Miracle-dz/UniFAR-FTUs huggingface dataset:
Reconciling geography and genealogy: phylogeography of giant freshwater prawns from the Lake Carpentaria region

There is convincing geological evidence for the historical existence of an ancient lake on the Australian–New Guinea continental shelf during the late Pleistocene. Lake Carpentaria was a vast fresh‐ to brackishwater lake that would presumably have provided habitat for, and facilitated gene flow among, aquatic taxa that tolerate low to moderate salinities in this region. Moreover, it has been argued that the outflow of Papua New Guinea's Fly River was diverted westward into Lake Carpentaria during this period, although this hypothesis is controversial. We predicted that these events, if a true history, would have promoted gene flow and population growth via range‐expansion events in the giant freshwater prawn (Macrobrachium rosenbergii) and restricted gene flow subsequently by way of a vicariant event as sea levels rose during the late Pleistocene, and a marine environment replaced Lake Carpentaria. We tested these hypotheses using phylogeographical and phylogenetic analyses of mitochondrial DNA variation in M. rosenbergii populations sampled from the Lake Carpentaria region. Our results support the hypothesis that Lake Carpentaria facilitated gene flow among populations of M. rosenbergii that are today isolated, but contest claims of a westward diversion of the Fly River. We inferred the timing of initial expansion in the ‘Lake Carpentaria lineage’ and found the timing of this event to be broadly concordant with geological dating of the formation of Lake Carpentaria. Reconciling geological and molecular data, as presented here, provides a powerful framework for investigating the influence of historical earth history events on the distribution of biological (i.e. molecular) diversity.
Analysis and modelling of glacial climate transitions using simple dynamical systems

Glacial climate variability is studied integrating simple nonlinear stochastic dynamical systems with palaeoclimatic records. Different models representing different dynamical mechanisms and modelling approaches are contrasted; model comparison and selection is based on a likelihood function, an information criterion as well as various long-term summary statistics. A two-dimensional stochastic relaxation oscillator model with proxy temperature as the fast variable is formulated and the system parameters and noise levels estimated from Greenland ice-core data. The deterministic part of the model is found to be close to the Hopf bifurcation, where the fixed point becomes unstable and a limit cycle appears. The system is excitable; under stochastic forcing, it exhibits noisy large-amplitude oscillations capturing the basic statistical characteristics of the transitions between the cold and the warm state. No external forcing is needed in the model. The relaxation oscillator is much better supported by the data than noise-driven motion in a one-dimensional bistable potential. Two variants of a mixture of local linear stochastic models, each associated with an unobservable dynamical regime or cluster in state space, are also considered. Three regimes are identified, corresponding to the different phases of the relaxation oscillator: (i) lingering around the cold state, (ii) rapid shift towards the warm state, (iii) slow relaxation out of the warm state back to the cold state. The mixture models have a high likelihood and are able to capture the pronounced time-reversal asymmetry in the ice-core data as well as the distribution of waiting times between onsets of Dansgaard–Oeschger events.
Supervised reranking for web image search

Visual search reranking that aims to improve the text-based image search with the help from visual content analysis has rapidly grown into a hot research topic. The interestingness of the topic stems mainly from the fact that the search reranking is an unsupervised process and therefore has the potential to scale better than its main alternative, namely the search based on offline-learned semantic concepts. However, the unsupervised nature of the reranking paradigm also makes it suffer from problems, the main of which can be identified as the difficulty to optimally determine the role of visual modality over different application scenarios. Inspired by the success of the "learning-to-rank" idea proposed in the field of information retrieval, we propose in this paper the "learning-to-rerank" paradigm, which derives the reranking function in a supervised fashion from the human-labeled training data. Although supervised learning is introduced, our approach does not suffer from scalability issues since a unified reranking model is learned that can be applied to all queries. In other words, a query-independent reranking model will be learned for all queries using query-dependent reranking features. The query-dependent reranking feature extraction is challenging since the textual query and the visual documents have different representation. In this paper, 11 lightweight reranking features are proposed by representing the textual query using visual context and pseudo relevant images from the initial search result. The experiments performed on two representative Web image datasets demonstrate that the proposed learning-to-rerank algorithm outperforms the state-of-the-art unsupervised reranking methods, which makes the learning-to-rerank paradigm a promising alternative for robust and reliable Web-scale image search.
A feasibility study: Use of actigraph to monitor and follow-up sleep/wake patterns in individuals attending community pharmacy with sleeping disorders

