Miracle-dz/UniFAR-FTUs huggingface dataset:
C‐Terminal Sequence Analysis

Carboxy‐terminal (C‐terminal) sequence analysis is used for direct confirmation of the C‐terminal sequence of native and expressed proteins, for detection and characterization of protein processing at the C‐terminus, for identification of post‐translational proteolytic cleavages, and for obtaining partial sequence information on N‐terminally blocked protein samples in order to facilitate design of oligonucleotide probes for gene cloning. This unit describes an automated chemical method and a manual enzymatic (carboxypeptidase digestion) method for determining C‐terminal sequence information. Carboxypeptidase digestion requires only a standard amino acid analysis method.
Evaluating a new method to estimate the rate of leaf respiration in the light by analysis of combined gas exchange and chlorophyll fluorescence measurements

Day respiration (Rd) is an important parameter in leaf ecophysiology. It is difficult to measure directly and is indirectly estimated from gas exchange (GE) measurements of the net photosynthetic rate (A), commonly using the Laisk method or the Kok method. Recently a new method was proposed to estimate Rd indirectly from combined GE and chlorophyll fluorescence (CF) measurements across a range of low irradiances. Here this method is tested for estimating Rd in five C3 and one C4 crop species. Values estimated by this new method agreed with those by the Laisk method for the C3 species. The Laisk method, however, is only valid for C3 species and requires measurements at very low CO2 levels. In contrast, the new method can be applied to both C3 and C4 plants and at any CO2 level. The Rd estimates by the new method were consistently somewhat higher than those by the Kok method, because using CF data corrects for errors due to any non-linearity between A and irradiance of the used data range. Like the Kok and Laisk methods, the new method is based on the assumption that Rd varies little with light intensity, which is still subject to debate. Theoretically, the new method, like the Kok method, works best for non-photorespiratory conditions. As CF information is required, data for the new method are usually collected using a small leaf chamber, whereas the Kok and Laisk methods use only GE data, allowing the use of a larger chamber to reduce the noise-to-signal ratio of GE measurements.
High-performance on-chip network platform for memory-on-processor architectures

Three Dimensional Integrated Circuits (3D ICs) are emerging to improve existing Two Dimensional (2D) designs by providing smaller chip areas, higher performance and lower power consumption. Stacking memory layers on top of a multiprocessor layer (logic layer) is a potential solution to reduce wire delay and increase the bandwidth. To fully employ this capability, an efficient on-chip communication platform is required to be integrated in the logic layer. In this paper, we present an on-chip network platform for the logic layer utilizing an efficient network interface to exploit the potential bandwidth of stacked memory-on-processor architectures. Experimental results demonstrate that the platform equipped with the presented network interface increases the performance considerably.
Challenging Assumptions for Strategic Information Systems Planning: Theoretical Perspectives

A number of well-documented, fundamental assumptions are associated with strategic information systems planning (SISP). A core activity for this domain is the alignment of an organisations systems and technology strategy with its business objectives. The difficulty is the complex and diverse nature of the strategy process itself that renders such a match increasingly problematic. The evidence within the literature relating to SISP suggests that it does not fully mirror contemporary business strategy and contains some fundamentally incorrect assumptions. This paper identifies eight such assumptions that propose a number of challenges for future research directions. Case examples are also presented which reflect the issues posed for exploiting the value of Information Technology (IT) as a strategic opportunity given the approaches adopted for SISP. Finally, a number of challenges to SISP are noted which relate to identified categories, through an ‘IS complexity framework’, of reviewing benefits, managing business change, and assessing organisational competencies for sustainable competitive advantage.
Rapid prototyping of PDMS microchannels for animal and plant cells using cutting plotter and double casting

