Miracle-dz/UniFAR-FTUs huggingface dataset:
Long-term outcome of autoimmune disease following allogeneic bone marrow transplantation.

OBJECTIVE To investigate the long-term outcome of autoimmune disease following allogeneic bone marrow transplantation (BMT), and its relationship to hemopoietic chimerism. METHODS Three previously described patients with rheumatoid arthritis (RA) who underwent allogeneic BMT for therapy-related severe aplastic anemia and 1 new patient with psoriasis who received BMT for chronic myeloid leukemia (CML) were followed up. Molecular studies were performed to assess hemopoietic and immune reconstitution in 3 cases. RESULTS In 2 of the RA patients, the RA remained in remission without treatment, with nonprogressive disease, 11 and 13 years after BMT. The third patient with RA had a relapse 2 years after BMT, although the previously aggressive disease subsequently ran an attenuated course with treatment-free remission for the last 11 years. Comparison with other cases of RA suggests that graft-versus-host disease may influence the long-term outcome, perhaps through ongoing inhibition of the immune system. In the patient with psoriasis, BMT was followed by remission, but the psoriatic rash recurred and arthropathy developed 12 months later. The psoriasis and arthropathy remained active 4.5 years post-BMT, although the CML remained in remission. Molecular studies in the 2 patients whose RA remained in continued remission and in the patient with psoriasis that relapsed confirmed complete donor hemopoietic reconstitution. CONCLUSION Long-term followup of autoimmune disease after allogeneic transplantation confirmed cure of the autoimmune disease in some, but eventual relapse in others. The occurrence of relapse despite complete donor hemopoietic reconstitution is evidence for the development of de novo, as opposed to persistent, disease, and is possibly related to intrinsic susceptibility of the transplanted stem cells or to host factors. There may be a relationship between remission of autoimmune disease and graft-versus-host reaction. These findings have relevance for the evolving application of stem cell transplantation as a therapy for autoimmune diseases.
Mutations in the mitochondrial genome confer resistance of cancer cells to anticancer drugs

The majority of cancer cells harbor homoplasmic somatic mutations in the mitochondrial genome. We show here that mutations in mitochondrial DNA (mtDNA) are responsible for anticancer drug tolerance. We constructed several trans‐mitochondrial hybrids (cybrids) with mtDNA derived from human pancreas cancer cell lines CFPAC‐1 and CAPAN‐2 as well as from healthy individuals. These cybrids contained the different mitochondrial genomes with the common nuclear background. We compared the mutant and wild‐type cybrids for resistance against an apoptosis‐inducing reagent and anticancer drugs by exposing the cybrids to staurosporine, 5‐fluorouracil, and cisplatin in vitro, and found that all mutant cybrids were more resistant to the apoptosis‐inducing and anticancer drugs than wild‐type cybrids. Next, we transplanted mutant and wild‐type cybrids into nude mice to generate tumors. Tumors derived from mutant cybrids were more resistant than those from wild‐type cybrids in suppressing tumor growth and inducing massive apoptosis when 5‐fluorouracil and cisplatin were administered. To confirm the tolerance of mutant cybrids to anticancer drugs, we transplanted a mixture of mutant and wild‐type cybrids at a 1:1 ratio into nude mice and examined the effect by the drugs on the drift of the ratio of mutant and wild‐type mtDNA. The mutant mtDNA showed better survival, indicating that mutant cybrids were more resistant to the anticancer drugs. Thus, we propose that mutations in the mitochondrial genome are potential targets for prognosis in the administration of anticancer drugs to cancer patients. (Cancer Sci 2009; 100: 1680–1687)
Pathophysiologic Observations and Histopathologic Recognition of the Portal Hyperperfusion or Small-for-Size Syndrome

