Miracle-dz/UniFAR-FTUs huggingface dataset:
The multi-resolution capability of Tchebichef moments and its applications to the analysis of fluorescence excitation-emission spectra

Fluorescence spectroscopy with an excitation-emission matrix (EEM) is a fast and inexpensive technique and has been applied to the detection of a very wide range of analytes. However, serious scattering and overlapping signals hinder the applications of EEM spectra. In this contribution, the multi-resolution capability of Tchebichef moments was investigated in depth and applied to the analysis of two EEM data sets (data set 1 consisted of valine-tyrosine-valine, tryptophan-glycine and phenylalanine, and data set 2 included vitamin B1, vitamin B2 and vitamin B6) for the first time. By means of the Tchebichef moments with different orders, the different information in the EEM spectra can be represented. It is owing to this multi-resolution capability that the overlapping problem was solved, and the information of chemicals and scatterings were separated. The obtained results demonstrated that the Tchebichef moment method is very effective, which provides a promising tool for the analysis of EEM spectra. It is expected that the applications of Tchebichef moment method could be developed and extended in complex systems such as biological fluids, food, environment and others to deal with the practical problems (overlapped peaks, unknown interferences, baseline drifts, and so on) with other spectra.
Orientation Changes of the Main Corneal Axes as a Function of Age

Purpose The purpose of this study was to assess the orientation of the anterior and posterior corneal surfaces with respect to the keratometric axis in the three-dimensional space. Methods A group of 407 normal corneas of 211 subjects with ages ranging from 4 to 79 years was analyzed by fitting their elevation topographies to a general three-axes ellipsoid model. Results The resulting average tilt (−1.20 degrees) and tip (1.83 degrees) of the anterior surface are consistent with previous findings. In addition, we found that the posterior surface is also misaligned with the anterior by a similar amount. The cornea seems to rotate as a solid body by 2 minutes of arc per year. Conclusions The misalignment between the cornea and the keratometric axis increases as a function of age. This tiny, but significant (p < 0.005), rotation may have an important impact on optical quality because it could cause an important increase of the higher order aberrations of the cornea with age.
Human microglial cell isolation from adult autopsy brain: Brain pH, regional variation, and infection with human immunodeficiency virus type 1

Microglia are the main source of productive infection by human immunodeficiency virus type 1 (HIV-1) in the central nervous system (CNS). Infection of microglia is difficult to study because nonhuman microglia are not infected by HIV-1, adult human microglia from surgically removed brain tissues are scarce, and fetal human microglial cells differ from adult cells in potentially important ways. Adult autopsies are a potential source of brain tissue for HIV-1 research, but the technique of isolating and infecting cells postmortem is not completely standardized. The authors determined optimal conditions for isolating and infecting adult microglial cells using 18 adult autopsy brain specimens from HIV-1-infected and noninfected decedents. The yield of mixed glial cells overall was on average 0.5 × 106 cells per gram of wet tissue. There was no correlation between the number of microglia isolated and the postmortem interval (PMI), HIV seropositivity, age, or gender. Brain pH accounted for about 41% of yield variability; a pH of less than 6.0 generally was not compatible with adequate cell recovery. The highest microglial cell yields were derived from anterior brain sectors (frontal lobe and temporal lobe) versus occipital lobe and cerebellum. A PMI of up to 25.5 h produced excellent cell yields in frontal lobe samples with high brain pH. HIV-1 infection of frontal lobe microglia was 100% successful using both CXCR4- and CCR5-tropic strains of HIV-1. With proper selection of cases and brain region, autopsy brain specimens are a dependable source of viable microglial cells to study CNS HIV-1 infection.
Effects of antibacterial agents and drugs monitored by atomic force microscopy.

