cssi/SciSciGPT-SciSciNet huggingface dataset:
Metabolism of α-Ketoglutarate by Roots of Woody Plants

The uptake and metabolism of alpha-ketoglutarate-5-(14)C by peach, apple, and privet root tissues were studied over various time intervals. As much as 80% of the absorbed (14)C appeared as (14)CO(2) in 320 minutes in peach roots. Apple and privet roots were less effective in this conversion with the bulk of the (14)C found in the organic acid fraction. This indicates differences in organic acid metabolism among species of woody plants.The (14)C accumulated in malate earlier and in larger quantities than in citrate. Both glutamate and aspartate were labeled in 10 minutes and glutamate was labeled as early as 3 minutes. The labeling pattern does not clearly distinguish between the synthesis of glutamate by glutamic dehydrogenase or by transamination with oxaloacetate.The rapid metabolism of alpha-ketoglutarate to glutamate by the 3 species studied indicates the presence of enzyme systems important in amino acid synthesis in the roots of woody plants.
Posttraining androgens' enhancement of cognitive performance is temporally distinct from androgens' increases in affective behavior.

Steroid hormone-induced variations in spatial learning and memory tasks have been reported. In this study, androgens’ effects in various cognitive and affective tasks were investigated in order to determine whether any observed differences in cognitive performance could be due to affective changes produced by the hormones. Ovariectomized rats (N = 72) received 0.0, 3.0, or 7.5 mg/kg subcutaneously, of testosterone (T), dihydrotestosterone (DHT), or 5α-androstane-3α, 17β-diol (3a-Diol) suspended in 10% ethanol/sesame oil v/v. For the cognitive tasks (Y maze, inhibitory avoidance, and object recognition), subjects were injected after training trials. For the affective tasks (open field, elevated plus maze, and tailflick), subjects were injected 1 or 24 h before testing. Posttraining injections that produced physiological concentrations of androgens - T, DHT, and 3α-Diol - 1 h later increased the percentage of correct choices in the Y maze, the latencies to cross to the shock-associated side of the inhibitory avoidance chamber, and percentage of time exploring novel objects 24 h later, when androgen levels were no longer increased. Administration of T, DHT, and 3α-Diol also increased the number of entries into the center squares of a brightly lit open field, open-arm time in the elevated plus maze, and tailflick latencies 1 but not 24 h following administration. These findings suggest that these androgens, when administered following training, can enhance cognitive performance in the tasks investigated 24 h later when androgen levels nadir, but overt changes in the affective behaviors examined occurred at the time of physiological concentrations 1 h but not 24 h following androgen administration. These findings suggest posttraining androgens can enhance consolidation and cognitive performance, independent of their anxiolytic actions.
Algorithms for the Simple Plant-Location Problem with Some Side Conditions

The algorithms of this paper belong to the direct-search or implicit-enumeration type. They compare to the recently proposed algorithm of Efroymson and Ray, as does the mixed integer algorithm proposed by C. E. Lemke and the author to that of Land and Doig. The general plan of procedure is expected to be equally valid for the capacitated plant-location problem and for transshipment problems with fixed charges; with some of the proposed devices more important for these difficult problems than for the simple plant location problem. Considerable computational experience has been accumulated and is discussed at some length. It suggests that additional work on the construction of "adaptive" programs, matching algorithm to data structure, is desirable.
Windowed mass selection method: a new data processing algorithm for liquid chromatography–mass spectrometry data

Abstract A number of preprocessing methods are tested on liquid chromatography–mass spectrometry (LC–MS) peptide map data, to determine the best and most efficient way to improve the signal to noise ratio in the data, especially at low analyte concentrations. Three methods are investigated, including an algorithm named “sequential paired covariance” (SPC), which was recently reported. An improvement to this algorithm is also reported here. This new, improved method, named the “windowed mass selection method” (WMSM), is shown to effectively eliminate random noise that occurs in the data. This method is shown to be particularly useful in improving signal to noise ratios in both chromatographic and mass spectra for data acquired in peptide mapping of recombinant DNA derived proteins.
Radial moment analysis of isovalent hybridization in N2

A radial moment analysis has been performed for the Hartree–Fock molecular orbitals of the nitrogen molecule. The objective of the analysis was to determine the extent of isovalent hybridization in even and odd sigma molecular orbitals. The radial moment analysis for the LC-SCF-AO fragments of the 2σg, 2σu, and 3σg molecular orbitals substantiates Mulliken's earlier conjecture concerning promotion into 3s atomic orbitals for the 3σg molecular orbital. The concept of free isovalent hybridization is discussed in terms of the atomic orbital shape defined by the extracted moments.
Adhesion of Staphylococcus aureus to Surface-Bound Platelets: Role of Fibrinogen/Fibrin and Platelet Integrins

