Miracle-dz/UniFAR-FTUs huggingface dataset:
Envelope Widths of Volcano‐Seismic Events and Seismic Scattering Characteristics Beneath Volcanoes

Volcanoes produce highly scattered seismic wavefields, which are characterized by the scattering mean free path (l0) and the quality factor of medium attenuation for S waves (Qi). Previous studies have estimated scattering mean free paths at various volcanoes to be around 100–1,000 m, but their depth distributions remain to be determined. We estimated one‐dimensional l0 and Qi structures using the envelope widths of volcano‐seismic events at Taal (Philippines) and at Nevado del Ruiz (Colombia) in a high‐frequency band (5–10 Hz). We performed Monte Carlo envelope simulations in various one‐dimensional models, and compared the simulated and observed envelope widths. Our results indicate that a highly heterogeneous (l0 = 1,000 m) and attenuative (Qi = 100) surface layer exists to a depth of 1 km, below which l0 and Qi are comparable to those in the normal crust. The surface layer may consist of unconsolidated materials with hydrothermal fluids and/or altered clay minerals, which cause strong scattering and attenuation effects beneath these volcanoes. Our results suggest that strong heterogeneities observed at volcanoes exist only in a thin surface layer.
Radioactive Fingerprinting of Microorganisms That Oxidize Atmospheric Methane in Different Soils

ABSTRACT Microorganisms that oxidize atmospheric methane in soils were characterized by radioactive labelling with14CH4 followed by analysis of radiolabelled phospholipid ester-linked fatty acids (14C-PLFAs). The radioactive fingerprinting technique was used to compare active methanotrophs in soil samples from Greenland, Denmark, the United States, and Brazil. The 14C-PLFA fingerprints indicated that closely related methanotrophic bacteria were responsible for the oxidation of atmospheric methane in the soils. Significant amounts of labelled PLFAs produced by the unknown soil methanotrophs coeluted with a group of fatty acids that included i17:0, a17:0, and 17:1ω8c (up to 9.0% of the total 14C-PLFAs). These PLFAs are not known to be significant constituents of methanotrophic bacteria. The major PLFAs of the soil methanotrophs (73.5 to 89.0% of the total PLFAs) coeluted with 18:1 and 18:0 fatty acids (e.g., 18:1ω9, 18:1ω7, and 18:0). The 14C-PLFAs fingerprints of the soil methanotrophs that oxidized atmospheric methane did not change after long-term methane enrichment at 170 ppm CH4. The 14C-PLFA fingerprints of the soil methanotrophs were different from the PLFA profiles of type I and type II methanotrophic bacteria described previously. Some similarity at the PLFA level was observed between the unknown soil methanotrophs and the PLFA phenotype of the type II methanotrophs. Methanotrophs in Arctic, temperate, and tropical regions assimilated between 20 and 54% of the atmospheric methane that was metabolized. The lowest relative assimilation (percent) was observed for methanotrophs in agricultural soil, whereas the highest assimilation was observed for methanotrophs in rain forest soil. The results suggest that methanotrophs with relatively high carbon conversion efficiencies and very similar PLFA compositions dominate atmospheric methane metabolism in different soils. The characteristics of the methane metabolism and the 14C-PLFA fingerprints excluded any significant role of autotrophic ammonia oxidizers in the metabolism of atmospheric methane.
The dynamic nature of the nuclear envelope

In eukaryotes, chromosomes are encased by a dynamic nuclear envelope. In contrast to metazoans, where the nuclear envelope disassembles during mitosis, many fungi including budding yeast undergo “closed mitosis,” where the nuclear envelope remains intact throughout the cell cycle. Consequently, during closed mitosis the nuclear envelope must expand to accommodate chromosome segregation to the two daughter cells. A recent study by Witkin et al. in budding yeast showed that if progression through mitosis is delayed, for example due to checkpoint activation, the nuclear envelope continues to expand despite the block to chromosome segregation. Moreover, this expansion occurs at a specific region of the nuclear envelope- adjacent to the nucleolus- forming an extension referred to as a “flare. ” These observations raise questions regarding the regulation of nuclear envelope expansion both in budding yeast and in higher eukaryotes, the mechanisms confining mitotic nuclear envelope expansion to a particular region and the possible consequences of failing to regulate nuclear envelope expansion during the cell cycle.
Kursus Pra-Nikah: Konsep dan Implementasinya (Studi Komparatif antara BP4 KUA Kecamatan Pontianak Timur dengan GKKB Jemaat Pontianak).

