Temporal Control of the TGF-β Signaling Network by Mouse ESC MicroRNA Targets of Different Affinities.

Although microRNAs (miRNAs) function in the control of embryonic stem cell (ESC) pluripotency, a systems-level understanding is still being developed. Through the analysis of progressive Argonaute (Ago)-miRNA depletion and rescue, including stable Ago knockout mouse ESCs, we uncover transforming growth factor beta (TGF-β) pathway activation as a direct and early response to ESC miRNA reduction. Mechanistically, we link the derepression of weaker miRNA targets, including TGF-β receptor 1 (Tgfbr1), to the sensitive TGF-β pathway activation. In contrast, stronger miRNA targets impart a more robust repression, which dampens concurrent transcriptional activation. We verify such dampened induction for TGF-β antagonist Lefty. We find that TGF-β pathway activation contributes to the G1 cell-cycle accumulation of miRNA-deficient ESCs. We propose that miRNA target affinity is a determinant of the temporal response to miRNA changes, which enables the coordination of gene network responses

New Opportunities for Automated Pedestrian Performance Measures

Pedestrian safety is an important concern when evaluating intersections. Previous literature has shown that exclusive pedestrian phases improve safety, but at the expense of imposing greater pedestrian and motorist delay. However, outside of crash data, there are no easily implementable performance measures for pedestrians at traffic signals. This study proposes two performance metrics: (1) a time-to-jaywalk measure, and (2) the Conflict Occupancy Ratio (COR) for evaluating concurrent pedestrian signal phasing with turning vehicles. The COR quantifies conflicts between turning vehicles and pedestrians in the crosswalk. The COR is based upon a commercially deployed video detection system that correctly identified the presence of pedestrians to within two per cycle in this study. This performance is likely sufficient for the current application, but as the technology matures it will provide a scalable screening tool to identify intersections that have opportunities for capacity adjustments or warrant further direct field investigation

Garbage Collection for General Graphs

Garbage collection is moving from being a utility to a requirement of every modern programming language. With multi-core and distributed systems, most programs written recently are heavily multi-threaded and distributed. Distributed and multi-threaded programs are called concurrent programs. Manual memory management is cumbersome and difficult in concurrent programs. Concurrent programming is characterized by multiple independent processes/threads, communication between processes/threads, and uncertainty in the order of concurrent operations. The uncertainty in the order of operations makes manual memory management of concurrent programs difficult. A popular alternative to garbage collection in concurrent programs is to use smart pointers. Smart pointers can collect all garbage only if developer identifies cycles being created in the reference graph. Smart pointer usage does not guarantee protection from memory leaks unless cycle can be detected as process/thread create them. General garbage collectors, on the other hand, can avoid memory leaks, dangling pointers, and double deletion problems in any programming environment without help from the programmer. Concurrent programming is used in shared memory and distributed memory systems. State of the art shared memory systems use a single concurrent garbage collector thread that processes the reference graph. Distributed memory systems have very few complete garbage collection algorithms and those that exist use global barriers, are centralized and do not scale well. This thesis focuses on designing garbage collection algorithms for shared memory and distributed memory systems that satisfy the following properties: concurrent, parallel, scalable, localized (decentralized), low pause time, high promptness, no global synchronization, safe, complete, and operates in linear time

A scalable hardware and software control apparatus for experiments with hybrid quantum systems

Modern experiments with fundamental quantum systems - like ultracold atoms, trapped ions, single photons - are managed by a control system formed by a number of input/output electronic channels governed by a computer. In hybrid quantum systems, where two or more quantum systems are combined and made to interact, establishing an efficient control system is particularly challenging due to the higher complexity, especially when each single quantum system is characterized by a different timescale. Here we present a new control apparatus specifically designed to efficiently manage hybrid quantum systems. The apparatus is formed by a network of fast communicating Field Programmable Gate Arrays (FPGAs), the action of which is administrated by a software. Both hardware and software share the same tree-like structure, which ensures a full scalability of the control apparatus. In the hardware, a master board acts on a number of slave boards, each of which is equipped with an FPGA that locally drives analog and digital input/output channels and radiofrequency (RF) outputs up to 400 MHz. The software is designed to be a general platform for managing both commercial and home-made instruments in a user-friendly and intuitive Graphical User Interface (GUI). The architecture ensures that complex control protocols can be carried out, such as performing of concurrent commands loops by acting on different channels, the generation of multi-variable error functions and the implementation of self-optimization procedures. Although designed for managing experiments with hybrid quantum systems, in particular with atom-ion mixtures, this control apparatus can in principle be used in any experiment in atomic, molecular, and optical physics.Comment: 10 pages, 12 figure

Physiology of chimpanzees in orbit. Part 1: Scientific Report

Major achievements and accomplishments are reported for the Physiology of Chimpanzees in Orbit Program. Scientific studies relate to behavior and physiology, and engineering studies cover telemetry, behavioral training, systems tests, life support subsystems, and program plan

Semilunar Spawning in Killifish, Fundulus Grandis.

