Miracle-dz/UniFAR-FTUs huggingface dataset:
Subclassifying atypical squamous cells in Thin-Prep cervical cytology correlates with detection of high-risk human papillomavirus DNA.

Recent studies have proposed subclassifying ASCUS into "favor reactive" (ASFR), "not otherwise specified" (ASNOS), and "favor squamous intraepithelial lesion (SIL)" (ASFS). This study explored the reproducibility of these diagnoses with Thin-Prep cytology and their association with high-risk human papillomavirus DNA (HRHPV). Three pathologists and 1 cytotechnologist with 2 to 25 years of experience reviewed 144 Thin-Prep (Cytyc, Boxborough, MA) specimens previously diagnosed as normal, ASFR, ASNOS, ASFS, and SIL. Interobserver reproducibility was computed with the kappa statistic. The original laboratory diagnosis was compared with the presence of HRHPV types. Interobserver reproducibility for a normal or SIL diagnosis was very good (kappa = .68 and .63). Reproducibility for ASFR, ASNOS, and ASFS ranged from poor to fair (kappa = .21, .19, and .32). In a weighted analysis, kappa values for ASFR/ASNOS and ASFS/SIL were . 36 and . 62, respectively. HRHPV-positivity for preparations originally diagnosed as N, ASFR, ASNOS, ASFS, and SIL were 5.7%, 8.8%, 17.4%, 47.8%, and 54.5%, respectively. The difference in index of HRHPV for either N or ASFR and ASFS or SIL was significant (P < .001). Reproducibility for ASCUS is generally poor, but better reproducibility is obtained by combining ASFS with SIL and, to a lesser degree, ASNOS with ASFR. ASFS and SIL confer a similar index of HRHPV and merit similar management. ASFR may be managed with cytologic follow-up; but this may depend upon the individual laboratory. HPV testing, in conjunction with cytologic and biopsy follow-up, appears useful for estimating the significance of ASCUS subgroups in laboratory practice.
American Journal of Epidemiology Original Contribution Context and Sequelae of Food Insecurity in Children's Development

The authors examined the role of food insecurity in the etiology of children's cognitive and mental health problems. Data from a prospective longitudinal study of 1,116 United Kingdom families with twins (sample constructed in 1999–2000) were used to test associations among household food insecurity; income; maternal personality ; household sensitivity to children's needs; and children's cognitive, behavioral, and emotional development. Food-insecure children had lower IQs and higher levels of behavioral and emotional problems relative to their peers. After differences in household income, the personalities of children's mothers, and the sensitivity of household organization to children's needs were accounted for, food-insecure children had moderately higher levels of emotional problems relative to food-secure children (b ¼ 0.22, P ¼ 0.02). Differences in children's cognitive development were accounted for by household income, and differences in their behavioral development were accounted for by their mothers' personalities and their households' sensitivity to children's needs. Results suggest that food insecurity was associated with school-aged children's emotional problems but not with their cognitive or behavioral problems after accounting for differences in the home environments in which children were reared. Mothers' personality and household sensitivity to children's needs may present challenges to improving outcomes of children with food insecurity. Children reared in poverty experience poor health outcomes and higher-than-usual mortality as adults (1–5). This health disparity is mediated partly by cognitive, behavioral, and emotional problems that emerge in childhood and is linked to a range of adverse outcomes later in life (6–10). Developing programs to safeguard and improve children's cognitive and mental health and thereby disrupt the cycle of life-course disease and disadvantage is a public health priority. However, opportunities for intervention remain elusive , in part because of a lack of clarity over the pathways linking socioeconomic disadvantage to cognitive and mental health problems in childhood. Elevated levels of cognitive, behavioral, and emotional problems among children living in poverty have been demonstrated (11, 12). However, weak findings regarding the causal effect of household income on these dimensions of children's mental health (13–15) have led investigators to pursue more direct measures of the privations poverty imposes on children and families. Specific ''material hardships ,'' shortages of physical resources needed for healthy development, have received attention for being more prox-imal to children's health than household income and more amenable to intervention than the general state of living in poverty (16–18). Among these measures, material hardship related to food—food insecurity, …
Cost minimizing sequential punishment policies for repeat offenders

This article discusses optimal sanctions for repeat offenders. We analysed a multi-period decision problem, where the regulator’s main objectives are to block any violations of law and to minimize the costs of crime control. We conclude that, when offenders are identical and wealth constrained, the government is resource constrained, can perfectly observe illicit gains and commits to a certain policy throughout the whole planning horizon, forward-looking solution implies that cost minimizing deterrence is decreasing in the number of offenses. This analysis is relevant in case when imprisonment is not commonly used, only monetary sanctions are allowed and limited liability of offenders plays an important role. The examples are tax evasion, violations of environmental regulations and violations of competition law.
Parameters Governing Invasive Disease Propensity of Non-M1 Serotype Group A Streptococci

