Miracle-dz/UniFAR-FTUs huggingface dataset:
Reactive Nodular Fibrous Pseudotumors of the Gastrointestinal Tract: Report of 8 Cases

Eight cases of reactive nodular fibrous pseudotumor of the gastrointestinal tract are presented. The patients included 6 males and 2 females between the ages of 1 and 68 years (mean age 41.5 years). Three tumors involved the small intestine, and 5 of the investigated lesions were located in the large bowel. Of these, 2 originated in the sigmoid colon, 1 in the cecum, 1 in the appendix, and 1 in the large bowel not otherwise specified. The tumors’ size varied from 3 to 10 cm in the greatest diameter (mean 6.2 cm). Histologically they were composed of stellate or spindle shaped cells resembling fibroblasts arranged haphazardly or in intersecting fascicles, embedded in a collagen-rich stroma, with sparse intralesional mononuclear cells frequently arranged in lymphoid aggregates. Immunohistochemically, the lesions were positive for vimentin (7/7), smooth muscle actin (8/8), muscle-specific actin (5/7), cytokeratins AE1/AE3 (6/7), and CAM 5.2 (1/7), and antigen CD68 (1/7). No case (0/8) reacted positively with antibody to CD117 (c-kit). Genetically no substitutions, deletions, or insertions occurred in exon 11 in all analyzed samples. Likewise, no deletions or insertions in part of exon 9 were observed. Ultrastructurally the tumor cells revealed features typical of myofibroblasts. According to the morphologic, immunohistochemical, and ultrastructural features mentioned above, especially to the positivity of low-molecular-weight cytokeratins, we propose this lesion to be related to a proliferation of multipotential subserosal cells rather than ordinary myofibroblasts or fibroblasts.
On combining disjoint caches

Following the ideas of Megiddo &Modha [9] for developing ARC (Adaptive Replacement Cache), we study how to best combine disjoint lists of pages in order to construct an adaptive paging algorithm that has a miss rate lower than LRU. This paper contains our preliminary results. The approach we use takes advantage of the Expert Framework from online learning[7, 5, 8, 4, 3]. It is also an interesting application of Path Kernels [11], which are used to keep track exponentially many combinations of the disjoint lists implicitly, by only maintaining polynomially many weights. We introduce the concept of rollover [6] in order to better track a dynamically changing cache. We compare our results to both ARC and LRU (the de facto standard policy which discards the least recently used page).
A Statewide Collaborative to Reduce Pediatric Surgical Site Infections

BACKGROUND: Surgical site infections (SSIs) are preventable events associated with significant morbidity and cost. Few interventions have been tested to reduce SSIs in children. METHODS: A quality improvement collaboration was established in Ohio composed of all referral children’s hospitals. Collaborative leaders developed an SSI reduction bundle for selected cardiac, orthopedic, and neurologic operations. The bundle was composed of 3 elements: prohibition of razors for skin preparation, chlorhexidine-alcohol use for incisional site preparation, and correct timing of prophylactic antibiotic administration. The incidence of SSIs across the collaborative was compared before and after institution of the bundle. The association between 1 of the bundle elements, namely correct timing of antibiotic prophylaxis, and the proportion of centers achieving 0 SSIs per month was measured. RESULTS: Eight pediatric hospitals participated. The proportion of months in which 0 SSIs per center was recorded was 56.9% before introduction of the bundle, versus 81.8% during the intervention (P < .001). Correct timing of preoperative prophylactic antibiotics also significantly improved; 39.4% of centers recorded correct timing in every eligible surgical procedure per month (“perfect timing”) before the intervention versus 78.7% after (P < .001). The achievement of 0 SSIs per center in a given month was associated with the achievement of perfect antibiotic timing for that month (P < .003). CONCLUSIONS: A statewide collaborative of children’s hospitals was successful in reducing the occurrence of SSIs across Ohio.
Multiple Routes to Smart Nanostructured Materials from Diatom Microalgae: A Chemical Perspective

