cssi/SciSciGPT-SciSciNet huggingface dataset:
Assays for determining poly(A) tail length and the polarity of mRNA decay in mammalian cells

This chapter describes several methods for measuring the length of the mRNA poly(A) tail and a novel method for measuring mRNA decay. Three methods for measuring the length of a poly(A) tail are presented: the poly(A) length assay, the ligation-mediated poly(A) test (LM-PAT), and the RNase H assay. The first two methods are PCR-based assays involving cDNA synthesis from an oligo(dT) primer. The third method involves removing the poly(A) tail from the mRNA of interest. A major obstacle to studying the enzymatic step of mammalian mRNA decay has been the inability to capture mRNA decay intermediates with structural impediments such as the poly(G) tract used in yeast. To overcome this, we combined a standard kinetic analysis of mRNA decay with a tetracycline repressor-controlled reporter with an Invader RNA assay. The Invader RNA assay is a simple, elegant assay for the quantification of mRNA. It is based on signal amplification, not target amplification, so it is less prone to artifacts than other methods for nucleic acid quantification. It is also very sensitive, able to detect attomolar levels of target mRNA. Finally, it requires only a short sequence for target recognition and quantitation. Therefore, it can be applied to determining the decay polarity of a mRNA by measuring the decay rates of different portions of that mRNA.
A Hardware-in-the-Loop Real-Time Testbed for Microgrid Hierarchical Control

To maintain a stable, flexible and economic operation of a microgrid, hierarchical control architecture consisting of primary, secondary and tertiary control is proposed. However, the differences in dynamics of microgrid, bandwidths of control levels and speed of communication channels make it difficult to comprehensively validate the performance of the hierarchical control schemes. In this paper we propose a hardware-in-the-loop real-time testbed for microgrid hierarchical control. The proposed testbed can be used to validate control performance under different microgrid operating modes (grid-tied or islanded), different primary control schemes (current or voltage mode) and different secondary control approaches (centralized or distributed). The integration of industry-grade hardware that runs primary and secondary control into the testbed allows for complete emulation of microgrid operation, and facilitates the study of the effects of measurement noise, sampling and communication delays.
Application of a New Paradigm for Cytomegalovirus Disease Prevention in Mayo Clinic’s First Face Transplant

The optimal approach to preventing cytomegalovirus (CMV) disease after face transplant is unknown. We report an individualized hybrid approach, initially using valganciclovir prophylaxis followed by surveillance and preemptive therapy guided by viral and immunologic markers. A 31-year-old man received a near-total face allotransplant for gunshot injury-related severe facial deformities. He was CMV seronegative, and the donor was CMV seropositive (D+/R- mismatch), and he received intravenous ganciclovir followed by oral valganciclovir prophylaxis. Monthly CD8+ T-cell immune competence assay revealed no CMV-specific CD8+ T-cell immunity development during valganciclovir prophylaxis. Because of severe leukopenia, valganciclovir was discontinued at 7 months after transplant when the patient had recovered and sustained normal global CD8+ T-cell function. Weekly CMV polymerase chain reaction testing detected asymptomatic CMV replication (plasma CMV, 549 IU/mL) 3 months later. Short-course preemptive valganciclovir treatment resulted in sustained virologic clearance. The patient had development of CMV-specific CD8+ T cells (12 cells/μL) together with CMV IgM and IgG. No rejection or infection relapse was detected 20 months after transplant. In conclusion, viral and immunologic monitoring allowed for an individualized approach to effective CMV disease prevention after face transplant. This case highlights the importance of understanding the interplay between the host immunity and the pathogen in determining the clinical course and outcome of CMV and other infectious disease syndromes.
Exploring the role of perception of social justice in predicting attitudes toward inclusive education for students with disabilities: a formative investigation of a theory

This formative study attempted to gather evidence for a theory postulating that inclusive education for students with disabilities is best facilitated by teachers with a strong sense of social just...
Signs of Free Peritoneal Air

Pneumoperitoneum is defined as free air in the peritoneal cavity. It is most commonly caused by rupture of a hollow viscus such as gastric or duodenal ulcer perforation. Other common causes include feeding tube insertion, bowel anastomotic leak, barotrauma, and intra-abdominal surgery. After a laparotomy, air is usually present for 3–7 days and should not increase in volume. An upright PA chest radiograph is traditionally the initial examination unless a patient is critically ill. In that circumstance, a supine decubitus radiograph is preferred. The diagnosis of pneumoperitoneum is critical because it is usually an indication for emergent surgery with exception of benign etiologies of free air. On radiographs, the signs of free peritoneal air are subtle and diverse. There are four major groups that these signs are categorized into: bowel-related, right upper quadrant, peritoneal ligament-related, and other signs.
Complex magnetic order in the decorated spin-chain system Rb 2 Mn 3 ( MoO 4 ) 3 ( OH ) 2