In an attempt to more completely define the histopathologic features of the portal vein hyperperfusion or small-for-size syndrome (PHP/SFSS), we strictly identified 5 PHP/SFSS cases among 39 (5/39; 13%) adult living donor liver transplants (ALDLT) completed between 11/01 and 09/03. Living donor segments consisting of 3 right lobes, 1 left lobe, and 1 left lateral segment, with a mean allograft-to-recipient weight ratio (GRWR) of 1.0±0.3 (range 0.6 to 1.4), were transplanted without complications, initially, into 6 relatively healthy 25 to 63-year-old recipients. However, all recipients developed otherwise unexplained jaundice, coagulopathy, and ascites within 5 days after transplantation. Examination of sequential posttransplant biopsies and 3 failed allografts with clinicopathologic correlation was used in an attempt to reconstruct the sequence of events. Early findings included: (1) portal hyperperfusion resulting in portal vein and periportal sinusoidal endothelial denudation and focal hemorrhage into the portal tract connective tissue, which dissected into the periportal hepatic parenchyma when severe; and (2) poor hepatic arterial flow and vasospasm, which in severe cases, led to functional dearterialization, ischemic cholangitis, and parenchymal infarcts. Late sequelae in grafts surviving the initial events included small portal vein branch thrombosis with occasional luminal obliteration or recanalization, nodular regenerative hyperplasia, and biliary strictures. These findings suggest that portal hyperperfusion, venous pathology, and the arterial buffer response importantly contribute to early and late clinical and histopathologic manifestations of the small-for-size syndrome.
Brain and heart magnetic resonance imaging/spectroscopy in duchenne muscular dystrophy

Duchenne muscular dystrophy (DMD) is an X‐linked muscle disorder characterized by progressive and irreversible loss of muscular function. As muscular disease progresses, the repair mechanisms cannot compensate for cellular damage, leading inevitably to necrosis and progressive replacement by fibrous and fatty tissue. Cardiomyopathy and respiratory failure are the main causes of death in DMD. In addition to the well‐described muscle and heart disease, cognitive dysfunction affects around 30% of DMD boys. Myocardial fibrosis, assessed by late gadolinium enhancement (LGE), using cardiovascular magnetic resonance imaging (CMR), is an early marker of heart involvement in both DMD patients and female carriers. In parallel, brain MRI identifies smaller total brain volume, smaller grey matter volume, lower white matter fractional anisotropy and higher white matter radial diffusivity in DMD patients. The in vivo brain evaluation of mdx mice, a surrogate animal model of DMD, showed an increased inorganic phosphate (P(i))/phosphocreatine (PCr) and pH. In this paper, we propose a holistic approach using techniques of magnetic resonance imaging, spectroscopy and diffusion tensor imaging as a tool to create a “heart and brain imaging map” in DMD patients that could potentially facilitate the patients’ risk stratification and also future research studies in the field.
, statistical methodology Meta-analysis of the technical performance of an imaging procedure : Guidelines and

Medical imaging serves many roles in patient care and the drug approval process, including assessing treatment response and guiding treatment decisions. These roles often involve a quantitative imaging biomarker, an objectively measured characteristic of the underlying anatomic structure or biochemical process derived from medical images. Before a quantitative imaging biomarker is accepted for use in such roles, the imaging procedure to acquire it must undergo evaluation of its technical performance, which entails assessment of performance metrics such as repeatability and reproducibility of the quantitative imaging biomarker. Ideally, this evaluation will involve quantitative summaries of results from multiple studies to overcome limitations due to the typically small sample sizes of technical performance studies and/or to include a broader range of clinical settings and patient populations. This paper is a review of meta-analysis procedures for such an evaluation, including identification of suitable studies, statistical methodology to evaluate and summarize the performance metrics, and complete and transparent reporting of the results. This review addresses challenges typical of meta-analyses of technical performance, particularly small study sizes, which often causes violations of assumptions underlying Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, Bethesda, MD, USA Department of Quantitative Health Sciences, Cleveland Clinic Foundation, Cleveland, OH, USA Department of Biostatistics and Bioinformatics/Department of Radiology, Duke University Medical School, Durham, NC, USA Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA Division of Biostatistics, Center of Devices and Radiological Health, Food and Drug Administration, Silver Spring, MD, USA Elucid Biomedical Imaging Inc., Wenham, MA, USA Department of Radiology, University of Washington, Seattle, WA, USA School of Electrical and Computer Engineering, Cornell University, Ithaca, NY, USA Department of Medical Physics, University of Wisconsin, Madison, WI, USA Massachusetts General Hospital, Boston, MA, USA F. Hoffmann-La Roche, Ltd., Basel, Switzerland Corresponding author: Erich P Huang, Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, 9609 Medical Center Drive, MSC 9735, Bethesda, MD 20892-9735, USA. Email: erich.huang@nih.gov Statistical Methods in Medical Research
Engine Knock Detection Based on Computational Intelligence Methods

