cssi/SciSciGPT-SciSciNet huggingface dataset:
Crystal Structures of the Sec1/Munc18 (SM) Protein Vps33, Alone and Bound to the Homotypic Fusion and Vacuolar Protein Sorting (HOPS) Subunit Vps16*

Intracellular membrane fusion requires the regulated assembly of SNARE (soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein receptor) proteins anchored in the apposed membranes. To exert the force required to drive fusion between lipid bilayers, juxtamembrane SNARE motifs zipper into four-helix bundles. Importantly, SNARE function is regulated by additional factors, none more extensively studied than the SM (Sec1/Munc18-like) proteins. SM proteins interact with both individual SNAREs and SNARE complexes, likely chaperoning SNARE complex formation and protecting assembly intermediates from premature disassembly by NSF. Four families of SM proteins have been identified, and representative members of two of these families (Sec1/Munc18 and Sly1) have been structurally characterized. We report here the 2.6 A resolution crystal structure of an SM protein from the third family, Vps33. Although Vps33 shares with the first two families the same basic three-domain architecture, domain 1 is displaced by 15 A, accompanied by a 40° rotation. A unique feature of the Vps33 family of SM proteins is that its members function as stable subunits within a multi-subunit tethering complex called HOPS (homotypic fusion and vacuolar protein sorting). Integration into the HOPS complex depends on the interaction between Vps33 and a second HOPS subunit, Vps16. The crystal structure of Vps33 bound to a C-terminal portion of Vps16, also at 2.6 A resolution, reveals the structural basis for this interaction. Despite the extensive interface between the two HOPS subunits, the conformation of Vps33 is only subtly affected by binding to Vps16.
Auditory evoked responses in the cerebrum (field l) and ovoid nucleus of the ring dove

Abstract Recording in the dove cerebrum showed a response to clicks and tone bursts consisting of a negative peak at 16–20 msec latency (later, variable slow potentials occurred under anesthesia but were very small in unanesthetized birds) in a region the same as or largely overlapping with Field L, shown by Karten 9 to receive a direct projection from the ovoid nucleus of the diencephalon. Below this region the response reversed to a positive peak at the same latency. Contralateral presentation of a click or tone burst produced a larger amplitude response than ipsilateral, and usually than bilateral, presentation. The amplitude vs. tone frequency curves obtained at different positions overlapped broadly, with peaks between 2500 and 4000 c/sec. Response amplitudes varied as a function of loud-speaker position, in contrast to those in the rostral acoustic field of Naumow and Iljitschew 10 . Attempts to record an evoked potential in the ovoid nucleus were usually unsuccessful; the slow potentials occasionally observed were associated with spi ke discharges as though they had to do with the spike-producing cells rather than being a widespread response like that of Field L. The Field L evoked response was somewhat similar to unit responses in ovoid nucleus, and may reflect arriving activity from that nucleus.
TLR7 and 9 agonists are highly effective mucosal adjuvants for norovirus virus-like particle vaccines.

Virus-like particles (VLPs) are an active area of vaccine research, development and commercialization. Mucosal administration of VLPs provides an attractive avenue for delivery of vaccines with the...
Preparation and Maintenance of Dorsal Root Ganglia Neurons in Compartmented Cultures

Neurons extend axonal processes that are far removed from the cell body to innervate target tissues, where target-derived growth factors are required for neuronal survival and function. Neurotrophins are specifically required to maintain the survival and differentiation of innervating sensory neurons but the question of how these target-derived neurotrophins communicate to the cell body of innervating neurons has been an area of active research for over 30 years. The most commonly accepted model of how neurotrophin signals reach the cell body proposes that signaling endosomes carry this signal retrogradely along the axon. In order to study retrograde transport, a culture system was originally devised by Robert Campenot, in which cell bodies are isolated from their axons. The technique of preparing these compartmented chambers for culturing sensory neurons recapitulates the selective stimulation of neuron terminals that occurs in vivo following release of target-derived neurotrophins. Retrograde signaling events that require long-range microtubule dependent retrograde transport have important implications for the treatment of neurodegenerative disorders.
Isothermal microcalorimetric study of the pH dependence of the interactions between a cellulase and a β-blocker

The influence of the pH on the complexation equilibria between (S)- or (R)-alprenolol and the cellulase Cel7A was investigated by isothermal titration calorimetry. The results obtained agree with those of previous, similar studies of the same equilibria in which the protein was immobilized on silica particles, packed in a chromatographic column. The association constant and the complexation enthalpy and entropy of the (S)-enantiomer increase with increasing pH. For (R)-alprenolol, the binding is endothermic at all pH values. Thus, for both enantiomers in the pH range 5.5-6.8, the binding is an entropically driven process.
Hepatic gene therapy for hemophilia B.

