Miracle-dz/UniFAR-FTUs huggingface dataset:
Parapatric subspecies of Macaca assamensis show a marginal overlap in their predicted potential distribution: Some elaborations for modern conservation management

Abstract Phylogenetic niche conservatism implies that sister taxa will have similar niches, although the niches of disjunct subspecies may evolve differently. This study uses Macaca assamensis, subspecies assamensis and pelops, to investigate the similarities of realized climatic niches of two disjunct subspecies (separated by the Brahmaputra River) along with a similarity analysis of their respective regions’ climate. Modeled distributions were used to quantify their potential distribution under current and future climate scenarios. The climatic similarity between regions of each subspecies was tested with principal component analysis (PCA), and the realized climatic niche overlap between two subspecies was tested with a multivariate analysis of variance (MANOVA) on a subset of the least correlated variables out of 24 publicly available topo‐bioclimatic variables. Tukey's honest significance difference (HSD) was used to test the range differences (on all 24 variables) between subspecies. The potential distribution of both taxa in the current climate and projected future climate was model‐predicted using MaxEnt and Random Forest. We found significantly different climatic ranges for 21 predictors (HSD; p < 0.05) for the two subspecies, significantly different climatic conditions for their regions (using PCA; p < 0.001), and significantly different realized climatic niches for the two subspecies (MANOVA; p < 0.001). The distribution models generated a larger potential area than the currently known distributions. Although literature show that the Brahmaputra River is an effective dispersal barrier, we found some of the neighboring geographic range for both subspecies appears to be potentially suitable for the other taxon. The projected future potential areas indicate that some parts of the currently occupied geography, mostly southern parts, may become climatically unsuitable, whereas other new geographical areas may become suitable. Most of these new potential areas will be toward the north where higher and fragmented mountains, which has conservation implications.
A vanishing theorem for twisted Alexander polynomials with applications to symplectic 4-manifolds

In this paper we show that given any 3-manifold N and any non-fibered class in H^1(N;Z) there exists a representation such that the corresponding twisted Alexander polynomial is zero. This is obtained by extending earlier work of the authors, together with results of Agol and Wise on separability of 3-manifold groups. This result allows us to completely classify symplectic 4-manifolds with a free circle action, and to determine their symplectic cones.
Targeting Melanoma with Dual Phosphoinositide 3-Kinase/Mammalian Target of Rapamycin Inhibitors

Phosphoinositide 3-kinase (PI3K)/protein kinase B/Akt and Ras/mitogen-activated protein kinase pathways are often constitutively activated in melanoma and have thus been considered as promising drug targets. Exposure of melanoma cells to NVP-BAG956, NVP-BBD130, and NVP-BEZ235, a series of novel, potent, and stable dual PI3K/mammalian target of rapamycin (mTOR) inhibitors, resulted in complete G1 growth arrest, reduction of cyclin D1, and increased levels of p27KIP1, but negligible apoptosis. In contrast, treatment of melanoma with the pan-class I PI3K inhibitor ZSTK474 or the mTORC1 inhibitor rapamycin resulted only in minor reduction of cell proliferation. In a syngeneic B16 mouse melanoma tumor model, orally administered NVP-BBD130 and NVP-BEZ235 efficiently attenuated tumor growth at primary and lymph node metastatic sites with no obvious toxicity. Metastatic melanoma in inhibitor-treated mice displayed reduced numbers of proliferating and significantly smaller tumor cells. In addition, neovascularization was blocked and tumoral necrosis increased when compared with vehicle-treated mice. In conclusion, compounds targeting PI3K and mTOR simultaneously were advantageous to attenuate melanoma growth and they develop their potential by targeting tumor growth directly, and indirectly via their interference with angiogenesis. Based on the above results, NVP-BEZ235, which has entered phase I/II clinical trials in patients with advanced solid tumors, has a potential in metastatic melanoma therapy. (Mol Cancer Res 2009;7(4):601–13)
Pessimism reduction in static timing analysis using interdependent setup and hold times