Diatoms are unicellular photosynthetic microalgae, ubiquitously diffused in both marine and freshwater environments, which exist worldwide with more than 100 000 species, each with different morphologies and dimensions, but typically ranging from 10 to 200 µm. A special feature of diatoms is their production of siliceous micro‐ to nanoporous cell walls, the frustules, whose hierarchical organization of silica layers produces extraordinarily intricate pore patterns. Due to the high surface area, mechanical resistance, unique optical features, and biocompatibility, a number of applications of diatom frustules have been investigated in photonics, sensing, optoelectronics, biomedicine, and energy conversion and storage. Current progress in diatom‐based nanotechnology relies primarily on the availability of various strategies to isolate frustules, retaining their morphological features, and modify their chemical composition for applications that are not restricted to those of the bare biosilica produced by diatoms. Chemical or biological methods that decorate, integrate, convert, or mimic diatoms' biosilica shells while preserving their structural features represent powerful tools in developing scalable, low‐cost routes to a wide variety of nanostructured smart materials. Here, the different approaches to chemical modification as the basis for the description of applications relating to the different materials thus obtained are presented.
HIV-specific CD 8 T cells express low levels of IL-7 R alpha : Implications for HIV-specific T cell memory

Chronic infections in mice can result in defects in memory CD8 T cell properties including low expression of the IL-7Rα (CD127). To determine whether defects in memory CD8 T cell formation exist during human chronic infections and to what extent these defects may be allele-or epitope-specific, we compared influenza (Flu), vaccinia (VV) and EBV-specific CD8 T cells to HIV-specific CD8 T cells, using a panel of 13 HIV tetramers. Compared to Flu, VV or EBV, HIV tetramer+ CD8 T cells expressed significantly lower levels of CD127, and this reduction was pervasive across all epitopes and alleles tested and over a wide range of viral loads and CD4 counts. These results indicate impaired HIV-specific memory CD8 T cell differentiation, regardless of level of control of viremia, epitopes targeted or restricting HLA alleles.
Receiver-Operating Characteristic Analysis for Evaluating Diagnostic Tests and Predictive Models

Receiver-operating characteristic (ROC) analysis was originally developed during World War II to analyze classification accuracy in differentiating signal from noise in radar detection.1 Recently, the methodology has been adapted to several clinical areas heavily dependent on screening and diagnostic tests,2–4 in particular, laboratory testing,5 epidemiology,6 radiology,7–9 and bioinformatics.10 ROC analysis is a useful tool for evaluating the performance of diagnostic tests and more generally for evaluating the accuracy of a statistical model (eg, logistic regression, linear discriminant analysis) that classifies subjects into 1 of 2 categories, diseased or nondiseased. Its function as a simple graphical tool for displaying the accuracy of a medical diagnostic test is one of the most well-known applications of ROC curve analysis. In Circulation from January 1, 1995, through December 5, 2005, 309 articles were published with the key phrase “receiver operating characteristic. ” In cardiology, diagnostic testing plays a fundamental role in clinical practice (eg, serum markers of myocardial necrosis, cardiac imaging tests). Predictive modeling to estimate expected outcomes such as mortality or adverse cardiac events based on patient risk characteristics also is common in cardiovascular research. ROC analysis is a useful tool in both of these situations. In this article, we begin by reviewing the measures of accuracy—sensitivity, specificity, and area under the curve (AUC)—that use the ROC curve. We also illustrate how these measures can be applied using the evaluation of a hypothetical new diagnostic test as an example. A diagnostic classification test typically yields binary, ordinal, or continuous outcomes. The simplest type, binary outcomes, arises from a screening test indicating whether the patient is nondiseased (Dx=0) or diseased (Dx=1). The screening test indicates whether the patient is likely to be diseased or not. When >2 categories are used, the test data can be on an ordinal rating …
YAP controls retinal stem cell DNA replication timing and genomic stability

