Miracle-dz/UniFAR-FTUs huggingface dataset:
Two‐Dimensional Blue Native Polyacrylamide Gel Electrophoresis

Multiprotein complexes play crucial roles in nearly all cell biological processes. Blue Native Polyacrylamide Gel Electrophoresis (BN‐PAGE) is a powerful method to study these complexes. It is a native protein separation method that relies on the dye Coomassie blue to confer negative charge for separation. It has a higher resolution than gel filtration or sucrose density ultracentrifugation and can be used for protein complexes from 10 kDa to 10 MDa. If a second‐dimension SDS‐PAGE is applied (two‐dimensional BN/SDS‐PAGE), the size, subunit composition, and relative abundance of the different multiprotein complexes can be studied. In recent years, there has been a large increase in the number of publications where BN‐PAGE was used to study protein‐protein interactions. Here, we give detailed protocols for the separation of multiprotein complexes by two‐dimensional BN/SDS‐PAGE and for a related technique to determine the stoichiometry of these complexes. Curr. Protoc. Cell Biol. 38:6.10. 1‐6.10. 21. © 2008 by John Wiley & Sons, Inc.
Comparison of all hand digit length ratios in left- and right-handed individuals

To compare and detect possible differences between the digit length and digit length ratios in left- and right-handed female and male students. One of the cerebral hemispheres is dominant over the other. Knowing a person’s dominant hemisphere can be a useful guide in some personal activities. Materials and methods: Digit lengths (D) of the students were measured, followed by calculating the ratio of each digit to the others (1D:2D, 1D:3D, 1D:4D, 1D:5D, 2D:3D, 2D:4D, 2D:5D, 3D:4D, 3D:5D, and 4D:5D). Results: In males, no significant difference was found between digit lengths and digit length ratios. Among left-handed females, the fifth digit length was significantly longer. The 2D:5D, 3D:5D, and 4D:5D ratios were significantly smaller in their left hands, which indicated that the fifth digit was longer in left-handed females. Conclusion: The results of this study suggest that left-handed women could be especially successful in sports that require grasping a ball. This criterion should be considered for left-handed women while selecting athletes.
Rho GTPase Activation Assays

The Rho GTPase family of signaling proteins controls a wide range of highly dynamic cellular processes. Activation of Rho GTPases can be investigated and quantified in cell extracts using so‐called pull‐down assays. Proteins that bind specifically to the activated form of the Rho GTPase are used to capture it onto a bead support. Western blotting of the captured samples with specific antibodies then allows for quantification of the level of Rho GTPase activation in the sample. This unit describes the techniques for preparing the reagents required for assays of RhoA, Rac, and Cdc42 and gives practical tips for the successful application of the assay in a range of situations. Curr. Protoc. Cell Biol. 38:14.8. 1‐14.8. 19. © 2008 by John Wiley & Sons, Inc.
Analysis of Protein Folding and Oxidation in the Endoplasmic Reticulum

Proteins that travel through the secretory pathway undergo post‐translational folding and oxidation steps that lead to correct conformation of the final protein. This unit focuses on methods for the analysis of folding and oxidation events and the factors responsible for their proper execution. Alkylation and nonreducing SDS‐PAGE is use to analyze disulfide bond formation in ER‐derived microsomes. If proteins are synthesized under reducing conditions, it is possible to initiate folding by addition of oxidizing agents, thus allowing analysis of factors necessary for the folding process. As folding progresses, the protein of interest shows a change in sensitivity to proteolysis. Co‐immunoprecipitation or crosslinking and denaturing immunoprecipitation are used to explore the role of molecular chaperones and other factors. Conformation‐specific antibodies can be used to probe folding. In addition, folding can be analyzed in intact or semi‐permeabilized adherent or suspension cells.
Does hemodiafiltration reduce vascular stiffness measured by aortic pulse wave velocity compared with high‐flux hemodialysis?