A methodology is proposed for interdependent setup time and hold time characterization of sequential circuits. Integrating the methodology into an industrial sign-off static timing analysis tool is described. The proposed methodology prevents optimism and reduces unnecessary pessimism, both of which exist due to independent characterization. Furthermore, the tradeoff between interdependent setup and hold times is exploited to significantly reduce slack violations. These benefits are validated using industrial circuits and tools
Patients’ adherence-related beliefs about methotrexate: a qualitative study of the role of written patient information

Objectives Methotrexate is effective in treating inflammatory arthritis, but both underadherence and overadherence can put patients at risk. Patients may fail to adhere due to practicalities including the unusual weekly dosing regimen, but medication beliefs also play a role. This study explored how both beliefs about necessity and concerns about methotrexate become established in patients with inflammatory arthritis and how patients use information in managing their beliefs and concerns. Design Semistructured interviews were conducted with patients taking oral methotrexate for inflammatory arthritis. Interviews were transcribed verbatim and analysed thematically. Setting Participants were recruited from a single Trust in the East Midlands. Participants Fifteen patients (4 male, 11 female) with inflammatory arthritis. Results Methotrexate was commonly prescribed at the time of diagnosis; at this point, experience of illness was influential for beliefs about medication necessity. Following prescription, patients absorbed information from written and verbal sources which reinforced beliefs about necessity but also raised concerns, including fear of side effects. Over time, beliefs were modified on the basis of personal experience, particularly of medication effectiveness and side effects. Some patients described tensions and dissonance in their beliefs and experiences of methotrexate, which put them at risk of non-adherence. Patients used information-seeking and information-avoidance as strategies to resolve these tensions. The available information did little to help suppress dissonance and sometimes exacerbated it. Conclusions Patients’ experiences of coming to terms with taking methotrexate are complex, and their experiences of dissonance are particularly problematic. Experiences might be improved by supporting patients to assess necessity (particularly in the presence of side effects) and by providing information to moderate unnecessary concerns. Improving recording and sharing of monitoring results may be one way to meet these needs.
The Infinite Markov Model

We present a nonparametric Bayesian method of estimating variable order Markov processes up to a theoretically infinite order. By extending a stick-breaking prior, which is usually defined on a unit interval, "vertically" to the trees of infinite depth associated with a hierarchical Chinese restaurant process, our model directly infers the hidden orders of Markov dependencies from which each symbol originated. Experiments on character and word sequences in natural language showed that the model has a comparative performance with an exponentially large full-order model, while computationally much efficient in both time and space. We expect that this basic model will also extend to the variable order hierarchical clustering of general data.
Drosophila melanogaster-Based Screening for Multihost Virulence Factors of Pseudomonas aeruginosa PA14 and Identification of a Virulence-Attenuating Factor, HudA

ABSTRACT Pseudomonas aeruginosa is an important opportunistic human pathogen that interacts with phylogenetically diverse nonmammalian hosts, including plants, nematodes, and insects. Here, we exploited the P. aeruginosa-induced killing of the fruit fly Drosophila melanogaster as an assay system to screen for virulence-attenuated mutants of P. aeruginosa PA14. Fifteen nonredundant mutants were isolated from 4,018 random transposon (TnphoA) insertion clones, and 13 out of them (86.7%) displayed significantly reduced virulence in a murine peritonitis model as well. The TnphoA insertion sites of the 15 mutants were determined; already known virulence genes (dsbA, pvdI, fhlB, pilF, and wspF) and new virulence genes such as PA0253 (hudR), PA0369, PA2077, PA0272, PA2113, PA2965 (fabF1), and PA2002 were identified; one insertion was located at the intergenic region between PA1928 and PA1929; and the other two insertions were located in the genes (PA14_35740 and PA14_36000) within a putative genomic island, indicating a potential pathogenicity island of PA14. Further characterization of hudR, a virulence gene which encodes a MarR/SlyA family transcription factor, revealed that elevated expression of PA0254 (hudA [homologous to UbiD]) was necessary and sufficient for the virulence attenuation of the hudR mutant. The HudR protein repressed the hudAR operon by directly binding to its upstream promoter region. Collectively, these results validate the relevance of the D. melanogaster model for the high-throughput identification of new virulence factors involved in the multihost pathogenesis of P. aeruginosa.
On Hyperspectral Classification in the Compressed Domain

