Microgeographic variation in morphology within populations of threespine stickleback

Local adaptation, the evolution of traits that make native individuals in a population have higher fitness than foreign individuals, is studied intensively in the field of evolutionary biology. For local adaptation to occur, different habitats must select for different traits, and this divergent selection must be stronger than the homogenizing effect of selection. However, at small spatial scales, gene flow is believed to be the stronger evolutionary force, eroding any local adaptation. Yet, local adaptation can still occur at small spatial scales (‘microgeographic divergence’) if selection is strong, if individuals proactively choose their habitat, or if philopatric individuals adjust their phenotypes to their local environment. The goal of my research is to test for microgeographic divergence within populations of threespine stickleback. I analyzed morphological and trap data of threespine stickleback collected in 2013, to test for among-trap differences in morphological traits. I show that stickleback morphology differs among traps within lakes, and within streams. This microgeographic variation is stronger for some traits than for others and is only partly attributable to isolation by distance within lakes. Overall, the results provide support of microgeographic divergence, a concept that may be more widespread than evolutionary biologists have previously believed.Integrative Biolog

Robust airline schedule design in a dynamic scheduling environment

In the past decade, major airlines in the US have moved from banked hub-and-spoke operations to de-banked hub-and-spoke operations in order to lower operating costs. In Jiang and Barnhart (2009), it is shown that dynamic airline scheduling, an approach that makes minor adjustments to flight schedules in the booking period by re-fleeting and re-timing flight legs, can significantly improve utilization of capacity and hence increase profit. In this paper, we develop robust schedule design models and algorithms to generate schedules that facilitate the application of dynamic scheduling in de-banked hub-and-spoke operations. Such schedule design approaches are robust in the sense that the schedules produced can more easily be manipulated in response to demand variability when embedded in a dynamic scheduling environment. In our robust schedule design model, we maximize the number of potentially connecting itineraries weighted by their respective revenues. We provide two equivalent formulations of the robust schedule design model and develop a decomposition-based solution approach involving a variable reduction technique and a variant of column generation. We demonstrate, through experiments using data from a major U.S. airline that the schedule generated can improve profitability when dynamic scheduling is applied. It is also observed that the greater the demand variability, the more profit our robust schedules achieve when compared to existing ones

Nexiwave case

Thesis (S.M. in Engineering and Management)--Massachusetts Institute of Technology, System Design and Management Program, 2009.Cataloged from PDF version of thesis.Includes bibliographical references (p. 82-83).Telecommunication technology has had a profound impact on our daily lives. It has enabled organizations to be more competitive by reducing the need for physical proximity and fostering collaboration. In recent years especially, data networks have been especially prominent, with the obvious example being the Internet. Work that was once conducted by phone and fax is now increasingly being done by VolP, e-mail and IM. For years telecommunication companies had focused in making available communication between person-to-person as well as multi-person and mobile communication, but none had focused on the content of the voice communication. This thesis presents a functioning product to address the needs of such users by applying a systems thinking approach to visualize and manage complexity through the whole process from the product idea generation to the business model. A detailed assessment of the users' needs and description of the product's user-centric design is provided. User experience design principles and legal constraints were considered throughout the development process. We propose to add value and differentiate the product by providing users with options to manage the content of their calls. At the most basic level, we give free audio-to-text transcripts with built-in features that could users save time and be more productive. nexiwave was built using principles promulgated in the System Design and Management Program classes.by Cynthia Munoz Jugo [and] Benjamin Jiang.S.M.in Engineering and Managemen

OPTIMIZATION APPROACHES TO AIRLINE INDUSTRY CHALLENGES: Airline Schedule Planning and Recovery

The airline industry has a long history of developing and applying optimization approaches to their myriad of scheduling problems, including designing flight schedules that maximize profitability while satisfying rules related to aircraft maintenance; generating cost-minimizing, feasible work schedules for pilots and flight attendants; and identifying implementable, low-cost changes to aircraft and crew schedules as disruptions render the planned schedule inoperable. The complexities associated with these problems are immense, including long-and short-term planning horizons; and multiple resources including aircraft, crews, and passengers, all operating over shared airspace and airport capacity. Optimization approaches have played an important role in overcoming this complexity and providing effective aircraft and crew schedules. Historical optimization-based approaches, however, often involve a sequential process, first generating aircraft schedules and then generating crew schedules. Decisions taken in the first steps of the process limit those that are possible in subsequent steps, resulting in overall plans that, while feasible, are typically sub-optimal. To mitigate the myopic effects of sequential solutions, researchers have developed extended models that begin to integrate som

Accuracy of IOL Power Calculation Formulas for AcrySof SN60WF versus Tecnis ZCB00 Intraocular Lenses

Purpose: To compare the accuracy of various intraocular lens power formulas for two monofocal hydrophobic foldable lenses, the AcrySof SN60WF and the Tecnis ZCB00. Methods: This retrospective study included 409 eyes from 409 patients who underwent uncomplicated cataract surgery (299 eyes with SN60WF and 110 eyes with ZCB00). Biometry was performed for all eyes with an IOLMaster 700. Predicted refraction from five different IOL power formulas (Barrett Universal II, Haigis, Hoffer-Q, Holladay 2, and SRK/T) was compared to postoperative refraction at one to three months for the following axial length strata: short eyes (<22.5 mm), medium eyes (22.5–25.5 mm), and long eyes (>25.5 mm). Results: In patients with medium eyes, there were no significant differences in the mean absolute error (MAE) and the percentage of eyes within ±0.5 D (%±0.5 D) between both IOLs. In short eyes, although MAE was similar between both lenses, %±0.5 D was significantly higher for Barrett Universal II in ZCB00 than in SN60WF (P = 0.01) while Hoffer-Q and Holladay 2 performed equally for both lenses. In long eyes, ZCB00 had a higher MAE than SN60WF for Barrett Universal II, Haigis, and Hoffer-Q. Additionally, in long eyes, the percentage of eyes within %±0.5 D was significantly higher for SN60WF than ZCB00 for all formulas (P < 0.001). Conclusion: Although there were no significant differences in the formula accuracy between these two lenses in medium eyes for all formulas and in short eyes for most formulas, the accuracy decreased significantly in long eyes for ZCB00 compared to SN60WF. The effect of IOL model on the postoperative outcomes should be further investigated

