Miracle-dz/UniFAR-FTUs huggingface dataset:
Synthetic peptides analogous to the fimbrillin sequence inhibit adherence of Porphyromonas gingivalis

Fimbriae are important in the adherence of many bacterial species to the surfaces they eventually colonize. Porphyromonas (Bacteroides) gingivalis fimbriae appear to mediate adherence to oral epithelial cells and the pellicle-coated tooth surface. The role and contribution of fimbriae in the binding of P. gingivalis to hydroxyapatite (HAP) coated with saliva as a model for the pellicle-coated tooth surface were investigated. 3H-labeled P. gingivalis or the radioiodinated purified fimbriae were incubated with 2 mg of HAP beads coated with whole human saliva (sHAP) and layered on 100% Percoll to separate unbound from sHAP-bound components. The radioactivity of the washed beads was a measure of the bound components. The binding of P. gingivalis 2561 (381) cells and that of purified fimbriae were concentration dependent and saturable at approximately 10(8) cells and 40 micrograms of fimbriae added, respectively. The addition of fimbriae inhibited binding of P. gingivalis to sHAP beads by 65%, while the 75-kDa protein, which is another major surface component of P. gingivalis 2561, did not show significant inhibition, suggesting that the fimbriae are important in adherence. Encapsulated and sparsely fimbriated P. gingivalis W50 did not bind to sHAP beads. On the basis of the predicted sequence of the fimbrillin, a structural subunit of fimbriae, a series of peptides were synthesized and used to localize the active fimbrillin domains involved in P. gingivalis adherence to sHAP beads. Peptides from the carboxyl-terminal one-third of the fimbrillin strongly inhibited P. gingivalis binding to sHAP beads. Active residues within the sequence of inhibitory peptide 226-245 (peptide containing residues 226 to 245) and peptide 293-306 were identified by using smaller fragments prepared either by trypsin cleavage of the peptide 226-245 or by synthesis of smaller segments of peptide 293-306. Hemagglutinin activity, lectinlike binding, and ionic interaction did not seem to be involved in this binding since lysine, arginine, carbohydrates, and calcium ions failed to affect the binding of P. gingivalis. The observation that poly-L-lysine, bovine serum albumin, and defatted bovine serum albumin, even at high concentrations, only partially blocked the binding of P. gingivalis indicates that hydrophobic interactions are not the major forces involved in P. gingivalis binding to sHAP beads. Protease inhibitors such as EDTA, leupeptin, pepstatin, 1,10-phenanthroline, and phenylmethylsulfonyl fluoride did not interfere with the binding of P. gingivalis. However, the binding of P. gingivalis to trypsin- or chymotrypsin-pretreated sHAP beads was reduced. (ABSTRACT TRUNCATED AT 400 WORDS)
Partner's understanding of affective–cognitive meta‐bases predicts relationship quality

Knowledge that partners have about each other's attitudes are consequential for relationship quality. This article extends prior research and examines whether knowledge regarding a partner's meta-attitudinal bases, or subjective perceptions of how one's attitudes are driven, can influence relationship quality. Given how meta-bases are reflective of information-processing goals, we hypothesized that partner understanding of meta-attitudinal bases would positively predict relationship quality. Self and partner ratings of how relationally relevant attitudes were driven, as well as perceptions of relationship quality, were assessed. Results revealed that a partner's knowledge of one's meta-bases positively predicts one's own reported relationship quality. Results remained significant when controlling for relationship duration and meta-bases similarity. Implications of meta-bases understanding for close relationship functioning are discussed.
Optical coherence tomography scan circle location and mean retinal nerve fiber layer measurement variability.

