cssi/SciSciGPT-SciSciNet huggingface dataset:
Kojak: efficient analysis of chemically cross-linked protein complexes.

Protein chemical cross-linking and mass spectrometry enable the analysis of protein–protein interactions and protein topologies; however, complicated cross-linked peptide spectra require specialized algorithms to identify interacting sites. The Kojak cross-linking software application is a new, efficient approach to identify cross-linked peptides, enabling large-scale analysis of protein–protein interactions by chemical cross-linking techniques. The algorithm integrates spectral processing and scoring schemes adopted from traditional database search algorithms and can identify cross-linked peptides using many different chemical cross-linkers with or without heavy isotope labels. Kojak was used to analyze both novel and existing data sets and was compared to existing cross-linking algorithms. The algorithm provided increased cross-link identifications over existing algorithms and, equally importantly, the results in a fraction of computational time. The Kojak algorithm is open-source, cross-platform, and f...
Attribution Retraining for Learning Disabled Students: Some Thoughts on the Practical Implications of the Evidence

Given a consistent interaction of student locus of attribution and mode of teacher response, this study sought to determine whether learning disabled students' attribution levels could be changed. ...
Candidate gene isolation and comparative analysis of a commonly deleted segment of 7q22 implicated in myeloid malignancies.

Abstract Monosomy 7 and deletion of 7q are recurring abnormalities in malignant myeloid diseases. Here we extensively characterize an ∼ 2-Mb commonly deleted segment (CDS) of 7q22 bounded by D7S1503 and D7S1841. Approximately 1.8 Mb of sequence have been generated from this interval, facilitating the construction of a transcript map that includes large numbers of genes and ESTs. The intron/exon organization of seven genes and expression patterns of three genes were determined, and leukemia samples were screened for mutations in five genes. We have used polymorphic markers from this region to examine leukemia cells for allelic loss within 7q22. Finally, we isolated mouse genomic clones orthologous to several of the characterized human genes. Fluorescence in situ hybridization studies using these clones indicate that a region of orthologous synteny lies on proximal mouse chromosome 5. These resources should greatly accelerate the pace of candidate gene discovery in this region.
WE-A-17A-04: Development of An Ultra-Fast Monte Carlo Dose Engine for High Dose Rate Brachytherapy

Purpose: Current clinical brachytherapy dose calculations are based on AAPM TG43 guidelines, which approximate the patient geometry as a large water phantom. This ignores heterogeneities and tends to overestimate skin dose. Although Monte Carlo (MC) dose calculations have been recognized as the most accurate method, its associated long computational time is a major bottleneck for routine clinical applications. This work aims to develop a GPU-based ultra-fast MC dose engine (gBMC) for HDR brachytherapy to provide clinical users with accurate sub-minute dose calculations. Methods: Standard photon transport with discrete events including: Compton scattering, Rayleigh scattering and Photoelectric effect, was implemented. Secondary electrons were transported under the continuous slowing down approximation. To reduce the GPU thread divergence, photons and electrons were separately transported. Transport of photons was grouped according to energy. The source model in gBMC can be either a phase-space file generated using Geant4 or a parameterized source model. This dose engine was validated against TG43 in a water phantom and against Geant4 calculations in heterogeneous patient geometries. Results: A phase space file was generated for the Varian VS2000 Ir-192 source. In a water phantom, the calculated radial dose function was within 0.6% of the TG43 calculations for radial distances from 1 cm to 20 cm. The anisotropy functions were within 1% for radial distances from 1 cm to 20 cm except for polar angles larger than 173°. Local point-dose differences were within 2%. In a Mammosite breast cancer case with 22 dwell locations, gBMC and Geant4 isodose lines compared well. The computation time was about 28 seconds using the phase-space file source and 20 seconds using the parameterized source to simulate 1 billion particles, yielding less than 1% statistical uncertainty. Conclusion: The gBMC dose engine makes it possible to use fast and accurate MC dose calculations for clinical work.
Interfirm cooperation and structural change in the European automobile industry

The past quarter-century has seen the rapid growth of interfirm cooperative arrangements, on a global scale. In the automobile industry, the forms of cooperation have ranged from mergers and acquisitions, with each partner firm retaining its corporate identity and brand name, to very informal strategic partnerships. Because of its past fragmentation, the consolidation of the European industry into “producer groups” has been a main feature of structural change. Arguably, this development and the formation of rent-seeking coalitions within the European Union were of greater significance than companies' purely technology-oriented cooperative ventures. As a result of the industry members' individual and collective rent-seeking, at the national and EU levels respectively, large price disparities among national markets have persisted. Regulatory barriers as well as the noncompetitive behavior of firms continue greatly to influence the automotive sector, despite the Union's ambitious vision of “Europe 92” as the final stage in the development of an open market for products and factors. Whatever benefits automobile producers may have derived from integration, it has done little so far to enhance consumer welfare.
Two aerobic pathways for the formation of unsaturated fatty acids in Pseudomonas aeruginosa

