Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematic Error in Seed Plant Phylogenomics

Resolving the closest relatives of Gnetales has been an enigmatic problem in seed plant phylogeny. The problem is known to be difficult because of the extent of divergence between this diverse group of gymnosperms and their closest phylogenetic relatives. Here, we investigate the evolutionary properties of conifer chloroplast DNA sequences. To improve taxon sampling of Cupressophyta (non-Pinaceae conifers), we report sequences from three new chloroplast (cp) genomes of Southern Hemisphere conifers. We have applied a site pattern sorting criterion to study compositional heterogeneity, heterotachy, and the fit of conifer chloroplast genome sequences to a general time reversible + G substitution model. We show that non-time reversible properties of aligned sequence positions in the chloroplast genomes of Gnetales mislead phylogenetic reconstruction of these seed plants. When 2,250 of the most varied sites in our concatenated alignment are excluded, phylogenetic analyses favor a close evolutionary relationship between the Gnetales and Pinaceae—the Gnepine hypothesis. Our analytical protocol provides a useful approach for evaluating the robustness of phylogenomic inferences. Our findings highlight the importance of goodness of fit between substitution model and data for understanding seed plant phylogeny.
A lower bound on outage probability of limited feedback MIMO beamforming systems

In this paper, the performance of multiple-input multiple-output (MIMO) beamforming-combining wireless systems employing limited feedback is studied from the point-of-view of outage probability. In the absence of perfect channel knowledge, the transmitter uses a quantized beamforming vector from a predesigned set of vectors, called codebook. A tight lower bound on the outage probability is derived for a system using an optimal codebook designed using maximizing minimum distance criterion. This analysis quantifies the impact of feedback rate and antenna systems. Simulations have shown that practical codebooks can closely achieve the lower bound.
CoNLL-2013 Shared Task: Grammatical Error Correction NTHU System Description

Grammatical error correction has been an active research area in the field of Natural Language Processing. This paper describes the grammatical error correction system developed at NTHU in participation of the CoNLL-2013 Shared Task. The system consists of four modules in a pipeline to correct errors related to determiners, prepositions, verb forms and noun number. Although more types of errors are involved that than last year’s Shared Task, leading to more complicated problem this year, our system still obtain higher F-score as compared to last year. We received an overall F-measure score of 0.325, which put our system in second place among 17 systems evaluated.
The Dynamics of Channel Slope, Width, and Sediment in Actively Eroding Bedrock River Systems

The evolution of rivers in eroding landscapes plays a key role in determining landscape relief and modulating climate‐tectonic interactions. A common approach to quantifying river system evolution uses a one‐dimensional, detachment‐limited stream power equation. One potential drawback of this model is that it does not incorporate the effects of changes in channel width or the role of sediment transport dynamics. Here I present a new method for modeling the influence of channel width on river dynamics to explore how variable width and sediment transport impact river profile evolution. With this approach, vertical river erosion can operate based on any number of river erosion models, such as a simple shear stress model (e.g., detachment limited), sediment cover‐shear stress hybrid models, or mechanistic saltation‐abrasion models. I explore the sensitivity of these three models to increases in rock‐uplift rate (i.e., 2, 3, 5, 10, and 20× increase). Generally, the results show that incorporating channel width adjustment or sediment transport dynamics lowers the sensitivity of a river profile to rock‐uplift rate. For the sediment transport‐dependent models, the degree of sensitivity depends on whether the system is limited by bedrock exposure or erosion potential (i.e., detachment potential). The approach produces transient responses that reveal distinct patterns of width and slope, which may provide valuable insight into the limiting physical mechanisms of bedrock erosion in a region. The implications of the work are broad and include the potential to distinguish underlying erosion controls from field observations of width and slope as well as understanding climate‐tectonic interactions.
On the Joint Evolution of Culture and Institutions

Explanations of economic growth and prosperity commonly identify a unique causal effect, e.g., institutions, culture, human capital, geography. In this paper we provide instead a theoretical modeling of the interaction between culture and institutions and their effects on economic activity. We characterize conditions on the socio-economic environment such that culture and institutions complement (resp. substitute) each other, giving rise to a multiplier effect which amplifies (resp. dampens) their combined ability to spur economic activity. We show how the joint dynamics of culture and institutions may display interesting non-ergodic behavior, hysteresis, oscillations, and comparative dynamics. Finally, in specific example societies, we study how culture and institutions interact to determine the sustainability of extractive societies as well as the formation of civic capital and of legal systems protecting property rights.
Antibiotic prophylaxis for permanent pacemaker implantation: a meta-analysis.

