Miracle-dz/UniFAR-FTUs huggingface dataset:
Stimulation of nitrogen-fixing cyanobacteria in a Baltic Sea plankton community by land-derived organic matter or iron addition

In the Baltic Sea, floating blooms of nitrogen-fixing cyanobacteria occur yearly during late summer. These blooms can sometimes be limited by iron. Due to extensive foresting around the Baltic Sea, iron is entering the Baltic Sea partly bound to dissolved organic material (DOM) via rivers. An experiment was performed in 300 l laboratory mesocosms to test the hypothesis that riverine high- molecular weight dissolved organic matter (HMWDOM), extracted by tangential flow filtration >1000 Da, stimulates the biomass of nitrogen-fixing cyanobacteria, by increasing the availability of iron. The addition of iron/EDTA and of DOM resulted in 5 to 10 times higher biomass of nitrogen- fixing cyanobacteria. Accordingly, higher primary production and particulate nitrogen concentration at the end of the experiment were observed in those treatments compared to the control. The removal of mesozooplankton grazers did not have a significant effect on the microphytoplankton biomass and species composition. Nodularia spumigena biomass was highest in the treatments receiving DOM, but addition of iron alone had no significant effect on this. N. spumigena was less positively affected by iron addition than Anabaena cf. inaequalis, suggesting that N. spumigena is a better competitor for iron. Separate microcosms comparing additions of iron, manganese and cobalt showed that iron was limiting for cyanobacterial biomass development. The results strongly suggest that iron bound to DOM can contribute to the iron demands of nitrogen-fixing cyanobacteria in the Baltic Sea.
Extended molecular dynamics of a c-kit promoter quadruplex

The 22-mer c-kit promoter sequence folds into a parallel-stranded quadruplex with a unique structure, which has been elucidated by crystallographic and NMR methods and shows a high degree of structural conservation. We have carried out a series of extended (up to 10 μs long, ∼50 μs in total) molecular dynamics simulations to explore conformational stability and loop dynamics of this quadruplex. Unfolding no-salt simulations are consistent with a multi-pathway model of quadruplex folding and identify the single-nucleotide propeller loops as the most fragile part of the quadruplex. Thus, formation of propeller loops represents a peculiar atomistic aspect of quadruplex folding. Unbiased simulations reveal μs-scale transitions in the loops, which emphasizes the need for extended simulations in studies of quadruplex loops. We identify ion binding in the loops which may contribute to quadruplex stability. The long lateral-propeller loop is internally very stable but extensively fluctuates as a rigid entity. It creates a size-adaptable cleft between the loop and the stem, which can facilitate ligand binding. The stability gain by forming the internal network of GA base pairs and stacks of this loop may be dictating which of the many possible quadruplex topologies is observed in the ground state by this promoter quadruplex.
THE JOHNSON COKERNEL AND THE ENOMOTO-SATOH INVARIANT

We study the cokernel of the Johnson homomorphism for the mapping class group of a surface with one boundary component. A graphical trace map simultaneously generalizing trace maps of Enomoto-Satoh and Conant-Kassabov-Vogtmann is given, and using technology from the author’s work with Kassabov and Vogtmann, this is is shown to detect a large family of representations which vastly generalizes series due to Morita and Enomoto-Satoh. The Enomoto-Satoh trace is the rank 1 part of the new trace. The rank 2 part is also investigated.
Crowding Effects on Amyloid Aggregation Kinetics

Biological protein self-assembly occurs in the cellular milieu, densely occupied by other macromolecules which do not participate directly in the aggregation process. Excluded volume effects arising in such a crowded environment deeply affect the thermodynamics and kinetics of biological processes, like protein folding, ligand binding, and protein aggregation. Here, Langevin dynamics simulations of a simplified model of an amphipathic polypeptide are used to investigate how macromolecular crowding influences the amyloid aggregation kinetics. The simulations show that the net influence of macromolecular crowding on the self-assembly process is the result of two competing effects: oligomer stabilization and solution viscosity increase. Notably, the net effect crucially depends on the aggregation propensity and pathways. Therefore, comparative studies of concentration and crowding effects on the kinetics of amyloid aggregation could shed light on the underlying self-assembly mechanism.
Group I Disynaptic Excitation in Flexor and Bifunctional Motoneurons during Locomotion