PURPOSE To investigate the effect on optical coherence tomography (OCT) retinal nerve fiber layer (RNFL) thickness measurements of varying the standard 3.4-mm-diameter circle location. METHODS The optic nerve head (ONH) region of 17 eyes of 17 healthy subjects was imaged with high-speed, ultrahigh-resolution OCT (hsUHR-OCT; 501 x 180 axial scans covering a 6 x 6-mm area; scan time, 3.84 seconds) for a comprehensive sampling. This method allows for systematic simulation of the variable circle placement effect. RNFL thickness was measured on this three-dimensional dataset by using a custom-designed software program. RNFL thickness was resampled along a 3.4-mm-diameter circle centered on the ONH, then along 3.4-mm circles shifted horizontally (x-shift), vertically (y-shift) and diagonally up to +/-500 microm (at 100-microm intervals). Linear mixed-effects models were used to determine RNFL thickness as a function of the scan circle shift. A model for the distance between the two thickest measurements along the RNFL thickness circular profile (peak distance) was also calculated. RESULTS RNFL thickness tended to decrease with both positive and negative x- and y-shifts. The range of shifts that caused a decrease greater than the variability inherent to the commercial device was greater in both nasal and temporal quadrants than in the superior and inferior ones. The model for peak distance demonstrated that as the scan moves nasally, the RNFL peak distance increases, and as the circle moves temporally, the distance decreases. Vertical shifts had a minimal effect on peak distance. CONCLUSIONS The location of the OCT scan circle affects RNFL thickness measurements. Accurate registration of OCT scans is essential for measurement reproducibility and longitudinal examination (ClinicalTrials.gov number, NCT00286637).
Views of People with Learning Difficulties about Current and Future Accommodation: The use of focus groups to promote discussion

There is growing emphasis on inclusion as a central philosophy in services for people with learning difficulties in the UK, Europe and the USA. Coupled with this is recognition of the need to actively involve people with learning difficulties in the research process through the use of more inclusive approaches. This paper reports the use of focus groups as a strategy for data collection from people with learning difficulties in a project that sought to review existing accommodation and support. A number of important key themes emerged relating to the importance of social networks, inclusion, reciprocal relationships, privacy and security. The implications arising from these findings for the provision of accommodation and support are considered. Furthermore, it was concluded that focus groups are potentially a valuable approach in research that seeks to actively involve people with learning difficulties.
learning to novel contexts Natural error patterns enable transfer of motor

[PDF] [Full Text] [Abstract] , July 15, 2013; 110 (2): 322-333. J Neurophysiol Tricia L. Gibo, Sarah E. Criscimagna-Hemminger, Allison M. Okamura and Amy J. Bastian Cerebellar motor learning: are environment dynamics more important than error size? [PDF] [Full Text] [Abstract] , August 15, 2013; 110 (4): 916-925. J Neurophysiol Sara J. Hussain, Angela S. Hanson, Shih-Chiao Tseng and Susanne M. Morton induces complete 24-hour retention A locomotor adaptation including explicit knowledge and removal of postadaptation errors [PDF] [Full Text] [Abstract] , June 15, 2014; 111 (12): 2414-2422. J Neurophysiol Sara J. Hussain and Susanne M. Morton Perturbation schedule does not alter retention of a locomotor adaptation across days [PDF] [Full Text] [Abstract] , August 15, 2014; 112 (4): 1010-1019. J Neurophysiol Yen-Ting Chen, MinHyuk Kwon, Emily J. Fox and Evangelos A. Christou older adults Altered activation of the antagonist muscle during practice compromises motor learning in
Reconsidering the effects of sibling configuration: Recent advances and challenges

▪ Abstract Until recently, social scientists were headed to consensus over the impact of the structural parameters of the sibling group, especially size and birth order, on educational and other status outcomes. New developments challenge this conventional wisdom, thus offering an opening for dialogue on this topic. We identify the utility and implications of studying the consequences of sibling configuration within sociology, across disciplines, and for public policy. Revisiting the association between sibship size and educational advancement, we evaluate challenges to long-held beliefs regarding this relationship. We then discuss the effects of birth order, highlighting recent declarations that these effects are more profound than previously believed. We next summarize scholarship on two less-explored components of the sibling matrix: spacing and sex composition. Finally, we consider generalizability of research done mostly in the United States to other countries. We hope examining and critiquing this r.
Common Threat and Common Response? The European Union's Counter-Terrorism Strategy and its Problems

