cssi/SciSciGPT-SciSciNet huggingface dataset:
Racial/ethnic differences in daily, nondaily, and menthol cigarette use and smoking quit ratios in the United States: 2002 to 2016.

Abstract In the United States (US), racial/ethnic groups differ in cigarette smoking behaviors. We examined changes in cigarette prevalence and quit ratios over 15 years by racial/ethnic group (Non-Hispanic (NH) White, NH Black, Hispanic, NH Other). Data were drawn from the 2002–2016 National Survey on Drug Use and Health (NSDUH) public use data files and analyzed in 2018. Linear time trends of the prevalence of daily, nondaily, and menthol cigarette use and quit ratios (i.e., proportion of former smokers among lifetime smokers) were assessed using logistic regression models. 19.35% of NH White persons were daily smokers in 2016; this prevalence was significantly higher than all other groups (NH Black 10.99%, Hispanic 6.81%, NH Other 9.10%). Menthol use was significantly more common among NH Black individuals than all other groups in every year from 2002 to 2016 (2016: NH Black 23.38%, NH White 14.52%, Hispanic 10.49%, NH Other 8.97%). From 2002 to 2016, daily and nondaily smoking decreased significantly among all groups. The rate of decline of nondaily smoking was more rapid among Hispanic than NH White individuals while the rate of menthol smoking decline was more rapid among NH White than among Hispanic individuals. The quit ratio did not change significantly from 2002 to 2016 among NH Black individuals (31% to 35%) in contrast to a significant increase among NH White (2002, 45%; 2016, 50%) and Hispanic (2002, 33%; 2016, 41%) individuals. Further progress in tobacco control for vulnerable groups may need to include innovative strategies to address these concerning trends.
Impact of cancer in pulmonary embolism presentation and outcomes: A large academic center study.

6613Background: The risk of venous thromboembolism is increased 4- to 7-fold in patients with malignancy, emphasizing the need to identify and treat these patients early to improve outcomes. We aim...
Mutagenic responses of tansy ragwort (Senecio jacobaea) plant, pyrrolizidine alkaloids and metabolites in goat milk with the Salmonella/mammalian-microsome mutagenicity test.

Tansy ragwort (Senecio jacobaea ) was evaluated for animal and human health hazard using the Salmonella/mammalian-microsome mutagenicity test. An acetone extract of tansy ragwort (TR) produced a negative mutagenic response for bacterial tester strains TA1535 and TA100 and a toxic response in tester strains TA1537 and TA98. Assay of this extract in the presence of mammalian liver microsomes (S-9) resulted in positive mutagenic responses in tester strains TA1535, TA1537, TA98 and TA100. Species differences were evaluated by use of liver microsome preparations from induced rat and uninduced sheep, beef, hamster, trout and rat. Only a slight species difference was demonstrated. A mixture of pyrrolizidine alkaloids (PA), extracted from TR flowers, produced a negative response in tester strains TA1535, TA1537, TA98 and TA100. A negative response was also demonstrated when the TR flower PA mixture was assayed with the Salmonella tester strains and induced rat liver microsomes ( IRLM ). A mixture of PA extracted from Senecio longilobus also produced a negative response. The major PA present in TR, jacobine , produced a negative response without and with IRLM exposure in tester strains TA1535, TA1537, TA98 and TA100. Another similar PA, monocrotaline, found in various Crotalaria species also gave a negative response. Milk from TR-fed goats was evaluated for mutagenic response. Milk from goats not receiving TR and from goats receiving TR at a level of 1% of their body weight/day via rumen cannula produced a negative response without liver microsomes present. Milk from TR-fed goats, however, yielded both negative and marginally positive responses for different combinations of tester strains and liver microsome preparations.
Discussion of “Accounting quality and the transmission of monetary policy”

Abstract Armstrong, Glaeser and Kepler (2019) examine whether accounting quality affects the sensitivity of a firm's stock returns to monetary policy news. The authors document that firms with lower accounting quality experience more pronounced responses to surprise changes in the target Federal funds rate, consistent with proposed balance-sheet channel of policy transmission. We first discuss how this paper fits with prior literature on the role of accounting quality and firm investment and with recent work examining information frictions and policy transmission. We then question the intuition behind the paper's symmetric prediction. In addition, we highlight potential measurement issues related to returns and accounting quality. Lastly, we consider the key takeaways of the paper and provide suggestions for areas of future research.
Persistent and sporadic Listeria monocytogenes strains do not differ when growing at 37 °C, in planktonic state, under different food associated stresses or energy sources

