Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid Fine Conformational Epitope Mapping Using Comprehensive Mutagenesis and Deep Sequencing*

Background: A new method using comprehensive mutagenesis libraries, yeast display, and deep sequencing is proposed to determine fine conformational epitopes for three antibody-antigen interactions. Results: For three separate antigens, the experimentally determined conformational epitope is consistent with orthogonal experimental datasets. Conclusion: We conclude that this new methodology is reliable and sound. Significance: With this new method, four antibody-antigen interactions can be mapped per day. Knowledge of the fine location of neutralizing and non-neutralizing epitopes on human pathogens affords a better understanding of the structural basis of antibody efficacy, which will expedite rational design of vaccines, prophylactics, and therapeutics. However, full utilization of the wealth of information from single cell techniques and antibody repertoire sequencing awaits the development of a high throughput, inexpensive method to map the conformational epitopes for antibody-antigen interactions. Here we show such an approach that combines comprehensive mutagenesis, cell surface display, and DNA deep sequencing. We develop analytical equations to identify epitope positions and show the method effectiveness by mapping the fine epitope for different antibodies targeting TNF, pertussis toxin, and the cancer target TROP2. In all three cases, the experimentally determined conformational epitope was consistent with previous experimental datasets, confirming the reliability of the experimental pipeline. Once the comprehensive library is generated, fine conformational epitope maps can be prepared at a rate of four per day.
Use of contraception in the United States: 1982-2008.

OBJECTIVE This report presents national estimates of contraceptive use and method choice based on the 1982, 1995, 2002, and 2006-2008 National Surveys of Family Growth (NSFG). METHODS Data for 2006-2008 were collected through in-person interviews with 13,495 men and women 15-44 years of age in the household population of the United States. This report is based on the sample of 7,356 women interviewed in 2006-2008. The response rate for women in the 2006-2008 survey was about 76%. RESULTS More than 99% of women 15-44 years of age who have ever had sexual intercourse with a male (referred to as "sexually experienced women") have used at least one contraceptive method. The percentage of women who have ever used emergency contraception, the contraceptive patch, and the contraceptive ring increased between 2002 and 2006-2008. Looking at contraceptive use in the month of interview, or current use, the leading method of contraception in the United States during 2006-2008 was the oral contraceptive pill, used by 10.7 million women; the second leading method was female sterilization, used by 10.3 million women. While contraceptive use is virtually universal in the United States, women with different characteristics make different choices of methods--for example, college educated women are much more likely to use the pill and less likely to use female sterilization than less educated women. Age, parity, marital status, and income are also closely related to the choice of method. These method choices are related to the risk of unintended pregnancy in these groups.
Structural and functional properties of the p60 proteins from different Listeria species

The major extracellular protein p60 of Listeria monocytogenes seems to be required for this microorganism's adherence to and invasion of 3T6 mouse fibroblasts but not for adherence to human epithelial Caco-2 cells. Western blot analysis with polyclonal antibodies against p60 of L. monocytogenes indicated the presence of cross-reacting proteins in the culture supernatants of all Listeria species. Protein p60 of L. monocytogenes could restore adhesion of the L. monocytogenes mutant RIII (impaired in the synthesis of p60) to mouse fibroblasts more efficiently than that of Listeria grayi. The amino acid sequences of the p60-related proteins of L. innocua, L. ivanovii, L. seeligeri, L. welshimeri, and L. grayi indicated highly conserved regions of about 120 amino acids at both the N-terminal and the C-terminal ends. The middle portions of these proteins, consisting of about 240 amino acids, varied considerably. These parts include the repeat domain consisting of repetitions of Thr (T) and Asn (N) which was present only, albeit in different arrangements, in the p60 proteins of L. monocytogenes and L. innocua. The p60-related proteins of L. grayi, L. ivanovii, L. seeligeri, and L. welshimeri each contained an insertion of 54 amino acids which was absent in the p60 proteins of L. monocytogenes and L. innocua.
The Unexplored Relationship Between Diet & Mental Health: A Review