The macroscopic magnetic properties and microscopic magnetic structure of ${\mathrm{Rb}}_{2}{\mathrm{Mn}}_{3}{({\mathrm{MoO}}_{4})}_{3}{(\mathrm{OH})}_{2}$ (space group $Pnma)$ are investigated by magnetization, heat capacity, and single-crystal neutron diffraction measurements. The compound's crystal structure contains bond-alternating ${[{\mathrm{Mn}}_{3}{\mathrm{O}}_{11}]}^{\ensuremath{\infty}}$ chains along the $b$ axis, formed by isosceles triangles of Mn ions occupying two crystallographically nonequivalent sites (the Mn1 site on the base and Mn2 site on the vertex). These chains are only weakly linked to each other by nonmagnetic oxyanions. Both superconducting quantum interference device magnetometry and neutron diffraction experiments show two successive magnetic transitions as a function of temperature. On cooling, it transitions from a paramagnetic phase into an incommensurate phase below 4.5 K with a magnetic wave vector near ${\mathbf{k}}_{1}=(0,\phantom{\rule{0.16em}{0ex}}0.46,\phantom{\rule{0.16em}{0ex}}0)$. An additional commensurate antiferromagnetically ordered component arises with ${\mathbf{k}}_{2}=(0,\phantom{\rule{0.16em}{0ex}}0,\phantom{\rule{0.16em}{0ex}}0)$, forming a complex magnetic structure below 3.5 K with two different propagation vectors of different stars. On further cooling, the incommensurate wave vector undergoes a lock-in transition below 2.3 K. The experimental results suggest that the magnetic superspace group is $Pnma.{1}^{\ensuremath{'}}(0b0)s0ss$ for the single-$\mathbf{k}$ incommensurate phase and is $P{n}^{\ensuremath{'}}ma(0b0)00s$ for the two-$\mathbf{k}$ magnetic phase. We propose a simplified magnetic structure model taking into account the major ordered contributions, where the commensurate ${\mathbf{k}}_{2}$ defines the ordering of the $c$-axis component of the Mn1 magnetic moment, while the incommensurate ${\mathbf{k}}_{1}$ describes the ordering of the $ab$-plane components of both Mn1 and Mn2 moments into elliptical cycloids.
Epidemiology and outcomes of non-HACEK infective endocarditis in the southeast United States.

Objectives Infective endocarditis (IE) with non-HACEK Gram-negative (GN) organisms is rare, but associated with poor outcomes. The purpose of this study was to quantify the microbiology, treatment strategies, and frequency of poor outcomes in patients with non-HACEK GN IE. Materials Retrospective cohort of adults with definite non-HACEK GN IE from 1/11-1/19. The primary endpoint was poor patient outcome, defined as a composite of all-cause death or infection-related readmission within 90-days of index infection. Results 43 patients were included: 51% patients were men, and the median (IQR) age was 40 (31-50) years. Forty patients reported injection drug use. The most common organisms were Pseudomonas aeruginosa (68%) and Serratia marcescens (9%). Seventy-six percent of patients received definitive combination therapy; the most common antibiotics used in combination with a β-lactam were aminoglycosides (50%) and fluoroquinolones (34%). Three patients discontinued combination therapy due to toxicity. Twelve-month, all-cause mortality and readmission was 30% and 54%, respectively. In multivariable logistic regression, variables independently associated with composite poor outcome were receipt of fluoroquinolone-based IE combination therapy and septic shock. Conclusions Long-term mortality and readmission rates were high. Patients who received fluoroquinolone-based IE combination therapy more frequently developed poor outcomes than those who did not.
A Survey of Korean Elementary Teachers’ Perceptions of and In-Service Needs for Gifted Education

AbstractThe purpose of this study was to examine Korean elementary teachers’ knowledge of and interest in gifted education, in-service training needs, and perceptions of gifted education to provide implications for developing in-service teacher training programs. Korean elementary teachers completed the survey, Korean Elementary Teachers: Perceptions of Gifted Education and In-service Needs in Gifted Education. The results of this study show teacher training is an essential factor for improving knowledge of and interest in gifted education. When in-service training for gifted education is planned, the findings of this study can help provide guidelines for the training including employing qualified staff who are experts in the gifted education field, developing appropriate length of training sessions, finding the best time for training, and providing relevant content during training.
A unified kinetic model for stress relaxation and recovery during and after growth interruptions in polycrystalline thin films

Abstract A model for the kinetics of residual stress evolution is described that can be applied to both the relaxation during a growth interruption and the recovery following resumption of growth. The stress is attributed to simple atomistic processes based on reversible diffusion of atoms in and out of the grain boundary. Each of these processes is considered separately to understand how the rates differ during relaxation and recovery and how they depend on grain size, film thickness, temperature, deposition rate, and initial stress. The model is compared with experimental data obtained by others for several materials (Fe, Ni and Au).
Integrating and Assessing Student Perceived Sustainability Literacy in an Integrated Marketing Communications Course.

