Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure and stability of β‐pleated sheets *

Beside α‐helices, β‐sheets are the most common secondary structure elements of proteins. In this article, the question of structure and stability of parallel and antiparallel sheets of various lengths is addressed. All data obtained are compared to a selected set of protein structures. In antiparallel β‐sheets, one of the two possible H‐bonded structures (containing 14 atoms in the H‐bonded pseudoring) is energetically more favored and also more abundant in proteins than the other one (with 10 atoms involved in the pseudoring). Parallel β‐sheets and their subunits are energetically less stable and indeed found to occur more rarely in proteins. Antiparallel hairpins are disfavored compared to β‐sheets formed by sequentially separated strands. Agreement between theory and experimental data indicates that characterization of structural building blocks at an appropriately accurate level of theory is a useful tool to get insight into fundamentals of protein structure. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1155–1168, 2005
Experience and Training of a First Person Shooter (FPS) Game Can Enhance Useful Field of View, Working Memory, and Reaction Time

To examine the effects of experience and training of a first person shooter (FPS) game on cognitive abilities, we conducted three experiments in which participants performed useful field of view (UFOV), visual working memory (VWM), and reaction time (RT) tasks. In Experiment 1, we compared performance on the three cognitive tasks between FPS players and non-FPS players. In Experiments 2 and 3, changes in task performance after 10-hr training or no training on the FPS game were examined. Experiment 1 showed that FPS players performed better than did non-FPS players on all cognitive tasks. Experiment 2 showed higher performance on all cognitive tasks after the training compared with those before it. Experiment 3 showed no enhancement of performance on all tasks. These results indicate that FPS game experience and/or training can enhance cognitive abilities at least for UFOV, VMW, and RT.
Uptake of Helicobacter pylori Outer Membrane Vesicles by Gastric Epithelial Cells

ABSTRACT Helicobacter pylori bacteria colonize the human stomach where they stimulate a persistent inflammatory response. H. pylori is considered noninvasive; however, lipopolysaccharide (LPS)-enriched outer membrane vesicles (OMV), continuously shed from the surface of this bacterium, are observed within gastric epithelial cells. The mechanism of vesicle uptake is poorly understood, and this study was undertaken to examine the roles of bacterial VacA cytotoxin and LPS in OMV binding and cholesterol and clathrin-mediated endocytosis in vesicle uptake by gastric epithelial cells. OMV association was examined using a fluorescent membrane dye to label OMV, and a comparison was made between the associations of vesicles from a VacA+ strain and OMV from a VacA− isogenic mutant strain. Within 20 min, essentially all associated OMV were intracellular, and vesicle binding appeared to be facilitated by the presence of VacA cytotoxin. Uptake of vesicles from the VacA+ strain was inhibited by H. pylori LPS (58% inhibition with 50 μg/ml LPS), while uptake of OMV from the VacA− mutant strain was less affected (25% inhibition with 50 μg/ml LPS). Vesicle uptake did not require cholesterol. However, uptake of OMV from the VacA− mutant strain was inhibited by a reduction in clathrin-mediated endocytosis (42% with 15 μg/ml chlorpromazine), while uptake of OMV from the VacA+ strain was less affected (25% inhibition with 15 μg/ml chlorpromazine). We conclude that VacA toxin enhances the association of H. pylori OMV with cells and that the presence of the toxin may allow vesicles to exploit more than one pathway of internalization.
Experiments with low power commodity hardware platforms for challenged networks

Wireless opportunistic connections are the primary mechanism for transferring data between disconnected nodes, such as vehicles, remote sensors, or village kiosks [6], [7] in a Delay Tolerant Network (DTN)[2]. Energy, being a scarce resource for such challenged environments, requires efficient management. We highlight the potential for accurate software-level energy modeling and prediction on commodity embedded computers for DTN deployments, such as KioskNet [6]. Our experiments confirm that accurate prediction of energy consumption, without relying on any hardware power measurement tool, is feasible. We performed controlled micro-benchmarks on the three major components of an embedded computing device: the processor, the storage, and the communication sub-systems. Results show that energy consumption in all three follow simple models. Analysis of such measurements provide strong hints to the system designers about potential areas of optimization to make the device operations more power-aware.
Concomitant chronic lymphocytic leukemia, acute myeloid leukemia, and thrombosis with protein C deficiency. Case report and review of the literature