Background: In order to understand eating behaviour of adolescents, insight into determinants of intake is necessary. Research has shown that anxiety and depression are associated with an increased risk for diabetes type 2, partly through their association with obesity and the metabolic syndrome, whereas both behavioral and biological mechanisms mediate such relations. Findings from existing research suggest that a more comprehensive approach to children & adolescents with obesity may provide novel methods of obesity management. Methods: Relevant Papers were identified from PubMed, Science Direct, Google Scholar, NCBI & Medline by using all combinations of the search terms: "mental health, dietary intake, eating disorders, obesity, underweight or adolescents & children". Research studies examining the relationship between mental health & food intake among children & adolescents were included in the review process. Based on inclusion - exclusion criteria full text papers were reviewed. Results: A number of behavioral and emotional parameters connect obesity to anxiety and depression in children. Similarly to adults, children suffering from anxiety and/or depression are typically characterized by poor adherence to self-care activities, by sedentary habits and lack of physical exercise, excessive television and internet viewing and disturbed eating behaviors, such as emotional eating and consumption of comfort foods. The association between diet and depression has previously mainly been studied in cross sectional studies, and only few prospective studies have been published. The evidence suggests that folate and long-chain n-3 polyunsaturated fatty acids (PUFAs) may be connected to the decreased risk of depression. Furthermore, only few studies have concentrated on the association between general dietary patterns and depression. Conclusion: Dietary intake may also have a direct impact on various biological systems and mechanisms that underpin depression, including oxidative processes, the functioning of the immune system, and levels of salient brain proteins. While considering the role of diet & depression, several points need to be considered. First, in general, evidence has been found for the effects of isolated nutrients or foods, and not for dietary patterns. Second, most previous studies have a cross-sectional design. Third, information is generally collected though questionnaires, increasing the risk of misclassification bias. Fourth, adequate control of confounding factors in observational studies is mandatory.
Kozai Migration Naturally Explains the White Dwarf Planet WD1856 b

The Jovian-sized object WD 1856 b transits a white dwarf (WD) in a compact 1.4 day orbit. Unlikely to have endured stellar evolution in its current orbit, WD 1856 b is thought to have migrated from much wider separations. Because the WD is old, and a member of a well-characterized hierarchical multiple, the well-known Kozai mechanism provides an effective migration channel for WD 1856 b. The tidal dissipation that makes this mechanism possible is sensitive to the mass of WD 1856 b, which remains unconstrained by observations. Moreover, the lack of tides in the star allows us to directly connect the current semimajor axis to the pre-migration one, from which we can infer the initial conditions of the system. By further requiring that planets must survive all previous phases of stellar evolution before migrating, we are able to constrain the main-sequence semimajor axis of WD 1856 b to have been ∼2.5 au, and its mass to be ≃0.7–3M J. These mass limits put WD 1856 b firmly within the planet category. Furthermore, our inferred values imply that WD 1856 b was born a typical gas giant. We further estimate the occurrence rate of Kozai-migrated planets around WDs to be (10−3−10−4) , suggesting that WD 1856 b is the only one in the TESS sample, but implying (102) future detections by the LSST survey. In a sense, WD 1856 b was an ordinary Jovian planet that underwent an extraordinary dynamical history.
Field-scale CH4 emission at a sub-arctic mire with heterogeneous permafrost thaw status

