Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparing ungulate dietary proxies using discriminant function analysis

A variety of tooth‐wear and morphological dietary proxies have been proposed for ungulates. In turn, they have been applied to fossil specimens with the purpose of reconstructing the diets of extinct taxa. Although these dietary proxies have been used in isolation and in combination, a consistent set of statistical analyses has never been applied to all of the available datasets. The purpose of this study is to determine how well the most commonly used dietary proxies classify ungulates as browsers, grazers, and mixed feeders individually and in combination. Discriminant function analysis is applied to individual dietary proxies (hypsodonty, mesowear, microwear, and several cranial dietary proxies) and to combinations thereof to compare rates of successful dietary classification. In general, the tooth‐wear dietary proxies (mesowear and microwear) perform better than morphological dietary proxies, though none are strong proxies in isolation. The success rates of the cranial dietary proxies are not increased substantially when ruminants and bovids are analyzed separately, and significance among the three dietary guilds is reduced when controlling for phylogenetic relatedness. The combination of hypsodonty, mesowear, and microwear is found to have a high rate of successful dietary classification, but a combination of all commonly used proxies increases the success rate to 100%. In most cases, mixed feeders bear the greatest resemblance to browsers suggesting that a morphology intermediate to browsers and grazers may represent a fitness valley resulting from the inability to exploit both browse and graze efficiently. These results are important for future paleoecological studies and should be used as a guide for determining which dietary proxies are appropriate to the research question. J. Morphol. , 2011. © 2011 Wiley‐Liss, Inc.
Translation of the Minor Capsid Protein of a Calicivirus Is Initiated by a Novel Termination-dependent Reinitiation Mechanism*

Caliciviruses represent a family of positive strand RNA viruses responsible for a variety of syndromes in man and animals. VP10, a minor structural protein of the calicivirus rabbit hemorrhagic disease virus, is encoded in the small 3′-terminal open reading frame (ORF) 2 and is translated with an efficiency of ∼20% of the preceding ORF1. The presence of the ORF1 termination codon is crucial for VP10 expression. Translation of VP10 starts at an AUG codon located at positions –5 to –3 of the ORF1 termination codon. However, VP10 was also expressed in the absence of an AUG initiation codon. The majority of ORF1 could be deleted or replaced by different sequences without significant influence on VP10 expression as long as translation terminated at the given position. The RNA sequence of the 3′-terminal 84 nucleotides of ORF1 but not the encoded peptide was found to be crucial for VP10 expression. In contrast, nearly the entire ORF2 could be replaced by a foreign sequence without abrogation of its translation. Accordingly, VP10 is expressed in a translation termination/reinitiation process that is particular because it is independent of an AUG translational start codon and requires the presence of a sequence element upstream of the initiation site.
A vector statistical piecewise polynomial approximation algorithm for environment compensation in telephone LVCSR

A vector statistical piecewise polynomial (VPP) approximation algorithm is proposed for environment compensation in speech signals that are degraded by both additive and convolutive noise. By investigating the model of the telephone environment, we address a piecewise polynomial, namely two linear polynomials and a quadratic polynomial, to approximate the environment function precisely. The VPP is applied either to stationary noise, or to non-stationary noise. In the first case, batch EM is used in the log-spectral domain; in the second case, recursive EM with iterative stochastic approximation is developed in the cepstral domain. Both approaches are based on the minimum mean squared error (MMSE) sense. Experimental results are presented on the application of this approach in improving the performance of Mandarin large vocabulary continuous speech recognition (LVCSR) in background noise and different transmission channels (such as fixed telephone line and GSM). The method can reduce the average character error rate (CER) by about 18%.
Stateful discovery of attack manifestations on networks and systems

Detection of attack manifestations on networks and systems via correlation of log information, is crucial for security. Speci cation-based solutions have been proposed as a promising paradigm that counters the high variability of attacks. In this study, a solution model using a form of Extended Finite State Automata is proposed, which is argued to be very e ective as a fundamental and precise primitive in sequence analysis of log events. Attack behaviour speci cations, are translated to runtime operations which show the viability of the approach. After an initial evaluation, these augmented state machines accompanied with a proof-of-concept Domain Speci c Language, o er a solid foundation for accurate conceptualization and classi cation of attack vectors; further applications with attack speci cation languages appear promising.
Performance comparison of an 80-km-per-span EDFA system and a 160-km hut-skipped all-Raman system over standard single-mode fiber