In the absence of locomotion, activation of extensor muscle spindle (Ia) and tendon organ (Ib) afferents evokes a widespread pattern of interneuronally mediated inhibition and excitation through the non-reciprocal reflex systems (1). During the extension phase of fictive locomotion, however, the same afferents evoke a disynaptic excitation of extensor motoneurons (2). Recently it has been reported that stimulation of flexor group I afferents also evokes a locomotor-dependent excitation of ankle flexor motoneurons (3). The present study further examined the distribution of locomotor-dependent group I excitation of flexor motoneurons and extended the analysis to motoneurons showing complex patterns of depolarization during locomotion, i.e. motoneurons innervating bifunctional muscles. Intracellular recordings of antidromically identified motoneurons were made (using glass microelectrodes filled with QX-314 to block action potentials) in decerebrate cats in which fictive locomotion was elicited by brainstem s timulation following neuromuscular blockade (see reference 2).
High Theta and Low Alpha Powers May Be Indicative of BCI-Illiteracy in Motor Imagery

In most brain computer interface (BCI) systems, some target users have significant difficulty in using BCI systems. Such target users are called ‘BCI-illiterate’. This phenomenon has been poorly investigated, and a clear understanding of the BCI-illiteracy mechanism or a solution to this problem has not been reported to date. In this study, we sought to demonstrate the neurophysiological differences between two groups (literate, illiterate) with a total of 52 subjects. We investigated recordings under non-task related state (NTS) which is collected during subject is relaxed with eyes open. We found that high theta and low alpha waves were noticeable in the BCI-illiterate relative to the BCI-literate people. Furthermore, these high theta and low alpha wave patterns were preserved across different mental states, such as NTS, resting before motor imagery (MI), and MI states, even though the spatial distribution of both BCI-illiterate and BCI-literate groups did not differ. From these findings, an effective strategy for pre-screening subjects for BCI illiteracy has been determined, and a performance factor that reflects potential user performance has been proposed using a simple combination of band powers. Our proposed performance factor gave an r = 0.59 (r2 = 0.34) in a correlation analysis with BCI performance and yielded as much as r = 0.70 (r2 = 0.50) when seven outliers were rejected during the evaluation of whole data (N = 61), including BCI competition datasets (N = 9). These findings may be directly applicable to online BCI systems.
When Truces Collapse: A Longitudinal Study of Price-Adjustment Routines

We analyze the microfoundations of the routine in a study of price-adjustment processes at a manufacturing firm. Existing theory says that truces balance cognitive and motivational differences across functions, but there is scant evidence on how truces work. We show both stability and change in routines. For minor price adjustments, routines incorporate truces in stable but separate market interpretations by the sales and marketing groups. Major price changes put truces at risk, as latent conflict over information and interests becomes overt. The ensuing battle shows how interests, information, and truces are intertwined in performing the routine. Routines are not just stable entities, but adaptive performances that include conflict. We illustrate how our approach addresses fundamental problems such as how firms perform economics, how routines incorporate economic theory, and how routines shape macroeconomic dynamics. We argue that our approach can be extended to any routine-based organizational work.
How Many Bits Are Needed To Store Probabilities for Phrase-Based Translation?

