cssi/SciSciGPT-SciSciNet huggingface dataset:
Mutagenesis and Functional Selection Protocols for Directed Evolution of Proteins in E. coli

The efficient generation of genetic diversity represents an invaluable molecular tool that can be used to label DNA synthesis, to create unique molecular signatures, or to evolve proteins in the laboratory. Here, we present a protocol that allows the generation of large (>1011) mutant libraries for a given target sequence. This method is based on replication of a ColE1 plasmid encoding the desired sequence by a low-fidelity variant of DNA polymerase I (LF-Pol I). The target plasmid is transformed into a mutator strain of E. coli and plated on solid media, yielding between 0.2 and 1 mutations/kb, depending on the location of the target gene. Higher mutation frequencies are achieved by iterating this process of mutagenesis. Compared to alternative methods of mutagenesis, our protocol stands out for its simplicity, as no cloning or PCR are involved. Thus, our method is ideal for mutational labeling of plasmids or other Pol I templates or to explore large sections of sequence space for the evolution of activities not present in the original target. The tight spatial control that PCR or randomized oligonucleotide-based methods offer can also be achieved through subsequent cloning of specific sections of the library. Here we provide protocols showing how to create a random mutant library and how to establish drug-based selections in E. coli to identify mutants exhibiting new biochemical activities.
A mechanomyographic frequency-based fatigue threshold test.

A B 5 T R ACT Theoretically, the mechanomyographic (MMG) mean power frequency fatigue threshold (MMGMPFFf ) describes the maximal isometric torque that can be maintained for an extended period of time with no change in the global firing rate of the unfused, activated motor units. Purpose: The purposes of this study were twofold: (1) to determine if the mathematical model for esti­ mating the electromyographic (EMG) MPFFf from the frequency of the EMG signal was applicable to the frequency domain of the MMG signal to estimate a new fatigue threshold called the MMG MPF Ff : and (2) to compare the mean torque levels derived from the MMG MPF Ff test for the vastus lateralis (VL), vastus medialis (VM), and rectus femoris (RF) muscles during isometric leg extension muscle actions. Methods: Nine adults (4 men and 5 women: mean ±S.D. age = 21.6 ± 1.2 years) performed three or four continuous, fatiguing, isometric muscle actions of the leg extensors at 30, 45, 60, and 75% of maximum voluntary isometric contraction (MVIC) to exhaustion. Surface MMG signals were recorded from the VL, VM,and RF muscles during each fatiguing isometric muscle action. The MMG MPFFf was defined as the y-intercept of the isometric torque versus slope coefficient (MMGMPF versus time) plot. Results: There were no significant differences among the MMG MPFFf values for the VL, VM, and RF
The polymorphism rs944289 predisposes to papillary thyroid carcinoma through a large intergenic noncoding RNA gene of tumor suppressor type

A genome-wide association study of papillary thyroid carcinoma (PTC) pinpointed two independent SNPs (rs944289 and rs965513) located in regions containing no annotated genes (14q13.3 and 9q22.33, respectively). Here, we describe a unique, long, intergenic, noncoding RNA gene (lincRNA) named Papillary Thyroid Carcinoma Susceptibility Candidate 3 (PTCSC3) located 3.2 kb downstream of rs944289 at 14q.13.3 and the expression of which is strictly thyroid specific. By quantitative PCR, PTCSC3 expression was strongly down-regulated (P = 2.84 × 10−14) in thyroid tumor tissue of 46 PTC patients and the risk allele (T) was associated with the strongest suppression (genotype [TT] (n = 21) vs. [CT] (n = 19), P = 0.004). In adjacent unaffected thyroid tissue, the genotype [TT] was associated with up-regulation of PTCSC3 ([TT] (n = 21) vs. [CT] (n = 19), P = 0.034). The SNP rs944289 was located in a binding site for the CCAAT/enhancer binding proteins (C/EBP) α and β. The risk allele destroyed the binding site in silico. Both C/EBPα and C/EBPβ activated the PTCSC3 promoter in reporter assays (P = 0.0009 and P = 0.0014, respectively) and the risk allele reduced the activation compared with the nonrisk allele (C) (P = 0.026 and P = 0.048, respectively). Restoration of PTCSC3 expression in PTC cell line cells (TPC-1 and BCPAP) inhibited cell growth (P = 0.002 and P = 0.019, respectively) and affected the expression of genes involved in DNA replication, recombination and repair, cellular movement, tumor morphology, and cell death. Our data suggest that SNP rs944289 predisposes to PTC through a previously uncharacterized, long intergenic noncoding RNA gene (PTCSC3) that has the characteristics of a tumor suppressor.
How accurate is the ultrasonic estimation of ventricular septal defect size

