Miracle-dz/UniFAR-FTUs huggingface dataset:
Lysine methylation modulates the protein–protein interactions of yeast cytochrome C Cyc1p

In recent years, protein methylation has been established as a major intracellular PTM. It has also been proposed to modulate protein‐protein interactions (PPIs) in the interactome. To investigate the effect of PTMs on PPIs, we recently developed the conditional two‐hybrid (C2H) system. With this, we demonstrated that arginine methylation can modulate PPIs in the yeast interactome. Here, we used the C2H system to investigate the effect of lysine methylation. Specifically, we asked whether Ctm1p‐mediated trimethylation of yeast cytochrome c Cyc1p, on lysine 78, modulates its interactions with Erv1p, Ccp1p, Cyc2p and Cyc3p. We show that the interactions between Cyc1p and Erv1p, and between Cyc1p and Cyc3p, are significantly increased upon trimethylation of lysine 78. This increase of interaction helps explain the reported facilitation of Cyc1p import into the mitochondrial intermembrane space upon methylation. This first application of the C2H system to the study of methyllysine‐modulated interactions further confirms its robustness and flexibility.
An empirical model for estimating annual consumption by freshwater fish populations

Abstract Population consumption is an important process linking predator populations to their prey resources. Simple tools are needed to enable fisheries managers to estimate population consumption. We assembled 74 individual estimates of annual consumption by freshwater fish populations and their mean annual population size, 41 of which also included estimates of mean annual biomass. The data set included 14 freshwater fish species from 10 different bodies of water. From this data set we developed two simple linear regression models predicting annual population consumption. Log-transformed population size explained 94% of the variation in log-transformed annual population consumption. Log-transformed biomass explained 98% of the variation in log-transformed annual population consumption. We quantified the accuracy of our regressions and three alternative consumption models as the mean percent difference from observed (bioenergetics-derived) estimates in a test data set. Predictions from our population-si.
Vulnerabilidade, impactos e adaptação à mudança do clima no semi-árido do Brasil

Este estudo apresenta uma revisao do estado da arte em estudos de clima, variabilidade e mudancas climaticas no semi-arido do Nordeste, e sao direcionadas principalmente aos aspectos de avaliacoes de vulnerabilidade e impactos, e com o intuito de fornecer subsidios para politicas regionais de adaptacao as mudancas climaticas. O trabalho representa uma atualizacao do que foi publicado no relatorio do Nucleo de Assuntos Estrategicos (NAE) em 2005. As evidencias observadas e o historico climatico da regiao sugerem que o semi-arido e vulneravel a variabilidade de clima, como evidenciadas pelas secas associadas aos eventos El Nino. Os cenarios futuros de clima sugerem ocorrencia de secas nesta regiao no futuro, sendo consequencia do aquecimento global, que podera afetar a populacao, a agricultura e os ecossistemas naturais. Este documento apresenta estudos das tendencias climaticas para a regiao, desenvolvidos durante os ultimos 50 anos e baseados em observacoes. Em seguida, e feita uma analise dos cenarios de clima do futuro (ate 2100) gerados pelos modelos usados no Quarto Relatorio de Painel Intergovernamental de Mudancas Climaticas (IPCC AR4) e a partir do recente Relatorio de Clima do Instituto Nacional de Pesquisas Espaciais (Inpe).
Accounting for the uncertainty of speech estimates in the complex domain for minimum mean square error speech enhancement

Uncertainty decoding and uncertainty propagation, or error propagation, techniques have emerged as a powerful tool to increase the accuracy of automatic speech recognition systems by employing an uncertain, or probabilistic, description of the speech features rather than the usual point estimate. In this paper we analyze the uncertainty generated in the complex Fourier domain when performing speech enhancement with the Wiener or Ephraim-Malah ﬁlters. We derive closed form solutions for the computation of the error of estimation and show that it provides a better insight into the origin of estimation uncertainty. We also show how the combination of such an error estimate with uncertainty propagation and uncertainty decoding or mod-iﬁed imputation yields superior recognition robustness when compared to conventional MMSE estimators with little increase in the computational cost.
Which types of hospital mergers save consumers money?