Platelets adhering to artificial or biologic surfaces have been implicated in the pathogenesis of catheter infections or endocarditis; however, the ligands involved in Staphylococcus aureus interaction with adherent platelets remain incompletely understood. Radiolabeled S. aureus Cowan I were incubated with purified platelets adherent to polymethylmethacrylate (PMMA) coverslips and washed, and adhesion was determined. Platelets promoted adhesion of S. aureus approximately 30-fold compared with adhesion to albumin-PMMA. In the presence of both plasma (1% vol/vol) and platelets, adhesion was extensively promoted, with 30% (of inoculated) S. aureus adherent (150-fold increase). Platelet pretreatment with anti-GPIIb/IIIa monoclonal antibodies or inhibitors of platelet activation decreased plasma-enhanced adhesion, suggesting a role of platelet activation in S. aureus adhesion. Plasma-enhanced adhesion was sensitive to thrombin antagonists, proteinase inhibitors, heparin, or antifibrinogen antibodies, indicating that fibrinogen/fibrin is necessary for bridging between adherent platelets and S. aureus. In conclusion, S. aureus adhesion to immobilized platelets may play a role in the pathogenesis of invasive bloodstream infections or endocarditis.
Investigation of mechanical impact effects on biological cells with scanned image microscopy

The objective of this study is to observe the behavior of the living cells after introducing impact, caused by an aluminum bullet shot out from an air gun, onto them via tungsten/polymer plate and culture liquid. An air gun type of apparatus shoots an aluminum bullet, wherein the shape of the bullet is substantially a sphere (diameter: 5 mm), and wherein the velocity of the bullet is controlled by the amount of air used for shooting. The aluminum bullet shot out from the air gun impacts onto the polymer/tungsten plate, located above the living cells grown on the bottom of the container (i.e., thin semi-transparent polymer membrane), which is located on the surface of a 200 kHz Panametrics transducer. The container is supported by a polymer member to prevent movement from shock caused by the bullet impact. The plate generates an acoustic wave (i.e., shock wave) by the mechanical impact (i.e., bullet impact) which is then converted into an electrical signal by the transducer. The amplitude of the electrical signal is measured and monitored by the digital oscilloscope. The transducer is calibrated by hydrophone with its peripheral equipment including computer software. The output voltage from transducer was monitored by the digital oscilloscope. The injury and recovery of the specimen are evaluated by scanned image microscopes. Furthermore, quantitative data showing the injury and recovery of the specimen can be obtained with the electromagnetic measurement.
Global and local molecular dynamics of a bacterial carboxylesterase provide insight into its catalytic mechanism

Carboxylesterases (CEs) are ubiquitous enzymes responsible for the detoxification of xenobiotics. In humans, substrates for these enzymes are far-ranging, and include the street drug heroin and the anticancer agent irinotecan. Hence, their ability to bind and metabolize substrates is of broad interest to biomedical science. In this study, we focused our attention on dynamic motions of a CE from B. subtilis (pnbCE), with emphasis on the question of what individual domains of the enzyme might contribute to its catalytic activity. We used a 10 ns all-atom molecular dynamics simulation, normal mode calculations, and enzyme kinetics to understand catalytic consequences of structural changes within this enzyme. Our results shed light on how molecular motions are coupled with catalysis. During molecular dynamics, we observed a distinct C-C bond rotation between two conformations of Glu310. Such a bond rotation would alternately facilitate and impede protonation of the active site His399 and act as a mechanism by which the enzyme alternates between its active and inactive conformation. Our normal mode results demonstrate that the distinct low-frequency motions of two loops in pnbCE, coil_5 and coil_21, are important in substrate conversion and seal the active site. Mutant CEs lacking these external loops show significantly reduced rates of substrate conversion, suggesting this sealing motion prevents escape of substrate. Overall, the results of our studies give new insight into the structure-function relationship of CEs and have implications for the entire family of α/β fold family of hydrolases, of which this CE is a member.
Spelling and dialect: Comparisons between speakers of African American vernacular English and White speakers

One characteristic of African American vernacular English (AAVE) is final obstruent devoicing, where the final consonant of a word likerigid is pronounced more like /t/ than /d/. To determine whether this dialect characteristic influences adults’ spelling, African American and White college students spelled words such asrigid andballot, pronounced by either a speaker of their own dialect or a speaker of the other dialect. African Americans, especially those who often devoiced final /d/, were more likely than Whites to confused andt. Both African American and White spellers made mored/t confusions when the words were spoken by an African American experimenter than by a White experimenter. Thus, the different phonological systems of AAVE and White speakers can cause them to make different types of spelling errors. Discussions of AAVE and literacy have focused on its syntax, but its phonology must also be considered.
Endothelial cell loss with ultrashort-pulse laser and manually generated full-thickness clear corneal incisions

