement of Cytometry
Sweat the small stuff

COMMENTARY Viruses are obligate intracellular parasites. How viral agents enter and replicate in cells are critical issues because of impact on cellular function and because of the need to find ways to block infection at different stages. Intermediate steps in entry and replication are hard to study. Conventional physical means of purification can be complex and time consuming. Even for the most intensively studied viruses such as HIV, it is not clear exactly how the virus loses its envelope once inside the cell or how the viral genome is shuttled around in the cytoplasm (1). In this issue, Loret et al. (page 950) show elegant flow cytometry that they use to detect and sort Herpes simplex virus (HSV-1) type I nuclear particles based on differential DNA staining and side scatter (90 ). HSV-1 is a large double stranded DNA virus which causes cold sores in humans. The major nuclear particles of HSV-1 (A, B, C) were identified and sorted for biochemical analysis. The viral particles that have the highest signal after DNA staining with syto 13 were shown to scatter more light at 90 perhaps indicating that structural changes occur in the nucleus as the viral particles mature. This work represents an extension of cytometry into a new arena and offers new strategies for analysis and separation that can be used by virologists and other seekers of intracellular components. In addition, this paper provides important lessons for how best to do cytometry with small particles. The lessons learned include:
The Chest Radiograph in Heart Disease

Abstract This contribution concentrates on the appearance of the adult chest radiograph in diseases of the heart and great vessels. It should be read in conjunction with MEDICINE 27:8 , 7, which discusses the chest radiograph in respiratory disorders. The ideal radiograph for assessing the heart and great vessels is the straight, erect, postero-anterior (PA) chest radiograph taken at full inspiration. PA radiographs image true heart size, as opposed to anteroposterior radiographs in which there is variable and indeterminate magnification. As a result of gravity, erect radiographs display small pulmonary vessels in the upper zone and larger ones in the lower; this important sign of normality cannot be assessed on a supine chest radiograph in which upper and lower zone vessels are equal in size. The high diaphragm and the commonly used short tube-to-film distance of supine radiographs also lead to magnification of heart size. In addition, heart size is affected by patient rotation. Because the long axis of the heart lies at about 45° to the sagittal plane, patient rotation with the right shoulder forward (RAO) enlarges the cardiac image, whereas the reverse rotation (LAO) reduces it. Rotations such as these along the major axis of the body also affect the prominence of various great vessels (aorta and pulmonary arteries), making their evaluation unreliable.
The monoterpene (–)‐carvone: A novel agonist of TRPV1 channels

(–)‐Carvone is an antinociceptive monoterpene found as the main active constituent of essential oils obtained from plants of the genus Mentha. Here, we have investigated the pharmacology of this monoterpene in dorsal root ganglia (DRG) neurons and TRPV1‐expressing HEK293 cells. (–)‐carvone at pharmacological active concentrations did not reveal significant cytotoxicity to the cells used in this study, as investigated by neutral red and propidium iodide flow cytometry assays. In calcium imaging experiments 1 mM (–)‐carvone increased the cytosolic calcium levels in DRG neurons from 120.6 ± 5.0 nM (basal) to 310.7 ± 23.1 nM (P < 0.05). These effects were completely abolished when neurons were preincubated with calcium‐free bath solution or ruthenium‐red (5 µM) and capsazepine (10 µM), suggesting the possibility of TRPV1 channel‐activation by (–)‐carvone. Activity of (–)‐carvone on TRPV1 channels was further investigated in HEK293 cells expressing recombinant human TRPV1 channels revealing dose‐dependent calcium transients with an EC50 of 1.3 ± 0.2 mM (Hill coefficient = 2.5). In conclusion, we show for the first time the ability of (–)‐carvone to induce increases in cytosolic calcium concentration through TRPV1 activation. © 2013 International Society for Advancement of Cytometry
Body Awareness, Eating Attitudes, and Spiritual Beliefs of Women Practicing Yoga

This research evaluated attitudes about body image and eating in women practicing postural yoga. Study 1 described scores from questionnaires on variables related to body awareness, intuitive eating, spirituality, and reasons for practicing. Scores were favorable on all measures with significant correlations (p < .01) among all main variables except between spiritual readiness and intuitive eating, and between BMI and both body awareness and spiritual readiness. Reasons for practicing did not affect scores. Study 2 evaluated interviews in a sub-sample. Qualitative data reported improvements in body satisfaction and disordered eating due in part to yoga and its associated spirituality.