In this paper, we present a comprehensive comparison of the performance of an 80-km-per-span erbium-doped fiber amplifier (EDFA) system and a hut-skipped (160-km-per-span) all-Raman system over standard single-mode fiber (SSMF) for the first time, using semianalytic models. The numerical results reveal that a hut-skipped all-Raman system (using one-order Raman pumping) can achieve comparable performance as the conventional 80-km-per-span EDFA system for a common 50-GHz-spaced 80 times 10 Gb/s nonreturn-to-zero (NRZ) wavelength division multiplexing (WDM) system at typical fiber loss of 0.22 dB/km. For 100-GHz-spaced 40 times 40 Gb/s carrier-suppressed return-to-zero (CS-RZ) WDM transmission, it was found that a hut-skipped all-Raman system can achieve even better performance than the current 80-km-per-span EDFA system. It was also found that the impact of pattern-dependent Raman crosstalk is more severe than interchannel cross-phase modulation (XPM) in a hut-skipped all-Raman system with 80 times 10 Gb/s capacity
The SPO11-C631T gene polymorphism and male infertility risk: a meta-analysis

Abstract To evaluate the association between the SPO11 gene C631T polymorphism and the risk of male infertility. We conducted a search on PubMed, Embase, Web of Science, Chinese National Knowledge Infrastructure (CNKI), China biology medical literature database (CBM), VIP, and Chinese literature database (Wan Fang) on 31 March 2016. Odds ratio (OR) and 95% confidence interval (95%CI) were used to assess the strength of associations. A total of five studies including 542 cases and 510 controls were involved in this meta-analysis. The pooled results indicated that the SPO11 gene C631T polymorphism was significantly associated with increased risk of male infertility (TT + CT vs. CC: OR = 4.14, 95%CI = 2.48–6.89; CT vs. CC: OR = 4.34, 95%CI = 2.56–7.34; T vs. C: OR = 4.35, 95%CI = 2.58–7.34). Subgroup analysis of different countries proved the relationship between SPO11 gene C631T polymorphism and male infertility risk in Chinese, but not in Iranian peoples. In conclusion, this study suggested that SPO11 gene C631T polymorphism may contribute as a genetic factor susceptible to cause male infertility. Furthermore, more large sample and representative population-based cases and well-matched controls are needed to validate our results.
Pooling of Unshared Information in Group Decision Making: Biased Information Sampling During Discussion

Decision-making groups can potentially benefit from pooling members' information, particularly when members individually have partial and biased information but collectively can compose an unbiased characterization of the decision alternatives. The proposed biased sampling model of group discussion, however, suggests that group members often fail to effectively pool their information because discussion tends to be dominated by (a) information that members hold in common before discussion and (b) information that supports members' existent preferences. In a political caucus simulation, group members individually read candidate descriptions that contained partial information biased against the most favorable candidate and then discussed the candidates as a group. Even though groups could have produced unbiased composites of the candidates through discussion, they decided in favor of the candidate initially preferred by a plurality rather than the most favorable candidate. Group members' pre- and postdiscussion recall of candidate attributes indicated that discussion tended to perpetuate, not to correct, members' distorted pictures of the candidates.
Indirect Proton MR Imaging and Kinetic Analysis of 17O-Labeled Water Tracer in the Brain