Purpose To compare the extent of corneal endothelial cell loss resulting from creating full-thickness clear corneal incisions manually using a diamond blade with that resulting from use of an ultrashort-pulse laser. Setting Lensar, Inc., Orlando, Florida, USA. Design Experimental study. Methods Ex vivo porcine globes were randomly assigned to groups for manual or laser-generated full-thickness CCIs. Standard 3-plane manual or laser incisions were made in freshly excised porcine globes. Two laser incision geometries were tested: with the exit incision perpendicular or 45 degrees to the posterior corneal surface. Corneas excised from the globe were measured immediately and after storage for 48 hours in Dulbecco modified Eagle media. Cell loss was assessed by measuring the area of damaged endothelial cells with a fluorescent microscope after cornea staining with a 3-component fluorescent live cell–dead cell assay. The percentage cell loss was expressed as the damaged area divided by the total area of a typical human corneal endothelium. Results Endothelial cell losses caused by manual and laser full-thickness CCIs were in the range of 0.8% to 1.4%. Although the mean endothelial cell loss percentages were lower for laser than for manual full-thickness CCIs, the measurements showed no statistically significant differences in the endothelial cell loss percentage between manual full-thickness CCIs and laser full-thickness CCIs with a perpendicular exit incision or 45-degree exit incision geometry. Conclusion Ultrashort-pulse laser–generated full-thickness CCIs resulted in the statistically equivalent levels of corneal endothelial cell loss as full-thickness CCIs created by standard manual methods. Financial Disclosure Dr. Teuma is an employee of Lensar, Inc. Dr. Bott is a Lensar, Inc. consultant and has a financial interest in the company. Dr. Edelhauser is a member of Lensar, Inc.'s Scientific Advisory Board and has a financial interest in the company.
Determination of cidofovir in human plasma after low dose drug administration using high-performance liquid chromatography–tandem mass spectrometry

Abstract A sensitive and specific method for the determination of cidofovir (CDV) in human plasma using high-performance liquid chromatography with tandem mass spectrometry (LC–MS/MS) was developed and validated. Plasma samples were processed by a solid phase extraction (SPE) procedure using Varian ® SAX extraction cartridges prior to chromatography. The internal standard was 13 C5-Folic acid ( 13 C5-FA). Chromatography was performed using a Luna C8(2) analytical column, 5 μm, 150 mm × 3.0 mm, using an isocratic elution with a mobile phase consisting of 43% methanol in water containing 12 mM ammonium acetate, at a flow rate of 0.3 mL/min. The retention times of CDV and 13 C5-FA were 2.1 min and 1.9 min, respectively, with a total run time of 5 min. The analytes were detected by a Micromass Quattro Micro triple quadrupole mass spectrometer in positive electron spray ionization (ESI) mode using multiple reaction monitoring (MRM). The extracted ions monitored following MRM transitions were m / z 280.0 → 262.1 for CDV and m / z 447.0 → 294.8 for 13 C5-FA (IS). The assay was linear over the range 20–1000 ng/mL. Accuracy (101.6–105.7%), intra-assay precision (4.1–5.4%), and inter-assay precision (5.6–6.8%) were within FDA limits. No significant variation in the concentration of CDV was observed with different sample storage conditions. This method is simple, adaptable to routine application, and allows easy and accurate measurement of CDV in human plasma.
Microassay of Phosphate Provides a General Method for Measuring the Activity of Phosphatases Using Physiological, Nonchromogenic Substrates Such as Lysophosphatidic Acid

Since measurement of lysophosphatidate phosphatase activity is important in studies of tumorigenesis, we attempted to develop a simpler alternative to the more complex methods currently available. Measuring the phosphate released would permit use of the same method for a variety of phosphatases with physiological substrates, many of which are nonchromogenic. The Malachite green method of K. Itaya and M. Ui (1966, Clin. Chim. Acta 14, 361) has adequate sensitivity for quantitating phosphatase activity in biological samples. In samples with high endogenous phosphate concentrations pretreatment with 50 mg Dowex 1 × 10 (100–200 mesh, OH− form) usually permitted reliable determination of phosphatase activity. For 34 consecutive runs the mean relative difference [(phosphorus activity − vitamer activity)/phosphorus activity] obtained from the simultaneous measurement of both the phosphate released and the corresponding organic product (pyridoxal and pyridoxine) was −0.03 ± 0.09. The within run and between run coefficients of variation (three runs of four to five replicates) were 0.05 and 0.04, respectively. Pyridoxine 5′-phosphate hydrolase activity (pH 10) in cultured skin cells (normal and cancerous) ranged from 2 to 12 nmol phosphorus/min · mg protein. Lysophosphatidate phosphatase activity (pH 7.4) ranged from 3 to 14 nmol phosphorus/min · mg protein. The current approach permits the measurement of phosphatase activity with a single method using a variety of substrates and incubation conditions.
Biomechanical analysis of anterior instrumentation for lumbar corpectomy.

