Miracle-dz/UniFAR-FTUs huggingface dataset:
The hydrochemistry of Lake Vostok and the potential for life in Antarctic subglacial lakes

Our understanding of Lake Vostok, the huge subglacial lake beneath the East Antarctic Ice Sheet, has improved recently through the identification of key physical and chemical interactions between the ice sheet and the lake. The north of the lake, where the overlying ice sheet is thickest, is characterized by subglacial melting, whereas freezing of lake water occurs in the south, resulting in ∼210 m of ice accretion to the underside of the ice sheet. The accreted ice contains lower concentrations of the impurities normally found in glacier ice, suggesting a net transfer of material from meltwater into the lake. The small numbers of microbes found so far within the accreted ice have DNA profiles similar to those of contemporary surface microbes. Microbiologists expect, however, that Lake Vostok, and other subglacial lakes, will harbour unique species, particularly within the deeper waters and associated sediments. The extreme environments of subglacial lakes are characterized by high pressures, low temperatures, permanent darkness, limited nutrient availability, and oxygen concentrations that are derived from the ice that provides the meltwater. Copyright © 2002 John Wiley & Sons, Ltd.
Quantitative comparison of single-cell sequencing methods using hippocampal neurons

Single-cell genomic analysis has grown rapidly in recent years and will find widespread applications in various fields of biology, including cancer biology, development, immunology, pre-implantation genetic diagnosis, and neurobiology. In this study, we amplified genomic DNA from individual hippocampal neurons using one of three single-cell DNA amplification methods (multiple annealing and looping-based amplification cycles (MALBAC), multiple displacement amplification (MDA), and GenomePlex whole genome amplification (WGA4)). We then systematically evaluated the genome coverage, GC-bias, reproducibility, and copy number variations among individual neurons. Our results showed that single-cell genome sequencing results obtained from the MALBAC and WGA4 methods are highly reproducible and have a high success rate. Chromosome-level and subchromosomal-level copy number variations among individual neurons can be detected.
T cell-dependent regulation of eotaxin in antigen-induced pulmonary eosinophila

T lymphocytes have been implicated in controlling the recruitment of eosinophils into the lung in murine models of allergic asthma. The mechanism by which T cells assist in the recruitment of eosinophils to the lung in these models is not completely understood. We hypothesized that eosinophil-active chemokines might be regulated by antigen (Ag)- induced T cell activation in vivo and thereby mediate T cell-dependent eosinophil recruitment. To test this hypothesis, we examined the effect of an anti-CD3 mAb on Ag-induced pulmonary eosinophilia and correlated this with the expression of three eosinophil-active chemokines: eotaxin, macrophage inflammatory protein (MIP)-1 alpha, and RANTES. We found that Ag-induced pulmonary eosinophilia was associated with the induction of eotaxin and MIP-1 alpha, but not RANTES mRNA. Prechallenge treatment with anti-CD3 mAb inhibited eotaxin, but not MIP-1 alpha and RANTES mRNA induction, and significantly reduced eosinophil accumulation in the lung. In addition, Ag-specific antibody responses and mast cell degranulation after Ag challenge in sensitized mice were not affected by T cell elimination, and were not sufficient to induce the expression of eotaxin and cause pulmonary eosinophilia. These findings suggest that eotaxin is one of the molecular links between Ag- specific T cell activation and the recruitment of eosinophils into the airways.
An open visualization toolkit for reverse architecting

Maintenance and evolution of complex software systems (such as large telecom embedded devices) involve activities such as reverse engineering (RE) and software visualization. Although several RE tools exist, we found their architecture hard to adapt to the domain specific requirements posed by our current practice in Nokia. We present an open architecture which allows easy prototyping of RE data exploration and visualization scenarios for a large range of domain models. We pay special attention to the visual and interactive requirements of the reverse engineering process. The article describes the basic architecture of our toolkit, compares it to the existing RE environments and present several visualizations taken from real cases.
Resurfacing shoulder arthroplasty for the treatment of severe rheumatoid arthritis

