cssi/SciSciGPT-SciSciNet huggingface dataset:
Lethality of glnD null mutations in Azotobacter vinelandii is suppressible by prevention of glutamine synthetase adenylylation

GlnD is a pivotal protein in sensing intracellular levels of fixed nitrogen and has been best studied in enteric bacteria, where it reversibly uridylylates two related proteins, PII and GlnK. The uridylylation state of these proteins determines the activities of glutamine synthetase (GS) and NtrC. Results presented here demonstrate that glnD is an essential gene in Azotobacter vinelandii. Null glnD mutations were introduced into the A. vinelandii genome, but none could be stably maintained unless a second mutation was present that resulted in unregulated activity of GS. One mutation, gln-71, occurred spontaneously to give strain MV71, which failed to uridylylate the GlnK protein. The second, created by design, was glnAY407F (MV75), altering the adenylylation site of GS. The gln-71 mutation is probably located in glnE, encoding adenylyltransferase, because introducing the Escherichia coli glnE gene into MV72, a glnD + derivative of MV71, restored the regulation of GS activity. GlnK-UMP is therefore apparently required for GS to be sufficiently deadenylylated in A. vinelandii for growth to occur. The ΔglnD GSc isolates were Nif−, which could be corrected by introducing a nifL mutation, confirming a role for GlnD in mediating nif gene regulation via some aspect of the NifL/NifA interaction. MV71 was unexpectedly NtrC+, suggesting that A. vinelandii NtrC activity might be regulated differently than in enteric organisms.
Effect of angiotensin II on energetics, glucose metabolism and cytosolic NADH/NAD and NADPH/NADP redox in vascular smooth muscle

Angiotensin II (AII) is a neurohormone and contractile agonist of vascular smooth muscle that has been shown to be involved in the pathogenesis of vascular disease, which may be partially caused by its effect on oxidant stress. Energy metabolism was examined in pig carotid arteries treated with AII, because the activity of pathways of intermediary metabolism of glucose determines the status of cytosolic NADH/NAD and NADPH/NADP redox, factors which are involved in oxidant stress. Contractile responses to AII were characterized by an increase in isometric force followed by a gradual decline to near-basal levels. Despite contractile activation, no change in glycolysis, lactate production, glucose oxidation, fatty acid oxidation, O2 consumption, glycogen content or high-energy phosphates was detected when compared to resting unstimulated arteries. Paradoxically, total uptake of glucose was inhibited by AII. Treatment with diphenylene iodinium, an inhibitor of NAD(P)H oxidase and superoxide production, reversed the inhibition of glucose uptake and revealed the expected increase in glucose uptake and oxidation upon contractile activation of smooth muscle by AII. The intracellular [lactate]/pyruvate] ratio was increased, reflecting an increase in cytosolic NADH/NAD redox, whereas NADPH/NADP redox was decreased by AII. No change in NADPH/NADP redox was observed when membrane depolarization with K+ was used as the contractile agent. It is concluded that the pattern of force generation, metabolism and energetics of AII-stimulated contraction are significantly different from that of other contractile agonists. Most notably AII inhibited glucose uptake. NAD(P)H oxidase and/or attendant superoxide may play a role in modulating glucose metabolism. AII induces opposite changes in NADH/NAD redox and NADPH/NADP redox, which may have important consequences for oxidant stress. (Mol Cell Biochem 262: 91–99, 2004)
Local resistance to oxidative stress by overexpression of copper-zinc superoxide dismutase limits neointimal formation after angioplasty.

PURPOSE To examine the effects of oxidative stress on neointimal hyperplasia through local overexpression of human copper-zinc superoxide dismutase (Cu-Zn SOD). METHODS The left common femoral arteries (CFA) of 18 New Zealand white rabbits were subjected to balloon overdilation injury. Each dilated CFA was then incubated with either a nonviral (buffer) or viral (adenovirus overexpressing beta-galactosidase) control or an adenovirus overexpressing Cu-Zn SOD. Animals were then sacrificed at 3, 7, or 28 days (3 arteries per group per time point) and the treated CFA segments were harvested for analysis of esterase-positive inflammatory cells and extracellular matrix elements. The intima-to-media ratio (I/M) was measured to assess the degree of neointimal formation. RESULTS At 3 days, local SOD levels in the Cu-Zn SOD-treated group were significantly elevated relative to both controls (p<0.01). Significant reductions in lipid peroxidation byproducts were also seen in the SOD group relative to viral and nonviral controls (p<0.05). Mean I/M at 28 days was 0.582+/-0.088 for the nonviral control group versus 0.565+/-0.133 for the viral control group. The SOD-treated group had a significant reduction relative to both controls: 0.259+/-0.045 (p<0.05). Statistically significant reductions in I/M were also demonstrated in the SOD group relative to control groups at 7 days (p<0.05). The SOD-treated group demonstrated significant preservation of elastin relative to controls, as well as a significant reduction in esterase-positive granulocytes relative to controls (p<0.05). CONCLUSIONS Direct buffering of oxidative stress in balloon-injured vessels can significantly alter postinjury response and limit neointimal hyperplasia.
Quantization bit rate reduction in scanning tomographic acoustic microscopy

