Miracle-dz/UniFAR-FTUs huggingface dataset:
Costs of detection and treatment of cervical cancer, cervical dysplasia and genital warts in the UK

ABSTRACT Objective: Infection with human Papillomavirus (HPV) is a necessary cause of cervical cancer (CC) and genital warts (GW). HPV vaccination studies have shown excellent efficacy against HPV-induced lesions. To assess the cost-effectiveness of a HPV quadrivalent (6, 11, 16 and 18) vaccine it is necessary to estimate the costs of managing current levels of HPV-related diseases. This study estimates the annual 2003 expenditures in the UK for CC screening, follow-up of abnormal findings, CC treatment and GW treatment. Design and methods: CC screening programmes provided the annual number of screening tests, their results and use of colposcopy procedures in women with abnormal findings. Incident CC cases and hospital admissions for CC in 2003 were used to estimate CC costs. Health Protection Agency data provided the annual number of new, recurrent or persistent cases of GW treated in Genitourinary Medicine (GUM) clinics. Treatment patterns for managing GW were estimated by GUM clinicians. The annual physician visits, tests, procedures, hospital admissions and topical genital wart medications were costed to estimate the total annual expenditures for CC and GW. Results: There were 4.8 million screening tests and 230 303 colposcopy procedures. Estimated costs for screening, management of abnormal and inadequate findings were £138.5 million. Annual management costs for incident and prevalent CC cases were £46.8 million. There were an estimated 76 457 incident and 55 657 recurrent/persistent GW cases in 2003. The costs for managing these cases were approximately £22.4 million. Total annual estimated costs for CC screening, management and treatment of GW were £208 million and ranged from £186.9 to £214 million based upon sensitivity analyses. Conclusions: The direct medical costs for the NHS associated with detection and management of CC, cervical dysplasia and treatment of GW in the UK are substantial. These medical costs are invaluable for future cost-effectiveness analyses of a quadrivalent HPV vaccine programme.
Automatic labeling of MR brain images by hierarchical learning of atlas forests.

PURPOSE Automatic brain image labeling is highly demanded in the field of medical image analysis. Multiatlas-based approaches are widely used due to their simplicity and robustness in applications. Also, random forest technique is recognized as an efficient method for labeling, although there are several existing limitations. In this paper, the authors intend to address those limitations by proposing a novel framework based on the hierarchical learning of atlas forests. METHODS Their proposed framework aims to train a hierarchy of forests to better correlate voxels in the MR images with their corresponding labels. There are two specific novel strategies for improving brain image labeling. First, different from the conventional ways of using a single level of random forests for brain labeling, the authors design a hierarchical structure to incorporate multiple levels of forests. In particular, each atlas forest in the bottom level is trained in accordance with each individual atlas, and then the bottom-level forests are clustered based on their capabilities in labeling. For each clustered group, the authors retrain a new representative forest in the higher level by using all atlases associated with the lower-level atlas forests in the current group, as well as the tentative label maps yielded from the lower level. This clustering and retraining procedure is conducted iteratively to yield a hierarchical structure of forests. Second, in the testing stage, the authors also present a novel atlas forest selection method to determine an optimal set of atlas forests from the constructed hierarchical structure (by disabling those nonoptimal forests) for accurately labeling the test image. RESULTS For validating their proposed framework, the authors evaluate it on the public datasets, including Alzheimer's disease neuroimaging initiative, Internet brain segmentation repository, and LONI LPBA40. The authors compare the results with the conventional approaches. The experiments show that the use of the two novel strategies can significantly improve the labeling performance. Note that when more levels are constructed in the hierarchy, the labeling performance can be further improved, but more computational time will be also required. CONCLUSIONS The authors have proposed a novel multiatlas-based framework for automatic and accurate labeling of brain anatomies, which can achieve accurate labeling results for MR brain images.
Ciona intestinalis: Chordate development made simple

