Miracle-dz/UniFAR-FTUs huggingface dataset:
Long-term direct and indirect effects of the 'Exxon Valdez' oil spill on pigeon guillemots in Prince William Sound, Alaska

We conducted a study to determine mechanisms constraining population recovery of pigeon guillemots Cepphus columba following the 1989 'Exxon Valdez' oil spill. We asked whether recovery was limited by continuing exposure to residual oil, reduced prey availability, or other causes. Our approach was to compare demographic, physiological, and behavioral parameters between an oiled site pre- and post-spill, and between the oiled site and an unoiled site post-spill. Adult mass, body condition, and nestling survival were significantly lower at the oiled site post-spill compared to pre-spill. After the spill, guillemots increased in number at the unoiled site and chicks fledged at significantly heavier weights than at the oiled site, where populations remained depressed. Elevated hepatic cytochrome P4501A (CYP1A), aspartate aminotransferase (AST), and lactate dehydrogenase (LDH) enzyme activities detected in adult guillemots a decade after the spill at the oiled site suggest that continued exposure to residual oil may have limited population recov- ery, although reduced availability of sand lance, a preferred forage fish, may have also played a role. Previous studies conducted at the oiled site demonstrated that guillemot chick growth and reproduc- tive success were positively related to the percentage of high-lipid forage fishes, such as sand lance, in the chick diet. Aspects of sand lance life history and the pattern of 'Exxon Valdez' oil deposition strongly suggest that sand lance were impacted by the spill, although we lack direct evidence of this, and reductions in this species' abundance may have also resulted from natural causes. Our study sug- gests that the recovery of a top-level generalist predator may be constrained by both direct effects (continued exposure to residual oil) and indirect effects (reduced availability of a key prey species) following a large-scale perturbation. Furthermore, it demonstrates that recovery following oil spills may take considerably longer for certain species than the few years that have been proposed as typical for marine birds.
The MEANING Project

Resumen: A pesar del progreso que se realiza en el Procesamiento del Lenguaje Natural (PLN) a un estamos lejos de la Comprensii on del Lenguaje Natural. Un paso importante hacia este objetivo es el desarrollo de t ecnicas y recursos que traten conceptos en lugar de palabras. Sin embargo, si queremos construir la prr oxima generacii on de sistemas inteligentes que traten Tecnolog a de Lenguaje Humano en dominios abiertos necesitamos resolver dos tareas intermedias y complementarias: Resolucii on de la ambiguedad l exica de las palabras y enriquecimeinto automm atico y a gran escala de bases de conocimiento l exico Abstract: Progress is being made in Natural Language Processing (NLP) but there is still a long way towards Natural Language Understanding. An important step towards this goal is the development of technologies and resources that deal with concepts rather than words. However, to be able to build the next generation of intelligent open domain Human Language Technology (HLT) application systems we need to solve two complementary and intermediate tasks: Word Sense Disambi-guation (WSD) and automatic large-scale enrichment of Lexical Knowledge Bases. Knowledge Technologies aim to provide meaning to petabytes of information content our societies will generate in a near future. Information and knowledge management systems need to evolve accordingly, to help release next generation of intelligent open domain HLT to deal with the growing potential of the knowledge-rich and multilingual society. To develop a trustable semantic web infrastructure and a multilingual ontology framework to support knowledge management it is required a wide range of techniques to progressively automate the knowledge lifecycle. In particular this include extracting high level meaning from the large collections of content data and its representation and management in a common knowledge bases. Even now, building large and rich knowledge bases takes a great deal of expensive manual eeort; this has severely hampered HLT application development. For example, dozens of person-years have been invest into the development of wordnets, but the data in these resources is still not suuciently rich to support advanced concept-based HLT applications directly. Furthermore, resources produced by introspection usually fail to register what really occurs in texts. Applications will not scale up to working in the open domain without more detailed and rich general-purpose and also domain-speciic linguistic knowledge. To be able to build the next generation of intelligent open domain HLT application systems we need to solve two complementary intermediate tasks: …
Niches and distributional areas: Concepts, methods, and assumptions