The imaging capability of the scanning laser acoustic microscope has been enhanced by the addition of a quadrature detector for holographic imaging and rotational and frequency-varying hardware for tomographic reconstruction. Because of the expansion of data acquisition capability, the memory-intensive demands placed on the processing computer by these modifications require efficient methods of representing and storing the tomographic data while retaining the quality of image reconstruction. This paper reports the performance evaluation of low bit-rate data acquisition. Results show the feasibility of high-quality imaging at bit-rate savings at the level of 33%. >
Reaction of (triphenylsilyl)lithium with some di- and trihalobenzenes

Abstract Reactions of (triphenylsilyl)lithium with some di- and trihalobenzenes include coupling and halogen-metal exchange transformations. Of particular significance is the reaction with 1,2,4-tribromobenzene which gives, additionally, some 1,3,5-tribromobenzene. The extent of this isomerization is apparently determined by the base involved.
Absence of chaos in Bohmian dynamics.

The Bohm motion for a particle moving on the line in a quantum state that is a superposition of $n+1$ energy eigenstates is quasiperiodic with n frequencies.
Coronary disease and stroke in patients with large-vessel peripheral arterial disease.

Previous reports have indicated an excess of mortality from coronary heart disease (CHD), cardiovascular disease (CVD), and all causes in subjects with large-vessel peripheral arterial disease (LV-PAD). However, there is little information available concerning the risk of nonfatal events (morbidity) in this patient group.
Consciousness, solidarity and hope as prevention and rehabilitation

This paper grapples with the question of how progressive criminologists might approach working with people who have committed violent or predatory crimes, or are ‘at risk’ of doing so. Progressives have often been uneasy about ‘intervention’ with people who offend: but in the face of the destructiveness of violence, especially in some parts of the world, a posture of simple non-intervention won’t suffice. I suggest three central principles – which I call consciousness, solidarity and hope – that may guide us in developing ways of working with offenders that are both progressive and effective.
Survey of Bartonella spp. in U.S. Bed Bugs Detects Burkholderia multivorans but Not Bartonella

Bed bugs (Cimex lectularius L.) have resurged in the United States and globally. Bed bugs are hematophagous ectoparasites of humans and other animals, including domestic pets, chickens, and bats, and their blood feeding habits contribute to their potential as disease vectors. Several species of Bartonella are re-emergent bacterial pathogens that also affect humans, domestic pets, bats and a number of other wildlife species. Because reports of both bed bugs and Bartonella have been increasing in the U.S., and because their host ranges can overlap, we investigated whether the resurgences of these medically important pathogens and their potential vector might be linked, by screening for Bartonella spp. in bed bugs collected from geographic areas where these pathogens are prevalent and from bed bugs that have been in culture in the laboratory for several years. We screened a total of 331 bed bugs: 316 bed bugs from 36 unique collections in 29 geographic locations in 13 states, 10 bed bugs from two colonies maintained in the laboratory for 3 yr, and 5 bed bugs from a colony that has been in culture since before the recent resurgence of bed bugs. Bartonella spp. DNA was screened using a polymerase chain reaction assay targeting the 16S–23S rRNA intergenic transcribed spacer region. Bartonella DNA was not amplified from any bed bug, but five bed bugs from four different apartments of an elderly housing building in North Carolina contained DNA sequences that corresponded to Burkholderia multivorans, an important pathogen in nosocomial infections that was not previously linked to an arthropod vector.
On the extraction of pattern features from continuous measurements

A suboptimum method of extracting features, by linear operations, from continuous data belonging to M pattern classes is presented. The set of features selected minimizes bounds on the probability of error obtained from the Bhattacharyya distance and the Hajek divergence. The random processes associated with the pattern classes are assumed to be Gaussian with different means and covariance functions. For M=2, in the two special cases in which, respectively, the means and the covariance functions are the same, both the above distance measures yield the same answer. The results obtained represent an extension of the existing results for two pattern classes with the same means and different covariance functions.
In vitro stability study of organophosphonic self assembled monolayers (SAMs) on cobalt chromium (Co-Cr) alloy.

Abstract Surface modification of cobalt chromium (Co–Cr) alloy is being investigated as a possible solution to the biomedical challenges arising from its usage. Self assembled monolayers (SAMs) of organophosphonic octadecylphosphonic acid (ODPA) were formed on the oxide surface of Co–Cr alloy by chemisorption using the solution deposition technique. High quality and well-ordered SAMs were formed which were characterized using Fourier transform infrared spectroscopy-attenuated total reflectance (FTIR-ATR), X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), contact angle measurements and ellipsometry. The resulting monolayers were then exposed to in vitro conditions using phosphate buffered saline (PBS) solution. The samples were analyzed for a period of 1, 3, 7 and 14 days. The resulting samples were characterized using XPS, AFM and Contact angle measurements. XPS atomic concentrations and detailed high energy elemental scans gave an insight into the trends of elemental concentrations over the duration of the study. SAMs were found to be strongly bound to the oxide surface after PBS exposure. AFM gave the topographic details of SAMs presence by island formation before and after SAM formation and also over the duration of the PBS exposure. Contact Angle Measurements confirmed the hydrophobicity of the surface after SAM formation and indicated a slight disorder of the SAM alkyl chain upon exposure to PBS. Thus, ODPA SAMs were successfully coated on Cobalt Chromium (Co–Cr) alloy surface and were found to be stable and strongly bound after PBS exposure.
Interactive publications: creation and usage

