cssi/SciSciGPT-SciSciNet huggingface dataset:
Introduction: To Vaccinate, or Not to Vaccinate

The impact of poliomyelitis, the search for a vaccine, and the formalization of mass vaccination it inaugurated continue to resonate in American society. Using the lens of polio allows us to gaze in the larger context of vaccine development which often endangered children. This introduction establishes the concepts of vulnerable and captive populations framing this study. It also analyzes how the public school system operated as an indispensable tool in the eradication of polio in the USA and continues to do so regarding general vaccination policy.
Heterogeneous Statistical QoS-Driven Resource Allocation for D2D Cluster-Caching Based 5G Multimedia Mobile Wireless Networks

To support the multimedia services over 5G mobile wireless networks, the heterogeneous statistical quality- of-service (QoS) technique has been designed to jointly guarantee the statistically delay-bounded video transmissions over different time-varying wireless channels, simultaneously. On the other hand, as one of the 5G-promising candidate techniques, device-to-device (D2D) technique has been shown to improve both energy efficiency and spectrum efficiency for multimedia communications. However, overuse of the D2D transmissions may cause the unnecessary interferences to the original base-station oriented cellular networks. Consequently, under heterogeneous statistical delay- bounded QoS constraints, in-network caching techniques, clustering algorithms, and resource allocation policies have been proposed for D2D cluster-caching based 5G multimedia wireless networks with new opportunities and challenges. To effectively overcome the above-mentioned challenges, we propose the heterogeneous statistical QoS-driven resource allocation scheme through applying the D2D cluster-caching based system. In particular, under the Nakagami-\textit{m} fading model, we establish the system models for the dynamic D2D clustering based video stream sharing and the wireless transmissions. Given the heterogeneous statistical QoS constraints, we derive and analyze the aggregate effective capacity under our developed optimal resource allocation policies for the heterogeneous QoS-driven D2D cluster-caching based 5G multimedia mobile wireless networks. Also conducted is a set of simulations which validate and evaluate our proposed D2D cluster-caching based scheme, compared with the other existing schemes in terms of effective capacity under heterogeneous statistical QoS constraints.
An Optimization Framework for Job Rotation to Better Assess the Impact on Overall Risk

We aim to study the potential of job rotation schemes to improve worker safety. To this end, we developed a novel optimization framework based on a recently proposed fatigue-failure model for muscu...
Marketing and the United States Supreme Court, 1965-1968

Important changes in marketing's legal environment have resulted from decisions of an extremely active U. S. Supreme Court during the past three years. The Court decisions have altered significantl...
"Implications of cost-sharing for observation care among Medicare beneficiaries: a pilot survey".

Medicare beneficiaries hospitalized under observation status have significant cost-sharing responsibilities under Medicare Part B. Prior work has demonstrated an association between increased cost-sharing and health care rationing among low-income Medicare beneficiaries. The objective of this study was to explore the potential impact of observation cost-sharing on future medical decision making of Medicare beneficiaries. Single-center pilot cohort study. A convenience sample of Medicare beneficiaries hospitalized under observation status care was surveyed. Out of 144 respondents, low-income beneficiaries were more likely to be concerned about the cost of their observation stay than higher-income respondents (70.7% vs29.3%, p = 0.015). If hospitalized under observation status again, there was a trend among low-income beneficiaries to request completion of their workup outside of the hospital (56.3% vs 43.8%), and to consider leaving against medical advice (AMA) (100% vs 0%), though these trends were not statistically significant (p = 0.30). The results of this pilot study suggest that low-income Medicare beneficiaries hospitalized under observation status have greater concerns about their cost-sharing obligations than their higher income peers. Cost-sharing for observation care may have unintended consequences on utilization for low-income beneficiaries. Future studies should examine this potential relationship on a larger scale.
Zika virus infection of pregnant rats and associated neurological consequences in the offspring

