Miracle-dz/UniFAR-FTUs huggingface dataset:
Oxygen isotopic fractionation and exchange during bacterial nitrite oxidation

We elucidate the controls on the δ18O values of microbially produced nitrate by tracking the δ18O of nitrite and nitrate during bacterial nitrite oxidation, which is the final step of the nitrification process. Aside from the δ18O values of the nitrite and water substrates, three factors can affect the δ18O value of nitrate produced during nitrite oxidation: (1) a kinetic isotope effect for nitrite oxidation (18εk,NO2), (2) a kinetic isotope effect for water incorporation by nitrite oxidoreductase (18εk,H2O,2), and (3) microbially mediated exchange of oxygen atoms between nitrite and water (×NOB). These parameters were quantified through batch culture experiments with species from three genera of marine nitrite‐oxidizing bacteria: Nitrococcus, Nitrobacter, and Nitrospira. Experiments conducted with 18O‐labeled water showed that less than 3% of the oxygen atoms in nitrite were exchanged with water and that 18εk,H2O,2 ranged from +12.8% to +18.2%. With the use of these parameters and the previously measured values of the δ18O of nitrite produced by ammonia‐oxidizing bacteria, the δ18O of newly produced nitrate in the ocean was estimated to fall between 28.3%to 20.7%, which is within the range necessary for balancing a deep ocean nitrate δ18O budget.
Differences in RNA formation and polyribosome metabolism in serum-starved normal and transformed cells.

Summary Comparative studies of RNA synthesis and polyribosome metabolism in normal (RFL) and transformed (RFL-T) cells under serum starvation show that their growth is more or less dependent upon serum factor. By limiting serum in the medium, 80 to 90% of RNA or protein synthesis is inhibited in RFL cells, while in RFL-T cells macromolecular synthesis proceeds at one-third to one-fourth the rate of control. Ribosomal RNA synthesis is more preferentially blocked in untransformed cells under decreased protein synthesis caused by serum deprivation than in transformed cells. However, when both RFL and RLF-T cell lines are treated with cycloheximide, 2 µg/ml, which inhibits over 90% protein synthesis, little if any ribosomal RNA is produced. Also, analysis of cytoplasmic extracts with isokinetic sucrose density gradient centrifugation shows the greater transition of polyribosomes into monosomes in RFL-T cells compared to that of RFL cells with time of serum deprivation. The prominent redistribution of polyribosomes, which occurred in serum-starved RFL-T cells but not in RFL cells, is restored by addition of 0.2 µg/ml to 2.0 µg/ml cycloheximide. Since nascent peptides are being made in polyribosomes of RFL-T starved for serum but little if and peptide chains are made in RFL, the ribosomal transition requires peptide formation at a reduced level.
Mitofusins: Disease Gatekeepers and Hubs in Mitochondrial Quality Control by E3 Ligases

Mitochondria are dynamic organelles engaged in quality control and aging processes. They constantly undergo fusion, fission, transport, and anchoring events, which empower mitochondria with a very interactive behavior. The membrane remodeling processes needed for fusion require conserved proteins named mitofusins, MFN1 and MFN2 in mammals and Fzo1 in yeast. They are the first determinants deciding on whether communication and content exchange between different mitochondrial populations should occur. Importantly, each cell possesses hundreds of mitochondria, with a different severity of mitochondrial mutations or dysfunctional proteins, which potentially spread damage to the entire network. Therefore, the degree of their merging capacity critically influences cellular fitness. In turn, the mitochondrial network rapidly and dramatically changes in response to metabolic and environmental cues. Notably, cancer or obesity conditions, and stress experienced by neurons and cardiomyocytes, for example, triggers the downregulation of mitofusins and thus fragmentation of mitochondria. This places mitofusins upfront in sensing and transmitting stress. In fact, mitofusins are almost entirely exposed to the cytoplasm, a topology suitable for a critical relay point in information exchange between mitochondria and their cellular environment. Consistent with their topology, mitofusins are either activated or repressed by cytosolic post-translational modifiers, mainly by ubiquitin. Ubiquitin is a ubiquitous small protein orchestrating multiple quality control pathways, which is covalently attached to lysine residues in its substrates, or in ubiquitin itself. Importantly, from a chain of events also mediated by E1 and E2 enzymes, E3 ligases perform the ultimate and determinant step in substrate choice. Here, we review the ubiquitin E3 ligases that modify mitofusins. Two mitochondrial E3 enzymes—March5 and MUL1—one ligase located to the ER—Gp78—and finally three cytosolic enzymes—MGRN1, HUWE1, and Parkin—were shown to ubiquitylate mitofusins, in response to a variety of cellular inputs. The respective outcomes on mitochondrial morphology, on contact sites to the endoplasmic reticulum and on destructive processes, like mitophagy or apoptosis, are presented. Ultimately, understanding the mechanisms by which E3 ligases and mitofusins sense and bi-directionally signal mitochondria-cytosolic dysfunctions could pave the way for therapeutic approaches in neurodegenerative, cardiovascular, and obesity-linked diseases.
White Matter Plasticity in Reading-Related Pathways Differs in Children Born Preterm and at Term: A Longitudinal Analysis