STUDY DESIGN: In vitro biomechanical assessment of spinal stability after corpectomy reconstruction. OBJECTIVES To gain a more thorough understanding of the biomechanical properties of anterior plate versus dual rod systems used for anterior lumbar corpectomy reconstruction. SUMMARY OF BACKGROUND DATA: Vertebral corpectomy is commonly required in the treatment of several types of spinal pathology (fracture, tumor, infection). Stabilization with strut allograft and anterior instrumentation can be accomplished with one of several anterior implant systems. These include plate systems and rod-based systems with theoretically different structural properties. METHODS: Two instrumentation systems, the ATL Z-plate and the Antares system, were each applied to 10 calf lumbar spines with a cortical strut graft reconstructing an L3 corpectomy defect. All spines were tested biomechanically to determine construct stiffness under physiologic loads in multiple planes and then tested in torsion to failure. RESULTS: There was greater stiffness (P < 0.05) in all directions of bending (flexion, extension, lateral bending) for the Antares dual rod construct compared to the Z-plate constructs. No significant difference was noted in either torsional testing under physiologic loads or torque to failure between the groups. CONCLUSIONS: Although there was significantly greater resistance to bending with the dual rod construct, the ultimate selection of a system will require an individual analysis of implant profile, construct demand, and ease of use. Both systems provided secure initial fixation following lumbar corpectomy; however, the Antares system may increase the likelihood of graft incorporation in cases with greater instability and higher load demands.
A maximum overlap orbital calculation of 13C-H coupling constants in the vinyl halides

The method of maximum overlap orbitals (MOO) has been employed to calculate all of the 13C - H coupling constants in the vinyl halides. The results indicate that values at the Β position depend primarily on mesomeric content of each halide, whereas the α couplings are predominately influenced by the nature of the C - X bond. By using only pure p-orbitals for X = C1, Br and I, the observed α couplings are predicted to within one cps, but in the fluoride ∼ 25% s-character is required to obtain satisfactory agreement. The results of these calculations are compared with those obtained for the methyl halides, and are also discussed in relation to relevant bonding inferences derived from microwave data.
Dietary agents for chemoprevention of prostate cancer

Prostate cancer (CaP) is the leading cause of cancer-related deaths in American men, responsible for over 29,000 deaths in the year 2007. Chemoprevention is a plausible and cost-effective approach to reduce cancer morbidity and mortality through inhibition of precancerous events before the occurrence of clinical disease. Indeed, CaP is an ideal candidate disease for chemopreventive intervention as it is typically diagnosed in the elderly population with a relatively slower rate of growth and progression. The potential of dietary substances to act as chemopreventive agents against CaP is increasingly appreciated. Further, epidemiological studies have identified significant correlations between CaP incidence and dietary habits. It is hoped that, combining the knowledge based on agents with targets, we will be able to build an armamentarium of naturally occurring chemopreventive substances that could prevent or slow down the development and progression of CaP. In this review, we have summarized the findings from clinical and preclinical studies on dietary agents including green tea, pomegranate, lupeol, fisetin, and delphinidin that are currently being investigated in our laboratory for their chemopreventive potential against CaP.
Feasibility of diode-array instruments to carry near-infrared spectroscopy from laboratory to feed process control.

Near-infrared calibrations were developed for the instantaneous prediction of the chemical and ingredient composition of intact compound feeds. Two rather different instruments were compared (diode array vs grating monochromator). The grating monochromator was used in a static mode in the laboratory, whereas the diode-array instrument-better adapted to online analysis-was placed on a conveyor belt to simulate measurements at a feed mill plant. Modified partial least squares (MPLS) equations were developed using the same set of samples analyzed in the two instruments. Sample set 1 (N = 398) was used to predict crude protein (CP) and crude fiber (CF), while sample set 2 (N= 393) was used for the prediction of one macroingredient (sunflower meal, SFM) and one microingredient (mineral-vitamin premix, MVP). The standard error of cross-validation (SECV) and the coefficient of determination (R 2 ) values for CF were better using the monochromator instrument. However, results obtained for CP, SFM, and MVP using the samples analyzed in the diode-array instrument showed similar or even greater accuracy than those obtained using samples analyzed in the grating monochromator. The excellent predictive ability [R 2 > 0.95; RPD (ratio of standard deviation to SECV) > 3] obtained for CP, CF, and SFM opens the way for the online use of NIRS diode-array instruments for surveillance and monitoring in the manufacture, processing, and marketing of compound feeds. R 2 , RPD, and SECV values for MVP showed similar performance for both instruments. Although RPD values did not reach the minimum recommended for quantitative analysis, results are encouraging for an ingredient present in feed compounds in such very low amounts.
Lobar Staphylococcal Pneumonia: An Unusual Variant

THE OFTEN described roentgenographic features of staphylococcal pneumonia1-3include a rapidly changing x-ray picture which may proceed from that of pneumonic infiltrate to one of large air-filled cavities within the space of a few hours.4Rupture of these pneumatoceles may produce a tension pyopneumothorax. The initial infiltrate may be focal, segmental, or lobar in distribution or may involve one or both lungs in their entirety and has almost always been described as being patchy in appearance but not as a homogenous lobar consolidation resembling neoplastic change. The following patients presented to us with x-ray findings initially thought to represent neoplastic involvement of the upper lobe area. Report of Cases Case 1 (59-42-46 [CHMC]). —This patient was admitted to the Children's Hospital on June 25, 1965, at the age of 1¾ years for management of "a mass in the upper lobe of the left lung." The patient was well
Infiltration rates and erosion associated with reclaimed coal mine spoils in west central New Mexico

