Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of In Situ Methods Used To Detect Mycobacterium avium subsp. paratuberculosis in Samples from Patients with Crohn's Disease

ABSTRACT In common with other diagnostic tests, detection of mycobacteria in tissue by microscopic examination is susceptible to spectrum bias. Since Crohn's disease is defined by the absence of detectable pathogenic organisms, the use of in situ techniques to search for Mycobacterium avium subsp. paratuberculosis in Crohn's disease samples requires validation of methods in a paucibacillary setting. To generate paucibacillary infection, C57BL/6 mice were artificially infected with Mycobacterium avium subsp. paratuberculosis strain K10 and M. tuberculosis H37Rv, yielding tissues harboring fewer than one bacillus per oil immersion field. Serial sections of organs were then studied by cell wall-based staining techniques (Ziehl-Neelsen and auramine rhodamine) and nucleic acid-based staining techniques (in situ hybridization [ISH] and indirect in situ PCR [IS PCR]). Microscopic examination and measurement of morphometric parameters of bacilli revealed that for all methods, Mycobacterium avium subsp. paratuberculosis bacilli were observed to be shorter, smaller, and less rod shaped than M. tuberculosis bacilli. Ziehl-Neelsen, auramine rhodamine stains, ISH targeting rRNA, and IS-PCR targeting the IS900 element afforded comparable sensitivities, but for all methods, visualization of individual bacterial forms required magnification ×1,000. Auramine rhodamine staining and IS-PCR generated positive signals in negative controls, indicating the nonspecificity of these assays. Together, our results indicate that detection of Mycobacterium avium subsp. paratuberculosis bacilli in tissue requires oil immersion microscopy, that rRNA-ISH provides sensitivity and specificity comparable to those of Ziehl-Neelsen staining, and that the microscopic detection limit for Mycobacterium avium subsp. paratuberculosis in tissue is governed more by bacterial burden than by staining method.
Rapid symptom relief in reflux oesophagitis: a comparison of lansoprazole and omeprazole

Background: Lansoprazole, a substituted benzimidazole, is a proton pump inhibitor which is highly effective in the control of 24‐h intragastric acidity. The aim of this multicentre, randomized, double‐blind study was to compare lansoprazole 30 mg once daily and omeprazole 20 mg once daily in the symptom relief and healing of patients with reflux oesophagitis.
The Relationship Between the Dim Light Melatonin Onset and Sleep on a Regular Schedule in Young Healthy Adults

The endogenous melatonin onset in dim light (DLMO) is a marker of circadian phase that can be used to appropriately time the administration of bright light or exogenous melatonin in order to elicit a desired phase shift. Determining an individual's circadian phase can be costly and time-consuming. We examined the relationship between the DLMO and sleep times in 16 young healthy individuals who slept at their habitual times for a week. The DLMO occurred about 2 hours before bedtime and 14 hours after wake. Wake time and midpoint of sleep were significantly associated with the DLMO (r = 0.77, r = 0.68 respectively), but bedtime was not (r = 0.36). The possibility of predicting young healthy normally entrained people's DLMOs from their sleep times is discussed.
Total White Blood Cell Count, Absolute Neutrophil Count, Absolute Lymphocyte Count, Neutrophil-to-Lymphocyte Ratio and the Risk of Breast Cancer: The NHANES I Epidemiologic Follow-up Study

The purpose of this study was to examine total white blood cell count (TWBCC), absolute neutrophil count (ANC), absolute lymphocyte count (ALC), and neutrophil-to-lymphocyte ratio’s (NLR) association with the risk of incident breast cancer (BCa). A prospective analysis was conducted among a cohort of 2,873 women from the First National Health and Nutrition Examination Survey (NHANES I) Epidemiologic Follow-up Study. In the present analysis, the association found between lower ALC and increased BCa risk was no longer statistically significant after adjusting for age. Additionally, no statically significant associations were found between any level of ANC, NLR, and TWBCC with incident BCa. Therefore, additional studies, which address the limitations encountered in the present analysis, are needed to validate, or rule out, their use as biomarkers of BCa risk in women.
Lumbar instability: an evolving and challenging concept

