cssi/SciSciGPT-SciSciNet huggingface dataset:
Systemic Air Embolism following Percutaneous Lung Biopsy

Systemic air embolism is a serious complication that may occur during a transthoracic percutaneous lung biopsy. Although rarely encountered, sequelae from systemic air embolism may result in a wide range of cardiac and neurologic presentations that are potentially fatal. Prompt clinical and radiologic recognition of systemic air embolism can prevent significant morbidity and mortality. The authors performed a transthoracic percutaneous lung biopsy that was complicated by seizures and transient neurologic deficits. In this article, a case of percutaneous lung biopsy complicated by a systemic arterial air embolism is presented, and strategies for prevention and management of this complication are discussed.
Dementia and cognitive impairment in ESRD: diagnostic and therapeutic strategies

Cognitive impairment, including dementia, is a common but poorly recognized problem among patients with end-stage renal disease (ESRD), affecting 16–38% of patients. Dementia is associated with high risks of death, dialysis withdrawal, hospitalization, and disability among patients with ESRD; thus, recognizing and effectively managing cognitive impairment may improve clinical care. Dementia screening strategies should take into account patient factors, the time available, the timing of assessments relative to dialysis treatments, and the implications of a positive screen for subsequent management (for example, transplantation). Additional diagnostic testing in patients with cognitive impairment, including neuroimaging, is largely based on the clinical evaluation. There is limited data on the efficacy and safety of pharmacotherapy for dementia in the setting of ESRD; therefore, decisions about the use of these medications should be individualized. Management of behavioral symptoms, evaluation of patient safety, and advance care planning are important components of dementia management. Prevention strategies targeting vascular risk factor modification, and physical and cognitive activity have shown promise in the general population and may be reasonably extrapolated to the ESRD population. Modification of ESRD-associated factors such as anemia and dialysis dose or frequency require further study before they can be recommended for treatment or prevention of cognitive impairment.
Small Fdu Strand Exhibits Salt-Dependent Stability

As shown in our previous work, F10 (a 10mer of Fdu - 5-fluoro-2′-deoxyuridine-5′-O-monophosphate) has a 40% likelihood of folding into a stable hairpin structure when Magnesium ions are used to neutralize the simulated system. Investigations of other counter ions revealed that F10 folds less than 10% of the time when neutralized with ions with a +1 charge and 40% of the time when neutralized with ions with a +2 charge. When simulated with biologically relevant combinations of K1+, Na1+ and Mg2+ ions, F10 folds into this hairpin structure approximately 10% of the time; however, once the strand of Fdu enters this folded state, it is 96% likely to stay in this kinetic trap. Here we present the data from microsecond timescale simulations and hypotheses on F10's behavior in the presence of various counter ions.
Western Margin of the Rocky Mountain Geosyncline in the Great Basin: ABSTRACT

The concept of an inner (miogeosynclinal) belt and an outer (eugeosynclinal) belt in the Paleozoic of the Great Basin is useful in a broad general way. It is impossible, however, to draw a well marked dividing line between the two troughs not only for the Paleozoic as a whole but also for the individual systems. It seems certain that no sharp uplift or even linear group of uplifts ever separated the troughs and that it is fruitless to search for sharply defined edges for either trough. The miogeosynclinal sediments are chiefly carbonates with minor shales and sandstones, the eugeosynclinal sediments are highly siliceous types such as chert, arkose, argillite, tuff, and black shale. Tongues of carbonate rock extend westward into the eugeosyncline, and, conversely, beds of black shale and chert are found in the miogeosyncline. On the basis of aggregate lithologic aspect the western edge of the Rocky Mountain geosyncline has roughly the following course through the Great Basin: commencing near Burley, Idaho, thence to the northwestern corner of Utah, continuing successively through Wells, Cortez, Manhattan, and Goldfield, Nevada, and ending near Owens Lake, California. Cover of Tertiary sediments and volcanic derivatives is thick and extensive over much of the eugeosyncline and unless deep wells are drilled there the exact nature of the older rocks may never be known. End_of_Article - Last_Page 2612------------
Basement membrane heterogeneity and variation in corneal epithelial differentiation.

Abstract We have previously shown that the expression of a major 64-Kda keratin (K3) in corneal cpithelium is site-related. It is found suprabasally in limbal epithelium, but uniformly (basal cells included) in central corneal epithelium. In the present study, we used a panel of antibodies against various components of corneal epithelial basement membrane to investigate a possible correlation between basement membrane heterogeneity and differential (basal vs . suprabasal) K3 keratin expression. One of these antibodies, AE27 , stains human conjunctival basement membrane weakly, limbal basement membrane heterogeneously, and central corneal basement membrane strongly. Basal cells resting on basement membrane that stains strongly with AE27 tend to stain with monoclonal antibody AE5 , which recognizes keratin K3. Basal cells on basement membrane staining weakly with AE27 tend not to stain with AE5 . No such correlation exists between AE5 staining and type IV collagen, which is detectable immunohistochemically in conjunctival and limbal basement membrane, but not in corneal basement membrane overlying Bowman's layer. These results suggest that basement membrane of human corneal/conjunctival epithelium can be divided into at least three domains: the conjunctival basement membrane (type IV collagen-positive, AE27 -weak), the limbal basement membrane (type IV collagen-positive, AE27 -strong), and corneal basement membrane (type IV collagennegative, AE27 -strong). The results also raise the possibility that basement membrane heterogeneity may play a functional role in regulating keratin expression and other aspects of differentiation of corneal epithelium; more experiments are needed to test this hypothesis.
A fast, higher-order solver for scattering by penetrable bodies in three dimensions