As envisioned here, an "interactive publication" has similarities to multimedia documents that have been in existence for a decade or more, but possesses specific differentiating characteristics. In common usage, the latter refers to online entities that, in addition to text, consist of files of images and video clips residing separately in databases, rarely providing immediate context to the document text. While an interactive publication has many media objects as does the "traditional" multimedia document, it is a self-contained document, either as a single file with media files embedded within it, or as a "folder" containing tightly linked media files. The main characteristic that differentiates an interactive publication from a traditional multimedia document is that the reader would be able to reuse the media content for analysis and presentation, and to check the underlying data and possibly derive alternative conclusions leading, for example, to more in-depth peer reviews. We have created prototype publications containing paginated text and several media types encountered in the biomedical literature: 3D animations of anatomic structures; graphs, charts and tabular data; cell development images (video sequences); and clinical images such as CT, MRI and ultrasound in the DICOM format. This paper presents developments to date including: a tool to convert static tables or graphs into interactive entities, authoring procedures followed to create prototypes, and advantages and drawbacks of each of these platforms. It also outlines future work including meeting the challenge of network distribution for these large files.
OXYGEN-INDEPENDENT INACTIVATION OF HAEMOPHILUS INFLUENZAE TRANSFORMING DNA BY MONOCHROMATIC RADIATION: ACTION SPECTRUM, EFFECT OF HISTIDINE AND REPAIR*

— The action spectrum for the oxygen-independent inactivation of native transforming DNA from Haemophilus influenzae with near-UV radiation revealed a shoulder beginning at 334 and extending to 460 nm. The presence of 0.2 M histidine during irradiation produced a small increase in inactivation at 254, 290 and 313 nm, a large increase at 334 nm and a decrease in inactivation at 365, 405 and 460 nm. Photoreactivation did not reverse the DNA damage produced at pH 7.0 at 334, 365, 405 and 460 nm, but did reactivate the DNA after irradiation at 254, 290 and 313 nm. The inactivation of DNA irradiated at 254, 290 and 313 nm was considerably greater when the transforming ability was assayed in an excision-defective mutant compared with the wild type, although DNA irradiated at 334, 365, 405 and 460 nm showed smaller differences. These results suggest that the oxygen-independent inactivation of H. influenzae DNA at pH 7 by irradiation at 334, 365, 405 and 460 nm is caused by lesions other than pyrimidine dimers.
Axenic Paramecium caudatum. I. Mass Culture and Structure

To establish and grow Paramecium caudatum in mass axenic culture the culture medium of Soldo, Godoy & van Wagtendonk was modified by substituting phosphatidylethanolamine (PE) for TEM-4T and by a 10-fold increase in folic acid. Population densities of 4000 to 6000 cells/ml and a generation time of 20-26 h are regularly obtained. Optimal growth is obtained with PE-stigmasterol ratios between 40:1 to 400:1. Cells from 1-day-old axenic cultures have many lipid bodies aggregated in clumps (which disappear in 2 to 3 days) as well as foci of rough endoplasmic reticulum bordered by dictyosomes. The latter suggests a very active metabolism. Crystalline sheets found in both food vacuoles and lysosomes presumably play a role in digestion. Axenically grown cells also have abundant Golgi bodies (dictyosomes) and by late log phase become filled with lysosomes.
MO-E-230A-01: Legal Issues

Research plays a prime role in the professional lives of many medical physicists, especially those in academic institutions. The prime goal of this research is to acquire new knowledge. Acquiring the knowledge, however, is not sufficient, in that the information must also be disseminated to the community. The standard vehicle for dissemination of research knowledge is the peer‐reviewed journal. In fact, a medical physicist's academic advancement is often based on the number of papers that have appeared in a peer‐reviewed journal. However, publication in a journal introduces significant restriction on the ability for subsequent dissemination of the research information. Prior to publication, the producer of the information is the complete owner of the information. Researchers may disseminate the information to anyone they please in any form they please. Publication, however, places significant limitations as to how information may be disseminated because of the existence of copyright laws. Often, the individual who has generated the information has turned over ownership of the information to the publisher of the journal and no longer has complete control over how the information may be distributed to others. Limits exist, however, on the extent that a publisher may control dissemination of the information in a journal article. In the distant past (>40 yr ago) the publisher exercised significant control over dissemination. If an author wished to provide others with copies of a paper, the author would have to purchase reprints of the article from the publisher and deliver the reprint to the recipient. In the more recent past, the author of the article, or anyone else for that matter, may photocopy the article from the journal. The ease of photocopying has established some principles of “fair use,” that is, scenarios where photocopying lies within the limitations of copyright restrictions, and other scenarios where photocopying violates copyright. For example, individuals may copy an article from a journal for their own use, but to make a large number of copies without permission for distribution to a class may violate copyright restrictions. Presently, most journal articles appear in electronic form, typically as a PDF file that can be downloaded and stored on an individual's computer. The same file can be emailed to many recipients. Because of the ease of dissemination of this information, a new paradigm for dissemination is necessary. It is necessary to balance the need to disseminate information against the need for the journal to recoup the expenses of publication and dissemination and, when appropriate, make sufficient profit to warrant remaining in business.
Deleterious effects of taurine in cats with digitalis-induced arrhythmias.