Background and purpose — There is no consensus on which type of shoulder prosthesis should be used in patients with rheumatoid arthritis (RA). We describe patients with RA who were treated with shoulder replacement, regarding patient-reported outcome, prosthesis survival, and causes of revision, and we compare outcome after resurfacing hemi-arthroplasty (RHA) and stemmed hemi-arthroplasty (SHA). Patients and methods — We used data from the national Danish Shoulder Arthroplasty Registry and included patients with RA who underwent shoulder arthroplasty in Denmark between 2006 and 2010. Patient-reported outcome was obtained 1-year postoperatively using the Western Ontario Osteoarthritis of the Shoulder index (WOOS), and rates of revision were calculated by checking revisions reported until December 2011. The patient-reported outcome of RHA was compared to that of SHA using regression analysis with adjustment for age, sex, and previous surgery. Results — During the study period, 167 patients underwent shoulder arthroplasty because of rheumatoid arthritis, 80 (48%) of whom received RHA and 34 (26%) of whom received SHA. 16 patients were treated with total stemmed shoulder arthroplasty (TSA), and 24 were treated with reverse shoulder arthroplasty (rTSA). 130 patients returned a completed questionnaire, and the total mean WOOS score was 63. The cumulative 5-year revision rate was 7%. Most revisions occurred after RHA, with a revision rate of 14%. Mean WOOS score was similar for RHA and for SHA. Interpretation — This study shows that shoulder arthroplasty, regardless of design, is a good option in terms of reducing pain and improving function in RA patients. The high revision rate in the RHA group suggests that other designs may offer better implant survival. However, this should be confirmed in larger studies.
A Personalized System for Conversational Recommendations

Searching for and making decisions about information is becoming increasingly difficult as the amount of information and number of choices increases. Recommendation systems help users find items of interest of a particular type, such as movies or restaurants, but are still somewhat awkward to use. Our solution is to take advantage of the complementary strengths of personalized recommendation systems and dialogue systems, creating personalized aides. We present a system - the ADAPTIVE PLACE ADVISOR - that treats item selection as an interactive, conversational process, with the program inquiring about item attributes and the user responding. Individual, long-term user preferences are unobtrusively obtained in the course of normal recommendation dialogues and used to direct future conversations with the same user. We present a novel user model that influences both item search and the questions asked during a conversation. We demonstrate the effectiveness of our system in significantly reducing the time and number of interactions required to find a satisfactory item, as compared to a control group of users interacting with a non-adaptive version of the system.
Immunomodulatory Effects of Balneotherapy with Hae-Un-Dae Thermal Water on Imiquimod-Induced Psoriasis-Like Murine Model

Background Balneotherapy, although not a well-established dermatological treatment, is thought to have therapeutic properties for psoriasis and is used as an alternative treatment modality throughout the world. Objective To evaluate the mechanism underlying the therapeutic immunologic effects of thermomineral water. Methods A murine model of imiquimod-induced psoriasis-like skin inflammation was used for evaluating the therapeutic effects of balneotherapy with Hae-Un-Dae hot spring mineral water. The clinical improvements were evaluated by a dermatologist. Lesional cytokines, including interleukin (IL)-17A, IL-23, and IL-22, were quantitatively measured by real-time reverse transcriptase polymerase chain reaction. Serum levels of interferon-γ, IL-4, IL-5, and IL-17A were measured by enzyme-linked immunosorbent assay. T cell proportions in the spleen were evaluated by flow cytometry, and histopathological evaluation of the skin was also performed. Results The mineral water balneotherapy group showed faster improvement in skin erythema and scales than the distilled water bathing group. A substantial reduction was observed in the lesional mRNA levels of IL-17A and IL-23 in the mineral water group. Serum levels of IL-4 and IL-5 were significantly decreased in the mineral water group but not in the distilled water group. Normalized T cell proportions were observed after bathing. Conclusion Balneotherapy showed immunomodulatory effects in a psoriasis-like murine model. Balneotherapy suppressed lesional IL-23 and IL-17A, which are important cytokines in the pathogenesis of psoriasis. These results suggest that balneotherapy can be used as an effective and safe treatment for psoriasis.
Inhibition of expression of major histocompatibility complex class II molecules in macrophages infected with Leishmania donovani occurs at the level of gene transcription via a cyclic AMP-independent mechanism

Among the important pleiotropic responses to gamma interferon (IFN-gamma) during the activation of macrophages (M phi) is the increased expression of major histocompatibility complex class II genes. In the present study, infection with Leishmania donovani was shown to inhibit in parallel the induction by IFN-gamma of H-2 A beta gene transcription, class II mRNA accumulation, and H-2 Ad protein expression in cells of the murine macrophage cell line P388D1. Treatment of P388D1 cells with either the adenylate cyclase activator cholera toxin or the protein kinase A activator N6-2'-O-dibutyryl cyclic AMP (dibutyryl cAMP) similarly inhibited the induction by IFN-gamma of class II protein expression, and in parallel with Leishmania infection, cholera toxin inhibited the induction of mRNA for the H-2 A alpha and H-2 A beta proteins. Concentrations of intracellular cAMP were significantly increased in cholera toxin-treated cells but not in leishmania-infected cells. These findings indicate that at least one mechanism by which Leishmania infection attenuates the activation of M phi by IFN-gamma involves selective, transcriptional inhibition of major histocompatibility complex class II genes via a cAMP-independent mechanism.
Discovering all most specific sentences