Assembly and architecture of the EBV B cell entry triggering complex.

Epstein-Barr Virus (EBV) is an enveloped double-stranded DNA virus of the gammaherpesvirinae sub-family that predominantly infects humans through epithelial cells and B cells. Three EBV glycoproteins, gH, gL and gp42, form a complex that targets EBV infection of B cells. Human leukocyte antigen (HLA) class II molecules expressed on B cells serve as the receptor for gp42, triggering membrane fusion and virus entry. The mechanistic role of gHgL in herpesvirus entry has been largely unresolved, but it is thought to regulate the activation of the virally-encoded gB protein, which acts as the primary fusogen. Here we study the assembly and function of the reconstituted B cell entry complex comprised of gHgL, gp42 and HLA class II. The structure from negative-stain electron microscopy provides a detailed snapshot of an intermediate state in EBV entry and highlights the potential for the triggering complex to bring the two membrane bilayers into proximity. Furthermore, gHgL interacts with a previously identified, functionally important hydrophobic pocket on gp42, defining the overall architecture of the complex and playing a critical role in membrane fusion activation. We propose a macroscopic model of the initiating events in EBV B cell fusion centered on the formation of the triggering complex in the context of both viral and host membranes. This model suggests how the triggering complex may bridge the two membrane bilayers, orienting critical regions of the N- and C- terminal ends of gHgL to promote the activation of gB and efficient membrane fusion

Approximating Human-Like Few-shot Learning with GPT-based Compression

In this work, we conceptualize the learning process as information compression. We seek to equip generative pre-trained models with human-like learning capabilities that enable data compression during inference. We present a novel approach that utilizes the Generative Pre-trained Transformer (GPT) to approximate Kolmogorov complexity, with the aim of estimating the optimal Information Distance for few-shot learning. We first propose using GPT as a prior for lossless text compression, achieving a noteworthy compression ratio. Experiment with LLAMA2-7B backbone achieves a compression ratio of 15.5 on enwik9. We justify the pre-training objective of GPT models by demonstrating its equivalence to the compression length, and, consequently, its ability to approximate the information distance for texts. Leveraging the approximated information distance, our method allows the direct application of GPT models in quantitative text similarity measurements. Experiment results show that our method overall achieves superior performance compared to embedding and prompt baselines on challenging NLP tasks, including semantic similarity, zero and one-shot text classification, and zero-shot text ranking

Boosting with intranasal dendrimeric Aβ1–15 but not Aβ1–15 peptide leads to an effective immune response following a single injection of Aβ1–40/42 in APP-tg mice

BACKGROUND: Immunotherapy for Alzheimer's disease (AD) is emerging as a potential treatment. However, a clinical trial (AN1792) was halted after adverse effects occurred in a small subset of subjects, which may have been caused by a T cell-mediated immunological response. In general, aging limits the humoral immune response, therefore, immunogens and vaccination regimes are required that induce a strong antibody response with less potential for an adverse immune response. METHOD: In the current study, we immunized both wildtype and J20 APP-tg mice with a priming injection of Aβ1–40/42, followed by multiple intranasal boosts with the novel immunogen dAβ1–15 (16 copies of Aβ1–15 on a lysine tree), Aβ1–15 peptide or Aβ1–40/42 full length peptide. RESULTS: J20 APP-tg mice primed with Aβ1–40/42 subcutaneously and subsequently boosted intranasally with Aβ1–15 peptide did not generate a cellular or humoral immune response. In contrast, J20 APP-tg mice boosted intranasally with dAβ1–15 or full length Aβ1–40/42 produced high levels of anti-Aβ antibodies. Splenocyte proliferation was minimal in mice immunized with dAβ1–15. Wildtype littermates of the J20 APP-tg mice produced higher amounts of anti-Aβ antibodies compared to APP-tg mice but also had low T cell proliferation. The anti-Aβ antibodies were mainly composed of IgG2b and directed to an epitope within the Aβ1–7 region, regardless of the immunogen. Examination of the brain showed a significant reduction in Aβ plaque burden in the J20 APP-tg mice producing antibodies compared to controls. Biochemically, Aβ40 or Aβ42 were also reduced in brain homogenates and elevated in plasma but the changes did not reach significance. CONCLUSION: Our results demonstrate that priming with full length Aβ40/42 followed by boosting with dAβ1–15 but not Aβ1–15 peptide led to a robust humoral immune response with a minimal T cell response in J20 APP-tg mice. In addition, Aβ plaque burden was reduced in mice producing anti-Aβ antibodies. Interestingly, wildtype mice produced higher levels of anti-Aβ antibodies, indicating that immune tolerance may be present in J20 APP-tg mice. Together, these data suggest that dAβ1–15 but not Aβ1–15 peptide may be useful as a boosting immunogen in an AD vaccination regime