Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional Analysis of the Terminase Large Subunit, G2P, of Bacillus subtilis Bacteriophage SPP1*

The terminase of bacteriophage SPP1, constituted by a large (G2P) and a small (G1P) subunit, is essential for the initiation of DNA packaging. A hexa-histidine G2P (H6-G2P), which is functional in vivo, possesses endonuclease, ATPase, and double-stranded DNA binding activities. H6-G2P introduces a cut with preference at the 5′-RCGG↓CW-3′ sequence. Distamycin A, which is a minor groove binder that mimics the architectural structure generated by G1P at pac, enhances the specific cut at bothbona fide 5′-CTATTGCGG↓C-3′ sequences withinpacC of SPP1 and SF6 phages. H6-G2P hydrolyzes rATP or dATP to the corresponding rADP or dADP and Pi. H6-G2P interacts with two discrete G1P domains (I and II). Full-length G1P and G1PΔN62 (lacking domain I) stimulate 3.5- and 1.9-fold, respectively, the ATPase activity of H6-G2P. The results presented suggest that a DNA structure, artificially promoted by distamycin A or facilitated by the assembly of G1P at pacL and/or pacR, stimulates H6-G2P cleavage at both target sites within pacC. In the presence of two G1P decamers per H6-G2P monomer, the H6-G2P endonuclease is repressed, and the ATPase activity stimulated. Based on these results, we propose a model that can account for the role of terminase in headful packaging.
Reducing Waste in Administrative Services with Lean Principles

Lean techniques have been applied for improving production systems in manufacturing processes over the last two decades and have had a profound impact on productivity. More recently, lean is used outside manufacturing; for example in hospitals, government agencies, and service organizations. This paper focuses on reducing waste in administrative processes in organizations. A lean approach for optimizing administrative processes is developed by adapting the conceptualization of waste and developing a set of lean principles for administrative processes. The method was field tested at a university. Waste in the current processes was identified and classified. Recommendations for reducing waste were then made according to lean principles. The study shows that the adapted conceptualizations of waste are applicable to administrative processes. Principles and techniques could also be transferred from manufacturing to administrative processes. Two additional principles were added to address recurrent problems found in administration: improving communication and designing information systems to support users in an optimal way.
An Intelligent Interface for Keyboard and Mouse Control -- Providing Full Access to PC Functionality via Speech

SUITEKeys is a speech user interface for motor-disabled computer users. This interface provides access to all available functionality of a computer by modeling interaction at the physical keyboard and mouse level. SUITEKeys is currently implemented for MS Windows platforms. Its architecture integrates a continuous, speakerindependent recognition engine with natural language processing components. It makes extensive use of dialog management to improve recognition accuracy. SUITEKeys extends the speech-keyboard metaphor through functionality visible on its graphical user interface, and accessible through speech. Experimental results indicate that speech input for alphanumeric data entry is a much more effective modality than existing alternatives for the target user group. Such alternatives include miniaturized keyboards, stylus "soft" keyboards, and handwriting recognition software.
Global Gene Expression Analysis of the Interaction between Cancer Cells and Osteoblasts to Predict Bone Metastasis in Breast Cancer