Abstract Large quantities of coal are extracted in New Mexico by surface mining that results in large areas of surface disturbance. Some goals of reclaiming these disturbances are to control erosion and consequent sediment yields by recontouring and revegetation. This study investigates the rates of infiltration and sediment removal on successfully reclaimed coal mine areas, and their relationship with analogous undisturbed rangeland. Reclaimed areas that had been revegetated for one, three and five years, and a nearby natural rangeland, were subjected to simulated rainfall. Ponding time and runoff time were similar between the non-disturbed lands and the areas reclaimed one and five years before for both dry and wet soil moisture scenarios. The area revegetated three years before required substantially longer time to pond and yield runoff than the rangeland. The reclaimed areas with three and five growing seasons displayed greater infiltration rates than the rangeland area on dry soils and wet soils. Infiltration rates for the reclaimed area with one growing season were similar to the natural rangeland area for both soil moisture conditions. Sediment production and concentrations on the newly reclaimed areas were equal to, or greater than, that for the rangeland on dry and wet soils, respectively. The reclaimed area with the most established vegetation yielded the least sediment of all the reclaimed sites, and significantly less than the rangeland site, regardless of soil moisture situations. Various vegetation, rock, soil, and surface roughness variables were found to influence ponding and runoff times, infiltration rates, sediment production, and sediment concentration. These variables include, in decreasing importance: foliar grass cover, grass production, bulk density, foliar shrub cover, shrub production, horizontal roughness, litter cover, vertical roughness, rock cover and organic matter content.
The fine structural localization of acetylcholinesterase at the myoneural junction.

A study of the cytochemical localization of acetylcholiriesterase activity, combining histochemistry with electron microscopy, showed that the final product of the reaction, which was deposited at or near enzyme sites, occurred at four places in the myoneural junction. These included: plasma membrane of the muscle covering the junctional folds, the primary and secondary synaptic clefts, parts of the plasma membrane covering the axon terminal, and vesicular structures in the terminal axoplasm. No reaction occurred in the presence of 10-4 eserine or DFP, whereas 10-5 DFP inhibited the reaction at all sites except in the vesicles of the terminal axon. These findings are discussed with reference to the histochemical method used and to the occurrence of esterolytic activity in the vesicles, as well as to some of the current hypotheses concerning the relationship of the site of acetylcholinesterase and synaptic transmission.
Evolving management of upper-tract transitional-cell carcinoma at a tertiary-care center.

Background and Purpose: Traditional management of upper-tract transitional-cell carcinoma (TCC) has been open nephroureterectomy. Minimally invasive options, including laparoscopic and endoscopic techniques, are being applied with increasing frequency, however. To assess the impact of these techniques on the current management of upper-tract TCC, we reviewed our experience managing this problem over the last 3 years. Patients and Methods: Since January 1998, 84 patients underwent definitive management of upper-tract TCC using open, laparoscopic, or endoscopic techniques. This study group includes 57 men and 27 women with a mean age of 69.9 years. Results: Fifty-three patients (63.9%) were treated by laparoscopic nephroureterectomy. Twelve patients (14.5%) were treated endoscopically, with percutaneous resection in 7 patients and ureteroscopic resection in 5 patients. The indications for nephron-sparing management in these 12 patients included solitary kidneys in 6 patients, significant comorbidities in 4 ...
Cervical Dorsal Spondylosis with Spinal Cord Compression in a Black Swan (Cygnus atratus)

Cervical dorsal spondylosis with spinal cord compression in a black swan (Cygnus atratus) was confirmed radiographically and morphologically. Clinically ataxia was associated. Noninflammatory, degenerative changes of the synovial joint cartilage were associated with the spondylosis.
The Stokes and Krasovskii conjectures for the wave of greatest height

Abstract : It is shown that there exists a solution to Nekrasov's integral equation which describes a wave of greatest height and of permanent form moving on the surface of a non-viscous, irrotational, infinitely deep flow. It is also shown that this wave can be obtained as the limit, in a specified sense, of waves of almost extreme form. Stokes conjectured, almost 100 years ago, that in the extreme case the wave is sharply crested and the wave surface makes an angle of pi/6 with the horizontal at the crest, and Krasovskii conjectured that, for waves of non-extreme form, which are smooth-crested, the angle between the surface and the horizontal at no point exceeds pi/6, the latter belief being widely held until some recent numerical calculations cast some doubt upon it. While the present paper makes only partial progress towards deciding Stokes' conjecture, it does confirm the numerical evidence and prove that the Krasovskii conjecture is false for waves sufficiently close to the extreme form, the angle exceeding pi/6 in a boundary layer.
The changing role of multinational corporations