Abstract On the basis of an analysis of the European Union's common definition of the post-9/11 terrorist threat, this article provides a critical assessment of the EU's response. The EU has arrived at a reasonably specific definition of the common threat that avoids simplistic reductions and is a response that is sufficiently multidimensional to address the different aspects – internal and external, legislative and operational, repressive and preventive – of this threat. Yet the definition is undermined by differences between national threat perceptions. The preference for instruments of cooperation and coordination rather than integration, and poor implementation are having a negative impact on the effectiveness of the common response, the legitimacy of which is also weakened by limited parliamentary and judicial control.
Annotating educational content by questions created by learners

Several approaches to educational web-based content enrichment have been devised. Annotations in form of comments and other types of remarks obviously supply these approaches. Annotations allow enriching the educational materials mainly by retaining key information or comments; they can support visual search and also collaboration. In this paper we present a method for an acquisition of new educational content created by learners. It is based on collaborative questions creation. We let the students to enrich educational materials with questions related to the selected text. We believe that this helps them to learn more effectively. It facilitates a collaboration and explicit rating to gain new quality content. This kind of annotations can be considered also as a source of semantics of the selected text and used for adaptation. To evaluate proposed method we experimented in domain of learning programming. We implemented the method within an existing web-based educational framework ALEF and provided several experiments.
An Empirical Comparison of Certain Techniques for Estimating the reliability of Speeded Tests

IT has been repeatedly demonstrated, both theoretically and empirically, that the reliability coefficients of speeded tests may be completely meaningless when computed by the usual single-trial, or &dquo;internal consistency,&dquo; procedures (1, 4, 6, 7, 10, 12). Split-half techniques and those based upon inter-item consistency, such as the Kuder-Richardson formulas, may yield spuriously high coefficients when applied to speed tests. An examination of the procedures followed in finding such reliability coefficients will show that these coefficients are based upon the consistency in number of errors made by the subject. In so far as individual differences in test scores depend upon speed of work, however, the measures of reliability must be based upon consistency in speed as well as in errors. In the
Cortical recruitment of nonmuscle myosin II in early syncytial Drosophila embryos

The nuclei of early syncytial Drosophila embryos migrate dramatically toward the poles. The cellular mechanisms driving this process, called axial expansion, are unclear, but myosin II activity is required. By following regulatory myosin light chain (RLC)–green fluorescent protein dynamics in living embryos, we observed cycles of myosin recruitment to the cortex synchronized with mitotic cycles. Cortical myosin is first seen in a patch at the anterocentral part of the embryo at cycle 4. With each succeeding cycle, the patch expands poleward, dispersing at the beginning of each mitosis and reassembling at the end of telophase. Each cycle of actin and myosin recruitment is accompanied by a cortical contraction. The cortical myosin cycle does not require microtubules but correlates inversely with Cdc2/cyclinB (mitosis-promoting factor) activity. A mutant RLC lacking inhibitory phosphorylation sites was fully functional with no effect on the cortical myosin cycle, indicating that Cdc2 must be modulating myosin activity by some other mechanism. An inhibitor of Rho kinase blocks the cortical myosin recruitment cycles and provokes a concomitant failure of axial expansion. These studies suggest a model in which cycles of myosin-mediated contraction and relaxation, tightly linked to Cdc2 and Rho kinase activity, are directly responsible for the axial expansion of the syncytial nuclei.
Early transcriptomic adaptation to Na₂CO₃ stress altered the expression of a quarter of the total genes in the maize genome and exhibited shared and distinctive profiles with NaCl and high pH stresses.

