cssi/SciSciGPT-SciSciNet huggingface dataset:
Defending against the Pirate Evolution Attack

A trace and revoke scheme is an encryption scheme for secure content distribution so that only authorized users can access the copyrighted content. When a clone device is recovered, the "trace" component detects the pirate users that have compromised the secret keys in their devices and participated in the construction of the clone device. The "revoke" component excludes the pirate users from accessing the future content. The state-of-art trace-revoke scheme is the very efficient subset difference based NNL scheme [11] which is also deployed in AACS [1], the industry new content protection standard for high definition DVDs. While its revocation and tracing are both very efficient, as pointed out by Kiayias and Pehlivanoglu from Crypto 2007, in its deployment NNL scheme may suffer from a new attack called pirate evolution attack . In this attack attackers reveal the compromised secret keys to the clone decoder very slowly through a number of generations of pirate decoders that will take long time to disable them all. They showed in a system with N users, the attacker can produce up to t *logN generations of pirate decoders given t sets of keys. In AACS context, that means a pirate can produce more than 300 generations of decoders by compromising only 10 devices. If this happens, it will indeed be a nightmare. In this paper we are interested in practical solutions that can defend well against the pirate evolution attack in practice. In particular we devise an easy and efficient approach for the subset difference based NNL scheme [11] to defend well against the potential pirate evolution attack. Indeed it takes as small as 2 generations to detect and disable a traitor in a coalition. This can be achieved by only negligibly increasing the cipher text header size in an application like AACS. The simplicity, efficiency and practicality of our approach has made AACS to adopt it to defend against the pirate evolution attack.
A global comparison of GEOS-Chem-predicted and remotely-sensed mineral dust aerosol optical depth and extinction profiles

[1] Dust aerosol optical depth (AOD) and vertical distribution of aerosol extinction predicted by a global chemical transport model (GEOS-Chem) are compared to space-borne data from the Moderate-resolution Imaging Spectroradiometer (MODIS), Multi-Angle Imaging SpectroRadiometer (MISR), and Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) for March 2009 to February 2010. Model-predicted and remotely-sensed AOD/aerosol extinction profiles are compared over six regions where aerosol abundances are dominated by mineral dust. Calculations indicate that over the regions examined in this study (with the exception of Middle Eastern dust sources) GEOS-Chem predicts higher AOD values compared to MODIS and MISR. The positive bias is particularly pronounced over the Saharan dust source regions, where model-predicted AOD values are a factor of 2 to 3 higher. The comparison with CALIPSO-derived dust aerosol extinction profiles revealed that the model overestimations of dust abundances over the study regions primarily occur below ∼4 km, suggesting excessive emissions of mineral dust and/or uncertainties in dust optical properties. The implementation of a new dust size distribution scheme into GEOS-Chem reduced the yearly-mean positive bias in model-predicted AOD values over the study regions. The results were most noticeable over the Saharan dust source regions where the differences between model-predicted and MODIS/MISR retrieved AOD values were reduced from 0.22 and 0.17 to 0.02 and −0.04, respectively. Our results suggest that positive/negative biases between satellite and model-predicted aerosol extinction values at different altitudes can sometimes even out, giving a false impression for the agreement between remotely-sensed and model-predicted column-integrated AOD data.
Should Decision Trees be Learned from Examples of from Decision Rules

A standard method for determining decision trees is to learn them from examples. A disadvantage of this approach is that once a decision tree is learned, it is difficult to modify it to suit different decision making situations. An attractive approach that avoids this problem is to learn and store knowledge in a declarative form, e.g., as decision rules, and then, whenever needed, generate from it a decision free that is most suitable in any given situation. This paper describes an efficient method for this purpose, called AQDT-1, which takes decision rules generated by the learning system AQ15 and builds from them a decision tree optimized according to a given quality criterion. The method is able to build conventional decision trees, as well as the so-called “skip noder” trees, in which measuring attributes assigned to some nodes may be avoided. It is shown that “skip-node” trees can be significantly simpler than conventional ones. In the experiments comparing AQDT-1 with C4.5, the former outperformed the latter both in terms of the predictive accuracy as well as the simplicity of the generated decision trees.
The Involvement of Glucose Metabolism in the Regulation of Inducible Nitric Oxide Synthase Gene Expression in Glial Cells: Possible Role of Glucose-6-Phosphate Dehydrogenase and CCAAT/Enhancing Binding Protein

In rat glial cells the lipopolysaccharide (LPS)-induced inducible nitric oxide synthase (iNOS) gene expression was enhanced by extracellular glucose concentration in a dose-dependent manner. On the other hand, 2-deoxy-d-glucose decreased the LPS-induced iNOS gene expression even in the presence of glucose (6 gm/l), suggesting that glucose metabolism is linked to the regulation of iNOS gene expression. The intracellular NADPH/NADP+ directly correlated with the extracellular glucose concentration, and the reduction of NADPH generation via a block of glucose-6-phosphate dehydrogenase (G6PD) by treatment with dehydroepiandrosterone or the antisense DNA oligomer of G6PD mRNA resulted in the inhibition of iNOS gene expression. Gel shift assays showed that CAAT/enhancing binding protein (C/EBP), rather than AP-1 or NF-kappaB, correlated better with a glucose-dependent increase in iNOS gene expression. The induction of C/EBP DNA binding activity by LPS and glucose was attributable mainly to the increase in C/EBP-delta protein. The cotransfection with wild-type C/EBP-delta increased the iNOS promoter activity to the level achieved with a higher glucose concentration in the presence of LPS. Therefore, our results suggest that C/EBP-delta may be a critical mediator in glucose-mediated regulation of iNOS gene expression.
Abstract 1588: Detectionin vivoof a novel endogenous etheno DNA adduct derived from arachidonic acid and the effects of antioxidants on its formation

Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA Previous studies showed that the 7-(1′,2′-dihydroxyheptyl) substituted etheno DNA adducts are products from reactions with epoxide of (E)-4-hydroxy-2-nonenal (HNE), an oxidation product of n-6 polyunsaturated fatty acids (PUFAs). In this work, we report the detection of 7-(1′,2′-dihydroxyheptyl)-1,N6-ethenodeoxyadenosine (DHHedA) in rodent and human tissues by two independent methods: a 32P-postlabeling/HPLC method and an isotope dilution liquid chromatography electrospray ionization tandem mass spectrometry method (ID-LC-ESI-MS/MS). This study demonstrated for the first time that DHHedA is a background DNA lesion in vivo. We showed that DHHedA can be formed upon incubation of arachidonic acid (AA) with deoxyadenosine (dA), supporting the notion that n-6 PUFAs are the endogenous source of DHHedA formation. Because the cyclic adducts are derived from the oxidation of PUFAs, we subsequently examined the effects of antioxidants, α-lipoic acid, polyphenon E and vitamin E on the formation of DHHedA and γ-hydroxy-1,N2-propanodeoxyguanosine (γ-OHPdG), a widely studied acrolein-derived cyclic adduct arisen from oxidized n-3 and n-6 PUFAs, in the livers of Long Evans Cinnamon (LEC) rats. LEC rats are inflicted with elevated lipid peroxidation and prone to the development of hepatocellular carcinomas. The results showed that while the survival of LEC rats was increased significantly by dietary α-lipoic acid, none of the antioxidants inhibited the formation of DHHedA and only polyphenon E treatment decreased the formation of γ-OHPdG. In contrast, vitamin E caused an increase in the formation of both γ-OHPdG and DHHedA in the livers of LEC rats. This work was supported by the NCI grant: RO1-CA-134892. Citation Format: Ying Fu, Marcin Dyba, Jishen Pan, Casey Schultz, Peiying Yang, Dhimant Desai, Shantu Amin, Fung-Lung Chung. Detection in vivo of a novel endogenous etheno DNA adduct derived from arachidonic acid and the effects of antioxidants on its formation. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1588. doi:10.1158/1538-7445.AM2014-1588
Speech errors in early child language production

Abstract There has been very little attention paid to nonsystemic errors in child language that closely resemble the speech errors made by adults. I have collected 576 such errors in the course of doing diary studies on my two children. Analyses reveal strong similarities with adult errors, suggesting that the language production system is set up in an adult-like fashion from a very early age. However, a number of differences suggest interesting ways in which the child's language production system differs from that of adults: a lower rate of decay for the activation of elements that have been accessed and less interdependence between different phonological elements in a word or segment. The data are useful for settling some of the controversies about adult language production that are based on error phenomena and support some of the predictions made by recent connectionist models.
Combustion-driven acoustic oscillations in a gas-fired burner

Longitudinal pressure oscillations in the acoustic modes of a cylindrical chamber can be excited and amplified by the combustion of premixed methane, nitrogen, and oxygen. In this study, the gas mixture was introduced through a stainless-steel frit at one end of the chamber; a blind flange closed the other end of the chamber, and a sonic vent was located in the cylindrical section midway between the ends. The exponential growth constant of the acoustic pressure amplitude, d(ln p)/dt, is taken as the measure of the tendency to oscillate—or, as is commonly said, a measure of the acoustic instability of the combustion system. Process variables that can be independently varied are pressure, oscillation frequency, mass-flow rate, and energy release per unit mass of gas. The effects on growth constant of frequency, flow rate, and mixture composition are such as to suggest that a sophisticated treatment of gas-phase kinetics will be required for an adequate explanation. This being the case with the gas-fired burner, one is led to suppose that similar considerations may be necessary for understanding the acoustic instability of solid rocket propellants.
PHYSICAL GROWTH AND MORTALITY RISK IN CHILDREN WITH PERINATALLY ACQUIRED HIV.681

