cssi/SciSciGPT-SciSciNet huggingface dataset:
Covert Communication with a Purely Random Spreading Function

This paper describes a method of communicating with a low probability of intercept by using a purely random spreading function. Binary message modulation is achieved by introducing appropriate delays and the message is recovered with a correlation operation. The performance of both binary and M-ary systems is analyzed and the bit error probability obtained as function of the system bandwidth and the receiver input signal-to-noise ratio. The analysis reveals that with adequate bandwidth it is possible to achieve acceptable bit error probabilities with receiver input signal-to-noise ratios on the order of ?30 to ?40 dB.
LOOKING AHEAD TO MORE SOCIO POLITICALLY-ORIENTED CASE STUDY RESEARCH IN L2 WRITING SCHOLARSHIP (BUT SHOULD IT BE CALLED POST-PROCESS?

Abstract In this essay I argue that three familiar areas of inquiry in future L2 writing research need to be investigated in more sociopolitically-oriented ways: written products, writing processes, and writer identity, and that qualitative case studies are well suited to explore the extraordinary diversity of L2 writers and writing contexts from an expanded sociopolitical perspective. However, although substantive changes in how we think about these areas of inquiry appear to be taking place, some resistance to these changes can be expected. Finally, I suggest caution in using the label “post-process” to describe the substantive changes in how we are beginning to view L2 writing scholarship.
Sexual-Minority, Gender-Nonconforming, and Transgender Youths

This chapter provides an overview of the key developmental and adjustment issues faced by sexual-minority youths (i.e., those with same-sex attractions, fantasies, or behaviors), gender nonconforming youths (i.e., those whose appearance, behavior, or interests violate traditional norms for masculinity or femininity), and transgender youths (i.e., those who adopt a gender identity that does not rigidly conform to their biological sex). Although these two populations are distinct from one another, they are considered together because of what they have in common: a set of complex psychosocial challenges deriving from the fact that their very existence challenges many of our culture’s most deeply held beliefs about “normal” sexual and gender development. The chapter reviews aspects of their experiences that are most relevant for efforts to promote their positive development, devoting particular attention to the mental health implications of youths’ exposure to stigma and social marginalization. The diversity of sexual-minority populations is emphasized, especially with respect to the prevalence of nonexclusive rather than exclusive same-sex attractions. The unique experiences and needs of youths whose gender presentation deviates from traditional norms are reviewed; this population includes youths who display mild to moderate forms of gender nonconformity, as well as those who identify as transgender. Throughout the chapter, the goal is to replace stereotyped portrayals of “youth at risk” with more accurate and nuanced scientific information that will be of greater use to those seeking to foster positive development in these populations.
Disease and Death in the Ancient City of Rome

This paper surveys textual and physical evidence of disease and mortality in the city of Rome in the late republican and imperial periods. It emphasizes the significance of seasonal mortality data and the weaknesses of age at death records and paleodemographic analysis, considers the complex role of environmental features and public infrastructure, and highlights the very considerable promise of scientific study of skeletal evidence of stress and disease.
Unusual cause of neck pain

A 69-year-old man with hyperlipidaemia presented to the emergency department with a 4-day history of new onset pain in the neck. The pain was severe (rated 9/10 in severity), constant, localised to the base of the skull and was associated with significant restriction of neck motion; any movements resulted in dramatic worsening of the pain. He also reported subjective fevers at home. He did not report trauma, photophobia, phonophobia, nausea, vomiting, insect bites, visual disturbances, trouble swallowing or speaking, jaw claudication or morning stiffness. There were no sick contacts. He did not have pain at any other sites. He had tried some topical diclofenac gel for the past 2 days without much relief. His only scheduled medication was atorvastatin. On physical examination, his temperature was 38.1°C, blood pressure was 128/82 mm Hg, heart rate was 82/min and respiratory rate was …
Experiments, Small Molecules, Unpaired Electrons

In this session there was representation from three different groups making contributions to our understanding of Van der Waals interactions in open shell systems. First, Benoit Soep discussed metal atom bimolecular cluster spectroscopy in Hg and Ca atom studies. The clusters are probed via LIF excitation of the complex using the bare metal atom electronic transition as the chromophore. Intermolecular energy transfer or chemical reaction in the complexes is then probed by total fluorescence and/or state resolved detection of products. The intermolecular potentials for these open shell systems, particularly between open shell atom+atom.and atom+diatom systems, can be directly probed by crossed beam scattering methods. Results from this experimental approach were presented by Piergorgio Cassevechia for a number of systems such as open shell halogen atoms, O(3P), and NO. A third perspective on recent developments in this field was provided by Marsha Lester with work in her group on complexes of OH radical with Ar atoms. These studies elucidate the dynamics of vibrational predissociation in the weakly bound, Ar + 2Π OH, ground and the relatively strongly bound, Ar + 2Σ OH, electronically excited state observed via laser induced florescence. A full description of these talks is provided in the following chapters. However, in the interest of providing as complete as possible an overview of the field, a short summary of the questions and answers that arose during the discussion periods between the talks is reproduced below.
Th3 BuilD: Immersive Learning Technology