Estimating actual and potential areas of distribution of species via ecological niche modeling has become a very active field of research, yet important conceptual issues in this field remain confused. We argue that conceptual clarity is enhanced by adopting restricted definitions of “niche” that enable operational definitions of basic concepts like fundamental, potential, and realized niches and potential and actual distributional areas. We apply these definitions to the question of niche conservatism, addressing what it is that is conserved and showing with a quantitative example how niche change can be measured. In this example, we display the extremely irregular structure of niche space, arguing that it is an important factor in understanding niche evolution. Many cases of apparently successful models of distributions ignore biotic factors: we suggest explanations to account for this paradox. Finally, relating the probability of observing a species to ecological factors, we address the issue of what objects are actually calculated by different niche modeling algorithms and stress the fact that methods that use only presence data calculate very different quantities than methods that use absence data. We conclude that the results of niche modeling exercises can be interpreted much better if the ecological and mathematical assumptions of the modeling process are made explicit.
Age‐Specific Fitness Components and Their Temporal Variation in the Barn Owl

Theory predicts that temporal variability plays an important role in the evolution of life histories, but empirical studies evaluating this prediction are rare. In constant environments, fitness can be measured by the population growth rate λ, and the sensitivity of λ to changes in fitness components estimates selection on these traits. In variable environments, fitness is measured by the stochastic growth rate λs, and stochastic sensitivities estimate selection pressure. Here we examine age‐specific schedules for reproduction and survival in a barn owl population (Tyto alba). We estimated how temporal variability affected fitness and selection, accounting for sampling variance. Despite large sample sizes of old individuals, we found no strong evidence for senescence. The most variable fitness components were associated with reproduction. Survival was less variable. Stochastic simulations showed that the observed variation decreased fitness by about 30%, but the sensitivities of λ and λs to changes in all fitness components were almost equal, suggesting that temporal variation had negligible effects on selection. We obtained these results despite high observed variability in the fitness components and relatively short generation time of the study organism, a situation in which temporal variability should be particularly important for natural selection and early senescence is expected.
Risk for Colorectal Cancer in Persons With a Family History of Adenomatous Polyps

BACKGROUND The risk for colorectal cancer (CRC) is unclear for persons who have first-degree relatives with adenomatous polyps (adenomas). PURPOSE To determine the validity of studies about this issue. DATA SOURCES MEDLINE and Cochrane databases from 1966 through 2011. STUDY SELECTION Sequential review of titles, abstracts, and text from retrieved articles. DATA EXTRACTION Study objective, study design, and numbers in study groups. DATA SYNTHESIS Ten studies were identified that have been used to answer the question, "Does having a first-degree relative with an adenoma increase the risk for CRC? " We determined that they instead answer the question, "Does having a first-degree relative with CRC increase the risk for an adenoma? " We identified 2 additional studies that provide more relevant information. One study showed that the risk for CRC in persons who have first-degree relatives with adenomas is greater than the risk in persons who do not have first-degree relatives with adenomas (2.31% vs. 0.53%; relative risk, 4.36 [95% CI, 1.60 to 10.21]). The other study showed that the risk for CRC or large adenomas (≥1 cm) in persons who have first-degree relatives with large adenomas is greater than the risk in persons whose first-degree relatives do not have adenomas or CRC (8.3% vs. 4.2%; adjusted odds ratio, 2.27 [CI, 1.01 to 5.09]). LIMITATION Even the 2 relevant studies have design problems that affect validity and generalizability. CONCLUSION Most studies that are cited for the risk for CRC when relatives have adenomas do not address the issue. The 2 studies that do address the issue suggest an increased risk but have important methodological limitations. Properly designed studies are needed to measure the risk and identify the factors that modify it.
Decline in Sulfadoxine-Pyrimethamine-Resistant Alleles after Change in Drug Policy in the Amazon Region of Peru

