Miracle-dz/UniFAR-FTUs huggingface dataset:
PSMC analysis of effective population sizes in molecular ecology and its application to black‐and‐white Ficedula flycatchers

Climatic fluctuations during the Quaternary period governed the demography of species and contributed to population differentiation and ultimately speciation. Studies of these past processes have previously been hindered by a lack of means and genetic data to model changes in effective population size (Ne) through time. However, based on diploid genome sequences of high quality, the recently developed pairwise sequentially Markovian coalescent (PSMC) can estimate trajectories of changes in Ne over considerable time periods. We applied this approach to resequencing data from nearly 200 genomes of four species and several populations of the Ficedula species complex of black‐and‐white flycatchers. Ne curves of Atlas, collared, pied and semicollared flycatcher converged 1–2 million years ago (Ma) at an Ne of ≈ 200 000, likely reflecting the time when all four species last shared a common ancestor. Subsequent separate Ne trajectories are consistent with lineage splitting and speciation. All species showed evidence of population growth up until 100–200 thousand years ago (kya), followed by decline and then start of a new phase of population expansion. However, timing and amplitude of changes in Ne differed among species, and for pied flycatcher, the temporal dynamics of Ne differed between Spanish birds and central/northern European populations. This cautions against extrapolation of demographic inference between lineages and calls for adequate sampling to provide representative pictures of the coalescence process in different species or populations. We also empirically evaluate criteria for proper inference of demographic histories using PSMC and arrive at recommendations of using sequencing data with a mean genome coverage of ≥18X, a per‐site filter of ≥10 reads and no more than 25% of missing data.
GemRBAC-DSL: A High-level Specification Language for Role-based Access Control Policies

A role-based access control (RBAC) policy restricts a user to perform operations based on her role within an organization. Several RBAC models have been proposed to represent different types of RBAC policies. However, the expressiveness of these models has not been matched by specification languages for RBAC policies. Indeed, existing policy specification languages do not support all the types of RBAC policies defined in the literature. In this paper we aim to bridge the gap between highly-expressive RBAC models and policy specification languages, by presenting GemRBAC-DSL, a new specification language designed on top of an existing, generalized conceptual model for RBAC. The language sports a syntax close to natural language, to encourage its adoption among practitioners. We also define semantic checks to detect conflicts and inconsistencies among the policies written in a GemRBAC-DSL specification. We show how the semantics of GemRBAC-DSL can be expressed in terms of an existing formalization of RBAC policies as OCL (Object Constraint Language) constraints on the corresponding RBAC conceptual model. This formalization paves the way to define a model-driven approach for the enforcement of policies written in GemRBAC-DSL.
High resolution range profile based extraction of radar target length

Radar target identification using high resolution range profile (HRRP), the target length is an important feature due to that it can reduce the time of identification and mitigate noise redundancy. Traditional threshold methods with the different operators are highly sensitive to noise. In this paper, we proposed an adaptive difference operator for target length feature extraction from HRRP. Experimental results confirmed the proposed method effectively acquire the radial projection length of the target with high precision even in case of lower Signal-to-Noise Ratio (SNR). Key words: Difference operator, target identification, HRRP, target length.
Achievable rates for multiple access relay channel with generalized feedback

We introduce the multiple access relay channel with generalized feedback (MARC-GF), which is more general than the known MARC (without feedback) and MAC-GF (without relay). In the MARC-GF, two sources, assisted by a common relay, send independent messages to a destination. The sources and relay each receives some feedback that may facilitate this communication. We propose and analyze a decode-and-forward scheme for the MARC-GF to obtain an achievable rate region. This scheme facilitates cooperation between the two sources, in addition to cooperation by the relay, via block Markov superposition encoding.
Convergence rate of inexact proximal point methods with relative error criteria for convex optimization

In this paper, we consider a framework of inexact proximal point methods for convex optimization that allows a relative error tolerance in the approximate solution of each proximal subproblem and establish its convergence rate. We then show that the well-known forward-backward splitting algorithm for convex optimization belongs to this framework. Finally, we propose and establish the iteration-complexity of an inexact forward-backward splitting algorithm for solving optimization problems whose objective functions are obtained by maximizing convex-concave saddle functions
CK2-mediated stimulation of Pol I transcription by stabilization of UBF–SL1 interaction