Abstract: Pre-Marriage Training: The Concept and Its Implementation (Comparative Study between BP4 KUA and GKKB Congregation in the Eastern District of Pontianak). This study compared the practices of pre-married Training conducted in KUA and in the GKKB Congregation in the Eastern District of Pontianak. This study is a field research using descriptive-comparative analysis. The goal is to see the similarities and the differences between the two practices that can be utilized for further study. The study finds out that the pre-marital courses, either that was conducted at KUA—known as Suscatin—or that was carried out in the GKKB Church—termed as Pre-Marriage Consultation—are not different in principle. The difference is only on technical matters. The two institutions, in fact, have similar goal of encouraging, preparing, dan guiding the prospective husband and wife to be able to establish harmonious household. Abstrak: Kursus Pra-Nikah: Konsep dan Implementasinya (Studi Komparatif Antara BP4 KUA Kecamatan Pontianak Timur dengan GKKB Jemaat Pontianak). Penelitian ini membandingkan praktik pemberian bimbingan bagi pasangan yang akan menikah yang dilaksanakan di KUA dengan yang dilaksanakan di lingkungan gereja. Studi ini adalah penelitian lapangan (field research) dengan menggunakan analisis deskriptif-komparatif. Tujuannya adalah untuk melihat perbedaan dan persamaan di antara kedua lembaga tersebut yang dapat dijadikan sebagai bahan untuk kajian lebih lanjut. Hasil penelitian menyimpulkan bahwa secara umum antara Kursus pra-nikah di KUA Kecamatan Pontianak Timur—yang dikenal dengan istilah Suscatin, dengan yang dilaksanakan di GKKB Jemaat Pontianak—dikenal dengan istilah Konseling Pra-Nikah—tidak memiliki perbedaan yang prinsip. Perbedaannya yang ada hanya pada hal-hal yang bersifat teknis. Keduanya memiliki tujuan yang sama yakni memberi arahan, gambaran persiapan, bimbingan, dan konseling kepada calon pasangan suami-istri untuk dapat membina rumah tangga yang sakinah, mawaddah, dan rahmah.
AutoISES: Automatically Inferring Security Specification and Detecting Violations

The importance of software security cannot be overstated. In the past, researchers have applied program analysis techniques to automatically detect security vulnerabilities and verify security properties. However, such techniques have limited success in reality because they require manually provided code-level security specifications. Manually writing and generating these code-level security specifications are tedious and error-prone. Additionally, they seldom exist in production software. In this paper, we propose a novel method and tool, called AutoISES, which Automatically Infers Security Specifications by statically analyzing source code, and then directly use these specifications to automatically detect security violations. Our experiments with the Linux kernel and Xen demonstrated the effectiveness of this approach - AutoISES automatically generated 84 security specifications and detected 8 vulnerabilities in the Linux kernel and Xen, 7 of which have already been confirmed by the corresponding developers.
Roles of PucR, GlnR, and TnrA in Regulating Expression of the Bacillus subtilisure P3 Promoter

ABSTRACT Expression of the P3 promoter of the Bacillus subtilis ureABC operon is activated during nitrogen-limited growth by PucR, the transcriptional regulator of the purine-degradative genes. Addition of allantoic acid, a purine-degradative intermediate, to nitrogen-limited cells stimulated transcription of ure P3 twofold. Since urea is produced during purine degradation in B. subtilis, regulation of ureABC expression by PucR allows purines to be completely degraded to ammonia. The nitrogen transcription factor TnrA was found to indirectly regulate ure P3 expression by activating pucR expression. The two consensus GlnR/TnrA binding sites located in the ure P3 promoter region were shown to be required for negative regulation by GlnR. Mutational analysis indicates that a cooperative interaction occurs between GlnR dimers bound at these two sites. B. subtilis is the first example where urease expression is both nitrogen regulated and coordinately regulated with the enzymes involved in purine transport and degradation.
Long-run and cyclical dynamics in the US stock market