The effect of perinatal HIV infection on somatic growth and mortality risk has not been evaluated systematically. We followed somatic growth in a cohort of Ugandan infants born to HIV-1 positive (HIV+) and HIV-1 negative (HIV-) mothers from birth to two years of age. 536 Ugandan infants born at term to 390 HIV+ and 146 HIV- mothers were enrolled. Weight and length measurements were performed at regular intervals. The generalized estimating equation approach was used to model longitudinal weight and length data. A total of 4225 measurements of weight and length were obtained (median of 7 measurements/child). Out of 84 HIV+ patients, 45 died before their second birthday. HIV+ infants were significantly lighter (p<.0005) and shorter(p<.0004) than both HIV-controls or seroeverters. In addition, HIV+ infants who died before their second birthday grew more poorly than HIV+ infants who lived to two years of age. Our finding of poor growth in HIV infected Ugandan infants as compared to seroeverters and negatives is consistent with other published reports. The mortality rate in our cohort is much higher than mortality rates reported from Europe and North America where median survival to about 4 years of age is reported. Poor nutrition may have shortened the symptom-free interval which would explain the high mortality. The determinants of this nutrition-immunity interaction remain to be delineated. Future interventional studies are needed to determine if progression of HIV infection to clinical ADIS can be delayed by early aggressive nutritional intervention.
Variability in suicidal ideation: a better predictor of suicide attempts than intensity or duration of ideation?

Abstract Background Much of the suicidology literature focuses on establishing contextual risk factors for suicidal behavior. However, the study of the parameters of suicidal behavior (e.g., intensity, duration, and variability) has been somewhat neglected [Joiner, T., Rudd, M.D., 2000. Intensity and duration of suicidal crises vary as a function of previous suicide attempts and negative life events. J. Consult. Clin. Psychol. 68, 909–916] . Having previously established a relationship between variability in suicidal ideation and a previous history of suicide attempts [ Witte, T.K., Fitzpatrick, K.K., Warren, K.L, Schatschneider, C., Schmidt, N.B., submitted for publication. Naturalistic Evaluation of Suicidal Ideation: Variability and Relation to Attempt Status ], we felt it important to assess the liability conferred by a variable pattern of ideation compared to the intensity and duration of suicidal thoughts. We also examined if there was an interaction between gender and the parameters of intensity, duration, and variability. Method One hundred eight participants (54 non-attempters, 35 single attempters, and 19 multiple attempters) completed the Suicide Probability Scale every day for 4 weeks, allowing us to measure the parameters of interest. These variables were entered into a regression model as predictors of previous suicide attempts. Results Consistent with prediction, high variability of ideation was the only significant predictor of previous attempt status. In addition, an interaction between gender and variability in suicidal ideation suggested that variability appeared more critical in predicting previous attempts for males. Limitations The limited number of multiple attempters in our sample and the use of college students limit the current study. Conclusions Variability appears to be the most potent predictor of attempt status among the parameters of suicidal ideation examined in the current study. This relationship appears to be particularly important in males, suggesting that fluctuating levels of suicidal ideation may confer future risk for suicide.
Response of Buddhism and Shintō to the Issue of Brain Death and Organ Transplant

Japan has no law recognizing the condition of brain death as the standard for determining that an individual has died. Instead, it is customary medical practice to declare a person dead when three conditions have been met: cessation of heart beat, cessation of respiration, and opening of the pupils. Of the developed nations, only Japan and Israel do not recognize brain death as the death of the human person.
Single scattering parameterizations for frozen hydrometeors at millimeter-wave frequencies

Physical approaches in microwave remote sensing to measure non-spherical frozen hydrometeors are frequently parameterized as spherical particles, assuming either dielectric mixing approximation or equivalent spheres, to make Mie-theory applicable. However, the applicability of those simplified approximations in millimeter-wave radar and radiometric remote sensing of frozen hydrometeors need to be evaluated. This study evaluates those fast approximations by comparing with single scattering parameters calculated by the Discrete Dipole Approximation (DDA) method.© (2004) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
HIV-related mental health nursing issues☆

UMAN immunodeficiency virus (HIV) has already challenged many oncology nurses to cope with new and pressing issues. Research to date indicates that progression from seropositivity to clinical acquired immunodeficiency syndrome (AIDS) will probably occur in most patients. This means that nurses in nearly all care settings will be affected by the epidemic. The prevalence of neuropsychiatric disorders in AIDS makes it imperative that oncology nurses be sensitive to HIVrelated mental health nursing issues. Adults with HIV are typically young, so they and their social networks are not well prepared to grapple with terminal illness. AIDS is heavily imbued with stigmas of contagion, sexual transmissibility, and intravenous drug use. Discrimination may be based on race, gender, ethnicity, and/or sexual orientation. Regardless of personal history, HIV positivity suggests to many the negative cultural stereotypes of homosexuality and/or drug addiction For some who contracted HIV via covert sexual activity or intravenous drug use, the disclosure of HIV seropositivity represents an unwanted disclosure of these previously covert activities. Such disclosures may provoke crises of personal identity, social discord, unemployment, and isolation. It is important to discuss HIV status directly with patients in order to understand the social context of their illness. Who else knows? How have those individuals responded? These are key questions in accurately evaluating the individual’s sup
Demonstration That Mast Cells, T Cells, and B Cells Bearing the Activating Kit Mutation D816V Occur in Clusters within the Marrow of Patients with Mastocytosis