In this paper, we introduce a new fast, higher-order solver for scattering by inhomogeneous media in three dimensions. As in previously existing methods, the low complexity of our integral equation method, O(NlogN) operations for an N point discretization, is obtained through extensive use of the fast Fourier transform (FFT) for the evaluation of convolutions. However, the present approach obtains significantly higher-order accuracy than these previous approaches, yielding, at worst, third-order far field accuracy (or substantially better for smooth scatterers), even for discontinuous and complex refractive index distributions (possibly containing severe geometric singularities such as corners and cusps). The increased order of convergence of our method results from (i) a partition of unity decomposition of the Green's function into a smooth part with unbounded support and a singular part with compact support, and (ii) replacement of the (possibly discontinuous) scatterer by an appropriate ''Fourier smoothed'' scatterer; the resulting convolutions can then be computed with higher-order accuracy by means of O(NlogN) FFTs. We present a parallel implementation of our approach, and demonstrate the method's efficiency and accuracy through a variety of computational examples. For a very large scatterer considered earlier in the literature (with a volume of 3648@l^3, where @l is the wavelength), using the same number of points per wavelength and in computing times comparable to those required by the previous approach, the present algorithm produces far-field values whose errors are two orders of magnitude smaller than those reported previously.
Siblings of children with mental retardation living at home or in residential placement

Severe retardation in a child surely has an effect on all family members. Studies of nondisabled siblings in these families have indicated both emotional risks and perceived benefits. Little is known about how out-of-home placement of the child with retardation affects the siblings. Adolescent siblings of children with retardation living at home (N = 25) or in residential placement (N = 20) were contrasted with siblings of children without retardation (N = 28), on measures obtained from their mothers and themselves. Despite their different situations, these siblings were highly similar on measures of psychological adjustment, self-esteem, and family environment. Sibling relationships, however, were less intense, with less warmth but also lower conflict, in families where the child lived out of the home. Most siblings of children with retardation reported positive personal growth experiences while also expressing realistic concerns about the future. Siblings of children with retardation had beliefs and attitudes about placement that were highly consistent with the child's current living situation.
USE OF ATOMIC FORCE MICROSCOPY FOR EXAMINING WET CLAY

Clays and their composites have been widely used for secondary containment walls for underground storage tanks and landfills. The pore-size changes occurring in the clay have a profound effect on its permeability. This study presents a new method for evaluating the use of an atomic force microscope (AFM) for studying wet clay in a non-aqueous state in order to determine the pore-size of clay at various water contents, a type of study typically performed by the more expensive environmental scanning electronic microscope. The method consists of mounting a sponge saturated with water under the sample in order to prevent drying by the heat generated by the AFM electronics. The micro-scale AFM image results show that the clay-particle separations reduce linearly as the water content increases. This change in pore-size is postulated to be attributed to the reduction in the size of the diffuse double layer and more extensive hydrogen bonds between clay particles and bipolar water molecules. The AFM was not able to produce nano-scale images due to excessive adhesion between the cantilever arm and the wet clay sample.
Coal solubilization by enhanced enzyme activity in organic solvents

Both oxidative and reductive enzymes can be utilized to enhance coal solubilization in aqueous and organic media. Aerobic solubilization was carried out with oxidases in a relatively polar medium, whereas solubilization in an anaerobic environment was conducted with reducing enzymes (dehydrogenase or hydrogenase) in aqueous and both polar and nonpolar organic media in the presence of hydrogen or a hydrogen donor. Solubilization of some enzymes in organic liquids was enhanced by complexation with polyethylene glycol. Enzyme concentration of 1–20 mg/mL was used, and most of the reactions occurred during the first 4 h, with up to 85% of the coal solubilized. There was some evidence of coal product inhibition and enzyme deactivation at higher temperatures.
Algorithms for extracting true phase from rotationally-diverse and phase-shifted DIC images

In this paper, we report on the status of our current algorithms and extensions for improved algorithms for extracting phase from images acquired with differential-interference-contrast (DIC) microscopy. Our algorithms are based on two different approaches for the computation of a specimen's phase function or optical path length (OPL) distribution from DIC images. The first approach uses an iterative phase-estimation method that minimize the I -divergence discrepancy measure using the conjugate-gradient technique to estimate the OPL from multiple DIC images acquired at different specimen rotations. The method is based on the assumption that the specimen does not absorb light. The second approach is a non-iterative method that is based on a geometric-optics model and the phase-shifting technique that allows separation of the amplitude and phase gradient information from DIC images thereby allowing computation of the desired phase from its gradient. We show results from both methods and discuss the tradeoff between complexity (with respect to data-acquisitiona and computation) and accuracy. Our long term goal is to develop a new and improved method based on a combination of our two approaches.
EOG and delta rhythmicity in human sleep EEG.