The facilitation of access to rapid and low-cost microfabrication methods is essential for improving the development cycles of testing new chip designs and research ideas. A simple fabrication method of biocompatible microchannels with a height of 0.3 mm is significant for biological scientists to study animal and plant cells (∼0.1 mm). Microfabrication using a cutting plotter and a knife blade provides a rapid and low-cost technology. In a previous study, designed cut pieces were used as a channel mold, but they were easy to deform during handling, and therefore the large-scale production of channels was difficult. Moreover, it is required to characterize the cutting process of 0.3-mm-thick sheets with a low-cost plotter. Here, we report the development of an easy fabrication method of 0.3-mm-high polydimethylsiloxane (PDMS) microchannels based on a desktop cutting plotter (300 USD) and an engraved sheet as follows. 1) A 0.3-mm thick sheet of cast-coated paper or silicone rubber was used as a mold material and patterns were created with a cutting plotter. 2) It was pasted to a double-sided tape to make a master mold of a flow channel. 3) The mold was replicated in PDMS to make a negative mold. 4) This PDMS mold was again transferred to a final PDMS chip. 5) It was bonded to a glass substrate to form a PDMS flow channel. We characterized the pattern transition of rectangular shapes from an engraved sheet mold to a final PDMS channel, that is essential for the design of a channel using this method. Iand Y-shaped microchannels (height: 0.3 mm) were fabricated and fluorescent particles and 0.2-mm diameter Volvox were introduced into the channels to show their performances. Keywords
The ecological consequences of unpalatable prey: phytoplankton response to nutrient and predator additions

Recent theoretical and laboratory studies have suggested that unpalatable prey modify the degree to which trophic levels are regulated by bottom-up or top-down forces such that primarily edible communities are regulated by predation and primarily unpalatable communities are regulated by resource supply. Despite the hypothesised importance of prey edibility, experiments have only rarely examined the response of primary producers to nutrient enrichment or the addition of a top trophic level following the reduction or elimination of inedible species. I performed two experiments in aquatic enclosures in which the prey (phytoplankton) had been manipulated to create treatments composed either nearly exclusively of only edible phytoplankton or with both edible and inedible phytoplankton. In the first experiment, the two types of phytoplankton community were subjected to either high or low nutrient concentrations. In the second experiment, the two types of phytoplankton community were present in enclosures with either 2 or 3 trophic levels. I found that the impact of both the nutrients and the number of trophic levels on total phytoplankton biomass was modified by the edibility of the phytoplankton community. Although enclosures with only edible phytoplankton were able to increase with enrichment, there was a greater overall phytoplankton biomass in enclosures with both edible and inedible phytoplankton. The addition of a third trophic level had a positive effect on phytoplankton biomass when only edible phytoplankton were present, but had no effect on phytoplankton biomass when both edible and inedible phytoplankton were present. These results therefore provide support for the hypothesis that the proportion of inedible phytoplankton determines the degree to which communities are regulated by top-down or bottom-up forces.
TNF Stimulates Nuclear Export and Secretion of IL-15 by Acting on CRM1 and ARF6

Interleukin (IL)-15 is a ubiquitously expressed cytokine that in the basal state is mainly localized intracellularly, including the nucleus. Unexpectedly, tumor necrosis factor-α (TNF) time-dependently induced nuclear export of IL-15Rα and IL15. This process was inhibited by leptomycine B (LMB), a specific inhibitor of nuclear export receptor chromosomal region maintenance 1 (CRM1). In the presence of TNF, LMB co-treatment led to accumulation of both IL-15Rα and IL-15 in the nucleus of HeLa cells, suggesting that CRM1 facilitates nuclear export and that TNF enhances CRM1 activity. Once in the cytoplasm, IL-15 showed partial co-localization with late endosomes but very little with other organelles tested 4 h after TNF treatment. IL-15Rα showed co-localization with both early and late endosomes, and to a lesser extent with endoplasmic reticulum and Golgi. This indicates different kinetics and possibly different trafficking routes of IL-15 from its specific receptor. The TNF-induced secretion of IL-15 was attenuated by pretreatment of cells by brefeldin A that inhibits ER-to-Golgi transport, or by use of domain negative ADP-ribosylation factor 6 (ARF6) that interferes with exocytotic sorting. We conclude that TNF abolishes nuclear localization of IL-15 and IL-15Rα by acting on CRM1, and it facilitates exocytosis of IL-15 with the involvement of ARF6.
Capacity of the noisy quantum channel