Mastocytosis is characterized by focal heterotypic clusters of mast cells and lymphocytes in the bone marrow and by a somatically acquired activating Kit mutation, D816V. The relationship of the occurrence of this mutation to the heterotypic clusters of mast cells and lymphocytes in bone marrow is unknown. We hypothesized that these two unique features of mastocytosis were related. To explore this hypothesis, laser capture microdissected mast cells, B cells, and T cells, from both lesional and non-lesional areas of bone marrow biopsy tissues from patients with mastocytosis, were examined for the D816V mutation in their DNA, using HinfI restriction digestion of nested PCR products amplified from extracts of dissected cells. The D816V mutation was detected in mast cells, B cells, and T cells from lesional but not non-lesional areas of bone marrow tissues. B cells obtained from lesional areas of tissue were also assessed for clonality and were found to at least represent an oligoclonal population. Thus, mast cells and lymphocytes within focal aggregates in the bone marrow of those with mastocytosis are more frequently positive for the codon 816 activating mutation. Further, the B cell population is oligoclonal, suggesting that clonal proliferation is unlikely to be the basis of clustering.
Optical properties of an outer membrane lipoprotein from Escherichia coli

Abstract The infrared spectrum of a structural lipoprotein from the Escherichia coli outer membrane indicated the lipoprotein had and α-helical conformation but no sign for the existence of β-structures. From circular dichroism spectra of the lipoprotein, the α-helical content of the protein was found to be as high as 88% in 0.01–0.03% sodium dodecyl sulfate in the presence of 10 −5 M Mg 2+ at pH 7.1 and 23° C. When sodium dodecyl sulfate concentration increased higher than 0.1%, the α-helical content of the lipoprotein decreased to about 57%. Divalent cations, such as Mg 2+ and Mn 2+ , were found to increase the helical content of the lipoprotein. The high α-helical content of the lipoprotein was observed in a wide range of temperatures (23 to 55° C). The significance of the high α-helical content of the lipoprotein is discussed in light of the three-dimensional molecular models of the lipoprotein proposed previously.
Ozone oxidation of surface-adsorbed polycyclic aromatic hydrocarbons: role of PAH-surface interaction.

The heterogeneous chemistry of surface-adsorbed polycyclic aromatic hydrocarbons (PAHs) plays key roles in nanoscience, environmental science, and public health. Experimental evidence shows that th...
Industry as a mechanism for urban technology transfer

This paper is based upon research done under the National Science Foundation sponsored study The Role of Industry in Urban Technology Transfer: A Comparative Profile. The purpose of the research is to investigate specific industries that serve the urban market of local governments. The research aim is to develop an understanding for the barriers and incentives that affect industry's ability and desire to produce and market technological innovations for cities.
Dynamic origin of non-Abelian Berry's-phase effects in a simple atomic system.

The full effect of adiabatically varying Hamiltonians on systems prepared in eigenstates of the stationary Hamiltonian often includes geometric Berry's phases. For degenerate systems these effects may result in transitions between distinct degenerate eigenstates that can be described in terms of a non-Abelian gauge potential. I demonstrate the explicit dynamic origin of such transitions between degenerate angular-momentum sublevels in an atom that is subject to collinear electric and magnetic fields that rotate adiabatically. The origin of the effects becomes clear when eigenstates of the total Hamiltonian, which includes the rotating fields, are calculated. The total Hamiltonian removes the degeneracy, and the eigenstates are in some cases linear combinations of the angular-momentum sublevels. Thus a system prepared in a specific sublevel may not remain in that sublevel, and the transition probability is exactly that given by an analysis of the geometric phase.
Impact of cardiac comorbidity on early outcomes after pancreatic resection.

Background In patients undergoing pancreatic resection (PR), identification of subgroups at increased risk for postoperative complications can allow focused interventions that may improve outcomes.
Processing of chemical solution-deposited BaTiO3-based thin films on Ni foils

BaTiO3 films on base metal foils are of interest for capacitor applications, but the processing requires reducing atmospheres that influence the film defect chemistry and density. In this study, powders dried from barium titanate solutions and barium titanate films were studied by X-ray diffraction, differential scanning calorimetry, thermal gravimetric analysis, infrared spectroscopy, and spectroscopic ellipsometry at various points in the processing. It was found that atmospheres designed to minimize Ni oxidation delay decomposition of organics, leading to retained carbonate phases. Thus, crystallization of the barium titanate occurs via decomposition of a barium carbonate phase. Retained organics that are present during high temperature processing can cause porosity in the films. On annealing at 1000 °C, there is slightly increase in the refractive index of the film due to further crystallization and densification. The final refractive index is comparable to that of 95% dense barium titanate ceramics. Re-oxidation did not change the refractive index of the film over the wavelength range from 350 to 650 nm.
Code alignment for architectures with pipeline group dispatching

