Miracle-dz/UniFAR-FTUs huggingface dataset:
Parity, age at first birth and the risk of carcinoma in situ of the breast

Epidemiological studies of in situ breast cancer are sparse, and the role of reproductive history, an established risk modifier for invasive breast cancer, remains incompletely investigated. To examine possible associations with parity and age at first birth, we undertook a case‐control study nested in a nationwide cohort of Swedish women. The reproductive history of 1,368 women aged 65 or younger with a diagnosis of carcinoma in situ of the breast were compared with that of 6,837 age‐matched controls drawn randomly from a population‐based Fertility Registry. Statistical analyses were performed by conditional logistic regression. Compared to nulliparous women, ever‐parous women were at a reduced risk of carcinoma in situ of the breast. The risk decreased with number of live births, with the estimated risk reduction in the highest parity group (5+), being of the same magnitude as that reported for invasive breast cancer. By contrast, a positive association with increasing age at first birth was somewhat less pronounced than that observed previously in the same data set with respect to invasive breast cancer. Our findings indicate that parity affects the risk of invasive breast cancer and carcinoma in situ similarly, whereas the effect of age at first birth appears to be weaker for the risk of carcinoma in situ. Int. J. Cancer 77:330–332, 1998. © 1998 Wiley‐Liss, Inc.
Spatiotemporal Structure of Molecular Evolution of H5N1 Highly Pathogenic Avian Influenza Viruses in Vietnam

Background Vietnam is one of the countries most affected by outbreaks of H5N1 highly pathogenic avian influenza viruses. First identified in Vietnam in poultry in 2001 and in humans in 2004, the virus has since caused 111 cases and 56 deaths in humans. In 2003/2004 H5N1 outbreaks, nearly the entire poultry population of Vietnam was culled. Our earlier study (Wan et al., 2008, PLoS ONE, 3(10): e3462) demonstrated that there have been at least six independent H5N1 introductions into Vietnam and there were nine newly emerged reassortants from 2001 to 2007 in Vietnam. H5N1 viruses in Vietnam cluster distinctly around Hanoi and Ho Chi Minh City. However, the nature of the relationship between genetic divergence and geographic patterns is still unclear. Methodology/Principal Findings In this study, we hypothesized that genetic distances between H5N1 viruses in Vietnam are correlated with geographic distances, as the result of distinct population and environment patterns along Vietnam's long north to south longitudinal extent. Based on this hypothesis, we combined spatial statistical methods with genetic analytic techniques and explicitly used geographic space to explore genetic evolution of H5N1 highly pathogenic avian influenza viruses at the sub-national scale in Vietnam. Our dataset consisted of 125 influenza viruses (with whole genome sets) isolated in Vietnam from 2003 to 2007. Our results document the significant effect of space and time on genetic evolution and the rise of two regional centers of genetic mixing by 2007. These findings give insight into processes underlying viral evolution and suggest that genetic differentiation is associated with the distance between concentrations of human and poultry populations around Hanoi and Ho Chi Minh City. Conclusions/Significance The results show that genetic evolution of H5N1 viruses in Vietnamese domestic poultry is highly correlated with the location and spread of those viruses in geographic space. This correlation varies by scale, time, and gene, though a classic isolation by distance pattern is observed. This study is the first to characterize the geographic structure of influenza viral evolution at the sub-national scale in Vietnam and can shed light on how H5N1 HPAIVs evolve in certain geographic settings.
Debugging GPU stream programs through automatic dataflow recording and visualization

