cssi/SciSciGPT-SciSciNet huggingface dataset:
Iconic eyesores: exploring do-it-yourself preservation and civic improvement at abandoned train stations in Buffalo and Detroit

This inquiry documents two citizen-driven campaigns to reclaim iconic train stations and their adjacent landscapes, assessing their effectiveness as agents of preservation and civic improvement, and potential as catalysts for local development. Examining grassroots efforts to conserve and reuse Buffalo’s Central Terminal and Detroit’s Michigan Central Station and the adjacent Roosevelt Park, it considers a unique form of preservation practice – one devoid of significant public sector funding and the conventional market-based adaptive reuse strategies that are ineffective in declining settings. Driven by idiosyncratic collectives of residents, business owners, cultural entrepreneurs, artists, designers, and planners, these groups coalesce around a shared desire to conserve local landmarks and play an active role in the physical rebuilding of their cities. Their incremental and incomplete transformations are driven by an ethic that transcends both typical market-oriented targets (private sector profits or “...
Repair of calcaneal tendon ruptures. A safe technique

A new method of repair of the calcaneal tendon, which uses a small transverse skin incision, is described. In 41 patients, there was only one minor wound problem and the clinical results were satisfactory.
Inductive effect of positively charged nitrogen on the addition of iodine monochloride to alkynamine hydrochlorides

During the course of a study to develop novel radio-iodination procedures, the authors investigated the addition of ICl to several propargylamine hydrochlorides and observed varying degrees of regioselectivity depending on the nature of the nitrogen substituents. In each case the major product was the chloroiodinated (E)-alkene in which chlorine was attached to the terminal carbon atom, as predicted by the extended Markovnikov rule. Due to the inconsistencies of this rule regarding ICl additions to alkynes, they decided to investigate the factors controlling the regiochemistry of these reactions. Based on the experimental results, they found the regioselectivity and rates of these reactions to be dependent upon the inductive effect of the positively charged nitrogen.
Climate regime shifts and community reorganization in the Gulf of Alaska: how do recent shifts compare with 1976/1977?

Litzow, M. A. 2006. Climate regime shifts and community reorganization in the Gulf ofAlaska: how do recent shifts compare with 1976/1977? e ICES Journal of Marine Science,63: 1386e1396.Climate regime shifts have recently occurred in the North Paciﬁc (1998e1999) and theArctic (2000), but the nature of biological reaction to these events is poorly understood.An index of local climate (1960e2005), and data from commercial ﬁshery catches(1960e2004) and from small-mesh trawl surveys (1972e2005) are used to assess the im-pacts of these climate events in the Subarctic Gulf of Alaska. Non-linear regression showedthat survey catch composition strongly responded to local climate at lags of 2 and 4 years,providing evidence of rapid ecological response to climate change in the system. A sequen-tial regime shift detection method identiﬁedrapid change in local climate, and in survey andcommercial catches following the well-documented regime shift to a positive state of thePaciﬁc Decadal Oscillation (PDO) in 1976/1977. However, the analysis failed to detectthe 1998/1999 regime shift in local climate, or in survey or commercial catches. This resultis consistent with the view that the 1998/1999 climate regime shift did not represent a rever-sion to a negative PDO state. Local temperature increased and local sea level pressure de-creased in the Gulf of Alaska during the years 2001e2005, consistent with anthropogenicwarmingand recent spatial reorganization in Arctic climate. There was no evidence of com-munity reorganization following this climate event. Further observation will be required toevaluate the persistence of this new climate pattern, and the nature of community reactionto it.
Pharmacology, Clinical Efficacy, and Adverse Effects of Sucralfate, A Nonsystemic Agent for Peptic Ulcer

Sucralfate, a complex salt of polyaluminum hydroxide with a sulfated disaccharide skeleton, has recently been approved by the Food and Drug Administration for the short-term treatment of duodenal ulcer. The drug is nonsystemic in action and apparently exerts its antiulcer effects by bonding with proteinaceous exudates in the ulcer crater, thereby protecting it from insult. In vitro and clinical studies have shown that the drug is not an antacid but does block the diffusion of acid. Inhibition of pepsin and bile acid activities have also been demonstrated. In double-blind clinical trials where patients used antacids as needed for pain, sucralfate 1 g 4 times a day was significantly more effective than placebo and as effective as cimetidine. No serious adverse effects have been caused by this locally-acting agent.
Orchestrating caGrid Services in Taverna

caBIGtrade (the cancer Biomedical Informatics Gridtrade) is an open-source, open-access information network enabling cancer researchers to share tools, data, applications, and technologies. caGrid is the underlying service-based grid software infrastructure for caBIG, integrating distributed data and analytic resources into a virtual collaborative platform for cancer research. Within caGrid, many cancer-related data analysis and aggregation tasks can make use of "canned" sets of service invocations, or workflows. As a result, there is a need to orchestrate the invocation of caGrid services through the use of both a workflow language and tooling. In this paper, we first explain why we select Taverna as a candidate for workflow authoring and invocation. We then review the development of Taverna plug-ins in general, and describe how we extend Taverna to use caGrid services. We then detail a real-world example and the lessons learned from our research. Finally we conclude with a summary and a description of potential next steps.
HEXEvent: a database of Human EXon splicing Events