Group A Streptococcus (GAS) causes rare but life-threatening syndromes of necrotizing fasciitis and toxic shock-like syndrome in humans. The GAS serotype M1T1 clone has globally disseminated, and mutations in the control of virulence regulatory sensor kinase (covRS) operon correlate with severe invasive disease. Here, a cohort of non-M1 GAS was screened to determine whether mutation in covRS triggers systemic dissemination in divergent M serotypes. A GAS disease model defining parameters governing invasive propensity of differing M types is proposed. The vast majority of GAS infection is benign. Nonetheless, many divergent M types possess limited capacity to cause invasive infection. M1T1 GAS readily switch to a covRS mutant form that is neutrophil resistant and frequently associated with systemic infection. Whilst non-M1 GAS are shown in this study to less frequently accumulate covRS mutations in vivo, such mutants are isolated from invasive infections and exhibit neutrophil resistance and enhanced virulence. The reduced capacity of non-M1 GAS to switch to the hypervirulent covRS mutant form provides an explanation for the comparatively less frequent isolation of non-M1 serotypes from invasive human infections.
Genome‐wide study identifies the regulatory gene networks and signaling pathways from chondrocyte and peripheral blood monocyte of Kashin–Beck disease

This investigation was designed to unravel gene networks in Kashin–Beck disease (KBD) and better identify target genes of KBD for gene therapy development. RNA was isolated separately from cartilage and peripheral blood samples of patients with KBD and healthy controls. Agilent 44K human whole‐genome oligonucleotide microarrays were used to detect differentially expressed genes. Three significant canonical pathways and nine chondrocyte networks from chondrocytic gene expression profiles were screened using ingenuity pathway analysis (IPA), but only one network and no canonical pathways from peripheral blood monocytic gene profile were identified. Bak1, APAF‐1, CASP6, IGFBP2, Col5a2 and TGFBI extracted from significant genes that involved in chondrocytic canonical pathways and networks may have closer relationship with the etiopathogenesis of KBD. Those genes may be potential targets for gene diagnosis and treatment. Six physiological functions were predominant and unique to the chondrocytic genes, whereas two were unique to peripheral blood monocytic genes. The identified genes may represent a source of potentially novel molecular targets, which may provide a better understanding of the molecular details in KBD pathogenesis and also provide useful pathways and network maps for the future research in osteochondrosis.
A controlled study on the cognitive effect of alpha neurofeedback training in patients with major depressive disorder

Cognitive deficits are core symptoms of depression. This study aims to investigate whether neurofeedback (NF) training can improve working memory (WM) performance in patients with major depressive disorder (MDD). The NF group (n = 40) underwent eight NF sessions and was compared to a non-interventional control group (n = 20). The NF protocol aimed to increase the individual upper alpha power in the parieto-occipital area of the scalp. Main cognitive variable was WM, which was measured pre- and post- training along with other variables such as attention and executive functions. EEG was recorded in both eyes closed resting state and eyes open task-related activity, pre- and post- NF training, and pre- and post- the NF trials within each session. A power EEG analysis and an alpha asymmetry analysis were conducted at the sensor level. Frequency domain standardized low resolution tomography (sLORETA) was used to assess the effect at brain source level. Correlation analysis between the clinical/cognitive and EEG measurements was conducted at both the sensor and brain source level. The NF group showed increased performance as well as improved processing speed in a WM test after the training. The NF group showed pre-post enhancement in the upper alpha power after the training, better visible in task-related activity as compared to resting state. A current density increase appeared in the alpha band (8–12 Hz) for the NF group, localized in the subgenual anterior cingulate cortex (sgACC, BA 25). A positive correlation was found for the NF group between the improvement in processing speed and the increase of beta power at both the sensor and brain source level. These results show the effectiveness of this NF protocol in improving WM performance in patients with MDD.
Handling Skew in Multiway Joins in Parallel Processing

Handling skew is one of the major challenges in query processing. In distributed computational environments such as MapReduce, uneven distribution of the data to the servers is not desired. One of the dominant measures that we want to optimize in distributed environments is communication cost. In a MapReduce job this is the amount of data that is transferred from the mappers to the reducers. In this paper we will introduce a novel technique for handling skew when we want to compute a multiway join in one MapReduce round with minimum communication cost. This technique is actually an adaptation of the Shares algorithm [Afrati et. al, TKDE 2011].
Polyspecific pyrrolysyl-tRNA synthetases from directed evolution

