Miracle-dz/UniFAR-FTUs huggingface dataset:
Colonic Phenotype of the Ileum in Crohn's Disease: A Prospective Study Before and After Ileocolonic Resection

Background:Colonic metaplasia has been described in pouchitis. In a prospective study, we investigated whether colonic phenotype may develop in Crohn's disease (CD) ileum. The expression of sulfomucins (colonic mucin), sialomucins, and CD10 (small intestine mucin and phenotype) was evaluated before and after ileocolonic resection for CD. Methods:From February 2007 to March 2010, 22 patients with CD undergoing surgery were enrolled. Clinical (Crohn's Disease Activity Index >150) and endoscopic recurrence (Rutgeerts score ≥1) rates were assessed at 6 and 12 months. Ileal samples were taken at surgery (T0), at 6 (T1), and 12 months (T2) for histology, histochemistry (High Iron Diamine-Alcian Blue), and immunohistochemistry (anti-CD10). Results:In 22 patients, recurrence was assessed at 6 and 12 months (clinical recurrence 9% and 18%; endoscopic recurrence 73% and 77%). In all 22 patients, ileal samples were taken at 6 and 12 months (involved area in patients with recurrence). In 19 of 22 (86.3%) patients, the involved ileum was also studied at surgery. At T0, T1, and T2, the expression of sialomucins and CD10 (small intestine mucin and phenotype) was comparable and higher (P < 0.0001) than the expression of sulfomucins (colonic mucin) (mean [range], T0:82 [35–100] versus 75 [0–100] versus 16 [0–50]; T1:96 [60–100] versus 94.7 [50–100] versus 3.89 [0–40]; T2:93.3 [60–100] versus 88.1 [25–100] versus 6.6 [0–40]). The expression of small-intestine mucin and phenotype was higher at T1 (P = 0.025) versus T0 (P = 0.026). Differently, the expression of colonic mucin was lower at T1 versus T0 (P = 0.027). Conclusions:In CD, the ileum involved by severe/established lesions develops a “metaplastic” colonic mucosa phenotype. Differently, CD ileum with no lesions or with early recurrence maintains the “native” small intestine type mucin secretion and phenotype.
Abnormal thickening as well as thinning of the photoreceptor layer in intermediate age-related macular degeneration.

PURPOSE To investigate the relationship between photoreceptor layers overlying and adjacent to large drusen in intermediate nonneovascular AMD. METHODS Patients with AMD (n = 41; aged 53-83 years) and elderly control subjects without eye disease (n = 10; aged 51-79 years) were studied with spectral-domain optical coherence tomography. Characteristics of large drusen (≥125 μm) were measured and the thickness of photoreceptor laminae overlying drusen and in retinal regions neighboring the drusen were quantified. RESULTS There were 750 large drusen in 63 intermediate AMD eyes studied. The width of the drusen sampled averaged 352 μm (SD = 153) and the height averaged 78 μm (SD = 31). There was significant reduction of the photoreceptor outer nuclear layer (ONL) thickness overlying 92% of the drusen. The thickness of the layer corresponding to photoreceptor inner and outer segments above drusen was also reduced, and the reduction was proportional to ONL thickness. In a substantial fraction (~20%) of normally laminated paradrusen locations sampled within ~300 μm of peak drusen height, ONL thickness was significantly increased compared with age and retinal location-matched normal values. Topographical analyses of the macula showed ONL thickening occurring in paradrusen regions as well as retinal locations distant from drusen. CONCLUSIONS Reductions in the photoreceptor laminae overlying drusen were detectable and this is consistent with histological studies revealing neuronal degeneration in AMD. ONL thickening in some macular areas of AMD eyes has not been previously reported and may be an early phenotypic marker for photoreceptor stress, as it has been speculated to be in hereditary retinal degenerations.
C4d staining in renal allograft biopsies with early acute rejection and subsequent clinical outcome.