An established model of digitalis toxicity was used to investigate the antiarrhythmic properties of taurine. I.v. doses of taurine ranging from 0.01 to 4.0 mmole/kg were ineffective in converting a deslanoside-induced arrhythmia to sinus rhythm. Indeed, taurine was found to aggravate the arrhythmia and in three experiments precipitated ventricular fibrillation. In addition, pretreatment with 5 mmole/kg taurine i.v. had no significant effect on the doses of deslanoside to produce ventricular arrhythmia and fibrillation.
Bhopal—A Case Study of International Disaster

This paper outlines what is known about the probable events leading up to the disaster in Bhopal, India, in 1984, wherein release of a gas cloud from an industrial plant killed over 3,800 people. It briefly reviews the toxicology of methyl isocyanate, a major component of the cloud; presents an overview of the acute and chronic health effects of the gas exposure from published human and animal studies; identifies some of the clinical dilemmas and medical management and epidemiologic issues being debated; provides an insight into national and transnational implications; and summarizes the lessons learned or not learned from this disaster of global significance.
Prediction of the viscosity and thermal conductivity coefficients of mixtures

Abstract A corresponding states procedure to predict the viscosity and thermal conductivity coefficients of a pure fluid or mixture is discussed. We show the transport properties of a fluid or mixture can be calculated to within experimental error given only corresponding values for a reference fluid and equation of state data. With methane, as the reference fluid, we consider nitrogen, ethane, propane, butane, carbon dioxide, and mixtures of these fluids. LNG is also included. It is shown that the conventional corresponding states approach is not sufficient to predict correctly the transport properties. The effect of internal degrees of freedom on the thermal conductivity coefficient and the enhancement in the critical region for this coefficient is discussed briefly.
Methanethiol Adsorption on Defective MoS2(0001) Surfaces

There have been relatively few studies that have used molybdenum sulfide single crystals as model HDS catalysts. MoS2(0001) single crystal surfaces are largely unreactive toward many organosulfur compounds but can be ion-bombarded to form chemically active surfaces with large densities of sulfur vacancies (coordinately unsaturated Mo sites). XPS and AES measurements confirm that sulfur is preferentially removed during ion-bombardment and that significant changes occur in the distribution of Mo oxidation states at the surface as a function of ion-bombardment time. Methanethiol adsorption studies were performed using TPD on ion-bombarded MoS2(0001) single-crystal surfaces. Methanethiol, methane, ethane, and ethylene were observed as decomposition products, which are thought to arise from methanethiolate and thioformaldehyde surface intermediates. Additionally, product selectivity varied as a function of cus Mo surface site densities.
Plasmapheresis-induced hemodilution and its effects on serum constituents.

Samples were obtained from 23 plasmapheresis donors before, during, and after double plasmapheresis. Seventeen chemical analyses were performed on these specimens and the results were subjected to statistical analysis. Representative samples can be obtained from plasmapheresis donors before the procedure has begun, immediately after the first unit of whole blood has been removed, or 15 minutes after the completion of the entire procedure. The sample obtained after the first unit of whole blood has been removed will show dilutional lowering of the uric acid concentration, and the 15-minute equilibration sample will show dilutional lowering of the inorganic phosphorus concentration. Short-term donors and long-term donors manifest a somewhat different hemodilutional response to plasmapheresis.
Demonstration of an Internal Pancreatic Fistula by Computed Tomography

The computed tomographic demonstration of a mediastinal pseudocyst communicating with the pancreatic duct in a patient with severe acute pancreatitis is reported. An awareness of this communication was essential in planning the appropriate surgical management.
Allelic complementation among nitrous acid-induced ad-3B mutants of Neurospora crassa

Abstract Complementation tests of a random sample of NA-induced ad-3B mutants of Neurospora crassa have shown that 72.1% show allelic complementation and have either nonpolarized or polarized complementation patterns, the majority (60.4%) being in the nonpolarized group. The ratio of nonpolarized to polarized complementation patterns is thus 5 to 1. In addition, a total of 24.3% are leaky, have nonpolarized patterns, and account for 40.3% of the mutants in this class. The facts that only 30 of the 65 mutants with nonpolarized patterns and only 5 of the 13 mutants with polarized patterns are different have been interpreted as indicating a nonrandom distribution of altered sites in the ad-3B locus. The discovery of many nonleaky NA-induced mutants with nonpolarized patterns has led to a revision of an earlier complementation map of the ad-3B cistron published previously 8 . A tester set of predominantly nonleaky ad-3B mutants with nonpolarized complementation patterns which define a linear complementation map of 17 complons has been selected for future work. The complementation data from the present analysis in combination with the reversion data of Malling 15 indicate a direct correlation between the percentage of mutations resulting from base-pair substitution and the percentage showing allelic complementation.
Pain control by image-guided radiosurgery for solitary spinal metastasis.