Gulf killifish, Fundulus grandis, spawned daily in aquaria exposed to 12-hr daylengths and 21 to 28\sp\circC temperatures. The number of eggs spawned varied daily producing a peak about every 13.7 days. Ovarian studies indicate that increased maturation of peripheral germinal-vesicle oocytes in preparation for spawning begins five days before the semilunar spawning peak. There is an increase in numbers of hydrated oocytes and ovulated eggs reaching a maximum on or a day before peak spawning. Semilunar spawning cycles of F. grandis are expressions of an endogenous rhythm. Although a specific phase of the semilunar cycle is maintained with respect to a tidal cycle in the natural environment, the spawning cycle freeruns in the laboratory with periods ranging from 12.7 to 14.1 days so that different phases occur respecting the concurrent tidal cycle. The period of the spawning cycle changes only slightly with temperatures (21 and 27\sp\circC) so that there is nearly complete temperature compensation (Q\sb{10} is not significantly different from 1.0). The period of the freerunning semilunar spawning cycle is apparently a long-term adaptation to the local environment. F. grandis, collected from the Louisiana coast of the Gulf of Mexico, and its close relative, F. heteroclitus, collected from the Delaware coast of the Atlantic ocean, were monitored side by side. The mean cycle periods were near 13.7 days for F. grandis and near 14.8 days for F. heteroclitus. The shorter duration in F. grandis closely approximates the tidal cycle in the Gulf of Mexico. The longer duration in F. heteroclitus closely approximates the tidal cycle along the Atlantic coast. Whereas endogenous freerunning semilunar cycles have been demonstrated previously in aquatic invertebrates, the present research is the first unequivocal evidence of such a cycle in fish. Contrary to mammalian reproductive cycles (e.g., estrual and menstrual) the semilunar cycle in F. grandis is not merely a reproductive rhythm, but rather an expression of a more basic periodicity of the fish neuroendocrine system. Otolith growth patterns indicate that a semilunar cycle of growth occurs in reproductively immature fish and in adult fish in or outside the breeding season

A design representation model for high-level synthesis

Design tools share and exchange various types of information pertaining to the design. The identification of a uniform design representation to capture this information is essential for the development of a successful design environment. We have done an extensive study on the representation needs of existing database tools in the UCI CADLAB; examples of which are graph compilers for high-level hardware specifications, state schedulers, hardware allocators, and microarchitecture optimizers. The result of this study is the development of a design representation model that will serve as a common internal representation (DDM) for all system and behavioral synthesis tools. DDM thus builds the foundation for a CAD Framework in which design tools can communicate via operating on this common representation. The design information is composed of three separate graph models: the conceptual model, the behavioral model and the structural model. The conceptual model (represented by a Design Entity Graph) captures the overall organization of the design information, such as, versions and configurations. The behavioral model (represented by an Augmented Control/Data Flow Graph) describes the design behavior. The structural model (represented by an Annotated Component Graph) captures the hierarchical data path structure and its geometric information. In this paper, we define the last two graph models. They both capture the actual design data of the application domain. Since VHDL has gained increasing popularity as hardware description language for synthesis, we give numerous examples throughout this report that show how the proposed design representation model can be used to represent VHDL specifications

Death of mixed methods?: Or the rebirth of research as a craft

The classification by many scholars of numerical research processes as quantitative and other research techniques as qualitative has prompted the construction of a third category, that of ‘mixed methods’, to describe studies that use elements from both processes. Such labels might be helpful in structuring our understanding of phenomena. But they can also inhibit our activities when they serve as inaccurate or limiting descriptors. Based on the observation that mixed methods is fast becoming a common research approach in the social sciences, this paper questions whether the assumptions that are used and perpetuated by mixed methods are valid. The paper calls for a critical change in how we perceive research, in order to better describe actual research processes. A more ethological taxonomy of the mechanisms underlying research structures and processes is posited to encourage creative thinking around alternatives to the three purported paradigms of quantitative, qualitative and mixed methods. This ‘return to basics’ seeks to encourage new and innovative research designs to emerge, and suggests a rebirth of research from the ashes of mixed methods