BRIEF SESSION DESCRIPTION: At George Mason University, immersive learning is part of the fun at Th3 BuilD! Embrace your inner nerd and join Instructional Technologists Jim McLean and Michelle Verneman for a hands-on encounter with some of Masonâs resident 3D technology tools. Get inspired to pump up your pedagogy by discovering new ways to create immersive learning experiences with virtual reality, augmented reality, 360 video, and more! Participants will be able to experience immersive technologies and list several possible educational and research applications for their discipline. ____________________________________________________________ FULL ABSTRACT: We will provide brief overview presentation (20 min) of several immersive technologies currently available to students and faculty for experimentation and course support at the collaborative learning hub's 3d learning space, Th3 BuilD . topics discussed will cover Virtual Reality (non- and semi immersive vs. full immersion), Augmented Reality, 360Â° Video capture, and digital capture (photogrammetry) with 3d Printing. For the remainder of the workshop attendees will interact with the technologies via 5 immersive hands on stations: Non-Immerssive VR (Leap Motion), VR & 360Â° content (VR Headsets with various applications), AR (Blippar and Aurasma), 360Â° cameras (with a 360 livestream of the workshop), and a Makerbot FDM 3d Printer and ReCap Photo workflow in process. 2 Instructional technologist will be on hand to answer specific questions and describe how the technologies can be used across disciplines. Participants will be able to experience immersive technologies and list several possible educational and research applications for their discipline.
Development and characterization of graphene oxide based electronics and actuators

Emerging interests in hardware security as well as environmental concerns have given rise to the field of transient or temporary electronics, which can be decommissioned by an external stimulus with minimal impact to the surrounding environment. In this study, an all graphene based film is produced by a one-step deposition process. The conversion of graphene oxide (GO) to reduced graphene oxide (rGO) depends on an interfacial reduction reaction. Control of processing conditions such as the underlying substrate, pH of GO and the film drying environment results in an ability to tailor the internal architecture of the films and their electronic properties. Furthermore, the ability to create masks for selective reduction of GO during deposition was also demonstrated, which was used to create intricate yet well-defined patterns and connections required in electronic circuits and devices. All graphene based freestanding films with selectively reduced GO were used in transient electronics application as circuitry and RFID tag patterns. Furthermore, the reversible and controllable hygromorphic actuation ability of GO films is demonstrated along with application in humidity sensing.
Effects of hearing loss and amplification device on infants’ perception of infant-directed speech

Caregivers typically speak to their infants in a speech register known as motherese or infant-directed speech (IDS; Fernald and Simon, 1984; Snow, 1977). Infants also prefer to listen to IDS over adult-directed speech (ADS) (Cooper and Aslin, 1990; Fernald, 1985; Singh et al.). Moreover, mothers adjust their IDS to factors such as infant age (e.g., Kitamura and Burnham, 2003; Newman and Hussain, 2006). Another factor that could potentially affect mother-infant interactions is infant hearing loss. Studies have shown that mothers adjust their speech based on infants’ hearing experience (e.g., Bergeson et al., 2006; Kondaurova and Bergeson, 2011; Wieland et al., 2015). Do infants with hearing loss pay attention to IDS? Two recent studies suggest that infants who use hearing aids or cochlear implants demonstrate increased attention to IDS over both ADS and silent trials (Wanget al., 2017; 2018). One feature that might regulate infant attention, namely target word repetition, is correlated with vocabulary skil...
Diagnostic and Prognostic Role of Fecal Calprotectin As a Biomarker for Gastrointestinal Graft Versus Host Disease: A Systematic Review of Literature

Abstract Introduction: Graft versus host disease (GVHD) is the most significant complication after allogeneic hematopoietic stem cell transplantation (HSCT) and a leading cause of morbidity and mortality. The incidence of acute gastrointestinal graft versus host disease (GI-GVHD) in HSCT patients is reported between 40% to 50%. Fecal calprotectin (FC) has an established role as a diagnostic modality and a biomarker of disease activity in patients with inflammatory bowel disease (IBD). It has been suggested that FC may also play an important role in diagnosing and assessing the severity of GVHD and in determining resistance and response to corticosteroid treatment. Methods: To study the diagnostic and prognostic role of FC in GVHD patients, we performed a systematic review, 19 articles published after 2004 were selected from following four databases (PubMed, Embase, Cochrane Library and Web of Science). Numeric data were summarized using means, medians, and ranges. Categorical data were summarized using absolute values and percentages. Results: A total of 494 patients were included. Two hundred fifty two patients (51%) developed acute GVHD. Hundred seventy nine patients (71%) had GI-GVHD and 73 patients (29%) had non GI-GVHD. In one of the cohorts (n=21), median FC (mFC) levels were 198.9 mg/kg [range(r) =58.4-500] in patients with GVHD versus 32.2 mg/kg (r=15.6-89) in patients without GVHD (p=0.0005). In a similar cohort (n=23), mFC levels were 504 mg/kg in patients with GVHD and 107.4 mg/kg in patients without GVHD (p= Conclusions: Our analysis demonstrates that FC levels are higher in patients with GI-GVHD. Furthermore, a linear correlation is present between FC levels and severity of GVHD. FC levels are higher in patients with steroid-resistant GVHD and can be useful to determine treatment response. Data on FC levels in these patients seem promising and future randomized prospective trials are needed. Disclosures No relevant conflicts of interest to declare.
Calibration of a common shortwave multispectral camera system for quantitative agricultural applications