Originally invented for topographic imaging, atomic force microscopy (AFM) has evolved into a multifunctional biological toolkit, enabling to measure structural and functional details of cells and molecules. Its versatility and the large scope of information it can yield make it an invaluable tool in any biologically oriented laboratory, where researchers need to perform characterizations of living samples as well as single molecules in quasi-physiological conditions and with nanoscale resolution. In the last 20 years, AFM has revolutionized the characterization of microbial cells by allowing a better understanding of their cell wall and of the mechanism of action of drugs and by becoming itself a powerful diagnostic tool to study bacteria. Indeed, AFM is much more than a high-resolution microscopy technique. It can reconstruct force maps that can be used to explore the nanomechanical properties of microorganisms and probe at the same time the morphological and mechanical modifications induced by external stimuli. Furthermore it can be used to map chemical species or specific receptors with nanometric resolution directly on the membranes of living organisms. In summary, AFM offers new capabilities and a more in-depth insight in the structure and mechanics of biological specimens with an unrivaled spatial and force resolution. Its application to the study of bacteria is extremely significant since it has already delivered important information on the metabolism of these small microorganisms and, through new and exciting technical developments, will shed more light on the real-time interaction of antimicrobial agents and bacteria.
High‐risk human papillomavirus DNA testing: A marker for atypical glandular cells

Cervical/endocervical cytology screening has decreased morbidity and mortality, and implementing adjunctive human papilloma virus (HPV) DNA testing for atypical squamous cells of undetermined significance has improved the specificity for detecting premalignant squamous lesions. Currently, there are no guidelines to perform HPV DNA testing on cervical/endocervical ThinPreps with atypical glandular cells (AGC). To assess the potential role of HPV DNA testing on AGC cases, Hybrid Capture 2 (Digene Corp.) testing was performed on 144 cervical/endocervical AGC specimens. One hundred three of 144 cases had follow‐up; 60/103 (58.3%) were high‐risk HPV negative and 43/103 (42.3%) were high‐risk HPV positive. Of 43 HPV‐positive patients, 37 had adenocarcinoma in situ (AIS), atypical squamous cells of undetermined significance (ASCUS), or cervical squamous intraepithelial neoplasia, while only one patient without high‐risk HPV had a squamous intraepithelial neoplasia. Furthermore, most high‐risk HPV positive AGC cases harbored high‐grade squamous intraepithelial lesion (HSIL) rather than AIS. Our data support HPV DNA testing of all AGC specimens to detect cervical, especially squamous, neoplasia. neoplasia. Diagn. Cytopathol. 2006; 34:235–239. © 2006 Wiley‐Liss, Inc.
Dietary problems in patients with severe chronic obstructive pulmonary disease.

BACKGROUND AND AIMS Low body weight and low fat-free mass-index (FFMI) are common in patients with severe chronic obstructive pulmonary disease (COPD). Several factors seem to contribute. The aims of the present observational study were to investigate dietary problems in patients with severe COPD and to compare dietary problems to nutritional status, energy intake and smoking habits. METHODS Nutritional status was assessed in 73 stable outpatients using body mass index and FFMI by single-frequency bioelectrical impedance. Lung function, smoking habits, energy intake and dietary problems were also assessed. RESULTS The most frequently reported dietary problems were 'anorexia', 'dyspeptic symptoms other than diarrhoea', 'slimming', 'fear of gaining weight', 'dyspnoea', 'diarrhoea', 'depression, anxiety, solitude'. Smoking habits and gender had impact on the kind of dietary problems reported. Reporting two dietary problems correlated to low FFMI, whereas reporting one or more dietary problems correlated to decreased energy intake. CONCLUSION Dietary problems are common in the group studied and related to smoking habits and gender. Dietary problems affect energy intake and FFMI negatively. It is important to recognize dietary problems and to offer intervention of the dietary problems as a part of the dietary intervention.
Complementary PTM Profiling of Drug Response in Human Gastric Carcinoma by Immunoaffinity and IMAC Methods with Total Proteome Analysis