Zika virus (ZIKV) is a mosquito-borne flavivirus associated with microcephaly and other neurological disorders in infants born to infected mothers. Despite being declared an international emergency by the World Health Organization, very little is known about the mechanisms of ZIKV pathogenesis or the long-term consequences of maternal ZIKV infection in the affected offspring, largely due to the lack of appropriate rodent models. To address this issue, our lab has developed a working model of prenatal ZIKV infection in rats. In this study, we infected immune competent pregnant female rats with 105-107 PFU of ZIKV (PRVABC59, Puerto Rico/Human/Dec 2015) in order to examine its pathogenesis in the dams and pups. We examined the febrile response and sickness behavior in the dams, in addition to neonatal mortality, microglia morphology, cortical organization, apoptosis, and brain region-specific volumes in the offspring. Here, we demonstrate that pregnant and non-pregnant female rats have a distinct febrile response to ZIKV infection. Moreover, prenatal ZIKV infection increased cell death and reduced tissue volume in the hippocampus and cortex in the neonatal offspring. For the first time, we demonstrate the efficacy and validity of an immunocompetent rat model for maternal ZIKV infection that results in significant brain malformations in the neonatal offspring.
Increasing value of autopsies in patients with brain tumors in the molecular era.

Pediatric brain tumors are associated with high morbidity and mortality, in part due to insufficient understanding of tumor biology. With limited tissue allocation for research from surgical specimens, a key barrier to improving biological understanding, brain tumor autopsies have become an increasingly valuable resource. This study reviews the brain tumor autopsy practice at our institution and describes specific emerging research utilization patterns beyond the clinical autopsy report. We performed a retrospective analysis of brain tumor autopsies at Boston Children’s Hospital (BCH) between 2007 and 2017 and reviewed their consents, neuropathology reports and final diagnoses. We reviewed the method of tissue triaging for research consented autopsies (bioregistry, frozen and fresh tissue) and documented their specific uses. Ninety-six deaths at BCH were due to brain tumors; 56 autopsies were performed (58.3%), of which 49 (87.5%) were consented for research. Tumor mapping was performed on all cases and tissue was allocated for DNA- and RNA-based sequencing studies (published and ongoing). Three tissue allocations with a postmortem interval of 8 h or less resulted in successful cell lines. Tissue from 14 autopsies was contributed to the National DIPG Registry. Our institutional pediatric brain tumor autopsy clinical experience demonstrates the increased utility and wide utilization of autopsy-derived tissue for multiple types of research. These results support the increased efforts to obtain research consent for brain tumor autopsy and active collection of unfixed autopsy material in the molecular era.
Oligometastatic Breast Cancer: Is This a Curable Entity? A Contemporary Review of the Literature.

Oligometastatic breast cancer (OMBC) remains a poorly understood entity for which no standard of care exists at this time. This review will focus on our biologic understanding of OMBC and provide an update on current treatment strategies. The introduction of micro RNA expression profiling has advanced our understanding of the biologic underpinnings of OMBC. Although most of the data regarding treatment have come from retrospective studies, there are now prospective randomized trials reporting progression-free survival and overall survival improvements with stereotactic ablative radiotherapy (SABR). Ongoing studies designed to evaluate addition of SABR as well as other novel agents will further develop this field and provide new treatment options. A “cure” for OMBC remains elusive. With further basic research coupled with novel prospective trials, patients will hopefully enjoy increased progression-free survival and overall survival, and ideally a delay to more toxic systemic therapy.
Benign adenoidal hypertrophy caused by adenovirus presenting as a nasopharyngeal mass concerning for malignancy

Abstract Benign adenoidal hypertrophy is the most common cause of nasopharyngeal obstruction. However, depending on size and location, masses may cause nasopharyngeal obstruction. We present our experiences with a ten-year-old female who presented with what appeared to be a large nasopharyngeal mass that was initially favored to be malignant and was ultimately found to be adenoid hypertrophy related to acute infection with adenovirus.
Elucidating the immune suppressive effects of antibiotics in cattle

The impact of antibiotic therapy on antimicrobial drug-resistance is well known in the cattle industry yet the potential effects of antibiotic administration on immune modulation is unknown. Data from various animal models indicate that some antibiotics can suppress adaptive immune responses. Azithromycin for example, can suppress inflammation and innate immune defenses inferring that indiscriminate use of antibiotics may paradoxically increase susceptibility to infection and interfere with vaccine immunity. For cattle, we aim to identify classes of immune modulatory antibiotics to determine whether treatment interferes with vaccine responses. We hypothesize that macrolide and tetracycline antibiotics will significantly suppress immune responses in cattle which will be tested using assays that evaluate immunity in vitro.
Neal Hoffman and the Mensch on a Bench