Children born preterm (PT) are at risk for white matter injuries based on complications of prematurity. They learn to read but on average perform below peers born full term (FT). Studies have yet to establish whether properties of white matter pathways at the onset of learning to read are associated with individual variation later in reading development in PT children. Here, we asked whether fractional anisotropy (FA) at age 6 years is associated with reading outcome at age 8 years in PT children in the same pathways as previously demonstrated in a sample of FT children. PT (n = 34, mean gestational age = 29.5 weeks) and FT children (n = 37) completed diffusion MRI and standardized measures of non-verbal IQ, language, and phonological awareness at age 6 years. Reading skills were assessed at age 8 years. Mean tract-FA was extracted from pathways that predicted reading outcome in children born FT: left arcuate fasciculus (Arc), bilateral superior longitudinal fasciculus (SLF), and left inferior cerebellar peduncle (ICP). We explored associations in additional pathways in the PT children: bilateral inferior fronto-occipital fasciculus, inferior longitudinal fasciculus, and uncinate fasciculus. Linear regression models examined whether the prediction of reading outcome at age 8 years based on mean tract-FA at age 6 years was moderated by birth group. Children born PT and FT did not differ significantly in tract-FA at age 6 years or in reading at age 8 years. Sex, socioeconomic status, and non-verbal IQ at age 6 years were associated with reading outcome and were included as covariates in all models. Birth group status significantly moderated associations between reading outcome and mean tract-FA only in the left Arc, right SLF, and left ICP, before and after consideration of pre-literacy skills. Microstructural properties of these cerebral and cerebellar pathways predicted later reading outcome in FT but not in PT children. Children born PT may rely on alternative pathways to achieve fluent reading. These findings have implications for plasticity of neural organization after early white matter injury.
Evolution of Resistance in Cancer: A Cell Cycle Perspective

Resistance of neoplastic cells to therapy is considered a key challenge in the treatment of cancer. Emergence of resistance is commonly attributed to the gradual mutational evolution of neoplastic cells. However, accumulating evidence suggests that exogenous stressors could significantly accelerate the emergence of resistant clones during the course of treatment. Herein, we review molecular mechanisms that regulate the evolution of resistance in a tumor with particular emphasis on the role of cell cycle.
The Policy Enabling Environment for Climate Smart Agriculture: A Case Study of California