ABSTRACT The frequency of alleles with triple mutations conferring sulfadoxine-pyrimethamine (SP) resistance in the Peruvian Amazon Basin has declined (16.9% for dhfr and 0% for dhps compared to 47% for both alleles in 1997) 5 years after SP was replaced as the first-line treatment for Plasmodium falciparum malaria. Microsatellite analysis showed that the dhfr and dhps alleles are of common origin.
Interleukin‐1α and brain inflammation

Acute brain injuries such as caused by stroke are amongst the leading causes of death and are the leading cause of disability. Despite this there are very limited therapeutic options, and new therapeutic strategies and targets are required. Inflammation is known to exacerbate brain injury and is now considered as a potential therapeutic target. The damaging inflammation that occurs after acute brain injury is driven by pro‐inflammatory members of the interleukin (IL)−1 cytokine family, namely, IL‐1α and IL‐1β. Previous research efforts have focussed on the biology and contribution of IL‐1β. However, we now recognise that IL‐1α is an early and important mediator of inflammation after injury. This review focuses on what is known about IL‐1α, its regulation and its contribution to brain injury. Inhibiting mechanisms regulating the processing and release of IL‐1α may offer new therapeutic targets for the treatment of devastating acute brain injuries. © 2015 IUBMB Life, 2015 67(5):323–330, 2015
Retroviral vector silencing during iPS cell induction: An epigenetic beacon that signals distinct pluripotent states

Retroviral vectors are transcriptionally silent in pluripotent stem cells. This feature has been potently applied in studies that reprogram somatic cells into induced pluripotent stem (iPS) cells. By delivering the four Yamanaka factors in retroviral vectors, high expression is obtained in fibroblasts to induce the pluripotent state. Partial reprogramming generates Class I iPS cells that express the viral transgenes and endogenous pluripotency genes. Full‐reprogramming in Class II iPS cells silences the vectors as the endogenous genes maintain the pluripotent state. Thus, retroviral vector silencing serves as a beacon marking the fully reprogrammed pluripotent state. Here we review known silencer elements, and the histone modifying and DNA methylation pathways, that silence retroviral and lentiviral vectors in pluripotent stem cells. Both retroviral and lentiviral vectors are influenced by position effects and often exhibit variegated expression. The best vector designs facilitate full‐reprogramming and subsequent retroviral silencing, which is required for directed‐differentiation. Current retroviral reprogramming methods can be immediately applied to create patient‐specific iPS cell models of human disease, however, future clinical applications will require novel chemical or other reprogramming methods that reduce or eliminate the integrated vector copy number load. Nevertheless, retroviral vectors will continue to play an important role in genetically correcting patient iPS cell models. We anticipate that novel pluripotent‐specific reporter vectors will select for isolation of high quality human iPS cell lines, and select against undifferentiated pluripotent cells during regenerative medicine to prevent teratoma formation after transplantation. J. Cell. Biochem. 105: 940–948, 2008. © 2008 Wiley‐Liss, Inc.
Heating effect of a one-dimensional molecular assembly on self-repairing capability in the nanoscopic channels of mesoporous silica

Self-repairable optoelectronic devices from a heat-induced structural damaged are potentially important for sensor [1] and display [2] applications. Recently, self-healing phenomena have attracted particular attention for developing sustainable structural materials [3], where extensive studies have been reported on polymeric materials capable of autonomous repairing macroscopic fractures or restoration lost mechanical strengths [4, 5]. On the other hand, for exploiting molecular devices that can self-repair elaborate functions, one may encounter different problems originating from much smaller size regimes. However, no rational strategies have yet been proposed for addressing this challenging issue. In our previous paper, when a phosphorescent columnar assembly of trinuclear gold(I) pyrazolate complex [Au3Pz3] is confined in the nanoscopic channel of hexagonal mesoporous silica [Au3Pz3]/silicahex (Fig. 1), upon stepwise heating from 20 °C to 140 °C in 45 min, the one-dimensional molecular assemblies are not only protected from thermal disruption but also strongly encouraged to self-recover to 100% in 5 h from a heat-induced structural damaged [6].
The sensitivity and specificity of clinical assessment compared with bitewing radiography for detection of occlusal dentin caries.

