cssi/SciSciGPT-SciSciNet huggingface dataset:
A NEW GENUS AND OTHER NOVELTIES IN COMPOSITAE

a separate genus. At that time I included them in a new section, Paragynoxys. Subsequent comparisons and careful examination of abundant material of Senecio and related genera have made it evident that the group is sufficiently defined to deserve the category of a genus. This decision seems to me justified by the concurrence of the following basic characters in Paragynoxys: (1) corolla-limb divided to its base; (2) corolla white or whitish; (3) style branches with slightly enlarged and acutely or obtusely conical tips, dorsally pilose with the hairiness increasing below the apex; (4) anthers sagittate; (5) discoid cylindric head with few (generally 5) involucral bracts and few flowers; (6) unbranched or scarcely branched trees with large, coriaceous, firm, alternate, entire, more or less bunched leaves. I wish to analyze summarily each of these characters in relation with their presence in other genera or groups: Senecio, Gynoxys, Pseudogynoxys, Psacalium, Pericalia, and Odontotrichum. Vvith regard to Cacalia I think that Rydberg's conclusion' to exclude this name from the American flora is correct, and I support in this paper his interpretation substituting Psacalium, Pericalia and Odontotrichum for it. 1. Corolla. In Senecio the disc corollas are tubular and dentate, the lobes shorter than one-fourth the limb. In Gynoxys and Pericalia the division of the corolla limb is deeper, reaching one-third or one-half (exceptionally exceeding the middle of the limb as in the singularly placed G. littleii). In Psacalium and Odontotrichum the split of the limb is complete to its base. Thus the laciniate corolla distinguishes the new genus from Senecio, Gynoxys, and Pericalia but not from Psacalium and Cdontotrichum; the herbaceous habit, leaf structure and anther bases chiefly differentiate it from the last ones. See figures 1-3. 2. White corolla. W'ithout doubt, the white or pale color of the corollas is an important character, never being present in Gynoxys and extremely rare in true Senec io. 3. Style branches. Senecio and some species included by Rydberg in Odontotrichum have the typical truncate and penicillate stylar tips; only exceptional isolated species (e.g. S. aberrans Greenm.) show conical stigmas. Groups of species with lanceolate or conical stylar tips occasionally included in Senecio, having in addition another common character, e.g. vegetative, should be segregated from Senecio. The fundamental importance of the form of the stigmatic branches in the taxonomy of Compositae is generally recognized. In this connection the slightly dilated, acutely or obtusely conical style tips, not precisely penicillate, distinguish Paragynoxys well from Senecio, reinforcing the other differential characters. The style branches of Paragynoxys approach those of Gynoxys, but in this latter genus the conical or lanceolate form is more pro
Pneumocystis colonization, airway inflammation, and pulmonary function decline in acquired immunodeficiency syndrome.

As a result of improved diagnosis, treatment, and supportive care for HIV-infected patients, AIDS in developed countries has now become a chronic infection with prolonged survival time, but long-term complications are increasing contributors to morbidity and mortality. HIV-infected patients are at increased risk for the development of pulmonary complications, including chronic obstructive pulmonary disease (COPD); however, the mechanisms associated with this increased susceptibility have not been defined. Infectious agents may contribute to the development of COPD by upregulating inflammatory mediators in the lung that act in concert with cigarette smoke to promote lung pathology. Studies in human subjects and non-human primate models of AIDS suggest that the inflammatory response to asymptomatic carriage or colonization by the opportunistic pathogen, Pneumocystis sp (Pc), is similar to that of COPD, which is characterized by influx of CD8+ T cells, neutrophils, and macrophages into the lungs. We have shown a high frequency of Pc colonization among asymptomatic HIV-infected subjects and in non-HIV infected subjects with COPD. To investigate the role Pc in the progression of obstructive lung disease in HIV infections, we developed a non-human primate model of Pc colonizatoin and infection in simian immunodeficiency virus (SIV)-infected macaques. These animals develop a prolonged colonization state characterized by a persistent influx of CD8+T cells and neutrophils, and local increases in IL-8, IFN-γ, and TNF-α. SIV-infected Pc-colonized monkeys show progressive decline in pulmonary function compared to SIV-infected monkeys. We hypothesize that in the context of AIDS-immune dysfunction, Pc colonization induces inflammatory responses leading to changes in pulmonary function and architecture similar to that seen in emphysema. Information gained from these studies will lead to the development of interventions to prevent lung injury associated with Pc colonization and the development of HIV-associated COPD.
Helicobacter pylori infection, gastritis, and the temperature of choice for hot drinks.