Summary The double bond in anaerobic unsaturated fatty acid (UFA) biosynthesis is introduced by the FabA dehy- dratase/isomerase of the bacterial type II fatty acid biosynthetic pathway. A D fabA mutant of Pseudomo- nas aeruginosa grew aerobically, but required a UFA supplement for anaerobic growth. Wild-type cells produced 18:1 D 11 as the principal UFA, whereas the D fabA strain produced only 16:1 D 9. The double bond in the 16:1 D 9 was introduced after phospholipid formation and was localized in the sn -2 position. Two predicted membrane proteins, DesA and DesB , pos- sessed the conserved histidine clusters charac- teristic of fatty acid desaturases. The D fabA D desA double mutant required exogenous fatty acids for growth but the D fabAdesB double mutant did not. Exogenous stearate was converted to 18:1 D 9 and supported the growth of D fabA D desA double mutant. A D fabA D desAdesB triple mutant was unable to desat- urate exogenous stearate and was an UFA auxotroph. We detected a 2.5-fold increase in desA expression in D fabA mutants, whereas desB expression was dere- pressed by the deletion of the gene encoding a tran- scriptional repressor DesT. These data add two aerobic desaturases to the enzymes used for fatty acid metabolism in proteobacteria: DesA, a 2-position phospholipid D 9-desaturase that supplements the anaerobic FabA pathway, and DesB, an inducible acyl- CoA D 9-desaturase whose expression is repressed by DesT.
Interface control: A modified rooting technique for enhancing field emission from multiwall carbon nanotube based bulk emitters

Abstract The unique properties of carbon nanotubes (CNTs) have raised hopes that these materials might find wide application as cold cathodes in various electron sources. The excellent field emission properties shown by CNT-based field emitters has further stimulated this expectation. However, efficient performance of a practical field emitter, which comprises a large number of randomly or regularly oriented CNTs, is restricted primarily due to poor junctions formed between CNTs and substrates. This study is aimed at enhancing the junction performance by way of a modified “rooting” technique—interface control. In this process, the interface between CNTs and substrate has been tailored with different metals in an attempt to improve the CNT–substrate junction performance. Multiwall carbon nanotubes (MWCNTs) were synthesized on different interface-controlled substrates, i.e. Cu, Al, W, Si and low-temperature co-fired ceramic. All the samples produced mat-type, randomly oriented MWCNT structures. Among the four different substrates studied, MWCNT-based field emitters on Cu substrate demonstrated the best field emission response, in terms of low turn-on field, high emission current, good field enhancement factor and excellent stability in long-term operation. Emitter structures and their field emission behavior were correlated and it was shown that interface control, as an advanced “rooting” process, plays an important role in determining the emission response from a bulk field emitter.
Teaching engineering ethics in the United States

The present academic discipline of engineering ethics originated in the mid-1970s when engineering and philosophy professors began to consider ethical problems facing engineers. In addition to the role played by these two primary disciplines, disciplines such as law, history, behavior and management sciences, and religious studies shaped the emerging field, as did parallel developments in other applied ethics fields treating professional responsibility, such as medical, legal, and business ethics. Courses in engineering ethics were developed at a number of universities. In addition to stand-alone courses in engineering ethics, many universities incorporated ethical components into technical or nontechnical courses. The article summarizes significant developments at a number of top engineering schools in the US, spurred in part by National Science Foundation funding. In addition, a spring 1997 search of the World Wide Web uncovered developments at a wide range of universities and colleges. Not all schools provide information on the Web. In addition, information on the Web is constantly changing and Web searches are imperfect. Nevertheless, the information provided here gives a good picture of the kinds of initiatives in engineering ethics pedagogy that now exist.
A radioimmunoassay for insulin-like growth factor II specific for the C-peptide region.

Insulin-like growth factor II (IGF-II) is a human plasma peptide whose sequence is homologous to both insulinlike growth factor I/somatomedin C (IGF-I/SM-C) and human proinsulin in the A and B regions. However, there is no obvious homology in the C (connecting peptide) region. The synthetic 8- amino acid C-peptide segment of IGF-II (Ser-Arg-Val-Ser-Arg- Arg-Ser-Arg) was covalently linked to thyroglobulin to render it more antigenic. Antiserum against the IGF-II C-peptide was generated which had a titer of 1:2000 determined with [125I]IGFII C-peptide. Half-maximum displacement was by 350 pg/ml IGF-II C-peptide or 80 ng/ml IGF-II. There was no displacement by IGF-I/SM-C, insulin, or a wide variety of peptides. There was also a high degree of species specificity of this antisera. Isoelectric focusing studies of immunoreactive IGF-II showed an apparent pi of 6–6.5. The mean (±SEM) level of IGF-II after acid chromatography of 28 normal adult males was 687.0 ± 31.9 ng/ml. The mean of 8 acromegalics was 600.5 ± ...
Robust window-based multi-node technology-independent logic minimization