Thanks to their transparent and rapidly developing mosaic embryos, ascidians (or sea squirts) have been a model system for embryological studies for over a century. Recently, ascidians have entered the postgenomic era, with the sequencing of the Ciona intestinalis genome and the accumulation of molecular resources that rival those available for fruit flies and mice. One strength of ascidians as a model system is their close similarity to vertebrates. Literature reporting molecular homologies between vertebrate and ascidian tissues has flourished over the past 15 years, since the first ascidian genes were cloned. However, it should not be forgotten that ascidians diverged from the lineage leading to vertebrates over 500 million years ago. Here, we review the main similarities and differences so far identified, at the molecular level, between ascidian and vertebrate tissues and discuss the evolution of the compact ascidian genome. Developmental Dynamics 233:1–19, 2005. © 2005 Wiley‐Liss, Inc.
Arterial input function and gray matter cerebral blood volume measurements in children

To investigate how arterial input functions (AIFs) vary with age in children and compare the use of individual and population AIFs for calculating gray matter CBV values. Quantitative measures of cerebral blood volume (CBV) using dynamic susceptibility contrast (DSC) magnetic resonance imaging (MRI) require measurement of an AIF. AIFs are affected by numerous factors including patient age. Few data presenting AIFs in the pediatric population exists.
Ontology Similarity Measure and Ontology Mapping Via Fast Ranking Method

By analyzing the fast algorithm for learning large scale preference relations, we propose the fast algorithm for ontology similarity measure and ontology mapping. Via the ranking learning algorithm, the ontology graph is mapped into a line consists of real numbers. The similarity between two concepts then can be measured by comparing the difference between their corresponding real numbers. The new algorithm has lower compute complexity and two experimental results show that the proposed algorithm has high accuracy and efficiency both on ontology similarity calculation and ontology mapping. Some issues are discussed in the last section as further works.
Chondroitin sulphation patterns in synovial fluid in osteoarthritis subsets

OBJECTIVES To determine concentrations of chondroitin sulphate (CS) disaccharides in knee synovial fluid (SF) from normal subjects and patients with osteoarthritis (OA) or rheumatoid arthritis (RA), to test whether these variables differ between different diseases and subsets of OA. METHODS OA was subdivided into large joint OA (LJOA), nodal generalised OA (NGOA), and OA with calcium pyrophosphate crystal deposition (CPA), with 25, 9, and 11 people in each subset respectively. The SF of 13 normal subjects was also volunteered for analysis along with 15 RA patients. Clinical assessment of inflammation (0–6) was undertaken on OA and RA knees. Concentrations of unsaturated CS disaccharides Δdi6S and Δdi4S were measured by capillary zone electrophoresis. RESULTS Concentrations of Δdi6S were lower in RA (5.90 ng/ml) and OA (13.24 ng/ml) fluids compared with normal (21.0 ng/ml) but no significant differences were seen between disease and normal fluids for Δdi4S (about 4–6 ng/ml). The ratio of Δdi6S:Δdi4S were RA<OA<normal subjects (p<0.001 for all comparisons). The disaccharide concentration values along with the ratios are below. Higher Δdi6S:Δdi4S ratios were obtained for LJOA and CPA compared with NGOA. Uninflamed knees had lower concentrations of Δdi6S than inflamed knees (p<0.01). In patients with bilateral samples, there were strong correlations between right and left knees for all SF variables. CONCLUSIONS Altered ratios of CS sulphation patterns occur in OA and within OA subsets. These further justify considering NGOA as a subset with a different aetiopathogenesis.
Analysis of Serum Haptoglobin Fucosylation in Hepatocellular Carcinoma and Liver Cirrhosis of Different Etiologies