BACKGROUND The role of the temperature of the diet as a potential etiological factor for gastritis or peptic ulcer disease has been postulated since the beginning of the century. Animal studies have demonstrated damage to gastric mucosa caused by hot water at 60 to 80 degrees C. In the pre-Helicobacter pylori era it was reported that the majority of ulcer patients preferred hot drinks. It also was reported that the temperature of choice for drinks increased with severity of histological grade of gastritis. We evaluated the association between the preferred temperature of hot drinks and the presence of H. pylori infection. METHODS We tested the temperature of choice for hot drinking liquids among 12 H. pylori-negative and 43 H. pylori-positive volunteers. We also compared the effect of H. pylori therapy on hot drink temperature preference and, in 32 individuals, whether there was a relation between temperature and the degree of gastric atrophy. RESULTS There was no difference in the preferred temperature for hot drinks between those volunteers with and without H. pylori infection (63.4 degrees +/- 6 degrees C compared to 61.3 degrees +/- 7 degrees C, respectively) (mean +/- 1 SD, p = .3). There was no change in preferred temperature after successful therapy of the H. pylori infection compared to unsuccessful H. pylori therapy, nor was there a correlation between the preferred temperature and the presence, absence, or degree of gastric atrophy (r2 < 0.001). CONCLUSION The temperature of preference for hot drinks was not influenced by H. pylori infection or by the presence of atrophic gastritis.
A Practical Guide to Estimating Cleanup Costs

Cost estimates are frequently developed to evaluate hazardous-waste-site cleanup options in support of a site investigation, remedy selection decision, or assessment of environmental liabilities. The accuracy of the cost estimate depends largely on the quality of the information available at the time it is prepared. This article presents a practical guide to developing a cleanup cost estimate. It includes information on how to document assumptions, use the latest technical resources, and perform basic adjustments to account for uncertainty and the time value of money. The content is based upon a recent guidance document issued by the U.S. Environmental Protection Agency and U.S. Army Corps of Engineers entitled A Guide to Developing and Documenting Cost Estimates during the Feasibility Study (USEPA, 2000). © 2001 John Wiley & Sons, Inc.
Deriving land surface temperature from Landsat 5 and 7 during SMEX02/SMACEX

A sequence of five high-resolution satellite-based land surface temperature (Ts) images over a watershed area in Iowa were analyzed. As a part of the SMEX02 field experiment, these land surface temperature images were extracted from Landsat 5 Thematic Mapper (TM) and Landsat 7 Enhanced Thematic Mapper (ETM) thermal bands. The radiative transfer model MODTRAN 4.1 was used with atmospheric profile data to atmospherically correct the Landsat data. NDVI derived from Landsat visible and near-infrared bands was used to estimate fractional vegetation cover, which in turn was used to estimate emissivity for Landsat thermal bands. The estimated brightness temperature was compared with concurrent tower based measurements. The mean absolute difference (MAD) between the satellite-based brightness temperature estimates and the tower based brightness temperature was 0.98 °C for Landsat 7 and 1.47 °C for Landsat 5, respectively. Based on these images, the land surface temperature spatial variation and its change with scale are addressed. The scaling properties of the surface temperature are important as they have significant implications for changes in land surface flux estimation between higher-resolution Landsat and regional to global sensors such as MODIS.
Germ line transmission of a yeast artificial chromosome spanning the murine alpha 1(I) collagen locus

Molecular complementation of mutant phenotypes by transgenic technology is a potentially important tool for gene identification. A technology was developed that allows the transfer of a physically intact yeast artificial chromosome (YAC) into the germ line of the mouse. A purified 150-kilobase YAC encompassing the murine gene Col1a1 was efficiently introduced into embryonic stem (ES) cells via lipofection. Chimeric founder mice were derived from two transfected ES cell clones. These chimeras transmitted the full length transgene through the germ line, generating two transgenic mouse strains. Transgene expression was visualized as nascent transcripts in interphase nuclei and quantitated by ribonuclease protection analysis. Both assays indicated that the transgene was expressed at levels comparable to the endogenous collagen gene.
Ventricular septal rupture after myocardial infarction : detection by transesophageal echocardiography

Acute rupture of the interventricular septum is a relatively unusual complication following acute myocardial infarction. The echocardiographic features depicted by transthoracic echocardiography are well described. However, transesophageal echocardiographic description of a ruptured septum has not been previously reported. This brief report illustrates the transesophageal features of such a defect. (Chest 1993; 103:1884-85)
Mineralogy of Martian atmospheric dust inferred from thermal infrared spectra of aerosols

[1] We have utilized optical constants derived from thermal infrared spectra acquired by the Mariner 9 Infrared Interferometer Spectrometer (M9 IRIS) and Mars Global Surveyor Thermal Emission Spectrometer (MGS TES), during periods of relatively high dust/low water ice opacity, to generate synthetic transmission and emission spectra of the atmospheric dust. Using libraries of transmission and emission spectra of common rock-forming minerals and their alteration products, we applied a linear deconvolution algorithm to the spectra to model the dust mineralogy. Models of the M9 IRIS transmission data generally are of poor quality, and the mineralogical results of these fits are unlikely to be valid. Fits to the TES transmission spectrum and TES and IRIS emission spectra are of better quality and suggest that the dust mineralogy is dominated by framework silicates (feldspar and/or zeolite) with carbonate, sulfate, pyroxene, and olivine, identified near, but below, generalized detection limits. Evidence for phyllosilicates is not robust. Our results, combined with those from in situ measurements and other visible to infrared spectral studies, suggest that framework silicates (probably feldspar) dominate the dust mineralogy, with lesser amounts of olivine, pyroxene, amorphous material, hematite, and magnetite, and that the dust largely is the product of mechanical weathering of basaltic rocks with minor chemical alteration.
Molecular pathways in dystonia