The relationship between the size of ventricular septal defects estimated from ultrasonic images and the actual size of the ventricular septal defects is currently unknown. Our goal was to image simulated defects of known size under conditions as physiological as possible with several two-dimensional ultrasonic instruments. The study was not viewed as a contest between instruments. A static heart model we tested consisted of a simulated chest wall-right ventricular anterior wall, a human septum or muscular septal equivalent, and a simulated left ventricular posterior wall. Model tissues were placed in holders in a water bath for imaging at 90° and 180° with respect to the ventricular septal defect. These angles tested the lateral and axial resolution necessary for imaging simulated ventricular septal defects. Actual ventricular septal defect sizes ranged from 5 to 17.5 mm. Images were obtained with a 30°, 3.5-MHz, mechanical sector scanner, a 2.4-MHz range focused phased array, and a prototype transmit and dynamically focused, 3.5-MHz phased array. Image quality of the defect varied at 90° but was generally poor at 180°. For studies conducted at 180°, phased arrays imaged sharp defect edges for larger holes, but the mechanical sector scanner did not. Signal attenuation appeared to be the major limiting factor for axial resolution. For imaging at 90°, the mechanical sector scanner approximated the actual defect size less 4 mm. The prototype phased array scanner approximated the defect size less 4 to 6 mm. With the range focused, phased array, imaged size was always less than one half actual size. The smallest defect imaged with our simulation with any instrument was 7 mm. These data or their regression equation should not be used to compute the actual size of a clinical ventricular septal defect, since different machines, transducers, and situations might alter the exact relationship between imaged and actual defect size. However, the data led to the conclusion that imaged size of a defect is instrument and transducer dependent and is always smaller than actual defect size.
First-principles calculation of the activation energy for diffusion in liquid sodium.

We have performed the first calculation of the activation energy for self-diffusion in a liquid metal which contains no adjustable parameters. The calculation uses the local-density-functional theory combined with the Car-Parrinello technique for molecular-dynamics simulation. The coefficient of self-diffusion agrees well with the experimental value and fits the form D=${\mathit{D}}_{0}$ i/rexp(-${\mathit{E}}_{\mathit{a}}$/${\mathit{k}}_{\mathit{B}}$T) with ${\mathit{E}}_{\mathit{a}}$=0.099 eV, ${\mathit{D}}_{0}$=0.84\ifmmode\times\else\texttimes\fi{}${10}^{\mathrm{\ensuremath{-}}3}$ ${\mathrm{cm}}^{2}$/sec, compared to the most recent experimental values of ${\mathit{E}}_{\mathit{a}}$=0.096 eV, ${\mathit{D}}_{0}$=0.86\ifmmode\times\else\texttimes\fi{}${10}^{\mathrm{\ensuremath{-}}3}$ ${\mathrm{cm}}^{2}$/sec.
Inhibition of desaturation of palmitic, linoleic and eicosa-8,11,14-trienoic acids in vitro by isomeric cis-octadecenoic acids.

The effects of the positional isomers of cis-18 : 1 acids on the desaturation of 18 : 2 omega 6 leads to 18 : 3 omega 6 (delta 6 desaturase), 20 : 3 omega 6 leads to 20 : 4 omega 6 (delta 5 desaturase) and 16 : 0 leads to 16 : 1 (delta 9 desaturase) were investigated using essential fatty acid deficient rat liver microsomes. The isomeric cis-18 : 1 acids were found to be inhibitory for the delta 6, delta 5 and delta 9 desaturases, and the position of the double bond is important in determining the degree of inhibition. The effects of the several cis-18 : 1 isomers on delta 6 and delta 5 desaturases were parallel in magnitude exept for the cis-delta isomer which gave 17.5% inhibition for delta 6 desaturase and no inhibition for delta 5 desaturase. The strongest inhibitor for delta 6 desaturase (cis-delta 8 18 : 1) was also the most potent inhibitor for delta 5 desaturase, and the weakest inhibitor for delta 6 desaturase (cis-delta 3 18 : 1) was the least effective inhibitor on delta 5 desaturase. The delta 9 desaturase was maximally inhibited by cis-delta 10 and delta 11 18 : 1 isomers. The cis-18 : 1 acid isomers in partially hydrogenated edible fats may have effects on the lipid metabolism through their inhibitory effects on the desaturases.
Missing data assumptions and methods in a smoking cessation study.

Aim A sizable percentage of subjects do not respond to follow-up attempts in smoking cessation studies. The usual procedure in the smoking cessation literature is to assume that non-respondents have resumed smoking. This study used data from a study with a high follow-up rate to assess the degree of bias that may be caused by different methods of imputing missing data. Design and methods Based on a large data set with very little missing follow-up information at 12 months, a simulation study was undertaken to compare and contrast missing data imputation methods (assuming smoking, propensity score matching and optimal matching) under various assumptions as to how the missing data arose (randomly generated missing values, increased non-response from smokers and a hybrid of the two). Findings Missing data imputation methods all resulted in some degree of bias which increased with the amount of missing data. Conclusion None of the missing data imputation methods currently available can compensate for bias when there are substantial amounts of missing data.
On listening where we look: the fragility of a phenomenon.