This paper examines the long-run dynamics and the cyclical structure of various series related to the US stock market using fractional integration. We implement a procedure which enables one to consider unit roots with possibly fractional orders of integration both at the zero (long-run) and the cyclical frequencies. We examine the following series: inflation, real risk-free rate, real stock returns, equity premium and price/dividend ratio, annually from 1871 to 1993. When focusing exclusively on the long-run or zero frequency, the estimated order of integration varies considerably, but nonstationarity is found only for the price/dividend ratio. When the cyclical component is also taken into account, the series appear to be stationary but to exhibit long memory with respect to both components in almost all cases. The exception is the price/dividend ratio, whose order of integration is higher than 0.5 but smaller than 1 for the long-run frequency, and is between 0 and 0.5 for the cyclical component. Also, mean reversion occurs in all cases. Finally, we use six different criteria to compare the forecasting performance of the fractional (at both zero and cyclical frequencies) models with others based on fractional and integer differentiation only at the zero frequency. The results show that the former outperforms the others in a number of cases.
Nuclear magnetic resonance spectra of adenosine di- and triphosphate. II. Effect of complexing with divalent metal ions.

The requirement of a divalent metal ion for all enzymatic reactions involving adenosine diand triphosphate is well established, but the role of the metal ion is not clearly understood. In some kinase reactions (1, 2) kinetic evidence has been presented that the metal complex of adenosine triphosphate is the true substrate in the enzymatic reaction. The present study was undertaken to obtain information concerning changes in the structure of adenosine diand triphosphate caused by interactions with various divalent metal ions. Such information might shed some light on the changes in the reactivity of specific bonds in the nucleotides induced by the met’al ions and would certainly impose limitations on any proposed structure of an enzyme-substrate complex for these compounds. In a previous paper (3), it was shown that chemical shifts of the nuclear magnetic resonance peaks of the phosphorus nuclei of adenosine diand triphosphate could be measured on 0.1 M solutions of the nucleotides. The same techniques have been applied in the present investigation to observe the changes in the chemical shifts of the phosphorus magnetic resonance spectra in the presence of metal ions to give direct evidence of the nature of the complexes formed. With the use of high resolution technique, the chemical shifts of the proton magnetic resonance spectra in the nucleotides could be compared with the shifts in the metal complexes to determine the interaction of the metal ion with the adenine ring. The measurements were extended to include the effect of paramagnetic ions such as Mn ++ and Cu++ at low concentrations of the order of 1O-4 to 1O-5 M on the width of the absorption lines of both phosphorus and protons. Such spectra revealed preferential interactions with particular phosphorus nuclei and protons, thus specifying the nature of the met.al complexes formed.
Existence and Control of Go/No-Go Decision Transition Threshold in the Striatum

A typical Go/No-Go decision is suggested to be implemented in the brain via the activation of the direct or indirect pathway in the basal ganglia. Medium spiny neurons (MSNs) in the striatum, receiving input from cortex and projecting to the direct and indirect pathways express D1 and D2 type dopamine receptors, respectively. Recently, it has become clear that the two types of MSNs markedly differ in their mutual and recurrent connectivities as well as feedforward inhibition from FSIs. Therefore, to understand striatal function in action selection, it is of key importance to identify the role of the distinct connectivities within and between the two types of MSNs on the balance of their activity. Here, we used both a reduced firing rate model and numerical simulations of a spiking network model of the striatum to analyze the dynamic balance of spiking activities in D1 and D2 MSNs. We show that the asymmetric connectivity of the two types of MSNs renders the striatum into a threshold device, indicating the state of cortical input rates and correlations by the relative activity rates of D1 and D2 MSNs. Next, we describe how this striatal threshold can be effectively modulated by the activity of fast spiking interneurons, by the dopamine level, and by the activity of the GPe via pallidostriatal backprojections. We show that multiple mechanisms exist in the basal ganglia for biasing striatal output in favour of either the `Go' or the `No-Go' pathway. This new understanding of striatal network dynamics provides novel insights into the putative role of the striatum in various behavioral deficits in patients with Parkinson's disease, including increased reaction times, L-Dopa-induced dyskinesia, and deep brain stimulation-induced impulsivity.
Conserved amino acids in each subunit of the heteroligomeric tRNA m1A58 Mtase from Saccharomyces cerevisiae contribute to tRNA binding