HEXEvent (http://hexevent.mmg.uci.edu) is a new database that permits the user to compile genome-wide exon data sets of human internal exons showing selected splicing events. User queries can be customized based on the type and the frequency of alternative splicing events. For each splicing version of an exon, an ESTs count is given, specifying the frequency of the event. A user-specific definition of constitutive exons can be entered to designate an exon exclusion level still acceptable for an exon to be considered as constitutive. Similarly, the user has the option to define a maximum inclusion level for an exon to be called an alternatively spliced exon. Unlike other existing splicing databases, HEXEvent permits the user to easily extract alternative splicing information for individual, multiple or genome-wide human internal exons. Importantly, the generated data sets are downloadable for further analysis.
Assessment of spectral, polarimetric, temporal, and spatial dimensions for urban and peri-urban land cover classification using Landsat and SAR data

Abstract Urban and peri-urban environments are composed of a wide variety of materials, making land cover classification challenging. The objective of this research is to determine how effectively multi-season Landsat Enhanced Thematic Mapper Plus (ETM+) and single-season Advanced Land Observing Satellite (ALOS) Phased Array type L-band Synthetic Aperture Radar (PALSAR) data can be combined to map 17 land cover categories in the Greater Boston area of, Massachusetts, USA. The key goal of this work is to test the integration of radar and optical data. The contribution of different dimensions of input data to a random forest classifier was evaluated with map accuracy statistics. PALSAR data produced a 30.99% overall classification accuracy. Higher classification accuracy (72.24%) was achieved by adding texture variables derived from the PALSAR data. A September Landsat image produced a map accuracy of 77.96%. The inclusion of Landsat images from other three seasons increased map accuracy to 86.86% and Landsat derived texture variables further increased the map accuracy to 92.69%. The highest map accuracy (93.82%) was achieved by combining Landsat and PALSAR. Though combining PALSAR and Landsat only increased the overall accuracy by 1.1%, it was a statistically significant increase, whose magnitude was limited by the high accuracy already achieved with Landsat data. Moreover, confusion matrices and land cover maps indicated that most of this increase was from three urban land cover types ( low density residential , high density residential , and commercial/industrial ). The results demonstrate the value of combining multitemporal Landsat imagery, ALOS PALSAR data, and texture variables for land cover classification in urban and peri-urban environments.
Ultraviolet photolysis and proton irradiation of astrophysical ice analogs containing hydrogen cyanide

Hydrogen cyanide (HCN) has been identified in the gas phase of the i nterstellar medium as well as in the comae of several comets. Terrestrially, HCN is a key component in the synthesis of biologically important molecules such as amino acids. In this paper, we report the results of low-temperature (18 K) ice energetic processing experiments involving pure HCN and mixtures of HCN with H2 Oa nd NH 3. Ice films, 0.1 to several microns in thickness, were exposed to either ultraviolet photons (110–250 nm) or 0.8-MeV protons to simulate the effects of space environments. Observed products include HCNO (isocyanic acid), NH + (ammonium ion), CN − (cyanide ion), OCN − (cyanate ion), HCONH2 (formamide), and species spectrally similar to HCN polymers. Product formation rates and HCN destruction rates were determined where possible. Results are discussed in terms of astrophysical situations in the ISM and the Solar System where HCN would likely play an important role in prebiotic chemistry. These results imply that if HCN is present in icy mixtures representative of the ISM or in comets, it will be quickly converted into other species in energetic environments; pure HCN seems to be polymerized by incident radiation.
Autophagy and the Immune System

Stressors ranging from nutrient deprivation to immune signaling can induce the degradation of cytoplasmic material by a process known as autophagy. Increasingly, research on autophagy has begun to focus on its role in inflammation and the immune response. Autophagy acts as an immune effector that mediates pathogen clearance. The roles of autophagy bridge both the innate and adaptive immune systems and include functions in thymic selection, antigen presentation, promotion of lymphocyte homeostasis and survival, and regulation of cytokine production. In this review, we discuss the mechanisms by which autophagy is regulated, as well as the functions of autophagy and autophagy proteins in immunity and inflammation.
Venture philanthropy and social entrepreneurship in community redevelopment