This paper examines whether marketing educators’ efforts in integrating sustainability-related issues in an undergraduate Integrated Marketing Communications (IMC) course affect students’ perceived...
Free-Breathing and Ungated Dynamic MRI Using Navigator-Less Spiral SToRM

We introduce a kernel low-rank algorithm to recover free-breathing and ungated dynamic MRI from spiral acquisitions without explicit k-space navigators. It is often challenging for low-rank methods to recover free-breathing and ungated images from undersampled measurements; extensive cardiac and respiratory motion often results in the Casorati matrix not being sufficiently low-rank. Therefore, we exploit the non-linear structure of the dynamic data, which gives the low-rank kernel matrix. Unlike prior work that rely on navigators to estimate the manifold structure, we propose a kernel low-rank matrix completion method to directly fill in the missing k-space data from variable density spiral acquisitions. We validate the proposed scheme using simulated data and in-vivo data. Our results show that the proposed scheme provides improved reconstructions compared to the classical methods such as low-rank and XD-GRASP. The comparison with breath-held cine data shows that the quantitative metrics agree, whereas the image quality is marginally lower.
Genome-wide estrogen receptor-α binding and action in human endometrial stromal cells

Objective To investigate the gene targets of estradiol (E2)–estrogen receptor-α (ESR1) in human endometrial stromal cells. Design Basic science. Setting University research center. Patient(s) Premenopausal women with or without endometriosis. Intervention(s) Primary cultures of human endometrial stromal cells from healthy endometrium, with or without small-interfering RNA (siRNA) knockdown of ESR1 expression, were treated with E2 or vehicle control. Main Outcome Measure(s) Genome-wide RNA expression by RNA sequencing was compared in endometrial stromal cells with or without siRNA knockdown of ESR1 in the presence or absence of E2. Genome-wide recruitment of ESR1 to chromatin was assessed by chromatin immunoprecipitation sequencing. Gene expression by real-time qualitative polymerase chain reaction of a potential E2-ESR1 target gene was determined in endometrial stromal cells and endometriotic stromal cells. Result(s) We identified several important pathways that are dependent on E2-ESR1 signaling in endometrial stromal cells, including progesterone signaling, cell–matrix adhesion, and cytoskeleton rearrangement, as well as paracrine signaling by members of the fibroblast growth factor family. We detected a total of 709 ESR1 target sites on chromatin. By integrating data on genome-wide transcriptomic changes and E2-ESR1 binding sites, we identified inositol polyphosphate phosphatase type II (INPP4B) as a candidate E2-mediated suppressor of proliferation in healthy endometrial cells. INPP4B was downregulated in endometriosis-derived stromal cells. Conclusion(s) E2-ESR1 activates genes involved in human endometrial stromal cell cycle regulation, progesterone response, and production of stromal growth factors. Understanding the direct role of estrogen on the endometrial stroma and identifying downstream targets of E2-ESR1 can inform the development of targeted therapies for endometriosis and diminished endometrial receptivity.
Database Operations in D4M.j1

Each step in the data analytics pipeline is important, including database ingest and query. The D4M-Accumulo database connector has allowed analysts to quickly and easily ingest to and query from Apache Accumulo using MATLAB®/GNU Octave syntax. D4M.jl, a Julia implementation of D4M, provides much of the functionality of the original D4M implementation to the Julia community. In this work, we extend D4M.jl to include many of the same database capabilities that the MATLAB®/GNU Octave implementation provides. Here we will describe the D4M.jl database connector, demonstrate how it can be used, and show that it has comparable or better performance to the original implementation in MATLAB®/GNU Octave.
COVID-19: Early Planning, Response & Lessons in OSH

Requests for participation made of leading North American safety foundations specifically for provision of select member data to maximize population size were either not answered or provided [ ]the survey instrument was distributed using the means immediately available to the researchers Figure 1 (p 36) provides consolidated data in which respondents reported their level of agreement to: * organizations' routine OSH program requirements being maintained, * adequate PPE supplies being maintained, * effective tracing procedures for possibly exposed workers being implemented, * control of exposed or symptomatic workers, * effective referral process for symptomatic or exposed workers being implemented, and * social distancing implemented per then-current CDC guidelines Figure 2 (p 36) consolidates data in which respondents report the degree that activities have been implemented in all work areas or for all workers, including: * scheduling of workers to minimize their physical interaction, * Adenosine Triphosphate (ATP) testing to confirm cleaning and disinfecting effectiveness, * increased sanitation and cleaning, * worker safe practices training, and * face coverings per CDC guidelines The first was to determine whether organization relative risk (Table 2, p 33) results in significant differences in respondents' perception of the pandemic's impact to operations, availability of PPE, continuance of safety routines and confidence in worker protective measures
Microfluidic Cooling for 3D-IC with 3D Printing Package

Microchannel cooling method for stacked 3D-IC has process and cost issues. The proposed method, the thermal fluid chamber, exploits the gap between the upper and lower stacks. The method advantages are achieving controllable coolant flow and low-cost process. The microfluidic cooling system is composed of a thermal test chip, thermal test board, 3D printing package, and microfluidic apparatus. The thermal test chip with C4 micro-bumps is attached on the test board. The thermal generator and sensor in the chip are operated by the test board. The microfluidic chamber of 68 μm thick is integrated between the chip and board. Thermal sensing and microfluidic tests demonstrate the validity of the thermal fluidic chamber.
Limitations of Fourier ring correlation as an image resolution metric