The role of eye position information has been the subject of some debate in the literature on the visual facilitation of auditory localization and attention. In one particularly compelling study, Reisberg, Scheiber, and Potemken (1981) found that fixation position strongly influenced sub­ jects' recall performance in a binaural selective-listening task. The present paper describes repeated failures to demonstrate the eye position effect under conditions similar to those of the original study, thus challenging the robustness of this oft-cited phenomenon of "listening where we look." Over the past several years, a number of studies have appeared which demonstrate that viewing conditions can affect auditory localization and attention. For example, performance in sound localization tasks is better when sub­ jects' eyes are kept open than when they are closed (Jones & Kabanoff, 1975; Warren, 1970). Voluntary eye move­ ments toward a sound source may facilitate sound localiza­ tion accuracy (Platt & Warren, 1972), whereas preven­ tion of eye movements or movements in the opposite direction may inhibit accuracy (Jones & Kabanoff, 1975). In dichotic listening tasks, subjects have been observed to direct their gaze in the direction of the attended chan­ nel, and they have reported that they deliberately did so in order to enhance performance (Gopher & Kahneman, 1971; see also Gopher's study, cited in Kahneman, 1973). Moreover, selective attention in otherauditory tasks ap­ pears to improve when subjects can visually fixate the sound source (Reisberg, 1978). A particularly compelling demonstration of the phenomenon of "listening where we look" was reported recently by Reisberg, Scheiber, and Potemken (1981). In their experiment, the subjects were asked to attend to one of two word lists played simultaneously over three iden­ tical vertically arrayed speakers. The subjects showed much better target-list (correct) recall and fewer distractor­ list (intrusion) errors when fixating the target speaker or a silent (control) speaker than when fixating the distrac­ tor speaker. These data were taken to suggest that eye position information is effective in directing auditory localization and attention. Reisberg et al. hypothesized that eye position information serves to help guide audi­ tory attention by permitting the construction of a spatial
Techniques for Scheduling I/O in a High Performance Multimedia-on-Demand Server

One of the key components of a multiuser multimedia-on-demand system is the data server. Digitalization of traditionally analog data such as video and audio, and the feasibility of obtaining network bandwidths above the gigabit-per-second range, are two important advances that have made possible the realization, in the near future, of interactive distributed multimedia systems. Secondary-to-main memory I/O technology has not kept pace with advances in networking, main memory, and CPU processing power. Consequently, the performance of the server has a direct bearing on the overall performance of such a system. In this paper, we present a highperformance solution to the I/O retrieval problem in a distributed multimedia system. We develop a model for the architecture of a server for such a system. Parallelism of data retrieval is achieved by striping the data across multiple disks. We present the algorithms for server operation when servicing a constant number of streams, as well as the admission control policy for accepting requests for new streams. The performance of any server ultimately depends on the data access patterns. Two modifications of the basic retrieval algorithm are presented to exploit data access patterns in order to improve system throughput and response time. Finally, we present preliminary performance results of these algorithms on the IBM SP1 and Intel Paragon parallel computers.
Valvular heart disease update.

An update on the many recent changes in the diagnosis and treatment of valvular disease, focusing on the most common problems.
Automatic and Programmed Tracking Systems for Optical Instrumentation

Instrumentation requirements of test programs involving rockets, rocket sleds, and other projectiles are often such that a capability of tracking the projectile with an optical system is highly desirable, both because of the economy of fewer cameras and equipment required for adequate coverage, and because of the more satisfactory data which can be obtained in this manner. Manual tracking of these projectiles is unsatisfactory and often im-practical due to the high accelerations and the fact that the duration of the tests is of the same order of time as the human reflex. Several proposed systems for automatic and programmed tracking utilizing both digital and analog techniques are discussed, and available results of tests of some of these systems are presented.
Regression analysis with dichotomous attributes

Abstract In recent years sociologists have become interested in mathematical models which are based on systems of recursive linear equations between a set of variables. The movement started with an article by Herbert Simon (1954) who translated certain findings of dichotomous algebra into quantitative terms. The idea was then extended by Hubert Blalock (1964). Raymond Boudon (1965) pointed out that path analysis introduced 40 years earlier by the biometrician Wright was really representing the same approach. Following his lead Otis Duncan (1967) then published a series of examples where path analysis was applied to social data. Path analysis has considerable attraction for for social scientists because its ideas can be graphically represented by the now well-known arrow scheme and because its algebra can be extended to any number of variables. But like any linear system it cannot reproduce conditional relations. 1 In many cases the advantage of dealing economically with many variates outweighs the loss of higher level information. For this reason Coleman (1964) developed a formalism by which we can translate the idea of linearity into dichotomous terms. In 1968 Boudon (1958) simplified considerably the computational aspect of his approach. The following paper recasts the Coleman-Boudon model in terms of dichotomous algebra. Leaving the main ideas of the two authors unchanged the present approach seems to provide further simplification. The paper is part of a larger presentation which shows that its theorems can be extended to apply the idea of path analysis to dichotomous systems. This generalization will be found in the proceedings of the 1970 UNESCO Seminar on mathematical social sciences (in preparation).
Novel computational methods for increasing PCR primer design effectiveness in directed sequencing