The multinational corporations’ (MNCs) environment and their international eminence have recently been threatened because of the turbulent international arena, the unlimited scope of information which they have to consider in their decision-making , and the accusations that they are a jeopardy to the political and economic independence of their host countries. Thus, they have to adopt a new strategy which is in contrast to the past where they were identified as the primary operators in their host environment and that they controlled to a great extent the political, economic and social environment in which they functioned.
Improving Semantic Concept Detection and Retrieval using Contextual Estimates

In this paper we introduce a novel contextual fusion method to improve the detection scores of semantic concepts in images and videos. Our method consists of three phases. For each individual concept, the prior probability of the concept is incorporated with detection score of an individual SVM detector. Then probabilistic estimates of the target concept are computed using all of the individual SVM detectors. Finally, these estimates are linearly combined using weights learned from the training set. This procedure is applied to each target concept individually. We show significant improvements to our detection scores on the TRECVID 2005 development set and LSCOM-Lite annotation set. We achieved on average +3.9% improvements in 29 out of 39 concepts.
An efficient method for large-scale slack allocation

This article concerns a timing or project graph, with given delays on the edges and given arrival times at the source and sink nodes. The arrival times at the other nodes are to be chosen; these determine the timing slacks, which must be non-negative, on the edges. The set of possible timing slacks is a polyhedron; to choose one, a separable concave utility function, such as the sum of the logarithms of the slacks, is maximized. This slack allocation problem, which can be given a simple statistical interpretation, is convex, and can be solved by a variety of methods. Gradient and coordinate ascent methods are simple and scale to large problems, but can converge slowly, depending on the topology and problem data. The Newton method, in contrast, reliably computes an accurate solution, but typically cannot scale beyond problems with a few thousand nodes. This article describes a custom truncated Newton method that efficiently computes an accurate solution, and scales to large graphs (say, with a million or m...
Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry

Liquid chromatography and tandem mass spectrometry (LC-MS/MS) has become the preferred method for conducting large-scale surveys of proteomes. Automated interpretation of tandem mass spectrometry (MS/MS) spectra can be problematic, however, for a variety of reasons. As most sequence search engines return results even for 'unmatchable' spectra, proteome researchers must devise ways to distinguish correct from incorrect peptide identifications. The target-decoy search strategy represents a straightforward and effective way to manage this effort. Despite the apparent simplicity of this method, some controversy surrounds its successful application. Here we clarify our preferred methodology by addressing four issues based on observed decoy hit frequencies: (i) the major assumptions made with this database search strategy are reasonable; (ii) concatenated target-decoy database searches are preferable to separate target and decoy database searches; (iii) the theoretical error associated with target-decoy false positive (FP) rate measurements can be estimated; and (iv) alternate methods for constructing decoy databases are similarly effective once certain considerations are taken into account.
An ab initio approach to the calculation of current-voltage characteristics of programmable molecular devices

Molecular electronics can be developed if we are able to program a random arrangement of molecules or a field-programmable molecular random array. The ansatz that small molecules can be programmed needs to be demonstrated; this means characterizing the smallest molecular system with programmable features. We demonstrate that even two molecules in a series conformation can have multivalued responses and, thus, is able to be programmed; we also indicate how to extend this programmability to other molecular circuit conformations. Current programs for the calculation of current-voltage characteristics of electronic circuits, needed for such demonstrations, are only capable of predicting single-valued characteristics. We present results from our ab initio procedures that couple the molecular approaches with a practical analysis of molecular circuits having strong nonlinearities.
ProDA: An End-to-End Wavelet-Based OLAP System for Massive Datasets

ProDA employs wavelets to support exact, approximate, and progressive OLAP queries on large multidimensional datasets, while keeping update costs relatively low. ProDA not only supports online execution of ad hoc analytical queries on massive datasets, but also extends the set of supported analytical queries to include the entire family of polynomial aggregate queries as well as the new class of plot queries.
The Rights of Migrants

Why do states provide migrants rights associated with citizenship? Existing accounts typically answer this question in terms of obligation - of a duty on the part of states to confer citizenship. Moreover, scholars tend to lump together the bundle of rights conventionally associated with citizenship when they answer this question. In contrast, this Article disaggregates the rights associated with citizenship, asks what both states and migrants want, and inquires into how the suite of rights associated with citizenship might advance those interests. States want to encourage migrants to enter their territory and to make country-specific investments, but have an interest in being able to remove immigrants or make their lives less comfortable if circumstances change. However, migrants will not enter and make country-specific investments if the state can easily remove them or change the conditions in which they live. Accordingly, the "optimal contract" reflects the trade-offs between commitment and flexibility. We discuss ways in which basic rights to liberty and property, political rights including voting, and other rights may embody the optimal contract in different circumstances.
A two‐stage model for incidence and prevalence in point‐level spatial count data