Multi-node optimization using Boolean relations is a powerful approach for network minimization. In this paper, we present an algorithm to perform Boolean relation-based multi-node optimization using a robust, fast and memory efficient algorithm. In particular, we simultaneously optimize two nodes at a time. The robustness of our approach arises from the use of a window-based technique for computing these Boolean relations. Secondly, we perform early quantification during the computation, keeping memory utilization low. Finally, we employ smart heuristics for selecting the node pair to be optimized simultaneously.These features allow the approach to scale well and provide good results for large designs. We perform experiments on a set of large benchmarks and compare our algorithm's performance to a recent SAT-based network optimization technique using complete don't cares. On average, we achieve a 15% reduction in literal count across all the large designs, compared to the complete don't care-based method while maintaining small runtimes and low memory usage.
Recent Advances in Humanized Mice: Accelerating the Development of an HIV Vaccine

Recent advances in the development of humanized mice hold great promise to advance our understanding of protective immunity to human immunodeficiency virus (HIV) infection and to aid in the design of an effective HIV vaccine. This supplement of the Journal of Infectious Diseases summarizes work in the humanized mouse model presented at an HIV Humanized Mouse workshop in Boston, Massachusetts, in November 2012, including recent advances in the development of humanized mice, the trafficking of human immune cells following mucosal HIV transmission, the role of immune activation and Toll-like receptor agonists in the control of HIV, the induction and efficacy of HIV-specific cellular and humoral immune responses, and the preclinical modeling of novel anti-HIV therapeutics. Many gaps remain in our understanding of how to design an effective HIV vaccine and novel therapeutics to eliminate the viral reservoir. Promising early results from studies in humanized mice suggest great potential and enthusiasm for this model to accelerate these critical areas of HIV research.
SUPREM 3.5-process modeling of GaAs integrated circuit technology

A computer program SUPREM 3.5, has been developed to simulate processes used to manufacture ion-implanted GaAs integrated circuits. The processes modelled in the present version of the simulator include ion implantation, diffusion, and activation. The simulator includes a routine to calculate the threshold voltage of a MESFET device based on the simulated processing results and on substrate properties. The models used for each dopant and process are based on physical mechanisms when possible, but empirical parameter fitting is sometimes used. Pearson IV distributions are used for the implantation modeling, concentration-independent diffusivities are used for n-type dopants, concentration-dependent diffusivities are used for p-type dopants, and concentration-dependent activation efficiencies are used for all dopants. The simulator models each process individually, as well as integrating the various processes and models together. >
Reciprocal Effects of Treatment-induced Increases in Exercise and Improved Eating, and Their Psychosocial Correlates, in Obese Adults Seeking Weight Loss: A Field-based Trial

Background A better understanding of interrelations of exercise and improved eating, and their psychosocial correlates of self-efficacy, mood, and self-regulation, may be useful for the architecture of improved weight loss treatments. Theory-based research within field settings, with samples possessing high probabilities of health risks, might enable rapid application of useful findings.
Sinus Floor Elevation Via the Maxillary Premolar Extraction Socket With Immediate Implant Placement: A Case Series

Background: When immediate implant placement is considered for teeth with close proximity to the sinus floor, apical extension of the osteotomy is significantly limited, and often a staged approach is used. Implant placement into fresh extraction sockets and sinus floor manipulation using bone-added osteotome sinus floor elevation with implant placement are techniques most often used independently or sequentially. Very few reports have described the combined use of immediate implant placement in fresh sockets and the bone-added osteotome sinus floor elevation technique.Methods: We present five cases in which a maxillary premolar was extracted and an implant placed into the extraction site with simultaneous abfracture of the sinus floor using osteotomes. All teeth were extracted atraumatically, and sockets carefully debrided and checked for integrity of the walls. After ideal osteotomy preparation, particulate bone graft was placed in the osteotomy and appropriately sized osteotomes were used for sinus flo...
Technique for very High Order Nonlinear Simulation and Validation

Finding the sources of sound in large nonlinear fields via direct simulation currently requires excessive computational cost. This paper describes a simple technique for efficiently solving the multidimensional nonlinear Euler equations that significantly reduces this cost and demonstrates a useful approach for validating high order nonlinear methods. Up to 15th order accuracy in space and time methods were compared and it is shown that an algorithm with a fixed design accuracy approaches its maximal utility and then its usefulness exponentially decays unless higher accuracy is used. It is concluded that at least a 7th order method is required to efficiently propagate a harmonic wave using the nonlinear Euler equations to a distance of 5 wavelengths while maintaining an overall error tolerance that is low enough to capture both the mean flow and the acoustics.
Extremely thermostable orotidine-5′-monophosphate decarboxylase from the archaeon Sulfolobus acidocaldarius