PURPOSE This prospective, cross-sectional study examined the sensitivity and specificity of clinical assessment compared to bitewing radiographs in the detection of occlusal dentin caries in permanent molars. METHODS Subjects were 481 children aged 5-12 years from a school-based dental clinic. Occlusal surfaces of 1929, sealed and unsealed first and second permanent molars were examined clinically and scored using specific criteria. Teeth with any type of restorations or proximal caries, including preventive resin restorations, were excluded from the study. Bitewing radiographs were exposed within 4 weeks of clinical examination and were assessed for dentin radiolucencies beneath the occlusal surface. The results of the clinical examinations were correlated with those of bitewing radiographs. Information provided by the parents on history forms, including systemic fluoride exposure, was also noted. RESULTS Of the 1833 teeth scored as clinically sound in the study, only 72 (4%) demonstrated a dentin radiolucency on bitewings, and 1761 (96%) were scored as sound. The sensitivity of the clinical examination was determined to be 0.96. In the teeth clinically scored as showing dentin caries, only 56/96 (58%) were found to have dentin radiolucencies on the radiographs. The specificity of the technique was determined to be 0.58. A positive history of a medical condition, or fluoride exposure, in the forms of toothpaste use, or water fluoridation did not affect the examination results. CONCLUSIONS Clinical examination of cleaned and dried, sealed, and unsealed teeth has a sensitivity of 0.96 and a specificity of 0.58 in the detection of dentin radiolucencies in bitewing radiographs. Dentin radiolucencies beneath clinically sound occlusal surfaces are not significantly associated with gender, medical conditions or fluoride.
Spatial and temporal complexity of the Amazon flood measured from space

Floodplain processes are driven by water flows that seasonally change in direction and consist of a myriad of interacting streams of varying depth, velocity, source, sediment concentration and chemistry. Here we show, using spaceborne interferometric synthetic aperture radar (SAR) JERS‐1 measurements, the first spatially dense hydraulic mapping of the passage of a flood wave through a large, topographically complex floodplain. We find that temporal changes in flood water heights (∂h/∂t) are more complex than typically assumed. During the passage of a flood wave, sharp variations in ∂h/∂t are localized along some floodplain channels. These channels separate adjacent locations with different rates of infilling. Near the peak of the flood wave, some of the channels are no longer evident as controls on ∂h/∂t. During the passage of the flood wave, flow paths change from bathymetrically influenced to hydraulically controlled (and back again), thus it is difficult to know the flow path a‐priori from bathymetry alone.
A PCA-based interpretation of ultrasonic data for accurately detecting a corridor wall

This paper introduces a validated model for the ultrasonic detection by processing sensor data and it presents a new approach for evaluating the orientation of a regular wall. The method described is based on the Principal Component Analysis (PCA) which gives the opportunity to make some geometrical considerations on the effectiveness of the scanning results. Several experiments are conducted scanning a regular corridor wall and also propagating ultrasonic waves towards a wall opening. In every instance these tests permit to confirm the applicability of the new proposed strategy.
Dural identity process for virtual community participation and impact of gender composition