Unmanned aerial systems (UAS) for collecting multispectral imagery of agricultural fields are becoming more affordable and accessible. However, there is need to validate calibration of sensors on these systems when using them for quantitative analyses such as evapotranspiration, and other modeling for agricultural applications. The results of laboratory testing of a MicaSense (Seattle, WA, USA) RedEdge™ 3 multispectral camera and MicaSense Downwelling Light Sensor (irradiance sensor) system using a calibrated integrating sphere were presented. Responses of the camera and irradiance sensor were linear over many light levels and became non-linear at light levels below expected real-world, field conditions. Simple linear corrections should suffice for most light conditions encountered during the growing season. Using an irradiance sensor or similar system may not properly account for light variability in cloudy or partly cloudy conditions as also identified by others. A simple stand for aiding in reference panel imaging was also described, which may facilitate repetitive, consistent reference panel imaging.
Experiences and Needs of African American Children and Adolescents in Supportive Care Roles for a Relative With Breast Cancer.

Purpose To explore the experiences and needs of African American (AA) children and adolescents who were identified by a cancer survivor in their family as providing substantial supportive care during diagnosis and treatment. Participants & setting 5 AA young adults who provided care and support to a family member with cancer when they were aged 7-19 years and 4 cancer survivors from a northeastern U.S. city. Methodologic approach Focus groups and interviews were conducted, recorded, transcribed, and analyzed using content analysis until thematic saturation was reached. Findings Themes focused on AA young supporters' lack of cancer-related information, reduced ability to communicate needs, and challenged views of themselves, relationships, faith, and the future at the time that they provided support. Implications for nursing Nurses can support AA children and adolescents in caregiving roles by assessing their needs and providing information on diagnosis and treatment. In addition, nurses can conduct research on culturally adapted interventions that can better support AA children and adolescents caring for a parent or grandparent with cancer.
Onomastic strategies: A pragmatic approach to the use of personal names among the kabye of northern togo

In this article I propose to analyze three verbal strategies underlying the use of personal names by the Kabye of northern Togo. Such strategies fulfill a variety of purposes, including attempts to influence the behavior of a name-bearer in the context of interpersonal or social relationships. They are often implemented with the intent to help name-bearers live up to their name. Among these strategies I examine (1) the choice of a name, (2) its intonation and (3) its amplification. All three strategies fall within the scope of the socio-pragmatic approach to naming (the giving of names as well as their use) defined here as essentially an act of interpellation.
Optimal Control applied to a SEIR model of 2019-nCoV with social distancing

Abstract Does the implementation of social distancing measures have merit in controlling the spread of the novel coronavirus? In this study, we develop a mathematical model to explore the effects of social distancing on new disease infections. Mathematical analyses of our model indicate that successful eradication of the disease is strongly dependent on the chosen preventive measure. Numerical computations of the model solution demonstrate that the ability to flatten the curve becomes easier as social distancing is strictly enforced. Based on our model, we also formulate an optimal control problem and solve it using Pontryagin’s Maximum Principle and an efficient numerical iterative method. Our numerical results of an optimal 2019-nCoV treatment protocol that yields a minimum disease burden from this disease indicates that social distancing is vitally important.
Attenuation of Submillimeter Radiation by Clouds and Rain

The scattering and extinction properties of cloud and rain elements for far-infrared and submillimeter radiation have been estimated on the basis of recently determined optical constants, by means of polydisperse Mie scattering theory and realistic drop-size distributions.
Symbolic Abstractions From Data: A PAC Learning Approach.

Symbolic control techniques aim to satisfy complex logic specifications. A critical step in these techniques is the construction of a symbolic (discrete) abstraction, a finite-state system whose behaviour mimics that of a given continuous-state system. The methods used to compute symbolic abstractions, however, require knowledge of an accurate closed-form model. To generalize them to systems with unknown dynamics, we present a new data-driven approach that does not require closed-form dynamics, instead relying only the ability to evaluate successors of each state under given inputs. To provide guarantees for the learned abstraction, we use the Probably Approximately Correct (PAC) statistical framework. We first introduce a PAC-style behavioural relationship and an appropriate refinement procedure. We then show how the symbolic abstraction can be constructed to satisfy this new behavioural relationship. Moreover, we provide PAC bounds that dictate the number of data required to guarantee a prescribed level of accuracy and confidence. Finally, we present an illustrative example.
Hunting and Gathering on the Legal Information Savannah

Research in massive online legal research platforms requires entering a multi-faceted construct, where user-interface design and an array of algorithms guide the experience. What is it like for novice researchers to research real-world legal problems and attempt to come to a legal conclusion in these four platforms: Bloomberg Law, Fastcase, Lexis Advance, and Westlaw? Researchers struggled where they could not find relevant secondary sources. Researchers did not improve their time to complete their research in the second, third, or fourth platform once they had resolved the issue in the first platform. The implications for teaching legal research seem clear: instruction on meta-strategies for entering a research universe are a critical component of what law students and young lawyers need to learn. And legal research platforms need to keep improving user guidance through their research universes.
Intensive preoperative ostomy education for the radical cystectomy patient.

