Miracle-dz/UniFAR-FTUs huggingface dataset:
Finding Top-k Min-Cost Connected Trees in Databases

It is widely realized that the integration of database and information retrieval techniques will provide users with a wide range of high quality services. In this paper, we study processing an l-keyword query, p1, p1, . , pl, against a relational database which can be modeled as a weighted graph, G(V, E). Here V is a set of nodes (tuples) and E is a set of edges representing foreign key references between tuples. Let Vi ⊆ V be a set of nodes that contain the keyword pi. We study finding top-k minimum cost connected trees that contain at least one node in every subset Vi, and denote our problem as GST-k When k = 1, it is known as a minimum cost group Steiner tree problem which is NP-complete. We observe that the number of keywords, l, is small, and propose a novel parameterized solution, with l as a parameter, to find the optimal GST-1, in time complexity O(3ln + 2l ((l + logn)n + m)), where n and m are the numbers of nodes and edges in graph G. Our solution can handle graphs with a large number of nodes. Our GST-1 solution can be easily extended to support GST-k, which outperforms the existing GST-k solutions over both weighted undirected/directed graphs. We conducted extensive experimental studies, and report our finding.
Exploring Lexical Network Development in Second Language Learners

This study explores how neural network models can simulate word production in second language (L2) learners. A neural network was trained to simulate L2 word production using a variety of word properties related to connectionist networks (hypernymy, polysemy, concreteness, and meaningfulness). The study demonstrates that a neural network can produce words to a similar degree as L2 learners. The findings are important for theories of L2 lexical growth and production.
Folding during soft-sediment deformation

Abstract The detailed analysis of folding in rocks was in part pioneered by John Ramsay, and resulted in a range of techniques and criteria to define folds. Although folding of unlithified or ‘soft’ sediments is typically assumed to produce similar geometries to those in ‘hard rocks’, there has to date been little detailed analysis of such folds. The aim of this paper is therefore to investigate folds developed during soft-sediment deformation (SSD) by applying techniques established for the analysis of tectonic folds during hard-rock deformation (HRD). We use the Late Pleistocene Lisan Formation exposed around the Dead Sea as our case study, as the laminated lake sediments record intricacies of fold detail generated during seismically triggered slumping of mass transport deposits (MTDs) towards the depocentre of the basin. While it is frequently assumed that folds created during SSD are chaotic and form disharmonic structures, we provide analyses that show harmonic fold trains may form during slumping, although larger upright folds cannot be traced for significant distances and are more typically disharmonic. Our analysis also reveals a range of fold styles, with more competent detrital-rich layers displaying buckles (Class 1B), as well as upright Class 1A folds marked by thickened limbs. Class 1A buckle folds are generally considered to be created by flattening that overprints folds with an original Class 1B geometry. As thickened fold limbs are truncated by overlying erosive surfaces, the vertical flattening is considered to have occurred during the slump event. Different fold shapes may partially reflect variable flattening, depending on the original orientation of upright or recumbent folds, together with continued downslope-directed simple-shear deformation that modifies the fold geometry. Analysis of fold wavelength, amplitude and bed thickness allows us to plot strain contour maps, and indicates that beds defining slump folds display viscosity contrasts in the range of 50–250, which are similar to values estimated from folds created during HRD in metamorphic rocks. A range of refold patterns, similar to those established by John Ramsay in metamorphic rocks, are observed within slumps, and are truncated by the overlying sediments, indicating that they formed during a single progressive slump event rather than distinct ‘episodes’ of superimposed deformation. This study confirms that techniques developed for the analysis of folds created during HRD are equally applicable to those formed during SSD, and that resulting folds are generally indistinguishable from one another. Extreme caution should therefore be exercised when interpreting the origin of folds in the rock record where the palaeogeographical and tectonic contexts become increasingly uncertain, thereby leading to potential misidentification of folds created during SSD.
Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma

