cssi/SciSciGPT-SciSciNet huggingface dataset:
Intrinsic toxicity of the cellular prion protein is regulated by its conserved central region.

The conserved central region (CR) of PrPC has been hypothesized to serve as a passive linker connecting the protein's toxic N-terminal and globular C-terminal domains. Yet, deletion of the CR causes neonatal fatality in mice, implying the CR possesses a protective function. The CR encompasses the regulatory α-cleavage locus, and additionally facilitates a regulatory metal ion-promoted interaction between the PrPC N- and C-terminal domains. To elucidate the role of the CR and determine why CR deletion generates toxicity, we designed PrPC constructs wherein either the cis-interaction or α-cleavage are selectively prevented. These constructs were interrogated using nuclear magnetic resonance, electrophysiology, and cell viability assays. Our results demonstrate the CR is not a passive linker and the native sequence is crucial for its protective role over the toxic N-terminus, irrespective of α-cleavage or the cis-interaction. Additionally, we find that the CR facilitates homodimerization of PrPC , attenuating the toxicity of the N-terminus.
Resilient Password Manager Using Physical Unclonable Functions

The offline dictionary attacks on the database of passwords (PW) or even hashed PW are damaging as a single server break-in leads to many compromised PWs. In this regard, using Physical Unclonable Functions (PUFs) to increase the security of PW manager systems has been recently proposed. Using PUFs allows replacing the hashed PW with PUF responses, which provide an additional hardware layer of security. In this way, even with accessing the database, an adversary should have physical control of the PUF to find the PWs. However, such a scheme cannot operate without a backup in case of catastrophic failure of the PUFs. The likelihood of a failure is low unless the opponent finds a way to destroy the PUF. The scheme used in this article includes a mechanism to make the system works consistently if the PUF fails, with redundant elements. In this method, two PUF outputs are saved in the database to register a user. In authentication, the first PUF output in the database is just checked. The second PUF output in the database is only checked in the exceptional cases when the first PUF does not work correctly; therefore, both false reject rates and latencies are not degraded. A PW manager node is implemented using a low-cost microcontroller, SRAM PUF, and nonvolatile SRAM. The nonvolatile SRAM is embedded in the PWM node circuit as a local database. Statistical tests on the applied commercial SRAM in this article show better PUF quality than those used in previous research. Also, to handle the error in PUF responses, only the stable SRAM cells are used. This article presents the first prototype of a resilient PW manager node with an embedded local database to the best of our knowledge.
Comparative Performance Evaluation of mmWave 5G NR and LTE in a Campus Scenario

The extremely high data rates provided by communications in the millimeter-length (mmWave) frequency bands can help address the unprecedented demands of next-generation wireless communications. However, atmospheric attenuation and high propagation loss severely limit the coverage of mmWave networks. To overcome these challenges, multi-input-multi-output (MIMO) provides beamforming capabilities and high-gain steerable antennas to expand communication coverage at mmWave frequencies. The main contribution of this paper is the performance evaluation of mmWave communications on top of the recently released NR standard for 5G cellular networks. Furthermore, we compare the performance of NR with the 4G long-term evolution (LTE) standard on a highly realistic campus environment. We consider physical layer constraints such as transmit power, ambient noise, receiver noise figure, and practical antenna gain in both cases, and examine bitrate and area coverage as the criteria to benchmark the performance. We also show the impact of MIMO technology to improve the performance of the 5G NR cellular network. Our evaluation demonstrates that 5G NR provides on average 6.7 times bitrate improvement without remarkable coverage degradation.
Clinical value of weight-bearing CT and radiographs for detecting patellofemoral cartilage visualized by MRI in the MOST study.

Summary Objective The patellofemoral joint is frequently affected by osteoarthritis (PFOA) and is incompletely imaged on radiographs (XR). Weight-Bearing CT (WBCT) could offer advantages for visualization. This study determined the sensitivity, specificity, and accuracy of axial WBCT and lateral XR for detection of PFOA features in comparison with cartilage damage on MRI. Design A convenience sample of 60 right knees from the MOST cohort were analyzed. WBCT and XR were read for OARSI JSN score and MRI for MOAKS cartilage score by two experienced musculoskeletal radiologists blinded to participant. Using MOAKS scoring on MRI (referent standard), the sensitivity, specificity and accuracy of patellofemoral OARSI JSN scores based on WBCT and XR were compared. Results The mean ± SD age and BMI for the participants included (66.7% women) were 67.6 ± 9.8 years and 30.0 ± 5.3 kg/m2 respectively. WBCT demonstrated significantly greater sensitivity (0.85–0.97 on WBCT vs 0.47–0.57 on XR) and accuracy (0.85–0.92 on WBCT vs 0.48–0.57 on XR) for all parameters except lateral full-thickness cartilage loss (McNemar's test p-values all Conclusion WBCT demonstrates significantly greater sensitivity and accuracy than radiographs for identification of PFOA. Given the same Relative Radiation Level as XR and improved visualization, WBCT holds promise to improve understanding of the weight-bearing patellofemoral joint.
Powerful Learning Strategies For Student Success