This article provides a case study of Tom Cousins, a social entrepreneur who used his own venture philanthropic investments and leveraged additional resources through extensive publicprivate partnerships for the sole intent of redeveloping an area of disinvestment and poverty. In the process, Cousins also provided the visionary, strategic, and operational leadership often associated with the actions and responsibilities of a social entrepreneur. The limited research to date has investigated social entrepreneurship and venture philanthropy as separate and often unrelated concepts. In this study, we analyze the sustained and intensive involvement by Cousins and his foundations and the continued leadership provided in the creation of public-private partnerships focused on the redevelopment of the East Lake area in Atlanta. V ENTURE PHILANTHROPY and social entrepreneurship are relatively new concepts and have only begun to be examined in the nonprofit and philanthropy literatures. This case study examines how a venture philanthropist and social entrepreneur used two nonprofit foundations, his own resources, and extensive partnerships to enact a strategy of redevelopment of a public housing project and its surrounding neighborhood. The specific focus is on the efforts of Atlanta developer Tom Cousins and the manner in which he used the resources of his own CF Foundation (CFF) and created the East Lake Community Foundation (ELCF) to revitalize an area of Atlanta known as East Lake Meadows, an area of concentrated poverty, crime, and disinvestment. Our analysis is of an entrepreneur and philanthropist who made a significant charitable investment designed to mitigate social need based on a theory of economic development,
Using aerial images to calibrate the inertial sensors of a low-cost multispectral autonomous remote sensing platform (AggieAir)

Even though small, low-cost unmanned aerial vehicles (UAVs) make good remote sensing platforms by reducing the cost and making imagery easier to obtain, there are also some tradeoffs. The low altitude, small image footprint and high number of images make it difficult and tedious to georeference the images based on features. Auto-orthorectification techniques based on the position and attitude of the UAV would work well except the inherent errors in the UAV sensors reduce the accuracy of the orthorectification significantly. This paper presents a method to improve the orthorectification accuracy by calibrating the UAV sensors. This is done by inverse or-thorectifing the images to find the actual position and attitude of the UAV using ground references setup in a square. Actual data from a test flight is used to validate this method.
Fatality Incidence Stratified by Driver Behavior: An Exploratory Analysis with FARS Data

Driver behavior indicators were used to stratify FARS (Fatal Accident Reporting System) data on occupant fatalities. Data for automobiles, vans, and light trucks were stratified by: single or multiple vehicle accident driver use of alcohol driver use of safety belt
Adjuvant induced destructive periodontitis in nonhuman primates. A comparative study.

Complete (CFA) and incomplete (IFA) Freund's adjuvant was injected into the periodontium of sensitized marmoset, capuchin and rhesus monkeys. All animals developed a proliferative granulomatous reaction at the injection sites. There were, however, species specific differences in the degree of destruction associated with the CFA injection. The marmosets and capuchins developed a destructive periodontitis. In the rhesus monkey, the lesion was both bone destructive and bone inductive. Tubercles containing typical Langhan's type giant cells, but without central necrosis, were only produced by the rhesus monkey. Granulation tissue with no necrosis was produced by the marmoset and capuchin monkeys. While there was some degree of periodontal destruction in all CFA injected animals, it was most severe in the marmoset followed in descending order by the capuchin and by the rhesus. The injection of IFA into the periodontium of the same animals resulted in the formation of nondestructive highly proliferative granulation tissue.
User Adaptation and Infusion of Information Systems

Today's complex information systems can be used to varying degrees by individuals. Information system infusion captures the degree to which the system is used deeply, or to its fullest extent, for improving organizational and individual performance. Theory suggests that infusion at the individual level depends on user adaptation to an information system; however, relationship between types of user adaptation and infusion has not been examined in extant research. This study draws on the Coping Model of User Adaptation to explore how various adaptation behaviors employed by information system users influence its infusion in their work. Results indicate that problem-focused adaptation behaviors directed toward changing the work-system-self dynamic promote infusion, while avoidance-oriented emotion-focused adaptation behaviors tend to diminish infusion. Theoretical and practical implications of these findings are discussed.
Measurement of the collisional depolarization cross section of the silver 5/sup 2/P/sub 1/2/ state by helium

We have measured the cross section for depolarization of the 5/sup 2/P/sub 1/2/ state of silver atoms by collisions with helium atoms using the Hanle-effect technique. We find the nuclear-spin-independent cross section to be sigma = 1.2 +- 0.15 x 10/sup -16/ cm/sup 2/, significantly smaller than the corresponding cross sections in rubidium and cesium. This is the first measurement of this quantity in any noble-metal atom.
Stable second-order nonlinearity in SiO 2 -based waveguide structures on Si

There is a need for inexpensive, manufacturable phase modulators and frequency converters, based on a second-order optical nonlinearity, that can be readily integrated with other optoelectronic components. Devices based on crystalline materials are difficult to integrate. Waveguides fabricated in polycrystalline materials generally suffer from excess losses. Organic and polymer- based nonlinear materials and devices have been the most successful, but have not yet provided a robust, broadly applicable solution. Thus, our initial report1 of a relatively large (χ(2) ~ 1 pm/V), stable nonlinearity formed in the near surface region of bulk fused silica materials by a combined temperature and electric field poling process has generated considerable interest. Subsequently, corona poling was used to induce a comparable nonlinearity in thin films of Corning 7059™ sputter-deposited on various glass substrates and unphase- matched waveguide second-harmonic generation (SHG) was demonstrated.2 Electron-beam irradiation of lead silicate glasses3 leads to a comparable nonlinearity. An electro-optic effect has been reported4 in waveguides formed by e-beam densification of bulk silica and poled by the temperature/field process. We have reported5 on corona poling of Si3N4/SiO2/Si waveguide structures; however, the nonlinearity was relatively unstable, decaying within several days, probably due to leakage of transient surface charges. In this paper, we report on the first observation of a stable second-order nonlinearity in a SiO2-based waveguide stack grown on a silicon substrate.
MEASURING POLLINATOR-MEDIATED SELECTION ON MORPHOMETRIC FLORAL TRAITS: BUMBLEBEES AND THE ALPINE SKY PILOT, POLEMONIUM VISCOSUM