In Saccharomyces cerevisiae, a two-subunit methyltransferase (Mtase) encoded by the essential genes TRM6 and TRM61 is responsible for the formation of 1-methyladenosine, a modified nucleoside found at position 58 in tRNA that is critical for the stability of tRNAiMet. The crystal structure of the homotetrameric m1A58 tRNA Mtase from Mycobacterium tuberculosis, TrmI, has been solved and was used as a template to build a model of the yeast m1A58 tRNA Mtase heterotetramer. We altered amino acids in TRM6 and TRM61 that were predicted to be important for the stability of the heteroligomer based on this model. Yeast strains expressing trm6 and trm61 mutants exhibited growth phenotypes indicative of reduced m1A formation. In addition, recombinant mutant enzymes had reduced in vitro Mtase activity. We demonstrate that the mutations introduced do not prevent heteroligomer formation and do not disrupt binding of the cofactor S-adenosyl-l-methionine. Instead, amino acid substitutions in either Trm6p or Trm61p destroy the ability of the yeast m1A58 tRNA Mtase to bind tRNAiMet, indicating that each subunit contributes to tRNA binding and suggesting a structural alteration of the substrate-binding pocket occurs when these mutations are present.
Predictors of Coronary and Carotid Atherosclerosis in Patients with Severe Degenerative Aortic Stenosis

Background. Patients with degenerative aortic stenosis (AS) exhibit elevated prevalence of coronary artery disease (CAD) and internal carotid artery stenosis (ICAS). Our aim was to investigate prevalence of significant CAD and ICAS in relation to demographic and cardiovascular risk profile among patients with severe degenerative AS. Methods. We studied 145 consecutive patients (77 men and 68 women) aged 49-91 years (median, 76) with severe degenerative AS who underwent coronary angiography and carotid ultrasonography in our tertiary care center. The patients were divided into two groups according to the presence of either significant CAD (n=86) or ICAS (n=22). Results. The prevalence of significant CAD or ICAS was higher with increasing number of traditional risk factors (hypertension, hypercholesterolemia, diabetes, smoking habit) and decreasing renal function. We found interactions between age and gender in terms of CAD (p=0.01) and ICAS (p=0.06), which was confirmed by multivariate approach. With the reference to men with a below-median age, the prevalence of CAD or ICAS increased in men aged >76 years (89% vs. 55% and 28% vs. 14%, respectively), whereas the respective percentages were lower in older vs. younger women (48% vs. 54% and 7% vs. 17%). Conclusions. In severe degenerative AS gender modulates the association of age with coronary and carotid atherosclerosis with its lower prevalence in women aged >76 years compared to their younger counterparts. This may result from a hypothetical “survival bias”, i.e., an excessive risk of death in very elderly women with severe AS and coexisting relevant coronary or carotid atherosclerosis.
Relations entre systèmes intrusifs et instabilités sur un volcan basaltique (Piton des Neiges, La Réunion)

L'etude des volcans basaltiques a demontre l'importance de leur architecture interne et de leur systeme intrusif dans le declenchement de destabilisations. Decoulant d'observations indirectes, les modeles elabores demeurent neanmoins interpretatifs. A La Reunion, l'importante erosion du Piton des Neiges, en rendant accessible sa structure interne, en fait un atout majeur pour combler ces lacunes d'observation. Ce travail s'est focalise sur le cirque de Salazie dans le but d'accroitre les connaissances de la structure interne du volcan. Nous proposons ainsi l'existence d'une chambre magmatique litee plurikilometrique situee a l'aplomb du cirque de Salazie qui appartiendrait a un edifice plus ancien estime a plus de 2 Ma. Cette chambre est recoupee par un detachement injecte de plusieurs dizaines d'intrusions basiques et surmonte par une breche d'avalanche de debris. La deformation cataclasique des mineraux primaires des roches plutoniques du detachement indique que cette structure s'est developpee dans le domaine fragile. Une deformation ductile posterieure de basse temperature (< 250 °C), caracterise par une cristallisation de chlorite, pumpellyite, zeolite et de calcite s'est ensuite developpee dans le detachement. Au toit de la pile de sills, des intrusions sont brechifies et dissemines dans la breche. Une analyse du sill au contact avec la breche montre l'existence d'une fabrique magmatique asymetrique revelatrice d'un deplacement co-intrusif de l'unite sus-jacente. Ces resultats suggerent que les volcans basaltiques s'effondrent par deformation le long de plans hydrothermalises et confirment le role majeur des sills dans la destabilisation des volcans boucliers.
Permanent Cardiac Pacing in Children: Choosing the Optimal Pacing Site A Multicenter Study