High levels of rRNA synthesis by RNA polymerase I are important for cell growth and proliferation. In vitro studies have indicated that the formation of a stable complex between the HMG box factor [Upstream binding factor (UBF)] and SL1 at the rRNA gene promoter is necessary to direct multiple rounds of Pol I transcription initiation. The recruitment of SL1 to the promoter occurs through protein interactions with UBF and is regulated by phosphorylation of UBF. Here we show that the protein kinase CK2 co-immunoprecipitates with the Pol I complex and is associated with the rRNA gene promoter. Inhibition of CK2 kinase activity reduces Pol I transcription in cultured cells and in vitro. Significantly, CK2 regulates the interaction between UBF and SL1 by counteracting the inhibitory effect of HMG boxes five and six through the phosphorylation of specific serines located at the C-terminus of UBF. Transcription reactions with immobilized templates indicate that phosphorylation of CK2 phosphoacceptor sites in the C-terminal domain of UBF is important for promoting multiple rounds of Pol I transcription. These data demonstrate that CK2 is recruited to the rRNA gene promoter and directly regulates Pol I transcription re-initiation by stabilizing the association between UBF and SL1.
Multi-document Summarization by Information Distance

Fast changing knowledge on the Internet can be acquired more efficiently with the help of automatic document summarization and updating techniques. This paper described a novel approach for multi-document update summarization. The best summary is defined to be the one which has the minimum information distance to the entire document set. The best update summary has the minimum conditional information distance to a document cluster given that a prior document cluster has already been read. Experiments on the DUC 2007 dataset and the TAC 2008 dataset have proved that our method closely correlates with the human summaries and outperforms other programs such as LexRank in many categories under the ROUGE evaluation criterion.
How Words and Money Cultivate a Personal Vote: The Effect of Legislator Credit Claiming on Constituent Credit Allocation

Particularistic spending, a large literature argues, builds support for incumbents. This literature equates money spent in the district with the credit constituents allocate. Yet, constituents lack the necessary information and motivation to allocate credit in this way. We use extensive observational and experimental evidence to show how legislators’ credit claiming messages—and not just money spent in the district—affect how constituents allocate credit. Legislators use credit claiming messages to influence the expenditures they receive credit for and to affect how closely they are associated with spending in the district. Constituents are responsive to credit claiming messages—they build more support than other nonpartisan messages. But contrary to expectations from other studies, constituents are more responsive to the total number of messages sent rather than the amount claimed. Our results have broad implications for political representation, the personal vote, and the study of U.S. Congressional elections.
The influence of rotor type and centrifugation time on the yield and purity of extracellular vesicles

Background Extracellular vesicles (EV), the collective term for vesicles released from cells, consist of vesicle species ranging in size from 30 nm to 5 µm in diameter. These vesicles are most commonly isolated by differential centrifugations, which pellets particles based on their differential movement through the liquid medium in which they are immersed. Multiple parameters, including the utilization of different rotor types, can influence the yield and purity of isolated vesicles; however, the understanding of how these factors affect is limited. Materials and methods Here, we compare the influence of multiple centrifugation parameters, including the use of swinging bucket and fixed angle rotors, as well as different centrifugation times, for the isolation of the smallest EVs, “exosomes. ” In particular, we determine the yields of exosomal RNA and protein, as well as the nature of the isolated vesicles and possible protein contamination with methods such as electron microscopy, western blot and flow cytometry. Results Our results show that application of a specific g-force or rotation speed by itself does not predict the ability of pelleting exosomes, and that prolonged centrifugation times can achieve greater yields of exosomal RNA and protein, whereas very long centrifugation times result in excessive protein concentrations in the exosome pellet. Conclusion In conclusion, rotor type, g-force and centrifugation times significantly influence exosome yield during centrifugation-based isolation procedures, and current commonly recommended isolation protocols may not be fully optimized for yield and purity of exosomes.
FIVE DEBRIS DISKS NEWLY REVEALED IN SCATTERED LIGHT FROM THE HUBBLE SPACE TELESCOPE NICMOS ARCHIVE