BACKGROUND Infection remains a serious complication after permanent pacemaker implantation. Antibiotic prophylaxis is frequently prescribed at the time of insertion to reduce its incidence, although results of well-designed, controlled studies are lacking. METHODS AND RESULTS We performed a meta-analysis of all available randomized trials to evaluate the effectiveness of antibiotic prophylaxis to reduce infection rates after permanent pacemaker implantation. Reports of trials were identified through a Medline, Embase, Current Contents, and an extensive bibliography search. Trials that met the following criteria were included: (1) prospective, randomized, controlled, open or blind trials; (2) patients assigned to a systemic antibiotic group or a control group; (3) end point events related to any infection after pacemaker implantation: wound infection, septicemia, pocket abscess, purulent secretion, right infective endocarditis, inflammatory signs, a positive culture, septic pulmonary embolism, or repeat operation for an infective complication. Seven trials met the inclusion criteria. They included 2023 patients with established permanent pacemaker implantation (new implants or replacements). The incidence of end point events in control groups ranged from 0% to 12%. The meta-analysis suggested a consistent protective effect of antibiotic pretreatment (P=.0046; common odds ratio: 0.256, 95% confidence interval: 0.10 to 0.656). CONCLUSIONS Results of the present meta-analysis suggest that systemic antibiotic prophylaxis significantly reduces the incidence of potentially serious infective complications after permanent pacemaker implantation. They support the use of prophylactic antibiotics at the time of pacemaker insertion to prevent short-term pocket infection, skin erosion or septicemia.
Object clauses, movement, and phrasal stress *

In this paper, we report the results of an experiment concerning the effect of object clauses on phrasal stress of the matrix verb. The presentation of the experiment is embedded in a discussion of the interaction of phrasal stress with movement in German. Section 2 includes some background on stress-assignment and an introduction to the interaction of syntactic movement with the assignment of phrasal stress. The experimental methods are laid out in Section 3, the results of the experiment in Section 4. The results are discussed in Section 5. Section 6 provides a summary.
Internalizing and externalizing behavior of children with enlisted Navy mothers experiencing military-induced separation.

OBJECTIVES To examine whether children with Navy mothers exhibit higher levels of internalizing and externalizing behavior than children in civilian families and whether deployment affects children's internalizing and externalizing behavior. METHOD Navy mothers who experienced deployment completed a measure assessing children's internalizing and externalizing behavior before and after a deployment (and at similar intervals for the Navy and civilian comparison groups). Data collection took place between 1996 and 1998. RESULTS Navy children with deployed mothers exhibited higher levels of internalizing behavior than children with nondeployed Navy mothers. Navy children whose mothers experienced deployment were more likely to exhibit clinical levels of internalizing behavior than Navy children with nondeployed mothers or civilian children. Group differences, however, were modest and overall mean scores were in the normal range. CONCLUSIONS Findings do not suggest greater pathology in children of Navy mothers; however, findings do indicate we should be particularly attentive of deployed mothers and their children.
A pattern classifier for interval-valued data based on multinomial logistic regression model

Interval-valued data arise in practical situations such as recording monthly interval temperatures at meteorological stations, daily interval stock prices, etc. This paper introduces a multinomial logistic regression method for interval-valued data in order to classify items described by interval-valued variables into a pre-defined number of a priori classes. Applications of the proposed approach on real as well as synthetic interval-valued data sets showed the usefulness of this approach.
On the (Mis) Understanding of the "this" Reference

The paper presents research conducted with high school (HS) students (N=86) learning object-oriented programming (OOP) and computer science HS teachers (N=48). The focus was on students' and teachers' understanding of the this reference. Proper conceptualization of this indicates an understanding of objects in general and of the current object, and it involves various aspects of programming variants. Students' preferences as to the use of the this reference were also examined. Findings revealed a lack of understanding of both the implication and the implementation of this; only 45% of the students expressed understanding of when we must use this; only 60% expressed understanding of when not to use this, and only 24% expressed clear understanding in their definition of this. Even correct answers do not necessarily indicate conceptual understanding, rather a repetition of definitions or programming habits, or a reliance on operative aspects of the implementation. The teachers expressed a considerable lack of clarity in accurately characterizing the correctness of students' answers.
Embodiment and psychopathology: a phenomenological perspective