A number of different cell types including keratinocytes, hepatodytes, fibroblasts, myoblasts, and endothelial cells have been targeted for factor IX (RIX) gene replacement therapy.1–7 Following gene transfer, these cells have produced functional RIX because of their ability to gamma-carboxylate the appropriate “gla” domains and secrete the functional protein. Most efforts to date have employed an ex vivo gene transfer method in rodents and involve transfer of the F.IX gene into the cells via a recombinant retroviral vector and subsequent transplantation of the cells back into the animal. Two major problems encountered in these studies have been the rather low concentration of circulating F.IX and/or the loss of F.IX expression over time. The inability to achieve long-term expression is primarily the result of loss of the transduced cells or inactivation of the expression vectors.
Probing Structure-Induced Optical Behavior in a New Class of Self-Activated Luminescent 0D/1D CaWO4 Metal Oxide–CdSe Nanocrystal Composite Heterostructures

In this report, we synthesize and characterize the structural and optical properties of novel heterostructures composed of (i) semiconducting nanocrystalline CdSe quantum dots (QDs) coupled with (ii) both one- and zero-dimensional (1D and 0D) motifs of self-activated luminescent CaWO4 metal oxides. Specifically, ∼4 nm CdSe QDs have been anchored onto (i) high-aspect ratio 1D nanowires, measuring ∼230 nm in diameter and ∼3 μm in length, as well as onto (ii) crystalline 0D nanoparticles (possessing an average diameter of ∼80 nm) of CaWO4 through the mediation of 3-mercaptopropionic acid (MPA) as a connecting linker. Composite formation was confirmed by complementary electron microscopy and spectroscopy (i.e., IR and Raman) data. In terms of luminescent properties, our results show that our 1D and 0D heterostructures evince photoluminescence (PL) quenching and shortened PL lifetimes of CaWO4 as compared with unbound CaWO4. We propose that a photoinduced electron transfer process occurs from CaWO4 to CdSe QDs...
Cystine Content and Enzyme Digestibility of Powdered Hoof Proteins.

SummaryConsiderably more than half of dried powdered cattle, horse, and hog hoof material was found to be digestible by proteolytic enzymes. Hog hoof proved the most readily digestible and horse hoof the least. The undigestible residue in each case contained more cystine than the original preparations. The soft part of the cattle hoof contained less cystine and was more readily digested than the horn-like front portion. Thus hoof powder consists of at least two and possibly a number of different kinds of proteins.
Zeste encodes a sequence-specific transcription factor that activates the Ultrabithorax promoter in vitro

Abstract Zeste is a Drosophila regulatory gene that is required for transvection at the bithorax complex. Here we find that purified zeste protein binds to multiple sites just 5′ of the initiation site of Ubx RNA. Zeste protein purified from Drosophila cells or from E. coli expressing the zeste gene activates Ubx transcription in vitro. This activation is dependent on the presence of zeste protein binding sites, as it is not observed with a Ubx promoter lacking these sites or with an Adh promoter. These results suggest that transvection involves regulatory elements that act at the level of transcriptional initiation and may be mechanistically similar to activation of transcription by enhancer elements, except that transvection occurs across paired chromosomes. These findings are consistent with the hypothesis that zeste may play a more important role in the normal regulation of Ubx and its other target genes than current genetic evidence implies.
Denoising diffusion-weighted magnitude MR images using rank and edge constraints.

Purpose To improve signal-to-noise ratio for diffusion-weighted magnetic resonance images. Methods A new method is proposed for denoising diffusion-weighted magnitude images. The proposed method formulates the denoising problem as an maximum a posteriori} estimation problem based on Rician/noncentral χ likelihood models, incorporating an edge prior and a low-rank model. The resulting optimization problem is solved efficiently using a half-quadratic method with an alternating minimization scheme. Results The performance of the proposed method has been validated using simulated and experimental data. Diffusion-weighted images and noisy data were simulated based on the diffusion tensor imaging model and Rician/noncentral χ distributions. The simulation study (with known gold standard) shows substantial improvements in single-to-noise ratio and diffusion tensor estimation after denoising. In vivo diffusion imaging data at different b-values were acquired. Based on the experimental data, qualitative improvement in image quality and quantitative improvement in diffusion tensor estimation were demonstrated. Additionally, the proposed method is shown to outperform one of the state-of-the-art nonlocal means-based denoising algorithms, both qualitatively and quantitatively. Conclusion The single-to-noise ratio of diffusion-weighted images can be effectively improved with rank and edge constraints, resulting in an improvement in diffusion parameter estimation accuracy. Magn Reson Med 71:1272–1284, 2014. © 2013 Wiley Periodicals, Inc.
Investigating controller performance in hybrid SOFC systems with unknown nonlinearities

Solid oxide fuel cells (SOFCs) offer many benefits over various other fuel cells as a result of their high operating temperatures. Our prior work has addressed the conflicting goals of preventing fuel starvation and improving load-following in SOFCs through a combination of current regulation and hybridization with an ultra-capacitor. The associated controllers are largely model independent, excepting certain generalized assumptions that were made about the unknown and nonlinear dynamics of the SOFC's fuel supply system (FSS). In this paper we formulate a generalized structure of the control problem and controller from our earlier work, and relax the conditions imposed on the FSS. Thereafter, we analytically determine conditions of instability. We obtain inequality conditions that impose restrictions on the controller gains and the unknown nonlinearity. The conditions are helpful in predicting the limits of performance of the controller. The results are verified through simulations and through hardware-in-the-loop tests.
Outcomes of Heart Transplantation in Small Children Bridged With Ventricular Assist Devices