State of the art in statistical machine translation is currently represented by phrase-based models, which typically incorporate a large number of probabilities of phrase-pairs and word n-grams. In this work, we investigate data compression methods for efficiently encoding n-gram and phrase-pair probabilities, that are usually encoded in 32-bit floating point numbers. We measured the impact of compression on translation quality through a phrase-based decoder trained on two distinct tasks: the translation of European Parliament speeches from Spanish to English, and the translation of news agencies from Chinese to English. We show that with a very simple quantization scheme all probabilities can be encoded in just 4 bits with a relative loss in BLEU score on the two tasks by 1.0% and 1.6%, respectively.
Habitat loss and raptor predation: disentangling long– and short–term causes of red grouse declines

The number of red grouse (Lagopus lagopus scoticus) shot in the UK has declined by 50% during the 20th century. This decline has coincided with reductions in the area of suitable habitat and recoveries in the populations of some avian predators. Here we use long–term records of shooting bags and a large–scale manipulation of raptor density to disentangle the effects of habitat loss and raptor predation on grouse populations. The numbers of grouse harvested on the Eskdale half of Langholm Moor in southern Scotland declined significantly during 1913–1990 and grouse bags from the whole moor from 1950 to 1990 exhibited an almost identical but non–significant trend. Hen harriers (Circus cyaneus) and peregrine falcons (Falco peregrinus) were absent or bred at low densities on this moor throughout this period but heather–dominant vegetation declined by 48% between 1948 and 1988. Harrier and peregrine breeding numbers on Langholm Moor increased to high levels following protection in 1990 whilst grouse density and grouse bags declined year after year until shooting was abandoned in 1998. The prediction of a peak in grouse bags on Langholm Moor in 1996 based on the patterns of bags during 1950–1990 was supported by the observed peaks in 1997 on two nearby moors with few raptors which formerly cycled in synchrony with Langholm Moor. This study demonstrates that, whilst long–term declines in grouse bags were most probably due to habitat loss, high levels of raptor predation subsequently limited the grouse population and suppressed a cycle. This study thus offers support to theoretical models which predict that generalist predators may suppress cycles in prey populations.
The Dunedin Multidisciplinary Health and Development Study: are its findings consistent with the overall New Zealand population?

AIMS To compare the health of the Dunedin Multidisciplinary Health and Development Study members with people of the same age in the nationally representative New Zealand Health and National Nutrition Surveys. METHOD Where similar information was obtained, means or proportions and confidence intervals were generated for both the age 26 assessment of the Dunedin sample and for the 25-26 year old participants in the national surveys. The populations were considered to differ when confidence intervals did not overlap. RESULTS For smoking habit, body mass index, waist-hip ratio, general practitioner and medical specialist consultations, and hospital admissions, the findings of the Dunedin Study were not significantly different to the nationally representative surveys. The Dunedin Study members also did not differ from their national counterparts on SF-36 subscales measuring physical functioning, bodily pain, general health, vitality, and mental health. They had better scores on the three interference subscales of the SF-36 compared to the national sample, and men in the Dunedin Study spent a little more time doing vigorous physical activity. DISCUSSION For most outcomes, the Dunedin Study members were very similar to the nationally representative samples. There was little evidence that the repeated assessments in the Dunedin Study had significantly altered the Study members' health, either in terms of responses to questionnaires or on physiological measures of health status. Findings from the Dunedin Study are likely to be generalisable to most young New Zealanders. However, the Dunedin Study is under-representative of Maori and Pacific peoples, so these findings need to be interpreted with caution in this context. Implications for the proposed national Longitudinal Study of New Zealand Children and Families are discussed.
Clinical outcomes of peripartum cardiomyopathy: a 15-year nationwide population-based study in Asia