We present a novel framework for debugging GPU stream programs through automatic dataflow recording and visualization. Our debugging system can help programmers locate errors that are common in general purpose stream programs but very difficult to debug with existing tools. A stream program is first compiled into an instrumented program using a compiler. This instrumenting compiler automatically adds to the original program dataflow recording code that saves the information of all GPU memory operations into log files. The resulting stream program is then executed on the GPU. With dataflow recording, our debugger automatically detects common memory errors such as out-of-bound access, uninitialized data access, and race conditions -- these errors are extremely difficult to debug with existing tools. When the instrumented program terminates, either normally or due to an error, a dataflow visualizer is launched and it allows the user to examine the memory operation history of all threads and values in all streams. Thus the user can analyze error sources by tracing through relevant threads and streams using the recorded dataflow. A key ingredient of our debugging framework is the GPU interrupt, a novel mechanism that we introduce to support CPU function calls from inside GPU code. We enable interrupts on the GPU by designing a specialized compilation algorithm that translates these interrupts into GPU kernels and CPU management code. Dataflow recording involving disk I/O operations can thus be implemented as interrupt handlers. The GPU interrupt mechanism also allows the programmer to discover errors in more active ways by developing customized debugging functions that can be directly used in GPU code. As examples we show two such functions: assert for data verification and watch for visualizing intermediate results.
Psychosexual trauma of an abnormal cervical smear

Summary. The psychosexual sequelae of diagnosis and treatment of pre‐invasive cervical atypia were assessed in three groups of women. The first group included 30 women referred to a colposcopy clinic with an abnormal cervical smear indicating cervical intraepithelial neoplasia (CIN), the second comprised 50 women who were traced as sexual partners of men with penile human papillomavirus (HPV) infection; 26 of them had histologically proven cervical atypia and 24 had no such evidence. The third group included 25 women traced as partners of men with non‐specific urethritis and who did not have cervical disease. Before and after questionnaires assessed six aspects of sexual behaviour and responses before diagnosis and 6 months after treatment in women with cervical atypia. These were compared with answers given by women investigated and treated, if necessary, as partners of men with sexually transmitted disease (control group). There were statistically significant adverse psychosexual sequelae associated with diagnosis and treatment of pre‐invasive cervical epithelial disease.
Efficacy of Corticosteroids and External Beam Radiation in the Management of Moderate to Severe Thyroid Eye Disease

Thyroid Eye Disease (TED, Graves ophthalmopathy, thyroid ophthalmopathy) is the most common cause of orbital inflammation and proptosis in adults. There is no agreement on its management although corticosteroids and external beam orbital radiation (XRT) have traditionally been believed to provide benefit in active inflammation. Our review of the published literature in English disclosed an overall corticosteroid-mediated treatment response of 66.9% in a total of 834 treated patients who had moderate or severe TED. Intravenous corticosteroids used in repeated weekly pulses were more effective (overall favorable response = 74.6%, n = 177) and had fewer side effects than daily oral corticosteroids (overall favorable response = 55.5%, n = 265). A combination of corticosteroid and radiation therapy seemed to be more effective than corticosteroids alone. Our conclusions are tempered by a notable lack of standardization within and between study designs, treatment protocols, and outcome measures. Accordingly, the North American Neuro-Ophthalmology Society (NANOS), American Society of Ophthalmic Plastic and Reconstructive Surgery (ASOPRS) and the Orbital Society, in conjunction with Neuro-Ophthalmology Research and Development Consortium (NORDIC), will investigate the design and funding of a multi-center controlled trial.
Cerebellitis in an adult with abnormal magnetic resonance imaging findings prior to the onset of ataxia.

BACKGROUND Brain magnetic resonance imaging (MRI) findings during acute cerebellar ataxia in cases of postinfectious cerebellitis are frequently normal. This has resulted in the use of other imaging modalities, such as single-photon emission computed tomography, to aid diagnosis. OBJECTIVE To illustrate the chronologic occurrence of cerebellar ataxia, abnormal findings on MRI, and cerebral spinal fluid pleocytosis in an adult case of postinfectious cerebellitis. METHODS Case report. RESULTS A patient with a 6-week history of occipital headaches and only mild tandem gait difficulty had abnormal MRI findings that were consistent with cerebellar inflammation. As cerebellar ataxia progressed in parallel with cerebral spinal fluid pleocytosis, MRI findings indicative of cerebellar inflammation resolved, while single-photon emission computed tomography showed cerebellar hyperperfusion. Recovery of neurologic function was accompanied by clearing of the pleocytosis and residual MRI-detected cerebellar atrophy. CONCLUSION This case demonstrates that transient abnormalities can be detected by MRI before clinical manifestations of cerebellitis appear, while hyperperfusion detected by single-photon emission computed tomography is prolonged.
Prevention of multidrug-resistant infections from contaminated duodenoscopes: Position Statement of the European Society of Gastrointestinal Endoscopy (ESGE) and European Society of Gastroenterology Nurses and Associates (ESGENA)