Polymerase chain reaction (PCR) is used in directed sequencing for the discovery of novel polymorphisms. As the first step in PCR directed sequencing, effective PCR primer design is crucial for obtaining high-quality sequence data for target regions. Since current computational primer design tools are not fully tuned with stable underlying laboratory protocols, researchers may still be forced to iteratively optimize protocols for failed amplifications after the primers have been ordered. Furthermore, potentially identifiable factors which contribute to PCR failures have yet to be elucidated. This inefficient approach to primer design is further intensified in a high-throughput laboratory, where hundreds of genes may be targeted in one experiment. We have developed a fully integrated computational PCR primer design pipeline that plays a key role in our high-throughput directed sequencing pipeline. Investigators may specify target regions defined through a rich set of descriptors, such as Ensembl accessions and arbitrary genomic coordinates. Primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the specified target regions. As part of the tiling process, primer pairs are computationally screened to meet the criteria for success with one of two PCR amplification protocols. In the process of improving our sequencing success rate, which currently exceeds 95% for exons, we have discovered novel and accurate computational methods capable of identifying primers that may lead to PCR failures. We reveal the laboratory protocols and their associated, empirically determined computational parameters, as well as describe the novel computational methods which may benefit others in future primer design research. The high-throughput PCR primer design pipeline has been very successful in providing the basis for high-quality directed sequencing results and for minimizing costs associated with labor and reprocessing. The modular architecture of the primer design software has made it possible to readily integrate additional primer critique tests based on iterative feedback from the laboratory. As a result, the primer design software, coupled with the laboratory protocols, serves as a powerful tool for low and high-throughput primer design to enable successful directed sequencing.
A signaling pathway coupled to T cell receptor ligation by MMTV superantigen leading to transient activation and programmed cell death

Abstract Stimulation of T cells by retroviral and bacterial superantigens is followed by specific T cell elimination, in contrast with stimulation of T cells by peptide, which is usually associated with clonal expansion. We show here that this differential response phenotype is apparent at the level of Individual T cell clones following TCR ligation with peptide or MTV antigen. We exploited selective coupling of apoptosis to TCR ligation by MTV7 to examine some of the intracellular biochemical events that underlie this response. MTV-dependent activation resulting in apoptosis was associated with activation of phosphollpase A, and the generation of reactive oxygen Intermediates. Inhibition of these biochemical events prevented both MTV-dependent activation and apoptosis without affecting the peptide-dependent response of the same T cell clones. These results Indicate that clonal expansion or programmed cell death following TCR ligation may be consequences of distinct TCR-coupled signaling pathways.
Educating the Women of Hainan: The Career of Margaret Moninger in China, 1915-1942

For Margaret Moninger - a brilliant, fun-loving, and dedicated young woman from Iowa - a career as a missionary in China promised adventure and the chance for responsibility and authority denied most American women of her time. In 1915 she went as a Presbyterian missionary to Hainan Island, China's southernmost territory, where she remained until repatriated in 1942. Kathleen Lodwick's biography, the first devoted to a single woman missionary, is based primarily on the long, newsy letters Moninger wrote her family every Sunday of her missionary years, and on those of a fellow missionary. It will be of interest to scholars in Asian Studies, religious studies, and anthropology.
Made in Heaven: Secondary Data Analysis and Interdisciplinary Collaborators.

Secondary data analysis and interdisciplinary collaboration have a great deal to offer developmentalists. The research traditions of economists and quantitative sociologists have produced large scale longitudinal studies using national samples, useful statistical techniques for approximating experimental conditions and interesting theoretical insights
Constitutive models of creep for lead-free solders

The constitutive modeling of creep has been extensively studied due to the important of the creep failure mode in solder joints. However, there are very few studies that considered room temperature aging contributions in their creep modeling studies. This study investigated constitutive modeling of creep of solders by taking into account the possible contribution room temperature aging. Lead-free solder (Sn–4.0Ag–0.5Cu) was found to have a higher creep resistance than Sn–Pb solder at the same stress level and testing temperature. The higher creep resistance was contributed by the second phase intermetallic compounds, Ag3Sn and Cu6Sn5. The precipitation of these intermetallic compounds can significantly block the movement of dislocations and increase the creep resistance of the material. Constitutive models of creep for both lead-free and Sn–Pb eutectic solders were constructed based on the experimental data. The activation energy for SAC405 is much higher than that of Sn–Pb, which also indicates that SAC405 possesses higher creep resistance. The constitutive models can be used in finite element analysis of actual electronic packages to predict solder joint failure. The creep mechanisms of both lead-free and Sn–Pb eutectic solders were also extensively discussed in this dissertation. Dislocation gliding and climb is believed to be the major failure mode at high stresses, while lattice diffusion and grain boundary diffusion is believed to be the major failure mode at low stress levels. Grain boundary sliding is believed to contribute to creep deformation at both high-stresses and low-stresses. For eutectic Sn–Pb, superplastic deformation is a major the creep mechanism at low-stresses and high-temperatures.
Regulation of cholesterol balance through control of half-life of the sterol nucleus.