A patient is reported who presented simultaneously with two distinct forms of leukemia: chronic lymphocytic leukemia (CLL) and acute myeloid leukemia (AML). The diagnosis of CLL was supported by the presence of lymphocytosis, lymphadenopathy, and splenomegaly with mature B‐cell markers on the population of lymphoid cells in the bone marrow. AML was documented by the presence of circulating blast cells and 50% blasts with myeloid markers and Auer rods in the bone marrow. A complete remission from both forms of leukemia was obtained after treatment for the AML. The patient also experienced the temporal occurrence of venous thrombosis for the first time at the age of 69 years, shortly before the diagnosis of leukemia. Protein C deficiency was documented and may have been hereditary as suggested by the strong family history of thrombosis or alternatively may have been the consequence of one of the leukemias.
Cramer-Rao bounds for data-aided sampling clock offset and channel estimation

We derive the Cramer-Rao bound (CRB) on the joint estimates of the sampling clock offset and the channel impulse response when a training sequence is available. Simple closed form expressions are obtained for the CRB in the case where the observation window is large, and furthermore in the case where the channel degree is large. Our derivations are suited for single-carrier as well as for multi-carrier orthogonal frequency division multiplexing (OFDM) schemes. Data-aided maximum-likelihood (ML) estimates are also carried out.
Impact of an educational intervention on smoking counseling practice among Nigerian dentists and dental students.

INTRODUCTION Oral health professionals are important in smoking cessation and prevention as their role is very crucial given the impact of smoking on oral health. Therefore, dental professionals need adequate education in tobacco use prevention and cessation skills to increase their confidence and be able to help patients to quit smoking. This study was aimed at determining the impact of an educational intervention on the attitudes, willingness, and perceived barriers of a group of Nigerian dental students and dentists to smoking cessation counseling in the dental clinic. METHODS A self-administered questionnaire-based study was conducted in September 2007 at the Lagos University Teaching Hospital Idi Araba, Lagos. This was followed by a series of lectures and seminars using the brief intervention strategies for patients willing to quit using the Ask, Advise, Assess, Assist, and Arrange of cessation. A repeat study was conducted in January 2009 using the same questionnaire. Post intervention attitudes were significantly improved over pre intervention values for each parameter used in the assessment. RESULTS A significantly higher proportion of the respondents were interested in providing cessation services after the intervention (P = 0.00002). Most (83.1%) of the respondents were willing to undergo training with a slight increase in the post intervention group from 80.9% to 86%. All the reported barriers were significantly reduced after the intervention (P = 0.000). CONCLUSION This study has shown that educational interventions such as didactic instructions and practical training in tobacco use cessation can help to increase the willingness, confidence, and ability to provide information, during encounters with patients.
Prm1 Prevents Contact-Dependent Lysis of Yeast Mating Pairs

ABSTRACT Membrane fusion requires localized destabilization of two phospholipid bilayers, but unrestrained membrane destabilization could result in lysis. prm1 mutant yeast cells have a defect at the plasma membrane fusion stage of mating that typically results in the accumulation of prezygotes that have fingers of membrane-bound cytoplasm projecting from one cell of each pair into its mating partner in the direction of the osmotic gradient between the cells. However, some prm1 mating pairs fuse successfully whereas the two cells in other prm1 mating pairs simultaneously lyse. Lysis only occurs if both mating partners are prm1 mutants. Osmotic stabilization does not protect prm1 mating pairs from lysis, indicating that lysis is not caused by a cell wall defect. prm1 mating pairs without functional mitochondria still lyse, ruling out programmed cell death. No excess lysis was found after pheromone treatment of haploid prm1 cells, and lysis did not occur in mating pairs when prm1 was combined with the fus1 and fus2 mutations to block cell wall remodeling. Furthermore, short (<1 μm) cytoplasmic microfingers indicating the completion of cell wall remodeling appeared immediately before lysis. In combination, these results demonstrate that plasma membrane contact is a prerequisite for lysis. Cytoplasmic microfingers are unlikely to cause lysis since most prm1 mating pairs with microfingers do not lyse, and microfingers were also detected before fusion in some wild-type mating pairs. The lysis of prm1 mutant mating pairs suggests that the Prm1 protein stabilizes the membrane fusion event of yeast mating.
Rotation Blurring: Use of Artificial Blurring to Reduce Cybersickness in Virtual Reality First Person Shooters

Users of Virtual Reality (VR) systems often experience vection, the perception of self-motion in the absence of any physical movement. While vection helps to improve presence in VR, it often leads to a form of motion sickness called cybersickness. Cybersickness is a major deterrent to large scale adoption of VR. Prior work has discovered that changing vection (changing the perceived speed or moving direction) causes more severe cybersickness than steady vection (walking at a constant speed or in a constant direction). Based on this idea, we try to reduce the cybersickness caused by character movements in a First Person Shooter (FPS) game in VR. We propose Rotation Blurring (RB), uniformly blurring the screen during rotational movements to reduce cybersickness. We performed a user study to evaluate the impact of RB in reducing cybersickness. We found that the blurring technique led to an overall reduction in sickness levels of the participants and delayed its onset. Participants who experienced acute levels of cybersickness benefited significantly from this technique.
Blind source separation for groundwater pressure analysis based on nonnegative matrix factorization

