cssi/SciSciGPT-SciSciNet huggingface dataset:
Loss of NEIL1 causes defects in olfactory function in mice.

Abstract Oxidative DNA damage accumulation has been implicated in neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease. The base excision repair pathway is a primary responder to oxidative DNA damage. Effects of loss of base excision repair on normal brain function is a relatively nascent area of research that needs further exploration for better understanding of related brain diseases. Recently, we found that loss of a versatile DNA glycosylase endonuclease 8-like 1 (NEIL1) causes deficits in spatial memory retention using the Morris water maze test. Furthermore, we found that there is a significant loss of NEIL1 enzyme levels and its activity in postmortem Alzheimer's disease brains. Based on the Allen Brain Atlas in situ hybridization data, the expression levels of Neil1 messenger RNA are higher in the olfactory bulb compared with other areas of the brain. Olfaction in mice is a central brain function that involves many central nervous system pathways. Here, we studied the effect of complete loss of Neil1 gene on olfactory function. We explored olfactory function in mice with 3 different behavioral tests namely, olfactory sensitivity, performance, and buried food tests. Neil1−/− mice performed poorly compared with wild-type mice in all 3 tests. Our data indicate that loss of Neil1 causes olfactory function deficits supporting our previous findings and that normal brain function requires robust DNA repair.
Bimodal induction of dopamine-mediated striatal neurotoxicity is mediated through both activation of D1 dopamine receptors and autoxidation

Abstract Striatal neurodegeneration occurs through unknown mechanisms in certain neurodegenerative disorders characterized by increased and sustained synaptic levels of dopamine (DA). Treatment of rat primary striatal neurons with DA causes profound neurotoxicity, with increased production of free radicals and accelerated neuronal death. DA effects were partly reduced by the antioxidant sodium metabisulfite (SMBS), and the D1 DA receptor antagonist, SCH 23390, and were completely blocked upon co-treatment with SMBS and SCH 23390. Part of DA effects were mimicked by either H2O2, or by the D1 agonist, SKF R-38393, indicating the existence of two distinct signaling pathways through which the neurotoxicity of DA is manifest. DA effects did not proceed through D2-like DA or β-adrenergic receptor signaling pathways. The D1 receptor-mediated and the autoxidative pathways of DA neurotoxicity converge to cause activation and/or increased synthesis of neuronal and inducible, but not endothelial, nitric oxide synthase (NOS). The reduction of DA striatal neurotoxicity through blockade of D1 DA receptors, suggests novel therapeutic approaches in the management of striatal neurodegeneration.
Library myths that affect performance

Purpose – To show that many of the old ways in which people think about libraries are not based on fact, but rather on fiction. Many ideas that library managers hold to be truths are, in fact, baseless assumptions about library operations.Design/methodology/approach – Uses six examples of how library management often applies old approaches to the detriment of the library's future. After describing these examples, the truth about them is revealed as each one is examined and their fallacies are laid out.Findings – There are many assumptions that play in managing a library. Some of these are not based on fact and, as such, need to be discarded.Originality/value – Challenges managers to seek out the facts rather than base library policy on assumed truths. Even paradigms that may have once been true are not necessarily valid in today's library environment.
fox hunting as ritual

The continuing cultural importance of hunting in modern Western societies, especially to some elites, justifies increased attention from anthropologists. English fox hunting can be seen as a ritual of social class, one dramatizing themes and images about the gentry and aristocracy, and about rural society as a whole. The present analysis stresses the importance of examining the symbolic forms of modern society in a historical perspective, and it raises the possibility that some key symbols may be second-best substitutes or approximations of an ideal. [hunting, ritual, symbolism, social class, England]
Azithromycin Does Not Cure Pityriasis Rosea

Objectives Pityriasis rosea (PR) is a common skin disorder in children. Its cause is unknown. A recent publication reported a 73% cure rate in patients with PR after treatment with erythromycin. To duplicate this result using a drug with fewer adverse effects and greater biological half-life, we set out to study the effect of azithromycin on PR. Azithromycin is an azalide antibiotic with a spectrum of antimicrobial activity very similar to that of erythromycin. Design We randomly assigned 49 children with PR to receive either azithromycin (12 mg/kg per day, up to a maximum of 500 mg/day) for 5 days or a similar-appearing placebo. Study physicians were blinded to patients' treatment type. Two pediatricians had to agree on the diagnosis of PR before patients could be enrolled. Subjects were seen at follow-up visits 1, 2, and 4 weeks after starting treatment. Outcome measures We measured the appearance of new lesions and resolution of lesions. Results Rates of cure and of partial resolution were similar in the azithromycin and placebo groups. Conclusion Azithromycin does not cure PR.
Spatial complexity and control of a bacterial cell cycle

A major breakthrough in understanding the bacterial cell cycle is the discovery that bacteria exhibit a high degree of intracellular organization. Chromosomal loci and many protein complexes are positioned at particular subcellular sites. In this review, we examine recently discovered control mechanisms that make use of dynamically localized protein complexes to orchestrate the Caulobacter crescentus cell cycle. Protein localization, notably of signal transduction proteins, chromosome partition proteins, and proteases, serves to coordinate cell division with chromosome replication and cell differentiation. The developmental fate of daughter cells is decided before completion of cytokinesis, via the early establishment of cell polarity by the distribution of activated signaling proteins, bacterial cytoskeleton, and landmark proteins.
Self‐organization and polyolefin nucleation efficacy of 1,3:2,4‐di‐p‐methylbenzylidene sorbitol