An upper limit is given to the amount of quantum information that can be transmitted reliably down a noisy, decoherent quantum channel. A class of quantum error-correcting codes is presented that allow the information transmitted to attain this limit. The result is the quantum analog of Shannon's bound and code for the noisy classical channel.
A semi-formal framework for describing interaction design spaces

Interactive system design is typically more successful if it is an iterative process involving collaboration between multi-disciplinary teams with different viewpoints. While some sub-teams may focus on the creative aspects of the user interface design and other sub-groups on the implementation of required functionality, all must ensure that they are working towards the same goal. They must also satisfy the requirements and needs of all stakeholders. Although many suggestions have been made as to how such design might be supported in a more formal way (such as by using a model-driven process), less focus has been given to managing the co-ordination of design sub-teams following a creative process. In this paper we propose a semi-formal framework to describe and to compare design spaces, and the external design representations within those spaces. The framework is based on ideas from interaction design and on formal refinement approaches. It suggests a distinction of design options into alternatives and variants to describe and guide processes of idea generation and convergence within, and between, different design sub-spaces and sub-groups. We provide a small example to illustrate our approach and to show how it can be implemented by using standard formal approaches alongside less formal design notations and human-computer interaction processes.
Blueprint for a High Performance NLP Infrastructure

Natural Language Processing (NLP) system developers face a number of new challenges. Interest is increasing for real-world systems that use NLP tools and techniques. The quantity of text now available for training and processing is increasing dramatically. Also, the range of languages and tasks being researched continues to grow rapidly. Thus it is an ideal time to consider the development of new experimental frameworks. We describe the requirements, initial design and exploratory implementation of a high performance NLP infrastructure.
Post-traumatic Stress Disorder and Cardiovascular Disease

This review provides an up-to-date summary of the evidence from clinical and epidemiologic studies indicating that persons with post-traumatic stress disorder (PTSD) may have an increased risk of coronary heart disease and possibly thromboembolic stroke. Persons with PTSD, a common anxiety disorder in both veteran and nonveteran populations, have been reported to have an increased risk of hypertension, hyperlipidemia, obesity, and cardiovascular disease. Increased activity of the sympathoadrenal axis may contribute to cardiovascular disease through the effects of catecholamines on the heart, vasculature, and platelet function. Reported links between PTSD and hypertension and other cardiovascular risk factors may partly account for reported associations between PTSD and heart disease. The associations observed between PTSD and cardiovascular diseases have implications for cardiology practice and research.
Computational Investigation of the Ionic Conductance through Molybdenum Disulfide (MoS2) Nanopores

Solid-state nanopores have emerged as versatile devices for probing single molecules. Because the channel conductance of the ionic flow through nanopores scales inversely with the membrane thickness, few-atoms thick materials are ideal candidates with an expected high signal-to-noise ratio. On one hand, graphene nanopores have been extensively studied because they exhibit the highest signal. However, they also exhibit high noise. On the other hand, transition metal dichalcogenides such as molybdenum disulfide (MoS2) are potentially advantageous due to their rich optoelectronic and mechanical properties. In this paper, we investigate the dynamics of KCl ions through MoS2 nanopores using non-equilibrium molecular dynamics (MD) simulations. MoS2 nanopores with different diameters, from 1.0 to 3.0 nm and nanoporous membranes with different thicknesses, from single-layer to trilayers MoS2 are studied. The structural properties of ions and water inside MoS2 nanopores are discussed and the performance of MoS2 nanopores to conduct ions at low voltages is quantified by computing I-V curves in order to extract open pore conductance and by comparing MD data to analytical models. This comparison reveals that ionic conductance and effective geometrical parameters for MoS2 nanoporous membranes extracted from models are overestimated. We provide open pore benchmark signals for further translocation simulations/experiments using MoS2 nanopores.
Prosody-enriched lattices for improved syllable recognition