Location: JC Room E According to CAART website, only 87.5% of freshmen return for their sophomore year. While this retention rate is better than the 81% average rate of 4-year degree granting institutions (NCES, 2018), George Mason University could be doing a better job at supporting students. In addition, over 2500 undergraduate students who responded to the Fall 2018 Patriot Success survey indicated that they wanted more information on better study habits. This session will present an overview of learning strategies that any staff or faculty member may share with students to support their learning. While this is the mission of Learning Services, the more people on campus who know about these strategies, the more students we can support and ultimately retain until degree completion. We will present information on a distributed learning model called the Study Cycle which provides students with a better understanding of the out-of-class learning activities in which professors expect students to be engaged. Next, we will engage participants in a discussion of the importance of self-testing (Brown, 2014) and present three study strategies designed to help students practice self-testing to improve memory retention. In addition, we will discuss how to incorporate discipline-specific learning strategy instruction into courses.
Priming with Cold-Adapted Influenza A Does Not Prevent Infection but Elicits Long-Lived Protection against Supralethal Challenge with Heterosubtypic Virus

We show in this study several novel features of T cell-based heterosubtypic immunity against the influenza A virus in mice. First, T cell-mediated heterosubtypic protection against lethal challenge can be generated by a very low priming dose. Second, it becomes effective within 5-6 days. Third, it provides protection against a very high dose challenge for >70 days. Also novel is the finding that strong, long-lasting, heterosubtypic protection can be elicited by priming with attenuated cold-adapted strains. We demonstrate that priming does not prevent infection of the lungs following challenge, but leads to earlier clearance of the virus and 100% survival after otherwise lethal challenge. Protection is dependent on CD8 T cells, and we show that CD4 and CD8 T cells reactive to conserved epitopes of the core proteins of the challenge virus are present after priming. Our results suggest that intranasal vaccination with cold-adapted, attenuated live virus has the potential to provide effective emergency protection against emerging influenza strains for several months.
Structure of the semiquinone form of flavodoxin from Clostridum MP. Extension of 1.8 A resolution and some comparisons with the oxidized state.

As part of a series of comparisons of the structures of the three oxidation states of flavodoxin from Clostridium MP, phases for the semiquinonc form were determined to 2.0 A resolution by isomorphous replacement ( = 0.725). Subsequently, the structure was refined at 1.8 A resolution by a combination of difference Fourier, real space and reciprocal space methods. After refining to an R of 0.194, we explored the conformation of the FMN binding site by real space refinement verau6 maps with Fourier coefficients of the form (2) F,I - 1 P,I ) exp (in,). To minimize bias in the fitting, groups of atoms were systematically omitted from the structure factors used in computat.ion of the (212”,1 - IF,\) maps. One-electron reduction of oxidized flavodoxin is accompanied by several changes at the FMN binding site: the conformation of residues in the reverse bend formed by Met56-Gly57-Asp58-Glu59 differs in the crystal structures of the oxidized and semiquinone species; further, backbone atoms in residues 55 and 89 shift by more than 0.5 A and the indole ring of Trp90 undergoes a significant displacement. The orientation of the peptide unit connecting Gly57 and Asp58 is consistent with the presence of a hydrogen bond between the carbonyl oxygen of Gly57 and the flavin N(5) in flavodoxin semiquinone. No equivalent bond is found in oxidized flavodoxin. In both the oxidized and semiquinone species of clostridial flavodoxin, the isoalloxazine ring is essentially planar : the bending angles about N(5)-N( 10) are -2.5” for the semiquinone structure and ~0’ in oxidized flavodoxin. The intensity changes resulting from t,he oxidized- ,semiquinone conversion (K, m= 0.33) arise in part from changes in molecular packing. Intermolecular contacts, including neighbors of the prosthetic group, are altered in the repacking. Maps or models of the two oxidation states can be brought into approximate coincidence by
Library user instruction in the curriculum : background and status update

Teaching patrons to use library resources unaided has long been recognized as highly desirable, yet the education of reference librarians to do this important instruction has been scattered and haphazard. Slow to develop and emerge as a separate course in library school curricula, this article reports that the situation has now changed, due primarily to the organized efforts and perseverance of practitioners and library and information science educators.
Filter banks and wavelets in signal processing: a critical review

This paper provides an overview of subband and wavelet theories. It emphasizes their strong relations. The practical merits of these decomposition techniques in signal processing are examined. The current status of this active research field is summarized and it concludes with the discussion of potential extensions for future study.
Mathematical Modeling of Facilitated Liquid Membrane Transport Systems Containing lonically Charged Species