Significance Pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNAPyl have emerged as ideal translation components for genetic code innovation. We found that a series of PylRS variants that were initially selected to be specific for the posttranslational modification Nε-acetyl-l-Lys displayed polyspecificity [i.e., activity with a broad range of noncanonical amino acid (ncAA) substrates]. Our structural and biochemical data indicate that the engineered tRNA synthetases can accommodate ncAA substrates in multiple binding modes. The data further suggest that in vivo selections do not produce optimally specific tRNA synthetases and that translation fidelity will become an increasingly dominant factor in expanding the genetic code far beyond 20 amino acids. Pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNAPyl have emerged as ideal translation components for genetic code innovation. Variants of the enzyme facilitate the incorporation >100 noncanonical amino acids (ncAAs) into proteins. PylRS variants were previously selected to acylate Nε-acetyl-Lys (AcK) onto tRNAPyl. Here, we examine an Nε-acetyl-lysyl-tRNA synthetase (AcKRS), which is polyspecific (i.e., active with a broad range of ncAAs) and 30-fold more efficient with Phe derivatives than it is with AcK. Structural and biochemical data reveal the molecular basis of polyspecificity in AcKRS and in a PylRS variant [iodo-phenylalanyl-tRNA synthetase (IFRS)] that displays both enhanced activity and substrate promiscuity over a chemical library of 313 ncAAs. IFRS, a product of directed evolution, has distinct binding modes for different ncAAs. These data indicate that in vivo selections do not produce optimally specific tRNA synthetases and suggest that translation fidelity will become an increasingly dominant factor in expanding the genetic code far beyond 20 amino acids.
Radioactive materials in recycled metals.

In recent years, the metal recycling industry has become increasingly aware of an unwanted component in metal scrap--radioactive material. Worldwide, there have been 35 instances where radioactive sources were unintentionally smelted in the course of recycling metal scrap. In some cases contaminated metal consumer products were distributed internationally. In at least one case, serious radiation exposures of workers and the public occurred. Radioactive material appearing in metal scrap includes sources subject to licensing under the Atomic Energy Act and also naturally occurring radioactive material. U.S. mills that have smelted a radioactive source face costs resulting from decontamination, waste disposal, and lost profits that range from 7 to 23 million U.S. dollars for each event. To solve the problem, industry and the government have jointly undertaken initiatives to increase awareness of the problem within the metal recycling industry. Radiation monitoring of recycled metal scrap is being performed increasingly by mills and, to a lesser extent, by scrap processors. The monitoring does not, however, provide 100% protection. Improvements in regulatory oversight by the government could stimulate improved accounting and control of licensed sources. However, additional government effort in this area must be reconciled with competing priorities in radiation safety and budgetary constraints. The threat of radioactive material in recycled metal scrap will continue for the foreseeable future and, thus, poses regulatory policy challenges for both developed and developing nations.
HmSearch: an efficient hamming distance query processing algorithm

Hamming distance measures the number of dimensions where two vectors have different values. In applications such as pattern recognition, information retrieval, and databases, we often need to efficiently process Hamming distance query, which retrieves vectors in a database that have no more than k Hamming distance from a given query vector. Existing work on efficient Hamming distance query processing has some of the following limitations, such as only applicable to tiny error threshold values, unable to deal with vectors where the value domain is large, or unable to attain robust performance in the presence of data skew. In this paper, we propose HmSearch, an efficient query processing method for Hamming distance queries that addresses the above-mentioned limitations. Our method is based on improved enumeration-based signatures, enhanced filtering, and the hierarchical binary filtering-and-verification. We also design an effective dimension rearrangement method to deal with data skew. Extensive experimental results demonstrate that our methods outperform state-of-the-art methods by up to two orders of magnitude.
Pulmonary and extrapulmonary acute respiratory distress syndrome are different

Acute respiratory distress syndrome (ARDS) can be derived from two pathogenetic pathways: a direct insult on lung cells (pulmonary ARDS (ARDSp)) or indirectly (extrapulmonary ARDS (ARDSexp)). This review reports and discusses differences in biochemical activation, histology, morphological aspects, respiratory mechanics and response to different ventilatory strategies between ARDSp and ARDSexp. In ARDSp the direct insult primarily affects the alveolar epithelium with a local alveolar inflammatory response while in ARDSexp the indirect insult affects the vascular endothelium by inflammatory mediators through the bloodstream. Radiological pattern in ARDSp is characterised by a prevalent alveolar consolidation while the ARDSexp by a prevalent ground-glass opacification. In ARDSp the lung elastance, while in ARDSexp the chest wall and intra-abdominal chest elastance are increased. The effects of positive end-expiratory pressure, recruitment manoeuvres and prone position are clearly greater in ARDSexp. Although these two types of acute respiratory distress syndrome have different pathogenic pathways, morphological aspects, respiratory mechanics, and different response to ventilatory strategies, at the present, is still not clear, if this distinction can really ameliorate the outcome.
A distinct group of north European Aedes vexans as determined by mitochondrial and nuclear markers