Fourier ring correlation was recently proposed in fluorescence microscopy as an objective measure of image resolution. In this study we show that FRC has serious limitations. For several common image processing techniques, we show that FRC can be made to be systematically biased to classify objectively lower resolution images as better resolved than objectively higher resolution images. Thus, rather than providing an objective, realistic measure of spatial resolution, care must be taken in interpreting FRC-based results. In revealing some of FRC’s limitations, this study also highlights the need for a more objective, principled approach to estimating resolution.
Flow Work and Sample Problems

In this lecture, we will solve Sample Problem 12.1 to calculate the reversible work of expansion or compression in flow systems (adapted from Chapter 2 in Denbigh). Second, we will solve Sample Problem 12.2 to analyze the operation of a Hilsch vortex tube (see below), which will allow us to crystallize material presented in Lectures 10, 11, and 12.
Post-discharge healthcare utilization in infants with neonatal opioid withdrawal syndrome.

Abstract The opioid epidemic in the United States has led to a significant increase in the incidence of neonatal opioid withdrawal syndrome (NOWS); however, the understanding of long-term consequences of NOWS is limited. The objective of this study was to evaluate post-discharge healthcare utilization in infants with NOWS and examine the association between NOWS severity and healthcare utilization. A retrospective cohort design was used to ascertain healthcare utilization in the first year after birth-related discharge using the CERNER Health Facts® database. ICD-9/ICD-10 diagnostic codes were used to identify live births and to classify infants into two study groups: NOWS and uncomplicated births (a 25% random sample). Evaluated outcomes included rehospitalization, emergency department (ED) visits within 30-days and one-year after discharge, and a composite one-year utilization event (either hospitalization or emergency department visit during that year). NOWS severity was operationalized as pharmacologic treatment, length of hospitalization, and medical conditions often associated with NOWS. In 3,526 infants with NOWS (restricted to gestational age ≥ 33 weeks), NOWS severity was associated with an increase in composite one-year utilization (OR: 1.1; 95% CI: 1.04–1.2) after adjusting for prematurity, sepsis, jaundice, use of antibiotics, infant sex, insurance status, race, hospital bed size, year of birth, and census division. In a subset of full-term infants (3008 with NOWS and 88,452 uncomplicated births), having a NOWS diagnosis was associated with higher odds of a 30-day (OR: 1.6; 95% CI: 1.03–2.4) and one-year rehospitalization (OR: 1.6; 95% CI: 1.1–2.4) after adjusting for infant sex, race, type of medical insurance, hospital location, census division, year of primary encounter, hospital bed size, and medical conditions. This study found higher healthcare utilization during the first year of life in infants diagnosed with NOWS, especially those with severe NOWS. Findings suggest a need for closer post-discharge follow-up and management of infants with NOWS.
A finite element investigation of quasi-static and dynamic asymptotic crack-tip fields in hardening elastic-plastic solids under plane stress

The asymptotic structures of crack-tip stress and deformation fields are investigated numerically for quasi-static and dynamic crack growth in isotropic linear hardening elastic-plastic solids under mode I, plane stress, and small-scale yielding conditions. An Eulerian type finite element scheme is employed. The materials are assumed to obey the von Mises yield criterion and the associated flow rule. The ratio of the crack-tip plastic zone size to that of the element nearest to the crack tip is of the order of 1.6 × 104. The results of this study strongly suggest the existence of crack-tip stress and strain singularities of the type rs (s < 0) at r=0, where r is the distance to the crack tip, which confirms the asymptotic solutions of variable-separable type by Amazigo and Hutchinson [1] and Ponte Castaneda [2] for quasi-static crack growth, and by Achenbach, Kanninen and Popelar [3] for dynamic crack propagation. Both the values of the parameter s and the angular stress and velocity field variations from the present full-field finite element analysis agree very well with those from the analytical solutions. It is found that the dominance zone of the rs-singularity is quite large compared to the size of the crack-tip active plastic zone. The effects of hardening and inertia on the crack-tip fields as well as on the shape and size of the crack-tip active plastic zone are also studied in detail. It is discovered that as the level of hardening decreases and the crack propagation speed increases, a secondary yield zone emerges along the crack flank, and kinks in stress and velocity angular variations begin to develop. This dynamic phenomenon observable only for rapid crack growth and for low hardening materials may explain the numerical difficulties, in obtaining solutions for such cases, encountered by Achenbach et al. who, in their asymptotic analysis, neglected the existence of reverse yielding zones along the crack surfaces.
The Color of Money or How to Redesign a “Monument in Your Pocket”:

In 2016, the Treasury Department announced that the redesigned $20 bill would feature Harriet Tubman on its front, sparking jubilation from women activists who had campaigned for female representat...
Perturbation of TM6SF2 Expression Alters Lipid Metabolism in a Human Liver Cell Line