Abstract Objectives Patients undergoing radical cystectomy with ileal conduit formation usually receive training on the use of their stoma during their initial hospitalization – while actively recovering from surgery – often with little follow-up or reinforcement. Many of these patients are not equipped to deal with these significant body changes, which can lead to additional clinic visits, stoma-related complications, and decreased patient satisfaction/health-related quality of life (HRQOL). In an effort to improve patient education, we sought to evaluate the feasibility of implementing a preoperative comprehensive stoma education session termed the “stoma bootcamp” for patients scheduled for a radical cystectomy and ileal conduit (RCIC). We tracked patient related outcomes to determine its impact. Methods We performed a longitudinal, quality-improvement feasibility study at the University of Kansas Health System. All patients who were scheduled to undergo a RCIC for bladder cancer were offered enrollment into the study at their preoperative clinic visit. The “stoma boot camp” consisted of a 3-hour group session within 2 weeks of the surgery date. Patients were given a short presentation by residents and advanced practice providers regarding the operation, recovery, and expectations for their post-operative care. Ostomy nurses then demonstrated basic urostomy care – pouching, sizing, emptying – along with trouble-shooting tips for common ostomy problems. Measurements of HRQOL questionnaires were completed at the initial visit, after “boot camp,” and at defined time points after surgery for 12 weeks. This included using an ostomy adjustment score. Length of stay, unplanned stoma-related interventions, and re-admissions within 30 days were also tracked. Results In this initial pilot program, 51 patients participated in the stoma bootcamp. The patients had an average ostomy adjustment score (OAS) of 150.4 (95% CI 142.0, 158.8) at discharge from the hospital, and these high OAS levels persisted throughout the 12 weeks of follow-up data without any significant decline. Short-form 36 (SF-36) scores demonstrated numerical improvements in each individual category at the 6-week mark above baseline. These improvements persisted at the 12-week mark. Conclusions In this study we were able to establish the feasibility of implementing a preoperative comprehensive stoma education session for patients scheduled for a RCIC. Additionally, we were able to document favorable HRQOL data and improved ostomy adjustment scores surrounding the education session.
The Unexpected Legacy

The last quarter of the twentieth century finds most of the world’s personal and public health services in disarray. The costs of medical care are widely thought to be exceeding the benefits; inequitable distribution abounds. Throughout the developed and developing worlds, many earlier triumphs of public health are forgotten. In comparison with “high-tech” clinical interventions, politicians, the practicing profession, and the public now accord public health a low priority.
Domestic Violence and the Black Church: Challenging Abuse One Soul at a Time

It was almost 5 years since they were married. Ryan was a church-going woman. She had been so ever since she was a child. Having grown up in the Black Church, she valued the importance of supporting her community, being a faithful wife and mother, and honoring her commitments. Accepting that the man is the spiritual leader of the home, she humbled herself to his direction and vision and attempted to support her husband—this black man who was highly regarded and well respected in the community. They had a beautiful home, a wonderful child, and belonged to numerous social and professional organizations. Fundamental to all of this was her belief in the word of God and her religious values. That was why she found herself confused and perplexed. How could God love me and let me go through so much pain? Didn’t “He” see the bruises, the blood, the torn skin or the scabs from previous abuse? Couldn’t “He” see the broken spirit, the phony smiles and make-up used to hide the residue of violence? She had prayed. She was anchored in the Word. She was saved. She didn’t wish bad things against her husband. She stayed the course, took the faith walk, and continued to support this man who said he loved her, yet was emotionally, physically, and psychologically abusive. So, where was God? Had “He” forgotten me? Doesn’t it matter that I’m one of the faithful? Or has God turned “His” back on me because my husband is the Chair of the Deacon’s Board?
Use of nutrient response techniques to assess the effectiveness of chlorination of rapid sand filter gravel

A direct viable counting method was used to rapidly assess the effectiveness of chlorination of biofilms on rapid sand filter gravel. A total of 50% of the cells were nutrient responsive after exposure to 0.5 mg of chlorine per liter, while this value was 25% after exposure to 25 mg of chlorine per liter. A large variation was seen in the numbers of nutrient-responsive cells on different rocks. More cells attached to the sandblasted side of marbles than to the smooth side, but there was no difference in eight of nine cases in the proportion of survival to chlorination between the two different sides. The effectiveness of chlorination appeared to be influenced by the species of bacterium in the biofilm.
Biodegradation and biotransformation of groundwater pollutant mixtures by mycobacterium vaccae