Orotidine-5′-monophosphate decarboxylase (E.C. 4.1.1.23) was purified from Sulfolobus acidocaldarius, one of the archaea that populates geothermal environments. The enzyme was determined to be a dimer of 22-kDa subunits and was readily separated from the orotate phosphoribosyl transferase of S. acidocaldarius. The purified orotidine-5′-monophosphate decarboxylase demonstrated a broad pH optimum centered about pH 8 and an optimal temperature above 98°C. In the absence of substrate and product, however, a considerable thermal inactivation was observed at 85°C or above. To our knowledge, this is the first orotidine-5′-monophosphate decarboxylase of a hyperthermophile or an archaeon to be purified. The S. acidocaldarius enzyme may offer special advantages for the detailed study of enzyme structure-function relationships at extremely high temperatures, due to the fact that either loss or gain of function can be genetically selected in vivo.
A Robust Audit Mechanism to Prevent Malicious Behaviors in Multi-robot Systems

Market-based mechanisms can be used to coordinate self-interested multi-robot systems in fully distributed environments, where by self-interested we mean that each robot agent attempts to maximize a payoff function that accounts for both the resources consumed and the contribution made by the robot. In previous work, we have studied the effect of various market rules and bidding strategies on the global performance of the multi-robot system. However, rather than use a central monitoring and enforcement mechanisms, we rely on agents to self-report their actions. This assumes that the agents act honestly. In this paper, we drop the honesty assumption, raising the possibility that agents may exaggerate their contribution in order to increase their payoff. To address the problem of such malicious behavior, we propose an audit mechanism to maintain the integrity of reported payoffs. Our algorithm extends previous work on preventing free-riding in peer-to-peer networks. Specifically, we consider locality and mobility in multi-robot systems. We show that our approach efficiently detects malicious behaviors with a high probability.
Electromagnetic and electrochemical response of geological conductors

Summary form only given. It is now realized that the Earth's crustal layers are not simple lossy dielectrics with fixed parameters. In fact, the effective permittivities of actual rocks and soils may exhibit values that are 10000 times free space at sufficiently low frequencies (e.g. less than 1000 Hz). Such effects, although less dramatic, extend all the way up to microwaves. Such highly dispersive phenomena greatly complicate quantitative analyses for transient electromagnetic propagation within the Earth. Various applications occur in mine communications, geophysical exploration, well logging, ground-penetrating radar, and ELF/VLF antenna transmitter design. >
Design of Spin-Torque Transfer Magnetoresistive RAM and CAM/TCAM with High Sensing and Search Speed

With a great scalability potential, nonvolatile magnetoresistive memory with spin-torque transfer (STT) programming has become a topic of great current interest. This paper addresses cell structure design for STT magnetoresistive RAM, content addressable memory (CAM) and ternary CAM (TCAM). We propose a new RAM cell structure design that can realize high speed and reliable sensing operations in the presence of relatively poor magnetoresistive ratio, while maintaining low sensing current through magnetic tunneling junctions (MTJs). We further apply the same basic design principle to develop new cell structures for nonvolatile CAM, and TCAM. The effectiveness of the proposed RAM, CAM and TCAM cell structures has been demonstrated by circuit simulation at 0.18 ?m CMOS technology.
Optimal Policies for Assembly Systems: Completing Rosling's Characterization

We study an assembly system with stochastic demand. This is the model studied in Rosling (1989), one of the classic papers in inventory theory, where the optimal policy is characterized as a balanced echelon base-stock policy, assuming that the initial state of the system possesses a certain property referred to as 'long-run balance.' We characterize the optimal policy starting with any arbitrary initial state, thereby completing the optimal policy description of Rosling (1989). The optimal policy is essentially a balanced echelon base-stock policy again, but with dynamically evolving echelon base-stock levels. We also show that the policy prescribed by Rosling (1989) is still optimal, if the initial echelon inventory positions are non-decreasing in item index, which is a milder condition than the long-run balance assumption and is easy to state and to check.
Protecting personal data: can IT security management standards help?

Compelled to improve information security by the introduction of personal data protection legislation, organizations worldwide are adopting standardized security management guidelines to inform their internal processes. We analyze whether existing security management standards support process requirements for personal data management, drawing from experience with security policies in private organizations and through an analysis of current European and US legislation. Various aspects of personal data management not commonly addressed by security standards are identified, and a number of generally applicable enhancements are proposed to one common standard, IS17799. The appropriateness of including data protection guidelines in security standards is discussed, showing how these enhancements could simplify the definition of personal data management procedures in organizations.
Obesity and the microbiome

Obesity constitutes a significant and rapidly increasing public health challenge and is associated with significant co-morbidities and healthcare costs. Although undoubtedly multifactorial, research over the last decade has demonstrated that the microbes that colonize the human gut may contribute to the development of obesity through roles in polysaccharide breakdown, nutrient absorption, inflammatory responses and gut permeability. Studies have consistently shown that the Firmicutes to Bacteroidetes ratio, in particular, is increased in obesity and reduces with weight loss. In addition, we and others have shown that the methanogenic Archaea may also contribute to altered metabolism and weight gain in the host. However, much remains to be learned about the roles of different gut microbial populations in weight gain and obesity and the underlying mechanisms before we can begin to approach targeted treatments.
AMPHIDROMY AND MIGRATIONS OF FRESHWATER SHRIMPS. I. COSTS, BENEFITS, EVOLUTIONARY ORIGINS, AND AN UNUSUAL CASE OF AMPHIDROMY