Background Ventricular assist devices (VADs) have been used with increasing frequency to bridge small children to heart transplantation (HTx), but outcomes in large cohorts are not well established. Methods Small children (≤ 10 kg) bridged to HTx with VADs between 2004 and 2010 were identified in the United Network for Organ Sharing database. Survival was modeled using the Kaplan-Meier method, and 2:1 propensity matching was used to compare outcomes with a well-matched control cohort of nonbridged HTx recipients. Results Of the 803 small children who underwent HTx during the study period, 59 (7%) were bridged with a VAD. The proportion of recipients that were bridged with a VAD increased from 3% in 2004 to 9% in 2010 ( p = 0.03). Kaplan-Meier 30-day, 6-month, and 1-year survival was comparable between those bridged with a VAD and 118 well-matched nonbridged children. Rates of postoperative renal failure, reoperation, infection, and rejection were also comparable. Those bridged with a VAD had a significantly higher rate of postoperative stroke (8.5% vs 0.9%; p = 0.008). Conclusions Small children bridged to HTx with a VAD have early survival rates that are comparable to nonbridged children; however, this is achieved at the expense of a higher rate of stroke. Identifying the risk factors for early death and stroke in small children bridged to HTx with VADs is prudent as more experience with this patient population accumulates.
BLAS Comparison on FPGA, CPU and GPU

High Performance Computing (HPC) or scientific codes are being executed across a wide variety of computing platforms from embedded processors to massively parallel GPUs. We present a comparison of the Basic Linear Algebra Subroutines (BLAS) using double-precision floating point on an FPGA, CPU and GPU. On the CPU and GPU, we utilize standard libraries on state-of-the-art devices. On the FPGA, we have developed parameterized modular implementations for the dot-product and Gaxpy or matrix-vector multiplication. In order to obtain optimal performance for any aspect ratio of the matrices, we have designed a high-throughput accumulator to perform an efficient reduction of floating point values. To support scalability to large data-sets, we target the BEE3 FPGA platform. We use performance and energy efficiency as metrics to compare the different platforms. Results show that FPGAs offer comparable performance as well as 2.7 to 293 times better energy efficiency for the test cases that we implemented on all three platforms.
Quantification of carbonyl compounds in oxidized low-linolenate, high-stearate and common soybean oils

The carbonyl compounds in five oxidized soybean oils (SBO) of various fatty acid compositions were determined. Three were from common normal soybean varieties, and two were from lines developed from new mutant varieties. One mutant line had a linolenate (18:3) content of 3.5% (A5), and one had a stearate (18:0) content of 24% (A6). SBO were stored at 28 C and 60 C. Trichlorophenylhydrazones (TCPH) of carbonyls formed during oxidation were quantified and tentatively identified by gas chromatography. The storage temperature and the composition of the oils affected the types and amounts of volatiles produced. Hexanal was the major volatile in the oils in both storage tests. After 60 C storage, 2- and/or 3-hexenal was present only in the oil with the highest 18:3 content (BSR 101, 18:3=9%). The amounts of the carbonyls formed in A5 were 2 to 5 times less than the amounts formed in BSR 101. The amounts of many of the carbonyls were converted into relative flavor potency by using reported data. Hexanal was the major contributor to flavor. After storage at 28 C, 2- and/or 3-hexenal was the second most intense flavor compound regardless of the 18:3 content of the oil. The amount of a compound and the threshold value did not always predict its flavor importance according to the flavor potency data.
Translucent ZrO2 prepared at high pressures

Abstract Submicron particles of monoclinic ZrO2, with and without stabilizing oxides of CaO or Y2O3, have been subjected to pressures ranging from 0.5 to 30 kbars and temperatures ranging from 1300° to 1750°C. Heating rates of 1000°C per hour followed by cooling rates of 500°C per hour at pressure were needed to achieve translucent monoclinic and cubic stabilized ZrO2. Specimens with essentially theoretical density were formed by high-pressure hot-pressing (monoclinic ZrO2 = 5.61 g/cm3, 15 mole % CaO-stabilized cubic ZrO2 = 5.54 g/cm3, and 15 mole % Y2O3-stabilized cubic ZrO2 = 6.05 g/cm3). Photometric measurements indicated an average of 12% in-line light transmission for both types of ZrO2. A uniform increase in grain size ranging from 1 μ to 5 μ going from the center of the specimen to the outer edge was observed, due to pressure gradients encountered at temperature. A dislocation density of 107–109 cm−2 was determined for monoclinic and cubic ZrO2 pressed to 30 kbars and 1750°C.
Studies on the binding of [3H-chloroethyl]-cyclophosphamide and 14[C-4] -cyclophosphamide to hepatic microsomes and native calf thymus DNA.