Purpose: The feasibility of steady-state sequences for 17O imaging was evaluated based on a kinetic analysis of the brain parenchyma and cerebrospinal fluid (CSF). Materials and Methods: The institutional review board approved this prospective study with written informed consent. Dynamic 2D or 3D steady-state sequences were performed in five and nine participants, respectively, with different parameters using a 3T scanner. During two consecutive dynamic scans, saline was intravenously administered for control purposes in the first scan, and 20% 17O-labeled water (1 mL/Kg) was administered in the second scan. Signal changes relative to the baseline were calculated, and kinetic analyses of the curves were conducted for all voxels. Region of interest analysis was performed in the brain parenchyma, choroid plexus, and CSF spaces. Results: Average signal drops were significantly larger in the 17O group than in the controls for most of the imaging parameters. Different kinetic parameters were observed between the brain parenchyma and CSF spaces. Average and maximum signal drops were significantly larger in the CSF spaces and choroid plexus than in the brain parenchyma. Bolus arrival, time to peak, and the first moment of dynamic curves of 17O in the CSF space were delayed compared to that in the brain parenchyma. Significant differences between the ventricle and subarachnoid space were also noted. Conclusion: Steady-state sequences are feasible for indirect 17O imaging with reasonable temporal resolution; this result is potentially important for the analysis of water kinetics and aquaporin function for several disorders.
Induction of the cyclic nucleotide phosphodiesterase PDE4B is essential for LPS-activated TNF-α responses

Lipopolysaccharide (LPS) stimulation of the innate immune response requires the activation of signaling cascades that culminate in the synthesis and secretion of proinflammatory cytokines. Given the inhibitory effects of phosphodiesterase (PDE) inhibitors on LPS-induced cytokine production, we have investigated LPS responses in mice deficient in PDE4 (type 4 cAMP-specific PDE)-B and PDE4D. LPS stimulation of mouse peripheral leukocytes induced PDE4B mRNA accumulation and increased PDE4 activity. This response was completely absent in mice deficient in PDE4B but not PDE4D. LPS induction of tumor necrosis factor-α secretion by circulating leukocytes was decreased by approximately 90% in mice deficient in PDE4B but not in mice lacking PDE4D. The impaired LPS response was evident regardless of the LPS dose used for stimulation and was associated with a more than 90% decrease in tumor necrosis factor-α mRNA accumulation. A decreased responsiveness to LPS was also present in other inflammatory cells, including peritoneal and lung macrophages. These findings demonstrate that PDE4B gene activation by LPS constitutes a feedback regulation essential for an efficient immune response.
adegenet 1.3-1: new tools for the analysis of genome-wide SNP data

SUMMARY While the R software is becoming a standard for the analysis of genetic data, classical population genetics tools are being challenged by the increasing availability of genomic sequences. Dedicated tools are needed for harnessing the large amount of information generated by next-generation sequencing technologies. We introduce new tools implemented in the adegenet 1.3-1 package for handling and analyzing genome-wide single nucleotide polymorphism (SNP) data. Using a bit-level coding scheme for SNP data and parallelized computation, adegenet enables the analysis of large genome-wide SNPs datasets using standard personal computers. AVAILABILITY adegenet 1.3-1 is available from CRAN: http://cran.r-project.org/web/packages/adegenet/. Information and support including a dedicated forum of discussion can be found on the adegenet website: http://adegenet.r-forge.r-project.org/. adegenet is released with a manual and four tutorials totalling over 300 pages of documentation, and distributed under the GNU General Public Licence (≥2). CONTACT t.jombart@imperial.ac. uk. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
The Second Type VI Secretion System of Pseudomonas aeruginosa Strain PAO1 Is Regulated by Quorum Sensing and Fur and Modulates Internalization in Epithelial Cells*