Abstract Maintenance of cholesterol balance under many conditions affecting rate of synthesis implies that control of cholesterol metabolism is related to turnover rate, rather than biosynthesis only. In this study, cholesterol biosynthesis was manipulated by drugs and rate of incorporation of acetate and rate of excretion of 4- 14 C-sterol nucleus were measured. Rats were given a bile acid binding polymer (cholestyramine) in the diet, an inhibitor of cholesterol biosynthesis (triiodothyropropionic acid), or both for varying lengths of time. Results indicate that cholesterol balance is maintained under the conditions studied. It appears that extrahepatic processes contribute substantially to maintenance of cholesterol balance.
The impact of relative tenure on newcomer socialization dynamics

Although many researchers have examined the impact of organizational tenure on newcomer socialization dynamics, few have explored whether relative tenure influences perceptions and behaviors inside organizations. This study introduces the concept of relative tenure and shows through a sociometric survey of 200 employees across four organizations that an individual's relative position in his or her firm's tenure distribution explains a significantly greater percentage of variance in newcomer status, social network position, and information-providing behavior than does absolute measures of tenure. The results suggest that organizational growth and turnover may have a bigger impact on newcomer socialization dynamics than has been discussed in the literature. The implications of the findings for socialization researchers and managers are discussed. Copyright © 2004 John Wiley & Sons, Ltd.
Orientation dependent elastic interaction between a truncated stacking fault tetrahedron and a glissile dislocation

Abstract The orientation dependence of elastic interaction between a stacking fault tetrahedron (SFT) and mobile dislocations is investigated for the possibility of unfaulting and subsequent absorption of the SFT. The obtained result indicates that 60° dislocations have stronger interaction with the spontaneously truncated SFT than pure screws or edges. Due to the high activation energy, the collapse and absorption of the SFTs seems to be limited to the cases where the approaching dislocations along 〈1 1 0〉 directly cut the SFTs symmetrically. The anisotropic energetics can contribute to the spatially limited growth of defect-cleared channels observed in the irradiated materials.
Enhanced Intellectual Property Protection for Digital Circuits on Programmable Hardware

The use of digital marks to provide ownership (watermarking) and recipient (fingerprinting) identification for intellectual property (IP) has become widespread. However, many of these techniques require a high complexity of copy detection, are vulnerable to mark removal after revelation for ownership verification, and are susceptible to reduced mark integrity due to partial mark removal. This paper presents a method for both watermarking and fingerprinting intellectual property, in the form of designs implemented on field programmable gate arrays (FPGAs), that achieves robustness by responding to these three weaknesses. The key techniques involve using secure hash functions to generate and embed multiple small marks that are more detectable, verifiable, and secure than existing FPGA IP protection techniques.
Lincoln, Race, and the Spirit of ’76

Abstract This essay examines how Lincoln dealt with race, slavery, and emancipation in antebellum America. It argues that despite a few controversial statements and policies regarding black Americans, Lincoln sought to preserve the American union and its system of self-government by reclaiming the ideals of the Declaration of Independence. Unlike U.S. Senator Stephen A. Douglas, who exploited white bigotry in his promotion of local “popular sovereignty” as a solution to the slavery controversy, Lincoln highlighted the natural rights of blacks as a way to prevent the spread of slavery and thereby save what he would later call “the last best hope of earth.”
Conceptual challenges and practical approaches to screening capacity for self-care and protection in vulnerable older adults

Identifying impairments in the capacity to make and execute decisions is critical to the assessment and remediation of elder self-neglect. Few capacity assessment tools are available for use outside of healthcare settings, and none have been validated in the context of elder self-neglect. Health and social services professionals are in need of validated tools to assess capacity for self-care and self-protection (SC&P) during initial evaluations of older adults with suspected self-neglect syndrome. Currently, legal and medical declarations of incapacity and guardianship rely on clinical evaluations and instruments developed to assess only decision-making capacity. This article first describes the conceptual and methodological challenges to assessing the capacity to make and execute decisions regarding safe and independent living. Second, the article describes the pragmatic obstacles to developing a screening tool for the capacity for SC&P. Finally, the article outlines the process for validation and field testing of the screening tool. Social services professionals can then use a valid and feasible screening tool during field assessments to screen for potential impairments in the capacity for SC&P in vulnerable older adults.
Emerging authenticity: the crafting of simulated parent–teacher candidate conferences