Neal Hoffman and his wife, Erin, were an interfaith couple out shopping when they ran right into the dilemma of how to balance Hanukkah and Christmas. Hoffmansaw his young son feeling left out by the Elf on the Shelf, a Christmas toy that was experiencing a huge amount of popularity in 2012. He suspected there were other Jewish and interfaith families that would appreciate a character for themselves.Hoffman decided to write a book to help Jewish kids appreciate and celebrate Hanukkah. He inserted a new character, Moshe, into the Hanukkah story. Moshe was a mensch—a good and honorable person in Yiddish—and Hoffman called his character the Mensch on a Bench. With a book and a character, Hoffman knew he could instill a sense of culture and celebration into his idea for a toy.This case details Hoffman's struggle to produce the Mensch--from earning money via Kickstarter and dealing with overseas production problems to trying to get the word out about the new holiday toy. Excerpt UVA-ENT-0205 Jul. 30, 2014 NEAL HOFFMAN AND THE MENSCH ON A BENCH Hoffman instinctively joked, “Jews don't do Elves on Shelves. We do Mensches on Benches.”Hoffman had a great name, but that wasn't enough reason to create a new toy. Hoffman saw his son feeling left out by the Elf on the Shelf craze, and he suspected there were other Jewish and interfaith families that would appreciate a character for themselves. But a mensch sitting on a bench wasn't a compelling idea on its own.Hoffman decided to write a book to help Jewish kids appreciate and celebrate Hanukkah. He inserted a new character into the story of the Maccabees, who returned from a fight to find they only had enough oil in the temple to last for one night. Hanukkah, the festival of lights, celebrates the fact that the oil lasted for eight nights instead of one. The new character Hoffman added was Moshe. He would watch over the oil and help everyone by letting the Maccabees know when the oil ran out. Moshe was a mensch—a good and honorable person in Yiddish, the historical language of Ashkenazi Jews. Hoffman instinctively joked, “Jews don't do Elves on Shelves. We do Mensches on Benches.” Hoffman had a great name, but that wasn't enough reason to create a new toy. Hoffman saw his son feeling left out by the Elf on the Shelf craze, and he suspected there were other Jewish and interfaith families that would appreciate a character for themselves. But a mensch sitting on a bench wasn't a compelling idea on its own. . . .
Accountability and effort among street-level bureaucrats: Evidence from a lab-in-the-field experiment

Governance reforms like decentralization and performance-based management aim to improve public services by increasing accountability among street-level bureaucrats: bureaucrats may be held to acco...
Delivering Health Information to Parents via a Theory-Informed SMS-Based Intervention: Development and Results from a Pilot Study.

Short message service (SMS), or text-based, health interventions offer a promising opportunity to deliver health education and have been shown to improve diet and exercise. However, few are theory-based or target low-income parents. This pilot study, informed by the Theory of Planned Behavior (TPB), primarily sought to determine if health education delivered via SMS was feasible and acceptable to low-income parents of young children. Using a one-group, pre- to post-test study design to assess a 12-week SMS-based health education program, parents enrolled in a health-related program at an early childhood development center for low-income families were sent three text messages per week that corresponded to a weekly diet or physical activity-related theme. Surveys assessed pre-post changes in TPB constructs and collected program feedback. Among the 119 eligible parents invited to participate, 109 were sent all text messages for the duration of the study. Participants were mostly Black (98.9%), 25–39 years old (83.9%), female (93.8%), and in single-parent households (63.8%). More than half (n = 59) completed the pre-survey, answered a bi-directional program text, or completed the post-survey. Twelve participants completed both the pre- and post-survey and at least one bi-directional text. Post-survey results revealed that most participants liked the program design and enjoyed their experience with the program. SMS-based interventions can simplify delivery of health information to low-income parents of young children. Although engagement was low, retention was high, and feedback was largely positive.
Disparate Impact: A Failed Remedy for Discrimination