Abstract A numerical model is presented which solves the transient nonlinear system of partial differential equations governing the facilitated transport of ionically charged species through a liquid membrane. The mathematical model is derived in dimensionless form and solved numerically. Facilitation factors and electrical potentials across the membrane are computed and compared to experimental results. This model is useful in predicting transient concentration, flux, and electrical potential gradients provided that the values of the required physical constants are known. It was noticed that transient facilitation factors are not affected by the transient electrical potential buildup, which indicates that both the pure diffusion and the faciltated transport of permeate are affected equally by the electrical effects of the ionically charged species.
Motor-vehicle safety in Europe and the USA: A public-health perspective

This article provides a public-health perspective on the motor-vehicle safety situation in Europe and in the United States. It will be argued that a prerequisite for such a perspective is the use of fatality rate per capita, instead of the usually employed rate per distance traveled. To illustrate the public-health perspective, two sets of analyses were performed. The first set of analyses compared motor-vehicle fatality rates to fatality rates from other causes of death. The second set contrasted the motor-vehicle fatality rates per population in different countries, providing information about traffic safety relative to other countries.
Experimental evaluation of moving sound diffusers for reverberant rooms

Abstract The acoustic power flowing from a monopole source is proportional to the radiation resistance presented to the source. This value is determined by the modal structure and the acoustic impedance of the walls of the chamber. The rotating sound diffuser modulates the modal structure and, with it, the radiation resistance. Comparison of the time average of the radiation resistance as the monopole source location is changed with and without the diffuser rotating indicates the effectiveness of a given diffuser design in removing the dependence of acoustic power output on the source position. The rotating sound diffuser evaluated was a symmetrical biconical surface of revolution rotating at speeds up to 30 rev/min. Fifty percent of the surface area of the diffuser was covered with ribbed glass fiber, the remainder was left uncovered. In order to measure the radiation resistance, an acoustic impedance head was fabricated from a modified loudspeaker. Displacement of the diaphragm was sensed using a non-contacting fiber-optic sensor. The resulting pressure generated in front of the diaphragm was measured by a condenser microphone. Instrumentation normally used for the measurement of complex mechanical impedance was adapted to record the real part of the radiation impedance.
Methane Oxycombustion for Low CO2 Cycles: Blowoff Measurements and Analysis

Increasing concerns about climate change have encouraged interest in zero-CO 2 emission hydrocarbon combustion techniques. In one approach, nitrogen is removed from the combustion air and replaced with another diluent, typically carbon dioxide or steam. In this way, formation of nitrogen oxides is prevented and the exhaust stream can be separated into concentrated CO 2 and water by a simple condensation process. The concentrated CO 2 stream can then be sequestered or used for enhanced oil recovery. Burning fuels in an O 2 /CO 2 diluent raises new combustion opportunities and challenges for both emissions and operability: this study focuses on the latter aspect. CH 4 /O 2 /CO 2 flames have slower chemical kinetics than methane-air flames and as such, flame stability is more problematic as they are easier to blow off. This issue was investigated experimentally by characterizing the stability boundaries of a swirl stabilized combustor. Near stoichiometric CO 2 and N 2 diluted methane/oxygen flames were considered and compared with lean methane/air flames. Numerical modeling of chemical kinetics was also performed to analyze the dependence of laminar flame speeds and extinction strain rates upon dilution by different species and to develop correlations for blowoff boundaries. Finally, blowoff trends at high pressure were extrapolated from atmospheric pressure data to simulate conditions closer to those of gas turbines.
Probabilistic structural analysis of adaptive/smart/intelligent space structures

A three-bay, space, cantilever truss is probabilistically evaluated for adaptive/smart/intelligent behavior. For each behavior, the scatter (ranges) in buckling loads, vibration frequencies, and member axial forces are probabilistically determined. Sensitivities associated with uncertainties in the structure, material and load variables that describe the truss are determined for different probabilities. The relative magnitude for these sensitivities are used to identify significant truss variables that control/classify its behavior to respond as an adaptive/smart/intelligent structure. Results show that the probabilistic buckling loads and vibration frequencies increase for each truss classification, with a substantial increase for intelligent trusses. Similarly, the probabilistic member axial forces reduce for adaptive and intelligent trusses and increase for smart trusses.
Investigation into the dynamics of physical properties of an epoxy resin during solidification

Results of experimental investigation into solidification of structures based on ED-20 epoxy resin with different contents of the polyethylene polyamine solidifier are presented. Continuous measurements using a specially developed automated system are presented. The data on changes of mechanical, acoustic, and electrical properties of epoxy amine compound during solidification are given.
Pattern goodness and redundancy revisited: Multidimensional scaling and hierarchical clustering analyses

Twenty subjects made all possible (136) pairwise-comparison judgments of pattern goodness between 17 five-dot patterns. Using multidimensional scaling and hierarchical clustering analyses, a two-dimensional representation was judged the most appropriate for the derived pattern space. The interpreted structure of the spatial-hierarchical configuration strongly supported previous findings that pattern redundancy is the most salient dimension underlying pattern goodness judgments and that patterns can be partitioned on this dimension according to the size of their equivalence sets, i.e., the number of patterns resulting from rigid rotations in 90-deg increments or reflection. A psychological mechanism that accounts for the effect of pattern redundancy on judged goodness was proposed.
“Place‐Framing” as Place‐Making: Constituting a Neighborhood for Organizing and Activism