Background High-throughput sequencing (HTS) analysis of microbial communities from the respiratory airways has heavily relied on the 16S rRNA gene. Given the intrinsic limitations of this approach, airway microbiome research has focused on assessing bacterial composition during health and disease, and its variation in relation to clinical and environmental factors, or other microbiomes. Consequently, very little effort has been dedicated to describing the functional characteristics of the airway microbiota and even less to explore the microbe-host interactions. Here we present a simultaneous assessment of microbiome and host functional diversity and host-microbe interactions from the same RNA-seq experiment, while accounting for variation in clinical metadata. Methods Transcriptomic (host) and metatranscriptomic (microbiota) sequences from the nasal epithelium of 8 asthmatics and 6 healthy controls were separated in silico and mapped to available human and NCBI-NR protein reference databases. Human genes differentially expressed in asthmatics and controls were then used to infer upstream regulators involved in immune and inflammatory responses. Concomitantly, microbial genes were mapped to metabolic databases (COG, SEED, and KEGG) to infer microbial functions differentially expressed in asthmatics and controls. Finally, multivariate analysis was applied to find associations between microbiome characteristics and host upstream regulators while accounting for clinical variation. Results and Discussion Our study showed significant differences in the metabolism of microbiomes from asthmatic and non-asthmatic children for up to 25% of the functional properties tested. Enrichment analysis of 499 differentially expressed host genes for inflammatory and immune responses revealed 43 upstream regulators differentially activated in asthma. Microbial adhesion (virulence) and Proteobacteria abundance were significantly associated with variation in the expression of the upstream regulator IL1A; suggesting that microbiome characteristics modulate host inflammatory and immune systems during asthma.
Limited Access to Iodized Salt among the Poor and Disadvantaged in North 24 Parganas District of West Bengal, India

Iodine deficiency is endemic in West Bengal as evident from earlier studies. This community-based, cross-sectional descriptive study was conducted in North 24 Parganas district during August-November 2005 to assess the consumption of adequately-iodized salt and to ascertain the various factors that influence access to iodized salt. In total, 506 households selected using the multi-stage cluster-sampling technique and all 79 retail shops from where the study households buy salt were surveyed. The iodine content of salt was tested by spot iodine-testing kits. Seventy-three percent of the households consumed salt with adequate iodine content (≥15 ppm). Consumption of adequately-iodized salt was lower among rural residents [prevalence ratio (PR): 0.8, 95% confidence interval (CI) 0.7-0.9], Muslims (PR: 0.8, 95% CI 0.7-0.9), and households with monthly per-capita income of ≤US$ 10 (PR: 0.7, 95% CI 0.6-0.8). Those who heard and were aware of the risk of iodine-deficiency disorders and of the benefit of iodized salt were more likely to use appropriate salt (PR: 1.2, 95% CI 1.1-1.3). Those who were aware of the ban on non-iodized salt were more likely to consume adequately-iodized salt (PR: 1.1, 95% CI 1.01-1.3). The iodine content was higher in salt sold in sealed packets (PR: 2.9, 95% CI 1.8-4.8) and stored on shelves (PR: 1.6, 95% CI 1.3-2.0). Seventy-two percent of the salt samples from the retail shops had the iodine content of ≥15 ppm. The findings indicate that elimination of iodine deficiency will require targeting the vulnerable and poor population.
Individual-Based Models in Ecology and Ecological Risk Assessments

This chapter introduces ABMs, their construction, and the pros and cons of their use. Although relatively new, agent-based models (ABMs) have great potential for use in ecotoxicological research – their primary advantage being the realistic simulations that can be constructed and particularly their explicit handling of space and time in simulations. Examples are provided of their use in ecotoxicology primarily exemplified by different implementations of the ALMaSS system. These examples presented demonstrate how multiple stressors, landscape structure, details regarding toxicology, animal behavior, and socioeconomic effects can and should be taken into account when constructing simulations for risk assessment. Like ecological systems, in ABMs the behavior at the system level is not simply the mean of the component responses, but the sum of the often nonlinear interactions between components in the system; hence this modeling approach opens the door to implementing and testing much more realistic and holistic ecotoxicological models than are currently used.
The World Health Organization's global strategy for prevention and assessment of HIV drug resistance

Antiretroviral treatment (ART) for HIV is being scaled up rapidly in resource-limited countries. Treatment options are simplified and standardized, generally with one potent first-line regimen and one potent alternate first-line regimen recommended. Widespread HIV drug resistance (HIVDR) was initially feared, but reports from resource-limited countries suggest that initial ART programmes are as effective as in resource-rich countries, which should limit HIV drug resistance if programme effectiveness continues during scale-up. ART interruptions must be minimized to maintain viral suppression on the first-line regimen for as long as possible. Lack of availability of appropriate second-line drugs is a concern, as is the additional accumulation of resistance mutations in the absence of viral load testing to determine failure. The World Health Organization (WHO) recommends a minimum-resource strategy for prevention and assessment of HIVDR in resource-limited countries. The WHO's Global Network HIVResNet provides standardized tools, training, technical assistance, laboratory quality assurance, analysis of results and recommendations for guidelines and public health action. National strategies focus on assessments to guide immediate public health action to improve ART programme effectiveness in minimizing HIVDR and to guide regimen selection. Globally, WHO HIVResNet collects and analyses data to support evidence-based international policies and guidelines. Financial support is provided by major international organizations and technical support from HIVDR experts worldwide. As of December 2007, 25 countries were planning or implementing the strategy; seven countries report results in this supplement.
Sexual selection gradients change over time in a simultaneous hermaphrodite