Mycobacterium vaccae can catabolize a number of major groundwater pollutants. When added singly, acetone, cyclohexane, styrene, benzene, ethylbenzene, propylbenzene, dioxane, and 1,2-dichloroethylene can be catabolized by M. vaccae. Catabolism of a number of these chemicals was monitored by gas-chromatographic analysis. Gas-chromatographic analysis indicated that the products of benzene degradation are phenol and hydroquinone. The products of chlorobenzene and ethylbenzene degradation are 4-chlorophenol and 4-ethylphenol. The extent that some compounds were catabolized when present as mixtures was also investigated. When toluene and benzene were present concomitantly, toluene was catabolized and benzene oxidation was delayed. Although toluene promoted the degradation of styrene, a lower rate of toluene degradation occurred when styrene was present. Both 4-chlorophenol and 4-ethylphenol had an antagonistic effect on the ability of M. vaccae to degrade other aromatic compounds. Studies with [14C]benzene indicated that M. vaccae can mineralize small amounts of this compound. These results suggest that components in mixtures may have a positive or a negative effect on the rates of biodegradation of other pollutants.
The development of the Drosophila larval body wall muscles.

Publisher Summary This chapter discusses the processes by which the two cell types that make a muscle in Drosophila—founder cells (FCs) and fusion competent myoblasts (FCMs)—are specified and describes how muscle identity is controlled by the expression of a group of transcriptional regulators termed “identity genes.” The way FCs fuse to surrounding FCMs to make a muscle of a specific size and the way a muscle grows and attaches to specialized tendon cells in the epidermis to form a muscle with the correct shape and orientation are also described. In addition, the way the muscle patterns are created and readied for their interaction with motoneurons from the central nervous system (CNS) is discussed in brief. The question regarding the specification of a muscle from a field of mesodermal cells is specifically addressed in the chapter, including a description of the cells' acquisition of their unique identity, growth of the muscle by cell–cell fusion, and the way the muscle attaches to specialized tendon cells within the epidermis. While some of these processes—such as cell–cell fusion—are unique to muscle development, many of the genes and mechanisms have parallel functions during CNS development.
Culturing American Life

Biologists and the Promise of American Life From Meriwether Lewis to Alfred Kinsey. Philip J. Pauly. Princeton University Press, Princeton, NJ, 2000. 329 pp. $29.95, £18.95. ISBN 0-691-04977-7. Examining the social history of biology in the United States, Pauly argues that scientists coupled their researches to their desires to improve plants, animals, and human life and thus build a nation of "prosperous, liberal, secular, and humane" people.
Pathogenesis of Intraventricular Hemorrhage

The article by Kenny et al ( Pediatrics 62:465, 1978) on the pathogenesis of intraventricular hemorrhage has prompted some thoughts regarding the role of rapid infusion of concentrated bicarbonate solutions and their relationship to neonatal intracranial hemorrhage. I should like to suggest that perhaps rather than the osmotic influences as has often been suggested, we may be dealing with the pharmacologic effect of excessive amounts of CO 2 transiently generated in the cerebral capillary bed by the reaction of these concentrated solutions with excessive free hydrogen ion.
Structure of neuroscience clerkships in medical schools and matching in neuromedicine

Objective: Due to the burden of neurologic disease, there is high demand for neurologists, child neurologists, and neurosurgeons. Only 2.6% of graduating medical students matched in neuromedicine residencies in 2014. This number will not likely meet the needs of the population or the projected shortfall. To compensate for this, the medical education system has an obligation to ensure competence in neuromedicine for all trainees and mentorship for students pursuing training in the field. We aim to evaluate the state of the neurology clerkship in US medical schools and how this impacts graduates entering the field. Methods: Publicly available curricula of 158 US medical schools were reviewed. Presence of a required neurology clerkship, its duration, and the year offered were tabulated, as were the availability of child neurology and neurosurgery electives and affiliated neuromedicine residencies. The total graduating students from each medical school matching into neuromedicine residencies for 2011–2014 were recorded. Repeated-measure analysis of variance was used to assess the relationship of these variables to number of students matching into the collective neuromedicine. Results: All but 4 schools (97%) published clerkship information. Neurology was a required clerkship at 56% of reporting institutions. Residency match data were not published from 53 schools (35%) and these were excluded from the analysis. In the remaining schools, all variables showed a relationship to students matching in neuromedicine residencies. Conclusions: The presence of a required neurology clerkship and opportunities for students to explore neuromedicine during medical school correlates with students matching into neuromedicine residencies.
Parallel Parsing Algorithms and VLSI Implementations for Syntactic Pattern Recognition