Many freshwater shrimps (Decapoda, Caridea) have amphidromous life histories, with extended planktonic larval development in the sea. Larvae either are hatched upstream to drift down to the sea or are carried and released there by females. After development, postlarvae (juveniles) must migrate back up to their adult freshwater habitat. An amphidromous life cycle thus involves long distance migrations between marine and fresh waters. Other freshwater shrimps have abbreviated (or direct) larval development (ALD) with a completely freshwater life cycle and without such migrations. The question of which life history pattern (amphidromy versus ALD) is ancestral in freshwater shrimps is discussed in terms of costs, benefits, and phylogeny. Competing hypotheses are presented to explain the unusual distribution of Macrobrachium ohione, an amphidromous shrimp with recently abundant populations located very far (>1500 km) from the sea.
King's Theory of Goal Attainment

This article presents an overview of the meaning of the terms concept, theory, and conceptual system. It gives a detailed description of King's conceptual system including personal systems, interpersonal systems, and social systems, and a description of the theory of goal attainment. A discussion of the philosophical assumptions underpinning King's theory as well as the concepts of the theory are also included. Research (both completed and ongoing) and changes that have taken place in her theory are examined.
An outcome analysis of intraoperative angiography for postmastectomy breast reconstruction.

Background: Intraoperative angiography is a useful tool for predicting both tissue perfusion during postmastectomy breast reconstruction and mastectomy flap and free flap survival. Objectives: The authors determine whether the routine use of laser-assisted indocyanine green (ICG) fluorescence angiography (SPY Imaging; LifeCell Corp, Branchburg, New Jersey) in breast reconstruction decreases the incidence of complications and whether this new technology is cost-effective. Methods: A retrospective review was conducted for 184 consecutive patients who underwent breast reconstruction using intraoperative ICG angiography from April 2009 to December 2011 at Emory University (Atlanta, Georgia). The incidence of complications (including mastectomy skin necrosis, flap necrosis, fat necrosis, unexpected reoperations, infections, and dehiscence) among these patients was compared with data for 184 consecutive patients who underwent breast reconstruction at Emory University from October 2007 to April 2009, prior to the introduction of ICG angiography. Patient data recorded included age, body mass index, smoking status, and history of preoperative radiation as well as the timing and type of reconstruction, along with complications. The cost of unexpected reoperations for perfusion-related complications and associated hospital stays was calculated. Results: The 184 patients who underwent procedures using ICG angiography imaging had a lower incidence of mastectomy skin necrosis (13% vs 23.4%; P = .010) and unexpected reoperations for perfusion-related complications (5.9% vs 14.1%, P = .009). The 184 patients who underwent procedures without ICG angiography had a higher mean degree of severity of mastectomy skin necrosis (2.22 vs 1.83 on a scale of 1–3; P = .065). There were no significant differences in the degree of flap necrosis, nipple necrosis, fat necrosis, dehiscence, infection, implant exposure, flap loss, seroma, hematoma, or the number of overall complications between the 2 groups. The use of ICG angiography saved patients an average of $610. Conclusions: The use of ICG angiography during postmastectomy breast reconstruction decreased the incidence and severity of mastectomy skin necrosis as well as the incidence of unexpected reoperations for perfusion-related complications. The technology was found to be cost-effective. Level of Evidence: 4 ![Graphic][1] [1]: /embed/inline-graphic-1.gif
"WE'VE ALL LEARNED A LOT OF WAYS NOT TO SOLVE THE PROBLEM": PERCEPTIONS OF SCIENCE AND ENGINEERING PATHWAYS AMONG TENURED WOMEN FACULTY

Women’s career development and socialization into the sciences and engineering is generally acknowledged to be uniquely guided by factors including having role models and mentors who provide useful guidance. This study examines aspects of department culture that encourage retention of women science and engineering majors through the perspectives of ten tenured women professors in Florida public university science and engineering departments. Interviewees refl ected on their personal experiences and those of their women colleagues and students to develop recommendations on social support and mentorship opportunities, improving treatment of women faculty, and developing departments that also function as a community and family. Tenured women faculty reject the pipeline approach and describe their own circuitous pathways into academia. They describe the strain of the role of “female professor” and its impact on research, teaching, and university service. These women explain how women and men together struggle to navigate divisions between departments based on research interest and with their bids for tenure and promotion to full professor. However, they explain that women emphasize community and collegiality more than men. Isolation and mistreatment of women and poor community in departments dissuade women junior faculty from continuing in the professoriate.
Structured Recurrent Temporal Restricted Boltzmann Machines