BACKGROUND AND OBJECTIVES Diffuse C4d staining in peritubular capillaries (PTCs) during an acute rejection episode (ARE) is the footprint of antibody-mediated rejection. In current clinical practice, diffuse C4d+ staining during acute rejection is regarded as an inferior prognostic sign. This case-control study investigated the prognostic role of mere C4d staining for graft outcome during an ARE in a well defined cohort of similarly ARE-treated patients. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS All kidney transplant recipients in the authors' center from January 1, 1995 to December 31, 2005 were reviewed. From these patients, 151 had a clinical ARE. Paraffin and/or frozen material was available for 128 patients showing a histologically proven ARE within the first 6 months after transplantation. All ARE patients were treated similarly with high-dose pulse steroids and in the case of steroid unresponsiveness with anti-thymocyte globulin. Biopsies were scored according to Banff criteria. Frozen and paraffin sections were stained by immunofluorescence (IF) and immunohistochemistry (IHC) for C4d, respectively, and scored for PTC positivity. RESULTS Diffuse C4d+ staining in PTCs was found in 12.5% and 4.2% sections stained by IF or by IHC, respectively. Four patients showed diffuse positive staining with both methods but showed no different risk profile from other patients. No relation between C4d staining and clinical parameters at baseline was found. C4d staining was not associated with steroid responsiveness, graft, or patient survival. CONCLUSIONS This study shows that C4d staining is not related to clinical outcome in this cohort of histologically proven early AREs.
Trace amounts of copper in water induce β-amyloid plaques and learning deficits in a rabbit model of Alzheimer's disease

Despite the crucial role played by cholesterol and copper in nutrition and normal brain function, recent evidence indicates that they may both be important factors in the etiology of Alzheimer's disease (AD). Here we provide critical evidence for the role of cholesterol and copper in AD by showing that the addition of trace amounts of copper (0.12 ppm) to water given to cholesterol-fed rabbits can induce β-amyloid (Aβ) accumulation, including senile plaque-like structures in the hippocampus and temporal lobe, and can significantly retard the ability of rabbits to learn a difficult trace conditioning task. The Aβ deposits do not affect the ability of rabbits to detect or respond to the training stimuli nor to learn a simpler delay conditioning task. Trace amounts of copper in drinking water may influence clearance of Aβ from the brain at the level of the interface between the blood and cerebrovasculature and combined with high cholesterol may be a key component to the accumulation of Aβ in the brain, having a significant impact on learning and memory. Cholesterol-fed rabbits have at least 12 pathological markers seen in AD, suggesting that the cholesterolfed rabbit is a good animal model for studying AD.
Automatic rhetorical sentence categorization on Indonesian meeting minutes

Meeting minutes contains much important information of meeting. Since meeting minutes is unstructured document, in order to easily get and summarize this information, classification for every sentence in meeting minutes should be conducted. Some works in this research area has been done for meeting minutes in English, but not conducted yet in Indonesian. Therefore, this paper aims to present the rhetorical sentence categorization from Indonesian meeting minutes by utilizing some features, i.e. length, position, previous label, significant terms, and cue phrases per class. Then, this paper shows the result of employing SMOTE and resampling for balancing the existing instances per class. Every experiment is tested in four classifiers, namely Naïve Bayes, SVM Linear, IBk, and J48 tree. It shows that the use of previous label and both of significant term and cue phrase per class improves performance. Then it shows also that resampling is better than SMOTE. After doing the 10-fold cross-validation in IBk classifier, model using SMOTE achieved F-measure of 85.22% and resampling model achieved 94.52%.
The Use of Fire in the Cerrado and Amazonian Rainforests of Brazil: Past and Present