The use of the electroencephalogram (EEG) is accepted as the only objective method of studying sleep. However, EEG sleep study may not be feasible, although it would be highly desirable, in some non-laboratory operational environments due to difficulties in EEG recordings. Results of the present study showed that the ultradian delta rhythmicity of sleep as defined by EEG could be obtained from electro-oculograms (EOGs) alone.
Total artificial heart

End-stage heart failure represents a highly morbid condition for the patient with limited treatment options. From a surgical perspective, the treatment options for effective long-term survival are usually limited to heart transplantation, heart–lung transplantation or implantation of a destination mechanical circulatory support device. Assuming an advanced heart-failure patient is indeed deemed a candidate for transplantation, the patient is subject to shortages in donor organ availability and thus possible further decompensation and potential death while awaiting transplantation. Various extracorporeal and implantable ventricular-assist devices (VADs) may be able to provide temporary or long-term circulatory support for many end-stage heart-failure patients but mechanical circulatory support options for patients requiring long-term biventricular support remain limited. Implantation of a total artificial heart (TAH) currently represents one, if not the best, long-term surgical treatment option for patients requiring biventricular mechanical circulatory support as a bridge to transplant. The clinical applicability of available versions of positive displacement pumps is limited by their size and complications. Application of continuous-flow technology can help in solving some of these issues and is currently being applied in the research towards a new generation of smaller and more effective TAHs. In this review, we discuss the history of the TAH, its development and clinical application, implications for anaesthetic management, published outcomes and the future outlook for TAHs.
Single longitudinal mode, diode-pumped Nd:YVO4 slab laser

Tunable, single longitudinal mode output has been obtained from a grazing-incidence grating- tuned Nd:YVO4 slab laser pumped by a quasi-cw diode laser bar. In order to compensate for the very high output coupling losses, a side pumping scheme using a single high angle of incidence reflection at the flat pump face is used to produce very high gain in the laser material. A pulse energy of up to 1 mJ in 200 microsecond(s) has been obtained for a 12 mJ pump pulse. The almost TEM00 output remained single longitudinal mode for periods of several minutes without active stabilization and could be tuned over a wavelength range of greater than 1 nm.© (1994) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
The consequences of Middle Paleolithic diets on pregnant Neanderthal women

Models of Neanderthal energetics and energy requirements suggest they required an average daily caloric intake well above the average for anatomically modern human foragers. The reasons stated for this include higher basic metabolic rates, less efficiency at thermoregulation, less efficiency at hunting, greater degrees of mobility, and reduced sexual division of labor in Neanderthal populations. These models suggest that Neanderthal Daily Energy Expenditure may have reached or exceeded 5500 calories per day. Given that most subsistence and isotope studies also suggest that Neanderthals focused their diet on large, terrestrial herbivores, this paper asks: what would be the nutritional consequences of such a diet on pregnant Neanderthal women? Applying a nutritional ecology perspective to the issue, a modeled diet consisting of 5500 calories per day derived exclusively from large, terrestrial herbivores indicates that such a diet would kill a pregnant Neanderthal woman and her developing fetus. This suggests that much remains to be learned about Neanderthal subsistence, mobility, and social relations, and that there is a long way to go before explaining the causes of Neanderthal extinction and modern human success in Europe and the Mediterranean region between 30,000 and 50,000 years ago.
Plasmonic Absorption Enhancement in a Dye-Sensitized Solar Cell Using a Fourier Harmonics Grating

A solid-state dye-sensitized solar cell with back-contact Fourier harmonics (FH) grating was studied theoretically, using the rigorous coupled-wave analysis. The FH grating was found to provide enhanced absorptance and enable efficient multiple surface–plasmon–polariton (SPP) wave excitations. The incident plane wave was considered to be TM-polarized with oblique incidence. The FH gratings were designed to excite multiple SPP waves at desirable wavelengths by solving a canonical boundary value problem. The excitation of SPP waves is indicated by the presence of peaks in the absorptance plots. The FH grating enables light trapping corresponding to the wave vectors of the constituting simple gratings, which may be useful for chemical sensing and communication applications as well.
Assessing Quality of Progression with Cyclic Coordination Functions

Quality of progression plays an important role in assessing the performance of urban streets with signalized intersections. The Highway Capacity Manual uses progression adjustment factors that modulate control delay at a signalized intersection approach in accordance with the quality of coordination. These factors correspond to six discrete arrival types that need to be estimated from given or observed flow data. However, this procedure is inaccurate and may lead to incorrect determination of level of service. This paper introduces an improved procedure for the determination of quality of progression that is sensitive to different traffic conditions, that can be easily calibrated, and that produces more accurate results. A periodic, continuously variable cyclic coordination function and associated coordination adjustment factors are developed to measure delay or travel time as a function of offsets along an urban street segment. Those measures depend on a variety of factors, including traffic flow charact...
Condensed phase route to polyacetylene