The recurrent temporal restricted Boltzmann machine (RTRBM) is a probabilistic time-series model. The topology of the RTRBM graphical model, however, assumes full connectivity between all the pairs of visible units and hidden units, thereby ignoring the dependency structure within the observations. Learning this structure has the potential for not only improving the prediction performance, but also revealing important dependency patterns in the data. For example, given a meteorological dataset, we could identify regional weather patterns. In this work, we propose a new class of RTRBM, which we refer to as the structured RTRBM (SRTRBM), which explicitly uses a graph to model the dependency structure. Our technique is related to methods such as graphical lasso, which are used to learn the topology of Gaussian graphical models. We also develop a spike-and-slab version of the RTRBM, and combine it with the SRTRBM to learn dependency structures in datasets with real-valued observations. Our experimental results using synthetic and real datasets demonstrate that the SRTRBM can significantly improve the prediction performance of the RTRBM, particularly when the number of visible units is large and the size of the training set is small. It also reveals the dependency structures underlying our benchmark datasets.
SpliceTrap: a method to quantify alternative splicing under single cellular conditions

MOTIVATION: Alternative Splicing (AS) is a pre-mRNA maturation process leading to the expression of multiple mRNA variants from the same primary transcript. More than 90% of human genes are expressed via alternative splicing. Therefore, quantifying the inclusion level of every exon is crucial for generating accurate transcriptomic maps and studying the regulation of alternative splicing. RESULTS: Here we introduce SpliceTrap, a method to quantify exon inclusion levels using paired-end RNA-seq data. Unlike other tools, which focus on full-length transcript isoforms, SpliceTrap approaches the expression-level estimation of each exon as an independent Bayesian inference problem. In addition, SpliceTrap can identify major classes of alternative splicing events under a single cellular condition, without requiring a background set of reads to estimate relative splicing changes. We tested SpliceTrap both by simulation and real data analysis, and compared it to state-of-the-art tools for transcript quantification. SpliceTrap demonstrated improved accuracy, robustness, and reliability in quantifying exon-inclusion ratios.Conclusions: SpliceTrap is a useful tool to study alternative splicing regulation, especially for accurate quantification of local exon-inclusion ratios from RNA-seq data.Availability and implementation: SpliceTrap can be implemented online through the CSH Galaxy server http://cancan.cshl.edu/splicetrap and is also available for download and installation at http://rulai.cshl.edu/splicetrap/. CONTACT: michael.zhang@utdallas.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
When males and hermaphrodites coexist: a review of androdioecy in animals.

Synopsis Androdioecy (populations consisting of males and hermaphrodites) is a rare mating system in plants and animals: up to 50 plants and only 36 animals have been described as being androdioecious, with most of the latter being crustaceans. To date, a thorough comparative analysis of androdioecy in animals has not been undertaken. Herein we present such an analysis. Androdioecy has only been extensively surveyed in 2 animal taxa: the nematode Caenorhabditis and the clam shrimp Eulimnadia. The other major taxon having androdioecious species is the Cirripedia (barnacles), but there are only limited studies on androdioecy in this group. In animals, androdioecy is found either in species that have morphologically and ecologically distinct sexes (that is, hermaphrodites and small, “complemental” males) that are derived from hermaphroditic ancestors (that is, the barnacles) or in species that have similarly-sized males and hermaphrodites that have been derived from dioecious ancestors (the remaining androdioecious species). We suggest that the barnacles have evolved a sexual specialization in the form of these complemental males that can more efficiently use the constrained habitats that these barnacles often experience. For the remaining species, we suggest that androdioecy has evolved as a response to reproductive assurance in species that experience episodic low densities. Additionally, we hypothesize that the development of mechanisms allowing reproductive assurance in species with a number of sexually differentiated traits is most likely to result in androdioecy rather than gynodioecy (mixtures of females and hermaphrodites), and that these species may be developmentally constrained to stay androdioecious rather than being capable of evolving into populations solely consisting of efficient, self-compatible hermaphrodites. We conclude by suggesting several areas in need of further study to understand more completely the evolution and distribution of this interesting mating system in animals.
Epigenetic mechanisms in cardiac development and disease

During mammalian development, cardiac specification and ultimately lineage commitment to a specific cardiac cell type is accomplished by the action of specific transcription factors (TFs) and their meticulous control on an epigenetic level. In this review, we detail how cardiac-specific TFs function in concert with nucleosome remodeling and histone-modifying enzymes to regulate a diverse network of genes required for processes such as cell growth and proliferation, or epithelial to mesenchymal transition (EMT), for instance. We provide examples of how several cardiac TFs, such as Nkx2.5, WHSC1, Tbx5, and Tbx1, which are associated with developmental and congenital heart defects, are required for the recruitment of histone modifiers, such as Jarid2, p300, and Ash2l, and components of ATP-dependent remodeling enzymes like Brg1, Baf60c, and Baf180. Binding of these TFs to their respective sites at cardiac genes coincides with a distinct pattern of histone marks, indicating that the precise regulation of cardiac gene networks is orchestrated by interactions between TFs and epigenetic modifiers. Furthermore, we speculate that an epigenetic signature, comprised of TF occupancy, histone modifications, and overall chromatin organization, is an underlying mechanism that governs cardiac morphogenesis and disease.
Searching biases in large interactive document retrieval systems