This study analyzes the changes in costs and prices from 1986 to 1994 for more than 3,500 U.S. short-term general hospitals, including 122 horizontal mergers. These mergers were generally financially beneficial to consumers, providing average price reductions of approximately 7 percent. Merger-related price reductions were considerably less in market areas with higher market concentration levels. Merger-related price reductions in areas with higher penetration by health maintenance organizations (HMOs) were approximately twice those in areas with lower HMO penetration. Merger-related price reductions were greater for low-occupancy hospitals, nonteaching hospitals, nonsystem hospitals, similar-size hospitals, and hospitals with greater premerger service duplication.
Solving structured segmentation of aerial images as puzzles

Traditional approaches to structured semantic segmentation employ appearance-based classifiers to provide a class-likelihood at each spatial location and then post-process it with Markov Random Fields (MRF) to enforce label smoothness and structure in the output space. The spatial support for such techniques is usually a patch of pixels, which makes the prediction over-smoothed because the borders of objects are not explicitly taken into account. This is further exacerbated by MRF post-processing employing the standard Potts model, which tends to further over-smooth predictions at boundaries. In this paper, we propose a different but related approach: we optimize an energy function finding the optimal combination of small ground truth (GT) tiles from training data over predictions at test time, effectively solving a puzzle. We optimize over a first configuration given by a Convolutional Neural Network (CNN) output.
Temporal regulation of human cytomegalovirus transcription at immediate early and early times after infection

The immediate early transcripts of human cytomegalovirus originated from restricted regions of the viral genome. In contrast, transcription at early times was complementary to all regions of the viral genome that were fractionated by restriction endonuclease treatment followed by agarose gel electrophoresis. The viral genome was also extensively transcribed when 2 h of protein synthesis or longer was permitted after infection in permissive cells treated with an inhibitor of viral DNA replication or in nonpermissive cells of animal origin that permit little or no viral DNA replication. The size and in vitro translation products of the cytomegalovirus-specified mRNA's at immediate early and early times after infection were determined. Discrete size classes of virus-specified polyadenylated RNA accumulated on the polyribosomes of cells infected in the presence of an inhibitor of protein synthesis. When 2 or 24 h of protein synthesis occurred after infection, there were changes in the relative abundance of the virus-specified RNAs that accumulated on polyribosomes. Treatment of nonpermissive cells had little effect on the size classes of viral RNA found associated with the polyribosomes at early times after infection. These viral mRNA's were assumed to represent early viral gene expression. In vitro translation of the viral mRNA isolated from polyribosomes at immediate early and early times after infection identified many of the virus-specified gene products and demonstrated (i) a switch from immediate early to early viral gene expression and (ii) a prolonged phase of early viral gene expression. The data also indicated that the initiation of viral RNA synthesis does not depend on the formation of viral protein, but that de novo viral protein synthesis may influence the extent of transcription of the viral genome.
Community structure promotes the emergence of persistence behavior in social networks

Cooperation phenomena are ubiquitous in social systems. In this paper, based on the Prisoner's dilemma game model, we study the evolution of cooperation in two social networks, namely, the scientific collaboration network (SCN) and the “Pretty-Good-Privacy” (PGP) trust network. Our investigation shows that due to the existence of community structures in real social networks, small-degree individuals tend to follow their local hubs' behavior and would adopt their strategies in the long run. Hence, the community structure promotes the emergence of persistence behavior. This provides a clue to understanding the evolution of cooperation in social systems.
Who is Using Chronic Acid Suppression Therapy and Why?

OBJECTIVES:Acid suppression medications have become one of the most commonly prescribed classes of therapeutic agents. Because little data exists describing the chronic use of these agents among a general population, we sought to determine the patterns of use of proton pump inhibitors (PPIs) and histamine type 2 receptor antagonists (H2RAs) in clinical practice, as well as the distribution and severity of symptoms in patients prescribed these therapies.METHODS:Pharmacy billing data from two insurers were used to identify all patients on chronic (>90 days) PPIs and H2RAs within a large, eastern Massachusetts provider network. Patient demographics, diagnoses, frequency of office visits, and information about diagnostic testing were obtained from billing databases. A questionnaire addressing recent upper GI symptoms, over-the-counter medication use, and gastroenterologist consultations was mailed to a 1,139 patient subset (35%) of eligible patients. We compared the diagnoses of patients on chronic therapy with those of the general population of the network. We also compared the frequency of symptoms and diagnostic testing between those prescribed H2RAs and PPIs.RESULTS:From a total population of 168,727 adult patients, we identified 4,684 (2.8%) prescribed chronic acid suppression therapy, with 47% taking H2RAs and 57% taking PPIs (4% filled prescriptions for both simultaneously). A relevant GI diagnosis was found using billing data for only 61% of patients, mainly for gastroesophageal reflux disease (38%) and dyspepsia (42%), with many patients carrying both diagnoses. Our survey (response rate 59%) revealed that more than 30% of responders experienced heartburn or reflux more than twice a week, and more than half experienced symptoms of dyspepsia at least once a week. Diagnostic testing was uncommon, with only 19% having undergone esophagogastroduodenoscopy within the prior 2 yr.CONCLUSIONS:Acid suppression medications were used chronically by a large number of patients within this population. A significant proportion of patients on chronic PPI or H2RA lacked definitive upper GI diagnoses in their billing data. The high symptom burden and low use of diagnostic testing indicates opportunities for improvement in the care of patients on chronic acid suppression therapy.
Ontogenetic growth rate responses of temperate marine copepods to chlorophyll concentration and light

