Miracle-dz/UniFAR-FTUs huggingface dataset:
The Irreversible Loss of a Decomposition Pathway Marks the Single Origin of an Ectomycorrhizal Symbiosis

Microbial symbioses have evolved repeatedly across the tree of life, but the genetic changes underlying transitions to symbiosis are largely unknown, especially for eukaryotic microbial symbionts. We used the genus Amanita, an iconic group of mushroom-forming fungi engaged in ectomycorrhizal symbioses with plants, to identify both the origins and potential genetic changes maintaining the stability of this mutualism. A multi-gene phylogeny reveals one origin of the symbiosis within Amanita, with a single transition from saprotrophic decomposition of dead organic matter to biotrophic dependence on host plants for carbon. Associated with this transition are the losses of two cellulase genes, each of which plays a critical role in extracellular decomposition of organic matter. However a third gene, which acts at later stages in cellulose decomposition, is retained by many, but not all, ectomycorrhizal species. Experiments confirm that symbiotic Amanita species have lost the ability to grow on complex organic matter and have therefore lost the capacity to live in forest soils without carbon supplied by a host plant. Irreversible losses of decomposition pathways are likely to play key roles in the evolutionary stability of these ubiquitous mutualisms.
The rapid intensification of Hurricane Guillermo (1997) as viewed with GPS dropwindsondes

On August 2 and 3 of 1997 the two NOAA WP-3D aircraft simultaneously sampled Hurricane Guillermo in the eastern Pacific as part of the Vortex Motion and Evolution Experiment. This was the first experiment to deploy Global Positioning System dropwindsondes (GPS sondes) into a hurricane. Over 80 GPS sondes were jettisoned from 500 and 700 hPa within 300 km of the hurricane center over the two days. On each day, the lower aircraft visited the center 10 times as the hurricane progressed steadily westward near 5 m s. This pattern allows for frequent monitoring of the reflectivity fields of the eyewall with the lower fuselage and tail radars. Sampling of the storm occurred just as rapid intensification (RI) commenced on August 2 with the hurricane deepening 25 hPa by the time the aircraft returned to a steadystate hurricane on August 3. Deepening may have been as much as 2 hPa h on the 2. The experiment provides us with a unique opportunity to observe how the inner core of a hurricane evolves during an RI period. Better understanding of how the eyewall interacts with the immediate environment during RI may aid in forecasting RI.
Mutual exclusion of roles as a means of implementing separation of duty in role-based access control systems

Role based access control (RBAC) is attracting increasing attention as a security mechanism for both commercial and many military systems. Much of RBAC is fundamentally different from multi-level security (MLS) systems, and the properties of RBAC systems have not been explored formally to the extent that MLS system properties have. This paper explores some aspects of mutual exclusion of roles as a means of implementing separation of duty policies, including a safety property for separation of duty; relationships between different types of exclusion rules; properties of mutual exclusion for roles; constraints on the role hierarchy introduced by mutual exclusion rules; and necessary and sufficient conditions for the safety property to hold. Results have implications for implementing separation of duty controls through mutual exclusion of roles, and for comparing mutual exclusion with other means of implementing separation of duty policies.
Mcph1-Deficient Mice Reveal a Role for MCPH1 in Otitis Media