Background— We evaluated the effects of the site of ventricular pacing on left ventricular (LV) synchrony and function in children requiring permanent pacing. Methods and Results— One hundred seventy-eight children (aged <18 years) from 21 centers with atrioventricular block and a structurally normal heart undergoing permanent pacing were studied cross-sectionally. Median age at evaluation was 11.2 (interquartile range, 6.3–15.0) years. Median pacing duration was 5.4 (interquartile range, 3.1–8.8) years. Pacing sites were the free wall of the right ventricular (RV) outflow tract (n=8), lateral RV (n=44), RV apex (n=61), RV septum (n=29), LV apex (n=12), LV midlateral wall (n=17), and LV base (n=7). LV synchrony, pump function, and contraction efficiency were significantly affected by pacing site and were superior in children paced at the LV apex/LV midlateral wall. LV dyssynchrony correlated inversely with LV ejection fraction (R=0.80, P=0.031). Pacing from the RV outflow tract/lateral RV predicted significantly decreased LV function (LV ejection fraction <45%; odds ratio, 10.72; confidence interval, 2.07–55.60; P=0.005), whereas LV apex/LV midlateral wall pacing was associated with preserved LV function (LV ejection fraction ≥55%; odds ratio, 8.26; confidence interval, 1.46–47.62; P=0.018). Presence of maternal autoantibodies, gender, age at implantation, duration of pacing, DDD mode, and QRS duration had no significant impact on LV ejection fraction. Conclusions— The site of ventricular pacing has a major impact on LV mechanical synchrony, efficiency, and pump function in children who require lifelong pacing. Of the sites studied, LV apex/LV midlateral wall pacing has the greatest potential to prevent pacing-induced reduction of cardiac pump function.
Characterization of New Spt3 and TATA-Binding Protein Mutants of Saccharomyces cerevisiae: Spt3–TBP Allele-Specific Interactions and Bypass of Spt8

The Spt-Ada-Gcn5-acetyltransferase (SAGA) complex of Saccharomyces cerevisiae is a multifunctional coactivator complex that has been shown to regulate transcription by distinct mechanisms. Previous results have shown that the Spt3 and Spt8 components of SAGA regulate initiation of transcription of particular genes by controlling the level of TATA-binding protein (TBP/Spt15) associated with the TATA box. While biochemical evidence exists for direct Spt8–TBP interactions, similar evidence for Spt3–TBP interactions has been lacking. To learn more about Spt3–TBP interactions in vivo, we have isolated a new class of spt3 mutations that cause a dominant-negative phenotype when overexpressed. These mutations all cluster within a conserved region of Spt3. The isolation of extragenic suppressors of one of these spt3 mutations has identified two new spt15 mutations that show allele-specific interactions with spt3 mutations with respect to transcription and the recruitment of TBP to particular promoters. In addition, these new spt15 mutations partially bypass an spt8 null mutation. Finally, we have examined the level of SAGA–TBP physical interaction in these mutants. While most spt3, spt8, and spt15 mutations do not alter SAGA–TBP interactions, one spt3 mutation, spt3-401, causes a greatly increased level of SAGA–TBP physical association. These results, taken together, suggest that a direct Spt3–TBP interaction is required for normal TBP levels at Spt3-dependent promoters in vivo.
The Cytoplasmic C-Terminal Domain of the Escherichia coli KdpD Protein Functions as a K+ Sensor

ABSTRACT The KdpD protein is a K+ sensor kinase located in the cytoplasmic membrane of Escherichia coli. It contains four transmembrane stretches and two short periplasmic loops of 4 and 10 amino acid residues, respectively. To determine which part of KdpD functions as a K+ sensor, genetic variants were constructed with truncations or altered arrangements of the transmembrane segments. All KdpD constructs were tested by complementation of an E. coli kdpD deletion strain for their ability to grow at a K+ concentration of 0.1 mM in the medium. A soluble protein composed of the C-terminal cytoplasmic domain was able to complement the kdpD deletion strain. In addition, analysis of the β-galactosidase activity of an E. coli strain which carries a transcriptional fusion of the upstream region of the kdpFABC operon and a promoterless lacZ gene revealed that this soluble KdpD mutant responds to changes in the K+ concentration in the extracellular medium. The results suggest that the sensing and response functions are both located in the C-terminal domain and might be modulated by the N-terminal domain as well as by membrane anchoring.