Artificial intelligence emerged from human thinking that has both logical and intuitive or subjective sides. The logical side has been developed and utilized, resulting advanced von Neumann type computers and expert systems, both constituting the hard computing domain. However, it is found that hard computing can’t give the solution of very complicated problems by itself. In order to cope with this difficulty, the intuitive and subjective thinking of human mind was explored, resulting the soft computing domain (also called computational intelligence). It includes neural networks, fuzzy logic and probabilistic reasoning, the last gathering evolutionary computation (including genetic algorithms with related efforts in genetic programming and classifier systems, evolution strategies and evolutionary programming), immune networks, chaos computing and parts of learning theory. In different kind of applications, all pure artificial intelligence methods mentioned above proved to be rather complementary than competitive, so that combined methods appeared in order to gather the advantages and to cope with the disadvantages of each pure method. The scope of this chapter is to study and finaly compare some representative classes of pure and combined computational intelligence methods applied in engine knock detection.
Bibliometric study of bioinformatics literature

Bioinformatics is a multidisciplinary and comparatively new area of science that has made a significant impact within a short period. A systematic analysis of the rise in bioinformatics literature is, however, not available. This study analyses the growth of the scientific literature in this area as available from NCBI PubMed using standard bibliometric techniques. Bradford’s law of scattering was used to identify core journals and Lotka’s law employed to analyze author’s productivity pattern. Study also explored publication type, language and the country of publication. Twenty core journals were identified and the primary mode of dissemination of information was through journal articles. Authors with single publication were more predominant (73.58%) contrary to that predicted by Lotka’s law. The study provides useful information to scientists wishing to undertake work in this area.
What is community archaeology?

Community archaeology, understood as a distinctive set of practices within the wider discipline, is a relatively new development. Its most important distinguishing characteristic is the relinquishing of at least partial control of a project to the local community. This introduction takes a preliminary look at where this kind of archaeology is being carried out around the world and outlines what marks it out as different from other kinds of archaeology. In conclusion, it is suggested that community archaeology has a unique, if not critical, contribution to make to the future development of archaeology as a genuinely worldwide discipline.
Effectiveness of Carisolv compared with sodium hypochlorite and calcium hydroxide

The aim of this study was to compare the effectiveness of Carisolv with that of two other alkaline substances: NaOCl and Ca(OH)2. Sixty extracted teeth were randomly divided into three groups and split down the center of a carious lesion. In group I, one half of the cavity was excavated with NaOCl (0.5%, pH 11.7), the corresponding half with Ca(OH)2 (pH 12.4); in group II with NaOCl and Carisolv; and in group III with Ca(OH)2 and Carisolv (n=20 in each case). Carisolv hand instruments were used. Histological specimens were subsequently produced from all cavities and analyzed with a light-microscope following Mallory-Azan staining. The thickness of the remaining caries was measured (<1 mm or >1 mm) and the locations were recorded. The data were statistically evaluated using the chi-square test. In group I, 50.5% of the specimens treated with NaOCl and 48.7% treated with Ca(OH)2 were evaluated to be caries-free. The results in group II were NaOCl 61.5% and Carisolv 75.4% caries-free, and in group III Ca(OH)2 61.2% and Carisolv 73.9%. No statistically significant differences were found between NaOCl and Ca(OH)2 excavation (group I: p=0.89). Compared to NaOCl and Ca(OH)2, Carisolv produced significantly better results for chemo-mechanical caries removal (groups II+III: p<0.05). In the NaOCl and Ca(OH)2 treated specimens, carious layers with a thickness >1 mm were found significantly more often than in the Carisolv-treated specimens (groups II+III: p<0.05), whereas there were no differences between NaOCl and Ca(OH)2 excavation (p=0.06). There were no statistically significant differences in the location of the remaining caries in any of the groups (p>0.05).
Genetic diversity and antibiotic resistance in Shigella dysenteriae and Shigella boydii strains isolated from children aged <5 years in Egypt