Precision and accuracy of image-guided spinal radiosurgery has been previously demonstrated. This study was carried out to determine the clinical efficacy of spine radiosurgery for the treatment of solitary spinal metastases with or without cord compression. A total of 49 patients with 61 separate spinal metastases were treated with radiosurgery. All patients had pathologically proven primary cancers and had either synchronous or metachronous metastasis to the spine. The majority of the patients presented with back pain. All patients received single-dose radiosurgery to the involved spine only. The radiosurgery dose ranged from 10 to 16 Gy. The primary endpoint was pain control, but outcomes in neurological status and radiological tumor control also were assessed. The median time to pain relief was 14 days and the earliest time of pain relief was within 24 hours. Complete pain relief was achieved in 46%, partial relief in 18.9%, and stable symptoms in 16.2%. Relapse of pain at the treated spinal segment was 6.9%. Median duration of pain relief at the treated spine was 13.3 months. Overall pain control rate for one year was 84%. This experience demonstrates that spinal radiosurgery can achieve rapid and durable pain relief. Single-dose radiosurgery has a potential to be a viable treatment option for single spinal metastasis.
Static scapholunate dissociation: a new reconstruction technique using a volar and dorsal approach in a cadaver model.

Abstract We used 4 fresh-frozen cadaver arms to assess a method of reconstruction we designed for static scapholunate dissociation. The dorsal scapholunate ligament, scapholunate interosseous ligament, radioscapholunate, and radioscaphocapitate ligaments were sectioned. Radiographs were taken before sectioning, after sectioning, and after reconstruction. Passive motion was also measured before sectioning and after the repair. The dorsal scapholunate ligament was repaired directly; the palmar radioscapholunate and radioscaphocapitate ligaments were reconstructed using a free flexor carpi radialis tendon autograft and Mitek mini suture anchors (1.8-mm diameter and 5.4-mm length; Mitek Products, Norwood, MA) for anatomic fixation. An independent board-certified hand surgeon analyzed the radiographs of the wrists taken before and after sectioning and after reconstruction. Assessment of the unsectioned wrists revealed an average scapholunate angle of 45°. After scapholunate dissociation was created the average scapholunate angle was 71°. Repair of the dorsal scapholunate ligament alone did not improve the scapholunate angle. Average scapholunate angle after repair of the dorsal scapholunate ligament and reconstruction of the palmar ligaments was 43°. Average range of motion on flexion, extension, and radial and ulnar deviation before ligament sectioning and after reconstruction was unchanged at 54°, 59°, 19°, and 40° respectively. This technique shows an improvement in scapholunate angle on lateral radiographs, and passive motion remained relatively unchanged. (J Hand Surg 2001;26A:749-754. Copyright © 2001 by the American Society for Surgery of the Hand.)
Nursing Home Social Services Directors and Elder Abuse Staff Training

In a nationally representative study of 1,071 nursing home social services directors 80% of social services departments provided resident rights training and 60–70% were involved in abuse training. Departments headed by recent grads and in chain nursing homes or in the northeast were more likely to be involved in training. Seventy-two percent of social services directors were able to provide one-on-one training about reporting suspected abuse; education and licensure were related to ability to train.
Light-ion production for medium-energy heavy-ion interactions

The unique radiation present in space is hard to completely reproduce for applications such as those needed for testing new shielding materials. Instead, the testing procedures involve transport model calculations that can simulate this radiation environment. Because these codes rely on experimental cross section data for validation and verification, it becomes necessary to expand or improve the cross section libraries in order to improve the accuracy of the models' predictions.
Binaural Beat Technology in Humans: A Pilot Study to Assess Neuropsychologic, Physiologic, And Electroencephalographic Effects

Objectives: When two auditory stimuli of different frequency are presented to each ear, binaural beats are perceived by the listener. The binaural beat frequency is equal to the difference between the frequencies applied to each ear. Our primary objective was to assess whether steady-state entrainment of electroencephalographic activity to the binaural beat occurs when exposed to a specific binaural beat frequency as has been hypothesized. Our secondary objective was to gather preliminary data on neuropsychologic and physiologic effects of binaural beat technology. Design: A randomized, blinded, placebo-controlled crossover experiment in 4 healthy adult subjects. Intervention: Subjects were randomized to experimental auditory stimulus of 30 minutes of binaural beat at 7 Hz (carrier frequencies: 133 Hz L; 140Hz R) with an overlay of pink noise resembling the sound of rain on one session and control stimuli of the same overlay without the binaural beat carrier frequencies on the other session. Outcome measu...
Grades of Cartesian innateness 1

(1993). Grades of Cartesian innateness. British Journal for the History of Philosophy: Vol. 1, No. 2, pp. 23-44.
Automatic loop transformations and parallelization for Java