Abstract In studies in vitro , ring labeled 14C-Cyclophosphamide (14C-CP) and side chain labeled 3H-Cyclophosphamide (3H-CP) became bound to native calf thymus DNA and/or microsomal proteins in the presence of rat hepatic microsomes and NADPH. Phenobarbital pretreatment of rats enhanced the binding to all macromolecules, whereas pretreatment with 3-methylcholanthrene decreased the binding. 3H-label from 3H-CP became bound to DNA and to some extent to proteins, whereas 14C-label from 14C-CP became bound essentially to proteins only. These data suggest involvement of some metabolic products of cyclophosphamide, most likely acrolein, in the binding of cyclophosphamide to proteins. Although the binding of acrolein to free sulfhydryl groups of cysteine and glutathione is very likely, binding to free amino groups in the proteins via the formation of Schiff bases is another likely mechanism suggested by our studies.
Acute morphine induces oscillatory discharge of noradrenergic locus coeruleus neurons in the waking monkey.

Abstract Neurons were recorded extracellularly from the locus coeruleus (LC) of a waking, chair-restrained cynomolgus monkey before and for 0.5–4 h after intramuscular injections of morphine sulfate (0.3–10 mg/kg). Tonic discharge of each LC neuron tested ( n = 11) decreased after morphine injection; this effect appeared to be dose-dependent for the range of 0.3–3.0 mg/kg. Unexpectedly, these same doses of morphine also induced a pronounced burst-pause discharge pattern in all LC neurons recorded. Thus, whereas in the naive animal pauses in discharge longer than 3 s were rare during waking, after morphine injection LC neurons frequently exhibited pauses in impulse activity of 10 s or longer during non-drowsy waking. The bursts in activity following morphine corresponded to orienting behaviors or apparent alertness, whereas pauses were associated with eye closure or slowly drifting gaze. Closer analysis revealed that this burst-pause activity pattern was somewhat regular, with a period of about 15–35 s. This observation was confirmed by autocorrelogram analysis. In view of previous findings in rodent LC, we suggest that acute morphine elicits a dual effect on primate LC neurons: inhibition of discharge by direct effects on opiate receptors located on LC cells, and periodic phasic activation mediated by excitatory afferents to the LC.
Dendrochemistry of White Mountain bristlecone pines: An investigation via Synchrotron Radiation Scanning X-Ray Fluorescence Microscopy

[1] Synchrotron Radiation Scanning X-Ray Fluorescence Microscopy (SXFM) was used for the first spatially/temporally resolved investigation of the multielemental chemistry of bristlecone pine (Pinus longaeva D.K. Bailey). A new protocol was designed to apply this nondestructive method of analysis to this unique palaeoclimatological resource, extracting previously inaccessible dendrochemical information at subannual resolution from tree rings ranging from 1400 to 40 μm. The potential of Pinus longaeva was assessed for the reconstruction of multicentennial annual resolution sequences of elemental change, with specific focus on the identification of multielemental markers for major, climatically effective volcanic eruptions. Increases in calcium (Ca), strontium (Sr), manganese (Mn), and zinc (Zn) were identified in association with frost rings around AD1601, following the eruption of Huaynaputina, Peru, but these could not be directly attributed to volcanogenic changes in environmental chemistry. Elemental patterns for 500 years from five trees demonstrated little agreement indicating that, for the elements detected, this species may be unsuitable for temporal reconstructions of external chemistry. Further development of SXFM dendrochemical technique, however, offers much potential for future work.
The kinetics of ozone-phenol reaction in aqueous solutions

Abstract The kinetics of the reaction of ozone and phenol in aqueous medium was studied. The reaction was first order with respect to both ozone and phenol. The rate constant was found to increase with increase in the pH of the reaction mixture. Four different catalysts were examined for their effect on the rate of reaction but none of them was found to have any appreciable effect. The presence of additional solutes like sodium chloride, sodium carbonate and sodium sulfate was found to affect the reaction significantly. The experiments indicated that hydroxyl radicals may not play a role in the attack of ozone on phenol and the reaction mechanism may be ionic rather than free radical.
Management of Bladder Neck Stenosis Secondary to Radical Prostatectomy or Radiation Treatment

Bladder neck stenosis (BNS) and posterior urethral stenosis (PUS) are uncommon but problematic complications of treatment for localized prostate cancer. Overall, BNS is less common following minimally invasive radical prostatectomy than open. Patients who develop PUS following radiation therapy (RT) (especially salvage RT) pose a greater challenge and tend to present longer after treatment. Regardless of etiology, treatment begins conservatively with endoscopic management but quickly progresses to more aggressive intervention if refractory. Urethral stents have been used with acceptable results. In patients who fail conservative therapy after radical prostatectomy (RP), open reconstruction should be considered. After RT, patients may ultimately benefit from urinary diversion or salvage prostatectomy. After treatment, many patients will require implantation of artificial urinary sphincter (AUS) for management of incontinence. Patient counseling prior to treatment selection for initial prostate cancer therapy is important; complications, future management, and potential for return to normal quality of life vary widely.
Matching pursuit data acquisition in magnetic resonance imaging