Recent studies have demonstrated that addition of a small quantity of dibenzylidene sorbitol (DBS) to a molten polymer may result in a physical gel if conditions permit the DBS molecules to self-organize into a three-dimensional network composed of highly connected nanofibrils. If the polymer crystallizes, DBS may also serve as a nucleating agent, promoting the formation of spherulites, especially in commercially important polyolefins such as polypropylene. We examine the thermal and mechanical properties, as well as the morphological characteristics, of an isotactic polypropylene copolymer with 3 wt % ethylene upon addition of less than 1 wt % of 1,3:2,4-di-p-methylbenzylidene sorbitol (MDBS). From dynamic rheological measurements, pronounced complex viscosity increases, attributed to MDBS nanofibril network formation, are observed at concentration-dependent temperatures above the melting point of the nucleated copolymer. Transmission electron micrographs of RuO4-stained sections confirm the existence of MDBS nanofibrils measuring on the order of 10 nm in diameter and, at higher concentrations, fibrillar bundles measuring up to about 200 nm across and several microns in length. The addition of MDBS at different concentrations is also found to promote increases in optical clarity, yield strength, tensile strength, and ultimate elongation of modified copolymer formulations. © 1997 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 35: 2617–2628, 1997
Basically Full Ideals in Local Rings

Abstract Let A be a finitely generated module over a (Noetherian) local ring ( R , M ). We say that a nonzero submodule B of A is basically full in A if no minimal basis for B can be extended to a minimal basis of any submodule of A properly containing B . We prove that a basically full submodule of A is M -primary, and that the following properties of a nonzero M -primary submodule B of A are equivalent: (a) B is basically full in A ; (b) B = ( MB ): A M ; (c) MB is the irredundant intersection of μ( B ) irreducible ideals; (d) μ( C ) ≤ μ( B ) for each cover C of B . Moreover, if B is an M -primary submodule of A , then B * := ( MB ): A M is the smallest basically full submodule of A containing B and B ↦ B * is a semiprime operation on the set of nonzero M -primary submodules B of A . We prove that all nonzero M -primary ideals are closed with respect to this operation if and only if M is principal. In relation to the closure operation B ↦ B *, we define and study the bf-reductions of an M -primary submodule D of A ; that is, the M -primary submodules C of D such that C ⊆ D ⊆ C *. If G ( M ) denotes the form ring of R with respect to M and G + ( M ) its maximal homogeneous ideal, we prove that M n = ( M n )* for all (resp. for all large) positive integers n if and only if grade( G + ( M )) > 0 (resp. grade( M ) > 0). For a regular local ring ( R , M ), we consider the M -primary monomial ideals with respect to a fixed regular system of parameters and determine necessary and sufficient conditions for such an ideal to be basically full.
Examination of some fermented foods for the presence of apparent total N‐nitroso compounds

The fermented foods yoghurt, bread and cheese were analysed for the presence of apparent total N-nitroso compounds (ATNC) by a group-selective procedure involving direct chemical denitrosation and chemiluminescence detection of the released nitric oxide. The levels of ATNC were below the 20 micrograms(N-NO)/kg detection limit in all 20 yoghurts, 23 of the 24 bread samples and 28 out of 31 different varieties of cheese analysed. ATNC were detected in most of those cheese samples manufactured with added nitrate, including Edam, Gouda and Havarti, in concentrations ranging from 30 to 210 micrograms(N-NO)/kg.
Account of scattering-independent contributions to the Hall conductivity in ferromagnets: A reply

The current-cancellation argument presented by Smit in the preceding paper is shown to collapse because of an ambiguity in the nature of his wave functions. The side-jump current survives as the main cause of the anomalous Hall effect.
Some Phases of the Life History of the Trout‐perch

The trout-perch, Percopsis omiscomaycus (Walbaum), is one of the more abundant forage fishes in the larger lakes of midwestern United States and central Canada where walleye, Stizostedion v. vitreum (Mitchill), yellow perch, Perca flavescens (Mitchill), and coregonids predominate. It has been suggested that it may have considerable effect on perch and walleye populations of these lakes. The present study describes growth, food habits, population structure, year-class strengths, and reproductive capacity of the trout-perch in relation to its population dynamics in lower Red Lake, Minnesota. The physical characteristics of Red Lake and the ecology of commercial species are described by Smith and Krefting (1954), Pycha and Smith (1955), Van Oosten and Deason (1957), and Smith and Pycha (1961). Lower Red Lake, located in Beltrami and Clearwater Counties in north-central Minnesota (Figure 1) has an area of 255 mi2 and a maximum
Vulcanized meadowfoam oil

The factice gelation time for meadowfoam oil, along with hardness, color, acetone extract and free sulfur content of the gelled products were compared with gelation time and product properties of factice prepared from seed oils of rapeseed, crambe, soybean, castor,Lesquerella and jojoba. The effect of additives, specifically zinc oxide, magnesium oxide, triethylamine, dicyclohexylamine, 2-mercaptobenzothiazole and iodine, was also investigated. Both white and brown factices could be prepared from meadowfoam oil and their properties were equivalent to or better than those from high erucic acid rapeseed oil used commercially for the highest quality factice.
Comment on “A new feedback control of a modified Chua's circuit system”