Today's architectures exploit long pipelines in order to increase instruction-level parallelism by grouping sets of consecutive instructions and feeding them into the pipeline with the purpose of executing them in a single cycle.The IBM Power architecture executes programs by dispatching groups of instructions where a dispatch group is fed as a whole into the pipeline to be executed in a single cycle.Such architecture, however, includes many cases of pipeline delays that result from dependencies between the resources of separate groups.As a result, there is a need to optimize the code in order to help the architecture place all the instructions in such a way that will produce as few delays as possible.Optimizing the alignment and the placement of the code is therefore, crucial to the performance of the program in such architectures.We show that in some cases, without proper code alignment, performance can degrade by 40% due to the impact of code alignment on the grouping and pipeline delays.We present a new binary-level and profile-based code alignment algorithm for architectures that make use of group dispatching. We show a steady performance gain of about 2--3% for fully optimized code running on IBM Power 6 while completely eliminating performance instability which can sometimes result in up to 40% variation in performance in the absence of the proposed code alignment algorithm.As the algorithm is based on gathered profiling and applies at binary-level, it can, therefore, be used as part of existing dynamic compilers and enabled on top of the operating system at runtime.
Sulphur removal from coal by electrolysis

Abstract Anodic oxidation of acidic coal slurries at potentials of 0.8–1.0 V, on the NHE scale, causes pyrite present in coal to react and dissolve while H2 is produced simultaneously at the cathode. If coal is filtered from unelectrolysed coal slurries, the filtrates show similar electrochemical reactivity. Cyclic voltammetry applied to either slurry orfiltrate indicates that the reversible, one-electron oxidation of Fe(II) to Fe(III) is a major reaction, but chemical assays reveal that sulphide also is oxidized, to S ° and SO42−.The electrochemical reactions may involve direct oxidation of pyrite when coal particles strike the anode; it is likely, in addition, that dissolved ionic Fe may act as an electron shuttle between solid pyrite and the anode. Other experiments without coal also indicate that Fe(III) (which can be produced from Fe(II) at the anode) can oxidize pyrite and thiophene. Preliminary experiments with lignite and a bituminous coal suggest that up to 40% of the total sulphur can be removed from coal by slurry electrolysis in acidic electrolyte with either platinum or graphite electrodes.
Biomechanical evaluation of rotator cuff fixation methods

Initial fixation strength and failure mode for various rotator cuff reattachment techniques (variations of the McLaughlin technique) were evaluated. Repair methods included standard suture (control), reinforced suture [expanded polytetrafluoroethylene (PTFE) patch and polydioxanone (PDS) tape augmentation] and stapling (nonarthroscopic and arthroscopic soft-tissue staples). The average strength of intact rotator cuff tissue (supraspinatus tendon) was also determined. The different rotator cuff repairs, including at least one control, were performed on fresh-frozen human cadaver shoulder pairs. Repairs were tested to failure in pure tension with the shoulder fixed in 60 degrees of abduction. Load and displacement data were normalized to controls, grouped according to failure modes, and statistically analyzed. The two basic failure modes observed were 1) bone failure, or suture tearing through the bone (indicating weak bone stock) and 2) tendon failure, or suture tearing of the rotator cuff. Gross comparisons between intact and repaired tendons indicated that the intact tendon was two to three times stronger than the repaired tendon. Based on the mode of failure and lack of increased strength after repair, the use of staples for cuff attachment is discouraged. PDS tape suture reinforcement did not increase fixation strength. In contrast, PTFE patch suture augmentation demonstrated statistically higher initial failure loads than did the control and was of specific benefit for shoulders with weak bone stock.
PILINIA EARLEAE N. SP. (CHLOROPHYCEAE, CHROOLEPIDACEAE) FROM THE FLORIDA WEST COAST1

Pilinia earleae n. sp. family Chroolepidaceae, was found in the Tampa Bay area of the Florida west coast in October, 1976, on the tunic of an ascidian, later on dead mollusc shells, a nylon faking line, plastic strips, and as an epiphyte of Gracilaria foliifera, a red alga. It is described on the basis of abundant material from the natural environment and laboratory cultures. The type locality is the southernmost known for the genus in the western North Atlantic.
Abstract 5412: Synergistic interactions between histone deacetylase inhibitors and aurora kinase inhibitor KW2449 Ph+ cells