The matching pursuit (MP) algorithm developed by S. Mallat and Z. Zhang is applied to magnetic resonance (MR) imaging. Since matching pursuit is a greedy algorithm to find waveforms which are the best match for an object-signal, the signal can be decomposed with a few iterations. In this paper, we propose an application of the MP algorithm to the MR imaging to reduce imaging time. Inner products of residual signals and selected waveforms in the MP algorithm are derived from the MR signals by excitation of RF pulses which are Fourier transforms of selected waveforms. Results from computer simulations demonstrate that the imaging time is reduced by using the MP algorithm and further a progressive reconstruction can be achieved.
Direct observation of heat dissipation in individual suspended carbon nanotubes using a two-laser technique

A two-laser technique is used to investigate heat spreading along individual single walled carbon nanotube (SWCNT) bundles in vacuum and air environments. A 532 nm laser focused on the center of a suspended SWCNT bundle is used as a local heat source, and a 633 nm laser is used to measure the spatial temperature profile along the SWCNT bundle by monitoring the G band downshifts in the Raman spectra. A constant temperature gradient is observed when the SWCNT bundle is irradiated in vacuum, giving direct evidence of diffusive transport of the phonons probed by the Raman laser. In air, however, we observe an exponentially decaying temperature profile with a decay length of about 7 μm, due to heat dissipation from the SWCNT bundle to the surrounding gas molecules. The thermal conductivity of the suspended carbon nanotube (CNT) is determined from its electrical heating temperature profile as measured in vacuum and the nanotube bundle diameter measured via transmission electron microscopy. Based on the exponent...
Using independent component analysis for material estimation in hyperspectral images

We develop a method for automated material estimation in hyperspectral images. The method models a hyperspectral pixel as a linear mixture of unknown materials. The method is particularly useful for applications in which material regions in a scene are smaller than one pixel. In contrast to many material estimation methods, the new method uses the statistics of large numbers of pixels rather than attempting to identify a small number of the purest pixels. The method is based on maximizing the independence of material abundances at each pixel. We show how independent component analysis algorithms can be adapted for use with this problem. We demonstrate properties of the method by application to airborne hyperspectral data.
Diabetes and perioperative outcomes following cervical fusion in patients with myelopathy.

Study design Database study using the Nationwide Inpatient Sample administrative data from 1988 through 2004. Objective To examine perioperative morbidity and mortality for patients diagnosed with myelopathy, with and without diabetes mellitus (DM) (and subclassifications) following cervical spinal fusion. Summary of background data DM has been associated with worse outcomes in a variety of orthopedic procedures including spinal surgery. Evidence that patients with DM have more complications following cervical fusion, specifically those treated for myelopathy, has been suggested within the literature but has been poorly explored. Methods Data from 37,732 patients within Nationwide Inpatient Sample database (1988-2004) with diagnostic codes specifying the presence of myelopathy and who underwent cervical fusion were included in the analysis. Patients were compared on the basis of the presence of DM, type of DM, and whether DM was controlled or uncontrolled. Bivariate statistical analyses compared postoperative complication rates while multivariate statistics were used to determine likelihood of complications with DM. Results Multivariate regression modeling outlined higher likelihoods of complications and hospital discharge variables with DM, particularly if it was diagnosed as uncontrolled disease. Fewer significant discrepancies in complications were noted in comparison of Type I versus Type II DM. Conclusion This nationally representative study of inpatients in the United States provides evidence that patients with DM who received cervical fusion secondary to myelopathy are associated with greater perioperative complications, nonroutine discharge, and increased total charges. Subanalyses suggest that uncontrolled DM is a significant associative factor in outcome.
Characterization and cloning of an (R)-specific trans-2,3-enoylacyl-CoA hydratase from Rhodospirillum rubrum and use of this enzyme for PHA production in Escherichia coli.

An (R)-trans-2,3-enoylacyl-CoA hydratase was purified to near-homogeneity from Rhodospirillum rubrum. Protein sequencing of enriched protein fractions allowed the construction of a degenerate oligonucleotide. The gene encoding the (R)-specific hydratase activity was cloned following three rounds of colony hybridization using the oligonucleotide, and overexpression of the gene in E. coli led to the purification of the enzyme to homogeneity. The purified enzyme used crotonyl-CoA, trans-2,3-pentenoyl-CoA, and trans-2,3-hexenoyl-CoA with approximately equal specificity as substrates in the hydration reaction. However, no activity was observed using trans-2,3-octenoyl-CoA as a substrate, but this compound did partially inhibit crotonyl-CoA hydration. Based on the nucleotide sequence, the protein has a monomeric molecular weight of 15.4 kDa and is a homotetramer in its native form as determined by gel filtration chromatography and native PAGE. The hydratase was expressed together with the PHA synthase from Thiocapsa pfennigii in E. coli strain DH5α. Growth of these strains on oleic acid resulted in the production of the terpolyester poly(3-hydroxybutyrate-co-3-hydroxyvalerate-co-3-hydroxyhexanoate).
The effectiveness of intensive mobilization technique combined with capsular distension for adhesive capsulitis of the shoulder