SUMMARY Diversity within Shigella dysenteriae (n=40) and Shigella boydii (n=30) isolates from children living in Egypt aged <5 years was investigated. Shigella-associated diarrhoea occurred mainly in summer months and in children aged <3 years, it commonly presented with vomiting and fever. Serotypes 7 (30%), 2 (28%), and 3 (23%) accounted for most of S. dysenteriae isolates; 50% of S. boydii isolates were serotype 2. S. dysenteriae and S. boydii isolates were often resistant to ampicillin, chloramphenicol and tetracycline (42%, 17%, respectively), although resistance varied among serotypes. Pulsed-field gel electrophoresis separated the isolates into distinct clusters correlating with species and serotype. Genetic differences in trimethoprim/sulfamethoxazole and β-lactam-encoding resistance genes were also evident. S. dysenteriae and S. boydii are genetically diverse pathogens in Egypt; the high level of multidrug resistance associated with both pathogens and resistance to the most available inexpensive antibiotics underlines the importance of continuing surveillance.
A link between endoplasmic reticulum stress‐induced β‐cell apoptosis and the group VIA Ca2+‐independent phospholipase A2 (iPLA2β)

Endoplasmic reticulum (ER) stress is becoming recognized as an important contributing factor in various diseases, including diabetes mellitus. Prolonged ER stress can cause β‐cell apoptosis; however, the underlying mechanism(s) that contribute to this process are not well understood. Early reports suggested that arachidonic acid metabolites and a Ca2+‐independent phospholipase A2 (iPLA2) activity play a role in β‐cell apoptosis. The PLA2 family of enzymes catalyse the hydrolysis of the sn‐2 substituent (i.e. arachidonic acid) of membrane phospholipids. In light of our findings that the pancreatic islet β‐cells are enriched in arachidonate‐containing phospholipids and express the group VIA iPLA2β, we considered the possibility that iPLA2β participates in ER stress‐induced β‐cell apoptosis. Our work revealed a novel mechanism, involving ceramide generation and triggering of mitochondrial abnormalities, by which iPLA2β participates in the β‐cell apoptosis process. Here, we review our evidence linking ER stress, β‐cell apoptosis and iPLA2β. Continued studies in this area will increase our understanding of the contribution of iPLA2β to the evolution of diabetes mellitus and will further our knowledge of factors that influence β‐cell health in diabetes mellitus and identify potential targets for future therapeutic interventions to prevent β‐cell death.
Mast cells and c‐Kit expression in liver allograft rejection

Aims : The pathogenesis of rejection following liver transplantation is not fully understood. It has been postulated that mast cells may play a role in acute and chronic rejection of a number of other solid organ grafts. The aim of this study was to assess the possible role of mast cells and c‐Kit+ cells in acute and chronic liver allograft rejection.
Clinical and microbiological effects of different antimicrobials on generalized aggressive periodontitis.

AIM To evaluate and compare the effects of adjunctive metronidazole plus amoxicillin, doxycycline and metronidazole on clinical and microbiological parameters in patients with generalized aggressive periodontitis. MATERIAL AND METHODS Forty-three patients participated in this randomized clinical trial divided into four groups. Six weeks after scaling and root planning (SRP), groups 1-3 received adjunctive metronidazole, plus amoxicillin, doxycycline and metronidazole respectively, and group 4 acted as controls. Clinical recordings concerning probing depth, probing attachment level and bleeding on probing were performed at baseline, 6 weeks after SRP and 6 months from baseline. Subgingival samples were analysed using the 'checkerboard' DNA-DNA hybridization for Porphyromonas gingivalis, Actinobacillus actinomycetemcomitans, Tannerella forsythia and Treponema denticola. RESULTS All treatments resulted in improvement of clinical parameters (ANOVA p > 0.05). Systemic administration of metronidazole plus amoxicillin or metronidazole resulted in statistically significant greater reduction of the proportion of sites > 6 mm than SRP (z-test, p < 0.05). These antimicrobials yielded a significant effect on levels of important periodontal pathogens for 6 months. CONCLUSION Adjunctive metronidazole plus amoxicillin or metronidazole alone (when A.actinomycetemcomitans is not involved) is effective in deep pockets of aggressive periodontitis patients.
Thymus-Independent Type-2 Antigen B-1a Cells in Adult Mice by Rapid Induction of Splenic and Peritoneal

