The limits of subfunctionalization

<p>Abstract</p> <p>Background</p> <p>The duplication-degeneration-complementation (DDC) model has been proposed as an explanation for the unexpectedly high retention of duplicate genes. The hypothesis proposes that, following gene duplication, the two gene copies degenerate to perform complementary functions that jointly match that of the single ancestral gene, a process also known as subfunctionalization. We distinguish between subfunctionalization at the regulatory level and at the product level (e.g within temporal or spatial expression domains).</p> <p>Results</p> <p>In contrast to what is expected under the DDC model, we use <it>in silico </it>modeling to show that regulatory subfunctionalization is expected to peak and then decrease significantly. At the same time, neofunctionalization (recruitment of novel interactions) increases monotonically, eventually affecting the regulatory elements of the majority of genes. Furthermore, since this process occurs under conditions of stabilizing selection, there is no need to invoke positive selection. At the product level, the frequency of subfunctionalization is no higher than would be expected by chance, a finding that was corroborated using yeast microarray time-course data. We also find that product subfunctionalization is not necessarily caused by regulatory subfunctionalization.</p> <p>Conclusion</p> <p>Our results suggest a more complex picture of post-duplication evolution in which subfunctionalization plays only a partial role in conjunction with redundancy and neofunctionalization. We argue that this behavior is a consequence of the high evolutionary plasticity in gene networks.</p

Meningeal Hemangiopericytoma with Intracranial Metastases in an HIV-Positive Male: Case Report and Review of the Literature

Background: Meningeal hemangiopericytoma is a rare, aggressive CNS tumor that tends to invade locally, metastasize, and has a high rate of recurrence. HIV classically increases the risk of 3 AIDS-defining malignancies: Kaposi’s sarcoma, non-Hodgkin’s lymphoma and invasive cervical cancer. More recently, considerable interest has been paid to the link between HIV and a wider range of non-AIDS-defining cancers. An HIV-positive patient with meningeal hemangiopericytoma is described. Case Description: A 36-year-old HIV-positive male presented with worsening headache and ataxia. The patient had experienced similar neurologic symptoms 4 months prior and MRI at that time had showed an extra-axial left cerebellar mass most consistent with benign meningioma. Repeat MRI showed the tumor had increased in size by a factor of greater than 20 in this 4-month period, with 4 small additional foci of similar enhancement. Subtotal resection was performed on the mass and final pathological diagnosis was meningeal hemangiopericytoma. Conclusions: This represents the first reported case of meningeal hemangiopericytoma in an HIV-positive patient. This is also the shortest time to intracranial metastasis ever reported for a meningeal hemangiopericytoma. Although the increased risk in the HIV-positive population of non-AIDS-defining cancers that has been observed in recent years can largely be attributed to cancers with a known viral pathogenesis, it is speculated that HIV infection in this patient may have contributed to the occurrence or unique behavior of this rare tumor

Determination of Operating Conditions and the Impact on Integrally Geared Centrifugal Air Compressor Selection and Performance

TutorialThis tutorial will provide several examples of how a users specified conditions impact the selection of the compressor along with discussions of how providing well-realized conditions can help reduce the compressors power consumption. The tutorial will also discuss the flexibility and limitations centrifugal compressor manufacturers have in meeting various operating conditions through the selection of aerodynamic hardware and the inlet control valve including variable inlet guide vanes. Finally, the paper will provide input from an end user of centrifugal air compressors offering their point of view of the conditions provided and the compressed air solutions they need. The overarching goal is to better educate end users and purchasers of centrifugal air compressors so they can make more informed requests and obtain machinery that more efficiently meets their year-round needs

Computing Tropical Varieties

The tropical variety of a $d$-dimensional prime ideal in a polynomial ring with complex coefficients is a pure $d$-dimensional polyhedral fan. This fan is shown to be connected in codimension one. We present algorithmic tools for computing the tropical variety, and we discuss our implementation of these tools in the Gr\"obner fan software \texttt{Gfan}. Every ideal is shown to have a finite tropical basis, and a sharp lower bound is given for the size of a tropical basis for an ideal of linear forms.Comment: 22 pages, 2 figure

Reflections on an Integrated Content and Language Project-Based Design of a Technical Communication Course for Electrical Engineering Students

Effective ways of teaching technical communication skills to engineering students have been much discussed. This article reflects on one setting, a first year course in Technical Communication at a university in Sweden, where electrical engineering teachers, language and communication teachers and student counsellors work in close, team-based cooperation using a project model which requires the students to analyse, implement and communicate technical problems. The paper discusses the change in this course - from an EAP course primarily prioritizing language training which ran parallel with a project course - to one unified ICL course. The progression is described through the changes in the organization of the course, and the article focuses on one learning activity: interdisciplinary tutorials on project reports. Through a pilot study where these sessions were video recorded and mapped, we conclude that the presence of different roles became an asset for the range of what the students see as relevant for their project report. In particular, the technical report genre was critically analysed, including problematic areas such as textual sequencing and display of technical problems; data visualisation and commentary; and referencing