Sweet-flowered plants of Polemonium viscosum in Colorado are visited by a fly-dominated pollinator fauna at timberline (krummholz), but almost exclusively by bumblebees in higher-elevation tundra habitats. Significant increases in flower size and height are associated with increasing elevation along this habitat gradient. This paper presents the results of an experiment designed to test whether bumblebees exert sufficient selection on morphometric floral phenotypes to account for the clinal shifts seen in natural populations. Two populations of sweet-flowered plants of krummholz origin were established: one randomly pollinated, the other solely bumblebee-pollinated. I tested the effects of two independent axes of floral variation, obtained by principal-components analysis, on mean seed set per flower of plants in each population. PC1, with strong correlations to corolla diameter, corolla length, and stem height, explained a significant amount of variance in seed set for bumblebee-pollinated plants but had no bearing on that of randomly pollinated plants. PC2, with strong correlation to flower number, did not influence seed set in either population. Bumblebee behavior was correlated with variation in PC1 scores of the selected population, yielding positive directional selection on morphometric floral traits associated with PC1. Selection coefficients for PC1, corolla length, corolla diameter, and inflorescence height were estimated, respectively, as 0.11, 0.09, 0.07, and 0.06 (P < 0.025 in all cases). These results support the hypothesis that pollinator-mediated selection can bring about changes in floral form, and can explain shifts in floral morphology of P. viscosum along natural habitat gradients.
Relation between platelet integrity and sulfhydryl groups.

Summary1. Incubation of freshly prepared human platelets with a variety of sulfhydryl inhibitors results in increased rate of platelet breakdown. 2. In all cases studied the effects of inhibitors can be decreased in extent by suitable concentrations of SH-containing substances such as cysteine or reduced glutathione. 3. Results obtained suggest a direct relationship between platelet sulfhydryl groups and platelet structure. The possible link of this relationship to platelet metabolism is briefly discussed.
SONG DIALECTS AND GENETIC DIFFERENCES IN WHITE-CROWNED SPARROWS (ZONOTRICHIA LEUCOPHRYS).

Song dialects have been described in several bird species (Marler and Tamura, 1962; Lemon, 1966; Nottebohm, 1969). Clear examples are found in the resident white-crowned sparrows (Zonotrichia leucophrys nuttalli) of coastal California and in populations of the chingolo (Zonotrichia capensis) of Argentina. Where dialects occur in these species an area of breeding habitat is occupied by territorial males that with few exceptions sing a very similar song. Contiguous and allopatric with this area males of another population sing a different song type. It has been shown (Marler and Tamura, 1964; Marler, 1970) that in the white-crown (Z. 1. nuttalli) the dialect is learned during the first few weeks of life. The contiguity of the populations with discretely different vocalizations could be related to several interesting questions in population genetics, vocal communication, and evolutionary processes. On a general level, however, the dialect phenomenon leads to two central issues: (1) How do dialects arise? and (2) What role, if any, do they play in the biology of the birds? In this paper I provide a speculation on the first question and some data that may clarify the second. Following a suggestion by Marler and Tamura (1962), Nottebohm (1969) proposed that females might preferentially mate with males of their own dialect, thereby constraining a locally adapted gene pool. This hypothesis, that dialects reduce gene migration, came from the observation that Z. capensis on altitudinal gradients in Argentina exhibits a series of dialect populations possibly corresponding to different selective regimes, whereas a single dialect is found over vast areas of lowland pampas where selection may be spatially homogeneous (Nottebohm, 1969; Nottebohm and Selander, 1972). There, are other possible explanations of song dialects in birds. First, song dialects, a consequence of vocal learning, may play no important role. Perhaps during the early learning phase, young birds acquire population specific calls that promote flocking, foraging efficiency, predator avoidance, or individual recognition, that are important for winter survival. Thus, the selective advantage of vocal learning would be explained by winter ecological conditions and not territorial breeding behavior. Second, dialects could maximize outcrossing in small populations. Females would mate with males having a song type unlike that of their early experience. Third, dialects may be a result of intrasexual selection and bear no direct relationship to mate selection. Perhaps vocal convergence bestows some advantage in gaining and holding a territory but females do not use dialect information for mate choice. Using an electrophoretic analysis of alloenzymes, I investigated populations of Nuttall's white-crowned sparrow (Z. 1. nuttalli) in California and populations of the mountain white-crown (Z. 1. oriantha) in Colorado to determine if song dialects were correlated with genetic differentiation.
Argon-Beam-Induced Defects in a Silica-Supported Single-Walled Carbon Nanotube