Introduction: Community pharmacists are in a suitable position to give advice and provide appropriate services related to sleep disorders to individuals who are unable to easily access sleep clinics. An intervention with proper objective measure can be used by the pharmacist to assist in consultation. Objectives: The study objectives are to evaluate: (1) The effectiveness of a community pharmacy-based intervention in managing sleep disorders and (2) the role of actigraph as an objective measure to monitor and follow-up individuals with sleeping disorders. Methods and Instruments: The intervention care group (ICG) completed questionnaires to assess sleep scale scores (Epworth Sleepiness Scale [ESS] and Insomnia Severity Index [ISI]), wore a wrist actigraph, and completed a sleep diary. Sleep parameters (sleep efficiency in percentage [SE%], total sleep time, sleep onset latency, and number of nocturnal awakenings) from actigraphy sleep report were used for consultation and to validate sleep diary. The usual care group (UCG) completed similar questionnaires but received standard care. Results: Pre- and post-mean scores for sleep scales and sleep parameters were compared between and within groups. A significant difference was observed when comparing pre- and post-mean scores for ISI in the ICG, but not for ESS. For SE%, an increase was found in the number of subjects rated as “good sleepers” at post-assessment in the ICG. Conclusions: ISI scores offer insights into the development of a community pharmacy-based intervention for sleeping disorders, particularly in those with symptoms of insomnia. It also demonstrates that actigraph could provide objective sleep/wake data to assist community pharmacists during the consultation.
Effect of platelet inhibition on bleeding complications in trauma patients on preinjury clopidogrel

BACKGROUND Use of antiplatelet medications for acute coronary syndromes and stroke prevention continues to rise as the population ages, although their effects on trauma outcomes remain unclear. This study sought to determine if trauma patients on preinjury clopidogrel with a higher degree of platelet inhibition (PI), as determined by the VerifyNow P2Y12 Test, experienced bleeding complications more frequently than did patients with a lower degree of PI. METHODS Retrospective, cohort study of adult trauma patients admitted to a Level 1 trauma center between October 1, 2009, and August 31, 2011, with documentation of clopidogrel as a home medication. Patients were excluded if they did not receive the P2Y12 assay, had a platelet count at the time of assay less than 100 × 109/L, or had warfarin, dabigatran, or other thienopyridine therapy documented as a concomitant home medication. The primary outcome compared a composite of bleeding complications between patients with 20% PI or greater and those with less than 20% PI. Bleeding complications were defined as the progression of neurologic insult, postoperative hemorrhage or initiation of the institutional massive blood transfusion protocol. RESULTS Baseline characteristics were similar between groups. The incidence of bleeding complications was not different between study groups (24.2% vs. 27.6%, p = 0.78). No difference in the secondary outcomes of length of stay, in-hospital mortality, and red blood cell transfusion were observed. Patients with 20% PI or greater received platelet transfusion more frequently than did patients with less than 20% PI (51.5% vs. 10.3%, p = 0.0008). CONCLUSION The VerifyNow P2Y12 Test may be a tool to stratify trauma patients at a higher risk of bleeding and who subsequently may benefit from transfusion. More frequent platelet transfusion in patients with 20% PI or greater may have resulted in fewer bleeding complications, although confirmation in a prospective, randomized trial is warranted. LEVEL OF EVIDENCE Prognostic study, level III.
Four steps to two sexes