Hemodialfiltration (HDF) has been reported to reduce the frequency of intradialytic hypotension compared with hemodialysis (HD). We wished to determine whether HDF resulted in improvement of arterial stiffness compared with HD. We reviewed peripheral blood pressure and pulse wave velocity measurements in a cross‐sectional analysis of stable HDF and HD outpatients. One hundred forty‐one HDF patients were matched to 148 HD patients in terms of age, sex, prevalence of diabetes, peripheral blood pressure, and body mass. Pulse wave velocity was not different between the HD and HDF cohorts (median 9.1 [8.0–10.7] m/s vs. 9.7 [8.5–11.6] m/s). Similarly, there were no differences in central aortic pressure (149.2 ± 30.9 mmHg vs. 151.9 ± 35.2 mmHg), or aortic (39 [25.1–51.2]% vs. 38.6 [25.8–51.4]%) and brachial (3.8 [−24.3 to 26.9]% vs. 3 [−22.4 to 27.1]%) augmentation indices, respectively. Pulse wave velocity did not differ between adult patients treated by HD and HDF, and similarly, there were no differences in central aortic pressure, aortic or brachial augmentation indices, and cardiac diastolic perfusion. Our study suggests that HDF does not appear to offer any benefit over HD in terms of vascular stiffness.
Rapid Inactivation of Proteins by Knocksideways

The knocksideways system inactivates proteins by using a small molecule to trap them onto mitochondria. It is typically ∼3 to 4 orders of magnitude faster than a knockdown. To get the best results out of a knocksideways, five parameters need to be optimized: the bait, the prey, the small molecule, the cell or organism, and the assay. Curr. Protoc. Cell Biol. 61:15.20. 1‐15.20. 7. © 2013 by John Wiley & Sons, Inc.
Analysis of the Stromal Cellular Components of the Solid Tumor Microenvironment Using Flow Cytometry

The tumor microenvironment consists of a variety of cell types. The contribution of each cell type to the tumor is an emerging subject in the field of cancer research. Here, we describe protocols for dissociating tumor tissues and Matrigel plugs into single cells for further analysis by flow cytometry. These protocols can be used for evaluating the cellular component of solid tumors from human or mouse origin or Matrigel plugs implanted in mice. The protocols describe the dissociation of tumor tissue with or without dissociation automatic devices. Subsequently, the use of flow cytometry for immunophenotypic analysis of host cells found in the tumor microenvironment, including myeloid derived suppressor cells, endothelial cells, and macrophages is provided. These methods can be used to broaden our understanding of the cross‐talk between tumor and host cells in the tumor microenvironment. © 2016 by John Wiley & Sons, Inc.
Veterinary Epidemiologic Research

First printing (Nov. 2009) After commencing shipping of the 2nd Edition of Veterinary Epidemiologic Research, we discovered that some of the lines in some of the Figures are printed very faintly (and in some cases are almost invisible). This was a surprise as the Figures had all printed perfectly well when the galley proofs were examined. In total, 20 figures are affected to some degree. To obtain a 2 page sheet with all of these figures printed correctly, go to: www.upei. ca/ver/errata
Sister Chromatid Exchange

Sister chromatid exchange (SCE) refers to the interchange of DNA between replication products. The technique for detecting such exchanges takes advantage of the semiconservative nature of DNA synthesis. 5′‐bromodeoxyuridine (BrdU) is incorporated into the newly synthesized DNA. Using standard culturing techniques, Colcemid is added to the culture and conventional cytogenetic preparations are made. Differential staining with Hoechst dye and Giemsa allows the newly synthesized DNA within a chromatid to be recognized, since BrdU incorporation results in much weaker staining. SCEs represent a point of DNA template exchange during strand synthesis, visualized as asymmetric chromatid staining or “harlequin” chromosomes.
Encyclopedia of Toxicology