Abstract Errors in Hwang et al. (1996) are pointed out. The correct results are presented. To demonstrate the errors, computer simulation results are provided.
COGNITIVE LINGUISTICS, SECOND LANGUAGE ACQUISITION, AND FOREIGN LANGUAGE TEACHING

COGNITIVE LINGUISTICS, SECOND LANGUAGE ACQUISITION, AND FOREIGN LANGUAGE TEACHING. Michel Achard and Susanne Niemeier (Eds.). Berlin: Walter De Gruyter, 2004. Pp. vi + 283. 98.00€, $118.00 cloth.Achard and Niemeier “hope that the different chapters in this volume will help establish the cognitive linguistics model as a valuable framework for the investigation of second language learning and teaching phenomena and provide the methodology to further extend the research” (p. 9). Not all of the chapters included realize that hope.
Iridium anomalies of late Eocene age at Massignano (Italy), and ODP Site 689B (Maud Rise, Antarctic)

Iridium anomalies of Late Eocene age are here reported in sequences from northern Italy and Weddell Sea, Antarctic. We have analyzed 270 samples of marly limestones from the Eocene/Oligocene boundary stratotype section at Massignano, Italy, ranging from 35.6 to 34.5 Ma (NP 18 Zone to NP 19/20 Zone). We discovered a distinct Ir peak of 156 ± 19 parts per trillion (ppt) in the lower calcareous nannofossil NP 19/20 Zone, corresponding to the mid-lower part of foraminiferal P16 Zone, and the top of magnetic Chron 16n2. The age of this Ir anomaly derived from several dated volcanic ashes found in the same section is 35.7 ± 0.4 Ma
Forward genetics uncovers Transmembrane protein 107 as a novel factor required for ciliogenesis and Sonic hedgehog signaling

Cilia are dynamic organelles that are essential for a vast array of developmental patterning events, including left-right specification, skeletal formation, neural development, and organogenesis. Despite recent advances in understanding cilia form and function, many key ciliogenesis components have yet to be identified. By using a forward genetics approach, we isolated a novel mutant allele (schlei) of the mouse Transmembrane protein 107 (Tmem107) gene, which we show here is critical for cilia formation and embryonic patterning. Tmem107 is required for normal Sonic hedgehog (Shh) signaling in the neural tube and acts in combination with Gli2 and Gli3 to pattern ventral and intermediate neuronal cell types. schlei mutants also form extra digits, and we demonstrate that Tmem107 acts in the Shh pathway to determine digit number, but not identity, by regulating a subset of Shh target genes. Phenotypically, schlei mutants share several features with other cilia mutants; however, spatial restriction of mutant phenotypes and lack of left-right patterning defects in schlei animals suggest differential requirements for Tmem107 in cilia formation in distinct tissues. Also, in contrast to mutants with complete loss of cilia, schlei mutants retain some function of both Gli activator and repressor forms. Together, these studies identify a previously unknown regulator of ciliogenesis and provide insight into how ciliary factors affect Shh signaling and cilia biogenesis in distinct tissues.
Adjuvant therapy of non small-cell lung cancer.

Multiple randomized prospective trials have failed to show a definitive survival advantage for the administration of adjuvant therapy following complete resection of non–small-cell lung cancer.
Competing Against the Unknown: The Impact of Enabling and Constraining Institutions on the Informal Economy

In addition to facing the known competitors in the formal economy, entrepreneurs must also be concerned with rivalry emanating from the informal economy. The informal economy is characterized by actions outside the normal scope of commerce, such as unsanctioned payments and gift-giving, as means of influencing competition. Scholars and policy makers alike have an interest in mitigating the impacts of such informal activity in that it might present an obstacle for legitimate commerce. Received theory suggests that country institutions can enable and constrain productive activity, and, in doing so, influence competitive obstacles in a country. Leveraging 13,670 responses from entrepreneurs distributed across 59 countries, we provide evidence that two particular types of enabling institutions, countries’ property rights regulations and cooperative actions, are useful for lowering the obstacles presented by informal activity. We also find evidence that two constraining institutions, economic and financial regulations lead to more obstacles presented by informal activity. We describe implications for entrepreneurs, policy makers, and future researchers stemming from these findings.
A Preliminary Study of Skylight Preferences

Previous research on environmental fenestration has generally neglected the study of people's preferences for skylights. In an attempt to fill this void, three studies were conducted to assess skyl...
Pediatric early warning score at time of emergency department disposition is associated with level of care.

ObjectiveThe objective of this study was to determine the association between the Pediatric Early Warning Score (PEWS) at time of emergency department (ED) disposition and level of care.MethodsWe conducted a prospective observational study with a convenience sample of patients aged 0 to 21 years in
Genetic causes of amyotrophic lateral sclerosis: new genetic analysis methodologies entailing new opportunities and challenges.