Otitis media is a common reason for hearing loss, especially in children. Otitis media is a multifactorial disease and environmental factors, anatomic dysmorphology and genetic predisposition can all contribute to its pathogenesis. However, the reasons for the variable susceptibility to otitis media are elusive. MCPH1 mutations cause primary microcephaly in humans. So far, no hearing impairment has been reported either in the MCPH1 patients or mouse models with Mcph1 deficiency. In this study, Mcph1-deficient (Mcph1tm1a /tm1a) mice were produced using embryonic stem cells with a targeted mutation by the Sanger Institute's Mouse Genetics Project. Auditory brainstem response measurements revealed that Mcph1tm1a /tm1a mice had mild to moderate hearing impairment with around 70% penetrance. We found otitis media with effusion in the hearing-impaired Mcph1tm1a /tm1a mice by anatomic and histological examinations. Expression of Mcph1 in the epithelial cells of middle ear cavities supported its involvement in the development of otitis media. Other defects of Mcph1tm1a /tm1a mice included small skull sizes, increased micronuclei in red blood cells, increased B cells and ocular abnormalities. These findings not only recapitulated the defects found in other Mcph1-deficient mice or MCPH1 patients, but also revealed an unexpected phenotype, otitis media with hearing impairment, which suggests Mcph1 is a new gene underlying genetic predisposition to otitis media.
Psychiatric comorbidity and suicide risk in patients with chronic migraine

The aim of this study was to explore the impact of mental illness among patients with migraine. We performed MedLine and PsycINFO searches from 1980 to 2008. Research has systematically documented a strong bidirectional association between migraine and psychiatric disorders. The relationship between migraine and psychopathology has often been clinically discussed rather than systematically studied. Future research should include sound methodologically-based studies focusing on the interplay of factors behind the relationship between migraine, suicide risk, and mental illness.
Glial Progenitors in Adult White Matter Are Driven to Form Malignant Gliomas by Platelet-Derived Growth Factor-Expressing Retroviruses

To test the gliomagenic potential of adult glial progenitors, we infected adult rat white matter with a retrovirus that expresses high levels of PDGF and green fluorescent protein (GFP). Tumors that closely resembled human glioblastomas formed in 100% of the animals by 14 d postinfection. Surprisingly, the tumors were composed of a heterogeneous population of cells, <20% of which expressed the retroviral reporter gene (GFP). The vast majority of both GFP+ and GFP– tumor cells expressed markers of glial progenitors. Thus, the tumors arose from the massive expansion of both infected and uninfected glial progenitors, suggesting that PDGF was driving tumor formation via autocrine and paracrine stimulation of glial progenitor cells. To explore this possibility further, we coinjected a retrovirus expressing PDGF-IRES-DsRed with a control retrovirus expressing only GFP. The resulting tumors contained a mixture of red cells (PDGF-expressing/tumor-initiating cells) and green cells (recruited progenitors). Both populations were highly proliferative and infiltrative. In contrast, when the control GFP retrovirus was injected alone, the animals never formed tumors and the majority of infected cells differentiated along the oligodendrocyte lineage. Together, these results reveal that adult white matter progenitors not only have the capacity to give rise to gliomas, but resident progenitors are recruited to proliferate within the mitogenic environment of the tumor and in this way contribute significantly to the heterogeneous mass of cells that compose a malignant glioma.
A Combined First-principles Calculation and Neural Networks Correction Approach for Evaluating Gibbs Energy of Formation

Despite of their successes, the results of first-principles quantum mechanical calculations contain inherent numerical errors that are caused by inadequate treatment of electron correlation, incompleteness of basis sets, relativistic effects or approximated exchange-correlation functionals. In this work, we develop a combined density-functional theory and neural-network correction (DFT-NEURON) approach to reduce drastically these errors, and apply the resulting approach to determine the standard Gibbs energy of formation ΔG 0 at 298 K for small- and medium-sized organic molecules. The root mean square deviation of the calculated ΔG 0 for 180 molecules is reduced from 22.3 kcal · mol-1 to 3.0 kcal · mol-1 for B3LYP/6-311+G(d,p). We examine further the selection of physical descriptors for the neural network.
Interferon-alfa as a comparative treatment for clinical trials of new therapies against advanced renal cell carcinoma.