Background The management of Adhesive Capsulitis(AC) is controversal. Both capsular distension after intraarticular injection and mobilization therapy are known as highly effective treatment of painful and limited shoulder joint. The aim of this study was to determine the synergistic effect of intensive mobilization technique combined with capsular distension for patients with adhesive capsulitis in improving shoulder ROM, pain and function.
Naproxen Interferes with the Assembly of Aβ Oligomers Implicated in Alzheimer's Disease

Experimental and epidemiological studies have shown that the nonsteroidal antiinflammatory drug naproxen may be useful in the treatment of Alzheimer's disease. To investigate the interactions of naproxen with Aβ dimers, which are the smallest cytotoxic aggregated Aβ peptide species, we use united atom implicit solvent model and exhaustive replica exchange molecular dynamics. We show that naproxen ligands bind to Aβ dimer and penetrate its volume interfering with the interpeptide interactions. As a result naproxen induces a destabilizing effect on Aβ dimer. By comparing the free-energy landscapes of naproxen interactions with Aβ dimers and fibrils, we conclude that this ligand has stronger antiaggregation potential against Aβ fibrils rather than against dimers. The analysis of naproxen binding energetics shows that the location of ligand binding sites in Aβ dimer is dictated by the Aβ amino acid sequence. Comparison of the in silico findings with experimental observations reveals potential limitations of naproxen as an effective therapeutic agent in the treatment of Alzheimer's disease.
Somatostatin cells regulate sensory response fidelity via subtractive inhibition in olfactory cortex

This study shows how somatostatin (SOM)-expressing interneurons contribute to odor coding in mouse olfactory cortex. Odor-tuned SOM cells regulate neuronal output through a purely subtractive operation that is independent of odor identity or intensity. This operation enhances the salience of odor-evoked activity without changing cortical odor tuning.
Primary Response Genes Induced by Growth Factors and Tumor Promoters

AND PERSPECTIVES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . 282 IDENTIFICATION OF THE FIRST MITOGEN-INDUCIBLE GENES . . . . . . . . .. . . . . . . . . . 286 THE FOS AND JUN GENE FAMILIES. . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . 287 PRIMARY RESPONSE GENES FROM CELLS TREATED WITH GROWTH FACTORS OR TUMOR PROMOTERS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. .. . . . . . . . . . 290 1. Nuclear Proteins . . . .. . . ......... 291 2. Cytoskeletal and Extracellular Matrix Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 295 3. Transmembrane Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . 295 4. Cytokines ... . . . . . . . . . .. . . . . . . . . . . . . . . . ..... . . .... . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . .. . . .. . . . . . 295 5. Proteins of Unknown Function . . . ... .. .. . .... . . . . . . . . . . . ... . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . 297 6. Primary Response Genes from a "Late" Library ... ........ .... 298 REGULATION OF PRIMARY RESPONSE GENE EXPRESSION. ......... . . . .. . . . . . . . . . 299 1. c-fos 299 2. c-jun 303 3. JE . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . 304 4. egr-lIz;if-268/krox24/NGFI-A/TIS8. 304 5. egr-2/ krox20. ..... ... 304 6. NlO/nur77/NGFI-B/TISI ..... . ...... . . . ... . .... ......... . ...... ......... 305 CELL-SPECIFIC RESTRICTION OF PRIMARY RESPONSE GENES . .. . . . . . . . . . . . . . . . . 305 SECONDARY RESPONSE GENES . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. .. . . . . . . . . . 306 DO PRIMARY RESPONSE GENES PLAY CAUSAL ROLES I N MODULATING SECONDARY RESPONSE GENES AND CELLULAR PHySIOLOGy? 306 COMMON PRIMARY RESPONSE GENES AND CELLAND LIGANDSPECIFIC RESPONSES . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . ... . . . . . . . . 307 PRIMARY RESPONSE GENE EXPRESSION IN THE NERVOUS SySTEM 309
What Spatial Mismatch? The Proximity of Blacks to Employment in Boston and Houston

We investigate the spatial mismatch hypothesis by analyzing detailed data on the spatial distributions of jobs and populations in Boston and Houston. Job potential measures calculated using data from the Urban Transportation Planning Package indicate that, on average, blacks are physically near more jobs than whites are. This finding holds despite analysis being restricted to consider only entry-level blue-collar jobs and allowances being made for group differences in search and commuting capabilities. This raises questions about the hypothesis that black-white employment differentials can be attributed to an inadequate supply of employment possibilities for African American workers resulting from shifts in the spatial distribution of jobs from the inner city to the suburbs. We investigate the spatial mismatch hypothesis by analyzing detailed data on the spatial distributions of jobs and populations in Boston and Houston. First advanced by Kain (1968), the spatial mismatch hypothesis argues that black access to employment has been adversely affected by the tendency for jobs in urban areas to shift toward locations distant from black residential centers. The idea is that because racial residential segregation has continued to disproportionately concentrate blacks in inner-city ghettos and because blacks have inferior access to automobiles, they'are less capable than whites of physically reaching suburban jobs and are thus more subject to unemployment. In the present article, we investigate spatial mismatch giving special attention to issues of conceptualization and measurement of mismatch. We draw on detailed data on the spatial location of employment taken from Urban
Improving Performance of Sparse Matrix-Vector Multiplication

