Miracle-dz/UniFAR-FTUs huggingface dataset:
Epitope mapping of the variable repetitive region with the MB antigen of Ureaplasma urealyticum

One of the major surface structures of Ureaplasma urealyticum recognized by antibodies of patients during infection is the MB antigen. Previously, we showed by Western blot (immunoblot) analysis that any one of the anti-MB monoclonal antibodies (MAbs) 3B1.5, 5B1.1, and 10C6.6 could block the binding of patient antibodies to MB. Subsequent DNA sequencing revealed that a unique six-amino-acid direct tandem repeat region composed the carboxy two-thirds of this antigen. In the present study, using antibody-reactive peptide scanning of this repeat region, we demonstrated that the amino acids defining the epitopes for MAbs 3B1.5 5B1.1 and 10C6.6 are EQP, GK, and KEQPA, respectively. Peptide scanning analysis of an infected patient's serum antibody response showed that the dominant epitope was defined by the sequence PAGK. Mapping of these continuous epitopes revealed overlap between all MAb and patient polyclonal antibody binding sites, thus explaining the ability of a single MAb to apparently block all polyclonal antibody binding sites. We also show that a single amino acid difference in the sequence of the repeats of serovars 3 and 14 accounts for the lack of reactivity with serovar 14 of two of the serovar 3-specific MAbs. Finally, the data demonstrate the need to obtain the sequences of the mba genes of all serovars before an effective serovar-specific antibody detection method can be developed.
The Child Asthma Link Line: A Coalition-initiated, Telephone-based, Care Coordination Intervention for Childhood Asthma

Background. Childhood asthma is a complex chronic disease that poses significant challenges regarding management, and there is evidence of disparities in care. Many medical, psychosocial, and health system factors contribute to recognized poor control of this most prevalent illness among children, with resultant excessive use of emergency departments and hospitalizations for care. Recent national guidelines emphasize the need for community-based initiatives to address these critical issues. To address health system fragmentation and impact asthma outcomes, the Philadelphia Allies Against Asthma coalition developed and implemented the Child Asthma Link Line, a telephone-based care coordination and system integration program, which has been in operation since 2001. This study evaluates the effectiveness of the Child Asthma Link Line integration model to improve asthma management by measuring utilization markers of morbidity. Methods. Medicaid Managed Care Organization claims data for 59 children who received the Link Line intervention in 2003 are compared to a matched sample of 236 children who did not receive the Link Line intervention. Children in the two study groups are ages 3 through 12 years and matched on 2003 emergency department visits, age, gender, and race/ethnicity. Primary outcome variables analyzed in this study are emergency department visits, hospitalizations, and office visit claims from the follow-up year (2004). Results. Link Line intervention children were significantly less likely to have follow-up hospitalizations than matched sample children (p = .02). Children enrolled in the Link Line were also more likely to attend outpatient office visits in the follow-up year (p = .045). In addition, Link Line children with multiple emergency department visits in 2003 were significantly less likely to have an emergency department visit in 2004 (p = .046). Conclusion. This coalition-developed, telephone-based, system-level intervention had a significant impact on childhood asthma morbidity as measured by utilization endpoints of follow-up hospitalizations and emergency department visits. Telephone-based care coordination and service integration may be a viable and economic way to impact childhood asthma and other chronic diseases.
Effects of caloric restriction with varying energy density and aerobic exercise on weight change and satiety in young female adults