The foodborne pathogen Listeria monocytogenes causes the potentially lethal disease listeriosis. Within food-associated environments, L. monocytogenes can persist for long periods and increase the risk of contamination by continued presence in processing facilities or other food-associated environments. Most research on phenotyping of persistent L. monocytogenes’ has explored biofilm formation and sanitizer resistance, with less data examining persistent L. monocytogenes’ phenotypic responses to extrinsic factors, such as variations in osmotic pressure, pH, and energy source availability. It was hypothesized that isolates of persistent strains are able to grow, and grow faster, under a broader range of intrinsic and extrinsic factors compared to closely related isolates of sporadic strains. To test this hypothesis, 95 isolates (representing 74 isolates of 20 persistent strains and 21 isolates of sporadic strains) from a series of previous studies in retail delis, were grown at 37 °C, in (i) stress conditions: salt (0, 5, and 10% NaCl), pH (5.2, 7.2, and 9.2), and sanitizer (benzalkonium chloride, 0, 2, and 5 μg/mL) and (ii) energy sources: 25 mM glucose, cellobiose, glycogen, fructose, lactose, and sucrose; the original goal was to follow up with low temperature experiments for treatments where significant differences were observed. Growth rate and the ability to grow of 95 isolates were determined using high-throughput, OD600, growth curves. All stress conditions reduced growth rates in isolates compared to control (p < 0.05). In addition, growth varied by the tested energy sources. In chemically defined, minimal media there was a trend toward more isolates showing growth in all replicates using cellobiose (p = 0.052) compared to the control (glucose) and fewer isolates able to grow in glycogen (p = 0.02), lactose (p = 2.2 × 10− 16), and sucrose (p = 2.2 × 10− 16). Still, at least one isolate was able to consistently grow in every replicate for each energy source. The central hypothesis was rejected, as there was not a significant difference in growth rate or ability to grow for retail deli isolates of persistent strains compared to sporadic strains for any treatments at 37 °C. Therefore, these data suggest that persistence is likely not determined by a phenotype unique to persistent strains grown at 37 °C and exposed to extrinsic stresses or variation in energy sources.
Infant environments in psychoanalysis: A cross-cultural view.

Freud was an avowed Darwinian, but the relationship between his theory and evolutionary biology is still being debated. Similarly, psychoanalysis is a developmental psychology, yet its connections with direct observations of child behavior remain problematic. This chapter examines certain psychoanalytic assumptions regarding the environments of infants in the light of direct observations made in culturally diverse human populations. Its aim is to provide a more secure base for a psychoanalytic contribution to the understanding of early experience and development and their place in human adaptation. In 1937 Heinz Hartmann presented to the Vienna Psychoanalytic Society his attempt to ground psychoanalytic ego psychology in a set of sophisticated assumptions concerning the biology, psychology, and sociology of individual development. Published two years later in German and two decades later in English, Hartmann's Ego Psychology and the Problem of Adaptation (1958) bridged many gaps between psychoanalysis and the biological and social sciences and influenced subsequent theory within psychoanalysis and to some extent outside it. One of its most influential concepts is “the average expectable environment of the child.” Hartmann did not specify what he meant by this nor did he state unequivocally whether it was supposed to be universal for all humans or variable across cultures. His strongest statement on the universal side was the following: Strictly speaking, the normal newborn human and his average expectable environment are adapted to each other from the very first moment. […]
Flat-histogram method comparison on the two-dimensional Ising model.

We compare the convergence of several flat-histogram methods applied to the two-dimensional Ising model, including the recently introduced stochastic approximation with a dynamic update factor (SAD) method. We compare this method to the Wang-Landau (WL) method, the $1/t$ variant of the WL method, and standard stochastic approximation Monte Carlo (SAMC). In addition, we consider a procedure WL followed by a ``production run'' with fixed weights that refines the estimation of the entropy. We find that WL followed by a production run does converge to the true density of states, in contrast to pure WL. Three of the methods converge robustly: SAD, $1/t$-WL, and WL followed by a production run. Of these, SAD does not require a priori knowledge of the energy range. This work also shows that WL followed by a production run performs superior to other forms of WL while ensuring both ergodicity and detailed balance.
Photoluminescence Excitation Spectroscopy Characterization of Surface and Bulk Quality for Early-Stage Potential of Material Systems

Photoluminescence Excitation Spectroscopy (PLE) is a contactless characterization technique to quantify Shockley-Reed-Hall (SRH) lifetimes and recombination velocities in direct band gap experimental semiconductor materials and devices. It is also useful as to evaluate surface passivation and intermediate fabrication processes, since it can be implemented without the need for development of effective contact technologies. In this paper, we present a novel experimental PLE system for precision-based quantification of the aforementioned parameters as well as a system for which absolute PLE characterization may occur. Absolute PLE measurements can be used to directly calculate VOC for new photovoltaic (PV) material systems and devices. Key system capabilities include a continuous excitation spectrum from 300 nm –1.1 μm, automated characterization, up to 1 nm wavelength resolution (up to 60x higher than prior work), and a reduced ellipsometry requirement for post-processing of data. We utilize a GaAs double heterostructure (DH) and an InP crystalline wafer as calibration standards in comparison with data from an LED-based PLE to demonstrate the validity of the results obtained from this new system.
Instabilities in a Self-Pumped Barium Titanate Phase Conjugate Mirror