Abstract This article uses social-movement theory to analyze how neighborhood organizations portray activism as grounded in a particular place and scale. I apply the concept of collective-action frames to a case study of four organizations in a single neighborhood in St. Paul, Minnesota. Using organizational documents such as annual reports, comprehensive plans, and flyers, I present a discourse analysis of the ways that organizations describe their goals and agenda. In particular, I assess the extent to which the organizations characterize the neighborhood in their justifications of organizational goals and actions. In order to legitimate their own agendas and empower community activism, neighborhood organizations foster a neighborhood identity that obscures social differences, such as ethnicity and class, among residents. They do so by describing the physical condition of the neighborhood and the daily life experiences of its residents. These “place-frames” constitute a motivating discourse for organiza...
Unified Mechanistic Approach for Modeling Tests of Unbound Pavement Materials

AbstractSeveral tests are used for the characterization of unbound materials for pavement applications. The resilient modulus has been one of the most common tests for design specification of unbound materials. The California bearing ratio (CBR) is another laboratory test that is frequently used. The dynamic cone penetrometer (DCP) test is a more common test for in situ quality assessment/quality control of unbound materials. For better connection between design and quality assurance (QA)/quality control (QC), it would be helpful to have a reliable, mechanistic method for correlating test results. This is particularly true for the use of new materials, for which there is not an extensive body of data to empirically draw such connections. This paper presents a framework for a unified approach for modeling these tests. A discrete-element method (DEM) is used to simulate the CBR test, the DCP test, and the resilient modulus test. An initial evaluation demonstrated that the simulations can account for the eff...
Comparison of stormflow responses of surface-mined and forested watersheds in the Appalachian Mountains, USA

The results of a hydrological analysis that was conducted as part of a larger, multifaceted, collaborative effort to quantify ecosystem functions in watersheds subjected to land-use and land-cover change are presented. The primary goal of the study was to determine whether a small watershed in the Appalachian region (USA) that was recently subjected to surface mining and reclamation practices produces stormflow responses to rain events that are different from those produced by a nearby reference watershed covered by young, second-growth forest. Water balances indicated that runoff yields did not vary significantly between the two watersheds on an annual basis. Statistically significant differences (p⩽0·05) in runoff responses were observed on an event basis, however, with the mined/reclaimed watershed producing, on average (a) higher storm runoff coefficients (2·5×), (b) greater total storm runoff (3×), and (c) higher peak hourly runoff rates (2×) when compared with the reference watershed. Results of a unit hydrograph analysis also showed, unexpectedly, that the modelled unit responses of the two watersheds to effective rainfall pulses were similar, despite the noted differences in land cover. Differences in stormflow responses were thus largely explained by dramatic reductions in cumulative rates of rainfall abstraction (measured using infiltrometers) attributable to soil compaction during land reclamation. Additional field hydrological measurements on other mined watersheds will be needed to generalize our results, as well as to understand and predict the cumulative hydrological impacts of widespread surface mining in larger watersheds and river basins. Copyright © 2006 John Wiley & Sons, Ltd.
UTE MRI of the Osteochondral Junction

The osteochondral junction is composed of numerous tissue components and serves important functions relating to structural stability and proper nutrition in joints such as the knee and spine. Conventional MR techniques have been inadequate at imaging the tissues of the osteochondral junction primarily because of the intrinsically short T2 nature of these tissues, rendering them “invisible” with the standard acquisitions. Ultrashort time to echo (UTE) MR techniques acquire sufficient MR signal of osteochondral tissues, thereby allowing direct evaluation. This article reviews the anatomy of the osteochondral junction of the knee and the spine, technical aspects of UTE MRI, and the application of UTE MRI for evaluation of the osteochondral junction.
Role of polymer morphology in the oxidation of polypropylene

The γ-initiated oxidation and presensitized photooxidation of polypropylene films and fibers are shown to be insensitive to sample thickness (if <150 μm) and a range of morphological parameters such as molecular orientation (in drawn samples) and fibrillar and void content. The relevance of these observations is discussed in the light of the many previous assertions as to the influence of morphological effects on oxidation rates. The γ-initiated oxidation was studied in preference to conventional thermal or photoinitiated oxidation because of the greater control over the rate of radical production available by this method.
Pin site cover: a simpleton’s approach

Pin site complications after orthopaedic procedures include skin indentation and wire migration.1 A simple technique can be incorporated into daily practice to offset the above. After the wire is fixed and the wire tip is bent, a Primapore® dressing (Smith & Nephew, Hull, UK) is cut in the middle and secured around the pin to prevent skin indentation. To further augment this, a second Primapore® is crimped and adhered over the tip to prevent the wire getting caught in the padding and migrating. This method is cheap, readily available and easy to apply. We have avoided the above complications in a series of 57 cases. Figure 1 Primapore® dressing secured around pin Figure 2 Second Primapore® dressing adhered over tip
Simulation of cardiac work transitions, in vitro: effects of simultaneous Ca2+and ATPase additions on isolated porcine heart mitochondria