Climate smart agriculture (CSA) provides a framework for balancing multiple dimensions of agriculture and food systems in an era of climate change: addressing agricultural contributions to global greenhouse gas emissions, vulnerabilities to climate change impacts, and the relationship between agricultural productivity, incomes and food security. As the global climate agenda more thoroughly integrates the CSA framework, policy makers often search for “triple wins” – practices that can mitigate emissions, increase resilience or adaptation, and increase productivity. Agriculture and food systems however, are complex systems with many agroecological and sociopolitical interdependencies. In many cases, there are necessary tradeoffs among the three CSA objectives, as advancement in one area may negatively impact another. A major challenge to implementing CSA across multiple geographies thus lies in the coordination of policies and programs that recognize these tradeoffs and allow for prioritization or reconciliation among the three objectives when there are conflicts. This paper describes California’s adoption of CSA principles to illustrate how synergies and trade-offs are addressed in a policy framework that spans regulatory measures, incentive programs, research and technological development, that is both climate specific and arising from other simultaneous environmental and economic priorities. We provide specific examples where agriculture has benefited and where it is constrained due to the balancing of CSA objectives, and discuss how the policy environment has evolved over time in attempts to deal with the complexity of the agriculture-climate nexus. This case serves to summarize and analyze the implemented CSA initiatives in one of most productive and well-resourced agricultural regions of the world; however, lessons learned from California can serve as transferable knowledge for other regions around the globe who are currently developing CSA policies and plans. Our findings suggest that cross-sectoral collaboration, policy coordination, and inclusion of a diverse set of stakeholders are fundamental to the efficacy of CSA strategies in complex and ever-evolving environmental and sociopolitical conditions.
Identification of Serum Biomarkers for Intestinal Integrity in a Broiler Chicken Malabsorption Model

Intestinal health is essential for feed efficiency and growth in animal agriculture and is dependent on barrier function, inflammation and dysbiosis. Our laboratory has published a nutritional model to induce gut inflammation using rye as a source of energy in poultry. More recently, we have used this model as an assessment of a nutritional rehabilitation model for better understanding of childhood undernutrition. The objective of this brief research report was to use a well-establish malabsorption model in broiler chickens using corn and rye as an energy source to identify several intestinal health biomarkers in the serum. To screen for inflammatory biomarkers, seven commercially available tests were used including Griess, superoxide dismutase, thiobarbituric acid reactive substances, Total antioxidant capacity, extracellular-signal-regulated kinase, Citrulline, and Interferon-ɤ; total IgA from cloacal swab was also measured. In the present study, chickens fed rye had a significant (P < 0.05) reduction in body weight and body weight gain at 10 day when compared with chickens that received the corn diet. In the second phase of the experiment, chickens that remain with the corn diet had significant differences in body weight and body weight gain. No significant differences were observed for any of the four antioxidant biomarkers evaluated in the sera (P > 0.05). However, significant differences were observed in serum citrulline and IFN-ɤ, as well as in cloacal IgA, in broiler chickens fed with rye, suggesting their potential use as biomarkers to study intestinal inflammation.
MRSA in Pigs and the Environment as a Risk for Employees in Pig-Dense Areas of Sri Lanka

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) is widely spread in intensive farming systems and considered an occupational risk for humans. MRSA is a common nosocomial pathogen in Sri Lanka, but information about prevalence of MRSA in pig farming in Sri Lanka is scarce. Farming is largely a small-scale confined system, and antimicrobial use in these systems is poorly regulated with no veterinary oversight for use. This study identified on 100 pig farms a MRSA prevalence of 10%, with MRSA-positive samples in pigs, farm workers, and dust of 1.2% (6/493), 2.2% (5/228), and 0.8% (1/119), respectively. The genotypes of these strains were compared with 22 human MRSA strains from a hospital; identified in pig farms were CC1/ST1/t127, CC5/ST5/t002, CC6/ST6/t304, or t4403, singleton ST3841/t10744, of which CC1/ST1/t127 and CC/ST5/t002 were present both in isolates from pigs and humans, suggesting a human origin. LA-MRSA types associated with intensive farming (ST398, ST9) were not detected. The low MRSA prevalence at farm level (10% vs. up to 70% in intensive farming systems) might be due to the management of these farms—open air and low dust. We conclude that in Sri Lanka the occupational risk for MRSA acquisition of people working with pigs in the described management systems is negligible.
Validation of bone segmentation and improved 3-D registration using contour coherency in CT data