The adult frog retina retains a reservoir of active neural stem cells that contribute to continuous eye growth throughout life. We found that Yap, a downstream effector of the Hippo pathway, is specifically expressed in these stem cells. Yap knock-down leads to an accelerated S-phase and an abnormal progression of DNA replication, a phenotype likely mediated by upregulation of c-Myc. This is associated with an increased occurrence of DNA damage and eventually p53-p21 pathway-mediated cell death. Finally, we identified PKNOX1, a transcription factor involved in the maintenance of genomic stability, as a functional and physical interactant of YAP. Altogether, we propose that YAP is required in adult retinal stem cells to regulate the temporal firing of replication origins and quality control of replicated DNA. Our data reinforce the view that specific mechanisms dedicated to S-phase control are at work in stem cells to protect them from genomic instability. DOI: http://dx.doi. org/10.7554/eLife.08488. 001
Molecular Phylogeny and Barcoding of Caulerpa (Bryopsidales) Based on the tufA, rbcL, 18S rDNA and ITS rDNA Genes

The biodiversity assessment of different taxa of the genus Caulerpa is of interest from the context of morphological plasticity, invasive potential of some species and biotechnological and pharmacological applications. The present study investigated the identification and molecular phylogeny of different species of Caulerpa occurring along the Indian coast inferred from tufA, rbcL, 18S rDNA and ITS rDNA nucleotide sequences. Molecular data confirmed the identification of 10 distinct Caulerpa species: C. veravalensis, C. verticillata, C. racemosa, C. microphysa, C. taxifolia, C. sertularioides, C. scalpelliformis, C. serrulata, C. peltata and C. mexicana. All datasets significantly supported the sister relationship between C. veravalensis and C. racemosa var. cylindracea. It was also concluded from the results that the specimen identified previously as C. microphysa and C. lentillifera could not be considered as separate species. The molecular data revealed the presence of multiple lineages for C. racemosa which can be resolved into separate species. All four markers were used to ascertain their utility for DNA barcoding. The tufA gene proved a better marker with monophyletic association as the main criteria for identification at the species level. The results also support the use of 18S rDNA insertion sequences to delineate the Caulerpa species through character-based barcoding. The ITS rDNA (5.8S-ITS2) phylogenetic analysis also served as another supporting tool. Further, more sequences from additional Caulerpa specimens will need to be analysed in order to support the role of these two markers (ITS rDNA and 18S insertion sequence) in identification of Caulerpa species. The present study revealed the phylogeny of Caulerpa as complete as possible using the currently available data, which is the first comprehensive report illustrating the molecular phylogeny and barcoding of the genus Caulerpa from Indian waters.
Degree of mineralization: its significance for the stability and treatment of excavated ironwork

Abstract The ratio weight:volume has been determined for ironwork from four archaeological sites. It is shown how this ratio can be used to determine the presence or absence of metallic iron in a corroded artifact. Experiments show that totally mineralized ironwork generally contains much less chloride than does ironwork retaining a metallic core. Accelerated corrosion experiments show that totally mineralized ironwork is not subject to a physical deterioration seen on objects retaining a metallic core. Therefore it is suggested that the ratio weight:volume can be used to predict the stability of ironwork following excavation. Costs of storage can be reduced since fewer environmental controls are necessary. Some aqueous chloride extraction methods were examined to determine if the weight:volume ratio influenced their efficiency but results were inconclusive.
Neopeptide Antibiotics That Function as Opsonins and Membrane-Permeabilizing Agents for Gram-Negative Bacteria