Earley's algorithm has been commonly used for the parsing of general context-free languages and the error-correcting parsing in syntactic pattern recognition. The time complexity for parsing is 0(n3). This paper presents a parallel Earley's recognition algorithm in terms of an ``X*'' operator. By restricting the input context-free grammar to be ?-free, the parallel algorithm can be executed on a triangular-shape VLSI array. This array system has an efficient way of moving data to the right place at the right time. Simulation results show that this system can recognize a string with length n in 2n + 1 system time. We also present a parallel parse-extraction algorithm, a complete parsing algorithm, and an error-correcting recognition algorithm. The parallel complete parsing algorithm has been simulated on a processor array which is similar to the triangular VLSI array. For an input string of length n the processor array will give the correct right-parse at system time 2n + 1 if the string is accepted. The error-correcting recognition algorithm has also been simulated on a triangular VLSI array. This array recognizes an erroneous string of length n in time 2n + 1 and gives the correct error count. These parallel algorithms are especially useful for syntactic pattern recognition.
Triplex Formation by Oligonucleotides Containing 5-(1-Propynyl)-2‘-deoxyuridine: Decreased Magnesium Dependence and Improved Intracellular Gene Targeting†

Oligonucleotides capable of sequence-specific triple helix formation have been proposed as DNA binding ligands useful for modulation of gene expression and for directed genome modification. However, the effectiveness of such triplex-forming oligonucleotides (TFOs) depends on their ability to bind to their target sites within cells, and this can be limited under physiologic conditions. In particular, triplex formation in the pyrimidine motif is favored by unphysiologically low pH and high magnesium concentrations. To address these limitations, a series of pyrimidine TFOs were tested for third-strand binding under a variety of conditions. Those containing 5-(1-propynyl)-2'-deoxyuridine (pdU) and 5-methyl-2'-deoxycytidine (5meC) showed superior binding characteristics at neutral pH and at low magnesium concentrations, as determined by gel mobility shift assays and thermal dissociation profiles. Over a range of Mg2+ concentrations, pdU-modified TFOs formed more stable triplexes than did TFOs containing 2'-deoxythymidine. At 1 mM Mg2+, a DeltaTm of 30 degreesC was observed for pdU- versus T-containing 15-mers (of generic sequence 5' TTTTCTTTTTTCTTTTCT 3') binding to the cognate A:T bp rich site, indicating that pdU-containing TFOs are capable of substantial binding even at physiologically low Mg2+ concentrations. In addition, the pdU-containing TFOs were superior in gene targeting experiments in mammalian cells, yielding 4-fold higher mutation frequencies in a shuttle vector-based mutagenesis assay designed to detect mutations induced by third-strand-directed psoralen adducts. These results suggest the utility of the pdU substitution in the pyrimidine motif for triplex-based gene targeting experiments.
The effect of extraneous radiation on photometric accuracy of infrared spectrophotometers

Recent advances in infrared spectrophotometry have led to increased concern with the effects of radiation emitted by elements other than the source, for example, samples, reference beam attenuators, and the monochromator itself. Present levels of precision of measurement and purity of radiation are in some cases good enough that the effects of extraneous radiation can become significant, even with room temperature samples. Of particular interest are the areas of far-infrared spectroscopy, the study of very dense or highly reflecting samples, and the use of rotating sectors for photometric calibration. The magnitude of the expected effects of extraneous radiation will be discussed for several photometer systems, and the results of some experimental measurements will be described.
Early anesthetic exposure and long-term cognitive impairment

Several lines of evidence from clinical cohort studies and animal studies have shown that early exposure to anesthetics is a significant risk factor for later development of learning disabilities. However, the underlying molecular mechanism is unclear. Recent studies have indicated that hippocampal neurogenesis and synaptogenesis may be involved in the mechanisms by which early anesthetic exposure produces long-term cognitive impairment. It is possible that synaptic scaffolding protein postsynaptic density-95 (PSD-95) PDZ (PSD 95/Discs large/Zona occludens-1) domain-mediated protein-protein interactions are involved in the regulation of neurogenesis and synaptogenesis in the central nervous system. PDZ domain-mediated protein-protein interactions are disrupted by clinically relevant concentrations of inhaled anesthetics. It will help us understand the molecular mechanism underlying anesthetic-induced long-term cognitive dysfunction if we can demonstrate the role of synaptic PDZ interactions in early anesthetic exposure-produced long-term cognitive impairment.
Role of P1 residues Arg336 and Arg562 in the activated-Protein-C-catalysed inactivation of Factor VIIIa

APC (activated Protein C) inactivates human Factor VIIIa following cleavage at residues Arg336 and Arg562 within the A1 and A2 subunits respectively. The role of the P1 arginine in APC-catalysed inactivation of Factor VIIIa was examined by employing recombinant Factor VIIIa molecules where residues 336 and 562 were replaced with alanine and/or glutamine. Stably expressed Factor VIII proteins were activated by thrombin and resultant Factor VIIIa was reacted at high concentration with APC to minimize cofactor inactivation due to A2 subunit dissociation. APC cleaved wild-type Factor VIIIa at the A1 site with a rate ∼25-fold greater than that for the A2 site. A1 mutants R336A and R336Q were inactivated ∼9-fold slower than wild-type Factor VIIIa, whereas the A2 mutant R562A was inactivated ∼2-fold slower. No cleavage at the mutated sites was observed. Taken together, these results suggested that cleavage at the A1 site was the dominant mechanism for Factor VIIIa inactivation catalysed by the proteinase. On the basis of cleavage at Arg336, a Km value for wild-type Factor VIIIa of 102 nM was determined, and this value was significantly greater than Ki values (∼9–18 nM) obtained for an R336Q/R562Q Factor VIIIa. Furthermore, evaluation of a series of cluster mutants in the C-terminal region of the A1 subunit revealed a role for acidic residues in segment 341–345 in the APC-catalysed proteolysis of Arg336. Thus, while P1 residues contribute to catalytic efficiency, residues removed from these sites make a primary contribution to the overall binding of APC to Factor VIIIa.
Mitomycin lung toxicity. Acute and chronic phases.