Abstract The genetic architecture of amyotrophic lateral sclerosis (ALS) is being increasingly understood. In this far-reaching review, we examine what is currently known about ALS genetics and how these genes were initially identified. We also discuss the various types of mutations that might underlie this fatal neurodegenerative condition and outline some of the strategies that might be useful in untangling them. These include expansions of short repeat sequences, common and low-frequency genetic variations, de novo mutations, epigenetic changes, somatic mutations, epistasis, oligogenic and polygenic hypotheses. This article is part of a Special Issue entitled ALS complex pathogenesis.
Inducing and observing the abstraction of a single hydrogen atom in bimolecular reactions with a scanning tunneling microscope

A variable-temperature scanning tunneling microscope (STM) was used to initiate and observe the abstraction of a single hydrogen atom in a simple bimolecular reaction. Dicarbon (CC) on the Cu(001) surface reacted separately with hydrogen sulfide (H2S) and water (H2O) to form CCH + SH and CCH + OH, respectively. At 9 K, hydrogen abstraction from H2O occurred spontaneously upon contact between CC and thermally diffusing H2O molecules. Hydrogen abstraction from H2S was effected at 9 K by inducing H2S diffusion via excitation with tunneling electrons. The thermal diffusion and reaction of H2S and CC were also observed at 45 K. By removing a single hydrogen atom from H2S and H2O using tunneling electrons, we established the identities of the sulfhydryl (SH) and hydroxyl (OH) reaction products. SH and OH did not react with CC under conditions that led to the reaction of the parent molecules. The bimolecular reactions H2O + O → 2OH and H2S + O → SH + OH did not occur thermally at 9 K but were induced by tunnelin...
How do athletes perceive and respond to change-events: An exploratory measurement tool

Abstract Objectives This study examined a new conceptual framework of change in the athletic career ( Samuel & Tenenbaum, in press ). An explorative perspective was assumed in order to: (a) develop a new measurement (Change-Event Inventory; CEI) to assess athletes’ experiences of certain change-events, and (b) examine athletes’ perceptions of and reactions to their change-event experiences, and the related effect of athletic identity. Design and method A cross-sectional design was used. The sample included adult athletes ( N = 338) from diverse athletic backgrounds who completed a measurement of athletic identity and the CEI. The psychometric properties of the CEI were established. Results Athletes reported experiencing various and multiple change-events in their careers, with a transition to a higher-level team or club and achieving a major accomplishment being the most frequently reported ones. Professional/international athletes experienced the highest variety of types of change-events ( M = 10.02, SD = 3.23). Certain change-events were experienced in different frequency rates as a function of athletes’ competitive level and sport discipline. Change-events were characterized by distinct profiles of perception, reaction, and coping. Athletic identity was associated with the perceived significance of change-events. Conclusions Athletes experience a variety of change-events in their careers, beyond the “traditional” athletic career transitions. Personal characteristics (e.g., competitive level, athletic identity) may affect athletes’ experience of and reaction to change-events. Educating coaches and parents about these types of events can be a valuable aspect of practitioners’ work.
Comparison of transrectal and transvaginal hybrid natural orifice transluminal endoscopic surgery partial nephrectomy in the porcine model.

Objective To compare the feasibility of porcine transrectal (TR) and transvaginal (TV) hybrid natural orifice transluminal endoscopic surgery (NOTES) partial nephrectomy (PN), as NOTES nephrectomy has recently been performed in the porcine model. Materials and Methods A total of 10 female pigs (weight 45 kg) underwent TR (n = 5) or TV (n = 5) NOTES PN. The pneumoperitoneum was created by a periumbilical 12-mm trocar, through which a laparoscope was advanced for intra-abdominal visualization. For TV-NOTES PN, a gastroscope was used to obtain TV peritoneal access. For TR-NOTES PN, a horizontal incision was made 2 cm above the dentate line, and a submucosal tunnel was created in the posterior rectal wall. The gastroscope was advanced through the submucosal tunnel and retroperitoneum to the kidney, and a peritoneal window was created. For both TR- and TV-NOTES PN, the gastroscope was exchanged for the SPIDER Surgical System. Flexible dissecting instruments and hook cautery introduced through the SPIDER Surgical System were used to mobilize the kidney. A harmonic scalpel introduced periumbilically was used to excise a portion of the lower pole. LAPRA-TY–secured sutured renorrhaphy was performed, followed by TR or TV specimen extraction. Results TR- and TV-NOTES PN was successfully performed in all 10 pigs. A comparison of TR- and TV-NOTES PN revealed no significant differences in the mean access time (29.2 vs 29.6 minutes, P = .944), operative time (196.0 vs 183.0 minutes, P = .631), and estimated blood loss (59.0 vs 54.0 mL, P = .861). Necropsy did not demonstrate abdominal injuries. Conclusion We have demonstrated proof-of-principle for TR and TV-NOTES PN in swine, with comparable perioperative parameters. Preclinical survival studies are requisite to assess the potential of TR-NOTES as an alternative to TV-NOTES.
Formation of preferences and strategic analysis

In some situations, players have to start analyzing the game before they have formed their preferences over the outcomes of the game. However, strategic analysis naturally depends on preferences. This dilemma will be discussed and some ideas for resolving it will be presented.
[F-18]-fluorodeoxyglucose positron emission tomography for targeting radiation dose escalation for patients with glioblastoma multiforme: clinical outcomes and patterns of failure.