Purpose Unlike the earlier research that examines gender impact at the individual level, the purpose of this paper is to examine whether and how gender composition of virtual communities (VCs) interact with identity-related needs, namely identification and identity confirmation in affecting VC participation. Design/methodology/approach Drawing on the theories and previous research of social identity and organizational identification, the study developed and tested a new research model through an online survey involving three male dominant VCs and one female-dominant VC. Findings The results show that identification and identity confirmation are two independent antecedents for VC participation. Identification is a significant and stable determinant for members’ VC participation regardless of gender composition, but the effect of identity confirmation on VC participation is only significant for those in a female-dominant VC. Research limitations/implications The results of the study represent the first attempt to empirically examine the dual identity processes for VC participation. The results also imply that gender composition shapes, to some extent, VC members’ communication strategies, contents, and social interaction norms. Gender composition also affects the expectations for VC participation in terms of identification and identity confirmation. Practical implications The results of the study offer practical value for VC design and management, marketing through social media, as well as online education such as virtual team learning and teaching. Originality/value This study extends and advances the existing research in several ways. To the best of the authors knowledge, the study is the first of its kind to address the interplays among identification, identity confirmation, and VC participation from a gender composition perspective.
Determination of the binding frame within a physiological ligand for the chaperone SecB

The hallmark of the class of proteins called chaperones is the amazing ability to bind tightly to a wide array of polypeptide ligands that have no consensus in sequence; chaperones recognize non‐native structure. As a step in the elucidation of the molecular mechanism of such remarkable binding, we have characterized complexes between the bacterial chaperone SecB and a series of ligands related to maltose‐binding protein. SecB interacts at multiple sites on its polypeptide ligand. The entire binding region covers approximately half of the primary sequence of maltose‐binding protein and comprises contiguous sites positioned around the center of the sequence.
A growth pattern of DG penetrations within LDC planning model in competitive energy environment

This paper presents a planning model for a local distribution company (LDC) providing electricity to meet its load growth in a competitive operational manner. Clean and renewable energy resources have been broadly deployed within LDC service territory and its asset and business managements are the main concern of current research efforts. A pattern function of distributed generation (DG) penetration within LDC is introduced. A market trend is investigated and defined in this paper where it can be involved in a planning problem. Based on a planner experience, annual budget thresholds are also discussed in order to measure gross costs of planning and their variations with new DG resources as an attractive planning option. The DG deployment index (DdgI-index) related to DGs growth function is introduced where it could be adjusted, particularly, from the budget limits and gross costs of investments taking into consideration the energy market trend. The mathematical model uses the full ac power flow formulations, and the planning problem is a dynamic one, designed to tackle all these issues simultaneously.
Structure and dynamics of the active site gorge of acetylcholinesterase: Synergistic use of molecular dynamics simulation and X‐ray crystallography

The active site of acetylcholinesterase (AChE) from Torpedo californica is located 20 Å from the enzyme surface at the bottom of a narrow gorge. To understand the role of this gorge in the function of AChE, we have studied simulations of its molecular dynamics. When simulations were conducted with pure water filling the gorge, residues in the vicinity of the active site deviated quickly and markedly from the crystal structure. Further study of the original crystallographic data suggests that a bis‐quaternary decamethonium (DECA) ion, acquired during enzyme purification, resides in the gorge. There is additional electron density within the gorge that may represent small bound cations. When DECA and 2 cations are placed within the gorge, the simulation and the crystal structure are dramatically reconciled. The small cations, more so than DECA, appear to stabilize part of the gorge wall through electrostatic interactions. This part of the gorge wall is relatively thin and may regulate substrate, product, and water movement through the active site.
Self-rated health and mortality: a review of twenty-seven community studies.

We examine the growing number of studies of survey respondents' global self-ratings of health as predictors of mortality in longitudinal studies of representative community samples. Twenty-seven studies in U.S. and international journals show impressively consistent findings. Global self-rated health is an independent predictor of mortality in nearly all of the studies, despite the inclusion of numerous specific health status indicators and other relevant covariates known to predict mortality. We summarize and review these studies, consider various interpretations which could account for the association, and suggest several approaches to the next stage of research in this field.