Schools of education struggle to provide future teachers with opportunities to engage in and practice parent–teacher conferences. This manuscript addresses the diffusion of a signature pedagogy from medical education to teacher education, specifically highlighting the design and implementation considerations surrounding simulated parent–teacher conferences. Focus group data center on the training of individuals to portray parents authentically during these simulated parent–teacher conferences. Pre‐service teachers’ interview data reflect on the authenticity of this new approach to novice teacher preparation. Implications center on the connections between medical and teacher education contexts and the further diffusion of this pedagogy to prepare future school leaders for complex social interactions with parents.
Appropriate pCO2 treatments in ocean acidification experiments

Experiments in which organisms are reared in treatments simulating current and future pCO2 concentrations are critical for ocean acidification (OA) research. The majority of OA exposure experiments use average atmospheric pCO2 levels as a baseline treatment. We conducted an ecoregion-scale analysis of global carbon chemistry datasets. For many locales, atmospheric pCO2 levels are not an appropriate characterization of marine carbon chemistry. We argue that atmospheric pCO2 should be disregarded when setting baseline treatment conditions and experimental design should rely on measurements of carbon chemistry in a study subject’s habitat. As carbon chemistry conditions vary with space and time, we suggest using a range of pCO2 values as a control rather than a single value. We illustrate this issue with data on the habitat of Euphausia pacifica, which currently lives in waters with a pCO2 around 900 μatm, a concentration much higher than the current global atmospheric mean.
Textractor: a hybrid system for medications and reason for their prescription extraction from clinical text documents.

Objective To describe a new medication information extraction systemdTextractorddeveloped for the ‘i2b2 medication extraction challenge’. The development, functionalities, and official evaluation of the system are detailed. Design Textractor is based on the Apache Unstructured Information Management Architecture (UMIA) framework, and uses methods that are a hybrid between machine learning and pattern matching. Two modules in the system are based on machine learning algorithms, while other modules use regular expressions, rules, and dictionaries, and one module embeds MetaMap Transfer. Measurements The official evaluation was based on a reference standard of 251 discharge summaries annotated by all teams participating in the challenge. The metrics used were recall, precision, and the F1-measure. They were calculated with exact and inexact matches, and were averaged at the level of systems and documents. Results The reference metric for this challenge, the system-level overall F1-measure, reached about 77% for exact matches, with a recall of 72% and a precision of 83%. Performance was the best with route information (F1-measure about 86%), and was good for dosage and frequency information, with F1-measures of about 82e85%. Results were not as good for durations, with F1-measures of 36e39%, and for reasons, with F1-measures of 24e27%. Conclusion The official evaluation of Textractor for the i2b2 medication extraction challenge demonstrated satisfactory performance. This system was among the 10 best performing systems in this challenge.
Positional envelope as a response parameter in caloric testing.

Bithermal caloric testing was carried out in 57 normal subjects and 374 patients presenting with subjective complaints of vertigo over a 4-year period from December 1984 to December 1988. Responses were quantitatively assessed using a DEC PDP 11/73 laboratory minicomputer. Patients were classified as normal and abnormal according to caloric responses based on standard methods of calculating unilateral hypoexcitability and directional preponderance using the maximum slow component velocity. Results obtained from the slow component velocity for unilateral hypoexcitability and directional preponderance were compared to the same values obtained from the overall positional envelope calculated by an integration of the slow component velocity vs. time curve. Although duration of nystagmus varies extensively in normal subjects and has not proven clinically useful in identifying abnormalities, the integral of response amplitude over time gives a more complete description of the vestibular response. However, when c...
Agrin is required for posterior development and motor axon outgrowth and branching in embryonic zebrafish

Although recent studies have extended our understanding of agrin's function during development, its function in the central nervous system (CNS) is not clearly understood. To address this question, zebrafish agrin was identified and characterized. Zebrafish agrin is expressed in the developing CNS and in nonneural structures such as somites and notochord. In agrin morphant embryos, acetylcholine receptor (AChR) cluster number and size on muscle fibers at the choice point were unaffected, whereas AChR clusters on muscle fibers in the dorsal and ventral regions of the myotome were reduced or absent. Defects in the axon outgrowth by primary motor neurons, subpopulations of branchiomotor neurons, and Rohon-Beard sensory neurons were also observed, which included truncation of axons and increased branching of motor axons. Moreover, agrin morphants exhibit significantly inhibited tail development in a dose-dependent manner, as well as defects in the formation of the midbrain-hindbrain boundary and reduced size of eyes and otic vesicles. Together these results show that agrin plays an important role in both peripheral and CNS development and also modulates posterior development in zebrafish.
Deconstructing civil wars: Beyond the new wars debate

The identification of intra-national armed conflict as a leading problem for the international community in the 1990s produced a wave of novel research into civil wars. Though these new civil war studies soon began to claim a degree of consensus on several key questions, the very concept and ontology of civil war has been implicitly and explicitly contested. An examination of the politics of naming civil wars likewise reveals the extent to which varying and sometimes conflicting definitions of civil war are still in circulation among various observer types. Instead of adjudicating these disputed definitions of civil war, this article details the way in which particular conceptions of civil war produce their object of analysis. The recent Algerian conflict stands as an excellent case study in the politics of naming civil wars and the ways in which the conceptual frameworks of the new civil war studies make Algeria into a civil war. To go beyond the contested definition of civil war, the new civil war studi...
THE GEOMETRY OF PLANT EPIDERMAL CELLS