We have spatially resolved five debris disks (HD 30447, HD 35841, HD 141943, HD 191089, and HD 202917) for the first time in near-infrared scattered light by reanalyzing archival Hubble Space Telescope (HST)/NICMOS coronagraphic images obtained between 1999 and 2006. One of these disks (HD 202917) was previously resolved at visible wavelengths using the HST/Advanced Camera for Surveys. To obtain these new disk images, we performed advanced point-spread function subtraction based on the Karhunen–Loève Image Projection algorithm on recently reprocessed NICMOS data with improved detector artifact removal (Legacy Archive PSF Library And Circumstellar Environments (LAPLACE) Legacy program). Three of the disks (HD 30447, HD 35841, and HD 141943) appear edge-on, while the other two (HD 191089 and HD 202917) appear inclined. The inclined disks have been sculpted into rings; in particular, the disk around HD 202917 exhibits strong asymmetries. All five host stars are young (8–40 Myr), nearby (40–100 pc) F and G stars, and one (HD 141943) is a close analog to the young Sun during the epoch of terrestrial planet formation. Our discoveries increase the number of debris disks resolved in scattered light from 19 to 23 (a 21% increase). Given their youth, proximity, and brightness (V = 7.2–8.5), these targets are excellent candidates for follow-up investigations of planet formation at visible wavelengths using the HST/Space Telescope Imaging Spectrograph coronagraph, at near-infrared wavelengths with the Gemini Planet Imager and Very Large Telescope/SPHERE, and at thermal infrared wavelengths with the James Webb Space Telescope NIRCam and MIRI coronagraphs.
Efficacy of Praziquantel against Schistosoma mekongi and Opisthorchis viverrini: A Randomized, Single-Blinded Dose-Comparison Trial

Background Schistosomiasis and opisthorchiasis are of public health importance in Southeast Asia. Praziquantel (PZQ) is the drug of choice for morbidity control but few dose comparisons have been made. Methodology Ninety-three schoolchildren were enrolled in an area of Lao PDR where Schistosoma mekongi and Opisthorchis viverrini coexist for a PZQ dose-comparison trial. Prevalence and intensity of infections were determined by a rigorous diagnostic effort (3 stool specimens, each examined with triplicate Kato-Katz) before and 28–30 days after treatment. Ninety children with full baseline data were randomized to receive PZQ: the 40 mg/kg standard single dose (n = 45) or a 75 mg/kg total dose (50 mg/kg+25 mg/kg, 4 hours apart; n = 45). Adverse events were assessed at 3 and 24 hours posttreatment. Principal Findings Baseline infection prevalence of S. mekongi and O. viverrini were 87.8% and 98.9%, respectively. S. mekongi cure rates were 75.0% (95% confidence interval (CI): 56.6–88.5%) and 80.8% (95% CI: 60.6–93.4%) for 40 mg/kg and 75 mg/kg PZQ, respectively (P = 0.60). O. viverrini cure rates were significantly different at 71.4% (95% CI: 53.4–84.4%) and 96.6% (95% CI: not defined), respectively (P = 0.009). Egg reduction rates (ERRs) against O. viverrini were very high for both doses (>99%), but slightly lower for S. mekongi at 40 mg/kg (96.4% vs. 98.1%) and not influenced by increasing diagnostic effort. O. viverrini cure rates would have been overestimated and no statistical difference between doses found if efficacy was based on a minimum sampling effort (single Kato-Katz before and after treatment). Adverse events were common (96%), mainly mild with no significant differences between the two treatment groups. Conclusions/Significance Cure rate from the 75 mg/kg PZQ dose was more efficacious than 40 mg/kg against O. viverrini but not against S. mekongi infections, while ERRs were similar for both doses. Trial Registration Controlled-Trials.com ISRCTN57714676
Data Cube Indexing of Large-Scale Infosec Repositories

