cssi/SciSciGPT-SciSciNet huggingface dataset:
A self-adaptive random walk algorithm to identify genetic epistatic effects

A novel search algorithm is developed for finding gene interaction, or epistasis, involved in determining quantitative traits. The algorithm is able to simultaneously find several epistatic effects involving any number of genetic loci. Several other search methods exist in the literature, but most search for epistasis involving two or less loci. For epistasis, especially epistasis involving more than two loci, traditional statistical tests have very low power. In the search algorithm, a series of random walks in the space of possible groups of epistatic effects is performed. The performance of the algorithm is measured while varying key parameters, including the length of the walk, the number of genetic markers available, and the sample size available. Two versions are described, one which restricts the search space to effects involving markers, and a newer approach that allows any locus to be considered. For the newer general locus version, the Expectation Maximization algorithm (EM algorithm) is used to find likelihoods of proposed models. The algorithm was designed to adapt between walks, allowing those loci associated with better models to be guessed more frequently. If the adaptation was gradual, limited and continuous, then the resulting algorithm was robust and improved performance greatly. In simulated data, the algorithm was successful at finding epistatic effects. When several epistatic effects were present in the simulated data, the method was able to simultaneously find all of them at low noise levels. The algorithm was tested in simulated data against a more exhaustive approach, effect bootstrapping, as well as a mainstream approach, Multiple Interval Mapping, and compared well to both approaches. In experimental data, the algorithm found strong evidence of several epistatic effects for most of the phenotypes that were analyzed. Strong evidence of several epistatic effects involving four loci were found, one with a p-value of less than 0.001 from a permutation test. To the best of our knowledge, this is the first time epistasis involving four loci has been explored for quantitative data.
Synergistic Biomass and Natural Gas Conversion to Liquid Fuel with Reduced CO2 Emissions

Abstract Towards reducing the CO 2 emissions associated with the transportation sector, we investigate the design of carbon and energy efficient processes for integrated biomass and natural gas (NG) conversion to liquid fuel. A process superstructure considering biomass conversion via gasification/Fischer-Tropsch (FT) synthesis and fast- hydropyrolsis/hydrodeoxygenation, and NG conversion via reforming followed by FT synthesis is established. Subsequently, a mixed integer nonlinear programming model (MINLP) is formulated to identify the process configurations that maximize the energy output as liquid fuel for different ratios of NG to biomass carbon feeds ( δ ng ). For 1 % ≤ δ ng ≤ 150 %, the optimal process configurations are capable of producing ~5–14 % more liquid fuel output than the combined fuel output of individual standalone processes converting the same amount of biomass and NG. This synergy originates from synthesizing additional liquid fuel by combining the residual biomass carbon with the excess hydrogen per carbon available from the NG feed. These integrated processes are also estimated to achieve up to 80 % reductions in greenhouse gas (GHG) emissions relative to petroleum-based fuels.
Pediatric preclinical testing program (PPTP) evaluation of the MEK1/2 inhibitor AZD6244 (ARRY-142886)

2998 Background : AZD6244 is a potent, selective, and uncompetitive inhibitor of MEK1/2 kinases that is currently in phase 2 clinical development. The activity of AZD6244 was evaluated against the PPTP’s in vitro and in vivo panels. Methods : The PPTP includes a molecularly characterized in vitro panel of cell lines (n=27) and in vivo panel of xenografts (n=61) representing most of the common types of childhood solid tumors and childhood acute lymphoblastic leukemia (ALL). AZD6244 was tested in vitro at concentrations from 1.0 nM to 10 μM and was tested against the PPTP in vivo panel using a BID schedule (excepting weekends for which a QD schedule was used), with oral administration for 6 weeks at a dose of 100 mg/kg. Three measures of antitumor activity were used: 1) an objective response measure modeled after the clinical setting; 2) a treated to control (T/C) tumor volume measure; and 3) a time to event (4-fold increase in tumor volume) measure based on the median event-free survival (EFS) of treated and control animals for each xenograft. Results : AZD6244 demonstrated a clear cytotoxic effect against Kasumi-1, an AML cell line with an activating KIT mutation. The IC50 for Kasumi-1 was 200 nM, similar to IC50 values for AZD6244 in adult cancer cell lines with activating BRAF or RAS family mutations. Several other cell lines showed a limited response to AZD6244 that was consistent with a primarily cytostatic effect, while 18 cell lines had IC50 values > 10 μM. AZD6244 was well tolerated in vivo with toxicity in 2.6% of treated animals compared to 0% of control animals. AZD6244 significantly increased EFS in 10 of 37 (27%) evaluable solid tumor xenografts. Significant differences in EFS distribution occurred in the majority of xenografts in the glioblastoma panel (3 of 4) and in one-half of the xenografts from the osteosarcoma panel (3 of 6). None of the 6 evaluable ALL xenografts demonstrated significant increases in EFS. The EFS T/C values were below the criteria for intermediate activity for the time to event measure of activity (EFS T/C > 2) in all but three evaluable lines: the GBM xenograft BT-39 and two osteosarcoma xenografts (OS-1 and OS-33). The best objective response was PD2 (progressive disease with growth delay), with PD2 activity concentrated in the glioblastoma panel (2 of 4) and the osteosarcoma panel (3 of 6). Conclusions : AZD6244 was highly active against a PPTP cell line with an activating KIT mutation, but was not active against the majority of the cell lines of the PPTP in vitro panel and did not significantly inhibit growth for most of the xenografts in the PPTP in vivo panel. These observations are consistent with the relative paucity of BRAF and RAS family mutations in the pediatric cancers included in this evaluation. Combinations of AZD6244 with agents targeting other signaling pathways involved in survival/proliferation are of interest for future PPTP evaluations of AZD6244. (Supported by NCI NO1CM42216)
Can naturally occurring nanoparticle-based targeted drug delivery effectively treat inflammatory bowel disease?