This paper describes a prototype Java compiler that achieves performance levels approaching those of current state-of-the-art Fortran compilers on numerical codes. We present a new transformation called alias versioning that takes advantage of the simplicity of pointers in Java. This transformation, combined with other techniques that we have developed, enables the compiler to perform high order loop transformations and parallelization completely automatically. We believe that our compiler is the first to have such capabilities of optimizing numerical Java codes. By exploiting synergies between our compiler and the Array package for Java, we achieve between 80 and 100% of the performance of highly optimized Fortran code in a variety of benchmarks. Furthermore, automatic parallelization achieves speedups of up to 3.8 on four processors. Our compiler technology makes Java a serious contender for implementing numerical applications.
The Ribosomal Pre State in Stalled vs. Actively Translating Ribosomes

During protein synthesis, tRNAs successively occupy three sites on the ribosome: A (aminoacyl), P (peptidyl), and E (exit). A proposed model based on observations of stalled ribosomes describes two distinct states before mRNA and tRNA translocation (PRE-translocation): a classical state in which the tRNAs occupy the same sites in the large and small ribosomal subunits (A/A and P/P), and a hybrid state in which the tRNAs occupy different sites in each subunit (A/P and P/E). To determine whether the exchange and partition between the classical and hybrid PRE states of stalled ribosomes is important for actively translating ribosomes, we conducted single molecule FRET experiments using ribosomes containing Cy5-labeled large subunit protein L11, and Val-tRNAVal(Cy3) or Phe-tRNAPhe(Cy3) in the A-site. We monitored FRET in stalled PRE complexes in the absence of EF-G•GTP, and during ongoing translation in the presence of EF-G•GTP. The mRNA contained a variable number (0, 4, or 8) of Tyr codons preceding Phe and Val codons. In stalled ribosomes, the histogram of L11-tRNA FRET values showed two peaks corresponding to the classical and hybrid states. In contrast, in actively translating ribosomes, the FRET histogram showed only one major peak, with a FRET efficiency that was intermediate between the two values for the stalled complexes. This distribution could correspond to an intermediate structure unique to active turnover, or to a transient state that, in the presence of EF-G, undergoes translocation more rapidly than it converts into the canonical classical and hybrid states. These results suggest that the PRE-translocation ribosomal state during active translation is distinct from the classical and hybrid states observed in stalled ribosomes, consistent with earlier results reported by our group (Rosenblum et al., JACS 2013). Supported by NIH grant GM080376 and AHA fellowship 12POST8910014 to CC.
Fine-structural characterization of the somatic innervation of the tympanic membrane in normal, sympathectomized, and neurotoxin-denervated rats.

The pars tensa of the rat tympanic membrane (TM) consists largely of a lamina propria of specialized unbanded collagen bounded on the outer surface by an unusually thin epidermal layer and on the inner surface by a flat, single-cell mucosal layer. The mucosal layer is innervated solely by unmyelinated (C) axons, whereas the cutaneous layer is supplied by both myelinated and C axons. The outer surface differs from general body skin, lacking dermal papillae, hairs, sweat glands, and distinctive dermal corpuscular structures.Epidermal innervation includes distinctive terminals in the basal layer, unassociated with Merkel cells, and deeper intraepidermal smaller endings containing accumulations of mitochondria and vesicles. The sensory nature of these endings can be inferred by their extensive, but not total, elimination following neonatal capsaicin treatment (a potent neurotoxin for thin sensory fibers) and their preservation following surgical or neurotoxin sympathectomy.The thin mucosal epithelium displays...
Must psychologists change the way they analyze their data

Wagenmakers, Wetzels, Borsboom, and van der Maas (2011) argued that psychologists should replace the familiar “frequentist” statistical analyses of their data with Bayesian analyses. To illustrate their argument, they reanalyzed a set of psi experiments published recently in this journal by Bem (2011), maintaining that, contrary to his conclusion, his data do not yield evidence in favor of the psi hypothesis. We argue that they have incorrectly selected an unrealistic prior distribution for their analysis and that a Bayesian analysis using a more reasonable distribution yields strong evidence in favor of the psi hypothesis. More generally, we argue that there are advantages to Bayesian analyses that merit their increased use in the future. However, as Wagenmakers et al.’s analysis inadvertently revealed, they contain hidden traps that must be better understood before being more widely substituted for the familiar frequentist analyses currently employed by most research psychologists.
Post-heparin phospholipase and post-heparin lipase have different tissue origins

Abstract Post-heparin phospholipase activity is reduced by 80% in the hepatectomized rat. In contrast, post-heparin lipase activity is unaffected by hepatectomy. Since the phospholipase originates mainly in the liver and the lipase originates entirely in extrahepatic tissues, these two activities must be different enzymes.
Optic atrophy after sildenafil use.