Proceedings: AACR 101st Annual Meeting 2010‐‐ Apr 17‐21, 2010; Washington, DC Resistance to tyrosine kinase inhibitors (imatinib, nilotinib, dasatinib) remains a major therapeutic challenge in Bcr/abl+ leukemia. Consequently, novel and more effective therapeutic strategies are urgently needed in this setting. KW-2449 is a multi-kinase inhibitor which inhibits Bcr/abl, aurora kinase, and FLT3, among other targets, and which has shown activity against T315I “gatekeeper” mutant Bcr/abl cells. Previous studies have shown that histone deacetylase inhibitors (HDACIs) such as vorinostat sharply promote the antileukemic effects of Bcr/abl and aurora kinase inhibitors such as MK-0457 in CML cells (Dai et al., Blood 112:793-804, 2008). However, MK-0457 is not currently under clinical development. The purpose of this study was to assess the effects of HDACIs (e.g., SBHA, MS-275) on responses to the dual aurora kinase-Bcr/abl inhibitor (KW-2449) in various Bcr/Abl + cells. Coadministration of HDACIs synergistically increased KW-2449 lethality in CML (K562, LAMA84) and Ph+ ALL cells (TOM-1, SD-1, SUP-B15, BV173). Notably, HDACI/KW-2449 regimens were also highly active against multiple imatinib resistant cells including BV-173/E255K, BaF3/Bcr-Abl/T315I, as well as Bcr/Abl -overexpressing and Bcr/abl-independent K562 cells. Combined treatment with HDACIs and KW-2449 was associated with inactivation and down-regulation of Bcr/Abl and its downstream target CrkL in CML and ALL cell lines including BaF3/T315I. Moreover treatment with KW-2449/HDACi resulted in a pronounced increase in DNA damage (γH2A.X) documented by Western blot and confocal microscopy. In addition, coadministration of HDACIs and KW-2449 strikingly blocked phosphorylation of histone H3, a marker of aurora kinase inhibition, and diminished HDACI-induced p21CIP1 expression. Notably, down-regulation of Bim by siRNA significantly diminished the lethality of the HDACI/KW-2449 regimen. Treatment of K562 cells with HDACIs alone resulted in G1S arrest, an effect abrogated by KW-2449, and which resulted in pronounced cellular endoreduplication. Furthermore, knockdown of either Aurora A or Aurora B in K562 cells dramatically increased the HDACI-mediated cell death. Finally, cotreatment with KW-2449 and HDACIs significantly increased cell death in seven CML primary samples (including both naive and imatinib-resistant specimens, one carrying the I242T, Y257C mutations) compared to treatment with either agent alone, while exhibiting minimal toxicity to normal CD34+ progenitors. Together, these findings indicate that HDACIs strikingly increase KW-2449 activity against IM-sensitive and -resistant Bcr/Abl+ cells, and suggest that this strategy warrants further attention in Bcr/abl+ leukemias. 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 5412.
Structural and functional diversity of paraoxonases

Several forms of a paraoxonase enzyme provide different degrees of protection against organophosphate chemicals.
Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites

Background Biologically active sequence motifs often have positional preferences with respect to a genomic landmark. For example, many known transcription factor binding sites (TFBSs) occur within an interval [-300, 0] bases upstream of a transcription start site (TSS). Although some programs for identifying sequence motifs exploit positional information, most of them model it only implicitly and with ad hoc methods, making them unsuitable for general motif searches.
ReSense: Mapping dynamic workloads of colocated multithreaded applications using resource sensitivity

To utilize the full potential of modern chip multiprocessors and obtain scalable performance improvements, it is critical to mitigate resource contention created by multithreaded workloads. In this article, we describe ReSense, the first runtime system that uses application characteristics to dynamically map multithreaded applications from dynamic workloads—workloads where multithreaded applications arrive, execute, and terminate continuously in unpredictable ways. ReSense mitigates contention for the shared resources in the memory hierarchy by applying a novel thread-mapping algorithm that dynamically adjusts the mapping of threads from dynamic workloads using a precalculated sensitivity score. The sensitivity score quantifies an application's sensitivity to sharing a particular memory resource and is calculated by an efficient characterization process that involves running the multithreaded application by itself on the target platform. To measure ReSense's effectiveness, sensitivity scores were determined for 21 benchmarks from PARSEC-2.1 and NPB-OMP-3.3 for the shared resources in the memory hierarchy on four different platforms. Using three different-sized dynamic workloads composed of randomly selected two, four, and eight corunning benchmarks with randomly selected start times, ReSense was able to improve the average response time of the three workloads by up to 27.03p, 20.89p, and 29.34p and throughput by up to 19.97p, 46.56p, and 29.86p, respectively, over the native OS on real hardware. By estimating and comparing ReSense's effectiveness with the optimal thread mapping for two different workloads, we found that the maximum average difference with the experimentally determined optimal performance was 1.49p for average response time and 2.08p for throughput.
Long lasting attenuation by prior sounds in auditory cortex of awake primates.

How the brain responds to sequences of sounds is a question of great relevance to a variety of auditory perceptual phenomena. We investigated how long the responses of neurons in the primary auditory cortex of awake monkeys are influenced by the previous sound. We found that responses to the second sound of a two-sound sequence were generally attenuated compared to the response that sound evoked when it was presented first. The attenuation remained evident at the population level even out to inter-stimulus intervals (ISIs) of 5 s, although it was of modest size for ISIs >2 s. Behavioral context (performance versus non-performance of a visual fixation task during sound presentation) did not influence the results. The long time course of the first sound’s influence suggests that, under natural conditions, neural responses in auditory cortex are rarely governed solely by the current sound.
Influence of ADH1B polymorphism on alcohol use and its subjective effects in a Jewish population.