Abstract Identification and management of chronic lumbar spine instability is a clinical challenge for manual physical therapists. Chronic lumbar instability is presented as a term that can encompass two types of lumbar instability: mechanical (radiographic) and functional (clinical) instability (FLI). The components of mechanical and FLI are presented relative to the development of a physical therapy diagnosis and management. The purpose of this paper is to review the historical framework of chronic lumbar spine instability from a physical therapy perspective and to summarize current research relative to clinical diagnosis in physical therapy.
Alterations in T-lymphocyte sub-set profiles and cytokine secretion by PBMC of systemic lupus erythematosus patients upon in vitro exposure to organochlorine pesticides

Chronic exposure to organochlorine pesticides (OCP) has been suspected of causing immunoregulatory abnormalities that eventually lead to development and progression of Systemic Lupus Erythematosus (SLE), but the role of these non-genetic stimuli has remained poorly understood. The objectives of the study were to quantify the levels of different OCP residues in the blood of SLE patients and to study the effects of in vitro treatment of peripheral blood mononuclear cells (PBMC) from these patients and healthy controls with OCP. Levels of different OCP residues in the blood were measured by gas-liquid chromatography. Isolated PBMC were treated in vitro with hexachlorocyclohexane (HCH), o,p’-dichlorodiphenyltrichloroethane (DDT), or phytohemagglutinin-M (PHA-M) for 72 h, then stained with different dye-labeled monoclonal antibodies to analyze alterations in T-lymphocytes using flow cytometry. Levels of different TH1 and TH2 cytokines were also estimated by ELISA. Significantly higher levels of p,p’-DDE and β-HCH were detected in the blood of SLE patients than in healthy controls. HCH exposure markedly increased the percentages of CD3+CD4+ T-lymphocytes and expression of CD45RO+ on CD4+ and CD8+ T-lymphocytes, but decreased CD4+CD25+ T-lymphocytes in SLE patients. DDT exposure increased the percentages of CD3+CD4+ T-lymphocytes and decreased those of CD4+CD25+ T-lymphocytes in SLE patients as compared to healthy controls. No significant responsiveness of patient PBMC to PHA-M stimulation was observed indicating suppression of T-lymphocytes by these OCP. Further, both HCH and DDT decreased the levels of IL-2 and IFNγ but had no effect on IL-4 levels in SLE patients. DDT also increased significantly the levels of IL-10 in patients. It is likely that higher levels and prolonged durations of exposure to HCH and DDT may significantly influence T-lymphocyte sub-sets and cytokine expression in vivo that could lead to the development or exacerbation of SLE.
Interest and Learning From Text

Dewey (1913) suggested some time ago that trying to find out what is of interest to students is an important part of schooling; on the other hand, “making things interesting” is artificial and often unsuccessful. Two studies investigating the placement of interesting detail in a text about a physicist and his scientific work are reported here. In both studies, undergraduate students were asked to read the science text under a variety of conditions and then to recall important information on a set of measures. Results indicated that attention of students was diverted from important generalizations in text to interesting, sometimes irrelevant, detail. Placement of the detail did not affect recall, but overall interestingness of the text did, particularly if students knew little about the topic of the text. Implications for instruction are discussed.
SPATIAL AND TEMPORAL VARIATION IN DETECTION PROBABILITY OF PLETHODON SALAMANDERS USING THE ROBUST CAPTURE–RECAPTURE DESIGN

Abstract Recent worldwide amphibian declines have highlighted a need for long-term, large-scale monitoring programs. Scientific or management objectives, appropriate spatial sampling, and detectability all must be considered when designing monitoring programs (Yoccoz et al. 2001). The ability to establish meaningful monitoring programs currently is compromised by a lack of information about amphibian detection probabilities. We used Pollock's robust design and capture–recapture models that included temporary emigration to test a priori hypotheses about spatial and temporal variation in salamander detection probability parameters for populations found in Great Smoky Mountains National Park (Tennessee/North Carolina), USA. We explored the effects of 3 large-scale habitat characteristics (disturbance history, elevation, vegetation type) and found that vegetation type and elevation were correlated with detection probabilities. Vegetation type was an important covariant in estimates of temporary emigration, conditional capture probability, and surface population size. Contrasts that isolated elevation effects were significant for all detection probability parameters except recapture probability, despite our small elevational range (330 m). When detection probability parameters have the potential to vary over time and space, investigators should develop monitoring designs that permit the estimation of detection probabilities.
Listeria phages