RECOMMENDATIONS Patients should be informed about the benefits and risks of endoscopic retrograde cholangiopancreatography (ERCP) Only specially trained and competent personnel should carry out endoscope reprocessing. Manufacturers of duodenoscopes should provide detailed instructions on how to use and reprocess their equipment. In the case of modifications to their equipment, manufacturers should provide updated instructions for use. Detailed reprocessing protocols based on the manufacturer’s instructions for use should clearly lay out the different reprocessing steps necessary for each endoscope model. Appropriate cleaning equipment should be used for duodenoscopes in compliance with the manufacturer’s instructions for use. Only purpose-designed, endoscope type-specific, single-use cleaning brushes should be used, to ensure optimal cleaning. As soon as the endoscope is withdrawn from the patient, bedside cleaning should be performed, followed by leak testing, thorough manual cleaning steps, and automated reprocessing, in order to: Remove debris from external and internal surfaces; Prevent any drying of body fluids, blood, or debris; Prevent any formation of biofilms. In addition to the leak test, visual inspection of the distal end as well as regular maintenance of duodenoscopes should be performed according to the manufacturer’s instructions for use, in order to detect any damage at an early stage. The entire reprocessing procedure in endoscope washer-disinfectors (EWDs) should be validated according to the European and International Standard, EN ISO 15883. Routine technical tests of EWDs should be performed according to the validation reports. Microbiological surveillance of a proportion of the department’s endoscopes should be performed every 3 months, with the requirement that all endoscopes used in the unit are tested at least once a year. In the case of suspected endoscopy-related infection, the relevant device (e. g., endoscope, EWD) should be taken out of service until adequate corrective actions have been taken. Outbreaks should be managed by a multidisciplinary team, including endoscopy, hygiene, and microbiology experts, manufacturers, and regulatory bodies, according to national standards and/or laws. In the case of suspected multidrug-resistant organism (MDRO) outbreaks, close cooperation between the endoscopy unit and the clinical health provider is essential (including infection control departments and hospital hygienists).
Optimal Electric Network Design for a Large Offshore Wind Farm Based on a Modified Genetic Algorithm Approach

The increasing development of large-scale offshore wind farms around the world has caused many new technical and economic challenges to emerge. The capital cost of the electrical network that supports a large offshore wind farm constitutes a significant proportion of the total cost of the wind farm. Thus, finding the optimal design of this electrical network is an important task, a task that is addressed in this paper. A cost model has been developed that includes a more realistic treatment of the cost of transformers, transformer substations, and cables. These improvements make this cost model more detailed than others that are currently in use. A novel solution algorithm is used. This algorithm is based on an improved genetic algorithm and includes a specific algorithm that considers different cable cross sections when designing the radial arrays. The proposed approach is tested with a large offshore wind farm; this testing has shown that the proposed algorithm produces valid optimal electrical network designs.
Molecular Shape of α-Connectin, an Elastic Filamentous Protein of Skeletal Muscle

Rotary shadowed image of α-connectin (titin 1; TI), mother molecule of the muscle elastic filament, was a long thin rod, approximately 1μm long and 3-4nm wide, with a globular head at one end. β-Connectin (titin 2; TII), the proteolytic product of α-connectin, was also a long rod, about 0. 85μm long and 3-4nm wide without the head. It appeared that both α-and β-connectin rods consisted of two laterally associated stands, approximately 1.5nm wide.
Modeling of the dynamics of R-11 blown polyurethane foam formation