The identification of the physical sources causing spatial and temporal fluctuations of aquifer water levels is a challenging, yet a very important hydrogeological task. The fluctuations can be caused by variations in natural and anthropogenic sources such as pumping, recharge, barometric pressures, etc. The source identification can be crucial for conceptualization of the hydrogeological conditions and characterization of aquifer properties. We propose a new computational framework for model‐free inverse analysis of pressure transients based on Nonnegative Matrix Factorization (NMF) method for Blind Source Separation (BSS) coupled with k‐means clustering algorithm, which we call NMFk. NMFk is capable of identifying a set of unique sources from a set of experimentally measured mixed signals, without any information about the sources, their transients, and the physical mechanisms and properties controlling the signal propagation through the subsurface flow medium. Our analysis only requires information about pressure transients at a number of observation points, m, where m≥r , and r is the number of unknown unique sources causing the observed fluctuations. We apply this new analysis on a data set from the Los Alamos National Laboratory site. We demonstrate that the sources identified by NMFk have real physical origins: barometric pressure and water‐supply pumping effects. We also estimate the barometric pressure efficiency of the monitoring wells. The possible applications of the NMFk algorithm are not limited to hydrogeology problems; NMFk can be applied to any problem where temporal system behavior is observed at multiple locations and an unknown number of physical sources are causing these fluctuations.
A Strong Constraint to the Joint Processing of Pairs of Cortical Signals

An important question in neuroscience is how the activity from spatially distributed cortical representations is integrated and processed together. In this study, we used a new approach to investigate the integration of distributed cortical activity. We used microstimulation to directly activate pairs of sites in primary visual cortex of rhesus monkeys. The sites were activated either singly or jointly, and the monkeys were trained to behaviorally report detection of the activation of either cortical site. We compared the detection performance with predictions from two different mathematical models of signal combination. Our data show that, at cortical separations <1 mm, signal integration is well described as a linear combination (d′ summation) of individual site activity. At larger separations, signal integration is better described as a maximum operation on the site signals. We compare our neurophysiological findings to existing psychophysical data and suggest the intriguing possibility that cortical activity originating at spatial separations greater than ∼1 mm is processed as if by parallel, independent circuits whose signals can be compared against each other but not summed. This in turn implies that there is a strong constraint to the kinds of computations the brain can perform with spatially distributed cortical activity.
Seed set variation in wild Clarkia populations: teasing apart the effects of seasonal resource depletion, pollen quality, and pollen quantity

Abstract In habitats where resource availability declines during the growing season, selection may favor early‐flowering individuals. Under such ephemerally favorable conditions, late‐blooming species (and individuals) may be particularly vulnerable to resource limitation of seed production. In California, a region prone to seasonal drought, members of the annual genus Clarkia are among the last to flower in the spring. We compared pollen limitation (PL) of seed set and outcrossing rates between early‐ and late‐flowering individuals in two mixed‐mating Clarkia taxa to detect whether flowering time is associated with changes in seed set due to resource depletion, PL, or increased selfing. In 2008–2010, we hand‐pollinated one flower on a total of 1855 individual plants either Early (near the onset of flowering) or Late (near the end of flowering) in the flowering season and compared seed set to adjacent, open‐pollinated flowers on the same stem. To assess the contribution of pollen quality to reproduction, we first (2008) used allozymes to estimate outcrossing rates of seeds produced by Early and Late open‐pollinated flowers. Second (2009), we conducted an anther‐removal experiment to estimate self‐pollen deposition. Seed set in Clarkia unguiculata was not pollen‐limited. Clarkia xantiana ssp. xantiana was pollen‐limited in 2008 and 2010, but not 2009. PL did not differ between Early and Late treatments. In both taxa, seed set of Early flowers was greater than Late flowers, but not due to PL in the latter. Reproduction was generally pollinator‐dependent. Most pollen deposition was xenogamous, and outcrossing rates were >0.7 – and similar between Early and Late periods. These results suggest that pollen receipt and pollen quality remain seasonally consistent. By contrast, the resources necessary to provision seeds decline, reducing the fitness benefits associated with resource allocation to ovules.
Stability and performance of networked control of quadrocopters formation flight

Stability conditions of the formation of linear SISO agents are described and applied to formation of 25 autonomous quadrocopters. The various information flow graphs are studied from the viewpoints of the formation stability and achievement of the consensus. A way for improving the system performance is proposed and demonstrated by the frequency response analysis and simulation.
The architecture of apophasis: exploring options for a cognitive scientific interpretation of the via negativa