Nanoparticle (NP)-based drug delivery is a promising approach for delivering drugs to target tissues by overcoming physiological barriers [1,2]. Traditionally formulated drugs (such as tablets or p...
Enhancing Intracellular Concentration and Target Engagement of PROTACs with Reversible Covalent Chemistry

Current efforts in the proteolysis targeting chimera (PROTAC) field mostly focus on choosing the appropriate E3 ligase for a certain targeted protein, improving the binding affinities towards the target protein and the E3 ligase, and optimizing the PROTAC linker. However, it is well known that due to the large sizes of PROTAC molecules, their cellular uptake level remains an issue, posing a challenge to translate PROTACs into therapeutics. Driven by our fundamental investigation to compare how different warhead chemistry, reversible noncovalent (RNC), reversible covalent (RC), and irreversible covalent (IRC) binders, may affect the degradation of a model protein Bruton Tyrosine Kinase (BTK), we serendipitously discovered that cyano-acrylamide-based reversible covalent chemistry can significantly enhance the intracellular concentration and target engagement of the PROTAC. Building on this discovery, we developed RC-1 as the first reversible covalent BTK PROTAC, which has high target occupancy and is effective as both an inhibitor and a degrader. Molecular dynamics calculations and phase-separation based ternary complex assays support that RC-1 forms a stable ternary complex with BTK and Cereblon (CRBN). Additionally, RC-1 compares favorably with other reported BTK degraders in cell viability and target engagement assays and has a reasonable plasma half-life for in vivo applications. Importantly, this reversible covalent strategy can be generalized and applied to improve other PROTACs. This work can not only help to develop optimal BTK degraders for clinical applications but also provide a new strategy to improve PROTAC efficacy.
Cyclic stability of lithium nitrate trihydrate in plate fin heat exchangers

Abstract Latent heat thermal energy storage systems based on hydrated salts are effective solutions for thermal management of transient thermal systems. Hydrated salts have relatively large specific and volumetric latent heat compared to paraffin phase change material. However, hydrated salts are not ubiquitous in energy storage systems because they exhibit inconsistent sub-cooling temperatures and tend to phase segregate due to incongruent melting which leads to degradation in the energy storage capacity. Here we demonstrate high stability of a congruently melting salt hydrate - lithium nitrate trihydrate, in a vacuum sealed plate-fin heat exchanger with water as heat transfer medium cycling between 40 °C and 20 °C, over 500 heating and cooling cycles. The specific latent heat of lithium nitrate trihydrate remained stable at 294 ± 37 J·g−1 and the sub-cooling temperatures increased only by 0.27 °C, demonstrating its stability in operational thermal energy storage systems.
Theoretical and experimental study of choline chloride-carboxylic acid deep eutectic solvents and their hydrogen bonds

Abstract In the field of green chemistry, deep eutectic solvents (DES) have seen extensive use and research in last two decades. Two carboxylic acid-choline chloride DES were studied using experimental Fourier Transform Infrared Spectroscopy (FTIR) and computational Density Functional Theory (DFT). Geometry optimization, vibrational analysis, and assignment of vibrational frequencies were performed using two DFT methods: B3LYP and BLYP. The resemblance to the experimental FTIR vibrations with calculated vibrations established that both the methods can be used to simulate experimental DES. Vibrations that would be impossible to identify and characterize using experimental methods were identified using DFT simulations. Optimized structures as well as experimental spectra were analyzed to prove the existence of hydrogen bonds and to study their lengths and changes when DES are synthesized from components. Atoms in Molecules theory was applied to study hydrogen bonding in these DES. The chlorine ion in choline chloride was found to form a strong hydrogen bond with acetic acid and formic acid in their DES formed with choline chloride. The choline ion was also found to act as a hydrogen bond donor in forming a strong hydrogen bond with acetic acid and formic acid.
The effects of strength and conditioning interventions on golf performance: A systematic review

There is a growing body of literature on strength and conditioning (S&C) interventions for golfers of various skill levels. The aim of this systematic review was to evaluate the effects of S&C inte...
Symbolic Boolean derivatives for efficiently solving extended regular expression constraints