Automatic recognition of syllables is useful for many spoken language applications such as speech recognition and spoken document retrieval. Short-term spectral properties (such as mel-frequency cepstral coefﬁcients, or MFCCs) are usually the features of choice for such systems, which typically ignore supra-segmental (prosodic) cues that manifest themselves at the syllable, word and utterance level. Previous work has shown that categorical representations of prosody correlate well with lexical entities. In this paper, we attempt to exploit this relationship by enriching syllable-level lattices, generated by a standard speech recognizer, with categorical prosodic events for improved syllable recognition performance. With the enriched lattices, we obtain a 2% relative improvement in syllable error rate over the baseline system on a read speech task (the Boston University Radio News Corpus).
Validation of low-accuracy quantization in massive MIMO and constellation EVM analysis

Massive MIMO is a promising approach in order to increase the data rate of cellular systems while reducing their power consumption. While the concept is elegant, many potential show-stoppers have to be investigated, in order to make sure that the idea keeps its promises. On such element is the claim that massive MIMO systems can operate with very low digital signal processing accuracy, and hence reduced implementation complexity and power consumption. In this paper, we investigate the impact of digital quantization of massive MIMO at low resolution. Simulations show that the system can operate correctly with as few as 2 or 3 bits of digital resolution at the end of the digital chain, while limiting the degradation to 1 dB in required signal-to-noise ratio.
Translational Research in Acute Lung Injury and Pulmonary Fibrosis TRIM 72 is required for effective repair of alveolar epithelial cell wounding

Seong Chul Kim,* Thomas Kellett,* Shaohua Wang, Miyuki Nishi, Nagaraja Nagre, Beiyun Zhou, Per Flodby, Konstantin Shilo, Samir N. Ghadiali, Hiroshi Takeshima, Rolf D. Hubmayr, and Xiaoli Zhao Division of Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio; Thoracic Diseases Research Unit, Mayo Clinic, Rochester, Minnesota; Department of Biological Chemistry, Kyoto University Graduate School of Pharmaceutical Sciences, Kyoto, Japan; Will Rogers Institute Pulmonary Research Center, Division of Pulmonary, Critical Care and Sleep Medicine, University of Southern California, Los Angeles, California; Thoracic Pathology Division, Department of Pathology, The Ohio State University, Columbus, Ohio; Biomedical Engineering Department, College of Engineering, The Ohio State University, Columbus, Ohio; and Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, College of Medicine, The Ohio State University, Columbus, Ohio
Symmetric piecewise planar object reconstruction from a single image

Recovering 3D geometry from a single view of an object is an important and challenging problem in computer vision. Previous methods mainly focus on one specific class of objects without large topological changes, such as cars, faces, or human bodies. In this paper, we propose a novel single view reconstruction algorithm for symmetric piece-wise planar objects that are not restricted to some object classes. Symmetry is ubiquitous in manmade and natural objects and provides rich information for 3D reconstruction. Given a single view of a symmetric piecewise planar object, we first find out all the symmetric line pairs. The geometric properties of symmetric objects are used to narrow down the searching space. Then, based on the symmetric lines, a depth map is recovered through a Markov random field. Experimental results show that our algorithm can efficiently recover the 3D shapes of different objects with significant topological variations.
Log Sanitization : Auditing a Database Under Retention Restrictions