Background: Three T6SSs are present in P. aeruginosa. H1-T6SS secretes bacteriolytic toxins. Results: H2-T6SS is regulated by quorum sensing and Fur and modulates internalization in epithelial cells through PI3K-Akt host pathway activation. Conclusion: H2-T6SS plays a role in virulence. Significance: In contrast to the anti-prokaryotic H1-T6SS, H2-T6SS targets human cells. Those T6SSs can carry out different functions important in establishing infection. The genome of Pseudomonas aeruginosa PAO1 contains three type VI secretion systems (T6SSs) called H1-, H2-, and H3-T6SS. The H1-T6SS secretes three identified toxins that target other bacteria, providing a fitness advantage for P. aeruginosa, and likely contributes to bacterial pathogenesis in chronic infections. However, no specific substrates or defined roles have been described for the two other systems. Here, we demonstrate that the expression of H2-T6SS genes of strain PAO1 is up-regulated during the transition from exponential to stationary phase growth and regulated by the Las and Rhl quorum sensing systems. In addition, we identify two putative Fur boxes in the promoter region and find that H2-T6SS transcription is negatively regulated by iron. We also show that the H2-T6SS system enhances bacterial uptake into HeLa cells (75% decrease in internalization with a H2-T6SS mutant) and into lung epithelial cells through a phosphatidylinositol 3-kinase-dependent pathway that induces Akt activation in the host cell (50% decrease in Akt phosphorylation). Finally, we show that H2-T6SS plays a role in P. aeruginosa virulence in the worm model. Thus, in contrast to H1-T6SS, H2-T6SS modulates interaction with eukaryotic host cells. Together, T6SS can carry out different functions that may be important in establishing chronic P. aeruginosa infections in the human host.
Software Design using Analogy and WordNet

Software design is a complex cognitive task. Given the lack of consistent and general methodologies, it often demands creative capacities that sometimes bring our insight closer to arts than to an engineering field. Much of the success obtained by software engineers in their designs, comes from their acquired know-how. One way to improve their work, is by providing CASE tools capable of assisting the software design task in two significant ways: storing past designs, and providing cognitive support for design space exploration. In this paper, we focus on the second aspect, presenting an approach to software design using analogy. We also describe how analogical reasoning can be combined with a general ontology – WordNet. This ontology provides object classification, and a conceptual network, in which we base our similarity mappings. An experimental study of the analogy-WordNet combination is also presented in this paper.
Characterization of Proteins Belonging to the CHAP-Related Superfamily within the Firmicutes

Cell division is a dynamic process ending by separation of the daughter cells. This final step requires the cleavage of the murein septum synthetized during cell division. In Streptococcus thermophilus, cse plays an important role in cell separation. Cse protein contains, at its N-terminal end, a signal peptide and a putative LysM motif suggesting that it is secreted and able to bind to the cell wall. Furthermore, the C-terminus of Cse carries a putative cysteine, histidine-dependent amidohydrolases/peptidases (CHAP) domain conferring to the protein a potential catalytic activity. To gain insight into the role of Cse in the cell division process, in silico analysis of the Firmicutes proteins displaying CHAP-related domain was undertaken. This work allowed us to distinguish and characterize within the Firmicutes the 2 families of proteins (CHAP and NlpC/p60) belonging to the CHAP superfamily. These 2 families regroup mainly peptidoglycan hydrolases. Data from the literature indicate that NlpC/p60 and CHAP proteins cleave distinct peptidoglycan bonds. Among the enzymes characterized within the Firmicutes, NlpC/p60 proteins are γ-D-glutamate-meso-diaminopimelate muropeptidase. Instead, CHAP enzymes involved in cell separation are N-acetylmuramoyl-L-alanine amidase and CHAP lysins have endopeptidase activity.
Adaptive evolution of cytochrome c oxidase subunit VIII in anthropoid primates

Cytochrome c oxidase (COX) is a 13-subunit protein complex that catalyzes the last step in mitochondrial electron transfer in mammals. Of the 10 subunits encoded by nuclear DNA (three are mtDNA products), some are expressed as tissue- and/or development-specific isoforms. For COX subunit VIII, previous work showed that expression of the contractile muscle-specific isoform gene, COX8H, is absent in humans and Old World monkeys, and the other isoform gene, COX8L, is expressed ubiquitously. Here, we show that COX8H is transcribed in most primate clades, but its expression is absent in catarrhines, that is, in Old World monkeys and hominids (apes, including humans), having become a pseudogene in the stem of the catarrhines. The ubiquitously expressed isoform, COX8L, underwent nonsynonymous rate acceleration and elevation in the ratio of nonsynonymous/synonymous changes in the stem of anthropoid primates (New World monkeys and catarrhines), possibly setting the stage for loss of the heart-type (H) isoform. The most rapidly evolving region of VIII-L is one that interacts with COX I, suggesting that the changes are functionally coadaptive. Because accelerated rates of nonsynonymous substitutions in anthropoids such as observed for COX8L are also shown by genes for at least 13 other electron transport chain components, these encoded amino acid replacements may be viewed as part of a series of coadaptive changes that optimized the anthropoid biochemical machinery for aerobic energy metabolism. We argue that these changes were linked to the evolution of an expanded neocortex in anthropoid primates.
User Preference Learning Based Edge Caching for Fog-RAN