Four steps through which parasitic intracellular symbionts could bring about the evolution of two sexes are considered. In the first step, a primitive host population has biparental cytoplasmic inheritance and lacks gametic differentiation: parasitic cytoplasmic elements readily invade and spread by vertical transmission through such host populations, even if they have major deleterious effects on their hosts. The second step leads to the establishment of a nuclear mutant in the host (locus A) that prevents inheritance of the cytoplasm in gametes in which it occurs. This mutant comes to equilibrium at an intermediate frequency, because a double dose of symbionts is more deleterious than a single dose, and zygotes lacking cytoplasm from both gametes are inviable. The third step involves the spread of a mutant at another nuclear locus (B), causing self-incompatibility of gametes in which it occurs. If this is closely linked to locus A, the mutant may become established by preventing the deleterious gamete unions. The mutant at locus B must, however, start both with an appreciable frequency and be in gametic disequilibrium with locus A. In the fourth step a second mutation causing self-incompatibility occurs at locus B. This allele spreads by becoming associated with the other allele at locus A, eventually leaving the population with two gamete types, or sexes, one predominantly transmitting the cytoplasm, and the other eliminating it. It is argued that this is a feasible mechanism for the origin of two sexes.
Superior Efficacy of a Combined Epigenetic Therapy against Human Mantle Cell Lymphoma Cells

Purpose: A deregulated epigenome contributes to the transformed phenotype of mantle cell lymphoma (MCL). This involves activity of the polycomb repressive complex (PRC) 2, containing three core proteins, EZH2, SUZ12, and EED, in which the SET domain of EZH2 mediates the histone methyltransferase activity. We determined the effects of 3-deazaneplanocin A (DZNep), an S-adenosylhomocysteine hydrolase inhibitor, and/or pan-histone deacetylase inhibitor panobinostat (PS) on cultured and primary MCL cells. Experimental Design: Following treatment with DZNep and/or PS, apoptosis and the levels and activity of EZH2 and PRC2 proteins in cultured and primary MCL cells were determined. Results: Treatment with DZNep depleted EZH2, SUZ12, and 3MeK27H3 in the cultured human MCL cells. DZNep also increased expression of p21, p27, and FBXO32, whereas it depleted Cyclin D1 and Cyclin E1 levels in MCL cells. In addition, DZNep treatment induced cell-cycle arrest and apoptosis in cultured and primary MCL cells. Furthermore, as compared with treatment with each agent alone, cotreatment with DZNep and PS caused greater depletion of EZH2, SUZ12, 3MeK27H3, and Cyclin D1 levels, whereas it induced greater expression of FBXO32, p16, p21, and p27. Combined treatment with DZNep and PS synergistically induced apoptosis of cultured and primary MCL cells while relatively sparing normal CD34 + cells. Cotreatment with DZNep and PS also caused significantly greater inhibition of tumor growth of JeKo-1 xenografts in NOD/SCID mice. Conclusions: These preclinical in vitro and in vivo findings show that cotreatment with DZNep and PS is an active combined epigenetic therapy worthy of further in vivo testing against MCL. Clin Cancer Res; 18(22); 6227–38. ©2012 AACR.
Induction of defeasible logic theories in the legal domain

Defeasible Logic is a promising representation for legal knowledge that appears to overcome many of the deficiencies of previous approaches to representing legal knowledge. Unfortunately, an immediate application of technology to the challenges of generating theories in the legal domain is an expensive and computationally intractable problem. So, in light of the potential benefits, we seek to find a practical algorithm that uses heuristics to discover an approximate solution. As an outcome of this work, we have developed an algorithm that integrates defeasible logic into a decision support system by automatically deriving its knowledge from databases of precedents. Experiments with the new algorithm are very promising -- delivering results comparable to and exceeding other approaches.
Outage Analysis of Multi-Relay Networks With Hardware Impairments Using SECps Scheduling Scheme in Shadowed-Rician Channel