Sparse matrix-vector multiplication (SpMxV) is one of the most important computational kernels in scientific computing. It often suffers from poor cache utilization and extra load operations because of memory indirections used to exploit sparsity. We propose alternative data structures, along with reordering algorithms to increase effectiveness of these data structures, to reduce the number of memory indirections. Toledo proposed handling the 1x2 blocks of a matrix separately, doing only one indirection for each block. We propose packing all contiguous nonzeros into a block to reduce the number of memory indirections further. This reduces memory indirections per block to one for the cost of an extra array in storage and a loop during SpMxV. We also propose an algorithm to permute the nonzeros of the matrix into contiguous locations. We state this problem as the traveling salesperson problem and use associated heuristics. Experiments verify the effectiveness of our techniques.
Archaeological Tourism: Looking for Answers along Mexico's Maya Riviera

Located on the Caribbean coast of Mexico's Yucatan Peninsula, the village of Cancun was radically transformed when mass tourism development began there in the early 1970s. Cancun and the surrounding “Maya Riviera” quickly became a wildly popular tourism destination offering a variety of cultural experiences, including visits to ancient Maya archaeological sites. Now, some of those archaeological sites are in danger of being “loved to death,” while others are only just beginning to appear on the tourist radar. There is increasing pressure to balance tourist accessibility with conservation of the ancient buildings and to find a balance that incorporates architectural and ecological conservation, management of the tourist procession through the site, and effective interpretation of the site to enhance the visitor experience. Sites need to be presented within historical, temporal, and geographical contexts, and tourists must be educated about the host region and local indigenous cultures to enhance the tourism experience and encourage tourist behaviors that promote sustainability at the site.
Comparative Effects of Half-Length Coded Wire Tagging and Ventral Fin Removal on Survival and Size of Pink Salmon Fry

Abstract The survival and adult size of pink salmon Oncorhynchus gorbuscha marked as recently emigrating fry with coded wire tags (CWTs) were compared with those of sibling groups that were either unmarked or marked by removing a ventral (pelvic) fin. Prerelease mortality was significantly higher for coded-wire-tagged fish. Survival from fry release to adult return was equal to or less than that of fish with ventral fin clips. Pink salmon marked with CWTs were similar in size at return to pink salmon with ventral fin clips but significantly smaller than unmarked fish. These results indicate that reduced growth after marking contributes to the lower survival reported in other studies of pink salmon marked with CWTs or fin clips. Marking pink salmon as recently emigrating fry with CWTs provides a powerful tool for differentiating between a large number of treatment groups and categories, but doing so will affect survival and size at return and is more detrimental to survival than ventral fin removal.
Annotated maps for autonomous land vehicles

The use of annotated maps to manage the information needed by autonomous mobile robots is discussed. Annotations tie specific information to particular locations of objects in the map, such as the description of a landmark or the proper control strategy for crossing an intersection. Descriptor annotations are retrieved on demand. Triggers are automatically sent to a specified process when the robot reaches a given location. The most ambitious runs involved navigating through a suburban neighborhood, including image processing to follow roads, 3-D perception for landmark identification, and inertial navigation to turn at intersections. Annotated maps were built by first driving the robot by hand and recording the location of roads and the location and description of objects along the way. During mission planning, triggers were added to specify how and where to drive and what to look for. While executing the mission, the triggers specified when to use image processing, when to slow down and identify landmarks, how to negotiate intersections, and when to stop at the goal. >
Spread spectrum for mobile communications

The characteristics of spread spectrum that make it advantageous for mobile communications are described. The parameters that determine both the performance and the total capacity are introduced, and an analysis which yields (approximately) the number of users that can simultaneously communicate, while maintaining a specified level of performance, is presented. Spread spectrum overlay, wherein a code-division multiple-access (CDMA) network shares a frequency band with narrow-band users, is analyzed, and it is seen that excision of the narrowband signals from the CDMA receivers before despreading can improve both performance and capacity. >
Doppler signatures of radar backscattering from objects with micro-motions

Radar backscattering from objects with micro-motions is subject to Doppler modulations that help determine dynamic properties of objects and provide useful information about the objects. Doppler modulations represented by joint time-frequency analysis provide useful time-varying Doppler characteristics and, thus, add additional time-dimension information to exploit motion characteristics. The author discusses how to simulate radar backscattering from objects with rigid body motions and objects with non-rigid body motions, and how to analyse, interpret and characterise Doppler signatures of objects that undergo these micro-motions. Precession heavy top and human locomotion are used as examples of rigid and non-rigid body motions, respectively. Radar micro-Doppler signatures derived from these motions illustrate the potential of the joint time-frequency analysis for exploiting kinetic and dynamic properties of objects.
Umbilical artery Doppler velocimetry--an update.