Gaining insight into normal cellular signaling and disease biology is a critical goal of proteomic analyses. The ability to perform these studies successfully to extract the maximum value and discovery of biologically relevant candidate biomarkers is therefore of primary importance. Many successful studies in the past have focused on total proteome analysis (changes at the protein level) combined with phosphorylation analysis by metal affinity enrichment (changes at the PTM level). Here, we use the gastric carcinoma cell line MKN-45 treated with the c-Met inhibitor SU11274 and PKC inhibitor staurosporine to investigate the most efficient and most comprehensive strategies for both total protein and PTM analysis. Under the conditions used, total protein analysis yielded few changes in response to either compound, while analysis of phosphorylation identified thousands of sites that changed differentially between the two treatments. Both metal affinity and antibody-based enrichments were used to assess phosphopeptide changes, and the data generated by the two methods was largely complementary (non-overlapping). Label-free quantitation of peptide peak abundances was used to accurately determine fold-changes between control and treated samples. Protein interaction network analysis allowed the data to be placed in a biologically relevant context, and follow-up validation of selected findings confirmed the accuracy of the proteomic data. Together, this study provides a framework for start-to-finish proteomic analysis of any experimental system under investigation to maximize the value of the proteomic study and yield the best chance for uncovering actionable target candidates.
Bullous Malignant Melanoma: An Unusual Differential Diagnosis of a Hemorrhagic Friction Blister

BACKGROUND A 66-year-old woman presented to our outpatient clinic with a 3×2.5-cm tense, hemorrhagic-appearing bulla on her forefoot. Histopathology and immunohistochemistry confirmed a transtumoral–transepidermal blister formation within an advanced acrolentiginous malignant melanoma (MM). OBJECTIVE To study bullous malignant melanoma. METHODS Blistering in MMs represents a rare but clinically important pitfall in clinical differential diagnosis. The blisters are typically due to the disruption of the cohesion between neoplastic cells and keratinocytes, but physical friction may also contribute. RESULTS Hemorrhagic blistering is, in many cases, a relatively insignificant finding in which frictional forces are imposed. CONCLUSION The case reported here underscores that in rare cases MMs, particularly if acrally located, can be complicated by hemorrhagic blistering. Because of the life-threatening consequences, one should be aware of this rare differential diagnosis.
Early and intermediate stage Hodgkin's lymphoma – report from the Swedish National Care Programme

Abstract: In Sweden a National Care Programme provides treatment principles for Hodgkin's lymphoma (HL) since 1985, for early and intermediate stages often less extensive than international recommendations. The purpose is to evaluate long‐term results of these principles. A total of 308 patients (167 men and 141 women), 17–59 yr old (median 31), diagnosed during 1985–92, pathological stage (PS) I‐III1A and I‐IIB and clinical stage (CS) I‐IIA, mean follow‐up 8.8 yr, were studied. Staging laparotomy was recommended in CS IIA. Recommended treatment was mantle or mini‐mantle radiotherapy (RT) alone in CS IA, and PS I‐IIA and subtotal nodal irradiation in PS III1A if the disease was not bulky. Patients in PS I‐IIA and III1A with bulky disease, and PS I‐IIB received one cycle of mechlorethamine, vincristine, prednisone, procarbazine/doxorubicin, bleomycin, vinblastine, lacarbazine (MOPP/ABVD) before irradiation. The remaining patients received three to four cycles of MOPP/ABVD with RT to bulky disease. Relapse‐free (RFS), Hodgkin specific (HLS), and overall survival (OS) at 10 yr were 74%, 92% and 85%. In the individual stages, RFS ranged from 53% (PSIII1A) to 90% (PS IA). RFS (P = 0.006), HLS, and OS were significantly better in patients treated with chemotherapy compared with those treated with RT alone, especially in patients with bulky disease (P = 0.0005). The international prognostic score did not provide any prognostic information. The OS rates are in agreement with results from international centres during that time. The recommended treatment was sufficient to produce the desired results of <20–30% recurrences, except in PS III1A. Most relapses could be salvaged. Patients with risk factors treated with one MOPP/ABVD and RT had an excellent outcome, superior to those without risk factors treated with RT alone. These results favour the trend to treat early and intermediate stages with a short course of chemotherapy followed by limited RT.
von Willebrand factor‐collagen binding activity is increased in newborns and infants