In this paper, we investigate the effect of hardware impairments on the performance of dual-hop amplify-and-forward (AF)/decode-and-forward (DF) multiple relaying networks using switch-and-examine combining with post-selection (SECps) scheduling scheme in shadowed-Rician (SR) channel. Moreover, we consider a more general network, where the hard impairments are both considered at source, relays, and destination. Specifically, to decrease the high-implementation cost, the SECps scheme is adopted to choose an appropriate relay. To evaluate the performance of the considered system, we derive the novel closed-form expression of the outage probability for the AF and DF protocol, respectively. We also derive the asymptotic outage probability results at high SNRs for the DF protocol, which provides a fast way to evaluate the impact of hardware impairments on the dual-hop relay networks in the SR channel. In addition, simulation results are given to validate the correctness of the analytical results.
Effect of wood flour and naphthenic oil on morphology, rheological and mechanical properties of EPDM/PP/AL composite

Abstract Thermoplastic elastomer (TPE), made from ethylene propylene diene monomer (EPDM) and polypropylene (PP) base on reactive blending, has an excellent processing performance and characteristics and a wide range of applications. In this paper, EPDM, PP and ammonium lignosulfonate (AL) were selected as raw materials, wood flour (WF) of poplar tree was used as filler, naphthenic oil was used as plasticizer, DCP vulcanization system with dynamic vulcanization was carried, to make a new kind of composite material. This research studied the influences of wood flour and naphthenic oil content on the microstructure, mechanical properties and rheological properties of the composite material. The result showed: the content of wood flour and naphthenic oil has big impact on composite material. With the increase of the wood flour content, the mechanical properties are increased firstly and then decreased. The viscosity and modulus of the composite is improved with the increase of wood flour. With of the increase of the amount of naphthenic oil, the mechanical properties, viscosity and modulus of the composites decreased. When the content of wood flour is between 30–60 parts and the content of naphthenic oil is less than 20, the EPDM/PP/AL composite is suitable for using as the core layer elastic material of composite floor.
Power-Sharing and Leadership Dynamics in Authoritarian Regimes

I examine a fundamental problem of politics in authoritarian regimes: the dictator and the ruling coalition must share power and govern in an environment where political influence must be backed by a credible threat of violence. I develop a model of authoritarian politics in which power-sharing is complicated by this conflict of interest: by exploiting his position, the dictator may acquire more power at the expense of the ruling coalition, which may attempt to deter such opportunism by threatening to stage a coup. Two power-sharing regimes, contested and established dictatorships, may emerge as a result of strategic behavior by the dictator and the ruling coalition. This theory accounts for the large variation in the duration of dictators' tenures and the concentration of power in dictatorships over time and it contributes to our understanding of the dynamics of power-sharing and accountability in authoritarian regimes.
An RNA recognition motif-containing protein is required for plastid RNA editing in Arabidopsis and maize

Significance Transcripts in plant organelles are altered by conversion of cytidines to uridines in a process termed RNA editing. Members of two protein families have been identified in the plant editosome, but its complete composition is unknown. Now a unique protein that contains an RNA recognition motif has been found to be essential for editing of multiple plastid transcripts in both Arabidopsis and maize. Phylogenetic analysis indicates that this protein belongs to a sub-family of RNA recognition-motif proteins predominantly predicted to be targeted to organelles and that are thus likely to play roles in organelle RNA metabolism. Plant RNA editing modifies cytidines (C) to uridines (U) at specific sites in the transcripts of both mitochondria and plastids. Specific targeting of particular Cs is achieved by pentatricopeptide proteins that recognize cis elements upstream of the C that is edited. Members of the RNA-editing factor interacting protein (RIP) family in Arabidopsis have recently been shown to be essential components of the plant editosome. We have identified a gene that contains a pair of truncated RIP domains (RIP-RIP). Unlike any previously described RIP family member, the encoded protein carries an RNA recognition motif (RRM) at its C terminus and has therefore been named Organelle RRM protein 1 (ORRM1). ORRM1 is an essential plastid editing factor; in Arabidopsis and maize mutants, RNA editing is impaired at particular sites, with an almost complete loss of editing for 12 sites in Arabidopsis and 9 sites in maize. Transfection of Arabidopsis orrm1 mutant protoplasts with constructs encoding a region encompassing the RIP-RIP domain or a region spanning the RRM domain of ORRM1 demonstrated that the RRM domain is sufficient for the editing function of ORRM1 in vitro. According to a yeast two-hybrid assay, ORRM1 interacts selectively with pentatricopeptide transfactors via its RIP-RIP domain. Phylogenetic analysis reveals that the RRM in ORRM1 clusters with a clade of RRM proteins that are targeted to organelles. Taken together, these results suggest that other members of the ORRM family may likewise function in RNA editing.
Working memory capacity as a moderator of load-related frontal midline theta variability in Sternberg task