Abstract Background It has been well-reported that phosphodiesterase-5 (PDE-5) inhibitors, originally investigated for their effect on smooth muscles and now used widely in treatment of erectile dysfunction, can cause mild transient visual disturbances because of their action on inhibiting enzymes involved in retinal transduction. Recently, these medications have been associated with the development of non-arteritic anterior ischemic optic neuropathy (NAAION) with attendant vision loss. Case report An older male patient, previously examined and ocularly healthy, presented asymptomatically with an occult optic neuropathy, not characteristic of NAAION. Neuroimaging and serology failed to reveal any other underlying cause. The patient did, however, report the use of sildenafil during the interval between his previously normal examination and the observation of his optic neuropathy. Conclusions This case details the development of an optic neuropathy with atrophy seemingly associated with the use of sildenafil, although no cause and effect could be conclusively found. This may indicate that medications used in the treatment of erectile dysfunction may be responsible for optic neuropathies other than NAAION.
GpMyoF, A WD40 REPEAT-CONTAINING MYOSIN ASSOCIATED WITH THE MYONEMES OF GREGARINA POLYMORPHA

This study presents the first characterization of a WD40 repeat-containing myosin identified in the apicomplexan parasite Gregarina polymorpha. This 222.7 kDa myosin, GpMyoF, contains a canonical myosin motor domain, a neck domain with 6 IQ motifs, a tail domain containing short regions of predicted coiled-coil structure, and, most notably, multiple WD40 repeats at the C-terminus. In other proteins such repeats assemble into a β-propeller structure implicated in mediating protein-protein interactions. Confocal microscopy suggests that GpMyoF is localized to the annular myonemes that gird the parasite cortex. Extraction studies indicate that this myosin shows an unusually tight association with the cytoskeletal fraction and can be solubilized only by treatment with high pH (11.5) or the anionic detergent sarkosyl. This novel myosin and its homologs, which have been identified in several related genera, appear to be unique to the Apicomplexa and represent the only myosins known to contain the WD40 domain. T...
Density functional theory of quantum mechanical systems. II. Accurate potential and energy functionals and their representations

The problem of generating accurate single-particle potentials in larger quantum mechanical systems is discussed. It is shown that representing the potential by Volterra series simplifies the relationships between the potential and energy functionals considerably.
HBCU efficiency and endowments: An exploratory analysis

Discussions of efficiency among Historically Black Colleges and Universities (HBCUs) are often missing in academic conversations. This article seeks to assess efficiency of individual HBCUs using Data Envelopment Analysis (DEA), a non-parametric technique that can synthesize multiple inputs and outputs to determine a single efficiency score for each institution. The authors hypothesized that institutions with higher endowments will have higher efficiency scores due to an increased ability to acquire more productive capital. To test this hypothesis, efficiency scores were regressed on endowments and HBCU status, with control variables denoting if institutions are public or religiously affiliated. From DEA, we found that HBCUs were on average slightly more efficient that Predominantly White Institutions. Endowment levels were found to be significant determinants of efficiency for both sets of institutions. This suggests (1) that the general perception of HBCUs as inefficient requires reconsideration and (2) that schools with the most endowment resources are generally more efficient. Less efficient HBCUs should perhaps devote resources to building endowment levels to increase efficiency. We can also see the importance of methodologies allowing for investigation of both differences among HBCUs and differences in operational contexts among HBCUs and other schools.
Assessing the potential for bias in direct observation of adult commuter cycling and helmet use

Objectives Bicycling and helmet surveillance, research, and programme evaluation depend on accurate measurement by direct observation, but it is unclear whether weather and other exogenous factors introduce bias into observed counts of cyclists and helmet use. Methods To address this issue , a time series was created of cyclists observed at two observation points in Washington, DC, at peak commuting times and locations between September 2012 and February 2013. Using multiple linear regression with Newey-West SEs to account for possible serial correlation, the association between various factors and cyclist counts and helmet use was investigated. Results The number of cyclists observed per 1 h session was significantly associated with predicted daily high temperature, chance of rain, and actual rain. Additionally, fewer cyclists were observed on Fridays. Helmet use was significantly lower during evening commutes than morning and also lower on Fridays. Helmet use was not associated with weather variables. Controlling for observable cyclists characteristics weakened the association between helmet use and the time of day and day of the week, but it did not eliminate that association. Conclusions Direct observation to measure commuter cycling trends or evaluate interventions should control for weather and day of week. Measurement of helmet use is unlikely to be meaningfully biased by weather factors, but time of day and day of week should be taken into account. Failing to control for these factors could lead to significant bias in assessments of the level of, and trends in, commuter cycling and helmet use.
Storing and querying XML data using denormalized relational databases

XML database systems emerge as a result of the acceptance of the XML data model. Recent works have followed the promising approach of building XML database management systems on underlying RDBMS’s. Achieving query processing performance reduces to two questions: (i) How should the XML data be decomposed into data that are stored in the RDBMS? (ii) How should the XML query be translated into an efficient plan that sends one or more SQL queries to the underlying RDBMS and combines the data into the XML result? We provide a formal framework for XML Schema-driven decompositions, which encompasses the decompositions proposed in prior work and extends them with decompositions that employ denormalized tables and binary-coded XML fragments. We provide corresponding query processing algorithms that translate the XML query conditions into conditions on the relational tables and assemble the decomposed data into the XML query result. Our key performance focus is the response time for delivering the first results of a query. The most effective of the described decompositions have been implemented in XCacheDB, an XML DBMS built on top of a commercial RDBMS, which serves as our experimental basis. We present experiments and analysis that point to a class of decompositions, called inlined decompositions, that improve query performance for full results and first results, without significant increase in the size of the database.
Time-dependent predictors of primary cardiac arrest in patients with acute myocardial infarction.