This study examines the combined effects of caloric restriction on body composition, blood lipid, and satiety in slightly overweight women by varying food density and aerobic exercise. Twenty-three women were randomly assigned to one of two groups for a four-week weight management program: the high-energy density diet plus exercise (HDE: n = 12, 22 ± 2 yrs, 65 ± 7 kg, 164 ± 5 cm, 35 ± 4 % fat) and low-energy density diet plus exercise (LDE: n = 11, 22 ± 1 yrs, 67 ± 7 kg, 161 ± 2 cm, 35 ± 4 % fat) groups. Subjects maintained a low-calorie diet (1,500 kcal/day) during the program. Isocaloric (483 ± 26 for HDE, 487 ± 27 kcal for LDE) but different weight (365 ± 68 for HDE, 814 ± 202 g for LDE) of lunch was provided. After lunch, they biked at 60% of maximum capacity for 40 minutes, five times per week. The hunger level was scaled (1: extremely hungry; 9: extremely full) at 17:30 each day. Before and after the program, the subjects' physical characteristics were measured, and fasting blood samples were drawn. The daily energy intake was 1,551 ± 259 for HDE and 1,404 ± 150 kcal for LDE (P > 0.05). After four weeks, the subjects' weights and % fat decreased for both LDE (-1.9 kg and -1.5%, P < 0.05) and HDE (-1.6 kg and -1.4%, respectively, P < 0.05). The hunger level was significantly higher for HDE (2.46 ± 0.28) than for LDE (3.10 ± 0.26) (P < 0.05). The results suggest that a low-energy density diet is more likely to be tolerated than a high-energy density diet for a weight management program combining a low-calorie diet and exercise, mainly because of a reduced hunger sensation.
An heuristic model for sea level rise due to the melting of small glaciers

Ice melt from glaciers and small ice caps (GSICs) is an important component of past and future sea level rise. Projections made to date of future GSIC-derived sea level rise have used a simple model that has conceptual weaknesses, calibrated using data that have since been revised. Here we devise a more satisfactory model that accounts for regional variations in the altitudinal ranges of the world's glaciers, calibrate it using recent data, and consider the implications for future sea level rise. Because of compensating factors, the new projections are similar to the earlier ones, but their methodological basis is far more sound. Wide uncertainties still remain.
Approximate least squares

We present a novel iterative algorithm for approximating the linear least squares solution with low complexity. After a motivation of the algorithm we discuss the algorithm's properties including its complexity, and we present theoretical results as well as simulation based performance results. We describe the analysis of its convergence behavior and show that in the noise free case the algorithm converges to the least squares solution.
Reordering Modeling using Weighted Alignment Matrices

In most statistical machine translation systems, the phrase/rule extraction algorithm uses alignments in the 1-best form, which might contain spurious alignment points. The usage of weighted alignment matrices that encode all possible alignments has been shown to generate better phrase tables for phrase-based systems. We propose two algorithms to generate the well known MSD reordering model using weighted alignment matrices. Experiments on the IWSLT 2010 evaluation datasets for two language pairs with different alignment algorithms show that our methods produce more accurate reordering models, as can be shown by an increase over the regular MSD models of 0.4 BLEU points in the BTEC French to English test set, and of 1.5 BLEU points in the DIALOG Chinese to English test set.
Safe navigation on hazardous terrain

Presents a strategy for autonomous navigation of field mobile robots on hazardous natural terrain using a fuzzy logic approach and a measure of terrain traversability. The navigation strategy comprises three simple, independent behaviors: seek-goal, traverse-terrain, and avoid-obstacle. The recommendations from these three behaviors are combined through appropriate weighting factors to generate the final steering and speed commands that are executed by the robot. The weighting factors are produced by fuzzy logic rules that take into account the current status of the robot. This navigation strategy requires no a priori information about the environment, and uses the on-board traversability analysis to enable the robot to select relatively easy-to-traverse paths autonomously. Field test results obtained from implementation of the proposed algorithms on the commercial Pioneer All Terrain rover are presented. These results demonstrate the real-time capabilities of the terrain assessment and fuzzy logic navigation algorithms.
XCML: A Runtime Representation for the Context Modelling Language

The context modelling language (CML), derived from object role modeling (ORM), is a powerful approach for capturing the pertinent object types and relationships between those types in context-aware applications. Its support for data quality metrics, context histories and fact type classifications make it an ideal design tool for context-aware systems. However, CML currently lacks a suitable representation for exchanging context models and instances in distributed systems. A runtime representation can be used by context-aware applications and supporting infrastructure to exchange context information and models between distributed components, and it can be used as the storage representation when relational database facilities are not present. This paper shows the benefits of using CML for modelling context as compared to commonly used RDF/OWL-based context models, shows that translations of CML to RDF or OWL are lossy, discusses existing techniques for serialising ORM models, and presents an alternative XML-based representation for CML called XCML
Association of serum vitamin D levels with inflammatory response following hip fracture: the Baltimore Hip Studies.