We consider the problem of modeling point-level spatial count data with a large number of zeros. We develop a model that is compatible with scientific assumptions about the underlying data-generating process. We utilize a two-stage spatial generalized linear mixed model framework for the counts, modeling incidence, resulting in 0–1 outcomes, and prevalence, resulting in positive counts, as separate but dependent processes and utilize a Gaussian process model for characterizing the underlying spatial dependence. We describe a Bayesian approach and study several variants of our two-stage model. We fit the models via Markov chain Monte Carlo methods. We study several Markov chain Monte Carlo algorithms, including a version of the Langevin–Hastings algorithm, for exploring the complicated posterior distribution efficiently and recommend an algorithm that is fairly efficient. Finally, we demonstrate the application of our modeling and computational approach on both simulated data and real data from an ecological field survey. Copyright © 2011 John Wiley & Sons, Ltd.
Impacts of fast flat fading channel on the performance of a primary-secondary user power control game for cognitive radios

Power control is an important concern in cognitive radio networks in which secondary users opportunistically compete to access spectrum allocated to primary users. However, most existing studies in this regard have ignored the impact of primary users and only considered the interactions between secondary users. In this study the novel primary-secondary game-theoretic scheme in [1] is extended to realistic wireless channels in which primary users are rewarded for sharing their spectrum with secondary users, allowing them to achieve energy-efficient transmissions. The proposed model is analyzed for both Rician and Rayleigh fast flat fading channels and closed-form expressions are also derived for the average utility functions and the existence of a unique Nash equilibrium is also shown. Finally, detailed simulation results are presented to verify the realistic performance of the scheme under those new channel conditions.
Of blood, bones, and ribosomes: is Swachman-Diamond syndrome a ribosomopathy?

Mutations in the human SBDS (Shwachman-Bodian-Diamond syndrome) gene are the most common cause of Shwachman-Diamond syndrome, an inherited bone marrow failure syndrome. In this issue of Genes & Development, Finch and colleagues (pp. 917–929) establish that SBDS functions in ribosome synthesis by promoting the recycling of eukaryotic initiation factor 6 (eIF6) in a GTP-dependent manner. This work supports the idea that a ribosomopathy may underlie this syndrome.
Evaluating the performance of active cache management schemes

In this paper we examine the performance of two multi-lateral cache schemes; one makes block allocation decisions correlated to the reference behavior of regions of memory (NTS), the other correlated to the reference behavior of memory accessing instructions (PCS). To determine the efficacy of exploiting these reference correlation schemes to improve cache management, we compare the performance of these multi-lateral schemes to a multi-lateral configuration that uses a near-optimal (but non-implementable) replacement policy, pseudo-opt. In addition to miss ratio, three metrics are used to evaluate the performance of these schemes, relative to pseudo-opt: 1) prediction accuracy in determining reference locality, 2) actual usage accuracy, i.e. how likely a block in an implementable scheme and the near-optimal scheme exhibit the same reuse characteristic, and 3) tour length of a line in the cache. Results show that while the NTS and PCS schemes outperform traditional cache management schemes, they fall short of the pseudo-opt performance; this is due to their simple prediction strategies and because their active management addresses only block allocation and not replacement.
‘I have never seen your equal’: Agricola, the Virgin, and the Creed

The chanson Je ne vis oncques la pareille enjoyed a certain renown in the years after 1454, when it was sung during the Feast of the Pheasant, an extravagant banquet entertainment hosted by the Burgundian Duke Philip the Bold. A consideration of the circumstances of the song’s performance then and its subsequent quotation in poetry by the Burgundian poet Jean Molinet reveals the potent multivalent nature of this chanson as paean to both courtly lady and Blessed Virgin. Among the company of masses and motets based on this song in the decades after its composition, two independent Credo settings by Alexander Agricola evince an especially intriguing Marian sensibility. Agricola’s manipulations of Je ne vis oncques la pareille suggest a deliberate effort on his part to co-ordinate certain musical events with particular narrative moments and theological declarations within the text of the Creed in which the Virgin was understood to participate.
Correction of Field Skid Measurements for Seasonal Variations in Texas

Findings are presented from a research study conducted in Texas to determine the significance of seasonal variation in skid measurements. Six bituminous highway pavement sections, two each from three different climatic regions, were monitored over a period of more than 18 months. Monitoring included collection of wet pavement skid resistance data using a locked-wheel skid trailer that met the specifications of ASTM E-274. These measurements were made at biweekly intervals in two of the three climatic regions and at monthly intervals in the remaining climatic region. The necessary climatic data were obtained from nearby National Climatic Data Centers. The data obtained indicated that significant variation in skid numbers occurs from one day of measurement to another. The maximum variations observed were on the order of 10 to 12 skid numbers. Furthermore, there were strong indications that the variations occurred in response to changes in temperature and precipitation. Finally, three methods of normalizing ...
Fast algorithm for modular reduction