We report the observation of intrinsic instabilities in the reflectivity of a barium titanate, self-pumped phase conjugate mirror (SPPCM). In such a device, a laser beam is focused into a crystal of barium titanate, and a beam is generated within the crystal that has been shown by FEINBERG [1] to be the phase conjugate of the incident laser beam. A model has been proposed [2] to explain this effect in terms of self beam fanning: the incident laser beam breaks up into new spatial components by self focusing. These components undergo total internal reflection at the corners of the crystal and are redirected in such a way that they intercept the incident laser beam, thereby forming the counterpropagating pump waves needed to create the phase conjugate beam by the usual four-wave mixing process. Since the pump waves grow from noise by a highly nonlinear process, and interact strongly with the incident and conjugate beams, it might be expected that the output beam would show unstable or even chaotic behavior. An alternative model for self-pumped phase conjugation has been presented by LAM [3]. According to this model, the phase conjugate return is formed by a two-beam stimulated scattering process. This process would not be expected to produce a chaotic output.
Delineation of clinical and biological factors associated with cutaneous squamous cell carcinoma among patients with chronic lymphocytic leukemia.

Background The incidence of cutaneous squamous cell carcinoma (SCC) in patients with chronic lymphocytic leukemia (CLL) is significantly higher compared with age- and sex-matched controls. Objective To evaluate the association of factors associated with SCC risk. Methods Clinical CLL and SCC data were obtained from Mayo Clinic CLL Resource and self-reported questionnaires among patients with newly diagnosed CLL. We computed the CLL International Prognostic Index (CLL-IPI) from CLL prognostic factors, and a polygenic risk score from SCC susceptibility variants. We used Cox regression to estimate hazard ratios (HRs) and 95% confidence intervals (CIs). Results Among 1269 patients with CLL, the median follow-up was 7 years, and SCC subsequently developed in 124 patients. Significant associations with SCC risk were history of skin cancer (HR=4.80; 95% CI: 3.37-6.83), CLL-IPI (HR=1.42; 95% CI: 1.13-1.80), and polygenic risk score (HR=2.58; 95% CI: 1.50-4.43). In a multivariable model, these factors were independent predictors (C statistic = 0.69; 95% CI: 0.62-0.76). T-cell immunosuppressive treatments were also associated with SCC risk (HR=2.29; 95% CI: 1.47-3.55; adjusted for age, sex, and prior SCC). Limitations The sample size decreases when combining all risk factors in a single model. Conclusion SCC risk includes history of skin cancer, an aggressive disease at time of CLL diagnosis, receiving T-cell immunosuppressive treatments, and high polygenic risk score. Future studies should develop prediction models that include these factors to improved screening guidelines.
Do Dental Implant Width and Length Matter

Achieving predictable outcomes in implant dentistry requires not only an understanding of surgical and prosthetic protocols but also knowledge of bone biology. Regarding implant stability, a distinction exists between non-osseointegrated and osseointegrated implants. Primary or mechanical stability at implant placement is different than secondary or biological stability. Bone quality, implant length, and implant width all influence the achievement of primary stability. This article reviews the contemporary literature on dental implant osseointegration, with the intent of presenting clinicians scientific information concerning the biomechanical parameters and limitations of endosseous implants and their components during the osseointegration phase, as well as their behavior once occlusal forces are present following osseointegration.
Cross‐Generational Effects of Parental Age on Offspring Longevity: Are Telomeres an Important Underlying Mechanism?

Parental age at offspring conception often influences offspring longevity, but the mechanisms underlying this link are poorly understood. One mechanism that may be important is telomeres, highly conserved, repetitive sections of non-coding DNA that form protective caps at chromosome ends and are often positively associated with longevity. Here, the potential pathways by which the age of the parents at the time of conception may impact offspring telomeres are described first, including direct effects on parental gamete telomeres and indirect effects on offspring telomere loss during pre- or post-natal development. Then a surge of recent studies demonstrating the effects of parental age on offspring telomeres in diverse taxa are reviewed. In doing so, important areas for future research and experimental approaches that will enhance the understanding of how and when these effects likely occur are highlighted. It is concluded by considering the potential evolutionary consequences of parental age on offspring telomeres.
Approach to Dyspnea

Dyspnea is a common patient presentation in outpatient or acute care settings. This teaching script leads the learner through a systematic approach to thinking through the causes of dyspnea. We emphasize the importance of including etiologies outside of pulmonary disorders when generating a differential diagnosis.
The Key to Combat Readiness Is a Strong Military-Civilian Partnership

Introduction In peacetime, it is challenging for Army Forward Resuscitative Surgical Teams (FRST) to maintain combat readiness as trauma represents Methods Over a 3-year period, all FRSTs were surveyed at one civilian center. Results Six hundred and thirteen FRST soldiers were provided surveys and 609 responded (99.3%), including 499 (81.9%) non-physicians and 110 (18.1%) physicians/physician assistants. The non-physician group included 69% male with an average age of 34 ± 11 years and consisted of 224 AR (45%) and 275 AD (55%). Rank ranged from Private to Colonel with officers accounting for 41%. For AD vs. AR, combat experience was similar: 50% vs. 52% had ≥1 combat deployment, 52% vs. 60% peri-deployment patient load was trauma-related, and 31% vs. 32% had ≥40 patient contacts during most recent deployment (all P > .15). However, medical experience differed for AD and AR: 18% vs. 29% had >15 years of experience in practice and 4% vs. 17% spent >50% of their time treating critically injured patients (all P Conclusions This is the first study of clinical practice patterns in AD vs. AR, non-physician members of Army FRSTs. In concordance with previous studies of military surgeons, FRST non-physicians seem to be lacking clinical experience as well. To maintain readiness and to provide optimal care for our injured warriors, the entire FRST, not just individuals, should embed within civilian centers.
Neutrophils significantly enhance pro-inflammatory cytokine release from airway epithelial cells in response to sars-COV-2 infection