Humans have been changing the natural fire regimes in most Brazilian vegetation types for over 4000 years. Natural lightning fires can easily happen in savannas and grasslands, but they are rare in the moist rainforests. Today, anthropogenic fires are frequent in both the fire-adapted cerrado (Brazilian savanna) and the fire-sensitive rainforest. In this paper, I compare two very different biomes concerning their susceptibilities and responses to fire: the Amazon rainforest and the cerrado. I present an overview of their fire history, especially regarding human-made fires for land management, and pull together information about the use of fire by indigenous peoples in the cerrado and the Amazon, as this information is very fragmented. Accordingly, I describe how fire regimes have changed in these biomes over time due to agricultural practices and the consequences of the current altered fire regimes. After European settlement, fire frequency greatly increased in the cerrado, especially related to cattle ranching, and more recently in the more seasonal landscapes in the Amazon. In cerrado natural preserves, however, managers try to keep fire away, but wildfires eventually come and develop into destructive events. Actions to reduce biodiversity loss and environmental deterioration due to inappropriate fire management are necessary and should be very distinct in both areas: in the Amazon they would include the development of policies to stimulate fire-free, small-scale agricultural projects, and in the cerrado, sustainable use of fire for cattle ranching is possible but the regimes must be fitted to local specific features in order to avoid land degradation. In cerrado conservation areas, proper fire management programs based on scientific knowledge and the incorporation of the traditional expertise of indigenous peoples are needed to maintain the biological diversity, to maintain the ecological processes, and to reduce wildfires.
Evidence-Based Behavioral Treatments for Diabetes: Problem-Solving Therapy

Problem solving is a basic human thinking process. Many general counseling and psychotherapy approaches, such as cognitive behavioral therapy, include problem solving as a component of treatment for managing life problems and emotional disorders.1 Similarly, educational and lifestyle interventions in diabetes often include elements of problem solving as part of broader intervention approaches.2 Among diabetes educators, problem solving is identified as necessary for patient mastery of diabetes self-management and as the skill most difficult to teach patients.3 This article describes the origins of problem-solving therapy (PST) as a formal, stand-alone intervention approach for behavior change; application of this technique to diabetes care; and evidence of its effectiveness in improving diabetes outcomes. Problem solving, which has its origins in the behavioral and cognitive basic sciences,4–8 is an identified intervention approach for behavior change.9,10 Cognitive psychology defines problem solving as involving the following components: the individual is goal-directed; reaching the goal requires a series of mental processes; and those processes are cognitive rather than automatic.6,7 Problem solving can perhaps be described more simply as a series of cognitive operations used to figure out what to do when the way to reach a goal is not apparent. Although problem solving is a counseling approach that may be incorporated within other intervention models, PST is a stand-alone intervention with a longstanding history. PST took root in clinical and counseling psychology in the 1960s and 1970s to address a variety of mental health disorders, including schizophrenia and psychotic disorders, depression and suicidality, social phobia, generalized anxiety disorder, and posttraumatic stress disorder.11,12 PST has also been used to address marital/family distress, lifestyle management in people with mental retardation, stress management, ineffective coping, and substance abuse.11 There is a substantial evidence …
Identifying severe bacterial infection in children with fever without source

For decades, many investigators have attempted to identify clinical or laboratory markers that can accurately differentiate severe bacterial from self-limiting viral infections in young children with fever without source. Unfortunately, no perfect marker has been discovered so far. Many guidelines recommend white blood cell count as a screening marker in fever without source, whereas compelling evidence in the literature emphasizes the superior characteristics of C-reactive protein and procalcitonin. One way to improve predictive value is the combination of prediction rules of different tests for clinical and laboratory markers. Several clinical decision rules, reviewed in this article, have been suggested but seem to be difficult to implement in practice due to their complexity. Recently, procalcitonin, C-reactive protein and urinary dipstick were combined in a simple risk index score that displayed promising predictive value in severe bacterial infections in children. Ultimately, impact analyses still have to be performed to show improved quality of care in this setting.
A Preliminary Assessment of Genetic Differentiation of Triatoma dimidiata (Hemiptera: Reduviidae) in Guatemala by Random Amplification of Polymorphic DNA-Polymerase Chain Reaction