The hereditary dystonias comprise a set of diseases defined by a common constellation of motor deficits. These disorders are most likely associated with different molecular etiologies, many of which have yet to be elucidated. Here we discuss recent advances in three forms of hereditary dystonia, DYT1, DYT6 and DYT16, which share a similar clinical picture: onset in childhood or adolescence, progressive spread of symptoms with generalized involvement of body regions and a steady state affliction without treatment. Unlike DYT1, the genes responsible for DYT6 and DYT16 have only recently been identified, with relatively little information about the function of the encoded proteins. Nevertheless, recent data suggest that these proteins may fit together within interacting pathways involved in dopaminergic signaling, transcriptional regulation, and cellular stress responses. This review focuses on these molecular pathways, highlighting potential common themes among these dystonias which may serve as areas for future research. This article is part of a Special Issue entitled "Advances in dystonia".
Writing About Defoe: What is a Critical Biography?

This essay considers traditional biographical approaches to literary figures and examines the validity of the connections that literary biography claims to make between life events and an author's writings. Proposing several exemplary instances of critical biographies of Samuel Johnson by Lipking and De Maria that focus instead on an author's writing, the essay compares their approaches to the assumptions that guide two biographies of Daniel Defoe by Novak and Backscheider. The essay examines Defoe's life and writings to explore just how his personal life can be clearly related to the writing, concluding that not enough is known about his life to warrant a purely biographical approach. Instead, the essay outlines a critical-biographical method that focuses on Defoe's writing and its political and social circumstances.
Segmental Takayasu (giant cell) aortitis with rupture and limited dissection

Takayasu arteritis is a chronic inflammatory disease of the aorta and its main branches, with variable extents of involvement. Rarely is it sharply localized in an isolated segment of the aorta, and it seldom occurs in an elderly person. Clinically, Takayasu arteritis produces symptoms of vascular insufficiency, predominantly because of the occlusive disease and less commonly because of aneurysmal disease of the affected arteries. An unusual case of segmental Takayasu arteritis confined to the infrarenal abdominal aorta in an elderly woman is described, in which rupture and fatal hemoperitoneum were the initial manifestations of the disease.
The Four Winds: A Shaman's Odyssey into the Amazon

The Four Winds: A Shaman's Odyssey into the Amazon. Alberto Villoldo and Erik Jendresen. San Francisco: Harper and Row, 1990. x + 265pp. $9.95 (paper). ISBN 0–06–250892-X.
Application of joint histogram and mutual information to registration and data fusion problems in serial sectioning microstructure studies

Serial sectioning has become a standard technique for creating three-dimensional representations of microstructures. Registering large numbers of images with respect to a common reference frame, in particular when images are taken by a number of different detectors, is a complex problem that cannot easily be solved using standard cross-correlation techniques. An alternative technique, based on image entropy and mutual information, is applied to the problem of multimodal image registration. Two examples of mutual information based image registration are provided.
Text Cueing and Comprehension

This is one in a series of studies concerned with the effectiveness of instructional assistance on comprehension of scrambled text. Subjects were General Psychology students at the University of Colorado. Subjects reconstructed one of two 26-sentence passages with the aid of signalling sentences which assisted in determining the original sequence. These sentences were placed in proper order prior to the reconstruction task. A third group of subjects read the scrambled discourse without reconstruction. Our major findings were: (1) recall of idea units was assisted by the use of signalling sentences, (2) recognition of original sentences and paraphrases was also assisted by signalling, and (3) degree of concordance (tau) between reconstructed order and the original sentence sequence was a function of passage content. The contribution of signalling alone as compared to signalling and feedback suggests that the amount of instructional assistance provided is not necessarily proportional to achievement. There a...
Specific steroid response from a nonspecific DNA element

A fundamental dilemma of steroid hormone regulation is how specific transcription is attained in vivo when several receptors recognize the same DNA sequence in vitro. We have identified an enhancer of the mouse sex-limited protein (Slp) gene that is activated by androgens but not by glucocorticoids in transfection. Induction requires a consensus hormone response element (HRE) and multiple auxiliary elements within 120 base pairs. Androgen specificity relies on a dual function to augment androgen but prevent glucocorticoid action from a site that both receptors can bind. The nonreceptor factors are the dominant force in transcriptional specificity, although HRE sequence variations can affect the stringency and magnitude of hormonal response. The effect of HRE variations suggests that receptor position is altered relative to the other factors. Thus protein interactions that elicit specific gene regulation are established by the array of DNA elements in a complex enhancer and can be modulated by subtle sequence differences that may influence precise protein contacts.
Cerebral Responses to Single and Multiple Cocaine Injections in Newborn Sheep