In this paper, we study the problem of hyperspectral pixel classification based on the recently proposed architectures for compressive whisk-broom hyperspectral imagers without the need to reconstruct the complete data cube. A clear advantage of classification in the compressed domain is its suitability for real-time on-site processing of the sensed data. Moreover, it is assumed that the training process also takes place in the compressed domain, thus, isolating the classification unit from the recovery unit at the receiver's side. We show that, perhaps surprisingly, using distinct measurement matrices for different pixels results in more accuracy of the learned classifier and consistent classification performance, supporting the role of information diversity in learning.
Relapse of aplastic anaemia after immunosuppressive treatment: a report from the European Bone Marrow Transplantation Group SAA Working Party

Summary This study was designed to determine the incidence of relapse and factors predictive for relapse in 719 patients with severe aplastic anaemia (SAA) after immunosuppressive treatment (IS). Patients developing myelodysplasia or acute leukaemia after IS, and patients receiving a transplant, were excluded from this analysis. Response was defined as reaching complete independence from transfusions, relapse was defined as becoming again transfusion dependent. This criteria was validated by similar figures when using other ‘relapse criteria’ such as drop in neutrophil or platelet counts.
THE DOSE‐RESPONSE RELATIONSHIP OF TUMORIGENESIS BY ULTRAVIOLET RADIATION OF 254 nm

Abstract— Groups of albino hairless mice, Skh‐hrl, were exposed daily to UVC radiation from low pressure Hg arcs (Philips TUV 40W). These lamps emit predominantly radiation of 254 nm. Three groups of animals were used in the experiments, each receiving a different daily dose.
Acute effects of the very low carbohydrate diet on sleep indices

Abstract Objective: We compared the effect of short-term consumption of a very low carbohydrate (VLC) diet over 48 h to a control mixed diet on sleep indices in healthy, non-obese men. Design: This study employed a repeated-measure design where subjects were given isocaloric (2400 kcal) diets and matching evening test meals (4 h before usual bed-time), which were either mixed low-fat, high carbohydrate (15.5%, 12.5% and 72% of energy from protein, fat and carbohydrate, respectively) or VLC (38%, 61% and < 1% of energy from protein, fat and carbohydrate, respectively). Polysomnographic testing was performed on the familiarization and control night, 4 h after the first VLC test meal (acute phase) and 48 h (ketosis phase) following commencement of the VLC diet. Subjects: Fourteen healthy, non-obese men (aged 18–35 years; body mass index 23.4 ± 1.9 kg/m2) who were good sleepers took part in the study. Measurement: Objective sleep was recorded using a computerized sleep system. Urine ketone level was monitored with reagent strips before the evening test meals and at bed-time on the control night, during the VLC acute and ketosis phases. Blood glucose level was measured with a glucometer before the evening test meal until 120 min following the meal. Hunger and fullness were assessed immediately after the meal until bed-time with Likert scales. Results: The proportion of rapid-eye movement (REM) sleep to total sleep time was significantly reduced at the VLC acute and VLC ketosis when compared to the control night (P = 0.006; n = 11 and P = 0.05; n = 14, respectively). The percentage of slow wave sleep (SWS) significantly increased for both the VLC acute (17.7 ± 6.7) and ketosis (17.8 ± 6.1) phases compared to control (13.9 ± 6.3), P = 0.02 for both phases. Conclusions: In healthy, good sleepers, the VLC diet over the short-term promotes increases in the percentage of SWS (deep sleep stage 4) and a reduction in the percentage of REM sleep ('dreaming' sleep) compared to the control mixed diet. The sleep changes may be linked to the metabolism of the fat content of the VLC diet.
The meaning of early intervention: A parent's experience and reflection on interactions with professionals using a phenomenological ethnographic approach