Purpose of review To survey recent developments in phenomenological psychopathology. Recent findings We present the concept of embodiment as a key paradigm of recent interdisciplinary approaches from the areas of philosophy, psychology, psychiatry and neuroscience. This requires a short overview on the phenomenological concept of embodiment; in particular, on the distinction of subject and object body. A psychopathology of embodiment may be based on these and other distinctions, in particular on a polarity of disembodiment and hyperembodiment, which is illustrated by the examples of schizophrenia and depression. Recent contributions to phenomenological accounts of these disorders are presented. Finally, the study discusses the relationship of phenomenological and neuropsychiatric perspectives on embodiment. Summary A phenomenology of embodiment may be combined with enactive approaches to cognitive neuroscience in order to overcome dualist concepts of the mind as an inner realm of representations that mirror the outside world. Phenomenological and ecological concepts of embodiment should also be conjoined to enable a new, advanced understanding of mental illness.
Maps of Subsurface Hydrogen from the High Energy Neutron Detector, Mars Odyssey

After 55 days of mapping by the High Energy Neutron Detector onboard Mars Odyssey, we found deficits of high-energy neutrons in the southern highlands and northern lowlands of Mars. These deficits indicate that hydrogen is concentrated in the subsurface. Modeling suggests that water ice–rich layers that are tens of centimeters in thickness provide one possible fit to the data.
Decrease in Irisin in Patients with Chronic Kidney Disease

Patients with chronic kidney disease have abnormal energy expenditure and metabolism. The mechanisms underlying altered energy expenditure in uremia are unknown and remain to be elucidated. Irisin is a peroxisome proliferator-activated receptor γ coactivator 1-α–dependent myokine, and it increases energy expenditure in the absence of changes in food intake or activity. We hypothesize that chronic kidney disease patients have altered irisin levels. We measured resting irisin levels in 38 patients with stage 5 chronic kidney disease and in 19 age- and sex-matched normal subjects. Plasma irisin levels were significantly decreased in chronic kidney disease patients (58.59%; 95% CI 47.9%–69.2%, p<0.0001). The decrease in irisin levels was inversely correlated with the levels of blood urea nitrogen and creatinine. Further association analysis revealed that irisin level is independently associated with high-density lipoprotein cholesterol level. Our results suggest that chronic kidney disease patients have lower than normal irisin levels at rest. Furthermore, irisin may play a major role in affecting high-density lipoprotein cholesterol levels and abnormal energy expenditure in chronic kidney disease patients.
Organ-specific Sulfation Patterns of Heparan Sulfate Generated by Extracellular Sulfatases Sulf1 and Sulf2 in Mice*

Background: Extracellular endosulfatases Sulf1 and Sulf2 hydrolyze 6-O-sulfate in heparan sulfate. Results: Disaccharide analysis showed that 2-O-, 6-O-, and N-trisulfated disaccharide units in heparan sulfate were increased to different degrees in different organs in Sulf1 and Sulf2 knock-out mice. Conclusion: Sulfs generate organ-specific sulfation patterns of heparan sulfate. Significance: This may indicate differences in activity between Sulf1 and Sulf2 in vivo. Heparan sulfate endosulfatases Sulf1 and Sulf2 hydrolyze 6-O-sulfate in heparan sulfate, thereby regulating cellular signaling. Previous studies have revealed that Sulfs act predominantly on UA2S-GlcNS6S disaccharides and weakly on UA-GlcNS6S disaccharides. However, the specificity of Sulfs and their role in sulfation patterning of heparan sulfate in vivo remained unknown. Here, we performed disaccharide analysis of heparan sulfate in Sulf1 and Sulf2 knock-out mice. Significant increases in ΔUA2S-GlcNS6S were observed in the brain, small intestine, lung, spleen, testis, and skeletal muscle of adult Sulf1−/− mice and in the brain, liver, kidney, spleen, and testis of adult Sulf2−/− mice. In addition, increases in ΔUA-GlcNS6S were seen in the Sulf1−/− lung and small intestine. In contrast, the disaccharide compositions of chondroitin sulfate were not primarily altered, indicating specificity of Sulfs for heparan sulfate. For Sulf1, but not for Sulf2, mRNA expression levels in eight organs of wild-type mice were highly correlated with increases in ΔUA2S-GlcNS6S in the corresponding organs of knock-out mice. Moreover, overall changes in heparan sulfate compositions were greater in Sulf1−/− mice than in Sulf2−/− mice despite lower levels of Sulf1 mRNA expression, suggesting predominant roles of Sulf1 in heparan sulfate desulfation and distinct regulation of Sulf activities in vivo. Sulf1 and Sulf2 mRNAs were differentially expressed in restricted types of cells in organs, and consequently, the sulfation patterns of heparan sulfate were locally and distinctly altered in Sulf1 and Sulf2 knock-out mice. These findings indicate that Sulf1 and Sulf2 differentially contribute to the generation of organ-specific sulfation patterns of heparan sulfate.
Empirical performance evaluation of concurrency and coherency control protocols for database sharing systems