Abstract. The Artic is exposed to faster temperature changes than most other areas on Earth. Constantly increasing temperature will lead to thawing permafrost and changes in the CH4 emissions from wetlands. One of the places exposed to those changes is the Abisko-Stordalen Mire in northern Sweden, where climate and vegetation studies have been conducted from the 1970s. In our study, we analyzed field-scale methane emissions measured by the eddy covariance method at Abisko-Stordalen Mire for three years (2014–2016). The site is a subarctic mire mosaic of palsas, thawing palsas, fully thawed fens, and open water bodies. A bimodal wind pattern prevalent at the site provides an ideal opportunity to measure mire patches with different permafrost statuses with one flux measurement system. The flux footprint for westerly winds is dominated by elevated palsa plateaus, while the footprint is almost equally distributed between palsas and thawing bog-like areas for easterly winds. As these patches are exposed to the same climatic conditions, we analyzed the differences in the responses of their methane emission for environmental parameters. The methane fluxes followed a similar annual cycle over the three study years, with a gentle rise during spring and a decrease during autumn and with no emission burst at either end of the ice-free season. The peak emission during the ice-free season differed significantly for the mire with two permafrost statuses: the palsa mire emitted 24 mg-CH4 m−2 d−1 and the thawing wet sector 56 mg-CH4 m−2 d−1. Factors controlling the methane emission were analyzed using generalized linear models. The main driver for methane fluxes was peat temperature for both wind sectors. Soil water content above the water table emerged as an explanatory variable for the three years for western sectors and the year 2016 in the eastern sector. Water table level showed a significant correlation with methane emission for the year 2016 as well. Gross primary production, however, did not show a significant correlation with methane emissions. Annual methane emissions were estimated based on four different gap-filing methods. The different methods generally resulted in very similar annual emissions. The mean annual emission based on all models was 4.2 ± 0.4 g-CH4 m−2 a−1 for western sector and 7.3 ± 0.7 g-CH4 m−2 a−1 for the eastern sector. The average annual emissions, derived from this data and a footprint climatology, were 3.6 ± 0.7 g-CH4 m−2 a−1 and 11 ± 2 g-CH4 m−2 a−1 for the palsa and thawing surfaces, respectively. Winter fluxes were relatively high, contributing 27–45 % to the annual emissions.
Bayesian data assimilation for improved modeling of road traffic

This thesis deals with the optimal use of existing models that predict certain phenomena of the road traffic system. Such models are extensively used in advanced traffic information systems (ATIS), dynamic traffic management (DTM) or model predictive control (MPC) approaches in order to improve the traffic system. As road traffic is the result of human behavior which is ever changing and which varies internationally, for each of these phenomena a multitude of models exist. The scientific literature generally is not conclusive about which of these models should be preferred. One common problem in road traffic science is therefore that for each application a choice has to be made from a set of available models. A second task that always needs to be performed is the calibration of the parameters of the models. A third and last task is the application of the chosen and calibrated model(s) to predict a part of the traffic system. The Bayesian framework for data assimilation is applied to three different phenomena: 1. car-following modeling; 2. travel time prediction and 3. traffic state estimation using a first order traffic flow model (the LWR model) and an extended Kalman filter (EKF). Finally, a part of the research is devoted to speeding up the EKF such that it can be applied together with the LWR model in real time to large networks.
Hydrodynamic Modeling, Optimization and Performance Assessment for Ducted and Non-ducted Tidal Turbines

This thesis examines methods for designing and analyzing kinetic turbines based on blade element momentum (BEM) theory and computational fluid dynamics (CFD). The underlying goal of the work was to assess the potential augmentation of power production associated with enclosing the turbine in an expanding duct. Thus, a comparison of the potential performance of ducted and non-ducted turbines was carried out. This required defining optimal turbine performance for both concepts. BEM is the typical tool used for turbine optimization and is very well established in the context of wind turbine design. BEM was suitable for conventional turbines, but could not account for the influence of ducts, and no established methodology for designing ducted turbines could be found in the literature. Thus, methods were established to design and analyze ducted turbines based on an extended version of BEM (with CFD-derived coefficients), and based on CFD simulation. Additional complications arise in designing tidal turbines because traditional techniques for kinetic turbine design have been established for wind turbines, which are similar in their principle of operation but are driven by flows with inherently different boundary conditions than tidal currents. The major difference is that tidal flows are bounded by the ocean floor, the water surface and channel walls. Thus, analytical and CFD-based methods were established to account for the effects of these boundaries (called blockage effects) on the optimal design and performance of turbines. Additionally, tidal flows are driven by changes in the water surface height in the ocean and their velocity is limited by viscous effects. Turbines introduced into a tidal flow increase the total drag in the system and reduce the total flow in a region (e.g. a tidal channel). An analytical method to account for this was taken from the field of tidal resource assessment, and along with the methods to account for ducts and blockage effects, was incorporated into a rotor optimization framework. It was found that the non-ducted turbine can produce more power per installed device frontal area and can be operated to induce a lesser reduction to the flow through a given tidal channel for a given level of power production. It was also found that by optimizing turbines for array configurations that occupy a large portion of the cross sectional area of a given tidal channel (i.e. tidal fences), the per-device power can be improved significantly compared to a sparse-array scenario. For turbines occupying 50% of a channel cross section, the predicted power improves is by a factor of three. Thus, it has been recommended that future work focus on analyzing such a strategy in more detail.
Effects of Dietary Coated Lysozyme on the Growth Performance, Antioxidant Activity, Immunity and Gut Health of Weaned Piglets