Abstract We present a versatile and convenient route to polyacetylene--the condensed phase metathesis polymerization of 1,3,5,7-cyclooctatetraene (COT). Dissolution of catalyst in “neat” cyclooctatetraene provides a means of transforming the liquid into a highly lustrous film at ambient temperature and pressure. New processing modes and novel morphologies (as observed by electron microscopy) have been found. The mechanism of polymerization, and its effect upon the stereochemical structure of the resulting polyacetylene, is discussed. Poly-COT films are shown to have physical and spectral properties very similar to polyacetylene prepared by the Shirakawa methodology. Iodine-doped films have conductivities greater than 300 ohm −1 /cm. Bromo-cyclooctatetraene has been polymerized to a strong, flexible golden film. The film is swollen in THF to a blue-black material; upon removal of the THF solvent the polymer shrinks to a golden film.
Estimating the prevalence and strength of non-independent predator effects

Understanding whether multiple predator species have independent effects on shared prey is critical for understanding community dynamics. We describe the prevalence and strength of non-independence between predators by quantifying the prey's risk of predation and the degree to which it deviates from the risk predicted from a null model of independent predator effects. Specifically, we document how frequently non-independent effects occur among ten different multiple predator combinations with mayfly larvae as prey. These predator combinations vary both predator density and predator species richness. Overall, the predator effects were non-independent and translated to an average of 27% fewer prey being consumed compared to independent predator effects. Non-independence of this magnitude is likely to have population level consequences for the prey and influence the distribution or prey preference of predators. Closer inspection shows that much of the risk reduction in this system is weak, to the point of being indistinguishable from independent predator effects, while few effects are strong. This pattern of many weak interactions and few strong ones parallels the pattern of interaction strengths documented previously in intertidal communities. Consequently, understanding strong interactors in multiple predator systems may help us understand the importance of a species.
Does Functional Reduction Need Bridge Laws? A Response to Marras

AbstractIn his recent article ‘Consciousness and Reduction’, Ausonio Marras argues that functional reduction must appeal to bridge laws and thus does not represent a genuine alternative to Nagelian...
Metamaterial-inspired, multi-functional, near-field resonant parasitic antennas

Several metamaterial-inspired, multi-functional, efficient, electrically small near-field resonant parasitic antennas have been designed and evaluated numerically. Single-band, dual-band, and quad-band monopole-like antennas; single-band and dual-band linearly and circularly polarized protractor antennas; and single-band and linearly and circularly polarized wire antennas have been obtained. Extensions to other multi-functional designs will be given in our presentation.
Talking Past the Middle

Challenge has published many pieces arguing that the standard of living in the United States has suffered in recent decades. But not everyone agrees there is a serious middle-class squeeze. Here is a counterargument.
Missing Thermochemical Groups for Large Unsaturated Hydrocarbons: Contrasting Predictions of G2 and CBS-Q

A total of 12 new thermochemical group additivity values (GAVs) needed to estimate the thermochemistry of large polyunsaturated hydrocarbons are derived from G2 calculations, including the nine missing hydrocarbon group values involving C-H bonds. The CBS-Q method is found to perform very poorly for the calculation of enthalpies of formation of alkynes and systems containing delocalized multiple bonds. The nonsystematic deviations between (i) CBS-Q and experimental values and (ii) CBS-Q and G2 values suggest errors in the CBS-Q extrapolation protocol rather than in the bond-additivity corrections. A few hydrocarbon groups are calculated to have surprisingly different stabilities than the others, and molecules containing these groups would be good targets for future experimental work.
CT-measured pore characteristics of surface and subsurface soils influenced by agroforestry and grass buffers