The relationship between growth rate and food concentration often differs between nauplii and copepodites of the same species, but the nature of these relationships varies between sys- tems and species. The artificial cohort method was used to calculate growth rates of Acartia hudson- ica and Eurytemora herdmani nauplii and copepodites in Passamaquoddy Bay, the Bay of Fundy, under a natural range of chlorophyll a concentrations and different light regimes. Of 3 predictive maximum growth rate relationships previously published, the Bˇ elehradek function provided the most precise maximum growth rates, while the others underestimated growth rates of both nauplii and copepodites. No growth rates were correlated with chlorophyll a concentration in any size fraction, but a wide range in growth rates, particularly for the copepodites, was observed. Growth rates of nauplii and copepodites were lower at reduced than at ambient light intensities, but the reason for this is not clear. In general, naupliar growth appears less likely to be food limited than copepodite growth rates. The lack of observed food limitation for the nauplii in this system could be due to (1) nauplii ingesting more food per unit respiration than copepodites, or (2) nauplii not having sufficient lipid reserves and, under food-limiting conditions, rather than responding to food-limiting conditions by lowering growth rates, simply dying. A lower maximum growth rate and a smaller food resource of nauplii compared to copepodites may also explain why nauplii are less susceptible to food limita- tion in other systems.
Comprehensive and general method for the analysis and synthesis of fiber Bragg gratings

In this paper, a comprehensive, general and unified method for the complete analysis and synthesis of fiber Bragg gratings is proposed. The formalism is based on the well-known multilayer thin-film filters and transfer-matrix theories, considering the Bragg grating structure as a linear and time-invariant system. The developed analysis and synthesis algorithms have been significantly improved to be used on any kind of complex perturbation profiles, allowing the characterization and ‘ad hoc’ designs in both time and frequency domains.
Preliminary comparison of direct electric current measurements in lightning rods and peak current estimates from lightning location systems

This work presents preliminary observations of the first lightning flash striking an instrumented lightning rod on the top of a common building in Brazil. The measurements include direct electric current in the lightning rod, high-speed recordings using different types of cameras and data from two lightning location systems (LLS) that operate in Brazil: RINDAT and BrasilDAT. The striking flash contained seven strokes. The current measurement of the first stroke had saturated and was not detected by both networks. We believe that the longer rise-time of the electric current prevented its detection by the LLS, since the lightning pulses are supposed to have a shorter rise time as shown in this work. The peak current of the detected strokes estimated by BrasilDAT and RINDAT networks were very close to the direct measurements. The average location error for BrasilDAT was 0.8 km (6 strokes detected, 86%) and for RINDAT was 0.4 km (2 strokes detected, 29%).
Efficiency of Government Social Spending in Croatia

This paper analyzes the relative efficiency of social spending and service delivery in Croatia by comparing social spending and key social (outcome) indicators in Croatia to those of comparator countries. The analysis finds evidence of significant inefficiencies in Croatia’s social spending, mainly related to inadequate cost recovery for health and education services, weaknesses in the financing mechanisms and institutional arrangements, weak competition in the provision of social services, and weaknesses in targeting benefits. The paper also identifies areas for cost recovery and reform.
Adjuvant activity of carbohydrate analogs of N-acetylmuramyl-L-alanyl-D-isoglutamine on the induction of delayed-type hypersensitivity to azobenzenearsonate-N-acetyl-L-tyrosine in guinea pigs

The adjuvant activity of 29 kinds of carbohydrate analogs of N-acetylmuramyl-L-alanyl-D-isoglutamine on the induction of delayed-type hypersensitivity to azobenzenearsonate-N-acetyl-L-tyrosine was examined in guinea pigs. It was found that the D-manno- and D-galacto-type muramyldipeptides were as active as the D-gluco-type muramyldipeptide (MDP). The structural requirement of the carbohydrate moiety of analogs of N-acetylmuramyl-L-alanyl-D-isoglutamine is discussed.
Evolutionary crossroads in developmental biology: annelids

Annelids (the segmented worms) have a long history in studies of animal developmental biology, particularly with regards to their cleavage patterns during early development and their neurobiology. With the relatively recent reorganisation of the phylogeny of the animal kingdom, and the distinction of the super-phyla Ecdysozoa and Lophotrochozoa, an extra stimulus for studying this phylum has arisen. As one of the major phyla within Lophotrochozoa, Annelida are playing an important role in deducing the developmental biology of the last common ancestor of the protostomes and deuterostomes, an animal from which >98% of all described animal species evolved.
Genetic Algorithm Based Visual Localization for a Robot PET in Home Healthcare System