During increases in cardiac work there are net increases in cytosolic [Ca(2+)] and ATP hydrolysis by myofiliments and ion transport ATPases. However, it is still unclear what role Ca(2+)or the ATP hydrolysis products, ADP and Pi, have on the regulation of mitochondrial ATP production. In this study, work jumps were simulated by simultaneous additions of Ca(2+) and ATPase to porcine heart mitochondria. The net effects on the mitochondrial ATP production were monitored by simultaneously monitoring respiration (mVo2), [NADH], [ADP] and membrane potential (deltapsi) at 37 degrees C. Addition of exogenous ATPase (300 mlU.ml(-1))]ATP (3.4 mM) was used to generate a 'resting' background production of ADP. This resting metabolic rate was 200% higher than the quiescent rate while [NADH] and deltapsi were reduced. Subsequent ATPase additions (1.3IU.ml(-)) were made with varying amounts of Ca(2+)(0 to 535 nM) to simulate step increases in cardiac work. Ca(2+) additions increased mVo2 and depolarized deltapsi, and were consistent with an activation of Fo/F1)ATPase. In contrast, Ca(2+) reduced the [NADH] response to the ATPase addition, consistent with Ca(2+)-sensitive dehydrogenase activity (CaDH). The calculated free ADP response to ATPase decreased \2-fold in the presence of Ca(2+). The addition of 172nM free Ca(2+)] ATPase increased mVo2 by 300% (P or =0.05, n=8), consistent with working heart preparations. The addition of Ca(2+) and ATPase combined increased the mitochondrial ATP production rate with changes in deltapsi, NADH and [ADP], consistent with an activation of CaDH and F o /F(1)ATPase activity. These balancing effects of ATPase activity and [Ca(2+)] may explain several aspects of metabolic regulation in the heart during work transitions in vivo.
99mTc-N-NOET Myocardial Uptake Reflects Myocardial Blood Flow and Not Viability in Dogs With Reperfused Acute Myocardial Infarction

Background—N-Ethoxy-N-ethyl-dithiocarbamato-nitrido-99mTc (99mTc-N-NOET) is a new neutral lipophilic 99mTc-labeled myocardial perfusion agent with a high first-pass extraction fraction and delayed redistribution kinetics after transient ischemia comparable to what is observed with 201Tl. It is unknown whether the uptake of this tracer reflects myocardial viability or just reperfusion flow in the setting of a reperfused myocardial infarction. Methods and Results—In 13 anesthetized open-chest dogs, the left anterior descending coronary artery was occluded for 180 minutes, followed by 180 minutes of reperfusion. 201Tl and 99mTc-N-NOET were injected after either 60 (group 1, n=9) or 175 (group 2, n=4) minutes of reperfusion. Myocardial blood flow was measured by radioactive microspheres, and 201Tl and 99mTc-N-NOET tissue activities were determined by gamma-well counting. Normalized myocardial blood flow in the central infarct zone fell from 0.80±0.03 (SEM) and 0.89±0.01 at baseline to 0.18±0.04 and 0.13±0.02 ...
AAOS Annual Meeting Roundup

The Annual Meeting of the American Academy of Orthopaedic Surgeons (AAOS) continues to be one of the largest meetings focused on the practice and science of orthopaedic and trauma surgery. It is characterised by a robust international attendance, with an academic program delivered by true leaders and innovators in the field. This year, the AAOS Annual Meeting was held from March 11 to 15 in New Orleans, Louisiana. The educational program offered a combination of a large collection of instructional course lectures, symposia, and scientific exhibits representing a wide range of orthopaedic subspecialties. This year, the Central Program Committee received a record number of original scientific abstracts and from a field of 5,646 abstracts submitted, a total of 825 abstracts were selected for podium presentations, and 569 abstracts were selected for poster presentations. Each subspecialty committee determined the best papers and posters presented in their respective subspecialty sections. These papers and posters were presented in a symposium moderated by Steven Frick, MD a-nd William Mihalko, MD, entitled “Best of the AAOS.” This session really represents a cross section of the finest orthopaedic research from the past year and each of these representative papers and posters deserves discussion. Five papers were selected from the program in adult hip reconstruction covering topics as varied as quality improvement programmes to bearing surfaces. An innovative use of the database of the American College of Surgeons National Surgical Quality Improvement Program (NSQIP) was used by Meddenick et al to identify risk factors for readmission following primary total hip replacement (THR).1 During the study period 9441 THR procedures were performed, and 345 unplanned re-admissions occurred giving an overall readmission rate of 3.65%. A number of independent predictive risk factors for re-admission were identified, including: low serum albumin, chronic steroid use, increased number of medical comorbidities, …
Perceptual categories for spatial layout