Background Bone metastasis is a main cause of morbidity in breast cancer. Since breast cancer is a heterogeneous disease, the interactions of cancer cells with the skeletal host cells might also be diverse. We hypothesized that gene expression signatures induced by heterotypic interaction of breast cancer cells and osteoblasts might be of clinical relevance. Methodology/Principal Findings We established an ex vivo co-culture model using benign breast epithelial cells or a panel of 5 malignant breast epithelial cells in combination with primary human osteoblasts and determined associated gene expression changes with HEEBO microarrays. Pretreatment gene expression profiles of 295 early stage breast cancers published from the Netherlands Cancer Institute with a median follow up of 12.6 years allowed evaluating in vitro effects in the in vivo situation.The effects of the interaction between osteoblasts and breast cancer cell lines of different origin were very heterogeneous. Hs578T cells started to proliferate in co-culture with osteoblasts, SKBR-3 induced a TGF-β response and MDA-MB231 cells showed two distinct sets of up-regulated genes: A set of interferon response genes associated with an up-regulation of STAT1 was in vivo remarkably coherent providing a basis for segregation of tumors into two groups. In a uni-variate analysis, early stage tumors with high expression levels (n = 136) of this gene set had a significantly lower overall survival rate (p = 0.005) (63% at 10 years) than tumors with low expression levels (n = 159) (overall survival: 77% at 10 years). The second gene set was associated with IL-6 and did not significantly change the overall survival rate (p = 0.165), but was significantly associated with a shorter time to bone metastasis (p = 0.049; 74% vs. 83% at 10 years). Conclusion/Significance An IL-6 gene expression pattern induced by heterotypic interaction of breast cancer cells with osteoblasts in vitro is associated with a higher rate of bone metastasis in vivo.
Arm Structure in Anemic Spiral Galaxies

Anemic galaxies have less prominent star formation than normal galaxies of the same Hubble type. Previous studies showed they are deficient in total atomic hydrogen but not in molecular hydrogen. Here we compare the combined surface densities of H I and H2 at mid-disk radii with the Kennicutt threshold for star formation. The anemic galaxies are below the threshold, which explains their lack of prominent star formation, but they are not much different than other early-type galaxies, which also tend to be below threshold. The spiral wave amplitudes of anemic and normal galaxies were also compared, using images in B and J passbands from the OSU Bright Spiral Galaxy Survey. Anemic galaxies have normal spiral wave properties too, with the same amplitudes and radial dependencies as other galaxies of the same arm class. Because of the lack of gas, spiral waves in early-type galaxies and anemics do not have a continuous supply of stars with low velocity dispersions to maintain a marginally stable disk. As a result, they are either short lived, evolving toward lenticulars and S0 types in only a few rotations at mid-disk, or they are driven by the asymmetries associated with gas removal in the cluster environment.
Autoreactive T cell clones specific for class I and class II HLA antigens isolated from a human chimera

T cell clones of donor origin that specifically react with recipient cells were obtained from a SCID patient successfully reconstituted by allogeneic fetal liver and thymus transplantation performed 10 yr ago. The majority of these clones displayed both cytotoxic and proliferative responses towards PBL and an EBV-transformed B cell line derived from the patient. In addition, these T cell clones had proliferative and cytotoxic responses towards the parental PBL, EBV cell lines, and PHA blasts. Blocking studies with anti-class I and anti-class II HLA mAbs indicated that the activity of the CD4+ T cell clones was specifically directed against class II HLA antigens of the recipient. On the other hand, the cytotoxic and proliferative responses of the CD8+ T cell clones were specific for class I HLA antigens which are ubiquitously expressed on the recipient cells. Thus, the establishment of transplantation tolerance observed in this stable human chimera is not due to the elimination of host-reactive T cells from the repertoire and suggests the presence of a peripheral autoregulatory suppressor mechanism.
Serious games for learning programming languages

In recent years, so-called serious games, where some kind of knowledge is gained through digital game play, have received significant attention and there has been an active movement toward games that effectively enrich the learning environment. Serious games are games that are developed according to the concept, “It is possible through game play to obtain some kind of knowledge while having fun. Through these serious games, there has been an active movement toward fun learning using games in education at school and internal training at organizations. In contrast, at universities the level of learning programming differs significantly depending on the academic background of the student and there are issues with traditional programming education learning because the student does not feel enjoyment and is not interested in information engineering. As a countermeasure, teaching methods and teaching aids etc. have been cited as themes and learning through the utilization of serious games and game development has been proposed to tackle these themes. In this paper we propose and evaluate serious games for programming learning based on the concept “Learning programming through gaming”.
Student Perceptions and Acceptance of Mobile Technology in an Undergraduate Nursing Program