ABSTRACT We suggest a novel approach to enhancing antimicrobial drug action by utilizing engineered peptide conjugates. Our most potent conjugates, [fMLF]PMBN and [fMLF]PMEN, are nonapeptides derived from polymyxin B's (PMB's) cyclic moiety (Thr-Dab-cyclo[Dab-Dab-d-Phe-Leu-Dab-Dab-Thr], where Dab is 2,4-diaminobutyric acid) and polymyxin E's (PME's) cyclic moiety (Thr-Dab-cyclo[Dab-Dab-d-Leu-Leu-Dab-Dab-Thr]), respectively, attached to a linear tail comprised of formyl-Met-Leu-Phe (fMLF). The cyclic part binds to gram-negative lipopolysaccharides, rendering the bacterial outer membrane permeable to hydrophobic antibiotics. The tail confers chemotactic and opsonic activities upon the conjugates. These two activities appear to be the basis for the conjugates' antibacterial activities. The conjugates are 8 to 10 times less toxic than the parent PMB or PME antibiotics. Fourteen of 18 mice lethally challenged with erythromycin-resistant Klebsiella pneumoniae survived following intraperitoneal administration of erythromycin and [fMLF]PMBN, whereas erythromycin or the peptide conjugate alone had no effect. Moreover, the clearance of Klebsiella from blood was markedly enhanced by intravenous injection of the [fMLF]PMEN peptide conjugate compared to the clearance of the organism from the mice treated with buffer alone as a control and was similar to that achieved by the PME antibiotic. Blood clearance was also significantly enhanced by administration of PMEN either alone or in a mixture with fMLF, although the effect was less than that produced by the peptide conjugate. Since resistance to polymyxins, the parent molecules of the synthetic cyclic peptides, is rare, the emergence of bacteria resistant to the antimicrobial properties of the peptide conjugates may be precluded as well.
Dementia screening questionnaire for individuals with intellectual disabilities.

BACKGROUND Many adults with Down's syndrome develop Alzheimer's dementia relatively early in their lives, but accurate clinical diagnosis remains difficult. AIMS To develop a user-friendly observer-rated dementia screening questionnaire with strong psychometric properties for adults with intellectual disabilities. METHOD We used qualitative methods to gather information from carers of people with Down's syndrome about the symptoms of dementia. This provided the items for the Dementia Screening Questionnaire for Individuals with Intellectual Disabilities (DSQIID), which we then tested for its psychometric properties. RESULTS The DSQIID was administered to carers of 193 adults with Down's syndrome, 117 of whom were examined by clinicians who confirmed a diagnosis of dementia for 49 according to modified ICD-10 criteria. We established that a total score of 20 provides maximum sensitivity (0.92) and optimum specificity (0.97) for screening. The DSQIID has sound internal consistency (alpha=0.91) for all its 53 items, and good test-retest and interrater reliability. We established a good construct validity by dividing the items into four factors. CONCLUSIONS The DSQIID is a valid, reliable and user-friendly observer-rated questionnaire for screening for dementia among adults with Down's syndrome.
High-Fidelity Correction of Mutations at Multiple Chromosomal Positions by Adeno-Associated Virus Vectors

ABSTRACT The gene targeting techniques used to modify chromosomes in mouse embryonic stem cells have had limited success with many other cell types, especially normal primary cells with restricted growth capacity outside the organism. This is due in large part to the technical problems and/or inefficiency of conventional DNA transfer methods, as well as the low rates of homologous recombination obtained in unselected cell populations. We recently described an alternative approach in which adeno-associated virus (AAV) vectors were used to modify homologous chromosomal sequences, and targeting rates close to 1% were observed at the single copy hypoxanthine phosphoribosyl transferase (HPRT) locus in normal human cells (D. W. Russell and R. K. Hirata, Nat. Genet. 18:325–330, 1998). Here we report experiments in which we used a retroviral shuttle vector system to introduce and characterize target loci in human chromosomes, and demonstrate that AAV vectors can correct several types of mutations with high fidelity, independent of chromosomal position. The gene targeting rates varied depending on the type of mutation being corrected, implicating cellular mismatch recognition functions in the reaction. Since AAV vectors can efficiently deliver DNA to many cell types both in vivo and ex vivo, our results suggest that AAV-mediated gene targeting will have wide applicability, including therapeutic gene correction.
Semantic analysis of SNOMED CT for a post-coordinated database of histopathology findings