Abstract Permanent vegetative buffers with grass and/or trees are expected to improve soil porosity compared to row crop management, yet little is known about the extent of changes in soil properties with depth and how rapidly these changes take place. The objective of this study was to compare the effects of agroforestry and grass buffers on computed tomography (CT)-measured macropore (diam. > 1000 μm) and coarse mesopore (diam. 200–1000 μm) parameters within 0.50 m soil profiles and to examine relationships between CT-measured pore parameters and saturated hydraulic conductivity ( K sat ). Undisturbed soil cores (76 mm diam. by 76 mm long) from a no-till corn ( Zea mays L.)-soybean ( Glycine max (L.) Merr.; RC) rotation, grass buffer (GB), and agroforestry buffer (AB) treatments were collected with six replicates from the 0- to 0.50-m depth in 0.10-m increments on a Putnam silt loam (fine, smectitic, mesic Vertic Albaqualf). Five CT images were acquired throughout each soil core using a medical CT scanner with 0.2 by 0.2 mm pixel resolution and 0.5 mm slice thickness. Soil pore parameters including number of pores, number of macropores, number of coarse mesopores, porosity, macroporosity, coarse mesoporosity, and fractal dimension were analyzed using ImageJ software. Treatment and depth effects were significant for all seven parameters. These seven pore parameters were different between row crop and buffer treatments as well as grass and agroforestry buffer treatments. The GB and AB treatments had 26 and 36 macropores per 2500-mm 2 area, respectively. These numbers were 2 and 2.6 times greater than 14 macropores in the RC treatment. No macropores were detected in the 40 to 50 cm depth of the RC treatment. The fractal dimension of macroporosity for the agroforestry treatment was 1.2 and 1.1 times greater than row crop and grass buffer treatments, respectively. Soil bulk density and saturated hydraulic conductivity were significantly different among the treatments. The fractal dimension accounted for 76% of the variability in K sat . This study concludes that establishment of permanent vegetative buffers improves CT-measured soil parameters and these CT-measured parameters may be used to quantify the effects of management relative to environmental benefits and improved water transport and retention models.
An Introduction to Dynamo : Diagrams for Evolutionary Game Dynamics

Dynamo: Diagrams for Evolutionary Game Dynamics is free, open-source software used to create phase diagrams and other images related to dynamical systems from evolutionary game theory. We describe how to use the software’s default settings to generate phase diagrams quickly and easily. We then explain how to take advantage of the software’s intermediate and advanced features to create diagrams that highlight the key properties of the dynamical system under study. Sample code and output are provided to help demonstrate the software’s capabilities.
Regulation of apoptotic signaling pathways in hepatocytes in vivo.

The mitochondrial pathway is critical for the efficient execution of death receptor-initiated apoptosis in certain cell types. Questions remain as to why the mitochondria are required in that scenario. We investigated the molecular events that determined the need for the mitochondria by using an in vivo model of anti-Fas-induced hepatocyte apoptosis. In wild-type mice, Fas stimulation resulted in normal activation of caspase-3, with the generation of the active p 19 -p 12 complex. In bid-deficient mice, caspase-3 activation was arrested after the initial cleavage at Asp 175 . This allowed the generation of the p 12 small subunit, but the p20 large subunit could not be further processed to the p 19 subunit. The p 20 -p 12 complex generated by Fas stimulation in bid-deficient hepatocytes was inactive, arresting the death program. Failure of p20/pl2 caspase-3 to mature and to exhibit activity was because of the inhibition by the inhibitor-of-apoptosis proteins (lAPs), such as XIAP, and also to a low caspase-8 activity. This block could be overcome in wild-type mice by two mechanisms. Smac was released from mitochondria early following Fas activation and was competitively bound to the IAPs to reverse their effects. XIAP could also be cleaved, and this occurred later and was likely mediated by enhanced caspase activities. Both mechanisms were dependent on Bid and thus were not operative in bid-deficient hepatocytes. In conclusion, mitochondrial activation by Bid is required for reversing the IAP inhibition through Smac release. It is also required for the alternative activation of caspases through cytochrome c release, as demonstrated previously. Together, these events ensure a successful progression of the death program initiated by the death receptor activation in the hepatocyte.
Quasi-brittle graphs, a new class of perfectly orderable graphs

Abstract A graph G is quasi-brittle if every induced subgraph H of G contains a vertex which is incident to no edge extending symmetrically to a chordless path with three edges in either H or its complement H¯ . The quasi-brittle graphs turn out to be a natural generalization of the well-known class of brittle graphs. We propose to show that the quasi-brittle graphs are perfectly orderable in the sense of Chvatal: there exists a linear order a , b , c , d and edges ab , bc , cd has a b and d c .
Nanomechanical properties of human prion protein amyloid as probed by force spectroscopy.

Amyloids are associated with a number of protein misfolding disorders, including prion diseases. In this study, we used single-molecule force spectroscopy to characterize the nanomechanical properties and molecular structure of amyloid fibrils formed by human prion protein PrP90-231. Force-extension curves obtained by specific attachment of a gold-covered atomic force microscope tip to engineered Cys residues could be described by the worm-like chain model for entropic elasticity of a polymer chain, with the size of the N-terminal segment that could be stretched entropically depending on the tip attachment site. The data presented here provide direct information about the forces required to extract an individual monomer from the core of the PrP90-231 amyloid, and indicate that the β-sheet core of this amyloid starts at residue ∼164–169. The latter finding has important implications for the ongoing debate regarding the structure of PrP amyloid.
What's on the horizon: the future of pain medicine.