We have developed herein a quantitative mass spectrometry-based approach to analyze the etiology-related alterations in fucosylation degree of serum haptoglobin in patients with liver cirrhosis and hepatocellular carcinoma (HCC). The three most common etiologies, including infection with hepatitis B virus (HBV), infection with hepatitis C virus (HCV), and heavy alcohol consumption (ALC), were investigated. Only 10 μL of serum was used in this assay in which haptoglobin was immunoprecipitated using a monoclonal antibody. The N-glycans of haptoglobin were released with PNGase F, desialylated, and permethylated prior to MALDI-QIT-TOF MS analysis. In total, N-glycan profiles derived from 104 individual patient samples were quantified (14 healthy controls, 40 cirrhosis, and 50 HCCs). A unique pattern of bifucosylated tetra-antennary glycan, with both core and antennary fucosylation, was identified in HCC patients. Quantitative analysis indicated that the increased fucosylation degree was highly associated with HBV- and ALC-related HCC patients compared to that of the corresponding cirrhosis patients. Notably, the bifucosylation degree was distinctly increased in HCC patients versus that in cirrhosis of all etiologies. The elevated bifucosylation degree of haptoglobin can discriminate early stage HCC patients from cirrhosis in each etiologic category, which may be used to provide a potential marker for early detection and to predict HCC in patients with cirrhosis.
[Features of chronic myeloid leukemia at diagnosis. Study of a series of 134 cases].

PURPOSE To analyse the clinico-biological features of 134 patients with chronic myelogenous leukaemia (CML) at presentation. MATERIAL AND METHODS The series is comprised of 134 patients from the Asturias Central Hospital and other hospital of the region, diagnosed of CML with conventional criteria between 1970 and 1989. A retrospective study was carried out revising the clinical records and the clinico-biological data at diagnosis. Cytogenetic studies were available in 62 cases. The statistical analysis was based upon descriptive statistics and comparison of means and proportions by the chi square and Student's tests. Univariate study was also performed for several variables. RESULTS The mean age of the group was 50 years, ranging between 2 and 81. The M/F ratio was 76/58. The commonest symptoms at onset were those secondary to hypermetabolism and splenomegaly, 8% of the patients being asymptomatic. Splenomegaly was present in 73.8% of the patients and hepatomegaly in 37.6%. The median white cell count was 132 x 10(9)/L. Absolute basophilia and eosinophilia were seen in 83% and 78% of the cases, respectively. Anaemia was found in 47.4% of the patients, usually mild, and 39% of them had nucleated red cells in peripheral blood. The median platelet count was 400 x 10(9)/L. Thrombocytosis was found in 48% of the cases, while 11% had thrombocytopenia. The mean number of blast cells in the bone marrow was 1.72%. The histopathologic study of the bone marrow revealed decreased red cells in 94.5% of the patients and decreased megakaryocytes in 29.5%; these last were increased in 50% of the patients. Increased reticulin fibres were found in 38.5% of the bone marrow samples. In addition to the Ph' chromosome, which was present in 51 patients, chromosomal abnormalities were seen in 15.6% of the cases in the chronic phase and in 69.2% in the terminal stages of the disease. Positive correlation could be established between the white cell count and the size of spleen (p < 0.001) and liver (p < 0.05), and there was a negative correlation between white blood cell count and haemoglobin rate and platelet count (p < 0.05 for both). CONCLUSIONS (1) The analysis of this series shows that the CML cases in this region have similar characteristics to those in other western world communities (2). The mean age of this group is somewhat higher than in other series, which should be re-evaluated after discarding the Ph'-negative cases. (3) There seems to be positive correlation between leucocyte count and spleen and liver enlargement, and negative correlation between leucocyte count and haemoglobin and platelet count.
The Iterated Prisoner's Dilemma on a Cycle

Pavlov, a well-known strategy in game theory, has been shown to have some advantages in the Iterated Prisoner's Dilemma (IPD) game. However, this strategy can be exploited by inveterate defectors. We modify this strategy to mitigate the exploitation. We call the resulting strategy Rational Pavlov. This has a parameter p which measures the "degree of forgiveness" of the players. We study the evolution of cooperation in the IPD game, when n players are arranged in a cycle, and all play this strategy. We examine the effect of varying p on the convergence rate and prove that the convergence rate is fast, O(n log n) time, for high values of p. We also prove that the convergence rate is exponentially slow in n for small enough p. Our analysis leaves a gap in the range of p, but simulations suggest that there is, in fact, a sharp phase transition.
Continuing rising trend in oesophageal adenocarcinoma