ABSTRACT: Newborn infants exposed to cocaine near birth display a wide range of neurologic abnormalities, but the mechanism or mechanisms for these injuries remain unknown. We studied the cerebral effects of a single acute dose (4 mg/kg; n = 7) and multiple binge doses (4 mg/kg hourly for 5 h; n = 7) of i.v. cocaine in unancsthetized newborn (5 ± 1 d old) sheep. We measured cerebral blood flow, mean arterial blood pressure, arterial blood gases, and cerebral O2 metabolism. Measurements were made at baseline; 30 s; and 5,15, and 60 min after a single injection of cocaine in the acute group and at the same time intervals after the 5th dose of cocaine in the binge group. CBF increased by 98 ± 68% (mean ± SD) at 30 s after a single acute dose and by 97 ± 94% at 30 s after the 5th of five hourly binge doses. Although it returned to baseline by 5 min in the acute group, cerebral blood flow remained elevated 5, 15, and 60 min after the 5th cocaine dose in the binge group. At 30 s, mean arterial blood pressure increased by 57 ± 21% in the acute group and 46 ± 15% in the binge group. In both groups, mean arterial blood pressure remained elevated at 5 min. Although no change occurred in cerebral O2 metabolism in the acute group, an increase in cerebral O2 consumption (7.4 ±1.3 mL/100 g/ min versus 5.5 ± 1.1 at baseline) was observed at 5 min in the binge group. Thus, injection of cocaine as a single acute dose or after multiple binge doses results in acute cerebral vasodilation and hypertension in newborn sheep. Acute cerebral vasodilation, when combined within hypertension, may partially explain the pathogenesis of cocaine-associated neonatal neurologic abnormalities.
An extension of the Overhauser model for nuclear matter

Abstract Overhauser has recently proposed a single-particle trial wave function for the ground state of a system of Fermi particles with attractive two-body point interactions. We have re-investigated this problem for the case of finite range attractive and repulsive two-body forces. It is shown that the magnitude of the energy gap above the ground state is diminished or disappears completely; the spatial density variations for both spin directions are smaller than for a point interaction. The two density functions oscillate in-phase when the two-body potential is attractive and in-phase opposition for repulsive forces. For certain potentials we are able to construct a Hartree-Fock ground state which has a lower energy than that obtained with simple Overhauser wave functions. This ground state has a region in momentum space, inside the Fermi sea, which is not occupied by any particles. However, for reasonable strengths and ranges of the two-body force the Overhauser ground state is the lowest one obtained and an energy gap occurs.
Quality assurance of PASADENA hyperpolarization for 13C biomolecules.

Define MR quality assurance procedures for maximal PASADENA hyperpolarization of a biological 13C molecular imaging reagent. An automated PASADENA polarizer and a parahydrogen generator were installed. 13C enriched hydroxyethyl acrylate, 1-13C, 2,3,3-d3 (HEA), was converted to hyperpolarized hydroxyethyl propionate, 1-13C, 2,3,3-d3 (HEP) and fumaric acid, 1-13C, 2,3-d2 (FUM) to hyperpolarized succinic acid, 1-13C, 2,3-d2 (SUC), by reaction with parahydrogen and norbornadiene rhodium catalyst. Incremental optimization of successive steps in PASADENA was implemented. MR spectra and in vivo images of hyperpolarized 13C imaging agents were acquired at 1.5 and 4.7 T. Application of quality assurance (QA) criteria resulted in incremental optimization of the individual steps in PASADENA implementation. Optimal hyperpolarization of HEP of P = 20% was achieved by calibration of the NMR unit of the polarizer (B 0 field strength ± 0.002 mT). Mean hyperpolarization of SUC, P = [15.3 ± 1.9]% (N = 16) in D 2O, and P = [12.8 ± 3.1]% (N = 12) in H 2O, was achieved every 5–8 min (range 13–20%). An in vivo 13C succinate image of a rat was produced. PASADENA spin hyperpolarization of SUC to 15.3% in average was demonstrated (37,400 fold signal enhancement at 4.7 T). The biological fate of 13C succinate, a normally occurring cellular intermediate, might be monitored with enhanced sensitivity.
Bacterial Conjugation Under Anaerobic Conditions

Chromosome transfer in Escherichia coli has been shown to occur at high frequencies in an anaerobic environment.
The Sec2 translocase of the chloroplast inner envelope contains a unique and dedicated SECE2 component.