Doppler ultrasonography was introduced into clinical obstetric practice over 20 years ago. It is also accepted that a variety of common obstetrical complications such as preeclampsia and intrauterine growth restriction have their origin in abnormal development of the placental vasculature and this could be reflected in abnormal Doppler velocimetry. Doppler velocimetry of the umbilical artery has been the subject of multiple clinical studies but results have often been disputed due to differences in study populations and methodologies. In recent years, meta-analysis of randomized clinical trials have shown that incorporation of Doppler velocimetry into clinical practice will reduce perinantal mortality in high-risk patients. This article reviews the data of the meta-analyses as it pertains to the management of high-risk pregnant patients.
Property Relations, Production Relations, And Inequality: Anthropology, Political Economy, And The Blackfeet

Political-economic concepts that privilege production over other dimensions of social life are inappropriate to the study of non-Western societies. Concepts suitable for non-Western societies must be based on the institutional specificity of those societies, just as production-based concepts (forces and relations of production) derive their analytical value from the institutional structure of industrial capitalism. In this article, “property relations” is advanced as such a concept and is used to explain the emergence of inequality from egalitarian social relations among the Blackfeet Indians on the northern plains of North America. [political economy, property relations, historical anthropology, legal anthropology, inequality, gender relations]
Prediction of vapor‐liquid equilibria of petroleum fractions

The thermodynamic treatment of phase equilibria proposed by Chueh and Prausnitz has been modified to extend their method to systems of petroleum fractions. These modifications, which include the use of a symmetric convention for normalizing activity coefficients and replacement of the dilated van Laar model with a regular solution model, were required because existing data were insufficient to establish the needed binary interaction parameters. The resulting correlation was compared with experimental data on a naphtha-furnace oil mixture at conditions up to 660°F. and 517 lb./sq.in.abs. The computed K values showed an average absolute deviation of 9.1%, while K values predicted by the Chao-Seader correlation deviated by 12.4%.
Multiple mechanisms account for genomic instability and molecular mutation in neoplastic transformation.

Neoplastic cells typically possess numerous genomic mutations and chromosomal aberrations, including point mutations, gene amplifications and deletions, and replication errors. Acquisition of such genomic instability may represent an early step in the process of carcinogenesis. Proteins involved in DNA replication, DNA repair, cell cycle progression, and others are all components of complex overlapping biochemical pathways that function to maintain cellular homeostasis. Therefore, mutational alteration of genes encoding proteins involved in these cellular processes could contribute to genomic instability. Loss of normal cellular mechanisms that guard against genomic mutation and the ensuing genomic instability might lead to accumulation of multiple stable mutations in the genome of affected cells, perhaps resulting in neoplastic transformation when some critical number of transformation-related target genes become damaged. Thus, interactions of fundamental cellular processes play significant roles in sustaining cellular normality, and alteration of any of these homeostatic processes could entrain cells to the progressive genomic instability and phenotypic evolution characteristic of carcinogenesis. Here, we discuss possible molecular mechanisms governing DNA mutation and genomic instability in genetically normal cells that might account for the acquisition of genomic instability in somatic cells, leading to the development of neoplasia. These include (a) molecular alteration of genes encoding DNA repair enzymes, (b) molecular alteration of genes responsible for cell-cycle control mechanisms, and (c) direct molecular alteration of dominantly transforming cellular protooncogenes. We also discuss normal cellular processes involved with DNA replication and repair that can contribute to the mutational alteration of critical genes: e.g., slow repair of damaged DNA in specific genes, and the timing of normal gene-specific replication.
Real-time hearing assessment device based on distortion product otoacoustic emissions

Real-time implementation of a recently introduced method of measurement of distortion product otoacoustic emissions (DPOAEs) for hearing assessment is presented. Development of the real-time application begins with the discretization of the DPOAE estimation algorithm in Matlab and then programming in C for final downloading onto a digital signal processor (DSP) platform. Aside from the signal processing task involved in the estimation process, the DSP platform controls a microphone/speaker system, which generates the acoustical stimuli for presentation to the ear canal and collects the acoustical responses recorded in the ear canal. The real-time results are compared with those obtained by a continuous-time off-line model of the DPOAE estimation algorithm. The developed DPOAE measurement system offers a high degree of noise immunity and a short measurement time, both of which are of importance in clinical applications of the DPOAE signals.
Mechanism of Molecular Ordering in Monolayer Liquid Crystal Films

Scanning tunneling microscopy and “molecule corrals” were used to measure the temperature dependence of the rate of molecular ordering in monolayer liquid crystal films. Molecule corrals are circular etch pits, 3.35 A deep on the basal surface of graphite formed by high-temperature oxidation. A strong negative relationship between temperature and nucleation rate was observed, consistent with a nucleation growth mechanism of molecular self-assembly. From a fit of classical nucleation theory the melting temperature of the film was found to be Tmelt = 318 ± 6 K, the thermodynamic driving force for nucleation ΔFn(Tmelt − T)/Tmelt = 1.1 ± 0.3 kcal mol-1, and the preexeponential factor A = (1.8 ± 0.8) × 108 A-2 s-1.