PURPOSE To define outcome data and prognostic criteria for patients with metastatic renal cell carcinoma (RCC) treated with interferon-alfa as initial systemic therapy. The data can be applied to design and interpretation of clinical trials of new agents and treatment programs against this refractory malignancy. PATIENTS AND METHODS Four hundred sixty-three patients with advanced RCC administered interferon-alpha as first-line systemic therapy on six prospective clinical trials were the subjects of this retrospective analysis. Three risk categories for predicting survival were identified on the basis of five pretreatment clinical features by a stratified Cox proportional hazards model. RESULTS The median overall survival time was 13 months. The median time to progression was 4.7 months. Five variables were used as risk factors for short survival: low Karnofsky performance status, high lactate dehydrogenase, low serum hemoglobin, high corrected serum calcium, and time from initial RCC diagnosis to start of interferon-alpha therapy of less than one year. Each patient was assigned to one of three risk groups: those with zero risk factors (favorable risk), those with one or two (intermediate risk), and those with three or more (poor risk). The median time to death of patients deemed favorable risk was 30 months. Median survival time in the intermediate-risk group was 14 months. In contrast, the poor-risk group had a median survival time of 5 months. CONCLUSION Progression-free and overall survival with interferon-alpha treatment can be compared with new therapies in phase II and III clinical investigations. The prognostic model is suitable for risk stratification of phase III trials using interferon-alpha as the comparative treatment arm.
Correlation research between osteoporosis and left ventricular hypertrophy in older men

Introduction The aim of the study was to correlate between osteoporosis and left ventricular hypertrophy (LVH) in older men. Material and methods One hundred and forty-six cases of senile male subjects were selected and divided into a normal bone mineral density group, an osteopenia group, and an osteoporosis group based on bone mineral density (BMD). Detailed history inquiry and clinical examination were used to determine biochemical indicators. Femoral neck BMD and lumbar BMD were determined. Electrocardiography was performed to calculate the left ventricular mass index (LVMI). One-way analysis of variance and multiple linear regression analysis were performed. Results With the bone mass reduced, LVMI was gradually increased (p < 0.05), incidence of left ventricular hypertrophy was increased, and there were significant differences (p < 0.05). With LVMI as the dependent variable, multiple linear regression analysis showed that lumbar bone density, body mass index, age and serum creatinine were associated with LVMI independently (p < 0.05). Conclusions In patients with osteoporosis and osteopenia, LVH rates were much higher than in normal bone mineral density patients. Moreover, there might be a relationship between osteoporosis and LVH.
Average State Observers for Large-Scale Network Systems

In this paper, we propose a novel observer, called the average state observer, for large-scale network systems. This observer estimates the average behavior of the system with an estimation error assurance. To design an average state observer with explicit consideration of the estimation error, we first derive a tractable representation of the estimation error system. On the basis of this representation, we provide a theoretical upper bound of the estimation error for the average state observer. As a result, a systematic procedure to design the average state observers with an estimation error assurance is presented. Finally, we show the efficiency of the average state observer through an example of spatially discretized thermal diffusion networks.
A newly identified fatty alcohol oxidase gene is mainly responsible for the oxidation of long-chain ω-hydroxy fatty acids in Yarrowia lipolytica.

Nine potential (fatty) alcohol dehydrogenase genes and one alcohol oxidase gene were identified in Yarrowia lipolytica by comparative sequence analysis. All relevant genes were deleted in Y. lipolytica H222ΔP which is lacking β-oxidation. Resulting transformants were tested for their ability to accumulate ω-hydroxy fatty acids and dicarboxylic acids in the culture medium. The deletion of eight alcohol dehydrogenase genes (FADH, ADH1-7), which may be involved in ω-oxidation, led only to a slightly increased accumulation of ω-hydroxy fatty acids, whereas the deletion of the fatty alcohol oxidase gene (FAO1), which has not been described yet in Y. lipolytica, exhibited a considerably higher effect. The combined deletion of the eight (fatty) alcohol dehydrogenase genes and the alcohol oxidase gene further reduced the formation of dicarboxylic acids. These results indicate that both (fatty) alcohol dehydrogenases and an alcohol oxidase are involved in ω-oxidation of long-chain fatty acids whereby latter plays the major role. This insight marks the first step toward the biotechnological production of long-chain ω-hydroxy fatty acids with the help of the nonconventional yeast Y. lipolytica. The overexpression of FAO1 can be further used to improve existing strains for the production of dicarboxylic acids.
Neural Multi-Source Morphological Reinflection