Sodium carbonate (Na₂CO₃) presents a huge challenge to plants by the combined damaging effects of Na⁺, high pH, and CO₃²⁻. Little is known about the cellular responses to Na₂CO₃ stress. In this study, the transcriptome of maize (Zea mays L. cv. B73) roots exposed to Na₂CO₃ stress for 5 h was compared with those of NaCl and NaOH stresses. The expression of 8,319 genes, representing over a quarter of the total number of genes in the maize genome, was altered by Na₂CO₃ stress, and the downregulated genes (5,232) outnumbered the upregulated genes (3,087). The effects of Na₂CO₃ differed from those of NaCl and NaOH, primarily by downregulating different categories of genes. Pathways commonly altered by Na₂CO₃, NaCl, and NaOH were enriched in phenylpropanoid biosynthesis, oxidation of unsaturated fatty acids, ATP-binding cassette (ABC) transporters, as well as the metabolism of secondary metabolites. Genes for brassinosteroid biosynthesis were specifically upregulated by Na₂CO₃, while genes involved in ascorbate and aldarate metabolism, protein processing in the endoplasmic reticulum and by N-glycosylation, fatty acid biosynthesis, and the circadian rhythm were downregulated. This work provides the first holistic picture of early transcriptomic adaptation to Na₂CO₃ stress, and highlights potential molecular pathways that could be manipulated to improve tolerance in maize.
Petticoats and Primary Sources: Lessons Learned through Public History

ABSTRACT The trend among public historians, educators, museum curators, and archivists is to find some means of making complex historical content readily accessible. At national sites, in the classroom, and on the Web, their efforts are aimed at drawing audiences and stimulating an engagement with history. While these efforts are laudable and surely promote a broad appreciation for the historic sites, artifacts and documents that are the essential elements of scholarship, the means of presentation (the form) that is employed may at times inadvertently color or distort the substance of the lessons they are intended to convey. In the following article, which is adapted from a talk given in Williamsburg, Virginia, at the Mid-Atlantic Regional Archives Conference in 2007, the author (an actress turned archivist) reviews her experiences as a first-person interpreter, addresses some of the merits and unintended consequences of this educational device, and—extrapolating from these experiences—concludes with a consideration of how archivists currently provide access to and present primary sources on the Web.
The Multitarget Monopulse CRLB for Matched Filter Samples

It has recently been found that by jointly processing multiple (sum, azimuth-, and elevation-difference) matched filter samples, it is possible to extract and localize several (more than two) targets spaced more closely than the classical interpretation of radar resolution. This paper derives the Cramer-Rao lower bound (CRLB) for sampled monopulse radar data. It is worthwhile to know the limits of such procedures; and in addition to its role in delivering the measurement accuracies required by a target tracker, the CRLB reveals an estimator's efficiency. We interrogate the CRLB expressions for cases of interest. Of particular interest are the CRLB's implications on the number of targets localizable: assuming a sampling-period equal to a rectangular pulse's length, five targets can be isolated between two matched filter samples given that the target's signal-to-noise ratios (SNRs) are known. This reduced to three targets when the SNRs are not known, but the number of targets increases back to five (and beyond) when a dithered boresight strategy is used. Further insight to the impact of pulse shape and of the benefits of oversampling are given.
Fostering deep and elaborative learning and generic (soft) skill development: the strategic use of case studies in accounting education

It is vital that accounting educators take responsibility for the development of students' generic (soft) skills in conjunction with, discipline-specific skills. Research indicates that the typical learning styles of accounting students are not suited to the acquisition of generic skills. In this paper learning theory is used to provide a framework to support the use of case studies as a tool to promote appropriate learning styles and thereby enhance generic skill development. The paper details a number of strategies that may be implemented with case studies to achieve these goals. The implications for accounting educators, which are significant, are discussed.
Reply to progression‐free survival: Does a correlation with survival justify its role as a surrogate clinical endpoint?