The purpose of this study is to describe how a parent's partnership with professionals progresses and evolves throughout the service provisioning process. Using a phenomenological ethnographic approach, the lived reality of a family is depicted as the parent walks through different stages of the Individualized Family Service Plan process over a 6-month period. Data concerning parent-professional interactions were obtained via observation notes and document reviews whereas data regarding parent perceptions were collected through multiple individual interviews. Overall, the parent conveyed her satisfaction with actual services especially regarding the professionals' knowledge and parental advocacy. However, the parent also indicated frustration with the early intervention planning process and ''obligated'' partnerships with providers. In particular, the providers' lack of sensitivity was noted, and greater emotional and psychological support was suggested. The overall process of developing partnerships with professionals can be excessively intrusive to the family's lives. Future research directions are offered as a contribution for the development of improved policies for early intervention programs regarding family-centered practice, utilizing the perspectives of families.
Memory Prefetching Using Adaptive Stream Detection

We present adaptive stream detection, a simple technique for modulating the aggressiveness of a stream prefetcher to match a workload's observed spatial locality. We use this concept to design a prefetcher that resides on an on-chip memory controller. The result is a prefetcher with small hardware costs that can exploit workloads with low amounts of spatial locality. Using highly accurate simulators for the IBM Power5+, we show that this prefetcher improves performance of the SPEC2006fp benchmarks by an average of 32.7% when compared against a Power5+ that performs no prefetching. On a set of 5 commercial benchmarks that have low spatial locality, this prefetcher improves performance by an average of 15.1%. When compared against a typical Power5+ that does perform processor-side prefetching, the average performance improvement of these benchmark suites is 10.2% and 8.4%. We also evaluate the power and energy impact of our technique. For the same benchmark suites, DRAM power consumption increases by less than 3%, while energy usage decreases by 9.8% and 8.2%, respectively. Moreover, the power consumption of the prefetcher itself is low; it is estimated to increase the power consumption of the Power5+ chip by 0.06%
Practical management of antibiotic allergy in adults

This review looks at the main issues around immediate hypersensitivity and the role and limitations of testing. The majority of literature on antibiotic hypersensitivity relates to β-lactam antibiotics, mainly because of the heavy usage of this class of drugs. Concerns around cross-reactivity always worry clinicians, particularly in the emergency situation. Reasonable data now exist in relation to β-lactam antibiotics and derivatives, which enable appropriate risk management to be undertaken. The available literature for other classes of antibiotics is also discussed.
DReggie: Semantic Service Discovery for M-Commerce Applications

The emergence of mobile devices and wireless networks has created a new path in the field of e-commerce: ``m-commerce''. Significant research needs to be done in the field of service discovery to support m-commerce applications. Various new applications, that would use services available to a mobile device from both the fixed network backbone and peer mobile devices in its proximity, are being developed. M-commerce applications have the challenging task of discovering services in a dynamically changing environment. To support dynamic service discovery, existing mechanisms need to move beyond trivial attribute or interface matching. Recently the DARPA Agent Markup Language (DAML) has been developed to semantically describe the content of the web. In this paper, we describe ongoing work in developing a dynamic service discovery infrastructure using DAML. This architecture is built on the Jini service discovery framework. Our service discovery infrastructure can find services in a semantically richer way, instead of using simple attribute or interface based matching. This increased flexibility in service discovery has the potential to enable a broad range of m-commerce applications.
Moving from Virtual Reality Exposure-Based Therapy to Augmented Reality Exposure-Based Therapy: A Review