Biogenesis of chloroplasts involves a series of protein trafficking events. Nuclear-encoded proteins are imported into the organelle, and then trafficked to various chloroplast locations by systems that are directly homologous to bacterial systems. Although the thylakoid-based systems have been studied extensively, much less is known about the systems that reside and function in the inner envelope membrane. One such system, the Sec2 system, is homologous to both the thylakoid-based Sec1 system and bacterial Sec systems, and may mediate both integration and translocation across the inner envelope. At a minimum, this system is expected to include three components, but only two, SCY2 and SECA2, have been identified in Arabidopsis. Bioinformatics and protein modeling were used to identify the protein encoded by At4g38490 as a candidate for the missing component (SECE2). Cellular localization, biochemistry, protein interaction assays in yeast, and co-immunoprecipitation experiments were used to establish that this protein is an integral membrane protein of the inner envelope, and specifically interacts with the SCY2 component in vivo. Sequence analyses indicated that SECE2 proteins are found in a variety of plants, and differ from the thylakoid SECE1 proteins in a stroma-exposed helical domain, which may contribute to their specificity. Finally, a genetic analysis indicated that SECE2 plays an essential role in plant growth and development.
Abstract 4029: Enhanced chemosensitivity of estrogen receptor-α (ERα)-negative breast cancer through soybean genistein-induced epigenetic reactivation ofERα

Estrogen receptor-α (ERα)-negative breast cancer is clinically aggressive and has a poor prognosis due to the lack of estrogen target-directed therapies. The soybean isoflavone, genistein (GE), has been shown to prevent and inhibit breast cancer and recent studies have suggested that GE can enhance the anticancer capacity of an estrogen antagonist, tamoxifen (TAM), especially in ERα-positive breast cancer cells. However, the role of GE in ERα-negative breast cancer remains unknown. In our current studies, we found that GE can reactivate ERα expression and this effect was synergistically enhanced when combined with a histone deacetylase (HDAC) inhibitor, trichostatin A (TSA), in ERα-negative MDA-MB-231 breast cancer cells. GE treatment also re-sensitized ERα-dependent cellular responses to activator 17β-estradiol (E2) and antagonist TAM. Further studies revealed that GE can lead to remodeling of the chromatin structure in the ERα promoter thereby contributing to ERα reactivation. The global enzymatic activities for HDACs and DNA methyltransferases (DNMTs) mediated by GE were altered to favor ERα up-regulation. Consistently, dietary GE significantly reduced the growth of ERα-negative mouse xenograft tumors due at least in part to ERα reactivation. The combination of GE with TAM had more prominent effects on delaying tumor growth than either treatment alone. Collectively, our studies suggest that soybean genistein can epigenetically restore ERα expression, which in turn increases TAM-dependent anti-estrogen chemosensitivity. The results from our studies revealed a novel chemotherapeutic combination approach using bioactive soybean product and anti-hormone therapy in refractory ERα-negative breast cancer which will provide more effective options in breast cancer therapy. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4029. doi:1538-7445.AM2012-4029
Detecting salient contours using orientation energy distribution

How does our visual system detect prominent contours? Our investigation begins with the observation that neurons in the visual cortex have receptive fields similar to oriented Gabor filters. Unlike plain gray-level intensity histograms which greatly vary across images, we found that Gabor orientation-response (or orientation-energy) histograms of natural images have a fairly uniform shape. Based on this observation, we derived a threshold criterion which only depends on the standard deviation of the orientation-energy distribution. Thus, the same principle could be uniformly applied to different natural images, either locally or globally. Comparison with thresholds chosen by humans showed that the criterion can accurately predict human performance. Further, the proposed criterion can be easily implemented in a neural network, which is currently under investigation.
Congenital persistent terminal ventricle and filar cyst.

A baby born prematurely at 34 weeks’ gestation had a sallow patch on the sacrum raising suspicion of spinal dysraphism. Physical examination including neurological examination was normal. Spinal US showed undulations and dilatation of the central echo complex at L1 in the conus medullaris consistent with a persistent terminal ventricle (PTV) (Fig. 1, arrow). Spinal US showed a PTV at L1 (Fig. 2, arrowhead) and a fusiform cystic structure in
Speeding up the convergence of online heuristic search and scaling up offline heuristic search

Heuristic search algorithms are popular Artificial Intelligence methods for solving the shortest-path problem. This research contributes new heuristic search algorithms that are either faster or scale up to larger problems than existing algorithms. Our contributions apply to both online and offline tasks. For online tasks, existing real-time heuristic search algorithms learn better informed heuristic values and sometimes eventually converge to a shortest path by repeatedly executing the action leading to a successor state with a minimum cost-to-goal estimate. In contrast, we claim that real-time heuristic search converges faster to a shortest path when it always selects an action leading to a state with a minimum f-value (i.e., a minimum estimate of the cost of a shortest path from start to goal via the state), just like in the offline A* search algorithm. We support this claim by implementing this new non-trivial action-selection rule in FALCONS and by showing empirically that FALCONS significantly reduces the number of actions to convergence of a state-of-the-art real-time search algorithm. For offline tasks, we scale up two best-first search approaches. First, a greedy variant of A* called WA* is known (1) to consume less memory to find solutions of equal cost when it is diversified (i.e., when it performs expansions in parallel), as in KWA*; and (2) to solve larger problems when it is committed (i.e., when it chooses the state to expand next among a fixed-size subset of the set of generated but unexpanded states), as in MSC-WA*. We claim that WA* solves even larger problems when it is enhanced with both diversity and commitment. We support this claim with our MSC-KWA* algorithm. Second, it is known that breadth-first search solves larger problems when it prunes unpromising states, resulting in the beam search algorithm. We claim that beam search quickly solves even larger problems when it is enhanced with backtracking based on limited discrepancy search. We support this claim with our BULB algorithm. We demonstrate the improved scaling of MSC-KWA* and BULB empirically in three standard benchmark domains. Finally, we apply anytime variants of BULB to the multiple sequence alignment problem in biology.
Elster's Marx