Non-alcoholic fatty liver disease (NAFLD) is caused by excess lipid accumulation in hepatocytes. Genome-wide association studies have identified a strong association of NAFLD with non-synonymous E167K amino acid mutation in the transmembrane 6 superfamily member 2 (TM6SF2) protein. The E167K mutation reduces TM6SF2 stability, and its carriers display increased hepatic lipids and lower serum triglycerides. However, the effects of TM6SF2 on hepatic lipid metabolism are not completely understood. We overexpressed wild-type or E167K variant of TM6SF2 or knocked down TM6SF2 expression in lipid-treated Huh-7 cells and used untargeted lipidomic analysis, RNAseq transcriptome analysis, and fluorescent imaging to determine changes in hepatic lipid metabolism. Both TM6SF2 knockdown and E167K overexpression increased hepatic lipid accumulation, while wild-type overexpression decreased acylglyceride levels. We also observed lipid chain remodeling for acylglycerides by TM6SF2 knockdown, leading to a relative increase in species with shorter, more saturated side chains. RNA-sequencing revealed differential expression of several lipid metabolizing genes, including genes belonging to AKR1 family and lipases, primarily in cells with TM6SF2 knockdown. Taken together, our data show that overexpression of TM6SF2 gene or its loss-of-function changes hepatic lipid species composition and expression of lipid metabolizing genes. Additionally, our data further confirms a loss-of-function effect for the E167K variant.
‘Let Me Tell the Story Straight On’: Middlemarch, Process-Tracing Methods and the Politics of Narrative

Much thought has been put into developing rationales for the process-tracing method, but proponents of this narrative method have been agnostic about the criterial demands for ‘writing up’ a case study. This article addresses that lack through a double reading. First, I show that ‘good’ process-tracing prose mirrors a narrative voice found in Victorian fiction, most notably in George Eliot's Middlemarch. Then, in the second reading, I critique this narrative approach through a close reading of Middlemarch. In doing so, I explain how this style attempts (and ultimately fails) to mask its own pre-theoretical political commitments. For process-tracing to seem effective, its practitioners must turn a blind eye to the theoretical consequences of narrative style and must remain silent on the instability inherent in their prose.
The MHC Class II Molecule I-Ag7 Exists in Alternate Conformations That Are Peptide Dependent

Insulin-dependent diabetes mellitus is an autoimmune disease that is genetically linked to the HLA class II molecule DQ in humans and to MHC I-A g7 in nonobese diabetic mice. The I-A g7 β-chain is unique and contains multiple polymorphisms, at least one of which is shared with DQ alleles linked to insulin-dependent diabetes mellitus. This polymorphism occurs at position 57 in the β-chain, in which aspartic acid is mutated to a serine, a change that results in the loss of an interchain salt bridge between αArg 76 and βAsp 57 at the periphery of the peptide binding groove. Using mAbs we have identified alternative conformations of I-A g7 class II molecules. By using an invariant chain construct with various peptides engineered into the class II-associated invariant chain peptide (CLIP) region we have found that formation of these conformations is dependent on the peptide occupying the binding groove. Blocking studies with these Abs indicate that these conformations are present at the cell surface and are capable of interactions with TCRs that result in T cell activation.
Structure-function relations of human hemoglobins

In 1949 Pauling and his associates showed that sickle cell hemoglobin (HbS) belonged to an abnormal molecular species. In 1958 Ingram, who used a two-dimensional system of electrophoresis and chromatography to break down the hemoglobin molecule into a mixture of smaller peptides, defined the molecular defect in HbS by showing that it differed from normal adult hemoglobin by only a single peptide. Since then, more than 200 variant and abnormal hemoglobins have been described. Furthermore, the construction of an atomic model of the hemoglobin molecule based on a high-resolution x-ray analysis by Dr. Max Perutz at Cambridge has permitted the study of the stereochemical part played by the amino acid residues, which were replaced, deleted, or added to in each of the hemoglobin variants. Some of the variants have been associated with clinical conditions. The demonstration of a molecular basis for a disease was a significant turning point in medicine. A new engineered hemoglobin derived from crocodile blood, with markedly reduced oxygen affinity and increased oxygen delivery to the tissues, points the way for future advances in medicine.
US Corporate Tax Reform and Financial Reporting Incentives

Under the current U.S. tax system, corporations have an incentive to defer the repatriation of their foreign earnings. This incentive is commonly referred to as the lock-out effect. The lock-out effect is significant, as estimates indicate that U.S. corporations hold nearly $2 trillion of earnings in foreign jurisdictions. While the U.S. tax system creates an incentive to retain these earnings abroad, research suggests that a non-tax factor, financial reporting incentives, exacerbates this lock-out effect. This study informs the debate regarding the lock-out effect by discussing evidence that financial reporting incentives significantly affect U.S. corporations’ tax policy responses.
Linkage disequilibria and the site frequency spectra in the su(s) and su(w(a)) regions of the Drosophila melanogaster X chromosome.