The dynamics of R-11 blown polyurethane foam formation depend on the rates of viscosity increase of the reacting mixture and R-11 evaporation, and both are controlled by the polymerization process. Detailed experiments were carried out to study the dynamics of foaming and the measurements made included the cream and rise times, the density change of the expanding foam with time, and the temperature rise during reaction. Dynamic temperature measurements at different points in the foaming mixture were also made to study the spatial variation of the temperature in the foam. The experimental results showed the rate of foaming, the final density, and the maximum temperature decreased with increasing R-11 concentration. The heat losses from the foam were also found to be significant towards the later stages of foaming when density was low. Theoretical models were developed to predict the temperature and density change with time and spatial variation of temperature in the foam due to heat losses, by considering the foaming dynamics to be either heat generation controlled or heat and mass transfer controlled. In the former, the foam was assumed to be a pseudohomogeneous phase and the approach was similar to that of Rojas, et al. (5). New features accounted for in the model were dilution of the reactant concentration due to the presence of liquid blowing agent and heat loss from the foam due to radiation. While excellent agreement between theoretical predictions and experimental results was obtained for temperature variation with time at different locations in the foam, the model gave a much sharper reduction in density with time as compared to the experimental data. In the second model, the rate of foaming was assumed to be controlled by the rate of heat and mass transfer to a single bubble in the foam. Assuming a film model for heat and mass transfer, the theoretical predictions for both temperature and density were found to be in very good agreement with experimental data.
Effect of thyroid hormone on the postnatal renal expression of NHE 8

Gattineni J, Sas D, Dagan A, Dwarakanath V, Baum M. Effect of thyroid hormone on the postnatal renal expression of NHE8. Am J Physiol Renal Physiol 294: F198–F204, 2008. First published October 31, 2007; doi:10.1152/ajprenal.00332. 2007. —We previously demonstrated that there are developmental changes in proximal tubule Na /H exchanger (NHE) activity. There is a maturational increase in postnatal brush-border membrane (BBM) vesicle NHE3 protein abundance and decrease in NHE8 protein abundance. The purpose of this study was to determine whether thyroid hormone plays a role in the rat renal maturational isoform switch from NHE8 to NHE3 and whether thyroid hormone regulates NHE8. Administration of thyroid hormone to neonatal rats, before the normal postnatal increase in serum thyroid hormone levels at 3 wk of age, resulted in a premature increase in NHE3/ -actin BBM protein abundance and mRNA abundance. Thyroid hormone also caused a premature decrease in BBM NHE8/ -actin protein abundance, whereas there was no change in mRNA expression (standardized to 28s). Rats made hypothyroid from birth were studied at 28 days, after the normal maturational increase in thyroid hormone. In these hypothyroid adult rats, the maturational increase in BBM NHE3 protein abundance and NHE3 mRNA expression was prevented. In contrast, the developmental decrease in BBM NHE8 protein abundance was prevented in hypothyroid adults, but mRNA expression was unchanged in hypothyroid rats. To determine whether the effect of thyroid hormone was due to a direct epithelial effect, we studied normal rat kidney cells in culture. We recently showed that this cell line expresses NHE8, but does not express NHE3. Thyroid hormone caused a decrease in surface expression of NHE8, determined by biotinylation, but total cellular abundance remained unchanged. NHE8 activity, measured as the sodium-dependent rate of intracellular pH recovery from an acid load, was less with thyroid treatment than control. In conclusion, thyroid hormone plays a potential role in the developmental isoform change from NHE8 to NHE3 and decreases NHE8 activity.
Topographic study of auditory event-related potentials in normal boys and boys with attention deficit disorder with hyperactivity.