A method is presented to validate the segmentation of computed tomography (CT) image sequences, and improve the accuracy and efficiency of the subsequent registration of the three-dimensional surfaces that are reconstructed from the segmented slices. The method compares the shapes of contours extracted from neighborhoods of slices in CT stacks of tibias. The bone is first segmented by an automatic segmentation technique, and the bone contour for each slice is parameterized as a one-dimensional function of normalized arc length versus inscribed angle. These functions are represented as vectors within a K-dimensional space comprising the first K amplitude coefficients of their Fourier Descriptors. The similarity or coherency of neighboring contours is measured by comparing statistical properties of their vector representations within this space. Experimentation has demonstrated this technique to be very effective at identifying low-coherency segmentations. Compared with experienced human operators, in a set of 23 CT stacks (1,633 slices), the method correctly detected 87.5% and 80% of the low-coherency and 97.7% and 95.5% of the high coherency segmentations, respectively from two different automatic segmentation techniques. Removal of the automatically detected low-coherency segmentations also significantly improved the accuracy and time efficiency of the registration of 3-D bone surface models. The registration error was reduced by over 500% (i.e., a factor of 5) and 280%, and the computational performance was improved by 540% and 791% for the two respective segmentation methods.
Coercion in psychiatric care: Can paternalism justify coercion?

Background: It has long been debated whether coercion can be justified as paternalism in the field of mental health and it is still a continuing issue of controversy today. Aims: This study analyses whether coercive intervention in mental health can be justified by the basic assumptions of paternalists: the assumption of incompetence, the assumption of dangerousness and the assumption of impairment. Method: This study involved 248 patients: 158 (63.7%) were diagnosed with schizophrenia and 90 (36.3%) were diagnosed with mood disorder. In this study, experiences of coercion were divided into legal status, subjective (perceived coercion) and objective experiences (experienced coercion). Results: The assumption of incompetence was justified in all three categories of coercion whereas the assumption of dangerousness was not justified in any. The assumption of impairment was not justified in legal status and perceived coercion, but provided a partial explanation to serve as a basis for justifying experienced coercive measures. Conclusions: It can be noted that mental health experts who support paternalism without question must reconsider their previous methods. Above all, the reason why the assumption of dangerousness was not justified in any of the categories of coercion was because coercive intervention used to prevent harm to oneself and others must be very carefully carried out.
Indexing Uncertain Categorical Data over Distributed Environment

Today, a large amount of uncertain data is produced by several applications where the management systems of traditional databases incuding indexing methods are not suitable to handle such type of data. In this paper, we propose an inverted based index method for effciently searching uncertain categorical data over distributed environments. We adress two kinds of query over the distributed uncertain databases, one a distributed probabilistic thresholds query, where all results sastisfying the query with probablities that meet a probablistic threshold requirement are returned, and another a distributed top k-queries, where all results optimizing the transfer of the tuples and the time treatment are returned.
Web 2 . 0 Traffic Measurement – Analysis on Online Map Applications

In recent years, web based online map applications have been getting more and more popular, such as Google Maps, Yahoo Maps. Many new Web 2.0 techniques such as mash-up and AJAX were adopted in these map applications to improve user experiences. But few researches have been done on traffic analysis of the Web 2.0 based online map applications. In this paper, we introduced our research on features of online map applications that previous studies hadn’t cover. In our research, we captured map application related HTTP traffic in a campus network while not violating user privacy. We introduced the traffic overview, mash-up and web caching characteristics of four map web sites (Google Maps, Yahoo Maps, Sogou Maps and Baidu Maps). For the first time, the mash-up characteristics of Google map traffic were analyzed using a new method proposed in this paper. The same method could be applied to other mash-up analysis works. These results can help us optimize the future web application designs and CDN based accelerating solution designs.
Language Identification based on a Discriminative Text Categorization Technique