The central problems of vision are often divided into object identification and localization. Object identification, at least at fine levels of discrimination, may require the application of top-down knowledge to resolve ambiguous image information. Utilizing top-down knowledge, however, may require the initial rapid access of abstract object categories based on low-level image cues. Does object localization require a different set of operating principles than object identification or is category determination also part of the perception of depth and spatial layout? Three-dimensional graphics movies of objects and their cast shadows are used to argue that identifying perceptual categories is important for determining the relative depths of objects. Processes that can identify the causal class (e.g. the kind of material) that generates the image data can provide information to determine the spatial relationships between surfaces. Changes in the blurriness of an edge may be characteristically associated with shadows caused by relative motion between two surfaces. The early identification of abstract events such as moving object/shadow pairs may also be important for depth from shadows. Knowledge of how correlated motion in the image relates to an object and its shadow may provide a reliable cue to access such event categories.
Phylogenetic Inferences from Molecular Sequences: Review and Critique

Conflicting results often accompany phylogenetic analyses of RNA, DNA, or protein sequences across diverse species. Causes contributing to these conflicts relate to ambiguities in identifying homologous characters of alignments, sensitivity of tree-making methods to unequal evolutionary rates, biases in species sampling, unrecognized paralogy, functional differentiation, loss of phylogenetic informational content due to long branches or fast evolution, and difficulties with the assumptions and approximations used to infer phylogenetic relationships. Attempts to surmount these conflicts by averaging over many proteins are problematic due to inherent biases of selected families, lack of signal in others, and events of lateral transfer, fusion, and/or chimerism. The process of assessing reliability of the results using the bootstrap method is strewn with obstacles because of lack of independence and inhomogeneity in the molecular data. Problems inherent to the three major procedures for developing phylogenetic trees--parsimony, likelihood, distance--are reviewed. Special attention is given to the problem of inferring evolutionary distances from patterns of similarity among sequences. The difficulties encountered by methods of phylogenetic reconstructions based on the analysis of divergent sequence families make new methods based on the analysis of complete genomes reasonable alternatives. Several of these are considered, including the signature sequences of Gupta and associates, the study of genome profiles, and the genomic signature set forth by Karlin and colleagues.
Paleobiological implications of shell repair in recent marine gastropods from the northern Gulf of California

Shell repair frequencies in eleven species of Recent gastropods from the northern Gulf of California vary with habitat, shell morphology and intensity of durophagous predation. Squat shells with la...
A pathway for the reduction of cytochrome b-559 by photosystem II in chloroplasts.

Abstract Cytochrome b-559, which is normally reduced in the dark, was oxidized by preillumination in the presence of N-methyl-phenazonium methosulfate with low intensity far-red light. The average half-time for the photoreduction of oxidized cytochrome b-559 by a long actinic flash ranged from 90 to 110 ms. In the presence of 0.25 μM 3-(3,4-dichlorophenyl)-1,1-dimethylurea the half-time for the photoreduction increased to 230 ms although the extent of the absorbance increase was unchanged. Under similar conditions inhibition of electron transport by 3-(3,4-dichlorophenyl)-1,1-dimethylurea and the increase in the chlorophyll fluorescence show that a large fraction of the Photosystem II reaction centers are blocked. These results are consistent with the concept that electrons are shared between different photosynthetic units by a common pool of plastoquinone and imply that the principle pathway for the reduction of cytochrome b-559 by Photosystem II occurs through plastoquinone. In the presence of the uncoupler gramicidin which stimulates non-cyclic electron transport, the rate of photoreduction of cytochrome b-559 is slower ( t 1 2 = 180 ms ), from which it is inferred that cytochrome b-559 competes with cytochrome f for electrons out of this pool. Comparison of cytochrome b-559 photoreduction and electron transport rates using untreated and KCN-treated chloroplasts indicate that, under conditions of basal electron transport from water to ferricyanide, approximately one-fifth of the electrons from Photosystem II go through cytochrome b-559 to ferricyanide. Further support for this pathway is provided by a comparison of the effect of 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (dibromothymoquinone) on the rates of reduction of cytochrome b-559 and ferricyanide.
Simultaneous determination of 5-hydroxytryptamine, its amino acid precursors and acid metabolite in discrete brain regions by high-performance liquid chromatography with fluorescence detection.

Abstract l -Tryptophan, 5-hydroxytryptophan (5-HTP), 5-hydroxytryptamine, and 5-hydroxyindoleacetic acid (5-HIAA) from discrete regions of brain can be resolved by isocratic elution on a C-18 reversed-phase column and quantitated by native fluorescence measurement. This method is rapid and simple and can reproduceably detect 5-hydroxytryptamine, tryptophan and 5-HIAA with picogram sensitivity. The detection of 5-HTP in brain extracts from untreated animals is difficult because of the extremely low endogenous levels of 5-HTP. Quantitation of 5-HTP presents no problem in animals injected with 5-HTP or with an inhibitor of l -aromatic amino acid decarboxylase. Brain tissue requires minimal treatment for assay and the hydroxyindoles are stable enough to allow automated processing.
The haustoria of Termitaria snyderi