We explore the task of multi-source morphological reinflection, which generalizes the standard, single-source version. The input consists of (i) a target tag and (ii) multiple pairs of source form and source tag for a lemma. The motivation is that it is beneficial to have access to more than one source form since different source forms can provide complementary information, e.g., different stems. We further present a novel extension to the encoder-decoder recurrent neural architecture, consisting of multiple encoders, to better solve the task. We show that our new architecture outperforms single-source reinflection models and publish our dataset for multi-source morphological reinflection to facilitate future research.
System development and performance investigation of mobile ad-hoc networks in vehicular environments

This paper presents the methodology of implementations and performance measurements of our mobile ad-hoc network (MANET) platforms. The work is prompted by the lack of published results concerning the issues associated with the implementation of MANET facilities on actual wireless networks, as opposed to results of simulation experiments. Our MANET is developed based on the settled IEEE 802.11b technology operating in the ad-hoc mode. The opportunity driven multiple access (ODMA), which is developed by IWICS Inc., is implemented on the platform and its performance has been examined through field tests along city streets. Based on the measurement results, ODMA-based MANET facilities are able to provide satisfactory wireless communication services in vehicular environments. The minimum data throughput of 20 kBytes/sec could be guaranteed in our testbed.
Landscape and local effects on avian habitat use and breeding success in bottomland hardwood forests of the Mississippi Alluvial Valley

Woodpeckers in North America are not widely recognized as nest predators. In this paper, we describe several eyewitness accounts of songbird nest predation by Redbellied Woodpeckers (Melanerpes carolinus), document evidence that songbirds recognize woodpeckers as nest predators, and show that our observations are consistent with previously published notes. We believe that this species, commonly overlooked, may be an important predator of songbird nests in many eastern North American forests. INTRODUCTION In the ornithological literature, there is much emphasis on determinants of nesting success because this is such a fundamental component of individual fitness, population dynamics, and avian conservation (e.g., Donovan and Thompson 2001; Martin 1998; Paton 1994 ). From a conservation standpoint, knowledge of the nest predator community is important for predicting how landscape changes (e.g., habitat fragmentation) will affect breeding bird communities (Andren 1995). Preconceived notions about which taxa are potential nest predators are likely to affect study design and interpretation. In discussions with researchers at ornithological conferences, we have found that woodpeckers are not generally recognized as nest predators. In a summary of nest predation studies, Paton (1994) listed various birds, mammals, and snakes as "primary predators". However, corvids were the only avian taxa listed. Gates and Gysel (1978) mentioned several species of mammals, snakes, corvids, and raptors as potential nest predators, but said nothing about woodpeckers. Among eastern North American
The process of enterprise resource planning implementation and business process re‐engineering: tales from two Chinese small and medium‐sized enterprises

Abstract. Using an innovative process model, we describe and analyse the process of introducing enterprise resource planning (ERP) systems in two Chinese small and medium‐sized enterprises and especially their decisions concerning business process re‐engineering. First we compared the results from our cases with Martinsons' earlier work (2004). One case seemed to fit most of the characteristics of a private venture (PV) whereas the other case, also a PV, had a very low degree of fit. We used the process model to offer further insights and features such as its predictive power. Second, and as predicted, we also observed the differential role of top management support in the two Chinese companies. But thirdly, and somewhat surprisingly, we found that cultural issues were only of limited importance. Finally, the ability of the project team to deal with unexpected events was seen as critical in ensuring the stability of a project. In contrast, project drift is shown to lead to a degree of chaos. We offer some suggestions as to how stakeholders can improve their chances of implementing ERP systems more successfully.
Discovering Protein-DNA Binding Cores by Aligned Pattern Clustering