The floodwater mosquito Aedes (Aedimorphus) vexans (Meigen, 1830) (Diptera: Culicidae) is common in several areas of Sweden and is predicted to become more abundant in the wake of expected changes in precipitation and temperature caused by climate change. As well as being a nuisance, Ae. vexans can act as a vector of over 30 viruses. In the event of an outbreak of disease caused by a vector‐borne virus, knowledge of the distribution, population structure and intermixing of populations from different locations will help direct resources to target locations to prevent spread of the pathogen. The present study analysed individual Ae. vexans from eight locations throughout Sweden. Based on the mitochondrial cytochrome oxidase I (COI) marker, a subset of the analysed mosquitoes cluster apart from the other samples. Similarly, two nuclear loci were sequenced and the same phylogenetic structure observed. These results indicate that this group represents a reproductively isolated population among Ae. vexans. Comparisons with COI sequences held in the Barcode of Life Database (BoLD) for Ae. vexans from around the world show that specimens collected in Belgium and Estonia group together with the Swedish group, suggesting that this genotype is present throughout northern Europe. These results suggest there is a cryptic taxonomic unit related to Ae. vexans in northern Europe.
Atopy is a risk factor for adult asthma in urban community of Southwestern Nigeria

Rationale: Factors affecting asthma course are not clearly elucidated in urban communities in developing countries. Furthermore, the interaction between factors such as atopy, environmental exposure, urbanization, and helminthic infections in modulating asthma have not been well investigated. Objectives: To determine factors, which affect asthma in adults being evaluated at urban tertiary health center of Southwestern part of Nigeria. Materials and Methods: A random sample of 24 (12 males, 12 females) consecutive asthmatics seen in the Outpatient Pulmonary Clinic of University College Hospital of Ibadan and 27 (13 males, 14 females) age and gender-matched controls underwent evaluation, which included blood tests for eosinophils, serum IgE, allergy skin tests to eight common environmental allergens, and spirometry. The modified version of the questionnaire of the International study of Asthma and Allergies in Children (ISAAC) Phase III used by the same study group of researchers in Nigeria was used to assess the asthma symptoms. Wilcoxon sign-rank tests were used to compare eosinophil counts, percentage eosinophils, and allergic skin test between the two groups, while paired t test was used to compare spirometry variables. Results: Asthmatics had significantly more positive skin reaction to house dust mite and mould than controls (P<0.05). Total serum IgE was also significantly higher in asthmatics than in controls (mean 210 vs 60 IU/mL; P=0.003). However, no significant differences were observed in total eosinophil counts. No significant difference in the degree of intestinal helminthes infection in the two groups, which means stool parasitism was similar. FEV1 % was significantly lower in asthmatics (P=0.02) but FEV1 was similar between the two groups (P=0.02). Conclusion: The elevated levels of IgE and positive skin reactions to some of the common environmental allergens suggests an important role of atopy in the expression of asthma in this developing country's urban setting. Intestinal parasites were seen in both, control and asthma subjects, but appear not to play any role in the course of asthma, so also is the blood group, genotype and G6PD status.
Globalization, economic policy and employment: Poverty and gender implications

When we speak of the impact of globalization on national and local economies, those economies are actually composed of a wide variety of individuals, each class of whom will be effected differently by large-scale economic forces. In this paper, produced for the U.N.'s International Labour Office, PERI Associate Director James Heintz demonstrates how global labor markets are segmented by gender and how any analysis of the impact of macroeconomic policies on growth, employment and poverty reduction needs to be undertaken with this segmentation in mind. Specifically, Heintz addresses how macroeconomic policies differentially effect women's and men's employment, looking at monetary policy, trade policy, exchange rate regimes and public sector restructuring. Heintz brings his findings together in recommendations for an alternative policy framework of employment-centered, poverty-reducing development.
Modular interpreters for the masses: implicit context propagation using object algebras

Modular interpreters have the potential to achieve component-based language development: instead of writing language interpreters from scratch, they can be assembled from reusable, semantic building blocks. Unfortunately, traditional language interpreters are hard to extend because different language constructs may require different interpreter signatures. For instance, arithmetic interpreters produce a value without any context information, whereas binding constructs require an additional environment. In this paper, we present a practical solution to this problem based on implicit context propagation. By structuring denotational-style interpreters as Object Algebras, base interpreters can be retroactively lifted into new interpreters that have an extended signature. The additional parameters are implicitly propagated behind the scenes, through the evaluation of the base interpreter. Interpreter lifting enables a flexible style of component-based language development. The technique works in mainstream object-oriented languages, does not sacrifice type safety or separate compilation, and can be easily automated. We illustrate implicit context propagation using a modular definition of Featherweight Java and its extension to support side-effects.