Physicians in each generation are convinced that the preceding eras of medicine were the glory days and that they are now living in trying times signaling the beginning of the end. All these generations couldn’t have been right. Instead, this sentiment is a symptom of the ever-changing landscape of medicine. Pain medicine is no exception to this rule. Despite being a young specialty, pain medicine and the role of physiatrists in the understanding and treatment of pain have evolved over a short period. Physical medicine and rehabilitation (PM&R) physicians have occupied the role of pain physicians since the inception of our specialty. In the beginning, physiatry served as the pillar of the biopsychosocial approach to understanding and treating pain and disability. This model has evolved to a functional biomechanistic approach, and in recent times, physiatrists have emphasized interventional approaches to pain. This transition was largely influenced by a shift in training and powerful remuneration incentives.
A comparison of polystyrene-poly(ethylene oxide) diblock copolymer and poly(ethylene oxide) homopolymer adsorption from aqueous solutions

Although amphiphilic polystyrene−poly(ethylene oxide) diblock copolymers (PS−PEO) adsorb from aqueous solutions to hydrophobic surfaces, they are unable to form an end-anchored brush. Four independ...
Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model

The application of phylogenetic inference methods, to data for a set of independent genes sampled randomly throughout the genome, often results in substantial incongruence in the single-gene phylogenetic estimates. Among the processes known to produce discord between single-gene phylogenies, two of the best studied in a phylogenetic context are hybridization and incomplete lineage sorting. Much recent attention has focused on the development of methods for estimating species phylogenies in the presence of incomplete lineage sorting, but phylogenetic models that allow for hybridization have been more limited. Here we propose a model that allows incongruence in single-gene phylogenies to be due to both hybridization and incomplete lineage sorting, with the goal of determining the contribution of hybridization to observed gene tree incongruence in the presence of incomplete lineage sorting. Using our model, we propose methods for estimating the extent of the role of hybridization in both a likelihood and a Bayesian framework. The performance of our methods is examined using both simulated and empirical data.
Rate-limiting steps and role of active site Lys443 in the mechanism of carbapenam synthetase.

Carbapenam synthetase (hereafter named CPS) catalyzes the formation of the β-lactam ring in the biosynthetic pathway to (5R)-carbapen-2-em-3-carboxylate, the simplest of the carbapenem antibiotics. Kinetic studies showed remarkable tolerance to substrate stereochemistry in the turnover rate but did not distinguish between chemistry and a nonchemical step such as product release or conformational change as being rate-determining. Also, X-ray structural studies and modest sequence homology to β-lactam synthetase, an enzyme that catalyzes the formation of a monocyclic β-lactam ring in a similar ATP/Mg2+-dependent reaction, implicate K443 as an essential residue for substrate binding and intermediate stabilization. In these experiments, we use pH−rate profiles, deuterium solvent isotope effects, and solvent viscosity measurements to examine the rate-limiting step in this complex overall process of substrate adenylation and intramolecular ring formation. Mutagenesis and chemical rescue demonstrate that K443 is...
No pain, no gain: Perceptions of calorie expenditures of exercise and daily activities

Reduction in physical activity is considered a major contributor to weight problems. Increasingly, people are expending less energy in household chores but joining fitness clubs. Do people perceive ordinary daily activities to expend less energy than exercise activities using similar amounts of calories? In the present study college students were asked to evaluate the calorie expenditure of 30 physical activities (i.e., exercises and household tasks). The household tasks were matched (in terms of caloric expenditure) to at least one exercise activity. When participants rated both exercise and daily activities, it appears that they focused on rate of caloric expenditure rather than type of activity (i.e., household task or exercise). In Study 2, college students evaluated the energy expenditure of light/leisure, moderate, and intense exercise. This emphasis concerning the benefit of intense physical activity was observed once again. College students appear to have assimilated the belief that intense physical activity expends more energy than longer sessions of lower intensity physical activity using similar amounts of calories. Perhaps one reason why people are not physically active is that they believe physical activities must be intense to be of benefit. At the same time they are automatizing household chores and, thus, become less active overall.
Avoidance System for Moving Obstacles

This paper presents a system which moves a robot through Cartesian space in the presence of objects which are also moving, in predictable trajectories. The method presented calculates a piecewise linear path with piecewise constant velocities. This is done by assuming a straight-line path from the start to the goal, and recursively planning smaller subpaths if collisions are detected. Two methods for generating subgoals are presented and compared. The first is a blind method employing little information on the location of the objects at collision time. The second is a method using Khatib's artificial potential functions for locating the subgoal. The algorithm currently is implemented in two dimensions, and represents an arbitrary number of objects by their bounding circles. The robot is represented by a point. The algorithm guarantees that all movement of the robot will take place in a specified workspace. In addition the robot is required to stay on a specified time schedule, within a certain tolerance. Obstacle trajectories are constrained to be represented as quadratic parametric equations in time. The paper points out some obvious extensions to this work. These include extensions to three dimensions, fine-motion planning with complex shapes, and use of the system with objects following unknown trajectories.
High-pressure effects in pyrene crystals: vibrational spectroscopy.