Abstract Peripartum cardiomyopathy (PPCM) is the development of heart failure during late pregnancy to months postpartum with potential fatal outcome. However, the disease is not well-studied in Asia. We aimed to investigate the epidemiology and clinical outcomes of PPCM in Taiwan. Electronic medical records were retrieved from Taiwan National Health Insurance Research Database from 1997 to 2011. Patients with PPCM were separated into 3 groups based on the timing of diagnosis. Early: PPCM diagnosed first to ninth month of pregnancy. Traditional: PPCM diagnosed last month of pregnancy till fifth month post-delivery. Late: PPCM diagnosed sixth to twelfth month post-delivery. Primary outcomes defined as cardiac death, all-cause mortality, and major adverse cardiovascular events (MACE) within 1 year. A total of 3,506,081 deliveries during 1997 to 2011 were retrieved and 925 patients with PPCM were identified. Overall incidence of PPCM was 1:3,790 during the 15 years. Early, Traditional, and Late group each had 88, 742, and 95 patients. Cardiac death occurred in 31 patients, all-cause mortality in 72 patients, and MACE in 65 patients. Late group had 2- to 3-fold event rates in cardiac death, all-cause mortality, and MACE compared with Early and Traditional groups. Cumulative incidence showed significant differences for cardiac death (P = .0011), all-cause mortality (P = .0031), and MACE (P = .0014) among 3 groups. Multivariate Cox model showed Late group had significantly worse outcomes after adjusted for clinical variables compared with 2 other groups. Our study is the largest national cohort among Asian countries that showed timing of diagnosis of PPCM had different outcomes. Late diagnosis portended significantly increased morbidity and mortality, even after adjusted for clinical variables.
Empirical Significance of Learning in a New Keynesian Model with Firm-Specific Capital

This paper examines the empirical significance of learning, a type of adaptive, boundedly rational expectations, in the U.S. economy within the framework of the New Keynesian model. Two popular specifications of the model are estimated: the standard three equation model that does not include capital, and an extended model that allows for endogenous capital accumulation. Estimation results for learning models can be sensitive to the choice for the initial conditions for agents expectations, so four different methods for choosing initial conditions are examined, including jointly estimating the initial conditions with the other parameters of the model. Maximum likelihood results show that learning under all methods for initial conditions lead to very similar predictions as rational expectations, and do not significantly improve the fit the model. The evolution of forecast errors show that the learning models do not out perform the rational expectations model during the run-up of inflation in the 1970s and the subsequent decline in the 1980s, a period of U.S. history which others have suggested learning may play a role. Despite the failure of learning models to better explain the data, analysis of the paths of expectations and structural shocks during the sample show that allowing for learning in the models can lead to different explanations for the data.
Self-Monitoring Interventions for At-Risk Middle School Students: The Importance of considering Function

Self-monitoring is a popular, efficient, and effective intervention that is associated with improved academic and social behavior for students across age and ability levels. To date, this is the first study to directly compare the outcomes of self-monitoring functionally relevant and nonrelevant replacement behaviors. Specifically, we used an experimental single-subject reversal design, with counterbalanced condition order, to document the relationship between types of self-monitoring (functionally relevant vs. nonrelevant) and off-task behavior for 2 at-risk middle school students. Across both participants, levels of off-task behavior were lower when a functionally relevant intervention was implemented than when a functionally nonrelevant intervention was implemented. Implications and limitations are discussed.
Incremental Validity of Personality Measures in Predicting Underwater Performance and Adaptation

Abstract Intelligence and personality traits are currently considered effective predictors of human behavior and job performance. However, there are few studies about their relevance in the underwater environment. Data from a sample of military personnel performing scuba diving courses were analyzed with regression techniques, testing the contribution of individual differences and ascertaining the incremental validity of the personality in an environment with extreme psychophysical demands. The results confirmed the incremental validity of personality traits (ΔR 2 = .20, f 2 = .25) over the predictive contribution of general mental ability (ΔR 2 = .07, f 2 = .08) in divers’ performance. Moreover, personality ( $R_L^2$ = .34) also showed a higher validity to predict underwater adaptation than general mental ability ( $R_L^2$ = .09). The ROC curve indicated 86% of the maximum possible discrimination power for the prediction of underwater adaptation, AUC = . 86, p < . 001, 95% CI (.82–.90). These findings confirm the shift and reversal of incremental validity of dispositional traits in the underwater environment and the relevance of personality traits as predictors of an effective response to the changing circumstances of military scuba diving. They also may improve the understanding of the behavioral effects and psychophysiological complications of diving and can also provide guidance for psychological intervention and prevention of risk in this extreme environment.
Apolipoprotein A-I Protection Against Atherosclerosis Is Dependent on Genetic Background