Our study provides an update of the incidence of oesophageal cancer in the West Midland region of England and Wales from 1992–96. A total of 2,671 cases of oesophageal cancer were identified during the 5‐year study period, with an age‐standardised annual incidence (ASR) of 5.24 per 100,000 (95% CI: 5.02, 5.45). Similar numbers of adenocarcinoma and squamous cell carcinoma were found. Only 152 (5.6%) had no histology. There was a 5‐fold difference in age‐standardised annual incidence rates between males and females for adenocarcinoma of oesophagus, but no gender difference for squamous cell carcinoma. The parallel but higher ASR in males compared to females for adenocarcinoma of both oesophagus and cardia merits further investigation. The similarities in the patterns of age‐ and sex‐specific rates and in the socioeconomic profiles could indicate a common aetiology for adenocarcinoma of oesophagus and gastric cardia. Quality control in Cancer Registries needs to focus on the accuracy and consistency of subsite classification to ensure that trends in incidence are identified. In the absence of accurate subsite classification of stomach cancers, the proportions of adenocarcinoma and squamous cell carcinoma of oesophagus (or the absolute rate of adenocarcinoma of oesophagus) may provide a useful tool in indicating whether adenocarcinoma of gastric cardia is likely to be increasing in incidence. © 2002 Wiley‐Liss, Inc.
Tumor protein D52 represents a negative regulator of ATM protein levels

Tumor protein D52 (TPD52) is a coiled-coil motif bearing hydrophilic polypeptide known to be overexpressed in cancers of diverse cellular origins. Increased TPD52 expression is associated with increased proliferation and invasive capacity in different cell types. Recent studies have reported a correlation between TPD52 transcript levels and G2 chromosomal radiosensitivity in lymphocytes of women at risk of hereditary breast cancer, and that TPD52 knockdown significantly reduced the radiation sensitivity of multiple cancer cell lines. In this study, we investigated possible roles for TPD52 in DNA damage response, and found that increased TPD52 expression in breast cancer and TPD52-expressing BALB/c 3T3 cells compromised ATM-mediated cellular responses to DNA double-strand breaks induced by γ-ray irradiation, which was associated with downregulation of steady-state ATM protein, but not transcript levels, regardless of irradiation status. TPD52-expressing 3T3 cells also showed significantly increased radiation sensitivity compared with vector cells evaluated by clonogenic assays. Furthermore, direct interactions between exogenous and endogenous ATM and TPD52 were detected by GST pull-down and co-immunoprecipitation assays. We also identified the interaction domains involved in this binding as TPD52 residues 111–131, and ATM residues 1–245 and 772–1102. Taken together, our results suggest that TPD52 may represent a novel negative regulator of ATM protein levels.
New Evaluation of the Electronically Activated Recorder (EAR): Obtrusiveness, Compliance, and Participant Self-selection Effects

The Electronically Activated Recorder (EAR) is a method for collecting periodic brief audio snippets of participants’ daily lives using a portable recording device. The EAR can potentially intrude into people’s privacy, alter their natural behavior, and introduce self-selection biases greater than in other types of social science methods. Previous research (Mehl and Holleran, 2007, hereafter M&H) has shown that participant non-compliance with, and perceived obtrusiveness of, an EAR protocol are both low. However, these questions have not been addressed in jurisdictions that require the consent of all parties to recording conversations. This EAR study required participants to wear a button bearing a microphone icon and the words “This conversation may be recorded” to comply with California’s all-party consent law. Results revealed self-reported obtrusiveness and non-compliance were actually lower in the present study than in the M&H study. Behaviorally assessed non-compliance did not differ between the two studies. Participants in the present study talked more about being in the study than participants in the M&H study, but such talk still comprised <2% of sampled conversations. Another potential problem with the EAR, participant self-selection bias, was addressed by comparing the EAR volunteers’ HEXACO personality dimensions to a non-volunteer sample drawn from the same student population. EAR volunteers were significantly and moderately higher in Conscientiousness, and lower in Emotionality, than non-volunteers. In conclusion, the EAR method can be successfully implemented in at least one all-party consent state (California). Interested researchers are encouraged to review this procedure with their own legal counsel.
Imaging different components of a tectonic tremor sequence in southwestern Japan using an automatic statistical detection and location method