This is the third rendition of this landmark work, the first and second editions having appeared in 1998 and 2005, respectively. It is produced in four hardbound volumes containing 1200 alphabetically arranged topics followed by the index. In addition to the editor-in-chief, there were 9 associate editors and nearly 1400 contributors. The topics comprise not just entries for specific chemicals and drugs (antimony, benomyl, carbamazepine, ethylene glycol, fluoxetine, etc.), but also numerous general headings for topics such as absorption, excretion, fetal alcohol syndrome, global environmental change, life cycle assessment, pharmacokinetic models, risk management and veterinary toxicology. The former type of entry is often just 2–3 pages; it lists the specific authors and their affiliations, the CAS number, synonyms, molecular formula, chemical structure, uses, brief history, routes of exposure, toxicokinetics, toxic mechanism, toxic effects in animals and humans, clinical management, environmental fate, exposure limits and a bibliography. The latter type may run from 1 to 10 or more pages and varies in scope depending on the topic in question. Some of the general heading contributions, Excretion, for example, are quite limited in their depth of coverage, but they do provide suggestions for further reading and this is an encyclopedia, of course, and not a textbook. The reader may find it worthwhile to first consult the index when searching for information, since many substances are listed in the contents under a general heading. Doxazosin, for instance, appears not under its own generic name but in a section on alpha blockers. Some other substances are not where you might expect them, for example, n-butyl alcohol was placed alphabetically among the N’s. The
Exploring Zebrafish Genomic, Functional and Phenotypic Data Using ZFIN

The zebrafish model organism database (ZFIN) provides a Web resource of zebrafish genomic, genetic, developmental, and phenotypic data. ZFIN curates and integrates data from current literature and from direct data submissions from laboratories. In addition, ZFIN collaborates with other bioinformatics organizations to provide links to other relevant data. These data can be accessed through a variety of Web‐based search and display tools. This unit focuses on some of the basic methods to search, visualize, and analyze ZFIN data, including genes, gene expression, mutants, morphants, transgenics, anatomical structures, and antibodies. ZFIN's GBrowse genome viewer, BLAST, and protocol and antibody wikis are also discussed. Curr. Protoc. Bioinform. 31:1.18. 1‐1.18. 44. © 2010 by John Wiley & Sons, Inc.
Psychodermatology: the psychological impact of skin disorders

Psychodermatology covers all aspects of how the mind and body interact in relation to the onset and progression of various skin disorders. This book is the first text written by a multidisciplinary team of psychiatrists, psychologists, child specialists and dermatologists for all the health professionals who treat patients with skin problems. They cover a broad range of issues affecting these patients, including: stigma, coping, relationships, psychological treatments, the impact on children, comorbidities, psychoneuroimmunology, quality of life and psychological treatments.
Using the Reactome Database

Pathway databases provide descriptions of the roles of proteins, nucleic acids, lipids, carbohydrates, and other molecular entities within their biological cellular contexts. Pathway‐centric views of these roles may allow for the discovery of unexpected functional relationships in data such as gene expression profiles and somatic mutation catalogues from tumor cells. For this reason, there is a high demand for high‐quality pathway databases and their associated tools. The Reactome project (a collaboration between the Ontario Institute for Cancer Research, New York University Langone Health, the European Bioinformatics Institute, and Oregon Health & Science University) is one such pathway database. Reactome collects detailed information on biological pathways and processes in humans from the primary literature. Reactome content is manually curated, expert‐authored, and peer‐reviewed and spans the gamut from simple intermediate metabolism to signaling pathways and complex cellular events. This information is supplemented with likely orthologous molecular reactions in mouse, rat, zebrafish, worm, and other model organisms. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.
MultiPipMaker: A Comparative Alignment Server for Multiple DNA Sequences

The MultiPipMaker World Wide Web server (http://www.bx.psu.edu) provides a tool for aligning multiple DNA sequences and visualizing regions of conservation among them. This unit describes its use and gives an explanation of the resulting output files and supporting tools. Features provided by the server include alignment of up to 20 very long genomic sequences, output choices of a true, nucleotide‐level multiple alignment and/or stacked, pairwise percent identity plots, and support for user‐specified annotations of genomic features and arbitrary regions, with clickable links to additional information. Input sequences other than the reference can be fragmented, unordered, and unoriented. Curr. Protoc. Bioinform. 30:10.4. 1‐10.4. 14. © 2010 by John Wiley & Sons, Inc.
Risk Assessment in Adult Cancer Patients with Febrile Neutropenia: A Review of Methods and of Risk-adapted Empiric Treatments