Over the last decade, surveys of DNA sequence variation in natural populations of several Drosophila species and other taxa have established that polymorphism is reduced in genomic regions characterized by low rates of crossing over per physical length. Parallel studies have also established that divergence between species is not reduced in these same genomic regions, thus eliminating explanations that rely on a correlation between the rates of mutation and crossing over. Several theoretical models (directional hitchhiking, background selection, and random environment) have been proposed as population genetic explanations. In this study samples from an African population ( n = 50) and a European population ( n = 51) were surveyed at the su(s) (1955 bp) and su(w a ) (3213 bp) loci for DNA sequence polymorphism, utilizing a stratified SSCP/DNA sequencing protocol. These loci are located near the telomere of the X chromosome, in a region of reduced crossing over per physical length, and exhibit a significant reduction in DNA sequence polymorphism. Unlike most previously surveyed, these loci reveal substantial skews toward rare site frequencies, consistent with the predictions of directional hitchhiking and random environment models and inconsistent with the general predictions of the background selection model (or neutral theory). No evidence for excess geographic differentiation at these loci is observed. Although linkage disequilibrium is observed between closely linked sites within these loci, many recombination events in the genealogy of the sampled alleles can be inferred and the genomic scale of linkage disequilibrium, measured in base pairs between sites, is the same as that observed for loci in regions of normal crossing over. We conclude that gene conversion must be high in these regions of low crossing over.
Small crater modification on Meridiani Planum and implications for erosion rates and climate change on Mars

A morphometric and morphologic catalog of ~100 small craters imaged by the Opportunity rover over the 33.5 km traverse between Eagle and Endeavour craters on Meridiani Planum shows craters in six stages of degradation that range from fresh and blocky to eroded and shallow depressions ringed by planed off rim blocks. The age of each morphologic class from <50–200 ka to ~20 Ma has been determined from the size-frequency distribution of craters in the catalog, the retention age of small craters on Meridiani Planum, and the age of the latest phase of ripple migration. The rate of degradation of the craters has been determined from crater depth, rim height, and ejecta removal over the class age. These rates show a rapid decrease from ~1 m/Myr for craters <1 Ma to ~ <0.1 m/Myr for craters 10–20 Ma, which can be explained by topographic diffusion with modeled diffusivities of ~10−6 m2/yr. In contrast to these relatively fast, short-term erosion rates, previously estimated average erosion rates on Mars over ~100 Myr and 3 Gyr timescales from the Amazonian and Hesperian are of order <0.01 m/Myr, which is 3–4 orders of magnitude slower than typical terrestrial rates. Erosion rates during the Middle-Late Noachian averaged over ~250 Myr, and ~700 Myr intervals are around 1 m/Myr, comparable to slow terrestrial erosion rates calculated over similar timescales. This argues for a wet climate before ~3 Ga in which liquid water was the erosional agent, followed by a dry environment dominated by slow eolian erosion.
Problem-oriented policing in public housing: The Jersey City evaluation

This paper examines the impact of a problem-oriented policing project on serious crime problems in six public housing sites in Jersey City, New Jersey. Representatives from the police department and the local housing authority, social service providers, and public housing tenants formed six problem-solving teams. Using systematic documentation of the teams' activities and calls for police service, we examine changes in serious crime both across and within the six sites over a 2 1/2-year period. We find that problem-oriented policing, as compared with traditional policing strategies used before the problem-oriented policing project, led to fewer serious crime calls for service over time and that two public housing sites in particular succeeded in reducing violent, property, and vehicle-related crimes.
Racial differences in disease activity and quality of life in patients with Crohn's disease.

The existing literature on racial differences in Crohn’s disease (CD) activity and quality of life (QOL) is limited and extrapolated from surrogate measures. The aim of our study was to compare objective markers of disease activity and QOL over time by race. A clinical data repository of inflammatory bowel disease (IBD) patients at University of Maryland, Baltimore IBD Program, was used. CD patients from 2004 to 2009 were included if they had greater than or equal to two clinic visits with disease activity and QOL scores during the study period. Differences in disease activity and QOL were compared by race over time. A total of 296 patients with CD met inclusion criteria; of these, 19 % (56/296) were African Americans (AA) and 81 % (240/296) were Caucasian. Baseline disease activity and QOL scores did not differ by race (p > 0.05). Caucasians had a steady decline in disease activity and increase in QOL. AA experienced a similar pattern of change in disease activity and QOL scores over time; however, the declines were not statistically significant between groups. At each time point post-baseline, disease activity and QOL scores were similar between races. We found that Caucasian and AA patients with CD had similar disease activity and QOL scores at initial presentation and over time. Thus, AA do not represent a more severe subgroup of CD patients to treat. These findings have important implications for clinicians that care for patients with CD.
High-sensitivity chemical derivatization NMR analysis for condition monitoring of aged elastomers

An aged polybutadiene-based elastomer was reacted with trifluoroacetic anhydride (TFAA) and subsequently analyzed via 19F NMR spectroscopy. Derivatization between the TFAA and hydroxyl functionalities produced during thermo-oxidative aging was achieved, resulting in the formation of trifluoroester groups on the polymer. Primary and secondary alcohols were confirmed to be the main oxidation products of this material, and the total percent oxidation correlated with data obtained from oxidation rate measurements. The chemical derivatization appears to be highly sensitive and can be used to establish the presence and identity of oxidation products in aged polymeric materials. This methodology represents a novel condition monitoring approach for the detection of chemical changes that are otherwise difficult to analyze.
Visibility of an afterimage alone and in the presence of, one or two additional afterimages