Listeria is an important foodborne pathogen and the causative agent of Listeriosis, a potentially fatal infection. Several hundred Listeria bacteriophages have been described over the past decades, but only few have actually been characterized in some detail, and genome sequences are available for less than twenty of them. We here present an overview of what is currently known about Listeria phage genomics, their role in host evolution and pathogenicity, and their various applications in biotechnology and diagnostics.
Antimicrobial resistance in Staphylococcus aureus, Streptococcus uberis and Streptococcus dysgalactiae from dairy cows with mastitis

Abstract AIMS: To determine the minimal inhibitory concentrations (MIC) of antimicrobials for common mastitis pathogens from dairy cows in New Zealand; and to assess the effect of source of the isolates, i.e. commercial veterinary laboratories or collected as part of research studies; the clinical status of the cow, i.e. subclinical or clinical mastitis; cow age and herd on the distribution of the MIC. METHODS: Minimal inhibitory concentrations for Staphylococcus aureus (n=364), Streptococcus dysgalactiae (n=65) and Streptococcus uberis (n=102) isolated from milk samples from dairy cows were determined for a variety of antimicrobials using broth microdilution. Isolates of S. aureus were sourced from research studies from both subclinically (n=161) and clinically (n=104) affected cows, as well as from commercial veterinary laboratories (n=101); while all the streptococcal isolates were from commercial laboratories. Resistance was defined using the cut-points provided by the Clinical and Laboratory Standards Institute (CLSI). RESULTS: The distribution of MIC varied among the bacterial species for every antimicrobial tested (p<0.001). Of the S. aureus isolates, 28, 2 and 0.5% were resistant to penicillin, ampicillin and trimethoprim/sulfamethoxazole, respectively. For S. dysgalactiae and S. uberis isolates, 17 and 13% were resistant to trimethoprim/sulfamethoxazole, respectively. One isolate (1%) of S. uberis was resistant to penicillin. The distribution of MIC of S. aureus varied with clinical status, between herds, and with age of cow (p<0.05). The distribution of MIC for S. aureus for penicillin, amoxicillin/clavulanic acid, cloxacillin and ampicillin were lower from clinical than subclinical cases, and those for amoxicillin/clavulanic acid and oxytetracycline from isolates from veterinary laboratories were lower than for those from research studies. CONCLUSIONS: Resistance to some beta-lactam antimicrobials and trimethoprim/sulfamethoxazole were found in isolates from cases of bovine mastitis. The distribution of MIC for isolates of S. aureus varied with clinical status of the cow, the age of the cow, the herd and with the source of isolate. CLINICAL SIGNIFICANCE: Resistance to penicillin was found in a quarter of S. aureus isolates, but in virtually no Streptococcus isolates; therefore microbial identification and sensitivity testing would be beneficial when assessing treatment options. The source of the isolates affected the estimated MIC, suggesting that selection of isolates for monitoring of resistance requires care and that use of routine submissions to commercial laboratories to assess antimicrobial resistance patterns may result in biased estimates of prevalence of resistance.
How will the court decide? Tax experts and the estimation of tax risk

Tax accounting and tax law concern the probability thresholds that can require the taxpayer to estimate the likelihood that a tax position would be upheld by a court. Tax complexity and the consequent ambiguity results in a reliance by most taxpayers on a tax expert estimate of this likelihood. This study examines whether the tax experts are able to accurately forecast the outcome of tax court decisions and compares tax expert predictions to those of laymen. Our results reveal no significant differences with respect to the forecasting performance of professional tax advisors and laymen. Moreover, the tax advisors exhibit a significantly higher level of overconfidence compared to laymen and the degree of overconfidence increases with professional experience. A comparison of two groups of tax experts, tax advisors and revenue agents demonstrates that the tax advisors exhibit the highest level of overconfidence and form stronger appeal recommendations that indicate a type of advisor bias.
The Diagnostic Value of EEG in Alzheimer Disease: Correlation With the Severity of Mental Impairment

