A Course in Critical Thinking for PhD Students in Biomolecular Sciences and Biotechnology: Classical Experiments in Biochemistry

This essay presents and discusses an eight-session seminar course designed to develop critical thinking skills in doctoral biochemistry students by exposing them to classical experiments in biochemistry. During each 2.5 session, different key topics of the discovery and development of biochemical concepts are discussed. Before each session, students are required to read the one or two classical papers. The size of the seminar course and the seating of the students are critical to make this a highly interactive environment for all students to participate in the critique and re-designing of key experiments, including control experiments, which helped formulate these classical concepts. Final student evaluation of the course’s goals has two equal components: Course participation and a final take home exam due two weeks after the course is completed. Together with the take home exam students are also required to write an evaluation of the course, preferably no longer than half a page. Students’ comments of the course have been uniformly positive. The author notes the sooner students are exposed to this manner of thinking, the better they will be equipped to choose an appropriate mentor and contribute creatively to attempt to solve the scientific problem of their PhD thesis

An Efficient Data Structure for Dynamic Two-Dimensional Reconfiguration

In the presence of dynamic insertions and deletions into a partially reconfigurable FPGA, fragmentation is unavoidable. This poses the challenge of developing efficient approaches to dynamic defragmentation and reallocation. One key aspect is to develop efficient algorithms and data structures that exploit the two-dimensional geometry of a chip, instead of just one. We propose a new method for this task, based on the fractal structure of a quadtree, which allows dynamic segmentation of the chip area, along with dynamically adjusting the necessary communication infrastructure. We describe a number of algorithmic aspects, and present different solutions. We also provide a number of basic simulations that indicate that the theoretical worst-case bound may be pessimistic.Comment: 11 pages, 12 figures; full version of extended abstract that appeared in ARCS 201

Dialogue Act Modeling for Automatic Tagging and Recognition of Conversational Speech

We describe a statistical approach for modeling dialogue acts in conversational speech, i.e., speech-act-like units such as Statement, Question, Backchannel, Agreement, Disagreement, and Apology. Our model detects and predicts dialogue acts based on lexical, collocational, and prosodic cues, as well as on the discourse coherence of the dialogue act sequence. The dialogue model is based on treating the discourse structure of a conversation as a hidden Markov model and the individual dialogue acts as observations emanating from the model states. Constraints on the likely sequence of dialogue acts are modeled via a dialogue act n-gram. The statistical dialogue grammar is combined with word n-grams, decision trees, and neural networks modeling the idiosyncratic lexical and prosodic manifestations of each dialogue act. We develop a probabilistic integration of speech recognition with dialogue modeling, to improve both speech recognition and dialogue act classification accuracy. Models are trained and evaluated using a large hand-labeled database of 1,155 conversations from the Switchboard corpus of spontaneous human-to-human telephone speech. We achieved good dialogue act labeling accuracy (65% based on errorful, automatically recognized words and prosody, and 71% based on word transcripts, compared to a chance baseline accuracy of 35% and human accuracy of 84%) and a small reduction in word recognition error.Comment: 35 pages, 5 figures. Changes in copy editing (note title spelling changed

Idealized digital models for conical reed instruments, with focus on the internal pressure waveform

International audienceTwo models for the generation of self-oscillations of reed conical woodwinds are presented. They use the fewest parameters (of either the resonator or the ex-citer), whose influence can be quickly explored. The formulation extends iterated maps obtained for loss-less cylindrical pipes without reed dynamics. It uses spherical wave variables in idealized resonators, with one parameter more than for cylinders: the missing length of the cone. The mouthpiece volume equals that of the missing part of the cone, and is implemented as either a cylindrical pipe (first model) or a lumped element (second model). Only the first model adds a length parameter for the mouthpiece and leads to the solving of an implicit equation. For the second model, any shape of nonlinear characteristic can be directly considered. The complex characteristics impedance for spherical waves requires sampling times smaller than a round trip in the resonator. The convergence of the two models is shown when the length of the cylindrical mouthpiece tends to zero. The waveform is in semi-quantitative agreement with experiment. It is concluded that the oscillations of the positive episode of the mouthpiece pressure are related to the length of the missing part, not to the reed dynamics

Interaction of reed and acoustic resonator in clarinetlike systems

Sound emergence in clarinetlike instruments is investigated in terms of instability of the static regime. Various models of reed-bore coupling are considered, from the pioneering work of Wilson and Beavers ["Operating modes of the clarinet", J. Acoust. Soc. Am. 56, 653--658 (1974)] to more recent modeling including viscothermal bore losses and vena contracta at the reed inlet. The pressure threshold above which these models may oscillate as well as the frequency of oscillation at threshold are calculated. In addition to Wilson and Beavers' previous conclusions concerning the role of the reed damping in the selection of the register the instrument will play on, the influence of the reed motion induced flow is also emphasized, particularly its effect on playing frequencies, contributing to reduce discrepancies between Wilson and Beavers' experimental results and theory, despite discrepancies still remain concerning the pressure threshold. Finally, analytical approximations of the oscillating solution based on Fourier series expansion are obtained in the vicinity of the threshold of oscillation. This allows to emphasize the conditions which determine the nature of the bifurcation (direct or inverse) through which the note may emerge, with therefore important consequences on the musical playing performances

Guanosine diphosphatase is required for protein and sphingolipid glycosylation in the Golgi lumen of Saccharomyces cerevisiae

Current models for nucleotide sugar use in the Golgi apparatus predict a critical role for the lumenal nucleoside diphosphatase. After transfer of sugars to endogenous macromolecular acceptors, the enzyme converts nucleoside diphosphates to nucleoside monophosphates which in turn exit the Golgi lumen in a coupled antiporter reaction, allowing entry of additional nucleotide sugar from the cytosol. To test this model, we cloned the gene for the S. cerevisiae guanosine diphosphatase and constructed a null mutation. This mutation should reduce the concentrations of GDP-mannose and GMP and increase the concentration of GDP in the Golgi lumen. The alterations should in turn decrease mannosylation of proteins and lipids in this compartment. In fact, we found a partial block in O- and N-glycosylation of proteins such as chitinase and carboxypeptidase Y and underglycosylation of invertase. In addition, mannosylinositolphosphorylceramide levels were drastically reduced

MC64: A web platform to test bioinformatics algorithms in a many-core architecture

New analytical methodologies, like the so-called "next-generation sequencing" (NGS), allow the sequencing of full genomes with high speed and reduced price. Yet, such technologies generate huge amounts of data that demand large raw computational power. Many-core technologies can be exploited to overcome the involved bioinformatics bottleneck. Indeed, such hardware is currently in active development. We have developed parallel bioinformatics algorithms for many-core microprocessors containing 64 cores each. Thus, the MC64 web platform allows executing high-performance alignments (Needleman-Wunsch, Smith-Waterman and ClustalW) of long sequences. The MC64 platform can be accessed via web browsers, allowing easy resource integration into third-party tools. Furthermore, the results obtained from the MC64 include time-performance statistics that can be compared with other platform