The manipulation of raw string data is ubiquitous in security-critical software, and verification of such software relies on efficiently solving string and regular expression constraints via SMT. However, the typical case of Boolean combinations of regular expression constraints exposes blowup in existing techniques. To address solvability of such constraints, we propose a new theory of derivatives of symbolic extended regular expressions (extended meaning that complement and intersection are incorporated), and show how to apply this theory to obtain more efficient decision procedures. Our implementation of these ideas, built on top of Z3, matches or outperforms state-of-the-art solvers on standard and handwritten benchmarks, showing particular benefits on examples with Boolean combinations. Our work is the first formalization of derivatives of regular expressions which both handles intersection and complement and works symbolically over an arbitrary character theory. It unifies existing approaches involving derivatives of extended regular expressions, alternating automata and Boolean automata by lifting them to a common symbolic platform. It relies on a parsimonious augmentation of regular expressions: a construct for symbolic conditionals is shown to be sufficient to obtain relevant closure properties for derivatives over extended regular expressions.
A 3D Computer Vision-Guided Robotic Companion for Non-Contact Human Assistance and Rehabilitation

With the rapid aging of the U.S. population, the mobility impairment is becoming a more and more challenging issue that affects a large number of individuals. The research presented in this paper aims at helping the mobility-challenged individuals with a novel robotic companion, which is a walker-type mobile robot capable of accompanying the human user and keeping user at the center for protection and possible power assistance. The robotic companion is equipped with a 3D computer vision system, which provides a unique capability of sensing the human-robot relative position/orientation without physical contact or the need for wearable sensors. As such, the robotic companion enables the user to walk freely with minimum disturbance to his/her normal gait, relieving the user from the physical and cognitive loads associated with the use of traditional assistive devices. For the development of the robotic companion, the authors designed and fabricated a low-cost, differentially steered mobile robotic platform, and also developed a unique image processing system to extract the position/orientation information from the 3D camera-captured images. Furthermore, an advanced motion control system was developed for the robotic companion, which provides novel solutions to the unique challenges such as sway reduction and noise reduction in digital differentiation. To quantify the performance, component and system-level experimentation was conducted, and the results demonstrated that robotic companion and its key components function as desired and the system is expected to reduce the user load and improve the user mobility in real-world scenarios.
A Parainfluenza Virus Vector Expressing the Respiratory Syncytial Virus (RSV) Prefusion F Protein Is More Effective than RSV for Boosting a Primary Immunization with RSV.

Live-attenuated pediatric vaccines for intranasal administration are being developed for human respiratory syncytial virus (RSV), an important worldwide pediatric respiratory pathogen that lacks a licensed vaccine or suitable antiviral drug. We evaluated a prime-boost strategy in which primary immunization with RSV was boosted by secondary immunization with RSV or with a chimeric recombinant bovine/human parainfluenza virus type 3 (rB/HPIV3) vector expressing the RSV fusion F protein. The vector-expressed F protein had been engineered (DS-Cav1 mutations) for increased stability in the highly immunogenic prefusion (pre-F) conformation, with or without replacement of its transmembrane and cytoplasmic tail domains with their counterparts from bovine parainfluenza virus type 3 (BPIV3) F protein to direct incorporation into the vector virion for increased immunogenicity. In hamsters that received a primary infection with RSV, a booster infection with RSV ∼6 weeks later was completely restricted for producing infectious virus but induced a significant increase in the serum RSV-plaque-reduction neutralizing antibody titer (RSV-PRNT). Boosting instead with the rB/HPIV3-RSV-pre-F vectors resulted in efficient replication and induced significantly higher RSV-PRNTs than RSV. In African green monkeys that received a primary infection with RSV, a booster infection with RSV ∼2, ∼6, or ∼15 months later was highly restricted, whereas booster infections with the vectors had robust replication. Compared with RSV, boosts with the vectors induced 7- to 15-fold higher titers of RSV-specific serum antibodies with high neutralizing activity, as well as significantly higher titers of RSV-specific mucosal IgA antibodies. These findings support further development of this heterologous prime-boost strategy. IMPORTANCE Immune responses to RSV in infants can be reduced due to immunological immaturity and immunosuppression by RSV-specific maternal antibodies. In infants and young children, two infections with wild-type RSV typically are needed to achieve the titers of RSV-specific serum antibodies and protection against illness that are observed in adults. Therefore, a boost might substantially improve the performance of live pediatric RSV vaccines presently being developed. Hamsters and African green monkeys received a primary intranasal infection with RSV and were given a boost with RSV or a parainfluenza virus (PIV) vector expressing RSV fusion protein engineered for enhanced immunogenicity. The RSV boost was highly restricted but induced a significant increase in serum RSV-neutralizing antibodies. The PIV vectors replicated efficiently and induced significantly higher antibody responses. The use of an attenuated PIV vector expressing RSV antigen to boost a primary immunization with an attenuated RSV warrants further evaluation.
Titanium Disulphide (TiS2) Dichalcogenide Thin Films as Inorganic Hole Transport Layer for Perovskite Solar Cells Synthesized from Ionic Liquid Electrodeposition