Objective—Inbred mouse strains have different susceptibilities to experimental atherosclerosis. The C57BL/6 strain is among the most sensitive and has, therefore, been the most widely used in atherosclerosis studies, whereas many strains are resistant. The FVB/N strain is highly resistant to atherosclerosis on the apolipoprotein E (apoE)– and low-density lipoprotein (LDL) receptor–deficient backgrounds. High-density lipoprotein and its major apoprotein, apoA-I, have been shown to be protective against atherogenesis on the C57BL/6 background. We here examine the influence of genetic background on the atheroprotective nature of apoA-I. Approach and Results—ApoE-deficient/apoA-I-deficient mice were generated in the C57BL/6 and FVB/N strains from apoE-deficient mice. After 6 to 10 weeks on a Western-type diet, plasma lipids and atherosclerotic lesion size were assessed. Macrophage recruitment, cholesterol regulation, and blood monocyte levels were examined as potential mechanisms driving lesion size differences. FVB/N knockout mice had higher plasma very-LDL/LDL cholesterol than their C57BL/6 counterparts. ApoA-I deficiency decreased very-LDL/LDL cholesterol in C57BL/6 mice but not in FVB/N mice. FVB/N single and double knockout mice had less lesion than C57BL/6 6 to 10 weeks on diet. ApoA-I deficiency augmented lesion development only in C57BL/6 mice. Macrophage recruitment to thioglycollate-treated peritoneum and diet-induced blood monocyte levels reflected the pattern of lesion development among the 4 genotypes. ApoA-I deficiency increased macrophage cholesterol content only in C57BL/6. FVB/N plasma was a better acceptor for macrophage cholesterol efflux than C57BL/6. Conclusions—ApoA-I is atheroprotective only in certain genetic contexts. In the C57BL/6 context, but not FVB/N, apoA-I decreases inflammatory macrophage recruitment and monocytosis, contributors to lesion formation.
Dual T cell receptor alpha chain T cells in autoimmunity

Allelic exclusion at the T cell receptor alpha locus TCR-alpha is incomplete, as demonstrated by the presence of a number of T lymphocyte clones carrying two expressed alpha chain products. Such dual alpha chain T cells have been proposed to play a role in autoimmunity, for example, because of a second TCR-alpha beta pair having bypassed negative selection by virtue of low expression. We examined this hypothesis by generating mice of various autoimmunity-prone strains carrying a hemizygous targeted disruption of the TCR-alpha locus, therefore unable to produce dual alpha chain T cells. Normal mice have a low but significant proportion of T cells expressing two cell-surface TCR-alpha chains that could be enumerated by comparison to TCR-alpha hemizygotes, which have none. Susceptibility to various autoimmune diseases was analyzed in TCR-alpha hemizygotes that had been backcrossed to disease-prone strains for several generations. The incidence of experimental allergic encephalomyelitis and of lupus is not affected by the absence of dual TCR-alpha cells. In contrast, nonobese diabetic (NOD) TCR alpha hemizygotes are significantly protected from cyclophosphamide-accelerated insulitis and diabetes. Thus, dual alpha T cells may play an important role in some but not all autoimmune diseases. Furthermore, since protected and susceptible NOD mice both show strong spontaneous responses to glutamic acid decarboxylase, responses to this antigen, if necessary for diabetetogenesis, are not sufficient.
ELECTROSTATIC-TUNING OF HERMETICALLY ENCAPSULATED COMPOSITE RESONATOR

MEMS resonators have promising future as frequency references with high levels of stability. In this paper, we present electrostatic-tuning of frequency for temperature compensation in Si-SiO2 composite resonators. This tuning technique uses the spring-softening effect for compensation. It is implemented by adjusting the DC bias voltage applied to the resonant structure. Electrostatic-tuning of silicon MEMS resonators has proven difficult because of the very large temperature induced frequency variation that must be overcome (2000 ppm). Si-SiO2 composite resonators have at least 10x less frequency variation over temperature, and lend themselves to electrostatic-tuning for compensation. This paper presents our first results for a tuning-based compensation approach over a full (70oC-wide) commercial temperature range.