The response of pyrene crystals to high pressure was examined using Raman and FTIR spectroscopies. Raman spectra of external and internal modes were measured up to 11 GPa. Changes in the external modes were observed at ∼0.3 GPa, indicating the onset of a phase transition. We demonstrated that at this pressure pyrene I( P21/a, 4 mol/unit cell) transforms to pyrene III (P21/a, 2 mol/unit cell). Further increase of pressure produced a gradual broadening of the internal modes and an increase of fluorescence background, indicating the formation of another phase above 2.0 GPa. Irreversible chemical changes were observed upon gradual compression to 40 GPa. FTIR spectroscopy of the recovered product indicated a transformation of pyrene into an amorphous hydrogenated carbon (a-C:H) structure.
High-Resolution Spectra of Intrinsic Absorption Lines in the Quasi-stellar Object UM 675

We discuss high-resolution (~9 km s-1) Keck Observatory spectra of the associated (za ≈ ze) absorption lines in the ze = 2.15 QSO UM 675. In a previous paper we showed that the time-variable absorption lines require a minimum gas density of ~4000 cm-3 and a maximum distance of ~1 kpc from the QSO. We also inferred metallicities of Z Z☉ from an assortment of measured column densities. The new data yield absorption-line profiles for Lyα, and C IV, more reliable column densities, and evidence for partial coverage of the background emission source(s). The za ≈ ze line profiles are dominated by broad (FWHM ≈ 470 km s-1) and relatively smooth components with centroids shifted roughly -1500 km s-1 from the emission-line redshift. Much weaker narrow-line components (with FWHM ≈ 55 and 29 km s-1) are also detected inside the broad C IV and N V profiles, but they contribute negligibly to the total equivalent widths and column densities. The complex of broad and narrow lines indicates formation in an outflow, possibly in discrete ejection events, where distinct regions have the same outflow velocity but different (nonthermal) velocity dispersions. The doublet ratios in C IV indicate that its broad and narrow components both cover less than 50% of the emission source(s). This is further strong evidence for absorption near the QSO by clouds that are 0.1 pc across. In contrast, the Lyα absorber covers 83% of the emission source(s) and O VI covers 60%, indicating that different ions can have different coverage fractions. Scaling all of the metallic column densities upward by amounts appropriate for the C IV coverage fraction implies a metallicity of 2 Z☉. However, the metallicity could be much lower if large H I columns are "hidden" in the Lyα profile.
Microradiographic characterization of bronchoconstriction after pulmonary embolism.

Abstract Bronchoconstriction after autologous pulmonary embolism has been documented with simultaneous radiologic and bronchial pressure measurements. Three study groups were employed utilizing aged clot, fresh clot, and inert (agarose) clot as emboli. Bronchoconstriction was demonstrated by both parameters in all groups and was essentially equivalent among all groups. The data indicate that at least 0.3 to 3.0-mm bronchi are involved in the constrictive response to pulmonary embolism. The data also suggest that mechanical obstruction is the predominant factor initiating bronchoconstriction in this model.
On valid and reliable identification of normal disfluencies and stuttering disfluencies: A response to Aram, Meyers, and Ekelman (1990)

Aram, Meyers, and Ekelman (1990, Brain and Language, 38, 105-121) recently reported finding that children with unilateral brain lesions produced more stuttering-type nonfluencies than their neurologically normal peers. However, they did not report inter- or intrajudge agreement for the nonfluency types or for their method of measuring speech rate. The speech rates they reported were also unusually fast. We argue that these problems with Aram et al.'s study imperil both their results and their conclusions regarding developmental stuttering.
Immunohistochemical study of neuropeptides in vagal and glossopharyngeal afferent neurons in the rat

The presence and distribution of multiple neuropeptides in vagal and glossopharyngeal afferent ganglia of the rat were studied using immunohistochemistry. Substance P-, calcitonin-gene related peptide-, cholecystokinin-, neurokinin A-, vasoactive intestinal polypeptide-, and somatostatin-immunoreactive neurons were detected in each visceral afferent ganglion. Neurotensin-immunoreactive cells were not observed. In the nodose ganglion (inferior ganglion of the vagus nerve) occasional immunoreactive cells were scattered throughout the main (caudal) portion of the ganglion with small clusters of cells seen in the rostral portion. The pattern of distribution of the various peptides in the nodose ganglion was similar, with the exception of vasoactive intestinal polypeptide-immunoreactive neurons which exhibited a more caudal distribution. The relative numbers of immunoreactive cells varied, with the greatest numbers being immunoreactive for substance P or vasoactive intestinal polypeptide, and the lowest numbers being immunoreactive for neurokinin A and somatostatin. A build-up of immunoreactivity for each of the peptides, except somatostatin and neurotensin, was detected in vagal nerve fibers of colchicine-injected ganglia. Numerous peptide-immunoreactive cells were also found in the petrosal (inferior ganglion of the glossopharyngeal nerve) and jugular (superior ganglion of the vagus nerve) ganglia. No specific intraganglionic distribution was noted although the relative numbers of cells which were immunoreactive for the different peptides varied considerably. Substance P and calcitonin-gene related peptide were found in large numbers of cells, cholecystokinin was seen in moderate numbers of cells, and neurokinin A, vasoactive intestinal polypeptide and somatostatin were seen in fewer cells. These data provide evidence for the presence and non-uniform distribution of multiple peptide neurotransmitters in vagal and glossopharyngeal afferent neurons. In general, relatively greater numbers of immunoreactive cells were located in the rostral compared with caudal nodose ganglion, and in the petrosal and jugular ganglia compared with the nodose ganglion. Thus, multiple neuropeptides may be involved as afferent neurotransmitters in the reflexes mediated by vagal and glossopharyngeal sensory nerves.
Dynamic changes in genome-wide histone H3 lysine 4 methylation patterns in response to dehydration stress in Arabidopsis thaliana