In high efficiency organic-inorganic perovskite solar cells formed as a multilayer structure, the hole transporting layer (HTL) at the perovskite absorber layer interface has a critical role. Organic HTLs based on Spiro-OMeTAD and PTAA have led to high efficiencies but displayed poor long-term stability and involves expensive purification processes that hinders universal low-cost commercialization goals for perovskite solar cells. Though as an inorganic alternative, transition metal chalcogenides have been investigated for HTL recently, the hot-injection method often used in synthesis has shown poor reproducibility and difficulty in scaling-up. In this work we demonstrate an ab initio facile inexpensive scalable synthesis of transition metal dichalcogenide (TiS2) by electrodeposition from ionic liquids as a low-cost inorganic HTL for perovskite solar cells. The TiS2 thin films were electrodeposited from choline chloride–urea eutectic based ionic liquid electrolytes at 80°C with Na2S2O3 as sulphur and TiCl4 as titanium source. From cyclic voltammetry studies the deposition potential of TiS2 was optimized at -0.8V vs Pt. The as-deposited TiS2 HTL exhibited polycrystalline structure with preferential growth along (001), (100), (002), (102), (110), (111) planes. The Raman spectroscopy of the films showed peaks around 225 cm−1 and 332 cm−1 attributed to the Eg and A1 g Raman modes respectively. The synthesized thin films demonstrated sharp optical bandgap edge along with bandgap tunability as the bandgap (direct) decreased from 1.53 eV to 1.49 eV, 1.40 eV, and 1.34 eV with gradual change in deposition potential from −0.8 V to −0.9 V, −1.0 V, and −1.1 V vs Pt, respectively. This aspect has potential for alignment of valance band edge in facilitating the hole transport at the perovskite-TiS2 interface. The absorption coefficient in visible-light range of the as-deposited TiS2 thin films likewise has shown a dependence on the synthesis potential which is highly conducive for application as an HTL in multilayer solar cell structure. The TiS2 thin films were observed to be p-type as shown from the Hall effect studies with a carrier mobility up to 14.4 cm2V−1s−1. A detailed study of the effect of the synthesis parameters on the structural, optical, band-edge, and electronic properties of TiS2 thin films suitable for application as HTL in perovskite solar cells is presented.
An Algorithm for Identifying High-Rank Singularities of Arbitrary Redundant Robots

This chapter presents an algorithm for identifying all singularities of a robot’s Jacobian, regardless of rank, for a robot of arbitrary kinematic structure. Unlike other approaches, the complexity of this algorithm is independent of the number of robot’s joints as well as rank of the singularity. It employs the gradient-descent technique on the singular values of the robot Jacobian to identify the singular configurations. It is able to efficiently identify high-rank singularities by accounting for the ill-defined singular vectors that occur when singular values are nearly equal. Also, this chapter addresses the use of Given’s rotation to determine the most natural singular directions for high-rank singularities. The algorithm is illustrated on two 7-DoF robots to show its ability to efficiently identify all singularities of all ranks for redundant manipulators.
Centering relational-meaning making and self-understanding

The Muslim woman who writes about Muslim women is never fully able to write away from the voyeuristic gaze fixated on saving, pitying, or vilifying the Muslim girl/woman. If one documents Muslim wo...
DEM modelling of 3D polyhedra with applications to gabion rockfall barriers

Rock particle shape plays a crucial role in shear resistance and energy consumption during transient loads. The dynamics of such granular materials are complex and cannot be properly described using closed-form solutions when the problem involves more than a few particles. Thus, for the sake of computational efficiency, it is common practice to implement simplified numerical models that involve a limited number of particle interactions. In this study, a novel approach is used to capture realistic particle shapes while maintaining a relatively high simulation efficiency. The geometry of the particles is determined by a Delaunay triangulation which operates on a set of vertices and returns the corresponding network of facets and grid connections. Inertial and material properties are assigned to the rock prototype which are representative of realistic gravel particles. The algorithm is validated by performing a series of numerical simulations for various particle configurations, demonstrating that mass and momentum are conserved. A potential application of this work is related to rockfall barriers and their response to rigid boulder impacts. This innovative model, based on the discrete element method, is shown to be capable of simulating rock particles with realistic shapes and complex physical interactions.
100 days of ELF/VLF generation via HF heating with HAARP