Purpose: [F-18]-fluorodeoxyglucose positron emission tomography (FDG-PET) imaging for brain tumors has been shown to identify areas of active disease. Radiation dose escalation in the treatment of glioblastoma multiforme may lead to improved disease control. Based on these premises, we initiated a prospective study of FDG-PET for the treatment planning of radiation dose escalation for the treatment of glioblastoma multiforme. Methods and Materials: Forty patients were enrolled. Patients were treated with standard conformal fractionated radiotherapy with volumes defined by MRI imaging. When patients reached a dose of 45–50.4 Gy, they underwent FDG-PET imaging for boost target delineation, for an additional 20 Gy (2 Gy per fraction) to a total dose of 79.4 Gy ( n = 30). Results: The estimated 1-year and 2-year overall survival (OS) for the entire group was 70% and 17%, respectively, with a median overall survival of 70 weeks. The estimated 1-year and 2-year progression-free survival (PFS) was 18% and 3%, respectively, with a median of 24 weeks. No significant improvements in OS or PFS were observed for the study group in comparison to institutional historical controls. Conclusions: Radiation dose escalation to 79.4 Gy based on FDG-PET imaging demonstrated no improvement in OS or PFS. This study establishes the feasibility of integrating PET metabolic imaging into radiotherapy treatment planning.
A microstructural study of a Nd15Fe77B8 magnetic alloy produced by liquid dynamic compaction (LDC)

Abstract Rapidly solidified bulk Nd 15 Fe 77 B 8 magnets were produced by liquid dynamic compaction (LDC), a rapid solidification, spray deposition technique. Results of transmission electron microscopic studies showed that in magnets produced at low atomization gas pressures, the Nd 2 Fe 14 B phase had an oriented dendritic structure, and that magnets produced at high atomization gas pressures had an amorphous structure. Heat treatment of the amorphous structure resulted in the precipitation of fine Nd 2 Fe 14 B crystallites and a very large increase in coercivity to i H c = 14.8 kOe.
Relay selection for joint scheduling, routing and power allocation in multiflow wireless networks

We study an integrated multiflow network model, in which physical-layer rate control and link-layer medium access and routing decisions are jointly optimized. In particular, we explore the challenges involved in incorporating the three-terminal cooperative paradigm into such a broader resource allocation problem. We present several methods for defining cooperative units within the larger network, all of which introduce various levels of complexity into the resource allocation algorithm. Results show the benefits of utilizing cooperation over traditional routing, and further demonstrate that the routing and cooperative grouping decisions must be taken jointly.
Comparison of observed and model‐computed low frequency circulation and hydrography on the New England Shelf

[1] The finite volume coastal ocean model (FVCOM) is configured to study the interannual variability of circulation in the Gulf of Maine (GoM) and Georges Bank. The FVCOM-GoM system incorporates realistic time-dependent surface forcing derived from a high-resolution mesoscale meteorological model (MM5) and assimilation of observed quantities including sea surface temperature and salinity and temperature fields on the open boundary. An evaluation of FVCOM-GoM model skill on the New England shelf is made by comparison of computed fields and data collected during the Coastal Mixing and Optics (CMO) Program (August 1996–June 1997). Model mean currents for the full CMO period compare well in both magnitude and direction in fall and winter but overpredict the westward flow in spring. The direction and ellipticity of the subtidal variability correspond but computed magnitudes are around 20% below observed, partially due to underprediction of the variability by MM5. Response of subtidal currents to wind-forcing shows the model captures the directional dependence, as well as seasonal variability of the lag. Hydrographic results show that FVCOM-GoM resolves the spatial and temporal evolution of the temperature and salinity fields. The model-computed surface salinity field compares well, except in May when there is no indication of the fresh surface layer from the Connecticut River discharge noted in the observations. Analysis of model-computed results indicates that the plume was unable to extend to the mooring location due to the presence of a westward mean model-computed flow during that time that was stronger than observed. Overall FVCOM-GoM captures well the dynamics of the mean and subtidal flow on the New England shelf.
Brahms' integration of traditional and progressive tendencies: A look at three sonata expositions

(1988). Brahms' integration of traditional and progressive tendencies: A look at three sonata expositions. Journal of Musicological Research: Vol. 8, No. 1-2, pp. 141-168.
Structural analysis of bovine pancreatic thread protein