Mobile technology allows healthcare students to access current evidence-based resources. The purpose of this study was to evaluate the student experience of implementing point-of-care (POC) smartphone applications in a first-semester undergraduate nursing program. Teaching methods included using case studies in the laboratory to familiarize students with the apps. At community screening sites, evidence-based guidelines were referenced when students discussed screening results with patients. Surveys were administered prior to implementing this innovation and after the students utilized the apps in direct patient interactions. Survey results were analyzed to evaluate student perceptions and acceptance of mobile technology. Students felt that healthcare smartphone apps were a helpful and convenient way to obtain evidence-based clinical information pertinent to direct care settings. Over 90% of students planned to continue using healthcare smartphone apps. In conclusion, healthcare smartphone apps are a way for students to become comfortable accessing evidence-based clinical resources. It is important to encourage students to use these resources early in the curriculum. Community screenings are an independent health promotion activity which assists in the attainment of health equity and fosters nursing leadership.
Interactive simulation of surgical needle insertion and steering

We present algorithms for simulating and visualizing the insertion and steering of needles through deformable tissues for surgical training and planning. Needle insertion is an essential component of many clinical procedures such as biopsies, injections, neurosurgery, and brachytherapy cancer treatment. The success of these procedures depends on accurate guidance of the needle tip to a clinical target while avoiding vital tissues. Needle insertion deforms body tissues, making accurate placement difficult. Our interactive needle insertion simulator models the coupling between a steerable needle and deformable tissue. We introduce (1) a novel algorithm for local remeshing that quickly enforces the conformity of a tetrahedral mesh to a curvilinear needle path, enabling accurate computation of contact forces, (2) an efficient method for coupling a 3D finite element simulation with a 1D inextensible rod with stick-slip friction, and (3) optimizations that reduce the computation time for physically based simulations. We can realistically and interactively simulate needle insertion into a prostate mesh of 13,375 tetrahedra and 2,763 vertices at a 25 Hz frame rate on an 8-core 3.0 GHz Intel Xeon PC. The simulation models prostate brachytherapy with needles of varying stiffness, steering needles around obstacles, and supports motion planning for robotic needle insertion. We evaluate the accuracy of the simulation by comparing against real-world experiments in which flexible, steerable needles were inserted into gel tissue phantoms.
Evaluating Mentoring Programs

Programs that promote mentoring should be regularly evaluated to determine whether they are proceeding as planned and achieving their intended objectives. The evaluation process begins by looking at the program's intended outcomes and targeted goals. It then measures progress, achievements, and effectiveness against those outcomes and goals. That is why it is essential to state mentoring program objectives when the program begins in a way that allows you to measure progress and results once it is under way.
Getting action from organizational surveys : new concepts, technologies, and applications