Abstract Haustorial mother cells of Termitaria snyderi are larger, thicker walled, more rounded, and deeper brown than surrounding cells of the basal layer of the thallus. Haustoria penetrate the cuticle and form lobed structures underneath. Parasite and host are separated by the host plasma membrane. The lobed, uninucleate protoplast of the haustorium is surrounded by a wall which is continuous around the haustorial neck and which extends through the cuticle to the haustorial mother cell. Haustoria contain mitochondria, rough and smooth endoplasmic reticulum, microbodies, lysosomes, microtubules, and multivesicular bodies. Unique minimicrotubules only 80–100A in diameter and having only six subunits in cross section are present between cisternae of the stacked smooth endoplasmic reticulum.
In Vitro Killing of Nosocomial Pathogens by Acid and Acidified Nitrite

Exposure to pH 1 or 2 buffers or acidic gastric contents resulted in the killing of vancomycin-resistant Enterococcus sp., Klebsiella pneumoniae, Staphylococcus aureus, and Candida glabrata but not Clostridium difficile spores. Nitrite enhanced killing under acidic conditions, but significant killing of C. difficile spores required nitrite concentrations above usual physiological levels.
Continuous Monitoring of Intraocular Pressure: An Overview of New Techniques

Elevated intraocular pressure (IOP) is the main risk factor for glaucoma and is currently the only treatable risk factor. IOP is dynamic with regular circadian variations and random short-term and long-term fluctuations. Current glaucoma management is mostly based on single IOP measurements during office visits which may not accurately represent a patient’s 24-h pressure profile. Most of glaucoma patients have their highest IOP outside clinic hours, usually during the nocturnal period. Currently, the only available approach for 24-h IOP monitoring is by using repeated tonometry which is inconvenient, expensive, and does not provide continuous monitoring of IOP. The goal of continuous IOP monitoring is to provide automated 24-h ambulatory recording of IOP. In this article, we review the existing technologies for IOP monitoring and evaluate new innovative methods for continuous 24-h IOP monitoring, including temporary non-invasive and permanent invasive approaches that currently being developed.
Probabilistic Fatigue: Computational Simulation

Fatigue is a primary consideration in the design of aerospace structures for long term durability and reliability. There are several types of fatigue that must be considered in the design. These include low cycle, high cycle, combined for different cyclic loading conditions - for example, mechanical, thermal, erosion, etc. The traditional approach to evaluate fatigue has been to conduct many tests in the various service-environment conditions that the component will be subjected to in a specific design. This approach is reasonable and robust for that specific design. However, it is time consuming, costly and needs to be repeated for designs in different operating conditions in general. Recent research has demonstrated that fatigue of structural components/structures can be evaluated by computational simulation based on a novel paradigm. Main features in this novel paradigm are progressive telescoping scale mechanics, progressive scale substructuring and progressive structural fracture, encompassed with probabilistic simulation. These generic features of this approach are to probabilistically telescope scale local material point damage all the way up to the structural component and to probabilistically scale decompose structural loads and boundary conditions all the way down to material point. Additional features include a multifactor interaction model that probabilistically describes material properties evolution, any changes due to various cyclic load and other mutually interacting effects. The objective of the proposed paper is to describe this novel paradigm of computational simulation and present typical fatigue results for structural components. Additionally, advantages, versatility and inclusiveness of computational simulation versus testing are discussed. Guidelines for complementing simulated results with strategic testing are outlined. Typical results are shown for computational simulation of fatigue in metallic composite structures to demonstrate the versatility of this novel paradigm in predicting a priori fatigue life.
Acetylcholine produces stimulus-specific receptive field alterations in cat auditory cortex.

Abstract Frequency receptive fields (RFs) were determined before and after pairing iontophorectic administration of acetylcholine (ACh) with a repeated single-frequency stimulus in the auditory cortex of barbiturate-anesthesized cats. In 58% of the cells, the paired ACh + tone treatment produced subsequent alterations of frequency RFs. In half of these cases, the RF modifications were highly specific to the frequency that had been paired with ACh. Atropine antagoized the frequency-effects of ACh, suggesting that they were mediated via muscarinic cholinergic receptors.
Quality of Life Assessment in Pain Management

Quality of life can be substantially affected by pain. While many pain control options are available, analgesics are the most common, and usually most effective, method used to manage moderate to severe pain. There are, however, potential adverse effects of these drugs that may reduce patients' willingness to take their analgesics as prescribed. Both pain and the modalities used to manage it can impact patients' quality of life. Quality of life measurements can be used to evaluate the effectiveness of pain treatment, and guide the selection of pharmacologic and non-pharmacologic therapies. A variety of instruments, developed from two different measurement approaches (psychometric and decision-making or economic) is available to measure quality of life. This article discusses the applications, dimensions, and benefits of psychometric and decision-making models and potential uses in evaluating pain therapies.
A Rationale for Differentiating Instruction in the Regular Classroom