Pulmonary toxicity is a rare but well described side effect of mitomycin C (MMC). We describe 14 cases of MMC pulmonary toxicity that were detected in four clinical trials performed at The Mayo Clinic using MMC-containing regimens for nonsmall cell lung cancer (NSCLC) and by reviewing the charts of patients treated at The Mayo Clinic with MMC-containing regimens for NSCLC from 1976 to 1995. The median age was 61 (range 44-84) years, with an M:F ratio of 1:1. The median number of cycles of MMC to develop toxicity was four (range two to five) with a median cumulative dose of MMC of 29 mg/m 2 . MMC toxicity occurred despite pre-medication with corticosteroids in 11 patients. At diagnosis of MMC lung toxicity, the median diffusing lung capacity (DLCO) was 9 and PaO 2 was 49 mm Hg. Of those having bronchoscopy, four patients had pulmonary histologic changes consistent with lung injury. Two patients had bronchioalveolar lavages that were nondiagnostic. All patients responded initially to corticosteroids, but approximately 40% had progressive pulmonary insufficiency despite high doses of corticosteroids. This chronic, progressive phase of MMC lung toxicity is a largely underestimated sequelae of MMC.
Mass, surface area and number metrics in diesel occupational exposure assessment

While diesel aerosol exposure assessment has traditionally been based on the mass concentration metric, recent studies have suggested that particle number and surface area concentrations may be more health-relevant. In this study, we evaluated the exposures of three occupational groups—bus drivers, parking garage attendants, and bus mechanics—using the mass concentration of elemental carbon (EC) as well as surface area and number concentrations. These occupational groups are exposed to mixtures of diesel and gasoline exhaust on a regular basis in various ratios. The three groups had significantly different exposures to workshift TWA EC with the highest levels observed in the bus garage mechanics and the lowest levels in the parking ramp booth attendants. In terms of surface area, parking ramp attendants had significantly greater exposures than bus garage mechanics, who in turn had significantly greater exposures than bus drivers. In terms of number concentrations, the exposures of garage mechanics exceeded those of ramp booth attendants by a factor of 5–6. Depending on the exposure metric chosen, the three occupational groups had quite different exposure rankings. This illustrates the importance of the choice of exposure metric in epidemiological studies. If these three occupational groups were part of an epidemiological study, depending on the metric used, they may or may not be part of the same similarly exposed group (SEG). The exposure rankings (e.g., low, medium, or high) of the three groups also changes with the metric used. If the incorrect metric is used, significant misclassification errors may occur.
MKK3, an upstream activator of p38, contributes to formalin phase 2 and late allodynia in mice

Spinal p38 mitogen activated (MAP) kinase plays a key role in chronic pain behavior. However, clinical development of p38 inhibitors has been hindered by significant toxicity. To evaluate alternative strategies of p38 regulation, we determined if known upstream activators of p38 (mitogen activated kinase kinase [MKK] 3 and MKK6), are involved in development and maintenance of pain and spinal p38 phosphorylation. Acute pain behaviors were not altered in MKK3 or MKK6 deficient mice. The phase 2 formalin response was delayed in MKK3-/- mice, but unchanged in magnitude, while the response remained normal in MKK6-/- mice. More striking, late formalin allodynia (3-18 days post-injection) was prominent in wild type and MKK6-/- mice, but was delayed for several days in MKK3-/- mice. In wild type, but not MKK3-/- mice, intraplantar formalin elicited increases in ipsilateral spinal MKK3/6 phosphorylation acutely and again at 9 days postinjection. Phosphorylation of MKK3/6 correlated with phase 2 formalin behavior. Wild type (WT) and MKK3-/- mice both expressed increases in spinal phosphorylated p38, however in WT mice this response began several days earlier, and was of higher magnitude and duration than in MKK3-/- mice. This phosphorylation correlated with the late allodynia. Phosphorylated MKK3/6 was detected only in astrocytes, given that phosphorylated p38 (P-p38) is usually not seen in astrocytes this argues for astrocytic release of soluble mediators that affect p38 phosphorylation in microglia. Taking these data together, MKK3, but not MKK6, is necessary for normal development of chronic pain behavior and phosphorylation of spinal p38.
Development of Finite Element Rat Head Model to Study the Effect of Incident Pressure and Skull Rigidity Under Blast-Induced Biomechanical Loading