Ion beams can be used to tailor the structure and properties of carbon nanostructures. Using molecular dynamics simulations, we explored the effects of irradiating silica-supported single-walled ca...
Abstract 4340: Increased cytokine and chemokine expression in U87MG glioblastoma cells after large clinically relevant single doses of ionizing radiation

BACKGROUND: Stereotactic radiosurgery is an established treatment option that uses high, single fraction doses of radiation to target tumors. Despite the best clinical strategies to eliminate brain tumors using this technique or others (surgery, chemotherapy and/or other radiotherapy techniques), post-therapy recurrence of brain tumors remains a major challenge in patients. To better understand the radiation response, we investigated how such high doses modulate the molecular signaling within glioblastoma cell populations from several days to months after irradiation. METHODS: The glioblastoma cell line, U87MG, was treated with single doses of ionizing radiation between 0 to 16Gy in vitro followed by: examination of cell proliferation; clonogenic survival; extraction of RNA; and subcutaneous injection into nude mice to monitor tumor growth 24 hours after cell irradiation. Genome-wide expression profiling was run on the Illumina HT-12 bead array platform and analysis for significant expressed genes was performed along with network analysis using Ingenuity Pathway Analysis and GenePattern platforms. RESULTS: As expected, high doses of radiation stunted growth of the U87MG cells from 0 to 14 days. Long term, single cell clonogenic survival of the irradiated cells was approximately 3% and 0.01% following 8Gy or 16Gy, respectively. Genome-wide gene expression at 1, 4 and 6 days after irradiation of 8 or 16Gy has revealed a dose-dependent increase in inflammatory cytokines and chemokines. Increased cytokine expression for IL-6 and IL-8 was validated in vitro using qRT-PCR. In vivo, 100% of the untreated U87MG cells formed tumors, whereas less than half of all irradiated treatment groups failed to form tumors. In those samples that did grow despite irradiation, the average time to tumor formation (volume = 300mm 3 ) was 13, 32, 58 and 88 days for 0, 8, 12, and 16Gy respectively while the exponential fits to tumor growth rate was shown to be accelerated after 8Gy but diminished after 12 and 16Gy. IL-6 gene expression was found to be elevated in tumors formed from irradiated cells versus control. CONCLUSION: The data presented here provides novel insight into the cellular and molecular modulation of glioblastoma cell populations by large, clinically relevant, single doses of ionizing radiation. A salient finding is the expression of inflammatory cytokines as a major player in the radiation response at periods long after the irradiation insult. This study was supported by NIH ICBP 1U54CA149233 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 4340. doi:1538-7445.AM2012-4340
Adrenocortical Function in Hypo- and Hyperthyroidism.∗:

Summary1. As a means of assessing adrenocortical function, the eosinopenic and adrenal ascorbic acid depletion responses of normal and thyroidectomized male rats, with and without thyroxine treatment, have been examined. 2. With nembutal sedation, the eosinopenic response to ACTH was the same in thyroidectomized as in normal rats and was not influenced by treatment with thyroxine in either group. 3. Under these conditions the eosinopenic response to epinephrine was less in thyroidectomized than in normal rats and was distinctly improved after thyroxine therapy. The response of normal rats to epinephrine was not modified by the administration of thyroxine in doses leading to hyperthyroidism. 4. In the second test used, adrenal ascorbic acid depletion in response to ACTH; the thyroidectomized rats showed a greater and more uniform depletion than did normal rats, with the same dose of ACTH. Hyperthyroid rats responded like the normals.
Very Thin Films of High Dielectric Constant Materials

An all-alkoxide route to SrBi2Ta2O9 (SBT) thin films and powders was developed. While stoichiometric gels transformed to single-phase SBT, excess bismuth was required to obtain single-phase SBT films on Pt substrates. An annealing temperature of 800 °C in O2 for 2 minutes was required to crystallize the films. Electrical measurements of SBT films produced under these conditions showed that films less than 2000 A in thickness were shorted, while films of 3000 to 5000 A had a dielectric constant of∼ 300. RBS measurements of a bismuth titanate film on Pt indicated that Pt diffuses into the dielectric layer when annealed at 700 °C in O2 for 1 minute, suggesting that interfacial reaction of these layered bismuth materials may be significant.
The NOAA Satellite Observing System Architecture study