BACKGROUND Vitamin D, known for its role in calcium homeostasis, may also regulate immune function. Whether vitamin D deficiency at the time of hip fracture is associated with the inflammatory response postfracture is not known. METHODS In a cohort from the Baltimore Hip Studies, women aged >or= 65 years were evaluated at baseline and 2, 6, and 12 months after hip fracture repair. Serum at baseline was analyzed for 25-hydroxyvitamin D [25(OH)D], and serum from all time points was analyzed for interleukin-6 (IL-6). Participants were divided into two groups based on their baseline 25(OH)D levels. Vitamin D deficiency was defined as a 25(OH)D level of <or= 15 ng/mL (<37.5 nmol/L). We examined IL-6 level as a function of vitamin D status using generalized estimating equations, adjusting for covariates. RESULTS Women deficient in vitamin D at baseline had higher IL-6 levels in the year postfracture (p=.02). On average, participants with low 25(OH)D levels had adjusted serum IL-6 levels that were 6.0 pg/mL (95% confidence interval [CI]: -6.7, 18.7 pg/mL), 11.9 pg/mL (95% CI: 3.5, 20.4), 13.1 pg/mL (95% CI: 4.6, 21.6), and 13.4 pg/mL (95% CI: 2.3, 24.5) higher at baseline, 2, 6, and 12 months after hip fracture, respectively. CONCLUSIONS Women with vitamin D deficiency at the time of hip fracture had higher serum IL-6 levels in the year after hip fracture. Whether the proinflammatory state of vitamin D deficiency explains the association of this deficiency with adverse outcomes in older adults warrants further study.
Biased random-key genetic algorithm for fiber installation in Optical Network Optimization

The problem of Fiber Installation in Optical Network Optimization consists in routing a set of lightpaths (all-optical connections), such that the cost of the optical components necessary to operate the network is minimized. We propose a genetic algorithm with random keys that extends the best heuristic in the literature by embedding it into an evolutionary framework. Computational results showed that the new heuristic improves the best heuristic in the literature.
Temporal Dynamics of Arthropods on Six Tree Species in Dry Woodlands on the Caribbean Island of Puerto Rico

Abstract The seasonal dynamics of foliage arthropod populations are poorly studied in tropical dry forests despite the importance of these studies for understanding arthropod population responses to environmental change. We monitored the abundance, temporal distributions, and body size of arthropods in five naturalized alien and one native tree species to characterize arthropod seasonality in dry novel Prosopis–Leucaena woodlands in Puerto Rico. A branch clipping method was used monthly to sample foliage arthropod abundance over 39 mo. Seasonal patterns of rainfall and abundance within various arthropod taxa were highly variable from year to year. Abundance for most taxa did not show significant seasonality over the 3 yr, although most taxa had abundance peaks each year. However, Homoptera displayed high seasonality with significant temporal aggregations in each year. Formicidae, Orthoptera, and Coleoptera showed high variation in abundance between wet and dry periods, whereas Hemiptera were consistently more abundant in the wet period. Seasonal differences in mean abundance were found only in a few taxa on Tamarindus indica L. , Bucida buceras L. , Pithecellobium dulce , and (Roxburgh) Benth. Mean arthropod abundance varied among tree species, with highest numbers on Prosopis juliflora , (Swartz) De Candolle, Pi. dulce , Leucaena leucocephala , and (Lamarck) de Wit. Abundance of Araneae, Orthoptera, Coleoptera, Lepidoptera larvae, and all arthropods showed weak relationships with one or more climatic variables (rainfall, maximum temperature, or relative humidity). Body size of arthropods was usually largest during the dry periods. Overall, total foliage arthropod abundance showed no consistent seasonality among years, which may become a more common trend in dry forests and woodlands in the Caribbean if seasonality of rainfall becomes less predictable.
Troubleshooting wireless mesh networks