Sexual selection is generally predicted to act more strongly on males than on females. The Darwin-Bateman paradigm predicts that this should also hold for hermaphrodites. However, measuring this strength of selection is less straightforward when both sexual functions are performed throughout the organism’s lifetime. Besides, quantifications of sexual selection are usually done during a short time window, while many animals store sperm and are long-lived. To explore whether the chosen time frame affects estimated measures of sexual selection, we recorded mating success and reproductive success over time, using a simultaneous hermaphrodite. Our results show that male sexual selection gradients are consistently positive. However, an individual’s female mating success seems to negatively affect its own male reproductive success, an effect that only becomes visible several weeks into the experiment, highlighting that the time frame is crucial for the quantification and interpretation of sexual selection measures, an insight that applies to any iteroparous mating system. DOI: http://dx.doi. org/10.7554/eLife.25139. 001
Novel human PDCD4 (H731) gene expressed in proliferative cells is expressed in the small duct epithelial cells of the breast as revealed by an anti‐H731 antibody

The novel gene H731 (approved name: PDCD4 (programmed cell death 4)) has been isolated as an antigen gene of the monoclonal antibody Pr‐28 which recognized a nuclear antigen in proliferating cells. The gene is homologous to the mouse gene (MA‐3/Pdcd4/A7–1) which was associated with apoptosis and was shown to suppress tumor promoter‐induced neoplastic transformation. A polyclonal antibody against H731‐protein derived from an extract of Escherichia coli transformed with an H731 expression plasmid was prepared, and the H731‐protein expression in human normal and tumor cells using the antibody was studied. The staining patterns of asynchronous cultures of human normal fibroblasts (MRC‐5) were heterogeneous but the antigen was accumulated in the nuclei at the G0 phase. On the contrary, the antigen was overproduced and localized in the cytoplasm during the cell cycle in tumor cell lines. Immunohistological studies revealed that the H731‐protein was highly expressed in bladder carcinoma and breast carcinoma tissues compared with the normal tissues so far tested. These results indicated that expression of the H731‐protein was up‐regulated or induced in the proliferative cells. Immunohistological studies also revealed that the protein was abundantly expressed in the small duct epithelial cells of the normal mammary gland.
Rehabilitation following cerebral anoxia: An assessment of 27 patients

Abstract Objectives: (1) To evaluate cognitive and emotional impairments, disability and quality-of-life for adults with cerebral anoxia institutionalized in residential care facilities. (2) To evaluate the efficacy of medication, psychotherapy, support group and therapeutic activities. Methods: Twenty-seven persons with cerebral anoxia were recruited, on average 8 years post-injury. Only 20 went through the whole study. Over three consecutive 2-month periods, they were assessed four times to evaluate: baseline observations (T1–T2), adjustment of their medication (T2–T3); and the effect of psychotherapy, support group and therapeutic activities such as physical and artistic or cultural activities usually proposed in the facilities involved (T3–T4). Examined variables at all time points were cognitive status, anxiety and depression, anosognosia, alexithymia, disability and quality-of-life. Results: All participants exhibited cognitive and emotional impairments comparable to those reported in the literature. Statistical analyses revealed good baseline stability of their condition and no significant effects of changes in medication (between T2 and T3). Conversely, following implementation of psychotherapy, support group and therapeutic activities (between T3 and T4), quality-of-life and social participation were significantly improved. Conclusion: Social participation and quality-of-life for persons instutionalized several years after cerebral anoxia were improved by psychotherapeutic and therapeutic activities.
Optimal channel probing and transmission scheduling for opportunistic spectrum access

In this study we consider optimal opportunistic spectrum access (OSA) policies for a transmitter in a multichannel wireless system, where a channel can be in one of multiple states. Each channel state is associated with either a probability of transmission success or a transmission rate. In such systems, the transmitter typically has partial information concerning the channel states, but can deduce more by probing individual channels, e.g. by sending control packets in the channels, at the expense of certain resources, e.g., energy and time. The main goal of this work is to derive optimal strategies for determining which channels to probe (in what sequence) and which channel to use for transmission. We consider two problems within this context,allthe constant data time (CDT) and the constant access time (CAT) problems. For both problems, we derive key structural properties of the corresponding optimal strategy. In particular, we show that it has a threshold structure and can be described by an index policy. We further show that the optimal CDT strategy can only take on one of three structural forms. Using these results we present a two-step lookahead CDT (CAT) strategy. This strategy is shown to be optimal for a number of cases of practical interest. We examine its performance under a class of practical channel models via numerical studies.
Influence of the Atlantic Meridional Overturning Circulation on the Northern Hemisphere Surface Temperature Response to Radiative Forcing