Objective This research investigated the use of SNOMED CT to represent diagnostic tissue morphologies and notable tissue architectures typically found within a pathologist's microscopic examination report to identify gaps in expressivity of SNOMED CT for use in anatomic pathology. Methods 24 breast biopsy cases were reviewed by two board certified surgical pathologists who independently described the diagnostically important tissue architectures and diagnostic morphologies observed by microscopic examination. In addition, diagnostic comments and details were extracted from the original diagnostic pathology report. 95 unique clinical statements were extracted from 13 malignant and 11 benign breast needle biopsy cases. Results 75% of the inventoried diagnostic terms and statements could be represented by valid SNOMED CT expressions. The expressions included one pre-coordinated expression and 73 post-coordinated expressions. No valid SNOMED CT expressions could be identified or developed to unambiguously assert the meaning of 21 statements (ie, 25% of inventoried clinical statements). Evaluation of the findings indicated that SNOMED CT lacked sufficient definitional expressions or the SNOMED CT concept model prohibited use of certain defined concepts needed to describe the numerous, diagnostically important tissue architectures and morphologic changes found within a surgical pathology microscopic examination. Conclusions Because information gathered during microscopic histopathology examination provides the basis of pathology diagnoses, additional concept definitions for tissue morphometries and modifications to the SNOMED CT concept model are needed and suggested to represent detailed histopathologic findings in computable fashion for purposes of patient information exchange and research. Trial registration number UNMC Institutional Review Board ID# 342-11-EP.
Supporting the emergence of dental informatics with an online community.

Dental Informatics (DI) is the application of computer and information science to improve dental practice, research, education, and program administration. As an emerging field, dental informatics faces many challenges and barriers to establishing itself as a full-fledged discipline; these include the small number of geographically dispersed DI researchers as well as the lack of DI professional societies and DI-specific journals. E-communities have the potential to overcome these obstacles by bringing researchers together at a resources hub and giving them the ability to share information, discuss topics, and find collaborators. In this paper, we discuss our assessment of the information needs of individuals interested in DI and discuss their expectations for an e-community so that we can design an optimal electronic infrastructure for the Dental Informatics Online Community (DIOC). The 256 survey respondents indicated they prefer electronic resources over traditional print material to satisfy their information needs. The most frequently expected benefits from participation in the DIOC were general information (85% of respondents), peer networking (31.1%), and identification of potential collaborators and/or research opportunities (23.2%). We are currently building the DIOC electronic infrastructure: a searchable publication archive and the learning center have been created, and the people directory is underway. Readers are encouraged to access the DIOC Website at www.dentalinformatics. com and initiate a discussion with the authors of this paper.
Parallel real-time numerical computation: beyond speedup. III

For pt. II see Technical Report No. 99-423, Dept. of Comput. and Inf. Sci., Queen's University, Kingston, Ontario, May 1999. Parallel computers can do more than simply speed up sequential computations. They are capable of finding solutions that are far better in quality than those obtained by sequential computers. This fact is demonstrated by analyzing sequential and parallel solutions to numerical problems in a real-time paradigm. In this setting, numerical data required to solve a problem are received as input by a computer system, at regular intervals. The computer must process its inputs as soon as they arrive. It must also produce its outputs at regular intervals, as soon as they are available. We show that for some real-time numerical problems a parallel computer can deliver a solution that is significantly more accurate than that computed by a sequential computer. Similar results were derived recently in the areas of real-time optimization and real-time cryptography.
Comprehensive analysis of current approaches to inhibit regulatory T cells in cancer

CD4+CD25+Foxp3+ regulatory T cells (Treg) have emerged as a dominant T cell population inhibiting anti-tumor effector T cells. Initial strategies used for Treg-depletion (cyclophosphamide, anti-CD25 mAb…) also targeted activated T cells, as they share many phenotypic markers. Current, ameliorated approaches to inhibit Treg aim to either block their function or their migration to lymph nodes and the tumor microenvironment. Various drugs originally developed for other therapeutic indications (anti-angiogenic molecules, tyrosine kinase inhibitors,etc) have recently been discovered to inhibit Treg. These approaches are expected to be rapidly translated to clinical applications for therapeutic use in combination with immunomodulators.