Pancreatic thread protein (PTP) forms double helical threads in the neutral pH range after purification, undergoing freely reversible, pH-dependent globule-fibril transformation. The purified bovine PTP consists on SDS gels of two carbohydrate-free polypeptide chains (Gross et al., 1985). Plasma desorption mass spectrometry and amino acid sequence analysis now confirm that bovine PTP contains two disulfide-bonded polypeptides, an A chain of 101 amino acid residues with a molecular weight of 11,073 and a B chain of 35 residues with a molecular weight of 3970. The intact protein exhibits a molecular weight of 15,036, agreeing greater than 99.9% with the molecular weight calculated from the sequence. The B chain sequence was determined by gas-phase Edman degradation of the intact polypeptide. The A chain sequence was determined from overlapping peptides generated by cleavage at lysyl, tryptophanyl, and aspartyl-prolyl residues. Based upon the bovine PTP cDNA structure, the two chains of the protein result from cleavage of a single polypeptide with removal of a dipeptide between the NH2-terminal A chain and COOH-terminal B chain. Comparison of bovine PTP with other proteins reveals significant structural relatedness with the single-chain homologues from human and rat pancreas and with the motif associated with Ca2(+)-dependent carbohydrate recognition domains. The physiological role of PTP has not yet been resolved. The protein is present in very high concentration in pancreatic secretion and it has been detected in brain lesions in Alzheimer's disease and Down syndrome and in regenerating rat pancreatic islets. The present results provide a firm protein base for ongoing molecular, physical-chemical, and structure-function studies of this unusual protein.
A boundary integral method for simulating the dynamics of inextensible vesicles suspended in a viscous fluid in 2D

We present a new method for the evolution of inextensible vesicles immersed in a Stokesian fluid. We use a boundary integral formulation for the fluid that results in a set of nonlinear integro-differential equations for the vesicle dynamics. The motion of the vesicles is determined by balancing the non-local hydrodynamic forces with the elastic forces due to bending and tension. Numerical simulations of such vesicle motions are quite challenging. On one hand, explicit time-stepping schemes suffer from a severe stability constraint due to the stiffness related to high-order spatial derivatives and a milder constraint due to a transport-like stability condition. On the other hand, an implicit scheme can be expensive because it requires the solution of a set of nonlinear equations at each time step. We present two semi-implicit schemes that circumvent the severe stability constraints on the time step and whose computational cost per time step is comparable to that of an explicit scheme. We discretize the equations by using a spectral method in space, and a multistep third-order accurate scheme in time. We use the fast multipole method (FMM) to efficiently compute vesicle-vesicle interaction forces in a suspension with a large number of vesicles. We report results from numerical experiments that demonstrate the convergence and algorithmic complexity properties of our scheme.
Phonon absorbing boundary conditions for molecular dynamics

With the goal of minimizing the domain size for molecular dynamics (MD) simulations, we develop a new class of absorbing boundary conditions (ABCs) that mimic the phonon absorption properties of an unbounded exterior. The proposed MD-ABCs are extensions of perfectly matched discrete layers (PMDLs), originally developed as an absorbing boundary condition for continuous wave propagation problems. Called MD-PMDL, this extension carefully targets the absorption of phonons, the high frequency waves, whose propagation properties are completely different from continuous waves. This paper presents the derivation of MD-PMDL for general lattice systems, followed by explicit application to one-dimensional and two-dimensional square lattice systems. The accuracy of MD-PMDL for phonon absorption is proven by analyzing reflection coefficients, and demonstrated through numerical experiments. Unlike existing MD-ABCs, MD-PMDL is local in both space and time and thus more efficient. Based on their favorable properties, it is concluded that MD-PMDL could provide a more effective alternative to existing MD-ABCs.
Control of volume shrinkage and residual styrene of unsaturated polyester resins cured at low temperatures. II. Effect of comonomer

Abstract The effect of a comonomer, methyl methacrylate (MMA), on volume shrinkage and residual styrene content of an unsaturated polyester (UP) resin with low profile additives (LPAs) cured at low temperature was investigated by an integrated reaction kinetics-morphology-property analysis. MMA affects the volume shrinkage and residual styrene content differently depending on MMA to styrene (St) CC bond molar ratio. At low MMA/St ratio, residual styrene decreases and the volume shrinkage of the resin system remains unchanged. At high MMA/St ratio, residual styrene can be substantially reduced, but the resin system suffers poor volume shrinkage control. Reactivity of the comonomer MMA and its compatibility to other components in the resin system can explain the observed results. A series of Seemann composites resin infusion molding process (SCRIMP) were conducted to study the relationship among materials, processing, and properties of molded composites in low temperature curing processes.
SU‐FF‐J‐51: Dosimetric Impact of Cone Beam Image Guided Setup for Paraspinal Patients

Purpose: To quantify the impact of kV cone beam CT (CBCT)‐guided setup on delivered dose to target and critical organs in patients receiving paraspinal irradiation and to compare the relative benefits of CBCT versus orthogonal kV radiograph (2D)‐guided setup. Method and Materials: Initial, pre‐ and post‐treatment CBCTs from ten patients receiving single‐fraction radiotherapy were evaluated. Delivered dose based on CBCT‐guided treatment was calculated after transferring target and critical organ contours from pre‐treatment CBCT to planning CT. Similarly, delivered dose from a simulated 2D setup was calculated by registering orthogonal DRRs created from the initial CBCT with planning DRRs using bony anatomy, and then applying the resulting shifts to the initial CBCT contours before transfer to the planning CT. The magnitude of residual setup errors and intra‐fractional motion were evaluated by registering pre‐treatment CBCT to planning CT and post‐ to pre‐treatment CBCT, respectively. Results:Dosimetric impact was evaluated using PTV D95% and maximum dose to critical structures. Even with CBCT‐guided setup, small residual setup errors combined with steep dose gradients led to increases up to 27% in maximum cord dose. Likewise, increases in esophagus maximum dose up to 34% (CBCT) and 20% (2D) were observed. PTV D95% decreased to 85% (CBCT) and 87% (2D) of planned dose for one patient with a low planned PTV D95% (73%) and a steep dose gradient. Magnitudes of the 3D vector of residual setup errors following 2D and CBCT setup were 2.3±0.5 mm and 1.5±0.4 mm, respectively. The intra‐fractional error was 1.6±0.3 mm. Conclusion: Since paraspinal lesions occur near stable bony anatomy with no significant anatomical deformation, CBCT provides no additional benefit over 2D techniques for accurate positioning. CBCT does provide easier visualization of the anatomy to facilitate setup and CBCT requires about the same effort as 2D setup based on orthogonal kV‐images.
Determination of laser damage initiation probability and growth on fused silica scratches