Analysts examining large-scale information security repositories for propagating network events are interested in quickly identifying temporal and spatial (IP address and/or port) regions containing interesting phenomena, or correlating events from different time periods. The size of these datasets strains current query capabilities provided by, for example, relational databases. We introduce a scalable, animated data cube representation and viewer, suitable for a broad range of observables, to permit coarsegrain detection and correlation in such data sets. We scale from the LAN to the Internet through flexible, locality-preserving hash algorithms mapping traffic source and destination (IP addresses or IP and port considered simultaneously). Data streams considered include inherently suspicious traffic such as packets rejected at a firewall, IDS alerts, or traffic to unused address space, as well as Netflow data. We display observables as intensity plots, where X and Y coordinates are the hashed source and target address and the intensity is proportional to traffic volume. Source and target address space may or may not be the same and may or may not be mapped the same way. Propagating events have distinct visual signatures that can be enhanced through matched filtering techniques. Future work will correlate cubes efficiently through cell-by-cell multiplication. An analyst will be able to, for example, examine whether plots representing two time periods (hours or days) exhibit similar patterns. Multiplication of a cube with its transpose permits identification of nodes that respond to potentially malicious probes. These data cubes permit coarse-grained detection and correlation without expensive data base queries.
Ubiquitin-H2AX fusions render 53BP1 recruitment to DNA damage sites independent of RNF8 or RNF168

The mammalian E3 ubiquitin ligases RNF8 and RNF168 facilitate recruitment of the DNA damage response protein 53BP1 to sites of DNA double-strand breaks (DSBs). The mechanism involves recruitment of RNF8, followed by recruitment of RNF168, which ubiquitinates histones H2A/H2AX on K15. 53BP1 then binds to nucleosomes at sites of DNA DSBs by recognizing, in addition to methyl marks, histone H2A/H2AX ubiquitinated on K15. We report here that expressing H2AX fusion proteins with N-terminal bulky moieties can rescue 53BP1 recruitment to sites of DNA DSBs in cells lacking RNF8 or RNF168 or in cells treated with proteasome inhibitors, in which histone ubiquitination at sites of DNA DSBs is compromised. The rescue required S139 at the C-terminus of the H2AX fusion protein and was occasionally accompanied by partial rescue of ubiquitination at sites of DNA DSBs. We conclude that recruitment of 53BP1 to sites of DNA DSBs is possible in the absence of RNF8 or RNF168, but still dependent on chromatin ubiquitination.
The impact of song-specific age and affective qualities of popular songs on music-evoked autobiographical memories (MEAMs)

Songs heard between the ages of 15 and 24 should be remembered better and have a stronger relationship to autobiographical memories when compared with music from other phases of life (“reminiscence bump effect”). Additionally, the proportion of music-evoked autobiographical memories (MEAMs) is at a maximum in these years of early adolescence and then declines up to the age of 60. In our study we tried both to replicate these important findings based on a German sample and to further investigate the influence of the affective characteristics of the songs on the frequency of participants’ autobiographical memories. In Experiment 1 a group of adults (N = 48, Mage = 67.1 years) listened to excerpts from 80, number-one, popular music hits from 1930 to 2010 and gave written self-reports on MEAMs. In Experiment 2 the affective characteristics were rated by another group of adults (N = 22, Mage = 66 years) and were used to predict the frequency of MEAMs. As a main result of Experiment 1, we confirmed the reminiscence bump and decline effect with a small effect size for the ratings of feelings evoked by the song and with a medium effect size for the song recognition performance of those songs released during the participants’ age range of 15 to 24 years. The total number of MEAMs was only marginally influenced by a memory bump and decline effect, and participants showed a significant proportion of MEAMs up to the fifth decade. Experiment 2 revealed that the affective ratings of the songs were unequally distributed over the two-dimensional emotion space unlike the average rate of MEAMs which was nearly equally distributed. In contrast to previous research, we therefore conclude that popular songs can be associated with autobiographical memory over five decades of life – independent of the affective character of the music.
Is testosterone the hormone of desire? For some women, some of the time