Effective network troubleshooting is critical for maintaining efficient and reliable network operation. Troubleshooting is especially challenging in multi-hop wireless networks because the behavior of such networks depends on complicated interactions between many factors such as RF noise, signal propagation, node interference, and traffic flows. In this paper we propose a new direction for research on fault diagnosis in wireless mesh networks. Specifically, we present a diagnostic system that employs trace-driven simulations to detect faults and perform root cause analysis. We apply this approach to diagnose performance problems caused by packet dropping, link congestion, external noise, and MAC misbehavior. In a 25 node mesh network, we are able to diagnose over 10 simultaneous faults of multiple types with more than 80% coverage.
Ocean Optics Protocols for Satellite Ocean Color Sensor Validation, Revision 4, Volume IV: Inherent Optical Properties: Instruments, Characterizations, Field Measurements and Data Analysis Protocols

The NASA STI Program Office … in ProfileSince its founding, NASA has been dedicated tothe advancement of aeronautics and spacescience. The NASA Scientific and TechnicalInformation (STI) Program Office plays a keypart in helping NASA maintain this importantrole.The NASA STI Program Office is operated byLangley Research Center, the lead center forNASA’s scientific and technical information. TheNASA STI Program Office provides access tothe NASA STI Database, the largest collection ofaeronautical and space science STI in the world.The Program Office is also NASA’s institutionalmechanism for disseminating the results of itsresearch and development activities. Theseresults are published by NASA in the NASA STIReport Series, which includes the followingreport types:• TECHNICAL PUBLICATION. Reports ofcompleted research or a major significantphase of research that present the results ofNASA programs and include extensive data ortheoretical analysis. Includes compilations ofsignificant scientific and technical data andinformation deemed to be of continuingreference value. NASA’s counterpart ofpeer-reviewed formal professional papers buthas less stringent limitations on manuscriptlength and extent of graphic presentations. • TECHNICAL MEMORANDUM. Scientificand technical findings that are preliminary orof specialized interest, e.g., quick releasereports, working papers, and bibliographiesthat contain minimal annotation. Does notcontain extensive analysis. • CONTRACTOR REPORT. Scientific andtechnical findings by NASA-sponsoredcontractors and grantees. • CONFERENCE PUBLICATION. Collectedpapers from scientific and technicalconferences, symposia, seminars, or othermeetings sponsored or cosponsored by NASA. • SPECIAL PUBLICATION. Scientific, techni-cal, or historical information from NASAprograms, projects, and mission, often con-cerned with subjects having substantial publicinterest. • TECHNICAL TRANSLATION.English-language translations of foreign scien-tific and technical material pertinent to NASA’smission.Specialized services that complement the STIProgram Office’s diverse offerings include creat-ing custom thesauri, building customized data-bases, organizing and publishing research results . even providing videos.For more information about the NASA STI Pro-gram Office, see the following:•Access the NASA STI Program Home Page athttp://www.sti.nasa.gov/STI-homepage.html•E-mail your question via the Internet tohelp@sti.nasa.gov• Fax your question to the NASA Access HelpDesk at (301) 621-0134•Telephone the NASA Access Help Desk at(301) 621-0390•Write to:NASA Access Help DeskNASA Center for AeroSpace Information7121 Standard DriveHanover, MD 21076–1320
Cellular levels of p120 catenin function as a set point for cadherin expression levels in microvascular endothelial cells

The mechanisms by which catenins regulate cadherin function are not fully understood, and the precise function of p120 catenin (p120ctn) has remained particularly elusive. In microvascular endothelial cells, p120ctn colocalized extensively with cell surface VE-cadherin, but failed to colocalize with VE-cadherin that had entered intracellular degradative compartments. To test the possibility that p120ctn binding to VE-cadherin regulates VE-cadherin internalization, a series of approaches were undertaken to manipulate p120ctn availability to endogenous VE-cadherin. Expression of VE-cadherin mutants that competed for p120ctn binding triggered the degradation of endogenous VE-cadherin. Similarly, reducing levels of p120ctn using siRNA caused a dramatic and dose-related reduction in cellular levels of VE-cadherin. In contrast, overexpression of p120ctn increased VE-cadherin cell surface levels and inhibited entry of cell surface VE-cadherin into degradative compartments. These results demonstrate that cellular levels of p120ctn function as a set point mechanism that regulates cadherin expression levels, and that a major function of p120ctn is to control cadherin internalization and degradation.
Synthesis of Property-Preserving Mappings