SUMMARY Six monolayer tissues from various plants were studied for the number of anticlinal walls of non-marginal, unspecialized cells. One class of tissues, including the abaxial epidermis of the scale of Allium cepa, the adaxial epidermis of the leaf of Euonymus fortunei var. vegetus, gametophytic cells of Dryopteris filix-mas, and the surface cells of the bud of Anacharis demo, is characterized by (a) a probability distribution curve with a peak at six walls having a frequency of around 0.40, and (b) tissue growth in two directions. A second class of tissues has the distribution peak of six walls at an approximate frequency of 0.58 and is formed by growth in either one dimension or with regular alternation in two directions, as in the leaf of Anacharis densa and for the colony of Volvox aureus. Models for both classes of tissues were constructed in order to identify those features associated with tissue proliferation that contribute to the variability of cell geometry. Geometric models give a pictorial representation of cell arrangement and are useful in ascertaining cell division patterns whereas algebraic models aid in clarifying spatial relationships between cells. The distinction between packing types and developmental types of models is discussed in the light of the concept of form in plant morphology.
The Effects of d0 on Rupture Propagation on Fault Stepovers

Abstract According to the slip‐weakening friction law (Andrews, 1976a), fault friction drops from a static value to a sliding value over some slip‐weakening distance ( d 0 ). Laboratory studies of fault friction confirm this weakening, but do not settle on a single value for d 0 . However, this parameter is a critical input in dynamic earthquake models, as it affects rupture nucleation and propagation. We use the 2D finite‐element method to test how the specific value of d 0 affects rupture behavior. We consider the ability of rupture to jump from segment to segment of a disconnected stepover, or to propagate through the double bends of a connected stepover, as a way to gauge rupture energy and behavior. We find the stepover width or bend angle through which rupture can propagate is affected by the choice of d 0 , but it is not a linear relationship. This is true regardless of whether the stepover is connected or disconnected, compressional or extensional, or whether the initial rupture velocity is supershear or subshear. We do find, however, that scaling the intensity of the regional stress field up or down does linearly correspond to scaling d 0 down or up. We interpret the nonlinearity of the d 0 scaling results to be related to the area of the secondary fault that intersects the lobe of failure‐level Coulomb stress change induced by rupture of the first fault segment because (1) the d 0 ‐controlled critical patch size for renucleation must be exceeded on the second segment and (2) the area of this overlap also does not change linearly with distance from the first fault.
Management of pelvic lymphoceles following robot-assisted laparoscopic radical prostatectomy

Pelvic lymphocele is a potential complication of radical prostatectomy. Although lymphoceles often regress spontaneously, many may progress, precipitate clinical symptoms, and ultimately require intervention. To date, the best treatment of pelvic lymphoceles has not yet been fully defined. However, laparoscopic marsupialization is a definitive and efficacious surgical alternative to percutaneous drainage. It is effective, results in minimal patient morbidity, and allows for rapid recovery. We report our experience with management of clinically symptomatic pelvic lymphoceles following robotic-assisted prostatectomy using laparoscopic marsupialization.
Aerodynamic aspects of helicopter blade-vortex interaction; the interaction with vortex streets considering the icing effect

Numerical investigations of helicopter blade-vortex mechanism of interaction are performed using large eddy simulation (LES). The simulations were performed for a Reynolds number, Re = 1.3 x 10 6 , based on the chord, c, of the airfoil (NACA0012). Computations are carried out for two different types of blade-vortex interactions, concerning single and respectively two vortices blade interaction. It was observed that for single vortex-blade interaction, the blade-vortex interaction becomes less significant with the increase of vertical miss distance. Larger amplitudes of aerodynamic coefficients were observed for the case of two vortices-blade interaction when compared with the single vortex blade interactions.
RNA Binding Proteins and the Genesis of Neurodegenerative Diseases

Recent advances in neurodegenerative diseases point to novel mechanisms of protein aggregation that revolve around the unique biology of RNA binding proteins. RNA binding proteins normally are present in the nucleus. Under conditions of cell stress these RNA binding proteins translocate to the cytoplasm where they form stress granules, which function in part to sequester specialized transcript and promote translation of protective proteins. Studies in humans show that pathological aggregates occurring in ALS, Alzheimer’s disease, and other dementias co-localize with stress granules. One increasingly appealing hypothesis is that mutations in RNA binding proteins or prolonged periods of stress cause formation of very stable, pathological stress granules. The consolidation of RNA binding proteins away from the nucleus and neuronal arbors into pathological stress granules might impair the normal physiological activities of these RNA binding proteins causing the neurodegeneration associated with these diseases. Conversely, therapeutic strategies focusing on reducing formation of pathological stress granules might be neuroprotective.
Using Surveillance to Evaluate Influenza Vaccine Effectiveness

Influenza vaccine is unique in that it is reformulated annually to include the viral strains predicted to be the most likely to circulate during the coming influenza season. During years when the predominant circulating strain is antigenically dissimilar from the corresponding vaccine strain, the effectiveness of trivalent inactivated influenza vaccine (TIV) may be diminished, but this variation is unpredictable, and during those years the benefit derived from TIV is difficult to estimate
Postweaning nutritional programming of ovarian development in beef heifers.