Class I alcohol dehydrogenases (ADHs) are the principal enzymes responsible for ethanol metabolism in humans. Genetic polymorphism at the ADH1B locus (old nomenclature ADH2) results in isozymes with quite different catalytic properties. The frequency of the ADH1B*2 allele varies among ethnic groups. ADH1B*2 is most often observed in Asian populations, and has been shown to be protective against alcoholism. The Jewish population has a higher frequency of the ADH1B*2 allele and lower rates of alcohol-related problems as compared to other Caucasian populations. Thus, it would be of interest to determine whether the ADH1B*2 allele is associated with alcohol consumption and its subjective effects in this group. Four groups of Jewish subjects (male and female college-age samples, and male and female general samples) were recruited from the same region of the United States. All subjects completed a questionnaire to delineate alcohol consumption and its subjective consequences. Genotype at the ADH1B locus was determined for each participant. ADH1B*2 allele frequencies were similar for the Jewish college-age and general population samples. Men in both the college-age and general population in the ADH1B*2 group reported more unpleasant reactions following alcohol consumption than men in the ADH1B*1 group. Men in the general population in the ADH1B*2 group drank alcohol less frequently than men who were homozygous ADH1B*1; there was a similar trend among the women. The ADH1B polymorphism is associated with unpleasant reactions after alcohol consumption, and frequency of alcohol consumption in these Jewish samples. © 2002 Wiley-Liss, Inc.
Computational Test Design for High-Speed Liquid Impact and Dispersal

Transportation accidents frequently involve liquids dispersing in the atmosphere. An example is that of aircraft impacts, which often result in spreading fuel and a subsequent fire. Predicting the resulting environment is of interest for design, safety, and forensic applications. This environment is challenging for many reasons, one among them being the disparate time and length scales that must be resolved for an accurate physical representation of the problem. A recent computational method appropriate for this class of problems has been developed for modeling the impact and subsequent liquid spread. This involves coupling a structural dynamics code to a turbulent computational fluid mechanics reacting flow code. Because the environment intended to be simulated with this capability is difficult to instrument and costly to test, the existing validation data are of limited scope, relevance, and quality. A rocket sled test is being performed where a scoop moving through a water channel is being used to brake a pusher sled. We plan to instrument this test to provide appropriate scale data for validating the new modeling capability. The intent is to get high fidelity data on the break-up and evaporation of the water that is ejected from the channel as the sled is braking. These two elements are critical to fireball formation for this type of event involving fuel in the place of water. We demonstrate our capability in this paper by describing the pre-test predictions which are used to locate instrumentation for the actual test. We also present a sensitivity analysis to understand the implications of length scale assumptions on the prediction results.Copyright © 2011 by ASME
Optic nerve degeneration in hamsters experimentally infected with scrapie.

Abstract Optic nerve degeneration occurred late in hamsters experimentally infected with scrapie. Disorganization and degeneration of myelin lamellae occurred in many of the axons of the orbital and prechiasmal regions of the nerve; a few axons showed swelling and degeneration of cytosol. Intracellular vacuoles similar to those seen in the brain were observed only in the nonmyelinated intraocular portion of the optic nerve.
Fracture and Permeability Enhancement With Pulse Tailoring

As part of a DOE program, SRI International performed 1) laboratory experiments to determine borehole-loading-dependent fracture phenomenology and to measure material and fracture properties and 2) computational simulations of fracturing in laboratory experiments and field tests. The fracture data obtained from the laboratory experiments was successfully used to computationally predict the ordering of fracture and permeability enhancement in field tests. 5 refs.
Congenital lobar emphysema documented by serial roentgenograms.

Summary A newborn infant with congenital lobar emphysema presented with an overdistended, overexpanded, airless upper lobe and an extreme shift of the mediastinal structures. In spite of these roentgenographic findings, the baby had minimal respiratory distress. Within a period of five days, the fluid within the overexpanded right upper lobe was replaced by air, resulting in the classic roentgenographic pattern of lobar emphysema. This case supports the concept of congenital origin of lobar emphysema and the belief that the fluid-filled lung is an early phase in the development of the overexpanded, hyperlucent, air-filled lobe.
Measurement of residual stresses in thin films by two-dimensional XRD

This paper introduces the recent progress in two-dimensional X-ray diffraction as well as its applications in residual stress analysis in thin films. The stress measurement with twodimensional x-ray diffraction can be done with low incident angle and is not limited to the peaks with high two-theta angles like the conventional method. When residual stresses of thin films are measured, a low incident angle is preferred to maximize the diffraction signals from the thin films surfaces instead of from the substrates and matrix materials. Since one stress measurement at one fixed incident angle is possible, stress gradients in depth can be measured by series of incident angles. Some experimental examples are given to show the stress measurement at low and fixed incident angle.
Characterization of Cysteine-containing Phosphoproteins from Human Submandibular-Sublingual Saliva

Members of a family of acidic proteins taken from human submandibular-sublingual saliva were designated cysteine-containing phosphoproteins, since they could be distinguished from other salivary phosphoproteins by the presence of half-cystine. These molecules consisted of a single peptide chain of ~ 14,000 daltons. Their isoelectric points ranged from 4.3 to 5.9. Two groups (C2 and C3) were 0-phosphorylated. Their charge heterogeneity was apparently due to variations in content of phosphate and acidic and basic amino acids.
Pervasive negabehavior games for environmental sustainability

Pervasive games - games that expand into everyday life - offer a potentially powerful method of promoting social good by encouraging people to perform new, positive actions. However, achieving some desired social goals (such as environmental sustainability) may also require people to stop performing undesirable actions - a form of behavior change that contrasts with common framings of pervasive game-play. I propose to create "Negabehavior Games" - games that encourage players to adopt "negabehaviors" (a manner of conducting oneself that supplants undesirable actions). This research offers a novel approach to designing pervasive games and other interactive experiences, as well as the potential to encourage people to live more environmentally sustainable lives.
Modification of the photosystem II acceptor side function in a D1 mutant (arginine-269-glycine) of Chlamydomonas reinhardti.