Summary The aim of our study was to analyze EEG changes in patients with Alzheimer disease (AD) and to determine how closely EEG reflects the progression of mental impairment in people with AD. Ninety-five patients with probable AD according to National Institute of Neurological and Communicative Disorders and Stroke/Alzheimer’s Disease and Related Disorders Association criteria treated in our Clinic for Memory Disorders were selected for this study. Patients were divided into three subgroups with mild, marked, and severe dementia according to the results of psychometric scales. The EEG findings were classified using an eight-degree scale according to the background activity, presence and amount of &thgr; and &dgr; waves, focal changes, lateralization of focal changes, synchronization, and presence of sharp and spike waves. A significant correlation between the degree of EEG abnormalities and cognitive impairment was found. We did not observe any correlation between the presence of &dgr; waves and the results of neuropsychological tests. Our study revealed an important diagnostic value of EEG in the estimation of the severity of dementia parallel to psychometric scales.
Multi-cue Perception for Robotic Object Manipulation : How Spatio-temporal Integration of Multi-modal Information Aids Task Execution

The thesis presents a robotic perception system for manipulation tasks in human living environments, that eases the deployment of autonomous service robots in new environments by enabling it to autonomously learn, model and localize the objects it perceives through the integration of geometric categorization and instance recognition. To do so, we designed, tested and analyzed novel methods for: (i) learning general object-related principles from the Internet based on their part composition, (ii) computing descriptors that facilitate generalization between instances of the same category, (iii) classification that is robust to large variations between training and testing data, (iv) and surface reconstruction capable of dealing with partial information and cluttered scenes, while respecting physical constraints. These enable robots to take advantage of their capability to explore their surroundings and that they are equipped with sensors with different advantages, by the integration of prior, spatio-temporal and multi-cue information. The developed system and the underlying modules and principles were shown to outperform alternative solutions in extensive experiments, and were applied in realworld robotic demonstration scenarios, proving the advantage of an embodied, taskadapting approach towards perception.
Differentiation of Leptospira interrogans isolates by IS1500 hybridization and PCR assays

Genetic variability among Leptospira interrogans (sensu stricto) serovars was assessed by Southern blot hybridization and PCR analyses. The experiments used probes directed to sequences in a recently described insertion element, IS1500. Hybridization analysis showed that IS1500 was present on polymorphic fragments and that differences in these patterns could be used to identify serovars. Hybridization analysis was also useful in discriminating between serovar pomona type kennewicki isolates, making possible the identification of 15 previously unrecognized genetic groups. A PCR assay was developed in which the primers are positioned near the terminal inverted repeats of the element and directed outward. This assay yielded characteristic amplification patterns from isolates, allowing them to be identified. We applied these assays to several new animal isolates of L. interrogans from Nicaragua, which recently had an outbreak of human leptospirosis. Three groups of isolates were identified: one strain of serovar pomona type kennewicki and two genetically distinct groups of isolates which may be genetic intermediates between serovars canicola and portlandvere. The IS-based typing assays described should be useful for epidemiological analysis of leptospirosis.
Disinfection of Hospital Rooms Contaminated With Vancomycin-Resistant Entemcocms faecium

ABSTRACT Sixteen percent of hospital room surfaces remained colonized by vancomycin-resistant enterococci (VRE) after routine terminal disinfection. Disinfection with a new "bucket method" resulted in uniformly negative cultures. Conventional cleaning took an average of 2.8 disinfections to eradicate VRE from a hospital room, while only one cleaning was required with the bucket method.
Stimulation Parameters Define the Effectiveness of Burst Spinal Cord Stimulation in a Rat Model of Neuropathic Pain

Although burst spinal cord stimulation (SCS) has been reported to reduce neuropathic pain, no study has explicitly investigated how the different parameters that define burst SCS may modulate its efficacy. The effectiveness of burst SCS to reduce neuronal responses to noxious stimuli by altering stimulation parameters was evaluated in a rat model of cervical radiculopathy.
Inpatient treatment of children and adolescents with severe obesity in the Netherlands: a randomized clinical trial.