Current methods for the manufacture of optical components inevitably leaves a variety of sub-surface imperfections including scratches of varying lengths and widths on even the finest finishes. It has recently been determined that these finishing imperfections are responsible for the majority of laser-induced damage for fluences typically used in ICF class lasers. We have developed methods of engineering subscale parts with a distribution of scratches mimicking those found on full scale fused silica parts. This much higher density of scratches provides a platform to measure low damage initiation probabilities sufficient to describe damage on large scale optics. In this work, damage probability per unit scratch length was characterized as a function of initial scratch width and post fabrication processing including acid-based etch mitigation processes. The susceptibility of damage initiation density along scratches was found to be strongly affected by the post etching material removal and initial scratch width. We have developed an automated processing procedure to document the damage initiations per width and per length of theses scratches. We show here how these tools can be employed to provide predictions of the performance of full size optics in laser systems operating at 351 nm. In addition we use these tools to measure the growth rate of a damage site initiated along a scratch and compare this to the growth measured on an isolated damage site.
Estimated quantities and trends of cadmium, lead, and mercury in US municipal solid waste based on analysis of incinerator ash.

Heavy metals are present in a variety of products and can be released to the environment during product life cycles. The concentration of metals in municipal solid waste (MSW) reflects the amount of metals in products and is directly related to the amount of metals transferred to disposal sites. Measured monthly mean concentrations of cadmium, lead, and mercury in the ash from May 1995 through October 2007 at the Essex County, NJ incinerator and from May 2004 through November 2007 at the Warren County, NJ incinerator were used, along with air emissions data for mercury, to estimate the content of these metals in MSW. Estimated mean concentration and 95% confidence limits for cadmium in MSW at the Essex and Warren facilities, respectively, were 17.4 ± 0.1 and 10.1 ± 1.2 ppm. For lead, the corresponding values were 408 ± 41 and 239 ± 42 ppm, and for mercury, they were 2.6 ± 0.2 and 0.9 ± 0.2 ppm. A trend of increasing cadmium concentrations was found at both facilities. No change vs. time was observed in lead concentrations. Mercury concentration was found to be decreasing over time at the Essex facility.
The Geography of Speciation: Case Studies from Birds

Our understanding of the origin of species, or speciation, is sometimes viewed as incomplete, a “mystery of mysteries.” We in fact know a lot about speciation, especially when we consider its two basic components, the geography of speciation and the biology of speciation (changes in phenotype and genotype that occur during the process). Our understanding of the geography of speciation is quite clear. The process involves the separation of a once-continuous range into two or more geographically isolated, or allopatric parts, which over time accrue genetic changes that result in new daughter species. Current distributions show that recently evolved species are currently allopatric, supporting the role of allopatry in speciation. However, many species originated in the early- to mid-Pleistocene, meaning that they persisted through the environmental perturbations of multiple glacial cycles. It has been assumed that species maintained allopatric distributions during these episodes of glacial advance and retreat. I used Grinnelian niche models to estimate species distributions at the Last Glacial Maximum and the Last Interglacial. For a pair of recently isolated warbler species, and a pair of relatively old sister species of gnatcatchers, allopatry was observed at all time periods. Thus, there is no mystery about the geography of speciation: at least in birds, allopatry predominates. The sentiment that speciation is mysterious comes, I argue, from the biological species concept, which requires populations to be reproductively isolated before recognizing them as species. Reproductive isolation is a complicated process that rarely occurs the same way twice, and I argue that this lack of generality has been misinterpreted as a mystery.
Current-voltage relation for asymmetric ballistic superconducting junctions.

We calculate the dc current-voltage ($I\ensuremath{-}V$) relation for a ballistic superconductor-normal metal-superconductor (${S}_{1}N{S}_{2}$) junction, where the two superconducting contacts have different energy gaps (${\ensuremath{\Delta}}_{2}g~{\ensuremath{\Delta}}_{1}g~0$). Several new features appear in the $I\ensuremath{-}V$ relation as it evolves from a $\mathrm{NS}$ junction (${\ensuremath{\Delta}}_{1}=0$) to the symmetric $\mathrm{SNS}$ junction (${\ensuremath{\Delta}}_{1}={\ensuremath{\Delta}}_{2}$). The dc current ${I}_{0}$ flowing at small voltages is ${I}_{0}=4\frac{e{\ensuremath{\Delta}}_{1}}{h}$, and is different from the critical current ${I}_{c}$. The differential conductance changes abruptly at $eV={\ensuremath{\Delta}}_{2}\ensuremath{-}{\ensuremath{\Delta}}_{1}$ due to the loss of a single Andreev reflection from the larger-gap superconductor. Finally, the voltages ${\ensuremath{\Delta}}_{n}$ at which subharmonic gap structures appear in the $I\ensuremath{-}V$ relation for temperatures ${k}_{B}T\ensuremath{\simeq}{\ensuremath{\Delta}}_{2}$ depend on both energy gaps ${\ensuremath{\Delta}}_{1}$ and ${\ensuremath{\Delta}}_{2}$. We find a systematic way to classify this subgap structure.
Ab initio relativistic effective potentials with spin–orbit operators. IV. Cs through Rn