The way that individuals construct and modify search queries on a large interactive document retrieval system is subject to systematic biases similar to those that have been demonstrated in experiments on judgments under uncertainty. These biases are shared by both naive and sophisticated subjects and cause the inquirer searching for documents on a large interactive system to construct and modify queries inefficiently. A searching algorithm is suggested that helps the inquirer to avoid the effect of these biases.
Dissimilarity of Scalar Transport in the Convective Boundary Layer in Inhomogeneous Landscapes

A land-surface model (LSM) is coupled with a large-eddy simulation (LES) model to investigate the vegetation-atmosphere exchange of heat, water vapour, and carbon dioxide (CO2) in heterogeneous landscapes. The dissimilarity of scalar transport in the lower convective boundary layer is quantified in several ways: eddy diffusivity, spatial structure of the scalar fields, and spatial and temporal variations in the surface fluxes of these scalars. The results show that eddy diffusivities differ among the three scalars, by up to 10–12%, in the surface layer; the difference is partly attributed to the influence of top-down diffusion. The turbulence-organized structures of CO2 bear more resemblance to those of water vapour than those of the potential temperature. The surface fluxes when coupled with the flow aloft show large spatial variations even with perfectly homogeneous surface conditions and constant solar radiation forcing across the horizontal simulation domain. In general, the surface sensible heat flux shows the greatest spatial and temporal variations, and the CO2 flux the least. Furthermore, our results show that the one-dimensional land-surface model scheme underestimates the surface heat flux by 3–8% and overestimates the water vapour and CO2 fluxes by 2–8% and 1–9%, respectively, as compared to the flux simulated with the coupled LES-LSM.
Sharp Bounds on the Spectral Radius of Nonnegative Matrices and Digraphs

Abstract The spectral radius ρ ( A ) of a matrix A is the maximum modulus of its eigenvalues. We present bounds on ρ ( A ) that are often tighter and are applicable to a larger class of nonnegative matrices than previously reported. The bounds are particularly suited to matrices which are sparse. We complete the paper by applying these bounds to digraphs, deriving the associated equality conditions which relate to the outdegree regularity of the digraph. Finally, we show that the equality conditions may be achieved only for very specific values of the digraph’s spectral radius.
Cottus paulus: A Replacement Name for the Pygmy Sculpin, Cottus pygmaeus Williams 1968

Abstract A replacement name, Cottus paulus, is proposed for the Pygmy Sculpin, Cottus pygmaeus. The name Cottus pygmaeus was preoccupied by Cottus quadricornis pygmaeus Lonnberg (1932).
Binocular Scanning Performance of Soldiers Wearing Chemical Biological Protective Masks

Future warfare may include the use of chemical weapons. Soldiers will be required to wear protective masks which impose restrictions in the field of view of optical devices. Two studies were conducted to examine the use of M19 binoculars when soldiers must wear protective masks. Targets were displayed over an area 21 degrees high by 60 degrees wide. The time required to scan the area was recorded and a relationship was developed between scan time and field of view by means of a simple linear regression analysis. The studies show that the use of protective masks will have a significant impact on the soldier's ability to find targets.
Acetone Precipitation of the Scrapie Agent Results in Successful Recovery of PrPSc but Decreased Infectivity

Bioassay is considered the most sensitive method for evaluating prion inactivation procedures. Because prions are resistant to methods effective at inactivating conventional microorganisms, prion inactivation research has focused on relatively harsh alternatives, such as concentrated sodium hypochlorite or sodium hydroxide. Often, bioassay for residual infectivity in these studies requires dilution or biochemical alteration of the treated sample in order to maintain subject health and survival. Ideally, prions from treated samples could be sufficiently separated from the inactivating agent without alteration of the sample and with negligible loss of infectivity prior to inoculation into the bioassay host. The current study was designed to evaluate acetone precipitation of the disease-associated form of the prion protein (PrPSc) from brain homogenate derived from mice with the RML (Rocky Mountain Laboratory) strain of scrapie. The ability to recover PrPSc was evaluated by Western blot. Dilutions of acetone...
NEW MUCOLYTIC AGENTS FOR SPUTUM LIQUEFACTION.

The ideal mucolytic agent would be inexpensive, stable, nonirritating and effective in liquefying mucus, purulent secretions and fibrin. Such an agent is not yet available, but one that approaches this ideal most closely so far is acetylcysteine. It effectively liquefies mucoid and purulent secretions, but not blood or fibrin. Care must be taken to assure evacuation of the liquefied secretions.
Maturational Patterns of Sigma Frequency Power Across Childhood and Adolescence: A Longitudinal Study.