The purpose of this study was to evaluate the effects of dietary coated lysozyme on growth performance, serum biochemical indexes, antioxidant activity, digestive enzyme activity, intestinal permeability, and the cecal microbiota in weaned piglets. In total, 144 weaned Large White × Landrace piglets were divided into six treatment groups, with 3 replicates and 8 piglets per replicate: CN, a basal diet; CL-L, CL-M, and CL-H, basal diet supplemented with 100, 150, 500 mg/kg coated lysozyme; UL, basal diet supplemented with 150 mg/kg lysozyme; and Abs, basal diet supplemented with 150 mg/kg guitaromycin for 6 weeks. Compared with the CN and UL diets, dietary CL-H inclusion increased the average daily gain (ADG) and decreased the feed/gain (F/G) ratio of piglets (p < 0.05). The addition of 500 mg/kg coated lysozyme to the diet significantly increased the total protein (TP) and globulin (Glob) plasma levels of weaned piglets (p < 0.05). Supplementation with 500 mg/kg coated lysozyme significantly increased the serum IgM concentration and increased lipase activity in the duodenum (p < 0.05). The addition of coated lysozyme and lysozyme significantly decreased the malondialdehyde (MDA) content, while the superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and total antioxidant capacity (T-AOC) levels all increased (p < 0.05). High-throughput sequencing results showed that CL-H treatment effectively improved the intestinal microbiome. The relative abundance of Terrisporobacter in the CL-H and CL-M groups was significantly lower than that in the other groups (p < 0.05). LEfSe analysis results showed that the relative abundance of Coprococcus_3 was higher in the CL-M treatment group. The marker species added to the CL-H treatment group was Anaerofilum. In summary, as a potential substitute for feed antibiotics, lysozyme is directly used as a dietary additive, which is inefficient. Therefore, we used palm oil as the main coating material to coat lysozyme. Lysozyme after coating can more effectively improve the growth performance of piglets by improving the intestinal flora, improving the activity of digestive enzymes, reducing the damage to intestinal permeability and oxidative stress in piglets caused by weaning stress, and improving the immunity of piglets.
The circa Model of Planning and Execution