[1] Extremely low frequency/very low frequency (ELF/VLF) radio waves are difficult to generate with conventional antennas. Ionospheric high frequency (HF) heating facilities generate ELF/VLF waves via modulated heating of the lower ionosphere. HF heating of the ionosphere changes the lower ionospheric conductivity, which in the presence of natural currents such as the auroral electrojet creates an antenna in the sky when heating is modulated at ELF/VLF frequencies. We present a summary of nearly 100 days of ELF/VLF wave generation experiments at the 3.6 MW High Frequency Active Auroral Research Program (HAARP) facility near Gakona, Alaska, at a variety of ELF/VLF frequencies, seasons, and times of day. We present comprehensive statistics of generated ELF/VLF magnetic fields observed at a nearby site, in the 500–3500 Hz band. Transmissions with a specific HF beam configuration (3.25 MHz, vertical beam, amplitude modulation) are isolated so the data comparison is self-consistent, across nearly 5 million individual measurements of either a tone or a piece of a frequency-time ramp. There is a minimum in the average generation close to local midnight. It is found that generation during local nighttime is on average weaker but more highly variable, with a small number of very strong generation periods. Signal amplitudes from day to day may vary by as much as 20–30 dB. Generation strengthens by ∼5 dB during the first ∼30 min of transmission, which may be a signature of slow electron density changes from sustained HF heating. Theoretical calculations are made to relate the amplitude observed to the power injected into the waveguide and reaching 250 km. The median power generated by HAARP and injected into the waveguide is ∼0.05–0.1 W in this baseline configuration (vertical beam, 3.25 MHz, amplitude modulation) but may have generated hundreds of watts for brief durations. Several efficiency improvements have improved the ELF/VLF wave generation efficiency further.
Exponential Autoregressive Models

This article focuses on exponential autoregressive time series models. A key feature of these models is that the observations have marginal exponential distributions. The models are described, and estimation of the model parameters and prediction are discussed. A review of other related models is also included. Keywords: exponential; Weibull; gamma; Laplace distributions; autoregressive; moving average models; conditional least squares estimation; prediction
Applying decomposition methods to Crossword Puzzle Problems

Structural decomposition methods have been proposed for identifying tractable Constraint Satisfaction Problems (CSPs)[1-5]. The basic principle is to decompose a CSP into tree-structured sub-problems. The subproblems are solved independently, then the original CSP is solved in a backtrack-free manner after the tree structure is made arc-consistent, as described in [1]. In [5], we proposed four decomposition methods: HINGE+, CUT, TRAVERSE, and CaT and tested these methods on randomly generated CSPs. We compare these techniques on instances of the fully interlocked Crossword Puzzle Problems (CPPs) [6] taken from a public library [7] and identify special cases of the constraint hypergraphs where some decomposition techniques yield better results than others although in general the opposite holds. Our future work includes: 1)Identifying more such configurations, and building hybrid decompositions techniques that exploit this information; 2)Tailoring existing decomposition methods for fully interlocked CPPs so that every sub-problem, after backtrack search, has few solutions; and 3)Designing a heuristic for applying local search for fully interlocked CPPs. This work is supported by CAREER Award #0133568 from the National Science Foundation.
Arp 158: A Study of the HI

We present here 21 cm observations of Arp 158. We have performed a study of the HI to help us understand the overall formation and evolution of this system and its role in galaxy evolution.
Isolation and Characterization of a Herpesvirus from Leukemic Guinea Pigs

Abstract A guinea pig herpesvirus (GPHV) has consistently been isolated from leukemic lymphoblasts of strain-2 guinea pigs. GPHV is serologically related to the guinea pig herpes-like virus isolated by Hsiung and Kaplow. The virions of GPHV consist of an icosahedral capsid containing a dense nucleoprotein core enclosed in a double-layered membrane. The average diameters of GPHV virion and capsid were 166 and 101 nm, respectively. Studies on the morphogenesis of GPHV revealed that, as in other herpesvirus infections, only the naked capsids with or without the nucleoprotein core were found in the infected cell nuclei; it was also learned that the virion acquired its envelope by budding from the nuclear membrane of the infected cells. However, GPHV-infected cell nuclei also contained dense fibrous rods, resembling nucleo-protein core outside the capsids, and tubules resembling viral core protein. The capsids were often embedded in dense granular antigen. GPHV deoxyribonucleic acid (DNA) has a density of 1.716 g/ml in cesium chloride compared to herpes simplex virus DNA (ρ = 1.728 g/ml) and cellular DNA (ρ = 1.700 g/ml).
Altered Trafficking of Mutant Connexin32

We examined the cellular localization of nine different connexin32 (Cx32) mutants associated with X-linked Charcot‐ Marie‐Tooth disease (CMTX) in communication-incompetent mammalian cells. Cx32 mRNA was made, but little or no protein was detected in one class of mutants. In another class of mutants, Cx32 protein was detectable in the cytoplasm and at the cell surface, where it appeared as plaques and punctate staining. Cx32 immunoreactivity in a third class of mutants was restricted to the cytoplasm, where it often colocalized with the Golgi apparatus. Our studies suggest that CMTX mutations have a predominant effect on the trafficking of Cx32 protein, resulting in a potentially toxic cytoplasmic accumulation of Cx32 in these cells. These results and evidence of cytoplasmic accumulation of other mutated myelin proteins suggest that diseases affecting myelinating cells may share a common pathophysiology.
An integrated acoustooptic Bragg heterodyning receiver module

A simple guided-wave architecture which utilizes wideband acoustooptic (AO) and electrooptic (EO) Bragg diffractions in cascade in an LiNbO/sub 3/ planar waveguide to perform efficient and wideband heterodyning detection, and thus realize integrated AO receiver modules, is described. A preliminary receiver module fabricated in a Y-cut LiNbO/sub 3/ waveguide 1 mm*8 mm*20 mm in size and operated at the optical wavelength of 0.6328 mu m has provided a bandwidth of 240 MHz centered at 350 MHz and single-tone instantaneous and two-tone third-order spurious free dynamic ranges of 44.6 and 36.0 dB, respectively. The working principles, design, fabrication, and measured results of the integrated AO heterodyning receiver module are presented. >
Zinc deficiency and child development