In this paper, we describe new results and improvements to a lan- guage identification (LID) system based on PPRLM previously introduced in (1) and (2). In this case, we use as parallel phone recognizers the ones provided by the Brno University of Technology for Czech, Hungarian, and Russian lan- guages, and instead of using traditional n-gram language models we use a lan- guage model that is created using a ranking with the most frequent and discrim- inative n-grams. In this language model approach, the distance between the ranking for the input sentence and the ranking for each language is computed, based on the difference in relative positions for each n-gram. This approach is able to model reliably longer span information than in traditional language models obtaining more reliable estimations. We also describe the modifications that we have being introducing along the time to the original ranking technique, e.g., different discriminative formulas to establish the ranking, variations of the template size, the suppression of repeated consecutive phones, and a new clus- tering technique for the ranking scores. Results show that this technique pro- vides a 12.9% relative improvement over PPRLM. Finally, we also describe re- sults where the traditional PPRLM and our ranking technique are combined.
DEFINITE POSSESSIVES AND DISCOURSE NOVELTY

Standard wisdom holds that in order for a use of a definite description to be felicitous, its referent must be familiar', either because it was mentioned in previous discourse or because it is otherwise salient in the non-linguistic context. I show that a grammatically-defined class of demonstrably definite NPs containing definite possessors (e.g., that man's daughter) are routinely able to describe novel (unfamiliar) entities. I propose to account for this systematic class of exceptions to the standard familiarity requirement by providing a refined notion of familiarity, one that determines when a use of a possessed NP as a whole will count as familiar based (in part) on whether its possessor phrase counts as familiar.
An animal model for Huntington's disease.

: In review is concerned with research done on an animal model for the hereditary neuropsychiatric disorder, Huntington's disease (HD). The neuropathology of HD involves primarily a selective degeneration of neurons with cell bodies in the striatum. Injection of kainic acid, a potent neuroexcitant structurally related to glutamic acid, into the rat striatum causes a selective neuronal degeneration resembling that of HD. Striatal cholinergic and GABAergic neurons, including their terminal projections in the substantia nigra, are affected by kainate; dopaminergic axons innervating the striatum as well as corticofugal fibers passing through the region are spared. The striatal kainate lesion has aided in the characterization of the neuronal circuitry in the nigrostriatal axis including the neuronal localization of dopamine-sensitive adenylate cyclase, neuroleptic binding sites, and GABA receptors. Studies in vivo and in vitro with kainate and its analogues suggest that the potent neurotoxicity of kainate involves a cooperative interaction between synaptically released glutamate and injected kainate on vulnerable neurons; prior destruction of cortico-striatal glutamatergic afferents attenuates kainate's neurotoxicity. The kainate model has been used to test drugs that may be of therapeutic benefit for HD. A better understanding of the mechanism of neurotoxicity of kainate may shed light on the cause of neuronal degeneration in HD.
Video2Cartoon: A System for Converting Broadcast Soccer Video into 3D Cartoon Animation

A system for converting broadcast soccer video into 3D cartoon animation is proposed. The system can provide viewers with a new experience that can not be acquired from the original soccer video, by taking advantage of computer vision and computer graphics techniques. Firstly, computer vision techniques are employed to estimate the 3D positions of players and the ball. Then, players, the ball and the playfield are modeled by computer graphics techniques. Finally, 3D cartoon animation is generated based on the extracted 3D information and the pre-constructed player motion database. The system allows users to watch the game at arbitrary viewpoint using a virtual camera. On the other hand, content service providers can distribute the generated cartoon animation on their Web portals or to mobile devices, for consumers to better enjoy the game.
A Study of Lateral Boundary Conditions for the NRL's Coupled Ocean/Atmosphere Mesoscale Prediction System (COAMPS)

Abstract : LONG-TERM GOALS. Our long-term goal is to improve lateral boundary conditions in local area models. OBJECTIVES. The treatment of lateral boundaries in regional models has been a perennial problem since the early days of numerical weather prediction. In a limited-area model the lateral edges are not physical boundaries of the flow but constitute artificial constraints imposed by computational considerations. Hence they do not have a physical counterpart. We must impose conditions at these artificial boundaries in order to solve the problem in an efficient and accurate manner. We have developed high order non-reflecting boundary conditions for the dispersive Klein-Gordon equation and the linearized shallow water equations.