Although testosterone (T) has been dubbed the “hormone of desire,” the link between T and sex drive has proven inconsistent among women. The mixed pattern of findings suggests that woman vary in the degree to which changes in T correspond to changes in sex drive (i.e., the T-drive linkage). Yet, to date no one has examined why this variation exists. The current study sought to answer 2 questions: First, within each individual woman, does T-drive linkage change as a function of ovulation? Second, is the overall degree of T-drive linkage higher in women with greater sexual motivation, greater average T, or greater daily variability in T, and among lesbian, bisexual or heterosexual women? We further explored how between-person and within-person characteristics interact to shape the T-drive linkage. To do this, we assessed daily T and daily sex drive over the middle 2 weeks of the menstrual cycle in a sample of 157 heterosexual, lesbian, and bisexual women. Multilevel modeling analyses demonstrated that lesbian and bisexual women showed a significant T-drive linkage, but only following ovulation, whereas heterosexual women had a significant T-drive linkage, but only prior to ovulation. Moreover, women with higher average T levels showed an inverse T-drive linkage prior to ovulation and a positive T-drive linkage following ovulation, whereas women with lower average T levels did not show a significant T-drive linkage during any ovulatory phase. Results suggest that considering menstrual cycle timing and trait-like characteristics are key to understanding variation in the T-drive linkage. To my sister and best friend, who have helped me articulate the ideas presented in this paper, and who shared their experiences in an effort to provide me with real-world examples for me to ponder in writing this thesis.
First Synthetic Carbohydrates with the Full Anticoagulant Properties of Heparin.

A single disaccharide building block is required to obtain synthetic carbohydrates that reproduce the anticoagulant activity of heparin and inhibit thrombin (n>6) and/or factor Xa (n≥2; see reaction scheme). Thus, there is evidence that heparin fragments with at least 15 saccharide units are required for thrombin inhibition. Lev=levulinoyl.
S-nitroso-N-acetylcysteine attenuates liver fibrosis in experimental nonalcoholic steatohepatitis

S-Nitroso-N-acetylcysteine (SNAC) is a water soluble primary S-nitrosothiol capable of transferring and releasing nitric oxide and inducing several biochemical activities, including modulation of hepatic stellate cell activation. In this study, we evaluated the antifibrotic activity of SNAC in an animal model of nonalcoholic steatohepatitis (NASH) induced in Sprague-Dawley rats fed with a choline-deficient, high trans fat diet and exposed to diethylnitrosamine for 8 weeks. The rats were divided into three groups: SNAC, which received oral SNAC solution daily; NASH, which received the vehicle; and control, which received standard diet and vehicle. Genes related to fibrosis (matrix metalloproteinases [MMP]-13, -9, and -2), transforming growth factor β-1 [TGFβ-1], collagen-1α, and tissue inhibitors of metalloproteinase [TIMP-1 and -2] and oxidative stress (heat-shock proteins [HSP]-60 and -90) were evaluated. SNAC led to a 34.4% reduction in the collagen occupied area associated with upregulation of MMP-13 and -9 and downregulation of HSP-60, TIMP-2, TGFβ-1, and collagen-1α. These results indicate that oral SNAC administration may represent a potential antifibrotic treatment for NASH.
Scheduling intense applications most 'surprising' first

Certain streaming applications are required to perform sophisticated analytics within bounded time on arriving streams of data. Such applications have the interesting characteristic that the total amount of work that could be performed is unbounded. We show how recent result from algorithmic theory are useful in scheduling such applications as they allow the efficient creation of synopses of unprocessed data. These synopses can then be used to schedule the processing of the stream. In particular, we describe a scheduler that optimizes the information rate available to applications by estimating the entropy of arriving streams. We describe the theory underlying such a scheduler and show how existing programming models can be extended to accommodate it.
Questions for Dr

It is indeed correct as the Senator suggests that I have criticized a few aspects of IPCC assessments, but then so too have nearly all scientists or policy analysts who honestly observe the complex issues involved. In fact, IPCC Lead Authors themselves are among the most vigorous critics of their own evolving assessment reports—as they should be. That is why IPCC assessments undergo several rounds of rigorous internal and external peer review—to maximize the likelihood of balanced assessment.