Understanding binding cores is of fundamental importance in deciphering Protein-DNA (TF-TFBS) binding and gene regulation. Limited by expensive experiments, it is promising to discover them with variations directly from sequence data. Although existing computational methods have produced satisfactory results, they are one-to-one mappings with no site-specific information on residue/nucleotide variations, where these variations in binding cores may impact binding specificity. This study presents a new representation for modeling binding cores by incorporating variations and an algorithm to discover them from only sequence data. Our algorithm takes protein and DNA sequences from TRANSFAC (a Protein-DNA Binding Database) as input; discovers from both sets of sequences conserved regions in Aligned Pattern Clusters (APCs); associates them as Protein-DNA Co-Occurring APCs; ranks the Protein-DNA Co-Occurring APCs according to their co-occurrence, and among the top ones, finds three-dimensional structures to support each binding core candidate. If successful, candidates are verified as binding cores. Otherwise, homology modeling is applied to their close matches in PDB to attain new chemically feasible binding cores. Our algorithm obtains binding cores with higher precision and much faster runtime ($\geq$ 1,600x) than that of its contemporaries, discovering candidates that do not co-occur as one-to-one associated patterns in the raw data. Availability: http://www.pami. uwaterloo.ca/~ealee/files/tcbbPnDna2015/Release.zip.
Swedish experience of the Dialock

Objective. To study the patency and complications associated with the Dialock, an access device for haemodialysis. Material and methods. The records of seven Swedish patients who were treated with the Dialock access device between 2000 and 2004 were studied retrospectively. Results. A total of 10 Dialock devices were used in seven patients. The mean period of patency was 16.3±13.8 months. Major complications observed were bleeding in the dose pocket in three patients and infection in four. Three patients experienced no complications. The 1-year patency was similar to that of a newly created arteriovenous fistula used in our unit. Conclusions. In spite of the associated complications, the Dialock is an acceptable access device for haemodialysis patients with vascular access problems. Although the Dialock is no longer available on the market, similar access devices may be of importance in the future.
Platelet storage lesion: An update

1 Platelets are unique blood cells that play a pivotal role in mediating hemostasis and thrombosis. Over the years, the demand for platelets is steadily rising because of their increased use in patients with thrombocytopenia and platelet function defects. The availability of platelets for transfusion is restricted by the markedly short shelf life of platelets owing to risk of bacterial contamination and storage-related deterioration known as platelet storage lesion (PSL). [1] PSL is best defi ned as the sum of all the deleterious changes in platelet structure and function that arise from the time the blood is withdrawn from the donor to the time the platelets are transfused to the recipient. [2] The mechanisms responsible for PSL are multifactorial and not clearly understood. Several factors including the methods of collection, processing, storage, and manipulation after collection can result in PSL. [3] These lesions are associated with decreased in vivo platelet recovery, survival, and hemostatic activity after transfusion. [4]
The Stability and Usability of Statistical Topic Models

Statistical topic models have become a useful and ubiquitous tool for analyzing large text corpora. One common application of statistical topic models is to support topic-centric navigation and exploration of document collections. Existing work on topic modeling focuses on the inference of model parameters so the resulting model fits the input data. Since the exact inference is intractable, statistical inference methods, such as Gibbs Sampling, are commonly used to solve the problem. However, most of the existing work ignores an important aspect that is closely related to the end user experience: topic model stability. When the model is either re-trained with the same input data or updated with new documents, the topic previously assigned to a document may change under the new model, which may result in a disruption of end users’ mental maps about the relations between documents and topics, thus undermining the usability of the applications. In this article, we propose a novel user-directed non-disruptive topic model update method that balances the tradeoff between finding the model that fits the data and maintaining the stability of the model from end users’ perspective. It employs a novel constrained LDA algorithm to incorporate pairwise document constraints, which are converted from user feedback about topics, to achieve topic model stability. Evaluation results demonstrate the advantages of our approach over previous methods.