RATIONALE: Novel coronavirus infectious disease (COVID-19) is caused by the severe acute respiratory distress syndrome related coronavirus 2 (SARS-CoV-2). Patients with underlying respiratory disease are considered at increased risk of contracting severe COVID-19. Many respiratory diseases including chronic obstructive pulmonary disease, asthma, and cystic fibrosis, have elevated inflammation driven by recruitment of neutrophils, known as neutrophilia, and contributes to disease pathogenesis. In response to viral infection, neutrophils are the first, and predominant, leukocyte recruited to the respiratory tract. Neutrophils release inflammatory mediators as part of the acute inflammatory response and contribute to pathogen clearance through virus internalization and killing, secretion of antimicrobial peptides and extracellular traps. It remains uncertain how critical the neutrophil response is in SARS-CoV-2 and to what extent this contributes to the cytokine response of the airways in COVID-19. We hypothesized that neutrophils are responsible for elevated inflammatory responses in patients who progress to severe COVID-19. Methods: To investigate, we developed a co-culture model of neutrophilic airways to study SARS-CoV-2 infection, combining primary human neutrophils and airway epithelial cells differentiated at the air-liquid interface. These cultures, with and without neutrophils, were infected with live SARS-CoV-2 and the inflammatory responses analyzed. In addition, extensive analysis of ACE2, neutrophils and inflammatory response, was performed comparing our models and COVID-19 patient and non-infected lung tissues. Results: ACE2 protein, the receptor binding to the S-protein of SARS-CoV-2, was predominantly expressed in submucosal glands, ciliated cells and in alveolar type 2 cells in human lung tissues. Surprisingly, substantial co-localization of ACE2 was also observed with neutrophil elastase and CD15 expressing neutrophils infiltrating the airways. Analysis of mono-and co-cultures of airway epithelial cells and neutrophils in the presence or absence of SARS-CoV-2 infection indicated significant increases in the expression of squamous epithelium associated cytokeratins, damage associated molecular patterns (DAMPS) and a downregulation of interleukin 8 (IL-8) specifically in the co-culture models. Airway supernatants from the basolateral and apical surfaces were profiled. In the neutrophil co-cultures significant increases in IFNγ, IL-1β, IL-6 and TNFα were observed in response to SARS-CoV-2 infection. Conclusions: In conclusion, we demonstrate that co-culture with neutrophils has a significant impact on SARS-CoV-2 infection, changing the inflammatory response and upregulating gene expression patterns associated with tissue remodeling and tissue damage. This study highlights the need to study SARS-CoV-2 infection in more complex, tissue-level models to fully understand the mechanisms driving the severe inflammatory response and the long-term consequences of infection.
Disruption of thioredoxin metabolism enhances the toxicity of transforming growth factor β-activated kinase 1 (TAK1) inhibition in KRAS-mutated colon cancer cells.

Transforming growth factor β-activated kinase 1 (TAK1) is critical for survival of many KRAS mutated colorectal cancer cells, and TAK1 inhibition with 5Z-7-oxozeaenol has been associated with oxidative stress leading to tumor cell killing. When SW 620 and HCT 116 human colon cancer cells were treated with 5 µM 5Z-7-oxozeaenol, cell viability, growth, and clonogenic survival were significantly decreased. Consistent with TAK1 inhibition being causally related to thiol-mediated oxidative stress, 10 mM N-acetylcysteine (NAC) partially reversed the growth inhibitory effects of 5Z-7-oxozeaenol. In addition, 5Z-7-oxozeaenol also increased steady-state levels of H2DCFDA oxidation as well as increased levels of total glutathione (GSH) and glutathione disulfide (GSSG). Interestingly, depletion of GSH using buthionine sulfoximine did not significantly potentiate 5Z-7-oxozeaenol toxicity in either cell line. In contrast, pre-treatment of cells with auranofin (Au) to inhibit thioredoxin reductase activity significantly increased levels of oxidized thioredoxin as well as sensitized cells to 5Z-7-oxozeaenol-induced growth inhibition and clonogenic cell killing. These results were confirmed in SW 620 murine xenografts, where treatment with 5Z-7-oxozeaenol or with Au plus 5Z-7-oxozeaenol significantly inhibited growth, with Au plus 5Z-7-oxozeaenol trending toward greater growth inhibition compared to 5Z-7-oxozeaenol alone. These results support the hypothesis that thiol-mediated oxidative stress is causally related to TAK1-induced colon cancer cell killing. In addition, these results support the hypothesis that thioredoxin metabolism is a critical target for enhancing colon cancer cell killing via TAK1 inhibition and could represent an effective therapeutic strategy in patients with these highly resistant tumors.
Abstract 2011: ETV4 promotes pancreatic cancer progression and metastasis

Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA Pancreatic cancer is a highly metastatic disease with a 5 year survival rate of ∼6.0% after diagnosis. The poor outcome of pancreatic cancer is largely due to its highly aggressive nature and lack of effective therapies against metastatic disease. Therefore, it is imperative to identify novel molecular targets driving metastatic progression of pancreatic cancer. ETV4, proto-oncogenic transcription factor, has been shown to be expressed aberrantly in various cancers types and to play important roles in pathobiology; however, its roles in pancreatic cancer have not been defined. We investigated the pathological significance of ETV4 in pancreatic cancer by its silencing in two highly metastatic pancreatic cancer cell lines, Colo357 and ASPC1, and by forced overexpression in weakly tumorigenic BXPC3 cells. Silencing of ETV4 led to decreases in growth, clonogenicity, motility and invasiveness of pancreatic cancer cells, whereas its overexpression had opposite effects. Furthermore, our data demonstrate a correlation with changes in the expression of mesenchymal (N-cadherin, Vimentin, Slug and Snail) and epithelial (E-cadherin) markers upon ETV4 modulation, indicating its role in epithelial to mesenchymal transition (EMT). More importantly, our in vivo studies in an orthotopic mouse model of pancreatic cancer demonstrated a direct association of ETV4 overexpression with tumorigenicity and metastatic potential of pancreatic cancer cells. In summary, our studies establish a functional role of ETV4 in pancreatic cancer pathogenesis. Citation Format: Nikhil Tyagi, Sanjeev K. Srivastava, Arun Bhardwaj, Sumit Arora, William E. Grizzle, Laurie B. Owen, Ajay P. Singh, Seema Singh. ETV4 promotes pancreatic cancer progression and metastasis. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2011. doi:10.1158/1538-7445.AM2014-2011
Laser driven electron acceleration

Issues pertaining to laser acceleration in vacuum, neutral gases and plasmas are discussed. For acceleration in vacuum the limitations due to electron slippage, laser diffraction, material damage and electron aperture effects are discussed. To achieve multi GeV electron energies in the laser wakefield accelerator (LWFA) it is necessary to propagate an intense laser pulse long distances in a plasma without disruption. It is shown that electron energies of /spl sim/GeV in a channel guided LWFA can be achieved by using short pulses where the forward Raman and modulation nonlinearities tend to cancel. Further energy gain can be achieved by tapering the plasma density to reduce electron dephasing.
Rate control for delay-constrained video transmission

We study the rate control problem for video transmission environments which require real-time encoding and transfer of the video data, and where rate-distortion (RD) optimal rate control approaches requiring a long encoding delay cannot be used. We propose two novel RD optimized rate control approaches based on dynamic programming and Lagrangian optimization.
Cost and Fee Allocation in Civil Procedure: United States of America National Report

This report summarizes critically the American practice of providing indemnity for court costs in litigation but not for attorneys' fees. It considers the basics, who pays, the rationals, exceptions,and modifications. It challenges the suggestion that the American no-indemnity practice reflects American values and debunks the assertion that it is used to promote access to justice. The report show that American jurists, just as their non-American counterparts, have pointed to a rational of full realization of rights to support complete indemnity. The reports notes the role of the bar in promoting no indemnity and the importance of viewing litigation as an event separate from the rights that it is to enforce.
Subtleties among subtilases

Prohormone processing was discovered 35 years ago with the observation that proinsulin is the precursor of both the A and the B chains of insulin (Steiner, 1969). During the next 15 years, many candidate proteases were proposed and rejected before genetic and biochemical evidence identified specific processing proteases in Saccharomyces cerevisiae that are involved in α‐factor biosynthesis (Julius et al ., 1983, 1984). The initial cleavages of the precursor—endoproteolytic scissions carboxyl to Lys‐Arg sites—are due to the action of Kex2 protease. Mammalian Kex2 homologues, known as furin, PC1/3, PC2, PC4, PACE4, PC5/6 and PC7/LPC were cloned throughout the 1990s. They were shown to process hormone and neuropeptide precursors, growth factors, receptors, metallo‐ and aspartyl proteases, envelope glycoproteins of many viruses including HIV, and bacterial toxins such as anthrax‐protective antigen (Zhou et al ., 1999; Thomas, 2002). These Kex2‐homologous prohormone convertases (PCs) are unrelated to the tryptic enzymes of the blood coagulation cascade that hydrolyse precursors carboxyl to basic amino acids. By contrast, PCs are related to degradative enzymes, such as subtilisin and proteinase K (Fuller et al ., 1989). Thus, accounting for the refined functions and specificity of PCs has been a major research problem. Molecular‐genetic studies have established a ‘P‐domain’ carboxyl to the subtilisin domain that is essential for the biosynthesis and/or activity of PCs. Biochemical analyses have further indicated …
Correlated Multinomial Data