The simultaneous localization and mapping technique is an important requirement in the development autonomous robot. Many localization algorithms for wheeled robots using various sensors have been proposed. In this article, we present a visual localization algorithm for a small home-use robot pet (legged robot). A low-resolution camera is equipped on the robot as the only sensor for localization. Challenges of visual localization for legged robots include: (1) Unmodeled motion errors due to leg slippages are common in legged robot, (2) as the oscillated walking motion of robot leads to fluctuated sensor data, the high degree of freedom of legged robot increases the complexity of the localization problem and (3) camera has limited field of view and image points lack of depth information. In the proposed algorithm, the localization for high-dimensional movement robot is modeled as an optimization. The objective function is then solved by a genetic algorithm. Approaches to (1) increase the efficiency of the search and (2) weaken the influence of noisy feature points to the localization results are presented. Results from simulations show that the proposed algorithm is able to localize the legged robot accurately and efficiently.
Consistency and stability of active contours with Euclidean and non-Euclidean arc lengths

External energies of active contours are often formulated as Euclidean arc length integrals. In this paper, we show that such formulations are biased. By this we mean that the minimum of the external energy does not occur at an image edge. In addition, we also show that for certain forms of external energy the active contour is unstable--when initialized at the true edge, the contour drifts away and becomes jagged. Both of these phenomena are due to the use of Euclidean arc length integrals. We propose a non-Euclidean arc length which eliminates these problems. This requires a reformulation of active contours where a single external energy function is replaced by a sequence of energy functions and the contour evolves as an integral curve of the gradient of these energies. The resulting active contour not only has unbiased external energy, but is also more controllable. Experimental evidence is provided in support of the theoretical claims.
United Kingdom national paediatric bilateral project: Demographics and results of localization and speech perception testing

Objectives: To assess longitudinal outcomes in a large and varied population of children receiving bilateral cochlear implants both simultaneously and sequentially. Methods: This observational non-randomized service evaluation collected localization and speech recognition in noise data from simultaneously and sequentially implanted children at four time points: before bilateral cochlear implants or before the sequential implant, 1 year, 2 years, and 3 years after bilateral implants. No inclusion criteria were applied, so children with additional difficulties, cochleovestibular anomalies, varying educational placements, 23 different home languages, a full range of outcomes and varying device use were included. Results: 1001 children were included: 465 implanted simultaneously and 536 sequentially, representing just over 50% of children receiving bilateral implants in the UK in this period. In simultaneously implanted children the median age at implant was 2.1 years; 7% were implanted at less than 1 year of age. In sequentially implanted children the interval between implants ranged from 0.1 to 14.5 years. Children with simultaneous bilateral implants localized better than those with one implant. On average children receiving a second (sequential) cochlear implant showed improvement in localization and listening in background noise after 1 year of bilateral listening. The interval between sequential implants had no effect on localization improvement although a smaller interval gave more improvement in speech recognition in noise. Children with sequential implants on average were able to use their second device to obtain spatial release from masking after 2 years of bilateral listening. Although ranges were large, bilateral cochlear implants on average offered an improvement in localization and speech perception in noise over unilateral implants. Conclusion: These data represent the diverse population of children with bilateral cochlear implants in the UK from 2010 to 2012. Predictions of outcomes for individual patients are not possible from these data. However, there are no indications to preclude children with long inter-implant interval having the chance of a second cochlear implant.
A location-adaptive virtual networked appliance

The paper presents a new way of constructing a Virtual Networked Appliance (VNA) middleware using location information. In the VNA architecture which we proposed in our previous work (J. Nakazawa et al., 2000), adaptation to the location of a user has not been clearly specified. We call such a location adaptive VNA "L-VNA". In L-VNA, location management is encapsulated in the runtime of VNA, thereby eliminating a user's explicit decision for location adaptation. We have implemented L-VNA over JDK1.2 and demonstrated its validity.
(E)-1-(4-Nitrophenyl)-2-(4-{[(E)-2-(4-nitrophenyl)hydrazinylidene]methyl}benzylidene)hydrazine dihydrate

The 30 non-H atoms in title dihydrazine compound, C20H16N6O4·2H2O, are close to coplanar, the r.m.s. deviation for these atoms being 0.096 Å. The conformation about each of the C=N bonds is E, and the molecule has non-crystallographic 2/m symmetry. The presence of O—H⋯O and N—H⋯O hydrogen bonding leads to a three-dimensional network in the crystal structure. A highly disordered solvent molecule is present within a molecular cavity defined by the organic and water molecules. Its contribution to the electron density was removed from the observed data in the final cycles of refinement and the formula, molecular weight and density are given without taking into account the contribution of the solvent molecule.