Database Sharing (DB-sharing) refers to a general approach for building a distributed high performance transaction system. The nodes of a DB-sharing system are locally coupled via a high-speed interconnect and share a common database at the disk level. This is also known as a “shared disk” approach. We compare database sharing with the database partitioning (shared nothing) approach and discuss the functional DBMS components that require new and coordinated solutions for DB-sharing. The performance of DB-sharing systems critically depends on the protocols used for concurrency and coherency control. The frequency of communication required for these functions has to be kept as low as possible in order to achieve high transation rates and short response times. A trace-driven simulation system for DB-sharing complexes has been developed that allows a realistic performance comparison of four different concurrency and coherency control protocols. We consider two locking and two optimistic schemes which operate either under central or distributed control. For coherency control, we investigate so-called on-request and broadcast invalidation schemes, and employ buffer-to-buffer communication to exchange modified pages directly between different nodes. The performance impact of random routing versus affinity-based load distribution and different communication costs is also examined. In addition, we analyze potential performance bottlenecks created by hot spot pages.
Blue Water in Europe: Estimates of Current and Future Availability and Analysis of Uncertainty

This study presents a regional assessment of future blue water availability in Europe under different assumptions. The baseline period (1960 to 1999) is compared to the near future (2020 to 2059) and the long-term future (2060 to 2099). Blue water availability is estimated as the maximum amount of water supplied at a certain point of the river network that satisfies a defined demand, taking into account specified reliability requirements. Water availability is computed with the geospatial high-resolution Water Availability and Adaptation Policy Assessment (WAAPA) model. The WAAPA model definition for this study extends over 6 million km2 in Europe and considers almost 4000 sub-basins in Europe. The model takes into account 2300 reservoirs larger than 5 hm3, and the dataset of Hydro 1k with 1700 sub-basins. Hydrological scenarios for this study were taken from the Inter-Sectoral Impact Model Inter-Comparison Project and included simulations of five global climate models under different Representative Concentration Pathways scenarios. The choice of method is useful for evaluating large area regional studies that include high resolution on the systems´ characterization. The results highlight large uncertainties associated with a set of local water availability estimates across Europe. Climate model uncertainties for mean annual runoff and potential water availability were found to be higher than scenario uncertainties. Furthermore, the existing hydraulic infrastructure and its management have played an important role by decoupling water availability from hydrologic variability. This is observed for all climate models, the emissions scenarios considered, and for near and long-term future. The balance between water availability and withdrawals is threatened in some regions, such as the Mediterranean region. The results of this study contribute to defining potential challenges in water resource systems and regional risk areas.
The Continuous Wagon Wheel Illusion and the ‘When’ Pathway of the Right Parietal Lobe: A Repetitive Transcranial Magnetic Stimulation Study

A continuous periodic motion stimulus can sometimes be perceived moving in the wrong direction. These illusory reversals have been taken as evidence that part of the motion perception system samples its inputs as a series of discrete snapshots –although other explanations of the phenomenon have been proposed, that rely on the spurious activation of low-level motion detectors in early visual areas. We have hypothesized that the right inferior parietal lobe (‘when’ pathway) plays a critical role in timing perceptual events relative to one another, and thus we examined the role of the right parietal lobe in the generation of this “continuous Wagon Wheel Illusion” (c-WWI). Consistent with our hypothesis, we found that the illusion was effectively weakened following disruption of right, but not left, parietal regions by low frequency repetitive transcranial magnetic stimulation (1 Hz, 10 min). These results were independent of whether the motion stimulus was shown in the left or the right visual field. Thus, the c-WWI appears to depend on higher-order attentional mechanisms that are supported by the ‘when’ pathway of the right parietal lobe.