Correlated multinomial data, including correlated binomial, arise from clustered sampling schemes such as grouped sampling or repeated measurements. Correlation induced by clustering can be of interest in its own right, but must be accounted for in statistical analyses to avoid inaccurate or inefficient inference. This article discusses common approaches to the treatment of correlated multinomial data and illustrates dose-response modeling via generalized estimating equations using an example from developmental toxicity experiment. Keywords: clustered sampling; mixture distribution; generalized estimating equations; developmental toxicity; dose-response
Distribution by Serological Type of Group B Streptococci Isolated from a Variety of Clinical Material over a Five-Year Period (with Special Reference to Neonatal Sepsis and Meningitis)

A total of 898 group B streptococci isolated from a wide variety of human clinical sources from July 1967 through June 1972 were typed by the Lancefield precipitin test. Only 11% of the strains were nontypable. Twenty-six percent of the group B strains were from respiratory sources, 22% were from cerebrospinal fluid (CSF) and blood, 13% were from the female genital tract, 12% were urine specimens, and the remaining 27% were from other varied sources. The clinical conditions reported for patients from whom these organisms were isolated included neonatal meningitis and sepsis, pharyngitis, urinary tract and female genital tract infections, and various skin and wound infections. Seventy percent of the CSF and blood cultures from patients with meningitis or sepsis, or both, were type III, whereas the overall percentage of this type was 32%. All but three CSF isolates were from patients under 2 years of age; the distribution of CSF isolates appeared to be the same for both sexes. In contrast, group B streptococci were isolated more frequently from the blood of males than from the blood of females. There were twice as many blood cultures from patients under 2 years of age than from those that were older. Images
A second-order backward difference time-stepping scheme for penalized Navier–Stokes equations modeling filtration through porous media

We investigate the stability and convergence of a fully implicit, linearly extrapolated second-order backward difference time-stepping scheme for the penalized Navier–Stokes equations modeling filtration through porous media. In the penalization approach, an extended Navier–Stokes equation is used in the entire computational domain with suitable resistance terms to mimic the presence of porous medium. It is widely used as an alternative to the heterogeneous approach in which different types of partial differential equations (PDEs) are used in fluid and porous subregions along with suitable continuity conditions at the interface. However, the introduction of extra resistance terms makes the penalized Navier–Stokes equations more nonlinear. We prove that the linearly extrapolated scheme is unconditionally stable and derive optimal order error estimates without any stability condition. To show feasibility and applicability of the approach, it is used to numerically solve a passive control problem in which flow around a solid body is controlled by adding porous layers on the surface.© 2015 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2015
Distribution and diversity of ribosome binding sites in prokaryotic genomes

Background Prokaryotic translation initiation involves the proper docking, anchoring, and accommodation of mRNA to the 30S ribosomal subunit. Three initiation factors (IF1, IF2, and IF3) and some ribosomal proteins mediate the assembly and activation of the translation initiation complex. Although the interaction between Shine-Dalgarno (SD) sequence and its complementary sequence in the 16S rRNA is important in initiation, some genes lacking an SD ribosome binding site (RBS) are still well expressed. The objective of this study is to examine the pattern of distribution and diversity of RBS in fully sequenced bacterial genomes. The following three hypotheses were tested: SD motifs are prevalent in bacterial genomes; all previously identified SD motifs are uniformly distributed across prokaryotes; and genes with specific cluster of orthologous gene (COG) functions differ in their use of SD motifs.
Post-disaster recovery dilemmas: challenges in balancing short-term and long-term needs for vulnerability reduction

Abstract Following disasters, governments often clamor to quickly reduce risk, rebuild communities and restore permanence. The pressure to urgently address complex, difficult decisions can result in reactive policies that may increase long-term vulnerability of affected populations. Sri Lanka in the aftermath of the 26 December 2004 tsunami represents such an example: a hastily designed coastal buffer zone policy has incited massive relocation of affected populations and resulted in social, economic and environmental problems that threaten the well-being of poor coastal communities. We review the impacts of this policy from its inception, days after the tsunami hit the island, until its revision, approximately 10 months following the disaster. We then apply a framework to conceptualize the components of vulnerability within Sri Lanka's coastal, human–environment system and to identify where post-disaster policies should focus to reduce vulnerability of coastal populations more effectively. From this analysis, it is apparent that the buffer zone policy gave disproportionate attention to reducing exposure to future tsunamis and, subsequently, did not address the critical social, economic and institutional factors that influenced sensitivity to the hazard. Post-disaster policies aimed at sustainable re-development should be informed by an analysis of the components of vulnerability that comprise a system and how these can be most effectively influenced during the separate short-term and long-term phases of rebuilding.
Molecular Dynamics Simulations of Pressure Effects on Hydrophobic Interactions