A central aim of Elster's Making Sense of Marx is to recover Marx for methodological individualism, to show that Marx, unlike many of his followers, sought to provide his explanations of macro‐phenomena with micro‐foundations. Though I largely share Elster's methodological commitments and his view that Marx also (intermittently) adhered to them, I question whether this makes Marx a methodological individualist. In my view, Marx practised in his best work both individualist and structuralist explanation simultaneously. In three briefer remarks I also comment on Marx's and Elster's treatment of the differences between workers’ and peasants’ propensities for collective action; the primacy in Marx's theories of dynamics internal to a society and his failure to recognize the importance for domestic developments of interactions with other societies and states; and finally Marx's ‘progressive’ values, which Elster seems to share.
Noise robust bird song detection using syllable pattern-based hidden Markov models

In this paper, temporal, spectral, and structural characteristics of Robin songs and syllables are studied. Syllables in Robin songs are clustered by comparing a distance measure defined as the average of aligned LPC-based frame level differences. The syllable patterns inferred from the clustering results are used for improving the acoustic modelling of a hidden Markov model (HMM)-based Robin song detector. Experiments conducted on a noisy Rocky Mountain Biological Laboratory Robin (RMBL-Robin) song corpus with more than 75 minutes of recordings show that the syllable pattern-based detector has a higher hit rate while maintaining a lower false alarm rate, compared to the detector with a general model trained from all the syllables.
Attempts to obtain neuroprotection in Parkinson's disease

It is suggested that oxidant stress is a contributing factor in the pathogenesis of Parkinson's disease (PD). Oxidant stress may contribute to cell death in PD because oxidative metabolism of dopamine has the potential to yield highly reactive and cytotoxic free radicals. Evidence for this hypothesis includes: (1) increased dopamine turnover with increased hydrogen peroxide formation; (2) decreased glutathione availability; and (3) increased reactive iron in the brains of patients with PD. Antioxidant therapies might be neuroprotective and could slow the clinical progression of the disease whereas metabolites of levodopa therapy may accelerate the rate of neuronal degeneration. Laboratory studies demonstrate that both selegiline and dopamine agonists can provide neuroprotective benefits. Selegiline-treated patients require less levodopa and have a delay in the progression of parkinsonian signs and symptoms. Dopamine agonists provide antiparkinson benefits and also diminish the need for levodopa.
Using data envelopment analysis for evaluating alternative software development process configurations

Summary form only given as follows. The goal of achieving better software depends on improvements in software development processes. This paper provides a nonparametric, quantitative methodology for evaluating alternative software development process configurations as a tool for process improvement. The methodology uses data envelopment analysis (DEA) for comparing the impact of varying degrees of software inspection on project schedule, cost and quality. Since every phase of the development process can be inspected at varying levels, a large number of process combinations become possible. Thus a manager's job to compare and select an efficient process configuration can become tedious. This is especially the case when several process configurations are being evaluated by comparing several productivity measures. Fortunately, data envelopment analysis (DEA) can be applied as a method to reduce the long list of candidates for best practices to a selected few process options for further analysis. In this study, 257 different process options were compared against each other. The input and output values for each process option were estimated and compared using DEA. Of this quantity, 7 models were identified as candidates for best practices. An extension to this model incorporated managerial preferences in the form of weight restrictions applied to input/output variables.
Biologic scaffolds composed of central nervous system extracellular matrix

Acellular biologic scaffolds are commonly used to facilitate the constructive remodeling of three of the four traditional tissue types: connective, epithelial, and muscle tissues. However, the application of extracellular matrix (ECM) scaffolds to neural tissue has been limited, particularly in the central nervous system (CNS) where intrinsic regenerative potential is low. The ability of decellularized liver, lung, muscle, and other tissues to support tissue-specific cell phenotype and function suggests that CNS-derived biologic scaffolds may help to overcome barriers to mammalian CNS repair. A method was developed to create CNS ECM scaffolds from porcine optic nerve, spinal cord, and brain, with decellularization verified against established criteria. CNS ECM scaffolds retained neurosupportive proteins and growth factors and, when tested with the PC12 cell line in vitro, were cytocompatible and stimulated proliferation, migration, and differentiation. Urinary bladder ECM (a non-CNS ECM scaffold) was also cytocompatible and stimulated PC12 proliferation but inhibited migration rather than acting as a chemoattractant over the same concentration range while inducing greater rates of PC12 differentiation compared to CNS ECM. These results suggest that CNS ECM may provide tissue-specific advantages in CNS regenerative medicine applications and that ECM scaffolds in general may aid functional recovery after CNS injury.
The Consistency of Rational Belief