Febrile neutropenia is a common complication of antineoplasic chemotherapy. It is a potentially serious event, sometimes lethal. However, it is well recognized that the population of patients with febrile neutropenia is heterogeneous in terms of prognosis. Simplified therapy, for instance oral antibiotic empiric treatment or ambulatory treatment, in comparison to the classical management of intravenously administered empiric antibiotics and in-hospital surveillance, has been the purpose of research for patients predicted at low-risk for serious complications development. However, for such a strategy to be successful an accurate identification of patients at low-risk is required. The objective of the present review is to present the available tools for risk assessment, in adult patients populations and to review the status of our knowledge regarding the efficacy and the safety of risk-adapted therapy.
Chronic Pain and Traumatic Brain Injury in OEF/OIF Service Members and Veterans

The co‐occurrence of chronic pain and traumatic brain injury (TBI) are 2 of the most common concerns among the Operations Enduring Freedom and Iraqi Freedom population and present unique challenges for evaluation and treatment. Previous research suggests that almost half the cohort report clinically significant pain, while up to 1 in 4 experiences some form of TBI. There is limited information regarding how TBI affects the presence and course of pain, and how pain impacts TBI and its symptoms. The present paper provides an overview of the range and degree of TBIs as well as a brief summary of current knowledge regarding the interaction between chronic pain and TBI, particularly in light of the numerous variables impacting it. Information on ways to best assess for and treat pain in the TBI population, including in those with multiple system injuries or associated affective symptoms, is provided. In addition, several innovative approaches for addressing the needs of this complex cohort of patients are described, which may stimulate further research and clinical innovation for this important subgroup.
Retrospective Study of Treatment for Peritonsillar Abscess

We reviewed the treatment of 86 patients with peritonsillar abscesses.We examined by m. a. whether the otolaryngological procedure and the antibiotics (cephems, penicillin, other f3-Ractums and clindamycin) used influenced the treatment period.We found that otolaryngological therapy is the best treatment for peritonsillar abscesses, especially incision and drainage. When aspiration is done, it is necessary to administer penicillin.Any intravenous antibiotics are effective for peritonsillar abscess after incision and drainage except for clindamycin alone.It is necessary to avoid clindamycin monotherapy, and to use clindamycin together with penicillin after aspiration.
FROM THERE TO HERE: USING PHOTOGRAPHY TO EXPLORE PERSPECTIVES OF RESETTLED REFUGEE YOUTH

Because refugee numbers are much smaller than those of other immigrant populations in the United States, researchers frequently group refugees with other immigrants in their studies. However, due to the traumatic circumstances that most refugees face prior to their arrival, they require separate consideration. We chose the medium of photography to help newcomer refugee students express themselves beyond their current capacities in English, and we used the students’ photographs as catalysts to interview them about their resettled lives in the United States. Through this process, we discovered themes central to the students’ lives, and ways in which they were working to reconcile important past and present elements, such as family, friends, cultures, and aspirations. Bronfenbrenner’s (1986) ecological theory provides a useful frame for exploring these students’ processes of acculturation. Their photos, and their commentaries, provide critically important information for teachers, social service providers, and others working with refugee youth.
Surgery for primary supratentorial intracerebral haemorrhage.