We report results on the pressure effects on hydrophobic interactions obtained from molecular dynamics simulations of aqueous solutions of methanes in water. A wide range of pressures that is relevant to pressure denaturation of proteins is investigated. The characteristic features of water-mediated interactions between hydrophobic solutes are found to be pressure-dependent. In particular, with increasing pressure we find that (1) the solvent-separated configurations in the solute−solute potential of mean force (PMF) are stabilized with respect to the contact configurations; (2) the desolvation barrier increases monotonically with respect to both contact and solvent-separated configurations; (3) the locations of the minima and the barrier move toward shorter separations; and (4) pressure effects are considerably amplified for larger hydrophobic solutes. Together, these observations lend strong support to the picture of the pressure denaturation process proposed previously by Hummer et al. (Proc. Natl. Aca...
On-line detection of random voltage perturbations in buses with multiple-threshold receivers

Random voltage changes on bus lines may lead to reading corrupted digital data. A novel methodology for detecting such anomalies is proposed. It uses multiple threshold voltages at the receiver-end. In our earlier work we have shown that multiple voltage thresholds improve the performance along buses, especially when they are coupled as is often the case in deep-submicron. This work shows that multiple thresholds can also be used to identify voltage perturbations on-line. The mechanism is presented assuming that each line can have only one aggressor. The efficiency of the methodology is evaluated for perturbations in single and multiple receiving nodes of a data bus.
Acquisition of rising intonation in pediatric cochlear implant recipients—a longitudinal study

Abstract This study examined how cochlear implant (CI) devices can facilitate pediatric users' post-implant acquisition of rising intonation of speech. Participants were 24 prelingually deafened individuals who received their implants from 2.5 to 11 years of age. A target utterance “Are you ready?” was imitatively produced by each of the participants following an examiner's model on an annual basis (up to 10 years post-implantation). Ten normal-hearing listeners perceptually judged these utterances (N=173) regarding whether the perceived utterances had an intonation of non-rise, partial rise, or full-rise. Listeners also judged each utterance with respect to its intonation contour appropriateness and speech intelligibility. Results indicated that pediatric CI recipients' production of rising intonation was unsatisfactory. Scores of both intonation category and contour appropriateness judgments did not appear to improve beyond 7 years post-implantation. These findings suggest that CI devices can be limited in its facilitation of acquisition of rising intonation. Further studies are required to help us understand the acquisition of speech intonation both in terms of perception and production in this population.
ACUTE CHEST SYNDROME (ACS) IN SICKLE CELL PATIENTS IS OFTEN DUE TO MYCOPLASMA PNEUMONIAE

ACS in sickle cell disease (SCD) includes the often indistinguishable processes of pneumonia and pulmonary infarction. 47 episodes of radiologically positive ACS in 18 months were studied prospectively to determine etiology and clinical consequences. None was associated with a positive blood culture or CIE test. 10 episodes (21%) were associated with positive viral cultures: 3 adenovirus, 2 CMV, and 1 each of RSV, herpes simplex, enterovirus, parainfluenza, and influenza B. 10 (21%) of the patients had ACS due to Mycoplasma pneumoniae (Mp) as documented by 4-fold or greater changes in specific antibody titer. When compared to other cases, ACS due to Mp was more severe with a lower hemoglobin on hospital admission (7.1±1.5 vs 8.0±1.5 g/dl, p=0.05) and a greater fall from the patients' usual level (1.5±1.3 vs 0.8±1.2 g/dl, p=0.05). 2/10 Mp patients and 1/37 other patients required red cell transfusions. Patients infected with Mp had prolonged fever (5.5±4.1 vs 3.2±2.0 days, p=0.009) and longer hospitalizations (8.0±3.7 vs 5.7±2.0 days, p=0.006). Cold agglutinin titers were ≥ 1:16 in 5/6 Mp episodes and in 1/22 other episodes (p=0.0007). In this study Mp caused ACS in many patients and was associated with significant morbidity. Early detection using cold agglutinin titers is usually possible. SCD patients with ACS should be screened with a cold agglutinin titers as a prognostic factor. Those with a high titer may benefit from early treatment with erythromycin.
USING GEOGRAPHIC INFORMATION SYSTEM TECHNOLOGY TO SYNTHESIZE CENSUS AREAWIDE AND LINEAR HIGHWAY DATA FOR LOCATION OF WEIGH-IN-MOTION SITES

A process is described that was developed by the New York State Department of Transportation to identify potential areas around the state for location of new weigh-in-motion sites. The procedure uses geographic information system (GIS) technology to synthesize census areawide travel and business data with linear highway system traffic and vehicle classification data from the Department's computer inventories. The conclusion is that GIS is a powerful tool for synthesizing and displaying diverse data sets for use in solving engineering problems.
Very slow relaxation in systems lacking translational symmetry, with emphasis on disordered insulators