This paper reviews the move from virtual reality exposure-based therapy to augmented reality exposure-based therapy (ARET). Unlike virtual reality (VR), which entails a complete virtual environment (VE), augmented reality (AR) limits itself to producing certain virtual elements to then merge them into the view of the physical world. Although, the general public may only have become aware of AR in the last few years, AR type applications have been around since beginning of the twentieth century. Since, then, technological developments have enabled an ever increasing level of seamless integration of virtual and physical elements into one view. Like VR, AR allows the exposure to stimuli which, due to various reasons, may not be suitable for real-life scenarios. As such, AR has proven itself to be a medium through which individuals suffering from specific phobia can be exposed “safely” to the object(s) of their fear, without the costs associated with programing complete VEs. Thus, ARET can offer an efficacious alternative to some less advantageous exposure-based therapies. Above and beyond presenting what has been accomplished in ARET, this paper covers some less well-known aspects of the history of AR, raises some ARET related issues, and proposes potential avenues to be followed. These include the type of measures to be used to qualify the user’s experience in an augmented reality environment, the exclusion of certain AR-type functionalities from the definition of AR, as well as the potential use of ARET to treat non-small animal phobias, such as social phobia.
Electron energy loss spectroscopy in advanced materials

The combination of a Transmission Electron Microscope (TEM) with an electron energy loss spectrometer (EELS) yields a powerful tool for the microcharacterization of materials. However, the application of this technique to advanced materials problems can only be fully appreciated when the information obtained using EELS is related to that obtained from other analytical spectroscopies. In this chapter, we briefly discuss the relative performance of X-ray, Auger and Photoelectron Spectroscopies with EELS pointing out the limitations and merits of each. This comparison is followed by examples of the application of EELS to investigations involving high {Tc} superconductors, artificial metallic superlattices, amorphous magnetic materials and the characterization of metallic hydride phases. 14 refs., 22 figs.
A Functional Screen Identifies Specific MicroRNAs Capable of Inhibiting Human Melanoma Cell Viability

Malignant melanoma is an aggressive form of skin cancer with poor prognosis. Despite improvements in awareness and prevention of this disease, its incidence is rapidly increasing. MicroRNAs (miRNAs) are a class of small RNA molecules that regulate cellular processes by repressing messenger RNAs (mRNAs) with partially complementary target sites. Several miRNAs have already been shown to attenuate cancer phenotypes, by limiting proliferation, invasiveness, tumor angiogenesis, and stemness. Here, we employed a genome-scale lentiviral human miRNA expression library to systematically survey which miRNAs are able to decrease A375 melanoma cell viability. We highlight the strongest inhibitors of melanoma cell proliferation, including the miR-15/16, miR-141/200a and miR-96/182 families of miRNAs and miR-203. Ectopic expression of these miRNAs resulted in long-term inhibition of melanoma cell expansion, both in vitro and in vivo. We show specifically miR-16, miR-497, miR-96 and miR-182 are efficient effectors when introduced as synthetic miRNAs in several melanoma cell lines. Our study provides a comprehensive interrogation of miRNAs that interfere with melanoma cell proliferation and viability, and offers a selection of miRNAs that are especially promising candidates for application in melanoma therapy.
Transient Reward Approximation for Continuous-Time Markov Chains

We are interested in the analysis of very large continuous-time Markov chains (CTMCs) with many distinct rates. Such models arise naturally in the context of reliability analysis, e.g., of computer network performability analysis, of power grids, of computer virus vulnerability, and in the study of crowd dynamics. We use abstraction techniques together with novel algorithms for the computation of bounds on the expected final and accumulated rewards in continuous-time Markov decision processes (CTMDPs). These ingredients are combined in a partly symbolic and partly explicit (symblicit) analysis approach. In particular, we circumvent the use of multi-terminal decision diagrams, because the latter do not work well if facing a large number of different rates. We demonstrate the practical applicability and efficiency of the approach on two case studies.