Foreword (Allan H. Church, Janine Waclawski). Preface (Allen I. Kraut). Acknowledgments. The Authors. 1 Moving the Needle: Getting Action After a Survey (Allen I. Kraut). Part One: New Concepts. 2 Connecting Employee Satisfaction to Business Unit Performance (James K. Harter, Frank L. Schmidt) 3 Employee Experiences and Customer Satisfaction: Toward a Framework for Survey Design with a Focus on Service Climate (William H. Macey, Benjamin Schneider). 4 Strategic Surveys: Linking People to Business Strategy (William A. Schiemann, Brian S. Morgan). 5 The Importance of Taking Action, Not Just Sharing Survey Feedback (Allan H. Church, David H. Oliver). 6 Organizational Surveys as Leverage for Organization Development and Change (W. Warner Burke). 7 Using Linkage Rsearch to Drive High Performance: A Case Study in Organization Development (Jack W. Wiley, Bruce H. Campbell). Part Two: New Technologies. 8 Online Surveys: Critical Issues in Using the Web to Conduct Surveys (Kristofer J. Fenlason, Kathleen Suckow-Zimberg). 9 Online Reporting: Real Time, Real Impact, Real Opportunities (Karen M. Barbera, Scott A. Young). 10 What Did They Really Mean? : New and Emerging Methods for Analyzing Themes in Open-Ended Comments (Patrick Kulesa, Ralph J. Bishop). 11 Pulse Surveys: A Limited Approach with Some Unique Advantages (Joe Colihan, Janine Waclawski). 12 Oversurveying: Causes, Consequences, and Cures (Sara P. Weiner, Anthony T. Dalessio). 13 Understanding Nonresponse and Facilitating Response to Organizational Surveys (Steven G. Rogelberg). 14 Relative Weights of Predictors: What is Important When Many Forces are Operating (Kyle M. Lundby, Jeff W. Johnson). 15 National Norms Versus Consortium Data: What Do They Tell Us? (William H. Macey, Larry D. Eldridge). 16 Preparing and Presenting Survey Results to Influence Audiences (Sarah Rassenfoss Johnson). 17 How to Create Presentations That Spark Action (Ingwer Borg, Matthias Zimmermann). Part Three: New Applications. 18 Measuring Employee Opinions During Mergers and Acquisitions (Mitchell Lee Marks, Daniel Baitch). 19 Leveraging Employee Surveys to Retain Key Employees: A Means to an End (Mitchelle A. Donovan, Scott M. Brooks). 20 Driving Change Around the World: Employee Surveys in Global Organizations (John C. Scott, Paul M. Mastrangelo). 21 Building an Inclusive Culture: The Communicating Managers Program (Robert J. Quinn). 22 Reengaging Employees During Turbulent Times (Sharon E. Parker, Michael J. Schroeder, J. Thomas Bowler, Jr., Patricia L. Muldoon). 23 Best Company Lists: Using Survey Data to Assess, Recognize, and Reward Organizations (Norman D. Costa, Peter Bachiochi). 24 An Executive and a Survey Model: A Follow-Up Action Success Story (Tracey Carsten Roll). Name Index. Subject Index.
Directing Differentiation of Pluripotent Stem Cells Toward Retinal Pigment Epithelium Lineage.

: Development of efficient and reproducible conditions for directed differentiation of pluripotent stem cells into specific cell types is important not only to understand early human development but also to enable more practical applications, such as in vitro disease modeling, drug discovery, and cell therapies. The differentiation of stem cells to retinal pigment epithelium (RPE) in particular holds promise as a source of cells for therapeutic replacement in age-related macular degeneration. Here we show development of an efficient method for deriving homogeneous RPE populations in a period of 45 days using an adherent, monolayer system and defined xeno-free media and matrices. The method utilizes sequential inhibition and activation of the Activin and bone morphogenetic protein signaling pathways and can be applied to both human embryonic stem cells and induced pluripotent stem cells as the starting population. In addition, we use whole genome transcript analysis to characterize cells at different stages of differentiation that provides further understanding of the developmental dynamics and fate specification of RPE. We show that with the described method, RPE develop through stages consistent with their formation during embryonic development. This characterization- together with the absence of steps involving embryoid bodies, three-dimensional culture, or manual dissections, which are common features of other protocols-makes this process very attractive for use in research as well as for clinical applications. SIGNIFICANCE This report describes a novel method of directed differentiation to generate retinal pigment epithelium (RPE) cells from pluripotent stem cells. The employed method is based on adherent monolayer culture using xeno-free conditions and manipulation of the Activin and bone morphogenetic protein signaling pathway using small molecules and recombinant proteins. Whole genome microarray analysis was performed to characterize the differentiation process and understand the developmental path of RPE generation in vitro. This method can be applied for generation of RPE for research as well as for clinical applications.
Supervised Composite Kernel Locality Preserving Projection Feature Extraction for Hyperspectral Image Classification

Locally preserving projection (LPP) does not take advantage of the spatial correlation of pixels in the image, and the pixels are considered as independent pieces of information. In this paper, a kernel based manifold learning feature extraction method which considers spatial relationship of neighboring pixels, called supervised composite kernel locality preserving projection (SCKLPP), is proposed for hyperspectral image feature extraction. The spatial information and spectral information from original hyperspectral image are combined using composite kernels weight matrix. The nearest neighbor graph is created with the prior class-label information of samples. Experimental results on AVIRIS data set show that the SCKLPP can not only efficiently reduce the dimensionality but also achieve higher accuracies. In addition, the proposed method opens a new field for future developments in which spatial information can be easily integrated into the feature extraction stage. Keywords-feature extraction; dimensionality reduction; locally preserving projection; composite kernel; hyperspectral image classification
Neither intact nor hydrolyzed soy proteins elicit intestinal inflammation in neonatal piglets.