NOAA is beginning a study, the NOAA Satellite Observing System Architecture (NSOSA) study, to plan for the future operational environmental satellite system that will follow GOES and JPSS, beginning about 2030. This is an opportunity to design a modern architecture with no preconceived notions regarding instruments, platforms, orbits, etc., but driven by user needs. The NSOSA study team will develop and evaluate architecture alternatives, to include partner and commercial alternatives that are likely to become available. The objectives will include both functional needs and strategic characteristics (e.g., resiliency, flexibility, responsiveness, sustainability). The study will be informed by the Space Platform Requirements Working Group (SPRWG), commissioned by NESDIS. The SPRWG is charged to assess new or existing user needs and to provide relative impacts from different candidate observing systems in the future architecture. SPRWG results will serve as input to the process for new foundational (Level 0 and Level 1) requirements for the next generation of NOAA satellites that follow the GOES-R, JPSS, DSCOVR, Jason-3, and COSMIC-2 missions.
The Beginning of Bioinformatics

Bioinformatics has become a buzzword in the post-genomic era. However, the discipline is not new. This chapter introduces the three scientists whose initiatives 50 years ago led to the birth of the science of bioinformatics, and briefly discusses their contributions. Although at the time it was not called bioinformatics, the application of computers in protein-sequence analysis and tracing protein evolution was the rudimentary form of contemporary bioinformatics. These three scientists were Margaret Dayhoff, Richard Eck, and Robert Ledley. Of these, Margaret Dayhoff’s contributions stood out the most and she is often credited as being the pioneer in bioinformatics for her varied contributions, including developing the first amino-acid substitution matrix for studying protein evolution. The chapter also discusses the scope and tools of bioinformatics.
Arms and the University: ROTC and the Ivies

What the radicals did not understand, according to John Updike, is that, in a world indelibly stained by Original Sin, peace “depends upon the threat of violence. The threat cannot always be idle.” – Janet Tassel, discussing and quoting Harvard graduate John Updike It is fitting to begin our empirical sojourn with the most politicized dimension of the relationship between the military and the university: the historical movement against ROTC and the subsequent efforts to bring it back from institutions that drove it away in the 1960s. Our focus is the Ivy League in general and Columbia University in particular. The reasons for this focus are threefold. First, Columbia and the Ivies offer the most prominent examples of the campus war truces that led to the abolition or abandonment of ROTC in the late 1960s and early 1970s. As we will see, there is some confusion as to the actual motives that lay behind this process, so the best way to express what happened has been offered by Columbia sociologist Allan Silver, who says that such universities “effectively barred” ROTC at the time. Second, the Ivies have emerged as a key home front for what we could call the “return of the soldier” to higher education in terms of both physical and mental presence. Columbia is a veritable ground zero for this movement. Third, because of their elite and self-proclaimed status as America’s most prestigious schools of preparing future leaders, Ivy institutions represent the most interesting and telling examples of the abandonment of the military by the nation’s elites – the “absent without leave” (AWOL) phenomenon that has occasioned the justifiable consternation of citizens committed to a common civic order.
Moving Money: Organizational Aspects of a Development Model

Introducing organizational theory into the analysis of the World Bank, one risks appearing to excuse its performance as a function of the perversity of large bureaucracies, a quirk of the organizational type. This chapter and the two that follow put forward an organizational analysis that deals not with bureaucratic quirks, but with the form and substance of the World Bank’s role in the global economy. The contribution of organizational analysis begins with the premise that organizations are not only created entities and tools of their creators, but also social entities, holding to values and priorities and working to preserve themselves and advance their own interests.
The English Stress Cycle and Interlexical Relations

The phonological cycle embodies the fundamental insight that words are derived not from raw morphological primitives, but from preexisting bases (i.e. actually occurring words), to which certain phonological processes have already been applied.1 For decades English stress has provided the most persuasive arguments for the transformational cycle. Despite occasional dissenters (notably Ross 1972, Hill-Nessly 1973, McCawley 1974, Schane 1975 and Selkirk 1980), virtually all current accounts of English accentuation assume some version of the cycle. The basic claim of a cyclic approach to stress assignment is this: the word base bequeaths its accentual pattern to its derivatives. This inherited accentual pattern may take the form of a residual stress (a la SPE (Chomsky-Halle 1968)), or simply a ‘+’ (Liberman-Prince 1977), a gridmark ‘x’ or asterisk ‘*’ (Prince 1983, Selkirk 1984, Halle-Vergnaud 1987), or an ‘S’ (for ‘strong’, Schane 1979). In the ‘arboreal’ model of metrical theory, what is passed on from one cycle to the next may be a more complex metrical organization encoded in the form of labelled trees (Kiparsky 1979, 1982, Hayes 1982). In this paper I propose to examine critically the cyclic approach to English stress assignment with reference to the tree model of metrical theory.
Climate-induced seasonal changes in smallmouth bass growth rate potential at the southern range extent