Author(s): Campbell, Ian G; Feinberg, Irwin | Abstract: Study objectivesTo further evaluate adolescent brain maturation by determining the longitudinal trajectories of nonrapid eye movement (NREM) sigma (11-15 Hz) power across childhood-adolescence.MethodsThe maturational trend for sigma (11-15 Hz) power was evaluated in an accelerated longitudinal study of three overlapping age cohorts (n = 92) covering ages 6 to 18 y. Semiannually, sleep electroencephalography (EEG) was recorded from participants sleeping at home in their normal sleep environment while keeping their current school night schedules.ResultsSigma frequencies became faster with age. The frequency of the 11-15 Hz spectral peak increased linearly. Sigma frequency power (SFP) declined with age, but its trajectory was complex (cubic). Power in a group of low sigma subfrequencies declined with age. Power in a group of high sigma frequencies increased with age. Power in subfrequencies within 11-15 Hz also showed different trends across the night, with lower frequencies increasing across NREM periods and higher frequencies decreasing across NREM periods. The upper and lower boundaries for the sigma frequencies that changed across NREMPs shifted upward with age.ConclusionsWe hypothesize that these maturational brain changes result from synaptic elimination which decreases sleep depth and streamlines circuits. SFP displays a maturational trajectory different from both delta and theta power. Theories on the function of sigma must be reconciled with its maturational trajectory. These findings further demonstrate the value of sleep EEG for studying noninvasively the complex developmental brain changes of adolescence.
Idraparinux was noninferior to standard therapy for deep venous thrombosis but inferior for pulmonary embolism.

Source Citation The van Gogh Investigators. Idraparinux versus standard therapy for venous thromboembolic disease. N Engl J Med. 2007;357:1094-104. 17855670
A New Method for Urban Spatial Analysis: Measuring Gaze, Attention, and Memory in the Built Environment

Ubiquitous computing technologies and an array of readily available sensors provide urban researchers with access to data acquisition and analysis tools related to the built environment. This paper presents the possibility of utilizing sensor data from a wearable eye-tracker to analyze human attention patterns when navigating urban environments. This is the outcome of a series of experiments conducted by students and researchers at the GSD Responsive Environments and Artifacts Lab in the spring of 2015. Through a comparative study of the test subjects' eye gaze data during a street walk and post-walk mapping exercise, this research shows and compares several layers of inconsistency: the difference between what exists in the built environment and what is seen, the portion of existing information that is both taken in through the eye (as determined by our eye tracking software) and what is remembered or processed into memory. An additional metric is drawn from the maps produced by the subjects, showing the elements that are remembered from prior experiences and those that pertain specifically to the testing period. These inconsistencies provide detailed clues when reexamined against Kevin Lynch's urban "imageability" studies of the individual: not only accounting for what leaves an impression on people's mind, but also allowing the opportunity to analyze why certain urban elements are more relevant than others.
3.21 – Neurophysiology of Motor Skill Learning

Significant advances have been made in the past several years in understanding the role of the various cortical motor areas in motor learning. It is clear that motor skill acquisition is associated with alterations in topographic maps of motor representations, structural changes in neuronal elements (synapses, dendrites, etc.), and differential expression of growth-related proteins. We now recognize that motor learning is a distributed process. While differentiation in response properties of various cortical areas demonstrates their unique functions, there is considerable overlap. Primary motor cortex is most associated with movement-related aspects of learning motor tasks. The mesial areas are more related to learning motor sequences, especially when they are self-initiated. The lateral motor areas are more related to externally guided movements, and the integration of sensory cues with motor commands, especially in forming conditional motor associations. Finally, the cingulate motor areas are involved in more cognitive and motivational aspects of motor learning. This chapter reviews the literature primarily from nonhuman primate neurophysiology studies, as well as human neuroimaging studies that demonstrate this distributed network underlying motor learning.
Directed Evolution Tools in Bioproduct and Bioprocess Development

Publisher Summary This chapter focuses on the strategies for diversity generation that are applicable to the development of bioproducts and bioprocesses via directed evolution. Microorganisms and the enzymes they hold have been exploited by man for thousands of years, for example, in the production of food products through fermentation. Directed evolution tools have been increasingly used to engineer new or improved enzymes, metabolic pathways, and whole genomes for various bioprocessing applications. In the past decade, numerous molecular biology techniques have been developed to create genetic diversity through random mutagenesis and/or homologous or nonhomologous recombination in the target genes, pathways, and genomes. Coupled with the development of powerful high-throughput screening or selection methods, these evolutionary techniques have been successfully used to solve challenging problems in protein engineering and metabolic engineering. In addition, directed evolution is highly complementary to rational design. Its capability is rapidly growing due to recent advances of structural genomics and computational biology. It seems that the combination of directed evolution and rational design represents the most powerful tool for protein engineering and metabolic engineering.