To understand predictors of cardiac arrest early in acute myocardial infarction (AMI), for the Thrombolytic Predictive Instrument, we developed a multivariable regression model predicting primary cardiac arrest using time-dependent variables based on a case-control study of emergency department (ED) patients with AMI: 65 cases with sudden cardiac arrest and 258 without cardiac arrest. Within the first hour of AMI symptom onset, adjusting for age, systolic blood pressure, serum potassium, and infarct size, increased risk of cardiac arrest was associated with electrocardiographic prolonged QTc interval and a greater sum of ST-segment elevation. After 1 hour, the effect of ST-segment elevation was much reduced and the effect of the QTc interval was reversed, so prolonged QTc appeared protective. Accordingly, for patients presenting 30 minutes after chest pain onset, compared with a QTc of 0.44, the risk for cardiac arrest for patients with QTc of 0.50 was more than doubled (odds ratio [OR] 2.20, 95% confidence intervals [CI] 1.17 to 4.13), whereas for those presenting after an hour, it was much lower (e.g., at 1.5 hours, OR 0.21, 95% CI 0.06 to 0.73). Patients presenting 30 minutes after chest pain onset with a sum of ST elevation of 20 mm had a threefold higher risk than patients with a sum of ST elevation of 5 mm (OR 3.37, 95% CI 1.83 to 6.20). However, if presenting 1.5 hours after chest pain onset, the risk was barely elevated (OR 1.18; 95% CI 1.09 to 1.29). Thrombolytic therapy was protective, halving the odds of cardiac arrest (OR 0.51, 95% CI 0.27 to 0.93). Thus, the relation of prolonged QTc interval and substantial ST segment elevation to cardiac arrest in AMI may be obscured because patients with these risks are more likely to die soon after AMI onset, before ED presentation, and are thereby unavailable for study. Those with prolonged QTc or substantial ST elevation who survive the initial 1.5-hour period are those less susceptible to these risks.
Selective Structural Transformation of Supramolecules to Multinuclear Heterosubstituted Pt Complexes via Ligand Exchange.

Abstract Selective triflate to chlorine ligand exchange reaction between ditriflate and dichloride Pt complexes producing pure heterosubstituted complexes is demonstrated. We show that this reaction can be applied for selective chlorination of supramolecules leading to their structural transformation into multinuclear mono-chlorinated Pt(II) complexes. The X-ray structure of complex of 4,4′-bipyridine with two molecules of (Et3P)2Pt(Cl)OTf is reported.
The effect of alteration in the sulcular environment upon the movement of 14C-diphenylhydantoin through rabbit sulcular tissues.

The kinetics of uptake and transport into blood after two hours of incubation of diphenylhydantoin (DPH) appears to be of the saturation type, (i.e. linear with the amount of DPH available for transport), but at higher DPH concentration the transport rate is markedly decreased. Insights into the properties of the transport system are gained by studying the effects of substances believed to alter cell membrane properties. The addition of 0.03 M potassium fluoride or 0.03 M sodium cyanide in gingival sulcus significantly alters the uptake of 14C-DPH by serum. These findings and use of this methodology have important implications in the study of sulcular tissue physiology and pathology.
Abstract 2051: DNA (cytosine-5-)-methyltransferases 3A (DNMT3A) is a direct target of miR-194 in breast cancer

Proceedings: AACR 101st Annual Meeting 2010‐‐ Apr 17‐21, 2010; Washington, DC microRNAs (miRNAs) are small non-coding RNAs of 19-25 nucleotides in length that can modulate gene expression that regulate biological and malignant processes. DNA methylation is catalyzed primarily by three DNMTs - DNMT1, DNMT3A, and DNMT3B and contributes to cancer initiation and progression. While DNMT3A protein overexpression has been detected in colon, lung, skin and testis cancers, its expression in breast cancer has not been previously reported. Targets and function for miR-194 have not been well defined. In this study, we investigated the expression of miR-194, DNMT3A, and the possible role of miR-194 in regulating DNMT3A in breast cancer cells. Expression of miR-194 precursor in breast cancer cell lines specifically downregulated DNMT3A mRNA and protein levels. miR-194 specifically inhibited the luciferase activity of wild type DNMT3A 3’-UTR construct, but not that of mutant vector, indicating that DNMT3A is a direct downstream target of miR-194. Furthermore, miR-194 expression appeared to correlate inversely with DNMT3A mRNA or protein expression in breast cancer cell lines and patient samples. An increase in miR-194 expression stimulated tumor suppressors cyclin G2, p27Kip1 and ADAM23 expression, which can be regulated by DNA methylation. Overexpression of miR-194 inhibited cell motility of breast cancer cells without alteration of the cell cycle distribution. Most DNMT3A protein localized in the nucleus, but a small fraction of DNMT3A protein was found in the cytoplasm. The prognostic value of miR-194 and DNMT3A in breast cancer is being studied using a breast cancer tissue array, quantitative real time PCR and immunohistochemical staining. In summary, this report demonstrates DNMT3A as a direct target of miR-194 in breast cancer cells. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2051.