The aim of this study was to investigate the relationship between working memory capacity (WMC) and frontal theta response to memory load in Sternberg task. We show that oscillatory activity in the theta band (4–6 Hz) related to Sternberg task performance may differentiate people characterized by high and low WMC. Specifically, there is a linear increase of frontal midline (FM) theta power with load, however, only in the high WMC group. Furthermore, a positive linear relationship was found between WMC (operation span task score) and average FM theta power increase from lower to higher loads which was not present at other scalp locations. The distinct patterns of high and low WMC individual’s FM theta response to memory load seem to support the assumption that theta activity during maintenance reflects not only the amount of information stored, but also the effort it takes to remember them and the efficiency of involved neural processes. This contributes to perceiving FM theta as an individual trait which can reflect individual working memory mechanism efficiency.
Multimodal imaging of posterior ocular involvement in McArdle's disease

Giuseppe Casalino* MD FEBO Wing Chan MD FRCOphth Clara McAvoy MD FRCOphth Michele Coppola MD Francesco Bandello MD FEBO Alan C Bird MD FRCOphth Usha Chakravarthy MD PhD *Royal Eye Unit, Kingston Hospital NHS Foundation Trust, London, UK Moorfields Eye Hospital NHS Foundation Trust, London, UK Ophthalmology Macular Service, Belfast Health and Social Care Trust, Belfast, UK Ophthalmology Unit, Ospedale di Desio, ASST Monza, Monza, Italy Department of Ophthalmology, Scientific Institute San Raffaele, Vita-Salute University, Milan, Italy E-mail: peppecasalino@gmail.com Submitted: 12 June 2017 Revised: 13 September 2017 Accepted for publication: 30 September 2017
Strategies of Eradicating Glioma Cells: A Multi-Scale Mathematical Model with MiR-451-AMPK-mTOR Control

The cellular dispersion and therapeutic control of glioblastoma, the most aggressive type of primary brain cancer, depends critically on the migration patterns after surgery and intracellular responses of the individual cancer cells in response to external biochemical and biomechanical cues in the microenvironment. Recent studies have shown that a particular microRNA, miR-451, regulates downstream molecules including AMPK and mTOR to determine the balance between rapid proliferation and invasion in response to metabolic stress in the harsh tumor microenvironment. Surgical removal of main tumor is inevitably followed by recurrence of the tumor due to inaccessibility of dispersed tumor cells in normal brain tissue. In order to address this multi-scale nature of glioblastoma proliferation and invasion and its response to conventional treatment, we propose a hybrid model of glioblastoma that analyses spatio-temporal dynamics at the cellular level, linking individual tumor cells with the macroscopic behaviour of cell organization and the microenvironment, and with the intracellular dynamics of miR-451-AMPK-mTOR signaling within a tumour cell. The model identifies a key mechanism underlying the molecular switches between proliferative phase and migratory phase in response to metabolic stress and biophysical interaction between cells in response to fluctuating glucose levels in the presence of blood vessels (BVs). The model predicts that cell migration, therefore efficacy of the treatment, not only depends on oxygen and glucose availability but also on the relative balance between random motility and strength of chemoattractants. Effective control of growing cells near BV sites in addition to relocalization of invisible migratory cells back to the resection site was suggested as a way of eradicating these migratory cells.