In this paper, the edge caching problem in fog radio access networks (F-RAN) is investigated. By maximizing the overall cache hit rate, the edge caching optimization problem is formulated to find the optimal edge caching policy. We consider content popularity in terms of time and space from the perspective of regional users. Taking into account that users request the contents they are interested in, we propose an online content popularity prediction algorithm by leveraging the content features and user preferences, and an offline user preference learning algorithm by using the "Online Gradient Descent" (OGD) method and the "Follow The (Proximally) Regularized Leader" (FTRL-Proximal) method. Our proposed edge caching policy not only can promptly predict the future content popularity in an online fashion with low computational complexity, but it also can track the content popularity with spatial and temporal popularity dynamics in time without delay. We theoretically derive the upper bound of the popularity prediction error, the lower bound of the cache hit rate, and the regret bound of the overall cache hit rate of our proposed edge caching policy. Furthermore, to implement our proposed edge caching policy, we design two learning based edge caching architectures for F-RAN, which have the capability of flexibly setting the monitoring cycle and is effective in various edge caching scenarios. Simulation results show that the overall cache hit rate of our proposed policy is superior to those of the traditional policies and asymptotically approaches the optimal performance.
Estimation of errors in determining intrathoracic blood volume using thermal dilution in pigs with acute lung injury and haemorrhage.

BACKGROUND Global end diastolic volume (GEDV) has a constant and predictable relationship to intrathoracic blood volume (ITBV). The present study assesses the difference between ITBV derived from GEDV and ITBV measured directly in pigs with acute lung injury (ALI) and mild haemorrhage. METHODS We caused ALI in 12 anaesthetized pigs by i.v. injection of oleic acid and removed 10% of estimated blood volume. EVLW, GEDV, ITBV (COLD; Pulsion Medical Systems), Pa(o(2))/Fi(o(2)), lung compliance and haemodynamic variables were measured at baseline (time 0) and at 30 and 120 min. All animals were volume-resuscitated, followed by measurements at 180 min. A linear equation estimated from the 44 pairs of ITBV and GEDV values in 11 animals was applied iteratively to the four GEDV measurements in the 12th animal, enabling 48 comparisons between measured (ITBVm) and derived ITBV (ITBVd) to be made. RESULTS Increase in extravascular lung water index (EVLWi) was associated with significant pulmonary hypertension, worsening of oxygenation and compliance (repeated measures ANOVA; P<0.05). There was good within-subject correlation and agreement between ITBV(m) and ITBV(d) (r=0.72, mean bias 0.8 ml; sd 32 ml). Mean error in deriving ITBV from GEDV was 4.5%. (sd 4.2%; range 0.05-19%). There were no significant differences in errors in the presence of small (up to 10%) deficits in blood volume (F=1.0; P=0.41). CONCLUSIONS ITBV estimated by thermodilution alone is comparable to measurements made by the thermo-dye dilution technique in the presence of pulmonary hypertension and mild deficits in total blood volume.
A taxonomy for measuring the success of open source software projects

Open Source Software (OSS) has been widely adopted by organizations as well as individual users and has changed the way software is developed, deployed and perceived. Research into OSS success is critical since it provides project leaders with insights into how to manage an OSS project in order to succeed. However, there is no universally agreed definition of “success” and researchers employ different dimensions ( e.g. , project activity and project performance) to refer to OSS success. By conducting a rigorous literature survey, this paper seeks to take a holistic view to explore various areas of OSS success that have been studied in prior research. Finally it provides a measurement taxonomy including six success areas for OSS projects. Implications for theory and practice are presented.