BACKGROUND There is considerable international variation in the rate and indications of surgery for primary supratentorial intracerebral haematoma, reflecting the uncertainty about the effects of surgery. Recently, some large randomised trials have appeared in the literature but the controversy over its role continues. This is an update of a Cochrane review first published in 1997, and previously updated in 1999. OBJECTIVES To assess the effects of surgery plus routine medical management, compared with routine medical management alone, in patients with primary supratentorial intracerebral haematoma. SEARCH STRATEGY We searched the Cochrane Stroke Group Trials Register (last searched June 2007), checked reference lists of relevant articles and contacted authors of relevant trials. In addition, for the original version of this review we handsearched two journals, Current Opinion in Neurology and Neurosurgery, and Neurosurgical Clinics of North America (1991 to July 1993), and three monographs. We contacted study authors for relevant information. SELECTION CRITERIA Randomised trials of routine medical treatment plus intracranial surgery compared with routine medical treatment alone in patients with CT-confirmed primary supratentorial intracerebral haematoma. Intracranial surgery included craniotomy, stereotactic endoscopic evacuation or stereotactic aspiration. DATA COLLECTION AND ANALYSIS Two review authors independently applied the inclusion criteria, assessed trial quality and extracted the data. MAIN RESULTS Ten trials with 2059 participants were included. The quality of most of the trials was acceptable but not high. Because of this and as the overall result was sensitive to the losses to follow up in the largest trial, the estimates of effect may not be robust and may be subject to bias. Surgery was associated with statistically significant reduction in the odds of being dead or dependent at final follow up (odds ratio (OR) 0.71, 95% confidence interval (CI) 0.58 to 0.88; 2P = 0.001) with no significant heterogeneity among the study results. Surgery was also associated with significant reduction in the odds of death at final follow up (OR 0.74, 95% CI 0.61 to 0.90; 2P = 0.003); however, there was significant heterogeneity for death as outcome. AUTHORS' CONCLUSIONS In patients with CT-proven primary supratentorial intracerebral haemorrhage, surgery added to medical management reduces the odds of being dead or dependent compared with medical management alone, but the result is not very robust. Hence, further randomised trials to identify which patients benefit from surgery and to evaluate less invasive methods are indicated.
Recruitment and Retention of Faculty of Color in Southern California Independent Schools

This qualitative study examined recruitment and retention of faculty of color in independent schools in Southern California. Seven administrator interviews captured the perspective of school leaders involved in hiring efforts at their schools, and nine faculty of color were interviewed to further explore themes that arose around recruitment practices and retention challenges in a faculty questionnaire completed by 84 respondents. The list of the highest priority factors candidates consider in choosing a school varies from person to person, but as a group the data show that faculty diversity, student diversity, and a commitment to professional development to allow for ongoing growth- on the personal and community level- are aspects of high value to candidates of color. Resilient candidates may still be successful at schools where they face challenges and cultural conflicts, but contentment and fulfillment happens only when a majority of a candidate’s personal values align with those of the school. Therefore the recruitment phase is critical in exploring this alignment, and support systems such as mentoring programs and faculty of color affinity groups are important in increasing retention after hiring. Ultimately a school’s commitment to diversity has to be supported by the school leadership. School leaders must take proactive measures in creating ongoing conversations, education for the community to address misconceptions around diversity, articulation that diversity strengthens teams, and thoughtful recruitment and retention procedures and systems to truly live out their school’s commitment to diversity.
Mental health related contact with education professionals in the British Child and Adolescent Mental Health Survey 2004

Purpose – The purpose of this paper is to describe mental health-related contact with educational professionals amongst children in the British Child and Adolescent Mental Health Survey (BCAMHS) 2004. Design/methodology/approach – BCAMHS 2004 was a community-based survey of 5,325 children aged 5-16, with follow-up in 2007. This paper reports the percentage of children with a psychiatric disorder that had mental health-related contact with education professionals (categorised as teachers or specialist education services) and the percentage with specific types of psychiatric disorders amongst those contacting services. Findings – Two-thirds (66.1 per cent, 95 per cent CI: 62.4-69.8 per cent) of children with a psychiatric disorder had contact with a teacher regarding their mental health and 31.1 per cent (95 per cent CI: 27.5-34.7 per cent) had contact with special education either in 2004 or 2007, or both. Over half of children reporting special education contact (55.1 per cent, 95 per cent CI: 50.0-60.2 p.