Many modeling studies have shown that the Atlantic meridional overturning circulation (AMOC) will weaken under increased greenhouse gas forcing, but the influence of AMOC internal variability on climate change in the context of a large initial condition ensemble has received less attention. Here, the Community Earth System Model Large Ensemble (CESM LE) is used to separate the AMOC-forced response from AMOC internal variability, and then assess their joint influence on surface warming. Similar to other models, the CESM LE projects a weakening AMOC in response to increased greenhouse gas forcing caused by freshening and decreased buoyancy fluxes in the North Atlantic. Yet if this forced response is removed using the ensemble mean, there is a positive relationship between global surface warming and AMOC strength. In other words, when the AMOC strengthens relative to the ensemble mean (i.e., weakens less), global surface warming increases relative to the ensemble mean response. This unforced surface warming occurs in northern Eurasia and in the Nordic and Barents Seas near the sea ice edge. Comparison of CESM simulations with and without a dynamic ocean shows that the unforced surface warming in the Nordic and Barents Seas results from both ocean and atmospheric circulation variability. In contrast, this comparison suggests that AMOC-associated Eurasian warming results from atmospheric circulation variability alone. In sum, the AMOC-forced response and AMOC internal variability have distinct relationships with surface temperature. Forced AMOC weakening decreases with surface warming, while unforced AMOC strengthening leads to surface warming.
Evaluation of the severity of chronic hepatitis C with 3-T1H-MR spectroscopy.

OBJECTIVE The purpose of this study was to compare the spectral characteristics of lipids, choline-containing compounds, and glutamine-glutamate complex assessed with (1)H-MR spectroscopy with the histologic findings in patients with chronic hepatitis C. SUBJECTS AND METHODS Nine healthy controls and 30 patients with biopsy-proven hepatitis C virus-related liver disease participated in this prospective study. Degree of fibrosis and histologic activity were scored according to the METAVIR classification. The percentage of involved hepatocytes was used to grade steatosis. Hepatic spectra were obtained with a 3-T spectroscopic system. Tenfold cross-validated stepwise discriminant analysis was performed to classify disease severity on the basis of the spectroscopic findings. RESULTS There was a strong correlation between (1)H-MR spectroscopically measured lipid concentration and the degree of steatosis at histologic examination (r = 0.9236, p < 0.0001). This finding enabled clear separation of groups according to degree of histologically determined steatosis. Variation in lipid concentration was consistent with the degree of steatosis (r = 0.7265, p < 0.0001) and stage of fibrosis (r = 0.8156, p < 0.0001). In univariate analysis, concentrations of both choline-containing compounds and glutamine-glutamate complex had a direct correlation with histologic grade (p < 0.0001) and degree of steatosis (p < 0.0001) but not with stage of fibrosis (p > 0.05). In multivariate analysis, the only factor independently associated with concentrations of choline-containing compounds and glutamine-glutamate complex was histologic grade. In cross-validated discriminant analysis based on choline-containing compound, glutamine-glutamate complex, and lipid resonance, 70% (21 of 30) of the histologic grade groups and 73% (22 of 30) of the steatosis groups were correctly classified. CONCLUSION Hydrogen-1 MR spectroscopy can be an alternative to liver biopsy in the evaluation of steatosis and necroinflammatory activity in liver disease but is not useful for complete evaluation of hepatic fibrosis.
Basket-Type Catheters: Diagnostic Pitfalls Caused by Deformation and Limited Coverage

Whole-chamber mapping using a 64-pole basket catheter (BC) has become a featured approach for the analysis of excitation patterns during atrial fibrillation. A flexible catheter design avoids perforation but may lead to spline bunching and influence coverage. We aim to quantify the catheter deformation and endocardial coverage in clinical situations and study the effect of catheter size and electrode arrangement using an in silico basket model. Atrial coverage and spline separation were evaluated quantitatively in an ensemble of clinical measurements. A computational model of the BC was implemented including an algorithm to adapt its shape to the atrial anatomy. Two clinically relevant mapping positions in each atrium were assessed in both clinical and simulated data. The simulation environment allowed varying both BC size and electrode arrangement. Results showed that interspline distances of more than 20 mm are common, leading to a coverage of less than 50% of the left atrial (LA) surface. In an ideal in silico scenario with variable catheter designs, a maximum coverage of 65% could be reached. As spline bunching and insufficient coverage can hardly be avoided, this has to be taken into account for interpretation of excitation patterns and development of new panoramic mapping techniques.