Temperature increases due to climate change over the coming century will likely affect smallmouth bass (Micropterus dolomieu) growth in lotic systems at the southern extent of their native range. However, the thermal response of a stream to warming climate conditions could be affected by the flow regime of each stream, mitigating the effects on smallmouth bass populations. We developed bioenergetics models to compare change in smallmouth bass growth rate potential (GRP) from present to future projected monthly stream temperatures across two flow regimes: runoff and groundwater-dominated. Seasonal differences in GRP between stream types were then compared. The models were developed for fourteen streams within the Ozark–Ouachita Interior Highlands in Arkansas, Oklahoma and Missouri, USA, which contain smallmouth bass. In our simulations, smallmouth bass mean GRP during summer months decreased by 0.005 g g−1 day−1 in runoff streams and 0.002 g g−1 day−1 in groundwater streams by the end of century. Mean GRP during winter, fall and early spring increased under future climate conditions within both stream types (e.g., 0.00019 g g−1 day−1 in runoff and 0.0014 g g−1 day−1 in groundwater streams in spring months). We found significant differences in change in GRP between runoff and groundwater streams in three seasons in end-of-century simulations (spring, summer and fall). Potential differences in stream temperature across flow regimes could be an important habitat component to consider when investigating effects of climate change as fishes from various flow regimes that are relatively close geographically could be affected differently by warming climate conditions.
Flexor Sheath Irrigation for Flexor Tenosynovitis

This chapter describes in detail the surgical steps for performing an incision, drainage and irrigation for suppurative flexor tenosynovitis. The operative note has been generalized so that it can be applied to various digits of the hand with appropriate modifications. The approach should allow for incision and drainage of the affected digit as well as placement of an apparatus amenable for postoperative irrigation of the tendon sheath. Indications, surgical steps, postoperative care, an operative dictation template, and suggested readings/references are included.
Giving Voice to Values: A Pedagogy for Behavioral Ethics:

Management education has had a long and somewhat conflicted relationship with the integration of ethics and values-driven leadership into its curriculum. This essay presents some of the key challen...
Containing errors in computations for neural sensing: Does a hierarchical-referencing strategy lead to energy savings?

Recent experimental evidence and theoretical results challenge the belief that ultra high-density EEG sensing will not yield higher spatial resolutions. It raises the exciting possibility that source-localization accuracy can be improved substantially with ultra high-density systems; however, these systems are hindered by implementation constraints in circuit volume and energy consumption. Recently, an information-theoretic hierarchical referencing mechanism has been proposed to exploit the decay of high-spatial frequencies during volume conduction from source to scalp — and the induced high local spatial correlations — to reduce the required circuit power and volume. In this paper, human EEG data is used to experimentally test and validate theoretical inter-electrode correlations and bit savings when employing a hierarchical referencing strategy. Extrapolating from electrodes that are at least 2 cm apart, we observe that on average savings can exceed 3 bits per electrode at inter-electrode distances of 3 mm.
Cabozantinib for the treatment of kidney cancer

ABSTRACTIntroduction: Cabozantinib is a small molecule tyrosine kinase inhibitor that initially showed activity in medullary thyroid cancer and was recently approved by the Food and Drug Administration for the treatment of metastatic renal cell carcinoma after progression on first line therapy.Areas covered: In the METEOR trial, cabozantinib demonstrated significantly improved efficacy in all three endpoints; response rates, progression free survival and overall survival in a randomized trial with everolimus as an active comparator. Cabozantinib also showed activity in the front line setting in RCC within the CABOSUN trial. The study randomized untreated metastatic RCC patients to either cabozantinib or sunitinib and the former showed improved progression free survival which was the primary endpoint. The future holds promise for indications in other malignancies, given the preliminary efficacy and unique mechanism of action of cabozantinib.In this review we address the mechanism of action, pharmacodynamic...
Decomposition of diverse solid inorganic matrices with molten ammonium bifluoride salt for constituent elemental analysis

Abstract Ammonium bifluoride (ABF, NH 4 F·HF) is a well-known reagent for converting metal oxides to fluorides and for its applications in breaking down minerals and ores in order to extract useful components. It has been more recently applied to the decomposition of inorganic matrices prior to elemental analysis. Herein, a sample decomposition method that employs molten ABF sample treatment in the initial step is systematically evaluated across a range of inorganic sample types: glass, quartz, zircon, soil, and pitchblende ore. Method performance is evaluated across two variables: duration of molten ABF treatment and ABF reagent mass to sample mass ratio. The degree of solubilization of these sample classes are compared to the fluoride stoichiometry that is theoretically necessary to enact complete fluorination of the sample types. Finally, the sample decomposition method is performed on several soil and pitchblende ore standard reference materials, after which elemental constituent analysis is performed by ICP-OES and ICP-MS. Elemental recoveries are compared to the certified values; results indicate generally good to excellent recoveries across a range of alkaline earth, rare earth, transition metal, and actinide elements.
Nonvitamin, Nonmineral Dietary Supplement Use among Adults with Fibromyalgia: United States, 2007–2012