The molecular mechanisms of genome reprogramming during transcriptional responses to stress are associated with specific chromatin modifications. Available data, however, describe histone modifications only at individual plant genes induced by stress. We have no knowledge of chromatin modifications taking place at genes whose transcription has been down-regulated or on the genome-wide chromatin modification patterns that occur during the plant's response to dehydration stress. Using chromatin immunoprecipitation and deep sequencing (ChIP-Seq) we established the whole-genome distribution patterns of histone H3 lysine 4 mono-, di-, and tri-methylation (H3K4me1, H3K4me2, and H3K4me3, respectively) in Arabidopsis thaliana during watered and dehydration stress conditions. In contrast to the relatively even distribution of H3 throughout the genome, the H3K4me1, H3K4me2, and H3K4me3 marks are predominantly located on genes. About 90% of annotated genes carry one or more of the H3K4 methylation marks. The H3K4me1 and H3K4me2 marks are more widely distributed (80% and 84%, respectively) than the H3K4me3 marks (62%), but the H3K4me2 and H3K4me1 levels changed only modestly during dehydration stress. By contrast, the H3K4me3 abundance changed robustly when transcripts levels from responding genes increased or decreased. In contrast to the prominent H3K4me3 peaks present at the 5'-ends of most transcribed genes, genes inducible by dehydration and ABA displayed atypically broader H3K4me3 distribution profiles that were present before and after the stress. A higher number (90%) of annotated Arabidopsis genes carry one or more types of H3K4me marks than previously reported. During the response to dehydration stress the changes in H3K4me1, H3K4me2, and H3K4me3 patterns show different dynamics and specific patterns at up-regulated, down-regulated, and unaffected genes. The different behavior of each methylation mark during the response process illustrates that they have distinct roles in the transcriptional response of implicated genes. The broad H3K4me3 distribution profiles on nucleosomes of stress-induced genes uncovered a specific chromatin pattern associated with many of the genes involved in the dehydration stress response.
A statistical model to correct systematic bias introduced by algorithmic thresholds in protein structural comparison algorithms

The identification of protein function is crucial to understanding cellular processes and selecting novel proteins as drug targets. However, experimental methods for determining protein function can be expensive and time-consuming. Protein partial structure comparison methods seek to guide and accelerate the process of function determination by matching characterized functional site representations, motifs, to substructures within uncharacterized proteins, matches. One common difficulty of all protein structural comparison techniques is the computational cost of obtaining a match. In an effort to maintain practical efficiency, some algorithms employ efficient geometric threshold-based searches to eliminate biologically irrelevant matches. Thresholds refine and accelerate the method by limiting the number of potential matches that need to be considered. However, because statistical models rely on the output of the geometric matching method to accurately measure statistical significance, geometric thresholds can also artificially distort the basis of statistical models, making statistical scores dependant on geometric thresholds and potentially causing significant reductions in accuracy of the functional annotation method. This paper proposes a point-weight based correction approach to quantify and model the dependence of statistical scores to account for the systematic bias introduced by heuristics. Using a benchmark dataset of 20 structural motifs, we show that the point-weight correction procedure accurately models the information lost during the geometric comparison phase, removing systematic bias and greatly reducing misclassification rates of functionally related proteins, while maintaining specificity.
The Downstream Transcriptional Enhancer, Ed, Positively Regulates Mouse Igκ Gene Expression and Somatic Hypermutation

The mouse Igkappa locus has three known transcriptional enhancers: the matrix association region/intronic enhancer, the 3' enhancer (E3'), and the further downstream enhancer (Ed). Previous studies have shown that both matrix association region/intronic and E3' enhancers are required for maximal gene rearrangement of the locus, and that E3' is also required for maximal expression and somatic hypermutation (SHM). To functionally elucidate Ed in vivo, we generated knockout mice with a targeted germline deletion of Ed. Ed deleted homozygous mice (Ed-/-) have moderately reduced numbers of Igkappa expressing B cells and correspondingly increased numbers of Iglambda expressing B cells in spleen. Ed-/- mice also have decreased Igkappa mRNA expression in resting and T cell-dependent activated splenic B cells and reduced Igkappa chains in sera. However, our analysis indicates that Igkappa gene rearrangement is normal in Ed-/- mice. In addition, our results show that Ed-/- mice exhibit reduced SHM in the Igkappa gene J-C intronic region in germinal center B cells from Peyer's patches. We conclude that Ed positively regulates Igkappa gene expression and SHM, but not gene rearrangement.