Auditing the changes to a database is critical for identifying malicious behavior, maintaining data quality, and improving system performance. But an accurate audit log is a historical record of the past that can also pose a serious threat to privacy. Policies which limit data retention conflict with the goal of accurate auditing, and data owners have to carefully balance the need for policy compliance with the goal of accurate auditing. In this paper, we provide a framework for auditing the changes to a database system while respecting data retention policies. Our framework includes a historical data model that supports flexible audit queries, along with a language for retention policies that hide individual attribute values or remove entire tuples from history. Under retention policies, the audit history is partially incomplete. We formalize the meaning of audit queries on the protected history, which can include imprecise results. We implement policy application and query answering efficiently in a standard relational system, and characterize (both theoretically and experimentally) the cases where accurate auditing can be achieved under retention restrictions.
CART AND BEST-ORTHO-BASIS: A CONNECTION'

We study what we call "dyadic CART"-a method of nonparametric regression which constructs a recursive partition by optimizing a complexity penalized sum of squares, where the optimization is over all recursive partitions arising from midpoint splits. We show that the method is adaptive to unknown degrees of anisotropic smoothness. Specifically, consider the anisotropic smoothness classes of Nikol'skii, consisting of bivariate functions f(xl, x2) whose finite difference of distance h in direction i is bounded in LP norm by Ch8i, i = 1, 2. We show that dyadic CART, with an appropriate complexity penalty parameter A - u2 Const log(n), is within logarithmic terms of minimax over every anisotropic smoothness class 0 < C < x, 0 < 81, 82 < 1. The proof shows that dyadic CART is identical to a certain adaptive best-ortho-basis algorithm based on the library of all anisotropic Haar bases. Then it applies empirical basis selection ideas of Donoho and Johnstone. The basis empirically selected by dyadic CART is shown to be nearly as good as a basis ideally adapted to the underlying f. The risk of estimation in an ideally adapted anisotropic Haar basis is shown to be comparable to the minimax risk over anisotropic smoothness classes. Underlying the success of this argument is harmonic analysis of anisotropic smoothness classes. We show that, for each anisotropic smoothness class, there is an anisotropic Haar basis which is a best orthogonal basis for representing that smoothness class; the basis is optimal not just within the library of anisotropic Haar bases, but among all orthogonal bases of L2[0, 1]2.
A Self-Sealing Suction Technology for Versatile Grasping

Title of dissertation: A SELF-SEALING SUCTION TECHNOLOGY FOR VERSATILE GRASPING Chad C. Kessens, Doctor of Philosophy, 2018 Dissertation directed by: Professor Jaydev P. Desai Department of Mechanical Engineering This thesis describes the design, development, and evaluation of a novel “selfsealing” suction technology for grasping. As humans desire robots capable of handling an increasingly diverse set of tasks, end effectors that are able to grasp the widest possible range of object shapes and sizes will be needed to achieve the desired versatility. Technologies enabling the exertion of local pulling contact forces (e.g. suction) can be extraordinarily useful toward this end by handling objects that do not have features smaller than the grasper, a challenge for traditional grippers. However, simple operation and cost effectiveness are also highly desirable. To achieve these goals, we have developed a self-sealing suction technology for grasping. A small valve inside each suction cup nominally seals the suction port to maintain a vacuum within the system. Through the reaction forces of object contact, a lever action passively lifts the valve to engage suction on the object. Any cups not contacting the object remain sealed. In this way, a system with a large number of cups may effectively operate using any subset of its cups, even just one, to grasp an object. All cups may be connected to a central vacuum source without the need for local sensors or powered actuators for operation, forming a simple, compact, cost effective system. This thesis begins with the detailed design and analysis of the self-sealing suction technology. An extensive evaluation of the technology’s robustness and performance demonstrates its features and limits. This includes self-seal quality and leakage, object seal and reseal, cycle performance, and normal and shear forcedisplacement, among other characterizations. It then describes the development of several devices utilizing the technology. The potential impact of the technology is highlighted through applications of human-controlled, robotic, and aerial grasping and perching. Finally, mathematical tools are developed to analyze potential grasps developed using the technology. A SELF-SEALING SUCTION TECHNOLOGY FOR VERSATILE GRASPING