In this study, we demonstrate the capability of an automatic network-based detection and location method to extract and analyse different components of tectonic tremor activity by analysing a 9-day energetic tectonic tremor sequence occurring at the downdip extension of the subducting slab in southwestern Japan. The applied method exploits the coherency of multiscale, frequency-selective characteristics of non-stationary signals recorded across the seismic network. Use of different characteristic functions, in the signal processing step of the method, allows to extract and locate the sources of short-duration impulsive signal transients associated with low-frequency earthquakes and of longer-duration energy transients during the tectonic tremor sequence. Frequency-dependent characteristic functions, based on higher-order statistics’ properties of the seismic signals, are used for the detection and location of low-frequency earthquakes. This allows extracting a more complete ( ∼ 6.5 times more events) and time-resolved catalogue of low-frequency earthquakes than the routine catalogue provided by the Japan Meteorological Agency. As such, this catalogue allows resolving the space–time evolution of the low-frequency earthquakes activity in great detail, unravelling spatial and temporal clustering, modulation in response to tide, and different
Robust Adaptive Fuzzy Tracking Control for Pure-Feedback Stochastic Nonlinear Systems With Input Constraints

This paper is concerned with the problem of adaptive fuzzy tracking control for a class of pure-feedback stochastic nonlinear systems with input saturation. To overcome the design difficulty from nondifferential saturation nonlinearity, a smooth nonlinear function of the control input signal is first introduced to approximate the saturation function; then, an adaptive fuzzy tracking controller based on the mean-value theorem is constructed by using backstepping technique. The proposed adaptive fuzzy controller guarantees that all signals in the closed-loop system are bounded in probability and the system output eventually converges to a small neighborhood of the desired reference signal in the sense of mean quartic value. Simulation results further illustrate the effectiveness of the proposed control scheme.
Extinction: bad genes or bad luck?

Extinctionofspecies and highertaxa is generally seenas aconstructive force in evolution because it is assumedthat the better adaoted oreanisms are most likelv to survive. It is possible, however, that most extinktion is-non-selective and thit changes observed in the taxonomic composition of the biota are the result of random effects. Two scenarios for non-selective exiinction are evaluated: one uses a time homogeneous birth-deathmodel andthe otherpostulates intermittenf catastrophic extermination of large numbers of species. In the present state of knowledge, neither scenana is mathematically plausible. This may be because extinction is, in fact, selective or it may be that our estimates of past diversities and evolutionary turnover rates are faulty. If extinction is selective, the time homogeneous model suggests that trilobites had species durations 14 to 28 percent shorter than normal for Paleozoic manne invertebrates.
Variability of the Ratio of Alfalfa to Grass Reference Evapotranspiration under Semiarid Climate

Crop evapotranspiration estimation is critical for sustainable water management under the semiarid and arid climate in New Mexico. While irrigation scheduling is based on daily evapotranspiration through the two step approach, reference evapotranspiration and crop coefficients should be determined with accuracy. The utilization of grass reference evapotranspiration (ETo) or alfalfa reference evapotranspiration (ETr) and the conversion from one to the other calls for an understanding of the relationship between ETr and ETo. The objectives of this study were to develop the ratio of ETr to ETo values (Kr) and to determine the variability of Kr during the year for six locations across the State of New Mexico (USA). The results showed long term annual Kr values to vary from 1.28 to 1.45 and the coefficient of determination varied from 0.96 to 0.98. Kr value decreases from January to July and increases from August to December and was at its lowest Kr value at the peak daily reference evapotranspiration. Annual average Kr values were 1.31, 1.38, 1.43, 1.38, 1.38 and 1.48 at Alcalde, Fabian Garcia, Farmington, Leyendecker, Las Cruces and Tucumcari locations and the growing season average Kr values were 1.24, 1.32, 1.38, 1.31, 1.32 and 1.42 at the respective locations. The strong correlation between ETr and ETo allows the conversion of the grass reference evapotranspiration to alfalfa reference evapotranspiration and vice versa however, caution should be taken when using the crop coefficient values to convert either ETo or ETr to actual crop evapotranspiration for irrigation scheduling and water management.