Abstract The population genetics of Triatoma dimidiata (Latreille, 1811) from five different provinces in Guatemala, including three sylvan and three domestic populations, was investigated by random amplification of polymorphic DNA-polymerase chain reaction. There is a high degree of genetic variation in all of the T. dimidiata populations as evidenced by high levels of average expected heterozygosity and polymorphism. Domestic populations are more closely related to each other (D = 0.05–0.085, Nei’s genetic distance) than are the sylvan (D = 0.121–0.189). Within the limited sample size of three populations, there was a correlation with geographic and genetic distance for the domestic populations, but not for the sylvan. Surprisingly, one of the sylvan populations was genetically very similar to the domestic populations. The FST demonstrated a high degree of differentiation at the country-wide level (FST = 0.175) and a moderate degree of differentiation within the sylvan (FST = 0.135) or domestic (FST = 0.097) populations. Although these results demonstrated that gene flow is limited between different provinces in Guatemala, hierarchical analysis showed that barriers between the Atlantic and Pacific drainage slopes were not biologically significant limiters of gene flow.
Proposed Use of Sharepoint to Improve New Employee In-processing

Microsoft SharePoint is an enterprise content management system that provides a collaborative platform for end users to design, monitor and execute business processes. This paper describes a workflow design methodology that if followed, end users can construct SharePoint workflows that implement a business process. As an example, we apply our methodology to a real-world business process, showing how we develop the final SharePoint workflows. Our methodology first develops UML models for the business process at hand. From these UML models, it then generates SharePoint workflows.
Assessment of the Relative Contribution of Different Protease Inhibitors to the Inhibition of Plasmin In Vivo

Summary It has been shown that the most important inhibitor of plasmin is α2-antiplasmin, however, other protease inhibitors are able to inhibit this proteolytic enzyme as well. The contribution of the various protease inhibitors to the inhibition of plasmin in vivo has never been quantitatively assessed. To assess the relative contribution of the different protease inhibitors on the inhibition of plasmin we developed a series of sensitive immunoassays for the detection of complexes between plasmin and the protease inhibitors α2-antiplasmin, α2-macroglobulin, antithrombin III, α1antitrypsin and C1-inhibitor, utilizing monoclonal antibodies that are specifically directed against complexed protease inhibitors and a monoclonal antibody against plasmin. It was confirmed that α2-antiplasmin is the most important inhibitor of plasmin in vivo, however, complexes of plasmin with α2-macroglobulin, antithrombin III, α1antitrypsin- and C1-inhibitor were also detected. Particularly during activation of fibrinolysis complexes between plasmin and inhibitors other than α2-antiplasmin were detected. It was observed that during different situations the inhibition profile of plasmin was not constant e.g. in patients with diffuse intravascular coagulation plasma levels of plasmin-α1-antitrypsin and plasmin-C1-inhibitor were increased whereas in plasma from patients who were treated with thrombolytic agents complexes of plasmin with α2-macroglobulin and with antithrombin III were significantly elevated. In conclusion, we confirmed the important role of α2-antiplasmin in the inhibition of plasmin, however, in situations in which fibrinolysis is activated other protease inhibitors also account for the inhibition of plasmin in vivo. Further investigations to assess the role of the various protease inhibitors in the fibrinolytic system can be assisted by the assays described in this study.
Melanin quantification by in vitro and in vivo analysis of near‐infrared fluorescence

Objective measurements of melanin can provide important information for differentiating melanoma from benign pigmented lesions and in assessing pigmentary diseases. Herein, we evaluate near‐infrared (NIR) fluorescence as a possible tool to quantify melanin. Various concentrations of in vitro Sepia melanin in tissue phantoms were measured with NIR fluorescence and diffuse reflectance spectroscopy. Similar optic measurements were conducted in vivo on 161 normal human skin sites. Diffuse reflectance spectroscopy was used to quantify the melanin content via Stamatas–Kollias algorithm. At physiologic concentrations, increasing in vitro melanin concentrations demonstrated higher fluorescence that was linearly correlated (R2 = 0.99, p < .001). At higher concentrations, the fluorescence signal plateaued. A linear relationship was also observed with melanin content in human skin (R2 = 0.59, p < .001). Comparing the fluorescence and reflectance signals with in vitro and in vivo samples, the estimated melanin concentration in human skin ranged between 0 and 1.25 mg/ml, consistent with previous quantitative studies involving invasive methods.
Reducing streak artifacts in computed tomography via sparse representation in coupled dictionaries.