The total time for which a circular afterimage is visible has been found to be increased by the presence of one or two additional afterimages. This increased’ visibility, which has been called “facilitation, ” is greater the nearer the afterimages are to one another, being optimum at .25 deg and declining to zero at 2.0 deg separation.
Dynamic acceleration management for SystemC emulation

Field-programmable gates arrays (FPGAs) have recently been used to emulate SystemC descriptions. Emulation of SystemC descriptions allows for in-system testing, and has been shown to compare favorably with SystemC simulations on a PC when acceleration engines are employed. A limit on the number of acceleration engines that can fit on a SystemC emulation platform creates new dynamic management problems involving decisions as to when and which acceleration engines to load with SystemC bytecode. We define an acceleration management problem for SystemC emulation platforms. In contrast to previous works that focus on statically improving SystemC (and the more general event-driven) simulations, we utilize dynamic online algorithms to manage the use of a limited number of SystemC acceleration engines in an emulation framework, where the kernel must adapt and react to a dynamically changing event queue. We test several online heuristics, and show that we can achieve 14X improvement over software-only emulation and 3.8X over statically preloading SystemC acceleration engines.
The indirect flight muscle of Drosophila accumulates a unique myosin alkali light chain isoform

Abstract Mapping of the 5′ and 3′ ends of the Drosophila myosin alkali light chain (MLC-ALK) mRNA by S1 nuclease and primer extension assays has shown that the primary transcripts are identical irrespective of the time in development that the RNA was prepared. As shown by S1 nuclease experiments these transcripts are alternatively spliced in a tissue-specific fashion generating mRNAs that encode tissue-specific protein isoforms. Antibodies were raised to synthetic peptides identical in sequence to the unique portion of each protein. Western blots of one-dimensional polyacrylamide gels using the type-specific antibodies confirmed and extended the results obtained from the S1 nuclease experiments. The indirect flight muscle is the only tissue in the adult that accumulates the alternatively spliced mRNA. The choice between splicing pathways involves the use of a nonconsensus 3′ splice junction in larvae and in the tubular muscles of adults, whereas in the indirect flight muscle of the adult only consensus sequences are utilized. The involvement of a trans -acting factor to activate the nonconsensus splice site in the myotubes of larvae and the tubular myotubes of adults is proposed.
Structural aspects of immune recognition of lysozymes. III. T cell specificity restriction and its consequences for antibody specificity.

We have studied the relationship between the determinants encountered by T cells on an antigenic molecule and the specificities of the antibodies eventually produced by the B cells with which these T cells cooperate. The number of epitopes on the hen lysozyme (HEL) molecule available to T cell receptors was functionally limited by inducing T cell tolerance to HEL in rabbits. Highly cross-reactive lysozymes were then used to challenge the HEL-unresponsive rabbits. Only T cells which recognize new epitopes on the challenge lysozymes could act as helpers in generating an anti-lysozyme response. Amino acid differences between Japanese quail lysozyme (JEL) and HEL are segregated within a single quadrant of this small antigen molecule. HEL-tolerant rabbits challenged with JEL produced antibodies which were totally cross-reactive with the tolerogen HEL. This result is in contrast to the result obtained in nontolerant rabbits which produced antibodies to JEL which were only 50–70 % cross-reactive with HEL. We conclude that T cells restricted to the JEL-unique epitopes were only capable of cooperating with B cells specific for common epitopes shared between JEL and the tolerogen HEL. Turkey lysozyme (TEL), on the other hand, bears different amino acids which are distributed over several regions on the surface of the molecule. Any one HEL-tolerant rabbit developed a restricted response to TEL; in some rabbits the anti-TEL was highly HEL cross-reactive, while in others little cross-reactivity with HEL was observed. Each of four HEL-tolerant rabbits injected with the minimally altered bob-white quail lysozyme possessed the reactive T cells necessary to mount a limited response to this challenge lysozyme, suggesting a diverse library of T cell specificities. Recognition of the small differences between the challenge lysozymes and the tolerogen HEL required the T cells of these tolerant rabbits to make a fine discrimination between minimally changed epitopes.
Solid state 13C and 1H NMR studies of the evolution of the chemical structure of coal char and tar during devolatilization

Solid-state 13 C and 1 H nuclear magnetic resonance (NMR) spectroscopy techniques are used to investigate the chemical structure of char particles and condensed tar vapors produced as pyrolysis products from an Illinois #6 coal at rapid heating conditions (≈10 4 K/s) at two gas conditions (maximum gas temperatures of 1250 K and 1050 K). The temperature history of particles in the flow reactor is determined using a unique infrared sizing-pyrometry system. The 13 C NMR analyses of the coal chars indicate that significant amounts of aliphatic material are released from the coal during devolatilization, with little change to the aromatic cluster size or number of attachments per cluster. At long residence times, and at higher temperatures, small increases in the cluster size in the char are observed. The 1 H NMR analyses indicate that thermal decomposition of tar vapor occurs at the 1250 K gas conditions, as evidenced by increases in the aromaticity and decreases in the peripheral aliphatic groups, such as methyl groups and aliphatic bridge material.
Phonon considerations in the reduction of thermal conductivity in phononic crystals

Periodic porous structures offer unique material solutions to thermoelectric applications. With recent interest in phonon band gap engineering, these periodic structures can result in reduction of the phonon thermal conductivity due to coherent destruction of phonon modes characteristic in phononic crystals. In this paper, we numerically study phonon transport in periodic porous silicon phononic crystal structures. We develop a model for the thermal conductivity of phononic crystal that accounts for both coherent and incoherent phonon effects, and show that the phonon thermal conductivity is reduced to less than 4% of the bulk value for Si at room temperature. This has substantial impact on thermoelectric applications, where the efficiency of thermoelectric materials is inversely proportional to the thermal conductivity.
Viral agglutination of saponin-lysed chicken erythrocytes.