ABSTRACT. von Willebrand factor (vWF) antigen (vWF:Ag) and vWF‐collagen binding activity (vWF:CBA) were measured in plasma by parallel quantitative ELISAs in normal newborns and infants (n=71). The medians for vWF:Ag (IUjml) and vWF:CBA (Ujml), respectively, were 1.46 and 1.91 for 2‐7 day‐old (n= 43), 1.22 and 1.40 for 2‐4 week‐old (n= 14), 1.22 and 1.15 for 2‐6‐month‐old (n= 14) infants and 0.98 and 1.08 (n= 36) in normal adults. Elevated levels of vWF:Ag, but particularly vWF:CBA were seen for up to 4 weeks of life reaching adult levels between 2 and 6 months of life. The elevated levels of the vWF parameters indicate that caution should be exercised when interpreting laboratory data and diagnosing von Willebrand disease in newborns and young infants and warrant the use of age‐specific reference ranges. The efficient haemostasis observed during early neonatal life may in part be due to the increased ability of vWF to interact with collagen.
A food-based dietary strategy lowers blood pressure in a low socio-economic setting: a randomised study in South Africa

Abstract Objective To assess the impact of a food-based intervention on blood pressure (BP) in free-living South African men and women aged 50–75 years, with drug-treated mild-to-moderate hypertension. Methods A double-blind controlled trial was undertaken in eighty drug-treated mild-to-moderate hypertensive subjects randomised to an intervention (n 40) or control (n 40) arm. The intervention was 8-week provision of six food items with a modified cation content (salt replacement (SOLO™), bread, margarine, stock cubes, soup mix and a flavour enhancer) and 500 ml of maas (fermented milk)/d. The control diet provided the same quantities of the targeted foods but of standard commercial composition and 500 ml/d of artificially sweetened cooldrink. Findings The intervention effect estimated as the contrast of the within-diet group changes in BP from baseline to post-intervention was a significant reduction of 6·2 mmHg (95 % CI 0·9, 11·4) for systolic BP. The largest intervention effect in 24 h BP was for wake systolic BP with a reduction of 5·1 mmHg (95 % CI 0·4, 9·9). For wake diastolic BP the reduction was 2·7 mmHg (95 % CI −0·2, 5·6). Conclusions Modification of the cation content of a limited number of commonly consumed foods lowers BP by a clinically significant magnitude in treated South African hypertensive patients of low socio-economic status. The magnitude of BP reduction provides motivation for a public health strategy that could be adopted through lobbying of the food industry by consumer and health agencies.
Using a Decision Wheel to Reduce Use of Restraints in a Medical-Surgical Intensive Care Unit.

BACKGROUND Little information is available on the use of tools in intensive care units to help nurses determine when to restrain a patient. Patients in medical-surgical intensive care units are often restrained for their safety to prevent them from removing therapeutic devices. Research indicates that restraints do not necessarily prevent injuries or removal of devices by patients. OBJECTIVES To decrease use of restraints in a medical-surgical intensive care unit and to determine if a decision support tool is useful in helping bedside nurses determine whether or not to restrain a patient. METHODS A quasi-experimental study design was used for this pilot study. Data were collected for each patient each shift indicating if therapeutic devices were removed and if restraints were used. An online educational activity supplemented by 1-on-1 discussion about proper use of restraints, alternatives, and use of a restraint decision tool was provided. Frequency of restraint use was determined. Descriptive statistics and thematic analysis were used to examine nurses' perceptions of the decision support tool. RESULTS Use of restraints was reduced 32%. No unplanned extubations or disruption of life-threatening therapeutic devices by unrestrained patients occurred. CONCLUSIONS With implementation of the decision support tool, nurses decreased their use of restraints yet maintained patients' safety. A decision support tool may help nurses who are undecided or who need reassurance on their decision to restrain or not restrain a patient.
When the Cycle Becomes the Trend: The Emerging Market Experience with Fiscal Policy During the Last Commodity Super Cycle