Zinc is a trace metal that is present in the brain and contributes to its structure and function. Limited evidence from both animal and human studies suggests that zinc deficiency may lead to delays in cognitive development. Although the mechanisms linking zinc deficiency with cognitive development are unclear, it appears that zinc deficiency may lead to deficits in children's neuropsychologic functioning, activity, or motor development, and thus interfere with cognitive performance. In this article a model is presented that incorporates the influence of social context and the caregiving environment and suggests that the relation between zinc deficiency and cognitive development may vary by age in children and may be mediated by neuropsychologic functioning, activity, and motor development. Suggestions for further research are provided.
Raman spectroscopic investigation of frozen and deparaffinized tissue sections of pediatric tumors: neuroblastoma and ganglioneuroma

Raman spectroscopy is a nondestructive technique that can provide information at the molecular level about the biochemicals in tissues. We have investigated the cellular regions in neuroblastoma and ganglioneuroma using Raman spectroscopy and compared their spectral characteristics with those of the corresponding normal adrenal gland. Thin sections from both the frozen and the corresponding formalin-fixed paraffin-processed (FFPP) tissues were studied in conjunction with the pathological examination of the tissues. Investigation of the spectral data shows that the normal adrenal gland tissues have higher levels of carotenoids,lipids,andcholesterolcomparedwith theneuroblastomaandganglioneuromafrozentissues.However, incomparisonwith the frozen tissues, the FFPP tissues show a significant alteration of several biochemicals, including the complete removal of carotenoids,lipids,and cholesterolin the adrenal tissues.A quantitative analysisusing chemometric methods of principalcomponent analysis and discriminant function analysis of the Raman spectral data obtained from the frozen tissues show a clear-cut classification among pathological groups with high sensitivity and specificity. We have validated the classification results of the FFPP tissues against a training set data obtained from the archived FFPP tissues of nine other patients. The validation process correctly identified and grouped the data with the training set of normal adrenal gland (>97% of the time) and neuroblastoma (100% of the time) tissues, whereas the validation was not so strong for ganglioneuroma. This study shows that Raman spectroscopycombinedwithchemometricmethodscanbesuccessfullyusedtodistinguishneuroblastomaandganglioneuromaatcellular levelinfrozentissuesections.Thisstudyalsoshowsthatformalin fixationandparaffinization/deparaffinizationoftissuescanalter their biochemical composition. Copyright © 2012 John Wiley & Sons, Ltd. Supporting information may be found in the online version of this article.
MetaRNA-Seq: An Interactive Tool to Browse and Annotate Metadata from RNA-Seq Studies

The number of RNA-Seq studies has grown in recent years. The design of RNA-Seq studies varies from very simple (e.g., two-condition case-control) to very complicated (e.g., time series involving multiple samples at each time point with separate drug treatments). Most of these publically available RNA-Seq studies are deposited in NCBI databases, but their metadata are scattered throughout four different databases: Sequence Read Archive (SRA), Biosample, Bioprojects, and Gene Expression Omnibus (GEO). Although the NCBI web interface is able to provide all of the metadata information, it often requires significant effort to retrieve study- or project-level information by traversing through multiple hyperlinks and going to another page. Moreover, project- and study-level metadata lack manual or automatic curation by categories, such as disease type, time series, case-control, or replicate type, which are vital to comprehending any RNA-Seq study. Here we describe "MetaRNA-Seq," a new tool for interactively browsing, searching, and annotating RNA-Seq metadata with the capability of semiautomatic curation at the study level.
STEATORRHEA AND HYPOALBUMINEMIA IN CIRRHOSIS WITH ASCITES.

Steatorrhea associated with advanced cirrhosis of the liver was studied by means of the I131-labeled oleic acid absorption test. The validity of the use of this test as a measure of fat absorption by the small intestine was reviewed. Malabsorption of oleic acid was demonstrated in each of the 6 cirrhotic patients examined. The impaired absorption of oleic acid was attributed to pathologic changes in the mucosa of the small intestine secondary to portal hypertension. The clinical implications of this finding were discussed. The possibility that a protein-losing enteropathy might contribute to the hypoalbuminemia of advanced cirrhosis was investigated by means of intravenously administered I131-labeled polyvinylpyrrolidone and I131-labeled serum albumin. However, no significant loss of protein through the gastrointestinal tract was demonstrated in the 4 cirrhotic patients examined for this condition.
Receipt of older RBCs does not predispose D-negative recipients to anti-D alloimmunization.