When are a man’s beliefs rational, and when are they irrational? A systematic answer to these questions constitutes a theory of the ethics of belief; that is, a theory which tells us what a man is obligated, permitted, and forbidden to believe, from the point of view of rationality. A theory of the rationality of belief will consist in large part of a system of rules which determine, in a given cognitive situation, what a man’s doxastic commitments ought to be. The most general form of a theory of rational belief will incorporate a set of rules that tell us what our doxastic commitments are once it has been determined which propositions, in a given cognitive situation, are justified, evident, reasonable, unreasonable, and so forth. A general theory of this sort becomes more exact when it is supplemented with a set of rules that also determine, in a given situation, which propositions are justified, evident, etc. This latter body of rules will generally incorporate, but not wholly consist of, criteria of inductive support. In addition to criteria of inductive support, such rules will generally incorporate criteria for determining which nonexperiential propositions, if any, are justified independently of the need for inductive support, and which experiential propositions are justified but not justified by any other propositions. These criteria might serve as explications of the general concepts Justified, Evident, Reasonable, and so forth.
Characterization of Proton Exchange Membrane Fuel Cells with Catalyst Layers Obtained by Electrospraying

Electrostatic polymer processing ~electro-spraying, electrospinning, and combinations of the two! represents a new and highly versatile approach for the fabrication of polymer-based electrochemical device components. 1,2 Electrospraying and electrospinning can afford particles and fibers with diameters of 100 nm or less, suggesting that nanostructured electrolytes and electrodes may be obtained by judicious choice of materials and electrostatic processing parameters. Moreover, these electrostatic processing approaches may have applicability to a wide variety of polymer-based electrochemical devices, including fuel cells, batteries, capacitors, and electrochromic and electroluminescent displays. We believe that electrostatic processing could be used for the construction of an entire proton-exchange membrane fuel cell ~PEMFC!, including the membrane, electro-catalyst layers, and gas diffusion layers. Particularly appealing is the potential ability to control composition, porosity, and wettability of these fuel cell components. As a first step in the development of this technology, Nafion was electrosprayed from solution to afford thin films and subsequently characterized as having physical properties ~water uptake, dimensional changes, electrical conductivity! similar to those of Nafion 117 films. 1 Following that, electrochemical properties of half-cells with commercial Nafion 117 and catalyst layers obtained by electrostatic processing were characterized. 2 The present research is focused on evaluation of PEM single cells with catalyst layers obtained by the electrospraying technique on commercial Nafion 112 films.
The biochemistry of acetaminophen hepatotoxicity and rescue: a mathematical model

Acetaminophen (N-acetyl-para-aminophenol) is the most widely used over-the-counter or prescription painkiller in the world. Acetaminophen is metabolized in the liver where a toxic byproduct is produced that can be removed by conjugation with glutathione. Acetaminophen overdoses, either accidental or intentional, are the leading cause of acute liver failure in the United States, accounting for 56,000 emergency room visits per year. The standard treatment for overdose is N-acetyl-cysteine (NAC), which is given to stimulate the production of glutathione. We have created a mathematical model for acetaminophen transport and metabolism including the following compartments: gut, plasma, liver, tissue, urine. In the liver compartment the metabolism of acetaminophen includes sulfation, glucoronidation, conjugation with glutathione, production of the toxic metabolite, and liver damage, taking biochemical parameters from the literature whenever possible. This model is then connected to a previously constructed model of glutathione metabolism. We show that our model accurately reproduces published clinical and experimental data on the dose-dependent time course of acetaminophen in the plasma, the accumulation of acetaminophen and its metabolites in the urine, and the depletion of glutathione caused by conjugation with the toxic product. We use the model to study the extent of liver damage caused by overdoses or by chronic use of therapeutic doses, and the effects of polymorphisms in glucoronidation enzymes. We use the model to study the depletion of glutathione and the effect of the size and timing of N-acetyl-cysteine doses given as an antidote. Our model accurately predicts patient death or recovery depending on size of APAP overdose and time of treatment. The mathematical model provides a new tool for studying the effects of various doses of acetaminophen on the liver metabolism of acetaminophen and glutathione. It can be used to study how the metabolism of acetaminophen depends on the expression level of liver enzymes. Finally, it can be used to predict patient metabolic and physiological responses to APAP doses and different NAC dosing strategies.
Anthropogenic noise affects risk assessment and attention: the distracted prey hypothesis

Many studies have focused on the effects of anthropogenic noise on animal communication, but only a few have looked at its effect on other behavioural systems. We designed a playback experiment to test the effect of noise on predation risk assessment. We found that in response to boat motor playback, Caribbean hermit crabs (Coenobita clypeatus) allowed a simulated predator to approach closer before they hid. Two hypotheses may explain how boat noise affected risk assessment: it masked an approaching predator's sound; and/or it reallocated some of the crabs' finite attention, effectively distracting them, and thus preventing them from responding to an approaching threat. We found no support for the first hypothesis: a silent looming object still got closer during boat motor playbacks than during silence. However, we found support for the attentional hypothesis: when we added flashing lights to the boat motor noise to further distract the hermit crabs, we were able to approach the crabs more closely than with the noise alone. Anthropogenic sounds may thus distract prey and make them more vulnerable to predation.
Role of blood coagulation in acute inflammation