BACKGROUND Efficacy of feeding hydrolyzed soy proteins to infants intolerant to cow milk proteins has not been determined fully. This study compared growth and intestinal responses of neonatal piglets fed formulas with hydrolyzed soy protein to piglets fed formulas with intact soy or cow milk (casein-whey) proteins. METHODS Piglets (n = 40, day 2 postpartum) were fed commercial milk replacer until day 7 postpartum (designated day 0) and then were assigned randomly to casein-whey (CW) or soy (intact, SI; hydrolyzed SH) formulas to evaluate intestinal responses on days 0, 2, 5, and 10. RESULTS Average daily gain was higher for CW (121 g/d; p < .05) compared with SI piglets 85 g/d); SH pig weight gain was intermediate (109 g/d). Villus height-to-crypt depth ratio in proximal jejunum was lower (p < .05) on day 2 than day 0 in soy-fed pigs and lower (p < .05) on day 5 than day 0 in CW pigs. Mucosal mast cells were generally higher in CW pigs compared with soy-fed pigs. Villus goblet cell numbers in the midjejunum of SH-fed piglets were lower (p < .05) on day 5 compared with day 0. On day 5, crypt goblet cell numbers were higher (p < .05) in the midjejunum of CW-fed piglets compared with SH-fed piglets with numbers intermediate for SI-fed piglets. Intestinal differences were not detected among dietary treatments for major histocompatibility complex class I and II gene expression, tissue concentrations of prostaglandin E2, or CD8+ T-cell numbers. CONCLUSIONS Hydrolyzed soy proteins do not elicit intestinal inflammatory responses in piglets and may be viable alternatives to milk and intact soy proteins for feeding infants.
Protein Friction Limits Diffusive and Directed Movements of Kinesin Motors on Microtubules

Friction in Microscopic Motor Friction arises because adhesive bonds between two bodies must be broken in order for them to move relative to each other. Now Bormuth et al. (p. 870; see the Perspective by Veigel and Schmidt) have used single molecule measurements to characterize the frictional drag force of kinesin-8 motor proteins interacting with their microtubule track. Friction, arising from rupture of bonds with the track, constrains the speed and efficiency of the motor protein. Rupture of bonds between a molecular machine and its track creates friction, which constrains speed and efficiency. Friction limits the operation of macroscopic engines and is critical to the performance of micromechanical devices. We report measurements of friction in a biological nanomachine. Using optical tweezers, we characterized the frictional drag force of individual kinesin-8 motor proteins interacting with their microtubule tracks. At low speeds and with no energy source, the frictional drag was related to the diffusion coefficient by the Einstein relation. At higher speeds, the frictional drag force increased nonlinearly, consistent with the motor jumping 8 nanometers between adjacent tubulin dimers along the microtubule, and was asymmetric, reflecting the structural polarity of the microtubule. We argue that these frictional forces arise from breaking bonds between the motor domains and the microtubule, and they limit the speed and efficiency of kinesin.
Making System User Interactive Tests Repeatable: When and What Should we Control?

System user interactive tests are widely used to evaluate the behavior of an application as a whole. To automate this process, many techniques are proposed whose effectiveness are evaluated by metrics such as code coverage and fault detection. However, most of previous work assumes determinism in the outputs of interactive tests. In this paper, we propose three layers of testing outputs to examine: the code layer (codecoverage), the behavioral layer (invariant detection) and the user interaction layer (fault detection with GUI oracle). We further study the impact of common set of factors such as operating system, Java version, initial starting state and time delay on these metrics. A comprehensive experiment has been conducted on Java Swing applications, and the results show that as many as184 lines can be covered differently and up to 96% false positives with respect to fault detection. We plan to study the repeatability of interactive tests on the Android platform.