Comment and ConclusionsFrom these experiments it would seem that saponin has no effect on the receptors responsible for the agglutination of chicken erythrocytes by influenza virus. Internal receptors, if such exist, are not exposed during the lytic process. The agglutinability of saponin-lysed cells by the virus is, in all probability, due to unaltered surface receptors and not to any substance associated with the nucleus. This interpretation is valid, however, only if it can be assumed that virus particles do not penetrate to the interior of the erythrocytes during treatment with the virus. That such a process could occur seems unlikely in view of present knowledge concerning the interaction between red cell and virus.
Autographa californica M nucleopolyhedrovirus chiA is required for processing of V-CATH.

Infection of permissive insect hosts by the baculovirus Autographa californica M nucleopolyhedrovirus results in liquefaction, a pathogenic effect that enhances the dispersal of progeny virions. Two viral gene products—a protease, V-CATH, and a chitinase, chiA—have been shown to be required for liquefaction to occur. It has been generally accepted that the primary functions of these proteins is to degrade the proteinaceous and chitinous components of the host cadaver, respectively. We have generated suggestive evidence, however, that chiA may also serve as a molecular chaperone for proV-CATH, the precursor of V-CATH. When cells were infected with virus lacking a functional chiA gene, proV-CATH failed to undergo processing in vivo and in vitro and formed insoluble aggregates in the endoplasmic reticulum of infected cells. Thus, expression of chiA may be required for the proper folding of the nascent V-CATH polypeptide in the endoplasmic reticulum. Identical results were obtained when tunicamycin was used to block N-linked glycosylation in cells infected with wildtype virus, suggesting that the putative chiA/V-CATH interaction is mediated by N-linked oligosaccharides.
Regulation of B cell entry into the cell cycle.

B cells are induced to enter the cell cycle by ligation of the B-cell receptor (BCR) complex and by Toll-like receptor (TLR) agonists. B-cell activation is regulated by molecules with several distinct modes of action: A first example, the adapter molecule Bam32 (B-lymphocyte adapter of 32 kDa), helps promote BCR-induced cell cycle entry, while the secondary messenger superoxide has the opposite effect. Bam32 and superoxide may fine tune BCR-induced activation by competing for the same limited resources including Rac1/2 and/or the plasma membrane phospholipid PI(3,4)P2. A second example, the BCR-associated co-receptor CD22, inhibits BCR-induced proliferation by binding to novel CD22 ligands on B cells and dendritic cells. Regulators of B-cell survival and death also influence B-cell transit through the cell cycle. Caspase 6 normally is simply classified as an effector caspase in cell death pathways; but in B cells caspase 6 negatively regulates CD40- and TLR-dependent G1 entry, in part by controlling levels of phosphorylated retinoblastoma (Rb) protein. Caspase 6 deficiency predisposes B cells to differentiate rather than proliferate after stimulation. The Bcl-2 family member, Bim, is normally classified as a 'pro-apoptotic' protein; but in B cells, it exerts a positive regulatory effect on cell cycle entry, which is opposed by Bcl-2. New insights into how B-cell transit through the cell cycle is controlled may lead to thoughtful design of drugs that selectively target pathogenic B cells.
Effects of Pressure-Sensitive Paint on Experimentally Measured Wing Forces and Pressures

Recent experiences with pressure-sensitive paint have shown that very thin paint layers on wind-tunnel models testedathighReynoldsnumberscansignie cantlyalterthepressuredistributions,andthustheforcesandmoments, on themodels.Thiswasobserved during two testsof transport-likewings:a “ clean” supercriticalwing at transonic cruise conditions in the NASA Ames High Reynolds Number Channel 2 and a high-lift wing, complete with slats and e aps, at landing conditionsin the NASA Ames 12-FootPressure Wind Tunnel. Theeffect of paint on the cruise wing was to displace the shock wave slightly upstream from its no-paint position. Smoothing the paint, and even removing it entirely from the leading edge, decreased this displacement slightly. Applying paint to only the slats of the high-lift wing caused the wing to stall prematurely at the highest Reynolds number. This effect could be eliminated by smoothing the paint. Adding paint to other parts of the model had little effect. Paint intrusiveness was much smaller and more ambiguous at lower Reynolds numbers. In both tests, paint intrusiveness occurred because the model surfaces were rougher when they were painted than when they were not, and this additional roughness altered the development of the turbulent boundary layers.