Auditory evoked potentials were recorded from 19 electrode sites in 20 children with Attention Deficit Disorder with Hyperactivity and 20 normal subjects in a two-choice discrimination task. N2 and Nd were found to be significantly smaller in subjects with Attention Deficit Disorder with Hyperactivity. The N2 abnormalities are discussed in relationship to the mismatch negativity component of the orienting response, poor discrimination of salient stimuli, neurotransmitter deficiency, and theories of “arousal. ’Nd findings are related to findings from studies of cerebral blood flow in children diagnosed as having Attention Deficit Disorder with Hyperactivity. These results suggest a problem with both automatic (not under conscious control) and controlled (under voluntary control) processing in children with Attention Deficit Disorder with Hyperactivity.
Coronary Computed Tomography Angiography Based Assessment of Endothelial Shear Stress and Its Association with Atherosclerotic Plaque Distribution In-Vivo

Purpose The relationship between low endothelial shear stress (ESS) and coronary atherosclerosis is well established. ESS assessment so far depended on invasive procedures. The aim of this study was to demonstrate the relationship between ESS and coronary atherosclerosis by using non-invasive coronary computed tomography angiography (CTA) for computational fluid dynamics (CFD) simulations. Methods A total number of 7 consecutive patients with suspected coronary artery disease who received CTA and invasive angiography with IVUS analysis were included in this study. CTA examinations were performed using a dual-source scanner. These datasets were used to build a 3D mesh model. CFD calculations were performed using a validated CFD solver. The presence of plaque was assumed if the thickness of the intima-media complex exceeded 0.3 mm in IVUS. Plaque composition was derived by IVUS radiofrequency data analysis. Results Plaque was present in 32.1% of all analyzed cross-sections. Plaque prevalence was highest in areas of low ESS (49.6%) and high ESS (34.8%). In parts exposed to intermediate-low and intermediate-high ESS few plaques were found (20.0% and 24.0%) (p<0.001). Wall thickness was closely associated with local ESS. Intima-media thickness was 0.43±0.34mm in low and 0.38±0.32mm in high ESS segments. It was significantly lower when the arterial wall was exposed to intermediate ESS (0.25±0.18mm and 0.28 ± 0.20mm) (p<0.001). Fibrofatty tissue was predominately found in areas exposed to low ESS (p≤0.023). Conclusions In this study a close association of atherosclerotic plaque distribution and ESS pattern could be demonstrated in-vivo. Adding CFD analysis to coronary CTA offers the possibility to gather morphologic and physiologic data within one non-invasive examination.
Tamoxifen-induced reduction in mammographic density and breast cancer risk reduction: a nested case-control study.

BACKGROUND Mammographic breast density is a strong risk factor for breast cancer. Tamoxifen, which reduces the risk of breast cancer in women at high risk, also reduces mammographic breast density. However, it is not known if tamoxifen-induced reductions in breast density can be used to identify women who will benefit the most from prophylactic treatment with this drug. METHODS We conducted a nested case-control study within the first International Breast Cancer Intervention Study, a randomized prevention trial of tamoxifen vs placebo. Mammographic breast density was assessed visually and expressed as a percentage of the total breast area in 5% increments. Case subjects were 123 women diagnosed with breast cancer at or after their first follow-up mammogram, which took place 12-18 months after trial entry, and control subjects were 942 women without breast cancer. Multivariable logistic regression was used to adjust for other risk factors. All statistical tests were two-sided. RESULTS In the tamoxifen arm, 46% of women had a 10% or greater reduction in breast density at their 12- to 18-month mammogram. Compared with all women in the placebo group, women in the tamoxifen group who experienced a 10% or greater reduction in breast density had 63% reduction in breast cancer risk (odds ratio = 0.37, 95% confidence interval = 0.20 to 0.69, P = .002), whereas those who took tamoxifen but experienced less than a 10% reduction in breast density had no risk reduction (odds ratio = 1.13, 95% confidence interval = 0.72 to 1.77, P = .60). In the placebo arm, there was no statistically significant difference in breast cancer risk between subjects who experienced less than a 10% reduction in mammographic density and subjects who experienced a greater reduction. CONCLUSION The 12- to 18-month change in mammographic breast density is an excellent predictor of response to tamoxifen in the preventive setting.