The effect of the age of RBCs on anti-RBC alloimmunization has not been investigated in previous studies of the RBC storage lesion. D-negative recipients of at least 1 D-positive RBC unit were identified. Responders produced an anti-D, while nonresponders had not made anti-D when the database was searched. The 2 groups were matched for age, sex, length of serologic follow-up, and hospital location. There were 29 responders and 58 nonresponders. The median number of all RBCs transfused to the responders was 6, vs 10 for the nonresponders ( P < .01); the median age of the RBCs was 15 vs 14 days, respectively ( P = .70). Responders received a median of 3 D-positive RBC units vs 4 D-positive RBCs for nonresponders ( P = .02); median ages of the D-positive RBCs were 16 vs 14 days, respectively ( P = .21). There was no association between the age of transfused RBCs and the likelihood of anti-D alloimmunization.
A note on the feeding of Calanus helgolandicus on detritus

Experiments on the feeding of Calanus helgolandicus females on detrital material were carried out. Natural detritus from the ocean was never ingested, whereas dead diatoms were readily eaten. Furthermore, it was shown that C. helgolandicus females ingested large amounts of fecal material produced by the same species in other vessels. These results indicate that the copepod C. helgolandicus feeds not only on living organisms, but also on dead particles.
A classification of biologic lipids based upon their interaction in aqueous systems

A classification of lipids is presented, based upon their physical properties in bulk aqueous systems and at the air-water or oil-water interface. This is supported by binary-phase diagrams of the various classes of lipids in water. The interactions of the lipids of each class with a lipid of another class is illustrated by a series of different ternary-phase diagrams of two lipids in water. The various types of association and the molecular relation of one lipid to another are indicated. The interaction of three classes of lipids with water is illustrated in two examples by quaternary-phase diagrams of the three lipids in water. As an example of the application of these invitro studies, the composition of bile is correlated with a quaternary-phase diagram cholesterollecithin-bile salt-water. The correlation shows that human bile behaves as a biologic four-component system the physical state of which is entirely predictable from the quaternary-phase diagram. Although bile is a special case, it is probable that the physical arrangement of the lipids in membranes, cellular organelles, lipoproteins, and adipose tissue can be suggested by studies of the interaction of lipid classes with themselves in water.
Measurement of spin memory lengths in PdNi and PdFe ferromagnetic alloys

length at 4.2K in sputtered Pd0.88Ni0.12 and Pd0.987Fe0.013 alloys using methods based on currentperpendicular-to-plane giant magnetoresistance. The alloys are incorporated into hybrid spin valves of various types, and the spin memory length is determined by fits of the Valet-Fert spin-transport equations to data of magnetoresistance vs. alloy thickness. For the case of PdNi alloy, the resulting values of the spin memory length are l P dNi sf = 2.8 ± 0.5nm and 5.4 ± 0.6nm, depending on whether or not the PdNi is exchange biased by an adjacent Permalloy layer. For PdFe, the spin memory length is somewhat longer, l P dF e sf = 9.6 ± 2nm, consistent with earlier measurements indicating lower spin-orbit scattering in that material. Unfortunately, even the longer spin memory length in PdFe may not be long enough to facilitate observation of spin-triplet superconducting correlations predicted to occur in superconducting/ferromagnetic hybrid systems in the presence of magnetic inhomogeneity.
Comparison of open and endovascular repair of ruptured abdominal aortic aneurysms from the ACS-NSQIP 2005-07.

The adoption of endovascular aneurysm repair (EVAR) for ruptured abdominal aortic aneurysms (RAAA) has lagged behind the technique's application for intact, elective abdominal aortic aneurysms (AAA).1 With emerging data from centers of excellence and community hospitals, it is apparent that EVAR for RAAA has shown a steady increase.2–8 Comparison of this method of repair to its traditional open repair counterpart is difficult, however, as preoperative differences in hemodynamic stability are likely to play a large role in the decision for one type of repair over the other. Early reports have been especially favorable in centers where a standardized treatment protocol has been established for EVAR as a first-line therapy for RAAA.2–5 Describing the results from one such program, Mehta et al.2 were able to show an 18% mortality rate following EVAR with a 95% success rate for the procedure, which compares favorably to prior repairs in which mortality for RAAA has hovered at 40% to 50% for the past 4 decades.9 Moreover, this and other small institutional studies may not be representative of the population at large. We therefore looked at the current outcomes of EVAR and open repair for RAAA within the National Surgical Quality Improvement Program (NSQIP), which is representative of community as well as academic medical centers. The NSQIP, developed for general and vascular surgical outcomes quality assessment, is a large database with contributions by over 200 hospitals nationwide. It contains a comprehensive list of preoperative comorbidities, preoperative variables reflecting hemodynamic stability, intraoperative variables, 30-day postoperative complications, and 30-day mortality, which makes it well suited for the comparison of RAAA repair methods.
Role of the pituitary–adrenal axis in granulocyte-colony stimulating factor-induced neuroprotection against hypoxia–ischemia in neonatal rats.