This article charts possibilities for discerning cognitive mechanisms that mediate apophatic cognition (and its purportedly self-transforming effects) in negative streams of Christian thought and practice. First, it tests the extent to which (1) Schjoedt’s et al. “cognitive depletion” model (Schjoedt et al., 2013) and (2) McNamara’s “decentering” model (McNamara, 2009) can explain, biologically and psychologically, why epistemic and existential loss is often said to precede and attend illumination in the via negativa – or negative way. While McNamara’s theory proves more convincing than Schjoedt’s et al. for shedding light on cognitive underpinnings of the negative way, neither theory is fully satisfactory because neither adequately accounts for the constitutive role of social and emotional dynamics at each step in the Christian apophatic journey. The final section introduces a cognitively informed account of the apophatic path consisting of four moments: Resonance, Rupture, Reappraisal, and Repair. This account is supported largely by a turn to neurocognitive, developmental, and clinical psychological research on relationality and emotion regulation.
School Identity in the Context of Alberta Charter Schools

ABSTRACT The central tenet of this investigation is that educational institutions possess their own school identity. Acknowledging that school identity is influenced by institutional mechanisms and personal dynamics, we examine school identity in the context of 13 Alberta charter schools. Narratives of 73 educational stakeholders across the network of Alberta charter schools reveal a heightening of trust and authenticity as related to school identity. We propose that lessons learned from this study can inform stakeholders within other school settings. In particular, that an explicitly articulated vision of school identity may challenge the entrenched norms and practices typical of large bureaucratic organizations.
Identification Of Prospective Science Teachers Mathematical-Logical Structures In Reference To Magnetism

This paper is a qualitative case study designed to identify prospective science teachers mathematical-logical structures on the basis of their knowledge and achievement levels in magnetism. The study also made an attempt to reveal the effects of knowledge-level variables and procedural variables, which were considered to be potential factors, on the teachers knowledge and achievement levels. The participants knowledge level was represented by the APS score (knowledge-level variable), whereas their achievement level was expressed by the ASS score (achievement level). The prospective teachers knowledge and achievement levels in mathematical logic were 0.204 and 0.305, respectively. The knowledge-level variables were given-asked, formula, and operation. On the other hand, the procedural variables consisted of formula knowledge, basic math knowledge, and scientific knowledge. The latter group of variables had the following values, respectively: 0.336, 0.758, and 0.199. The findings indicated that basic math knowledge led the participants to have an achievement level higher than their knowledge level. The other variables had values similar to those of the knowledge and achievement levels.
Disentangling prenatal and inherited influences in humans with an experimental design

Exposure to adversity in utero at a sensitive period of development can bring about physiological, structural, and metabolic changes in the fetus that affect later development and behavior. However, the link between prenatal environment and offspring outcomes could also arise and confound because of the relation between maternal and offspring genomes. As human studies cannot randomly assign offspring to prenatal conditions, it is difficult to test whether in utero events have true causal effects on offspring outcomes. We used an unusual approach to overcome this difficulty whereby pregnant mothers are either biologically unrelated or related to their child as a result of in vitro fertilization (IVF). In this sample, prenatal smoking reduces offspring birth weight in both unrelated and related offspring, consistent with effects arising through prenatal mechanisms independent of the relation between the maternal and offspring genomes. In contrast, the association between prenatal smoking and offspring antisocial behavior depended on inherited factors because association was only present in related mothers and offspring. The results demonstrate that this unusual prenatal cross-fostering design is feasible and informative for disentangling inherited and prenatal effects on human health and behavior. Disentangling these different effects is invaluable for pinpointing markers of prenatal adversity that have a causal effect on offspring outcomes. The origins of behavior and many common complex disorders may begin in early life, therefore this experimental design could pave the way for identifying prenatal factors that affect behavior in future generations.
Toddlers’ Use of Grammatical and Social Cues to Learn Novel Words

ABSTRACT By their second birthday, children have begun using grammatical cues to decipher the meaning of newly encountered words. By 3 years of age, there is evidence that children are more reliant on grammatical than social cues to decipher verb meaning (Nappa, Wessel, McEldoon, Gleitman, & Trueswell, 2009). Here, we investigate children’s reliance on grammatical and social information to infer the meaning of a novel noun. First we investigate the emergence of children’s use of grammatical number markings to infer noun meaning. Then we explore how children integrate this cue with other (social) cues to word meaning. In Experiment 1, we demonstrate that children begin using grammatical number markings to resolve referential ambiguity by 24 months of age. In Experiment 2, we pit the grammatical number cue against a well-established social cue and find that 2-year-olds’ reliance on grammatical number markings is already strong enough to compete with social eye gaze cues.