We thank Becker et al for their thoughtful editorial on our article describing progression-free survival (PFS) as a surrogate endpoint for overall survival (OS) in renal cancer clinical trials. We agree that our data do not necessarily support the use of PFS as a surrogate endpoint for OS across the entire renal cancer therapeutic spectrum. We further concur that additional work needs to be done to establish PFS as a pragmatic endpoint for regulatory purposes. However, we disagree with Becker et al that it is necessary to fulfill Prentice criteria to establish surrogacy. More specifically, fulfilling Prentice’s third criterion that the treatment effect on the surrogate (PFS) should capture the full effect of treatment on the clinical endpoint (OS) is an extremely high bar. Multiple authors have argued for and suggested different approaches to the validation of the surrogate. Although a full discussion is beyond the scope of this correspondence, we would like to point out that one alternative approach is the adjusted association h. The adjusted association first estimates the dependency parameter within each treatment arm and then aggregates the information by a weighted average. As we demonstrated in our article, the adjusted association was a highly statistically significant measure that strongly suggests that PFS is a surrogate endpoint for OS, at least within the context of the trials analyzed.
Age‐related impeded regeneration of mouse minced anterior tibial muscle

The effect of increasing age on the completeness of anterior tibial muscle regeneration from autotransplants of minced muscle has been studied in Swiss Webster and C57/B6J mice aged 18 to 120 days. A progressively declining capability to regenerate new myofibers was associated with a decreasing phagocytic clearance of implanted myofiber debris. Concurrently, there was decreased presumptive myoblast proliferation and new myofiber formation. The importance of age‐related host factors, including nonspecific macrophage activity, in muscle mince regeneration was demonstrated by: (1) the successful regeneration of muscle in hetero‐transplanted muscle minces from older mice implanted in younger animals and (2) the failure of muscle regeneration when the reverse experiment was performed in syngeneic animals. Heterologous striated muscle from the diaphragm regenerated in the bed of the excised anterior tibial muscle, whereas heterologous cardiac muscle failed to regenerate as expected because of the absence of satellite cells. The failure of phagocytic clearance of implanted myofiber mince and concurrent retardation of regeneration suggests a major age‐related nonimmune role of phagocytic macrophages in the early stages of regeneration of anterior tibial muscle from isotopic minced muscle implants.
Pediocin PA-1, a Wide-Spectrum Bacteriocin from Lactic Acid Bacteria

Referee: Dr. Helen Dodd, Food Safety Science Division, Institute of Food Research, Norwich Research Park, Colney NR4 7UA, Norwich, United Kingdom Pediocin PA-1 is a broad-spectrum lactic acid bacteria bacteriocin that shows a particularly strong activity against Listeria monocytogenes, a foodborne pathogen of special concern among the food industries. This antimicrobial peptide is the most extensively studied class IIa (or pediocin family) bacteriocin, and it has been sufficiently well characterized to be used as a food biopreservative. This review focuses on the progress that have been made in the elucidation of its structure, mode of action, and biosynthesis, and includes an overview of its applications in food systems. The aspects that need further research are also addressed. In the future, protein engineering, genetic engineering and/or chemical synthesis may lead to the development of new antimicrobial peptides with improved properties, based on some features of the pediocin PA-1 molecule.
Reduced capacity to sustain positive emotion in major depression reflects diminished maintenance of fronto-striatal brain activation

Anhedonia, the loss of pleasure or interest in previously rewarding stimuli, is a core feature of major depression. While theorists have argued that anhedonia reflects a reduced capacity to experience pleasure, evidence is mixed as to whether anhedonia is caused by a reduction in hedonic capacity. An alternative explanation is that anhedonia is due to the inability to sustain positive affect across time. Using positive images, we used an emotion regulation task to test whether individuals with depression are unable to sustain activation in neural circuits underlying positive affect and reward. While up-regulating positive affect, depressed individuals failed to sustain nucleus accumbens activity over time compared with controls. This decreased capacity was related to individual differences in self-reported positive affect. Connectivity analyses further implicated the fronto-striatal network in anhedonia. These findings support the hypothesis that anhedonia in depressed patients reflects the inability to sustain engagement of structures involved in positive affect and reward.