Several reports indicate that the activity of the hypothalamic–pituitary–adrenal axis (HPA) is increased after a brain insult and that its down-regulation can improve detrimental outcomes associated with ischemic brain injuries. Granulocyte-colony stimulating factor (G-CSF) is a neuroprotective drug shown in the naive rat to regulate hormones of the HPA axis. In this study we investigate whether G-CSF confers its neuroprotective properties by influencing the HPA response after neonatal hypoxia–ischemia (HI). Following the Rice–Vannucci model, seven day old rats (P7) were subjected to unilateral carotid ligation followed by 2.5 h of hypoxia. To test our hypothesis, metyrapone was administered to inhibit the release of rodent specific glucocorticoid, corticosterone, at the adrenal level. Dexamethasone, a synthetic glucocorticoid, was administered to agonize the effects of corticosterone. Our results show that both G-CSF and metyrapone significantly reduced infarct volume while dexamethasone treatment did not reduce infarct size even when combined with G-CSF. The protective effects of G-CSF do not include blood brain barrier preservation as suggested by the brain edema results. G-CSF did not affect the pituitary released adrenocorticotropic hormone (ACTH) levels in the blood plasma at 4 h, but suppressed the increase of corticosterone in the blood. The administration of G-CSF and metyrapone increased weight gain, and significantly reduced the Bax/Bcl-2 ratio in the brain while dexamethasone reversed the effects of G-CSF. The combination of G-CSF and metyrapone significantly decreased caspase-3 protein levels in the brain, and the effect was antagonized by dexamethasone. We report that G-CSF is neuroprotective in neonatal HI by reducing infarct volume, by suppressing the HI-induced increase of the Bax/Bcl-2 ratio, and by decreasing corticosterone in the blood. Metyrapone was able to confer similar neuroprotection as G-CSF while dexamethasone reversed the effects of G-CSF. In conclusion, we show that decreasing HPA axis activity is neuroprotective after neonatal HI, which can be conferred by administering G-CSF.
Topology and elastic properties of depleted media

Random structures can be taken as models for many structures that occur in nature. Here we consider such structures from the standpoint of their topology, and suggest the utility of an easily calculated quantity, the Euler number, as a means of assessing connectivity and mechanical performance.
Quantifying the Exposure of Street Segments to Drinking Places Nearby

Introduce and test the relative efficacy of two methods for modeling the impact of cumulative ‘exposure’ to drinking facilities on violent crime at street segments. One method, simple count, sums the number of drinking places within a distance threshold. The other method, inverse distance weighted count, weights each drinking place within a threshold based on its distance from the street segment. Closer places are weighted higher than more distant places. Distance is measured as the street length from a street segment to a drinking place along the street network. Seven distance thresholds of 400, 800, 1,200, 1,600, 2,000, 2,400 and 2,800 feet are tested. A negative binomial regression model controlling for socio-economic characteristics, opportunity factors and spatial autocorrelation is used to evaluate which of the measure/threshold combinations produce a better fit as compared to a model with no exposure measures. Exposure measured as an inverse distance weighted count produces the best fitting model and is significantly related to violent crime at longer distances than simple count (from 400 to 2,800 feet). Exposure to drinking places using a simple count is significantly related to violent crime up to 2,000 feet. Both models indicate the influence of drinking places is highest at shorter distance thresholds. Both researchers and practitioners can more precisely quantify the influence of drinking places in multivariate models of street segment level violent crime by incorporating proximity in the development of a cumulative exposure measure. The efficacy of using exposure measures to quantify the influence of other types of facilities on crime patterns across street segments should be explored.
Single machine scheduling with nonlinear cost functions

Abstract The problem of scheduling n jobs with a single machine where each job has a differentiable cost function and the total cost being minimized is studied. A heuristic solution procedure is proposed. The algorithm is also applicable when the cost functions are piecewise diflerentiable. Running time of the algorithm is O ( n 2 ). The effectiveness of the algorithm is evaluated and is shown that in many cases the algorithm picks an optimal order. The algorithm proposed here empirically is compared with linearized algorithm by Fisher and Krieger [1].
Three facets of satisfaction and their influence on the performance of innovation teams

Abstract This study investigates and demonstrates the mediating effect of job satisfaction between team deftness and team comprehension and the performance of 168 project teams involved in major innovation projects for their companies. The study demonstrates that there are at least three independent facets of job satisfaction: instrumental satisfaction with the way the task is progressing, social satisfaction with the way the team members interact with one another and the organization, and egocentric satisfaction with the individuals' perceived benefits to themselves. Previous studies have shown that innovation team performance is directly correlated with the two antecedents of performance: team deftness, which reflects how effectively the team works to achieve the innovation's purpose and team comprehension, which reflects how the team understands the linkages among key variables driving the innovation outcome. The study argues that these different facets of satisfaction differentially affect the ways in which team performance is affected by deftness and comprehension. There are three major results: 1. 1. Social satisfaction mediates the relation between team deftness and performance—as social dissatisfaction of the team increases, it appears to impede the ability of the team to deploy its deftness in accomplishing the project's purpose. 2. 2. Instrumental satisfaction mediates the relation between team comprehension and project performance—as instrumental dissatisfaction increases, it appears to impede the ability of the team to deploy its comprehension to accomplish the project's purpose. 3. 3. Egocentric satisfaction does not appear to mediate the relation between team deftness and project performance. Some managerial implications of these results are discussed.