System development often involves decisions about how a high-level design is to be implemented using primitives from a low-level platform. Certain decisions, however, may introduce undesirable behavior into the resulting implementation, possibly leading to a violation of a desired property that has already been established at the design level. In this paper, we introduce the problem of synthesizing a propertypreserving mapping : A set of implementation decisions ensuring that a desired property is preserved from a high-level design into a low-level platform implementation. We provide a formalization of the synthesis problem and propose a technique for synthesizing a mapping based on symbolic constraint search. We describe our prototype implementation, and a case study demonstrating the application of our technique to synthesizing secure mappings for OAuth, a popular family of authorization protocols on the web.
Geodesics using Waves: Computing Distances using Wave Propagation

In this paper, we present a new method for computing approximate geodesic distances. We introduce the wave method for approximating geodesic distances from a point on a manifold mesh. Our method involves the solution of two linear systems of equations. One system of equations is solved repeatedly to propagate the wave on the entire mesh, and one system is solved once after wave propagation is complete in order to compute the approximate geodesic distances up to an additive constant. However, these systems need to be pre-factored only once, and can be solved efficiently at each iteration. All of our tests required approximately between 300 and 400 iterations, which were completed in a few seconds. Therefore, this method can approximate geodesic distances quickly, and the approximation is highly accurate.
Preference-Based Query Answering in Datalog+/- Ontologies

The study of preferences has a long tradition in many disciplines, but it has only relatively recently entered the realm of data management through their application in answering queries to relational databases. The current revolution in data availability through the Web and, perhaps most importantly in the last few years, social media sites and applications, puts ontology languages at the forefront of data and information management technologies. In this paper, we propose the first (to our knowledge) integration of ontology languages with preferences as in relational databases by developing PrefDatalog+/-, an extension of the Datalog+/- family of languages with preference management formalisms closely related to those previously studied for relational databases. We focus on two kinds of answers to queries that are relevant to this setting, skyline and k-rank (a generalization of top-k queries), and develop algorithms for computing these answers to both DAQs (disjunctions of atomic queries) and CQs (conjunctive queries). We show that DAQ answering in PrefDatalog+/- can be done in polynomial time in the data complexity, as in relational databases, as long as query answering can also be done in polynomial time (in the data complexity) in the underlying classical ontology.
Photoreactivation compensates for UV damage and restores infectivity to natural marine virus communities

We investigated the potential for photoreactivation to restore infectivity to sunlight-damaged natural viral communities in offshore (chlorophyll a, < 0.1 microgram liter-1), coastal (chlorophyll a, ca. 0.2 microgram liter-1), and estuarine (chlorophyll a, ca. 1 to 5 micrograms liter-1) waters of the Gulf of Mexico. In 67% of samples, the light-dependent repair mechanisms of the bacterium Vibrio natriegens restored infectivity to natural viral communities which could not be repaired by light-independent mechanisms. Similarly, exposure of sunlight-damaged natural viral communities to > 312-nm-wavelength sunlight in the presence of the natural bacterial communities restored infectivity to 21 to 26% of sunlight-damaged viruses in oceanic waters and 41 to 52% of the damaged viruses in coastal and estuarine waters. Wavelengths between 370 and 550 nm were responsible for restoring infectivity to the damaged viruses. These results indicate that light-dependent repair, probably photoreactivation, compensated for a large fraction of sunlight-induced DNA damage in natural viral communities and is potentially essential for the maintenance of high concentrations of viruses in surface waters.
The Adaptive Control for a Class of Nonlinear Systems Based on Dynamic Approximate Non-Linearization

The adaptive control algorithm, its parameter adaptive recursive predicting and noise estimator is presented for a class of nonlinear discrete-time systems with multiple time delays based on dynamic approximate second-order nonlinear increment minimized recursive predicting model method. The adaptive control is employed for nonlinear systems with heavy multiple time delays. The simulation result for several typical nonlinear systems are given to demonstrate the correctness and effectiveness of approach proposed.