Photo repair and 3d structure from flatbed scanners

We introduce a technique that allows 3D information to be captured from a conventional flatbed scanner. The technique requires no hardware modification and allows untrained users to easily capture 3D datasets. Once captured, these datasets can be used for interactive relighting and enhancement of surface detail on physical objects. We have also found that the method can be used to scan and repair damaged photographs. Since the only 3D structure on these photographs will typically be surface tears and creases, our method provides an accurate procedure for automatically detecting these flaws without any user intervention. Once detected, automatic techniques, such as infilling and texture synthesis, can be leveraged to seamlessly repair such damaged areas. We first present a method that is able to repair damaged photographs with minimal user interaction and then show how we can achieve similar results using a fully automatic process

Tuning magnetic frustration on the diamond lattice of the A-site magnetic spinels CoAl2−x_{2-x}Gax_xO4_4: Lattice expansion and site disorder

The spinels CoB$_2$O$_4$ with magnetic Co$^{2+}$ ions on the diamond lattice A site can be frustrated because of competing near-neighbor ($J_1$) and next-near neighbor ($J_2$) interactions. Here we describe attempts to tune the relative strengths of these interactions by substitution on the non-magnetic B-site. The system we employ is CoAl$_{2-x}$Ga$_x$O$_4$, where Al is systematically replaced by the larger Ga, ostensibly on the B site. As expected, Ga substitution expands the lattice, resulting in Co atoms on the A-site being pushed further from one other and thereby weakening magnetic interactions. In addition, Ga distributes between the B and the A site in a concentration dependent manner displacing an increasing amount of Co from the A site with increasing $x$. This increased inversion, which is confirmed by neutron diffraction studies carried out at room temperature, affects magnetic ordering very significantly, and changes the nature of the ground state. Modeling of the magnetic coupling illustrates the complexity that arises from the cation site disorder.Comment: 9 pages, 10 figure

Large-Scale Discovery of Promoter Motifs in Drosophila melanogaster

A key step in understanding gene regulation is to identify the repertoire of transcription factor binding motifs (TFBMs) that form the building blocks of promoters and other regulatory elements. Identifying these experimentally is very laborious, and the number of TFBMs discovered remains relatively small, especially when compared with the hundreds of transcription factor genes predicted in metazoan genomes. We have used a recently developed statistical motif discovery approach, NestedMICA, to detect candidate TFBMs from a large set of Drosophila melanogaster promoter regions. Of the 120 motifs inferred in our initial analysis, 25 were statistically significant matches to previously reported motifs, while 87 appeared to be novel. Analysis of sequence conservation and motif positioning suggested that the great majority of these discovered motifs are predictive of functional elements in the genome. Many motifs showed associations with specific patterns of gene expression in the D. melanogaster embryo, and we were able to obtain confident annotation of expression patterns for 25 of our motifs, including eight of the novel motifs. The motifs are available through Tiffin, a new database of DNA sequence motifs. We have discovered many new motifs that are overrepresented in D. melanogaster promoter regions, and offer several independent lines of evidence that these are novel TFBMs. Our motif dictionary provides a solid foundation for further investigation of regulatory elements in Drosophila, and demonstrates techniques that should be applicable in other species. We suggest that further improvements in computational motif discovery should narrow the gap between the set of known motifs and the total number of transcription factors in metazoan genomes

Overcoming status quo bias in the human brain

Humans often accept the status quo when faced with conflicting choice alternatives. However, it is unknown how neural pathways connecting cognition with action modulate this status quo acceptance. Here we developed a visual detection task in which subjects tended to favor the default when making difficult, but not easy, decisions. This bias was suboptimal in that more errors were made when the default was accepted. A selective increase in subthalamic nucleus (STN) activity was found when the status quo was rejected in the face of heightened decision difficulty. Analysis of effective connectivity showed that inferior frontal cortex, a region more active for difficult decisions, exerted an enhanced modulatory influence on the STN during switches away from the status quo. These data suggest that the neural circuits required to initiate controlled, nondefault actions are similar to those previously shown to mediate outright response suppression. We conclude that specific prefrontal-basal ganglia dynamics are involved in rejecting the default, a mechanism that may be important in a range of difficult choice scenarios

Determination of Operating Conditions and the Impact on Integrally Geared Centrifugal Air Compressor Selection and Performance

TutorialThis tutorial will provide several examples of how a users specified conditions impact the selection of the compressor along with discussions of how providing well-realized conditions can help reduce the compressors power consumption. The tutorial will also discuss the flexibility and limitations centrifugal compressor manufacturers have in meeting various operating conditions through the selection of aerodynamic hardware and the inlet control valve including variable inlet guide vanes. Finally, the paper will provide input from an end user of centrifugal air compressors offering their point of view of the conditions provided and the compressed air solutions they need. The overarching goal is to better educate end users and purchasers of centrifugal air compressors so they can make more informed requests and obtain machinery that more efficiently meets their year-round needs