Abstract The inflammatory process is a response to many different kinds of tissue injury. One event thay may be common to many apparently unrelated irritants is the deposition of fibrin. Three experimental designs have considered the significance of fibrin in acute inflammation, but only the third will be discussed extensively (details of the other approaches have been published). In the first approach, the biochemical profile of proteins concerned in fibrin formation was defined quantitatively for inflammatory fluids obtained from acutely inflamed joints of humans with arthritic diseases. Quantitative differences appeared to reflect degress of inflammation rather than to define a profile unique for the types of arthritis. The second experimental approach attempted to correlate the type of exudative leucocytes with the presence of fibrin in human joint disease and experimental skin windows on dogs. The granulocyte phase of inflammation was maintained and prolonged by the presence of fibrin. The third experimental approach was a quantitative study of leucocyte response to the chemotactic power of fibrin, fibrinogen, and their proteolysis products. By a skin window collection chamber technique with dogs, the leucocyte responses to fibrin-related material. other protein aggregates (albumin, γ-globulin, antigen-antibody complexes), and several inert particulate or structured preparations were compared. Fibrin-related materials were the most potent chemotactic agents for granulocyte (predominantly neutrophil) emigration in acute inflammation.
Octree-based Finite Element Method for electromagnetic scattering problems

Currently Finite Element Methods (FEM) fall into one of two categories: FEMs based on structured meshes, and those based on unstructured meshes. Work by Hill, Farle, et. al [1] has explored nonconformal unstructured meshes to aid in the application of adaptive mesh refinement (AMR) and geometric multigrid methods on tetrahedral meshes. Demkowicz, Kurtz, et. al [2] have worked with nonconformal hexahedral meshes. This work proposes an octree mesh based FEM which enjoys fast, robust meshing, as well as simplified matrix assembly. There is the potential to reap large benefits when applied to AMR and multigrid methods, since the overhead of local refinements on unstructured meshes is avoided, and projections between differing levels of mesh refinement are simplified. The stair-casing prevalent in structured meshes, while still present, is mitigated by the nonconformal nature of the octree mesh.
Timing of events during deglutition after chemoradiation therapy for oropharyngeal carcinoma.

Background The purpose of this study was to determine if persistent changes in the duration of bolus movement through the pharynx and bolus movement coordination with pharyngeal swallowing gestures occur after treatment of oropharyngeal carcinoma with chemoradiation therapy. Methods The timing of bolus movement and coordination with swallowing gestures was evaluated in 30 patients using a modified barium swallowing study at least 1 year after completion of treatment. Patients were recruited irrespective of any swallowing complaints. The mean of each measure from the study subjects was compared to those from a group of age-matched controls. Results Bolus transit duration in the study population was unchanged compared with normal controls. Unlike normal controls, the patients were found to allow the bolus to arrive in the vallecula before the initiation of swallowing gestures that resulted in a swallow. Earlier opening of the upper esophageal sphincter was found for a 1-cc bolus (p = .004). For the 20 cc bolus size, the onset of hyoid and aryepiglottic fold elevation was delayed (p = .029 and .037, respectively). Gesture timing did not change to accommodate larger bolus sizes, as it normally does, resulting in a delay in airway protection for the 20-cc bolus. Conclusion Patients are able to move a liquid bolus through the pharynx in a timely manner. However, patients are unable to modify swallowing gestures to safely protect the airway. © 2014 Wiley Periodicals, Inc. Head Neck 37: 1193–1199, 2015
Temperature-aware clock tree synthesis considering spatiotemporal hot spot correlations

Temperature variation in microprocessors is a workload dependent problem. In such a design, the clock skew should be minimized with respect to temperature variation. Existing work has studied clock tree embedding perturbation considering time variant temperature variation. There is no existing method that can reduce skew variation. This paper develops an efficient yet effective simultaneous hotspot avoid embedding and thermal aware routing (TMST) method, where hotspot embedding avoid tree topology located in area with high temperature possibility and thermal aware routing reduce skew in tree path with more smooth temperature area. With a thermally tolerable tree structure, our method can reduce not only delay skew but also skew variation (skew violation range). Compared with existing temperature-aware clock tree method, our TMST solution reduces skew variation by 2X compared with the greedy-DME (GDME) method of Edahiro and existing thermal aware clock synthesis TACO and PECO. With the scale from 100 down to 1 temperature maps, our TMST also guarantees the smallest wire length overflow. TMST reduces the worst case skew up to 4X than PECO and 5X than TACO.
Arteriotracheal fistula in patients treated for lymphoma

Exsanguinating hemorrhage is an unusual cause of death in patients who are being treated for neoplasms. We report two cases of adolescents with mediastinal non-Hodgkin's lymphoma who each developed a fistula between the right brachiocephalic trunk and the trachea following mediastinal irradiation and systemic chemotherapy. During the hospital course, the patients had each suffered a respiratory arrest and undergone difficult endotracheal intubation. The tracheal ulcerations at the fistula sites were unsuspected prior to autopsy.