We have produced a transgenic mouse (PV1TgL) that can only generate B lymphocytes with an Ig receptor speciﬁc for the synthetic polymer polyvinyl pyrrolidinone. Before immunization, bone marrow B cell numbers are very low, and peripheral lymphoid organs are almost devoid of B cells, conﬁrming the role of positive selection by Ag in the development of mature B cell populations. The predominant population of B cells in the spleens of naive adult PV1TgL mice have most of the characteristics of marginal zone B cells, including anatomical location in the peripheral areas of the splenic white pulp. After immunization, a new population of B cells appears in the spleen with the characteristics of B-1 cells. Similar cells also appear somewhat later in the peritoneal cavity. Our ﬁndings suggest that immunization with a thymus-independent Ag can lead to the appearance and expansion of Ag-reactive B-1 cells in an adult mouse. The Journal of Immunology, 2004, 173: 5406–5414.
Native Speaker Response to Non-Native Accent: A Review of Recent Research

Introduction Research has generally shown that without early exposure, non-native speakers cannot achieve a native-like accent in a foreign language (Gass & Selinker, 2001, p. 336). Differences in pronunciation, stress, rhythm, and intonation remain. Nevertheless, accent has been shown to affect how native speakers (NSs) evaluate non-native speakers (NNSs). This single speech characteristic has been openly cited as justification for much broader judgments about individuals. Lippi-Green (1997), for example, highlights several cases in the U.S. in which NNSs lost jobs due to their accents, such as that of an Indian woman (who had studied English for over 20 years) deemed unfit for a librarian’s position because of her “‘heavy accent’” and “‘speech patterns’” (p. 153). Matsuda (1991) reports on U.S. doctors who lost their malpractice insurance because the company felt accent would prevent them from successfully defending themselves in a lawsuit (p. 1346). In light of the potentially high-stakes consequences of accent-based evaluation, particularly in major immigrant-receiving countries like the U.S., the goal of this paper is to examine recent contributions of language research to understanding NS attitude toward NNS accent. Specifically, this paper will address two questions relevant to the work of the past decade. First, what are the factors that affect NS attitudes toward accented speakers? This question has been investigated by a number of researchers, and the variety of accents, locations, and contexts examined in pursuit of an
Dynamics of pneumococcal carriage among healthy Icelandic children attending day-care centres

Invasive pneumococcal disease and antimicrobial (AM) resistance in pneumococci are important public health concerns. With the advent of new pneumococcal vaccines, information on serotype prevalence and their temporal fluctuations is important. Information on AM use and consent for participation was obtained by a questionnaire to parents of children at 5 day-care centres in Reykjavik from 1992 to 1999, and nasopharyngeal swabs were cultured selectively for pneumococci. The pneumococci were serotyped and pulsed field gel electrophoresis used to determine clonality. Of 1228 nasopharyngeal swabs, 640 (52.1%) yielded pneumococci of which 89 (13.9%) had decreased susceptibility to penicillin and 1 was resistant. Children receiving AMs during the month preceding nasopharyngeal sampling and children attending a day-care centre where AM use was high were significantly more likely to carry penicillin non-susceptible isolates. Serotypes 6A, 6B and 23F were most common (48%), and 74% of serotyped isolates belonged to 1 of the 7 most common serotypes. Almost all penicillin non-susceptible isolates were of serotype 6B or 19A. Serotype prevalence fluctuated markedly between y. In conclusion, there was significant variation in serotype prevalence between y, and only 51% of the pneumococci belonged to serotypes covered by the current 7-valent conjugated vaccine.