PURPOSE Reducing the number of acquired projections is a simple and efficient way to reduce the radiation dose in computed tomography (CT). Unfortunately, this results in streak artifacts in the reconstructed images that can significantly reduce their diagnostic value. This paper presents a novel algorithm for suppressing these artifacts in 3D CT. METHODS The proposed algorithm is based on the sparse representation of small blocks of 3D CT images in learned overcomplete dictionaries. It learns two dictionaries, the first dictionary (D(a)) is for artifact-full images that have been reconstructed from a small number (approximately 100) of projections. The other dictionary (D(c)) is for clean artifact-free images. The core idea behind the proposed algorithm is to relate the representation coefficients of an artifact-full block in D(a) to the representation coefficients of the corresponding artifact-free block in D(c). The relation between these coefficients is modeled with a linear mapping. The two dictionaries and the linear relation between the coefficients are learned simultaneously from the training data. To remove the artifacts from a test image, small blocks are extracted from this image and their sparse representation is computed in D(a). The linear map is then used to compute the corresponding coefficients in D(c), which are then used to produce the artifact-suppressed blocks. RESULTS The authors apply the proposed algorithm on real cone-beam CT images. Their results show that the proposed algorithm can effectively suppress the artifacts and substantially improve the quality of the reconstructed images. The images produced by the proposed algorithm have a higher quality than the images reconstructed by the FDK algorithm from twice as many projections. CONCLUSIONS The proposed sparsity-based algorithm can be a valuable tool for postprocessing of CT images reconstructed from a small number of projections. Therefore, it has the potential to be an effective tool for low-dose CT.
Assessment of periodontal conditions and systemic disease in older subjects. II. Focus on cardiovascular diseases.

BACKGROUND Panoramic radiographs (PMX)s may provide information about systemic health conditions. AIMS i). To study clinical periodontal conditions and collect self-reported health status in a cohort of 1084 older subjects; ii). to study signs of alveolar bone loss and carotid calcification from panoramic radiographs obtained from these subjects; and iii). to study associations between study parameters. MATERIAL AND METHODS PMXs from 1064 adults aged 60-75 (mean age 67.6, SD +/- 4.7) were studied. Signs of alveolar bone loss, vertical defects, and molar furcation radiolucencies defined periodontal status. Medical health histories were obtained via self-reports. Signs of carotid calcification were identified from panoramic radiographs. RESULTS The PMX allowed assessment of 53% of the films (Seattle 64.5% and Vancouver 48.4%). A self-reported history of a stroke was reported by 8.1% of men in Seattle and 2.9% of men in Vancouver (P < 0.01). Heart attacks were reported by 12% of men in Seattle and 7.2% in Vancouver (N.S.). PMX evidence of periodontitis was found in 48.5% of the subjects, with carotid calcification in 18.6%. The intraclass correlation score for PMX findings of carotid calcification and stroke was 0.24 (95% CI: 0.10-0.35, P < 0.001). The odds ratio for PMX carotid calcification and periodontitis was 2.1 (95% CI: 1.3-3.2, P < 0.001), and for PMX carotid calcification and stroke 4.2 (95% CI: 1.9-9.1, P < 0.001). The associations disappeared when smoking was accounted for. A history of a heart attack was associated with stroke, gender, age, and PMX scores of alveolar bone loss. CONCLUSIONS PMXs may provide valuable information about both oral conditions and signs of carotid calcification, data that are consistent with self-reported health conditions. Alveolar bone loss as assessed from PMXs is associated with cardiovascular diseases.