Background. Fibromyalgia (FMS) is a pain condition affecting 2–6% of US adults; effective treatment remains limited. Determinants of nonvitamin, nonmineral dietary supplement (NVNM) use among adults with FMS are not well-studied. We investigated the relation of NVNM use to FMS, and trends, in two nationally representative samples of US adults ≥18 years. Methods. Data were drawn from 2007 and 2012 National Health Interview Surveys (’s = 20127 and 30672, resp.). Logistic regression was used to examine associations of FMS to NVNM use (past 12 months) and evaluate potential modifying influences of gender and comorbidities. Multivariate models adjusted for sampling design, demographic, lifestyle, and health-related factors. Results. FMS was significantly higher in 2012 than in 2007 (1.7% versus 1.3%), whereas NVNM use decreased (57% versus 41%; ). Adults reporting diagnosis were more likely to use NVNMs within 12 months, 30 days, or ever relative to adults without; positive associations remained significant after controlling for demographics, lifestyle characteristics, medical history, and other confounders (ranges: 2007 and 2012 AORs = 2.3–2.7; 1.5–1.6, resp.; ’s < 0.0001). Conclusion. In this cross-sectional study of two national samples, NVNM use was strongly and positively associated with FMS, highlighting the need for further study.
HIGH REYNOLDS NUMBER OSCILLATING FLOW BY CYLINDERS

In order to determine the added mass, drag and lift coefficients of a smooth cylinder at various distances from a plane boundary, the forced cylinder oscillation tests at high Reynolds number 105 to 106 and the wave force tests at moderate Reynolds number 101* to 105 have been carried out at the Wave Research Facility at Oregon State University. It is found that the drag, lift and added mass coefficients are all strongly Reynolds number dependent. The effect of the near by plane boundary is to increase all of the force coefficients two to four times as compared to the free stream flow values. This is a most important factor to be aware of for design purposes.
Management of epistaxis in patients with ventricular assist device: a retrospective review

Patients with a ventricular assist device (VAD) are at risk for epistaxis due to the need for anticoagulation. Additionally, these patients develop acquired von Willebrand syndrome (AvWS) due to these devices. Management is complicated by the risk of thrombosis if anticoagulation is reversed. This study sought to characterize the clinical features and management of epistaxis in this high-risk population. Retrospective review of adults with VAD and epistaxis necessitating inpatient consultation with the otolaryngology service were included. 49 patients met inclusion criteria. All patients had a presumed diagnosis of AvWS. An elevated INR (> 2.0) was present in 18 patients (36.7%). Anticoagulation was held in 14 (28.6%) patients, though active correction was not necessary. Multiple encounters were required in 16 (32.7%) patients. Spontaneous epistaxis was associated with multiple encounters (p = 0.02). The use of hemostatic material was associated with a lower likelihood of bleeding recurrence (p = 0.05), whereas cauterization with silver nitrate alone was associated with a higher likelihood of re-intervention (p = 0.05). Surgery or embolization was not required urgently for any patient. Endoscopy under general anesthesia was performed for one patient electively. Mean follow up time was 16.6 months (σ = 6.3). At six months, 18 (36.7%) patients were deceased. While these patients are at risk for recurrent spontaneous epistaxis, nonsurgical treatment without active correction of INR or AvWS was largely successful. Placement of hemostatic material, as opposed to cautery with silver nitrate, should be considered as a first-line treatment in this group. Multidisciplinary collaboration is critical for successful management.
Impact of Epicardial Adipose Tissue in Heart Failure with Preserved Ejection Fraction

Introduction Obesity is a strong risk factor for heart failure (HF) with preserved ejection fraction (HFpEF). HFpEF patients with obesity display distinct structural and functional changes in the heart compared to non-obese HFpEF. In addition to generalized obesity, fat distribution may also be important. Prior studies have shown that epicardial adipose tissue (EAT) is associated with inflammation, atrial fibrillation and cardiac fibrosis. Based upon its location, EAT might also influence hemodynamics and ventricular interaction via direct mechanical effects. However, no study has directly evaluated the impact of EAT content in HFpEF. Hypothesis We hypothesized that among patients with obesity and HFpEF, those with excess EAT (EAT+, n=77) would display more deranged hemodynamics compared to obese HFpEF patients without excess EAT (EAT−, n=92). Methods Patients underwent invasive hemodynamic cardiopulmonary exercise testing and echocardiography. Obesity was defined by BMI≥30 kg/m2 and excess EAT was defined by EAT thickness ≥9mm by echocardiography. Ventricular interaction was assessed by the left ventricular eccentricity index (LVecc), where higher values indicate greater interdependence. Results EAT+ and EAT− patients displayed similar cardiac structure and function (Table). However, compared to EAT−, LVecc were elevated in EAT+. Right atrial (RA), pulmonary artery (PA), and pulmonary capillary wedge pressures (PCWP) were higher at rest and during exercise in EAT+ compared to EAT−, despite similar diastolic chamber stiffness (β) among EAT+ and EAT−. Peak VO2 was reduced in both groups, but was significantly lower in EAT+ compared to EAT−. Conclusion Among patients with the obese phenotype of HFpEF, the presence of increased EAT is associated with more profound hemodynamic derangements at rest and exercise, greater pericardial restraint, and poorer exercise capacity (VO2). Further study is needed to understand the biology and potential treatment of excessive EAT in patients with HFpEF.