Peripubertal caloric restriction increases primordial follicle numbers at breeding, which may improve reproductive potential. Our hypothesis was that feed restriction was changing primordial follicle number through stimulation of follicle formation via leptin, roundabout axon guidance receptor, homolog 4 (), or or through inhibition of follicle activation via anti-Mullerian hormone (). Heifers ( = 30) were fed a ration consisting of 30% alfalfa hay, 69.8% corn silage, and 0.2% salt as DM. Heifers received the control diet for 42 d before an initial 6 heifers were ovariectomized at 8 mo of age. The remaining 24 heifers were divided into 2 treatment groups. Controls were offered 97.9 g DM/kg BW over the entire feeding period. Stair-step heifers received 67.4 g DM/kg BW for 84 d. Following the 84-d restriction, heifers were stepped up to receive 118.9 g DM/kg BW over a 15-d period and were held at this feeding level 68 d. At the end of the feed restriction (11 mo of age), ovaries were collected from 6 heifers per treatment, and at the end of the refeeding period (13 mo of age), ovaries were collected from 6 heifers per treatment. Plasma leptin concentrations were greater in control heifers than in stair-step heifers at 11 mo of age ( 0.10). In conclusion, developing heifers on a stair-step compensatory growth scheme resulted in larger ovarian reserve before the onset of breeding, which may have beneficial effects on increasing reproductive lifespan.
Bone marrow transplantation with major ABO blood group incompatibility using erythrocyte depletion of marrow prior to infusion

Twenty-five patients with major ABO blood group incompatibility between donor and recipient underwent allogeneic bone marrow transplantation using erythrocyte depletion of the bone marrow infusate prior to administration. Over 95% of the original erythrocyte content of the marrows was removed, while retaining 75% of the mononuclear cell content and 57% of the granulocyte-monocyte colony-forming units. Recipients, well hydrated and premedicated with corticosteroids, diphenhydramine, and mannitol, tolerated infusions well. The frequency of engraftment, rate of recovery of peripheral blood leukocytes, granulocytes, and platelets, and the incidence of graft-versus-host disease was similar to that observed following ABO blood group compatible bone marrow transplantation. Erythroid development following ABO blood group incompatible transplantation was significantly impaired until hemagglutinins fell to 1:4 or lower, at which time recovery of erythrocytes was detected in the peripheral blood. The erythrocyte hypoplasia associated with incompatible hemagglutinins was temporary. Erythrocyte purging is a safe and effective technique to perform bone marrow transplantation across major ABO blood group incompatibilities.
Effects of structured controversy on students' perceptions of their skills in discussing controversial issues.

The teaching strategy that educators use when addressing controversial issues can help students develop the skills they need to deal effectively with controversial issues. Structured controversy is designed to allow students to practice these skills. This study measured the change in students' perceptions of their skills in perspective-taking, logical arguing, and reaching consensus after using structured controversy on two controversial issues. Results of two-factor analyses of variance and comparison of means indicate significant positive changes in 51 senior nursing students' perceptions of their skills in perspective-taking (less than .001), logical arguing (less than .01), and reaching consensus (less than .01). These results are consistent with findings of previous research studies on the effectiveness of structured controversy.
Electronically regulated thermally and light-gated electron transfer from anions to naphthalenediimides.

Anion-induced electron transfer (ET) to π-electron-deficient naphthalenediimides (NDIs) can be channeled through two distinct pathways by adjusting the Lewis basicity of the anion and the π-acidity...
Deposition of Dielectric Thin Films by Irradiation of Condensed Reactant Mixtures

Results of ongoing investigations of a new method for processing molecular solids to form refractory thin films are presented. We have extended past work on boron nitride and alumina growth from molecular solids induced by synchrotron radiation (SR), to silica growth from tetramethylsilane and water at 80 K. Also reported are experiments where alumina is formed using 4.64 eV laser irradiation. The majority of the results suggest that with SR, the film growth is induced by secondary electrons from the substrate, whereas laser light excites the film growth by direct photolysis. Implications of this will be discussed.
Conflicting Consensus: Public Reaction to a Domestic Violence Pro-Arrest Policy

Limited research exists on the extent to which the public supports the criminalization of domestic violence, and whether people believe police pro-arrest policies will deter future offending. Based...
Label-free Molecular Binding Assays using Holographic Video Microscopy

Inline holographic video microscopy’s resolution for single particle characterization is fine enough to detect avidin coating on biotinylated colloidal surfaces, without requiring staining or fluorescent labeling.