Data mining can be viewed, in many instances, as the task of computing a representation of a theory of a model or a database, in particular by finding a set of maximally specific sentences satisfying some property. We prove some hardness results that rule out simple approaches to solving the problem.The a priori algorithm is an algorithm that has been successfully applied to many instances of the problem. We analyze this algorithm, and prove that is optimal when the maximally specific sentences are "small". We also point out its limitations.We then present a new algorithm, the Dualize and Advance algorithm, and prove worst-case complexity bounds that are favorable in the general case. Our results use the concept of hypergraph transversals. Our analysis shows that the a priori algorithm can solve the problem of enumerating the transversals of a hypergraph, improving on previously known results in a special case. On the other hand, using results for the general case of the hypergraph transversal enumeration problem, we can show that the Dualize and Advance algorithm has worst-case running time that is sub-exponential to the output size (i.e., the number of maximally specific sentences). We further show that the problem of finding maximally specific sentences is closely related to the problem of exact learning with membership queries studied in computational learning theory.
Early Pathologic Findings of Bronchiolitis Obliterans after Allogeneic Hematopoietic Stem Cell Transplantation: A Proposal from a Case

Bronchiolitis obliterans (BO) is one of the serious, noninfectious pulmonary complications after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Early diagnosis of BO is usually difficult because patients are often asymptomatic at an initial stage of the disease and pathologic findings are available mostly at the late stages. Therefore, the diagnosis of the disease is based on the pulmonary function test using the National Institute of Health consensus criteria. Here, we report a case of slowly progressive BO. A biopsy specimen at an early stage demonstrated alveolar destruction with lymphocyte infiltration in bronchial walls and mild narrowing of bronchioles without fibrosis, those were strongly indicative of initial pathologic changes of BO. Definitive BO followed, which was proven by both clinical course and autopsy. While alloreactive lymphocytes associated with chronic graft-versus-host disease are believed to initiate BO, we present a rare case that directly implies such a scenario.
Edoxaban versus placebo, aspirin, or aspirin plus clopidogrel for stroke prevention in atrial fibrillation

Summary As non-valvular atrial fibrillation (AF) brings a risk of stroke, oral anticoagulants (OAC) are recommended. In ‘real world’ clinical practice, many patients (who may be, or perceived to be, intolerant of OACs) are either untreated or are treated with anti-platelet agents. We hypothesised that edoxaban has a better net clinical benefit (NCB, balancing the reduction in stroke risk vs increased risk of haemorrhage) than no treatment or anti-platelet agents. We performed a network meta-analysis of published data from 24 studies of 203,394 AF patients to indirectly compare edoxaban with aspirin alone, aspirin plus clopidogrel, and placebo. Edoxaban 30 mg once daily significantly reduced the risk of all stroke, ischaemic stroke and mortality compared to placebo and aspirin. Compared to aspirin plus clopidogrel, there was a lower risk of intra-cranial haemorrhage (ICH). Edoxaban 60 mg once-daily had a reduced risk of any stroke and systemic embolism compared to placebo, aspirin, and aspirin plus clopidogrel. Mortality rates for both edoxaban doses were estimated to be lower compared to any anti-platelet, and significantly lower compared to placebo. With overall reduced risk of ischemic stroke and ICH, both edoxaban doses bring a NCB of mean (SD) 1.68 (0.15) saved events per 100 patients per year compared to anti-platelet drugs in a clinical trial population. The NCB was demonstrated to be lower, at 0.77 (0.12) events saved (p< 0.01) when modeled to data from a ‘real world’ cohort of AF patients. In conclusion, edoxaban is likely to provide even better protection from stroke and ICH than placebo, aspirin alone, or aspirin plus clopidogrel in both clinical trial populations and unselected community populations. Both edoxaban doses would also bring a positive NCB compared to anti-platelet drugs or placebo/non-treatment based on ‘real world’ data. Note: The review process for this paper was fully handled by Christian Weber, Editor in Chief.
Development and implementation of a remote-sensing and in situ data-assimilating version of CMAQ for operational PM2.5 forecasting. Part 1: MODIS aerosol optical depth (AOD) data-assimilation design and testing