Abstract The paper addresses the problem of very slow relaxations of electrons observed in a large variety of materials. Three aspects of the slow relaxations are explicitly considered: a.c. conductivity, dispersive transport, and the electron glass. Interactions have previously been proposed as the primary cause for the very slow relaxation process. It is argued here that while interactions are important in making slow rates even slower, the primary cause for the very slow relaxations is localization, and thus lack of translational symmetry. Specifically, it is shown that the appropriate a.c. conductivity, dispersive transport, as well as the electron glass can exist without interactions. The time evolution of the entropy and of the polarizability are calculated for non-interacting electrons in a disordered insulator. It is found that a temperature exists where the polarizability changes dramatically, but the entropy varies smoothly. The effects of interactions are discussed on a qualitative level.
The incidence of scintigraphically viable and nonviable tissue by rubidium-82 and fluorine-18-fluorodeoxyglucose positron emission tomographic imaging in patients with prior infarction and left ventricular dysfunction

Background Although reversible perfusion defects, perfusion-metabolism mismatch and match patterns are important for differentiating viable from nonviable myocardium, the frequency of these scintigraphic patterns has not been reported. The study objective was to establish the incidence of these scintigraphic patterns to estimate the clinical need for metabolic positron emission tomography for evaluating tissue viability in patients with prior myocardial infarction (MI).
Seasonal comparisons of daily activity budgets of gray squirrels (Sciurus carolinensis) in urban areas

Gray squirrels (Sciurus carolinensis) use trees for various resource needs in urban and nonurban settings; particularly, mast producing trees which are the preferred and supplemental foods for the species. During periods of abundant mast availability, less time will be invested in foraging because of the higher success rate stemming from the increased ability to locate food items. Conversely, in periods of reduced mast availability, more time will be invested in foraging. However, correlations between food availability and foraging effort are only supported under the assumption that gray squirrels rely significantly on mast as a preferred or supplemental food source (Nixon et al, J Wildl Manag 39:1–25, 1975). Therefore, given the seasonal variation in the availability of mast, there should also be correlating seasonal variations in foraging effort. In this paper, we will examine daily and seasonal time-activity budgets of gray squirrels in urban areas. We studied the time-activity budgets of gray squirrels in six urban parks in Baltimore, MD. Seasonal frequencies of activities were expressed as percent occurrence and seasonal differences in activities were analyzed using a Tukey Studentized multiple range test for significance. We found that the activity with highest percent occurrence was forage (2003, summer: 23.8 %, fall: 25.9 %; 2004, summer: 23.1 %, fall: 25.2 %), followed by feed and store, all activities associated with food. Results of the Tukey Studentized multiple range test for seasonal differences of activities yielded significant results (P < 0.05) for rest: fall 2003 and summer 2004 (P = 0.003); fall 2003 and fall 2004 (P = 0.048).
Remembering Bruce: the early years.

This paper summarizes Merrifield-Stewart interactions during the years 1952–1968. © 2007 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 90: 185–187, 2008. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
History of the diabetic foot

In the first half of this century serious foot problems in diabetic patients were described in standard text books under the general description of ‘diabetic gangrene’ Inevitably with the passage of time and a greater understanding of the diabetic process, changes in clinical classification and description have occurred. Choyce’ in 1923 regarded diabetic gangrene as senile gangrene due to arteriosclerosis, but the condition was rendered more severe by the lowered vitality of the tissues in a diabetic subject. No mention is made of the use of insulin in its management as at that time insulin was not universally available. A decade later in 1933, Rose and Carless’ emphasized the importance of impaired resistance of the tissues to bacterial invasion, but considered that sclerosing endarteritis and peripheral neuritis played an important part. Aird3 in 1957 considered that in young patients, diabetic gangrene was essentially an infective process occurring in tissue of low bacterial resistance, while in older subjects the cause was mainly arteriosclerotic. Of more recent date, Bailey and Love4 in 1965 give equal importance to neuropathy, arteriosclerosis and infection. The clinical presentation of gangrene in diabetics showed wide variations. In elderly patients the foot was cold and pale, the toes became dark and painful, and with the passage of time the blackened and shrunken digits tended to separate and ultimately the wound healed. The condition was described as ‘dry’ gangrene. On the other hand a much more progressive and dangerous condition could occur. The foot became swollen and dusky in appearance. Patches of gangrene occurred in the skin and ulcers developed on the sole of the foot in the region of the heads of the metatarsal bones. Though pain was not a marked feature, the condition was very toxic as infection spread in the foot and leg. Without effective treatment the condition could prove fatal. This condition was regarded as wet gangrene. It was realized that ‘dry’ gangrene could progress to wet gangrene though it was rare for wet gangrene to become ‘dry’. Treatment varied according to the type of gangrene.
High ciliary neuronotrophic specific activity in rat peripheral nerve

Ciliary neuronotrophic factors (CNTFs) are proteins defined by their ability to promote the survival in tissue culture of chick embryo ciliary ganglionic neurons. CNTF activity has been reported in several source materials. Among these sources, the highest specific activity, i.e. 16,000 TU/mg, has been found in the intraocular tissue innervated by the ciliary ganglionic neurons. We now report that extracts of adult rat peripheral nerve and spinal nerve roots contain CNTF at a specific activity equal to or greater than the intraocular tissue. Equally high concentrations of CNTF activity are found in both motor and sensory nerves. The possible cellular source(s) of this mammalian CNTF is discussed.