Providence, Rhode Island, July 28, 1997 The CIRCA Model of Planning and Execution Robert P. Goldman and David J. Musliner and Mark S. Boddy and Kurt D. Krebsbach Automated Reasoning Group Honeywell Technology Center 3660 Technology Drive Minneapolis, MN 55418 fgoldman,musliner,boddy,krebsbacg@htc.honeywell. com Introduction We are working to develop intelligent agents, using the CIRCA architecture (Musliner, Durfee, & Shin 1993; 1995), that construct and execute plans for controlling embedded real-time systems. By \embedded," we mean that these systems are interacting with a dynamic environment including uncontrolled, exogenous events. By \real-time," we mean that catastrophic failure is possible if a timely control action is not taken in certain situations. For these systems, control plans must provide guarantees that failures will not occur. In this position paper we discuss our revised version of the CIRCA planning model. We start by reviewing the CIRCA architecture, which couples a deliberative planning component with a scheduler and a real-time executive. A distinctive feature of CIRCA is that it is based on a memoryless and unclocked reactive execution engine, but nevertheless manages to meet hard real-time constraints. A deliberative component of the architecture reasons about control actions, sensing actions, exogenous events and timing in order to achieve real-time behavior. After reviewing the key features of CIRCA, we discuss a new planning technique, Dynamic Abstraction Planning (Goldman et al. 1997), that provides us with more e cient planning. We review the planning model that allows us to generate reactive controllers that provably meet real-time execution constraints. Finally, we discuss some ongoing extensions to the model. These extensions will allow CIRCA agents to take advantage of reliable processes in their environment, making them more capable controllers and allowing them to interact with other agents. CIRCA CIRCA is designed to support both hard real-time response guarantees and unrestricted AI methods that can guide those real-time responses. Figure 1 illustrates the architecture, in which an AI subsystem (AIS) reasons about high-level problems that require its powerful but potentially unbounded planning methods, while a separate real-time subsystem (RTS) reactively sensor data Environment
The Oxford handbook of multicultural identity

Chapter 1: Introduction V. Benet-Martinez & YY. Hong PART I: DEFINITIONAL ISSUES AND BASIC PROCESSES Chapter 2: Dynamic multiculturalism: The interplay of social cognitive, neural, and genetic mechanisms YY. Hong & M. Khei Chapter 3: The bilingual brain: Language, culture, and identity N. Ramirez-Esparza & A. Garcia-Sierra Chapter 4: The identity dynamics of acculturation and multiculturalism S. Schwartz, V. Vignoles, R. Brown, & H. Zagefka PART II: THE SOCIAL-PSYCHOLOGICAL CONTEXT Chapter 5: Multicultural societies J. Berry & D. Sam Chapter 6: The social psychology of multiculturalism: Identity and intergroup relations K. Deaux & M. Verkuyten Chapter 7: Exploring the Identity Autonomy Perspective (IAP): An Integrative theoretical approach to multicultural and multiracial identity D. T. Sanchez, M. J. Shih & L. S. Wilton Chapter 8: Multiple groups, multiple identities, and intersectionality I. H. Settles & N. T. Buchanan Chapter 9: Psychological science of globalization A. K-y Leung, L. Qiu, & C. Chiu PART III: MEASUREMENT & VALIDITY ISSUES Chapter 10: Assessment of psychological acculturation and multiculturalism O. Celenk & F. Van de Vijver Chapter 11: Implicit multicultural identities T. Devos & T. Vu PART IV: INDIVIDUAL DIFFERENCES Chapter 12: Personality and multicultural effectiveness K. van der Zee & J.P. van Oudenhoven Chapter 13: Variations in multicultural identity: Socio-cognitive processes and Bicultural Identity Integration (BII) CY. Cheng, F. Lee, V. Benet-Martinez, & Q. Huyn Chapter 14: Multiculturalism and adjustment J. Ponterotto & A. Fietzer PART V: DEVELOPMENT, EDUCATION, & COUNSELING Chapter 15: Identity formation in bicultural youth P. Vedder & J. Phinney Chapter 16: Childhood socialization and academic performance of bicultural youth J. Mistry, M. Contreras, & E. Pufall-Jones Chapter 17: Multicultural education and global citizens J. A. Banks Chapter 18: Multicultural counseling & therapy L. Perez-Gualdron & C. Yeh PART VI: APPLIED PERSPECTIVES Chapter 19: Bridging cultural divides: Traversing organizational and psychological perspectives on multiculturalism M.Y. Brannen & F. Lee Chapter 20: Cultural diversity and marketing: The multicultural consumer L. A. Peracchio, M. G. Bublitz, & D. Luna Chapter 21: Policies for managing cultural diversity C. Novoa & F. Moghaddam Chapter 22: Managing identity issues in intercultural conflict communication S. Ting-Toomey