The paper presents an algorithm for computing the residue R = X mod M. The algorithm is based on a sign estimation technique that estimates the sign of a number represented by a carry-sum pair produced by a carry save adder. Given the (n + k)-bit X and the n-bit M, the modular reduction algorithm computes the n-bit residue R in O(k + log n) time, and is particularly useful when the operand size is large. We also present a variant of the algorithm that performs modular multiplication by interleaving the shift-and-add and the modular reduction steps. The modular multiplication algorithm can be used to obtain efficient VLSI implementations of exponentiation cryptosystems.
Niche separation of seven lemur species in the eastern rainforest of Madagascar

This study examines segregation of seven lemur species in an eastern rainforest of Madagascar by a numerical analysis of microhabitats using structural and phenological data. These data are combined with the results of a previous study on food selection by these species in relation to plant chemistry. Description of some 441 10×10 m2 microhabitats yields clear separation of the frugivorous from the more folivorous guild of lemurs. Within each guild there are subgroups of two species each, which use similar microhabitats. The two species of the subgroups are separated by their different reactions towards food chemicals. Thus food chemistry and microhabitat structure are two complementary axes sufficient to separate lemur species in the Malagasy rainforest. Species using the same microhabitats choose food items with different chemical properties and species eating the same food differ in their utilization of microhabitats. Only Cheirogaleus major can not be separated from the other lemur species based on habitat utilization and the chemical composition of their food. This species, however, is active only at times of food abundance and reduces its activity at times of scarcity thus avoiding potential competition. The folivorous species Avahi laniger and Indri indri use similar micro habitats for feeding and for resting, reflecting the strategy of low energy cost and fow energy return. A more folivorous species, Lemur fulvus, discriminates between feeding and resting sites based on phenological and structural variables, representing an example for behavior shaped by high cost and high energy return. Feeding sites of this species are linked to fruit abundance but the need to see but not to be seen seems to determine their choice of resting sites. This discrimination is similar to habitat choices of frugivorous primates in other tropical rainforests which have been linked to anti-predator behavior and suggests convergent evolution due to similar evolutionary selection pressure.
Social computing networks: a new paradigm for engineering self-adaptive pervasive software systems

Software systems are increasingly permeating a variety of domains including medical, industrial automation, and emergency response. The advances in portable and embedded computing devices and the recent advances in wireless network connectivity have paved the way for the proliferation of smart spaces in such domains. At the same time, the emergence of service-oriented technology (e.g., web services [10]) and interoperability standards (e.g., WSDL [11], UDDI [5]) has made it possible to develop pervasive software systems intended for execution in smart spaces that were not even conceivable a few years back.
Beads, Exchange Networks and Emerging Complexity: A Case Study from Cambodia and Thailand (500 bce–ce 500)

Control over the exchange of prestige goods is an important component of emerging socio-political complexity in many ancient societies. During the Iron Age period (500 bce–ce 500), communities in mainland Southeast Asia were undergoing rapid socio-political changes, due in part to new interactions with societies from South Asia. As objects made from exotic raw materials and using complex technologies, stone and glass beads are one type of prestige object from South Asia that were exchanged widely across Southeast Asia. This study examines beads from 12 sites in Cambodia and Thailand. Morphological and compositional analyses using LA-ICP-MS resulted in the identification of different bead types that were circulated in distinct exchange networks. Initially, beads were exchanged within a pre-existing South China Sea network. However, as trade with South Asia intensified in the late Iron Age, exchange networks in Southeast Asia expanded, with an increase in the quantities of beads circulated. These results show the utility of studying beads as a means of examining trade and emerging socio-political complexity. Lastly, in considering evidence for control over the exchange of beads, I propose looking to an emerging state in the Mekong Delta.
A generalized electrocardiographic spherical shells model with emphasis on the paced infarcted heart

The spherical shells model (SSM) is a useful tool for qualitative investigations of the electrical events in the thorax during a heart beat. The authors present a scheme to extend the SSM to allow for general dipolar source configurations. A model is suggested to simulate the depolarization phase of a paced ventricular beat, the source being a propagating dipole layer. The computer simulations from the SSM are compared to measured intracavitary potentials from a paced dog heart, and the SSM is shown to reproduce the main features of the experimental data. It is also illustrated how infarctions might affect the signal. >
A Longitudinal Study of Attempted Religiously Mediated Sexual Orientation Change

The authors conducted a quasi-experimental longitudinal study spanning 6-7 years examining attempted religiously mediated sexual orientation change from homosexual orientation to heterosexual orientation. An initial sample was formed of 72 men and 26 women who were involved in a variety of Christian ministries, with measures of sexual attraction, infatuation and fantasy, and composite measures of sexual orientation and psychological distress, administered longitudinally. Evidence from the study suggested that change of homosexual orientation appears possible for some and that psychological distress did not increase on average as a result of the involvement in the change process. The authors explore methodological limitations circumscribing generalizability of the findings and alternative explanations of the findings, such as sexual identity change or adjustment.