Fiscal buffers have shrunk across the world. This paper argues that limited fiscal room in emerging market economies today is partly due to the commodity super cycle of 2000-15. The super cycle created the mirage that economic performance had structurally improved, mistaking a long, commodity-fueled uptick in the business cycle for higher trend growth. This thinking supported fiscal expansions. When the commodity boom ended, it became apparent that countries had saved less than they should have, and that fiscal policy had, perhaps inadvertently, been pro-cyclical. It left countries with depleted fiscal buffers and large budgets when the cycle came to an end, limiting room for fiscal stimulus when needed. The paper illustrates the argument with reference to the South African experience.
Assessing the performance of four different categories of histological criteria in brain tumours grading by means of a computer‐aided diagnosis image analysis system

Brain tumours are considered one of the most lethal and difficult to treat forms of cancer, with unknown aetiology and lack of any realistic screening. In this study, we examine, whether the combination of descriptive criteria, used by expert histopathologists in assessing histologic tissue samples, and quantitative image analysis features may improve the diagnostic accuracy of brain tumour grading. Data comprised 61 cases of brain cancers (astrocytomas, oligodendrogliomas, meningiomas) collected from the archives of the University Hospital of Patras, Greece. Incorporating physician's descriptive criteria and image analysis's quantitative features into a discriminant function, a computer‐aided diagnosis system was designed for discriminating low‐grade from high‐grade brain tumours. Physician's descriptive features, when solely used in the system, proved of high discrimination accuracy (93.4%). When verbal descriptive features were combined with quantitative image analysis features in the system, discrimination accuracy improved to 98.4%. The generalization of the proposed system to unseen data converged to an overall prediction accuracy of 86.7% ± 5.4%. Considering that histological grading affects treatment selection and diagnostic errors may be notable in clinical practice, the utilization of the proposed system may safeguard against diagnostic misinterpretations in every day clinical practice.
Defining Thresholds for the Patient Acceptable Symptom State for the IKDC Subjective Knee Form and KOOS for Patients Who Underwent ACL Reconstruction

Background: A clinically meaningful change in patient-reported outcome (PRO) may not be associated with an acceptable state that corresponds to “feeling well,” also known as the patient acceptable symptom state (PASS). The PASS thresholds for the International Knee Documentation Committee Subjective Knee Form (IKDC-SKF) and the Knee injury and Osteoarthritis Outcome Score (KOOS) have not been determined for individuals after anterior cruciate ligament (ACL) reconstruction. Purpose: To determine the PASS thresholds for the IKDC-SKF and KOOS in individuals at 1 to 5 years after ACL reconstruction. Study Design: Cohort study (diagnosis): Level of evidence, 2. Methods: Individuals 1 to 5 years after primary ACL reconstruction completed a survey that included the IKDC-SKF and KOOS. All subjects assessed satisfaction with their current state by answering the question, “Taking into account all the activity you have during your daily life, your level of pain, and also your activity limitations and participation restrictions, do you consider the current state of your knee satisfactory? ” Results: A total of 251 participants (mean age ± SD, 26.1 ± 9.9 years) completed the survey at an average of 3.4 ± 1.3 years after ACL reconstruction. Of these, 223 (89.2%) individuals indicated that they were in an acceptable symptom state (PASS-Y). Analysis of the receiver operating characteristic curve revealed that the IKDC-SKF and each of the KOOS subscales (pain, symptoms, activities of daily living [ADL], sport and recreation [sport/rec], and quality of life [QoL]) were significantly better identifiers of PASS than chance as indicated by the significance of the area under the curves. The PASS threshold (sensitivity, specificity) was 75.9 (0.83, 0.96) for the IKDC-SKF, 88.9 (0.82, 0.81) for the KOOS pain, 57.1 (0.78, 0.67) for the KOOS symptoms, 100.0 (0.70, 0.89) for the KOOS ADL, 75.0 (0.87, 0.88) for the KOOS sport/rec, and 62.5 (0.82, 0.85) for the KOOS QoL. In addition, the difference between PASS-Y and PASS-N was statistically significant (P < .001) for all PROs. Conclusion: To our knowledge, this is the first study to identify the PASS thresholds for the IKDC-SKF and the KOOS subscales for individuals 1 to 5 years after ACL reconstruction. By identifying threshold values for the PASS, this study provides additional information to facilitate interpretation of the IKDC-SKF and KOOS in daily practice and clinical research related to ACL reconstruction.