A refined version of the ‘‘shape consistent’’ effective potential procedure of Christiansen, Lee, and Pitzer was used to compute averaged relativistic effective potentials (AREP) and spin‐orbit operators for the atoms Li through Ar. These are tabulated in analytic form. Small optimized Gaussian basis sets with expansion coefficients for the lowest energy state for each atom are given and the reliability of the potentials relative to all electric calculations is discussed. Finally a procedure for computing molecular moments and Breit corrections is suggested.
Signal transduction in a compliant thick ascending limb

In several previous studies, we used a mathematical model of the thick ascending limb (TAL) to investigate nonlinearities in the tubuloglomerular feedback (TGF) loop. That model, which represents the TAL as a rigid tube, predicts that TGF signal transduction by the TAL is a generator of nonlinearities: if a sinusoidal oscillation is added to constant intratubular fluid flow, the time interval required for an element of tubular fluid to traverse the TAL, as a function of time, is oscillatory and periodic but not sinusoidal. As a consequence, NaCl concentration in tubular fluid alongside the macula densa will be nonsinusoidal and thus contain harmonics of the original sinusoidal frequency. We hypothesized that the complexity found in power spectra based on in vivo time series of key TGF variables arises in part from those harmonics and that nonlinearities in TGF-mediated oscillations may result in increased NaCl delivery to the distal nephron. To investigate the possibility that a more realistic model of the TAL would damp the harmonics, we have conducted new studies in a model TAL that has compliant walls and thus a tubular radius that depends on transmural pressure. These studies predict that compliant TAL walls do not damp, but instead intensify, the harmonics. In addition, our results predict that mean TAL flow strongly influences the shape of the NaCl concentration waveform at the macula densa. This is a consequence of the inverse relationship between flow speed and transit time, which produces asymmetry between up- and downslopes of the oscillation, and the nonlinearity of TAL NaCl absorption at low flow rates, which broadens the trough of the oscillation relative to the peak. The dependence of waveform shape on mean TAL flow may be the source of the variable degree of distortion, relative to a sine wave, seen in experimental recordings of TGF-mediated oscillations.
Document categorization in legal electronic discovery: computer classification vs. manual review

In litigation in the US, the parties are obligated to produce to one another, when requested, those documents that are potentially relevant to issues and facts of the litigation (called “discovery”). As the volume of electronic documents continues to grow, the expense of dealing with this obligation threatens to surpass the amounts at issue and the time to identify these relevant documents can delay a case for months or years. The same holds true for government investigations and third-parties served with subpoenas. As a result, litigants are looking for ways to reduce the time and expense of discovery. One approach is to supplant or reduce the traditional means of having people, usually attorneys, read each document, with automated procedures that use information retrieval and machine categorization to identify the relevant documents. This study compared an original categorization, obtained as part of a response to a Department of Justice Request and produced by having one or more of 225 attorneys review each document with automated categorization systems provided by two legal service providers. The goal was to determine whether the automated systems could categorize documents at least as well as human reviewers could, thereby saving time and expense. The results support the idea that machine categorization is no less accurate at identifying relevant-responsive documents than employing a team of reviewers. Based on these results, it would appear that using machine categorization can be a reasonable substitute for human review. © 2010 Wiley Periodicals, Inc.
Forest recovery in a tropical landscape: what is the relative importance of biophysical, socioeconomic, and landscape variables?

Socioeconomic changes in many areas in the tropics have led to increasing urbanization, abandonment of agriculture, and forest re-growth. Although these patterns are well documented, few studies have examined the drivers leading to landscape-level forest recovery and the resulting spatial structure of secondary forests. Land cover transitions from agricultural lands to secondary forest in the island of Puerto Rico have been ongoing since the 1940s. This study is a glimpse into this landscape level trend from 1991 to 2000. First, we relied on Landsat images to characterize changes in the landscape structure for forest, urban, and agricultural land classes. We found that although forest cover has increased in this period, forest has become increasingly fragmented while the area of urban cover has spread faster and become more clustered. Second, we used logistic regression to assess the relationship between the transition to forest and 21 biophysical, socioeconomic, and landscape variables. We found that the percentage of forest cover within a 100 m radius of a point, distance to primary roads and nature reserves, slope, and aspect are the most important predictors of forest recovery. The resulting model predicts the spatial pattern of forest recovery with accuracy (AUC-ROC = 0.798). Together, our results suggest that forest recovery in Puerto Rico has slowed down and that increasing pressure from urbanization may be critical in determining future landscape level forest recovery. These results are relevant to other areas in the tropics that are undergoing rapid economic development.