This two-part paper reports on the development, implementation, and improvement of a version of the Community Multi-Scale Air Quality (CMAQ) model that assimilates real-time remotely-sensed aerosol optical depth (AOD) information and ground-based PM2.5 monitor data in routine prognostic application. The model is being used by operational air quality forecasters to help guide their daily issuance of state or local-agency-based air quality alerts (e.g. action days, health advisories). Part 1 describes the development and testing of the initial assimilation capability, which was implemented offline in partnership with NASA and the Visibility Improvement State and Tribal Association of the Southeast (VISTAS) Regional Planning Organization (RPO). In the initial effort, MODIS-derived aerosol optical depth (AOD) data are input into a variational data-assimilation scheme using both the traditional Dark Target and relatively new “Deep Blue” retrieval methods. Evaluation of the developmental offline version, reported in Part 1 here, showed sufficient promise to implement the capability within the online, prognostic operational model described in Part 2. In Part 2, the addition of real-time surface PM2.5 monitoring data to improve the assimilation and an initial evaluation of the prognostic modeling system across the continental United States (CONUS) is presented. Implications: Air quality forecasts are now routinely used to understand when air pollution may reach unhealthy levels. For the first time, an operational air quality forecast model that includes the assimilation of remotely-sensed aerosol optical depth and ground based PM2.5 observations is being used. The assimilation enables quantifiable improvements in model forecast skill, which improves confidence in the accuracy of the officially-issued forecasts. This helps air quality stakeholders be more effective in taking mitigating actions (reducing power consumption, ride-sharing, etc.) and avoiding exposures that could otherwise result in more serious air quality episodes or more deleterious health effects.
Distributed Sparse Random Projections for Refinable Approximation

Consider a large-scale wireless sensor network measuring compressible data, where n distributed data values can be well-approximated using only k <g n coefficients of some known transform. We address the problem of recovering an approximation of the n data values by querying any L sensors, so that the reconstruction error is comparable to the optimal fc-term approximation. To solve this problem, we present a novel distributed algorithm based on sparse random projections, which requires no global coordination or knowledge. The key idea is that the sparsity of the random projections greatly reduces the communication cost of pre-processing the data. Our algorithm allows the collector to choose the number of sensors to query according to the desired approximation error. The reconstruction quality depends only on the number of sensors queried, enabling robust refinable approximation.
Expert testimony in a child sex abuse case: Translating memory development research

In this paper we describe a custody case that centred on allegations of child sexual abuse. A pair of preschool-aged sisters accused their biological father of various sexual acts, though their allegations were made under problematic conditions and were contradicted by other statements they made. In an affidavit written by one of us (MB), we describe the relevant memory development research in the course of presenting the court with a scientific analysis. We find compelling evidence of multiple risk factors in the way the daughters' recollections were elicited. Although the “ultimate question” of guilt is beyond our purview, our identification of risks was instrumental in the legal system's decision that the children's allegations were not valid. We put this analysis forward as an example of evidence-based testimony in which scientific findings from the memory literature can be used to frame an expert's analysis.
Multiple-Valued Computing Using Field Emission - Based Carbon Nanotube Controlled Switching

A new carbon nanotube (CNT) - based controlled switch is introduced. The new CNT device is a field emission - based device that uses field electron emission from the CNT to implement the functionality of controlled switching. To implement the field emission CNT controlled switch, four field emission CNTs that have single carbon nanotubes as the emitters were tested; two with single-walled CNT and two with multi-walled CNT. A tube with a tungsten tip was also used for comparison. The Fowler-Nordheim analysis of the DC current- voltage data provided reasonable values for the local fields at the emitters and the sizes of the emitters. It is also shown within the new implementation of the controlled switch that square- wave pulses from a single laser diode with 20 mW power and 658 nm wavelength which is focused on each emitter increased the emitted current by 5.2% with the CNT and 0.19% with the compared tungsten tip. The extension of the new device from the two-valued to the general m-valued case is introduced, and the implementation of multiple-valued Galois circuits and systems utilizing the new CNT field emission - based device is also shown. Since the controlled switch is a basic block in the design of modern digital systems, the new CNT device can have a wide range of applications in a wide variety of nano circuits.
Life strategies of fishes in European estuaries: the functional guild approach

The structure and functioning of estuarine fish assemblages have been analysed using data sets for 38 transitional waters covering all European latitudes, including NE Atlantic estuaries, Mediterranean lagoons and Scandinavian fjords. The fish species were assigned to functional guilds covering estuarine use, mode of feeding and reproductive strategy, thus describing the use made of transitional waters by fishes. The importance of estuaries as temporary biotopes (migration and nurs- ery routes) for fish species has been identified together with the predominance of feeding on the detritivorous hyperbenthos and infauna. The high incidence of protective breeders in estuaries, as a mechanism to prevent the flushing out of young, has also been identified. These findings allow the validation of the functional guild approach, emphasising its use for the understanding of the function- ing of estuaries and for their management and the protection of their ecological goods and services.
Dynamic congestion-based load balanced routing in optical burst-switched networks

In optical burst-switched networks, data loss may occur when bursts contend for network resources. There have been several proposed solutions to resolve contentions in order to minimize loss. These localized contention resolution techniques react to contention, but do not address the more fundamental problem of congestion. Hence, there is a need for network level contention avoidance using load balanced routing techniques in order to minimize the loss. In this paper, we propose two dynamic congestion-based load balanced routing techniques to avoid congestion. Our simulation results show that the proposed contention avoidance techniques improve the network utilization and reduce the packet loss probability.