This article articulates what might be called a value-based argument, a philosophical statement, one that emphasizes principles and perspectives that have remained precious to the author throughout 40 years in the field of education. It is the author's perspective on research and the school experience rather than a review of the research literature and, as such, strongly reflects a point of view. The author argues that heterogeneous classrooms and differentiated instruction must form the core of the classroom experience for students in a democracy that works.
Automated Custom Code Generation for Embedded, Real-time Second Order Cone Programming

Abstract In this paper, we discuss the development of an Interior Point Method (IPM) solver for Second Order Cone Programming optimization problems that is capable of producing customized ANSI-C code for embedded, real-time applications. The customized code is generated for a given problem structure and makes use of no dynamic memory allocation, minimizes branching, wastes no mathematical or logical computations, and has minimal dependencies to standard libraries. The resulting software is designed to be easy to implement on embedded hardware with limited computing capabilities, while still providing accurate results rapidly enough for real-time use. The core IPM algorithm is a fairly standard primal-dual IPM, which makes use of Mehrotra predictor-corrector method with Nesterov-Todd scalings and Newton search directions. We make use of the Approximate Minimum Degree heuristic to maximize the sparsity of the Cholesky factorizations that are ultimately used to solve for the search directions. We conclude the paper by presenting the computational performance results from two example problems: a Mars landing optimal control problem and a reaction wheel allocation problem. The code generated for the Mars landing problem was successfully validated in three flights onboard a NASA test rocket, and was used in real-time to generate the optimal landing trajectories that guided the rocket. To the best of our knowledge, this was the first time that a real-time embedded convex optimization algorithm was used to control such a large vehicle, where mission success and safety critically relied on the real-time optimization algorithm.
The effects of silver nanoparticles on fathead minnow (Pimephales promelas) embryos

Nanoparticles are being used in many commercial applications. We describe the toxicity of two commercial silver (Ag) nanoparticle (NP) products, NanoAmor and Sigma on Pimephales promelas embryos. Embryos were exposed to varying concentrations of either sonicated or stirred NP solutions for 96 h. LC50 values for NanoAmor and Sigma Ag NPs were 9.4 and 10.6 mg/L for stirred and 1.25 and 1.36 mg/L for sonicated NPs, respectively. Uptake of Ag NPs into the embryos was observed after 24 h using Transmission Electron Microscopy and Ag NPs induced a concentration-dependent increase in larval abnormalities, mostly edema. Dissolved Ag released from Ag NPs was measured using Inductively Coupled-Mass Spectrometry and the effects tested were found to be three times less toxic when compared to Ag nitrate (AgNO3). The percentage of dissolved Ag released was inversely proportional to the concentration of Ag NPs with the lowest (0.625 mg/L) and highest (20 mg/L) concentrations tested releasing 3.7 and 0.45% dissolved Ag, respectively and percent release was similar regardless if concentrations were stirred or sonicated. Thus increased toxicity after sonication cannot be solely explained by dissolved Ag. We conclude that both dissolved and particulate forms of Ag elicited toxicity to fish embryos.
A double-blind randomized crossover trial of two loop diuretics in chronic kidney disease.

A double-blind randomized crossover trial of two loop diuretics in chronic kidney disease. Background Torsemide has predictable absorption compared to furosemide. Thereby, torsemide results in more constant exposure to active drug. Our hypothesis was that this pharmacokinetic difference between these commonly used loop diuretics may translate into disparate antihypertensive responses in patients with chronic kidney disease (CKD). Methods We conducted a randomized, double-blind, two-period, crossover trial to compare the pharmacodynamics of torsemide and furosemide, in 14 subjects with stage 2 or 3 CKD. We first performed an inpatient study, where after the subjects were brought into sodium balance on a 200mEq per day diet, a single bioequivalent dose of oral loop diuretic was administered with an intervening washout period. Measurements of urinary electrolytes were made. Subjects then participated in an outpatient study, wherein they received daily therapy for 3weeks with the loop diuretics in random order. Twenty four-hour ambulatory blood pressure monitoring was performed before and after each drug to assess the antihypertensive response. Results In the inpatient phase, furosemide increased urinary sodium excretion from average (±SD) 199 ± 49mEq/day to 357 ± 96mEq/day and torsemide increased urinary sodium excretion from 213 ± 79mEq/day to 398 ± 142mEq/day. These differences between the diuretics were not significant, confirming bioequivalence. In the outpatient phase, furosemide reduced 24-hour ambulatory blood pressure from 147 ± 17/78 ± 11mm Hg to 138 ± 21/74 ± 12mm Hg ( P = 0.021) and torsemide reduced it from 143 ± 18/75 ± 10mm Hg to 133 ± 19/71 ± 10mm Hg ( P = 0.007). Although each diuretic was effective in reducing ambulatory blood pressure, the differences between diuretics were not statistically significant. Conclusion Bioequivalent doses of torsemide and furosemide given in a randomized, double-blind design fail to demonstrate superiority of torsemide with respect to natriuresis or 24-hour ambulatory blood pressure control in subjects with stages 2 and 3 CKD.