Blast waves generated by improvised explosive devices (IEDs) cause traumatic brain injury (TBI) in soldiers and civilians. Currently, in vivo animal models are extensively used to study blast TBI, to identify mechanisms of injury, and to develop injury thresholds. This work focuses on the study of the effect of Incident Pressure (IP), skull rigidity on the measured Intracranial Pressure (ICP) and maximum principle strain measured on the skull using a validated finite element model of the rat head. Our results indicate that the ICP has a negative correlation with the skull rigidity; i.e., with increase in the skull rigidity the ICP tends to decrease. Similarly, ICP linearly increases with an increase in the IP. Finally, the strain has a negative non linear relationship with the skull rigidity.Copyright © 2013 by ASME
A Method to Image Flame Index in Partially Premixed Flames

This paper describes a new method to image the flame index in partially premixed flames. To improve modeling of partially premixed flames, such as those in gas turbines and scramjets, there is a need to measure the flame index. CHEMKIN modeling of both premixed and non-premixed methane (CH4) / air flames determined that acetone (CH3COCH3) and nitrogen dioxide (NO2) were good tracers of methane and oxygen (O2). Using simultaneous acetone and NO2 Planar Laser-Induced Fluorescence (PLIF), flame index was measured in a CH4 / air co-flow burner with acetone and NO2 seeding. The application of the method to turbulent flames is discussed, as well as the signal-to-noise ratio.
Production of ethylene from hydrous ethanol on H-ZSM-5 under mild conditions

Due to the dramatic rise in the use of ethers as fuel oxygenates, an alternative process for the production of ethyl tert-butyl ether (ETBE) based solely on biomass-derived ethanol feedstock is proposed. The first step in this process is ethanol dehydration on H-ZSM-5 to produce ethylene. Hydrous ethanol is a particularly attractive feedstock for this step since the production of anhydrous ethanol is very energy/cost intensive. In fact, the presence of water in the ethanol feed enhances the steady-state activity and selectivity of H-ZSM-5 catalysts. Reaction kinetic data were collected in a microreactor at temperatures between 413 and 493 K, at ethanol partial pressures of less than 0.7 atm, and at water feed molar ratios of less than 0.25. A sharp initial decline in catalyst activity observed within a few minutes on stream was attributed to the formation of “low-temperature coke” from ethylene oligomerization. Deactivation occurred at a much slower rate after 100 min on stream, allowing near-steady-state...
Sorption dynamics of hydrophobic pollutants in sediment suspensions

Sorption of hydrophobic organic chemicals in natural sediment suspensions was found to frequently require extended time periods (days to weeks) for complete equilibrium. Sorption dynamics could be described by a two-compartment model that distinguished a rapid or labile exchange(requiring at most a few hours to achieve) from highly retarded or nonlabile sorption requiring days or weeks to occur. For highly hydrophobic chemicals and high solid concentrations, the labile fraction decreased to 0.1 or less in some systems. The kinetic exchange constant for nonlabile sorption varied inversely with the sorption equilibrium constant. An understanding of sorption dynamics is important in describing the fate of highly sorbed pollutants in aquatic systems.
SEX AND DELINQUENCY: A Partial Test of the Masculinity Hypothesis

With increasing frequency, commentators assert that attitudes associated with occupying the male status or “masculinity” contribute to criminal/delinquent involvement. Despite the ubiquity with which this “masculinity hypothesis” appears, it has received few empirical assessments, and those that do exist typically are flawed by what amounts to the ecological fallacy. Using individual level data, this research attempted to test the masculinity proposition. In general, our data lent some support to the hypothesis, indicating that independent of gender, having masculine attributes positively affected the commission of different types of delinquent offenses.
PhosphoSVM: prediction of phosphorylation sites by integrating various protein sequence attributes with a support vector machine

Phosphorylation is one of the most essential post-translational modifications in eukaryotes. Studies on kinases and their substrates are important for understanding cellular signaling networks. Because of the cost in time and labor associated with large-scale wet-bench experiments, computational prediction of phosphorylation sites becomes important and many computational tools have been developed in the recent decades. The prediction tools can be grouped into two categories: kinase-specific and non-kinase-specific tools. With more kinases being discovered by the new sequencing technologies, accurate non-kinase-specific prediction tools are highly desirable for whole-genome annotation in a wider variety of species. In this manuscript, a support vector machine is used to combine eight different sequence level scoring functions to predict phosphorylation sites. The attributes used by this work, including Shannon entropy, relative entropy, predicted protein secondary structure, predicted protein disorder, solvent accessible area, overlapping properties, averaged cumulative hydrophobicity, and k-nearest neighbor, were able to obtain better results than the previously used attributes by other similar methods. This method achieved AUC values of 0.8405/0.8183/0.7383 for serine (S), threonine (T), and tyrosine (Y) phosphorylation sites, respectively, in animals with a tenfold cross-validation. The model trained by the animal phosphorylation sites was also applied to a plant phosphorylation site dataset as an independent test. The AUC values for the independent test dataset were 0.7761/0.6652/0.5958 for S/T/Y phosphorylation sites, which compared favorably with those of several existing methods. A web server based on our method was constructed for public use. The server, trained model, and all datasets used in the current study are available at http://sysbio.unl.edu/PhosphoSVM .