Bicarbonate anions have a strong positive influence on the electron and proton transfers in photosystem II (PS II). It has been suggested that bicarbonate binds to the non-heme iron and the QB binding niche of the PS II reaction center. To investigate the potential amino acid binding environment of bicarbonate, an arginine residue (R269) of the D1 protein of PS II of Chlamydomonas reinhardtii was mutated into a glycine; our characterization of the resultant mutant (D1-R269G) shows that both the TyrD+ and QA- Fe2+ EPR signals are substantially reduced and assembly of the tetranuclear Mn is lost (R.S. Hutchison, J. Xiong, R.T. Sayre, Govindjee, Biochim. Biophys. Acta 1277 (1996) 83-92). In order to understand the molecular implications of this mutation on the electron acceptor side of PS II, we used chlorophyll (Chl) a fluorescence as a probe of PS II structure and function, and herbicide binding as a probe for changes in the QB binding niche of PS II. Chl fluorescence measurements with the heterotrophically grown D1-R269G mutant cells (or thylakoids), as compared to that of the wild type, show that: rate of electron transfer from QA to the plastoquinone pool, measured by flash-induced Chl a fluorescence decay kinetics, is reduced by - 17 fold; the minimum Chl a fluorescence yield when all QA- is oxidized, is elevated by 2 fold; the level of stable charge separation as inferred from variable Chl fluorescence is reduced by 44%; binary oscillation pattern of variable Chl a fluorescence obtained after a series of light flashes is absent, indicative of the loss of functioning of the two-electron gate on the PS II acceptor side; 77 K PS II Chl a fluorescence emission bands (F685 and F695) are reduced by 20-30% (assuming no change in the PS I emission band). Thermoluminescence data with thylakoids show the absence of the S2QA- and S2QB- bands in the mutant. Herbicide 14C-terbutryn binding measurements, also with thylakoids, show that the QB niche of the mutant is significantly modified, at least 7-8 fold increased terbutryn dissociation constant is shown (220 nM in the mutant versus 29 nM in the wild type); the PS II sensitivity to bicarbonate-reversible formate inhibition is reduced by 5 fold in the mutant, although the formate/bicarbonate binding site still exists in the mutant. This suggests that D1-R269 must play some role in the binding niche of bicarbonate. On the basis of the above observations, we conclude that the D1-R269G mutation has not only altered the structure and function of PS II (QB niche being abnormal), but may also have a decreased net excitation energy transfer from the PS II core to the reaction center and/or an increased number of inactivated reaction center II. We also discuss a possible scenario for these effects using a recently constructed three dimensional model of the PS II reaction center.
Regulation and synthesis of selected bacteria-induced proteins in Manduca sexta

Abstract The levels of different induced immune proteins in feeding larvae peak at different times following induction with bacteria. If induction is within a few days of wandering, relatively high levels of immune proteins, induced in the feeding larval stage, persist into the wandering larva stage. A period exists, during the feeding-larva to wandering larva transition, when the larva are apparently unable to effectively induce the immune proteins; the larvae are unusually susceptible to bacterial attack during this period. The regulation of several proteins, inducible in larvae, is altered; proteins denoted M4 and M11 which are inducible in larvae are constitutively synthesized in wandering larvae, as well as the subsequent prepupal and pupal stages. The detailed protein analysis here has identified a second component of the larva-specific scolexin (formerly denoted M13), tentatively assumed to be an additional subunit or modified form; two other larva-specific, inducible proteins have been identified. Two non-bactericidal inducible proteins, denoted M11 and scolexin, were found to be induced by abdominal ligation; other immune proteins, including those which are bactericidal, were not. Ligation did not, however, interfere with the induction of all the immune complement of proteins when the ligated larvae were injected with bacteria. These data would suggest that the synthesis of some bacteria-induced proteins are also subject to different regulatory stimuli, and permit one to tentatively assume that neither JH or ecdysteroid synthesis is required for induction to take place. In vitro translations with feeding and wandering larval mRNA tend to support earlier data which indicated that the epidermis is the main source of scolexin.
Science policy and the geographic preferences of stem cell scientists: understanding the appeal of China and Singapore

As scientific advances increasingly pose ethical questions, policymakers must decide how, if at all, to integrate controversial lines of inquiry into existing national innovation systems. This study examines human embryonic stem cell science, a controversial but promising field characterized by an unusually heterogeneous policy environment. This study first assesses this policy environment's impact on stem cell scientists' geographic preferences and finds that permissive policies are a statistically significant predictor of stem cell scientists' preferred countries. Next, China and Singapore, two “emerging leaders” in the field, are examined in greater detail. China appeals to US scientists across biomedical research fields, but this appeal is largely limited to members of the Chinese disapora. In contrast, Singapore's appeal is more specific to stem cell scientists.