IMPORTANCE Severe childhood obesity has become a major health problem, and effective, evidence-based interventions are needed. The relative effectiveness of inpatient compared with ambulatory treatment remains unknown. OBJECTIVE To determine whether an inpatient treatment program is more effective than an ambulatory treatment program at achieving a sustained weight loss in children and adolescents with severe obesity. DESIGN, SETTING, AND PARTICIPANTS We conducted a randomized clinical trial with a 2-year follow-up at a tertiary referral center for pediatric obesity in the Netherlands. We recruited 90 children and adolescents aged 8 to 18 years with severe obesity (body mass index [BMI] z score, ≥3.0 or >2.3 with obesity-related health problems). INTERVENTIONS Patients were randomly assigned to an inpatient (6 months of hospitalization on working days) or an ambulatory (12 days of hospital visits at increasing intervals during a 6-month period) treatment program. Both treatment programs involved an intensive, family-based, lifestyle intervention, including exercise, nutritional education, and behavior modification for the patients and their caregiver(s). MAIN OUTCOMES AND MEASURES Change in BMI z score. Secondary outcomes included fasting insulin, fasting plasma glucose, 2-hour plasma glucose, and lipid levels, insulin sensitivity, liver function test results, waist circumference, blood pressure, body composition, and aerobic fitness (peak oxygen consumption, Vo₂). Outcomes were analyzed by intention to treat. RESULTS Immediately after treatment, reductions in the BMI z score were significantly larger for the inpatient than the ambulatory groups (mean [SE] difference, -0.26 [0.12; 95% CI, -0.59 to -0.01]; P = .04). Change from baseline for the BMI z score in the inpatient group was -18.0% (P = .001) immediately after treatment, -8.5% (P = .008) at 18 months, and -6.3% (P = .38) at 30 months; in the ambulatory group, changes from baseline were -10.5% (P = .001), -6.2% (P = .39), and -1.5% (P > .99), respectively. The favorable outcomes of the inpatient group could not be sustained at 12 and 24 months after treatment. In addition, significant differences in favor of the inpatient group immediately after treatment were found for levels of fasting insulin (-6.37 IU/L; P = .02), total cholesterol (-19.51 mg/dL; P = .01), low-density lipoprotein cholesterol (-13.48 mg/dL; P = .03), and triglycerides (-25.39 mg/dL; P = .01), and insulin sensitivity (-1.37; P = .02), fat mass (-3.31%; P = .03), and peak Vo₂ (378.2 mL/min; P = .01). CONCLUSIONS AND RELEVANCE In severely obese children and adolescents, inpatient treatment was superior to ambulatory treatment immediately after treatment, but effects were not sustained at long-term follow-up. These findings stress the need to further study maintenance strategies for sustainable weight loss. TRIAL REGISTRATION trialregister.nl Identifier: NTR1172.
Gimme 5 Fruit and Vegetables for Fun and Health: Process Evaluation

Gimme 5 (Georgia) was a school-based nutrition education effectiveness trial to help fourth- and fifth-grade students eat more fruit, 100% juice, and vegetables (FJV). Process evaluation assessed fidelity of implementation, reach, and use of intervention materials and environmental mediators: teacher training, curriculum delivery, participation in family activities, attendance at evening point-of-purchase grocery store activities, and availability and accessibility of FJV at home. Approximately half of the curriculum activities were implemented in fourth and fifth grades. The lowest proportion completed were those most pertinent to behavior change. Eighty-seven percent of parents reported participating in homework activities with their fourth grader, 66% with fifth graders. Sixty-five percent of parents reported viewing a video with their child in both grades. Ten percent attended evening point-of-purchase grocery store activities. The low level of implementation and modest level of participation in family activities suggest that higher levels of behavior change may have occurred if exposure to the intervention had been higher.