Per the regulatory guidelines espoused by the EEOC, the necessity of disparate treatment as the mode of remedying disparate impact claims is unavoidable. As such, the Ricci standard of a “strong-basis-in-evidence” to balance the practice of disparate treatment to remedy disparate impact is holding. However, the EEOC, in creating racial classifications in order to adjudicate claims, is bound by Fourteenth Amendment jurisprudence to abide by the strict-scrutiny standard. The consequence of these conflicting standards in disparate impact adjudication is a detriment to racial groups as well as the American legal system. In the case of Ricci, a group of firefighters were deprived of a promotion due to the promotion tests enabling the disproportionate promotion of white firefighters. The fear that disparate impact claims instill in those employment decisions creates social backlash. The psychological categorization by employers of racial groups in an increasingly conscious attempt to solicit disparate impact claims creates a psychological over-exaggeration of race. This over-exaggeration, as studies show, tends to elicit decision-making based more-so on stereotypes. The low standard of scrutiny permits the EEOC to create these racial classifications more pervasively. As a result, the fear that disparate impact claims instill into employers creates a society that is in turn more discriminatory rather than less – defeating the remedial purpose of disparate impact doctrine.
Plutonium in Manhattan Project workers: Using autopsy data to evaluate organ content and dose estimates based on urine bioassay with implications for radiation epidemiology

Purpose Radiation dose estimates in epidemiology typically rely on intake predictions based on urine bioassay measurements. The purpose of this article is to compare the conventional dosimetric estimates for radiation epidemiology with the estimates based on additional post-mortem tissue radiochemical analysis results. Methods The comparison was performed on a unique group of 11 former Manhattan Project nuclear workers, who worked with plutonium in the 1940s, and voluntarily donated their bodies to the United States Transuranium and Uranium Registries. Results Post-mortem organ activities were predicted using different sets of urine data and compared to measured activities. Use of urinalysis data collected during the exposure periods overestimated the systemic (liver+skeleton) deposition of 239Pu by 155±134%, while the average bias from using post-exposure urinalyses was –4±50%. Committed effective doses estimated using early urine data differed from the best estimate by, on average, 196±193%; inclusion of follow-up urine measurements in analyses decreased the mean bias to 0.6±36.3%. Cumulative absorbed doses for the liver, red marrow, bone surface, and brain were calculated for the actual commitment period. Conclusion On average, post-exposure urine bioassay results were in good agreement with post-mortem tissue analyses and were more reliable than results of urine bioassays collected during the exposure.
Association Meeting Planners' Perceptions of Five Major Convention Cities

Abstract The purpose of this study is to report the pre-test results of a questionnaire designed to examine association meeting planners' site selection criteria and performance of five major convention cities. Pre-testing is necessary to ensure face (content) validity of the instrument by assessing the meaning of questions (ambiguity and bias), continuity and flow, question sequence, scale variability, and length and timing. The findings from the pre-test provided significant feedback for content validity of selection criteria used in the study, measurement and scaling, and flow of the questionnaire. The implications were discussed.
Keyboard Instruction for Students with a Disability

Abstract Projected employment reports indicate that most new jobs will involve occupations in which computer skills are essential, but surveys reveal that many people with a disability currently lack these computer skills. One way to address the gap is to prepare students while they are attending primary and secondary school. The National Business Education Association developed technology standards for all students in grades K–12 and recommend that keyboarding instruction begin in third or fourth grade. However, research studies indicate that general education teachers, special educators, and business education teachers do not feel prepared to teach keyboarding to students with a disability. This article reviews current practices in keyboarding instruction and provides suggestions for adaptations for students with disabilities.
Confessions after Connelly: An Evidentiary Solution for Excluding Unreliable Confessions

The subject matter of this Article - the criminal justice system’s treatment of unreliable confessions in light of Connelly - is especially appropriate for two reasons. First, and as noted above, Connelly recently celebrated its twentieth anniversary. This passage of time is long enough to allow for an informed retrospective of the decision but not so long that the opportunity for meaningful reform has lapsed. Second, an examination of how to better exclude unreliable and false confessions, which this Article undertakes, is an appropriate companion piece to “Rethinking Police Interrogation: Encouraging Reliable Confessions While Respecting Suspects’ Dignity,” published in 2006. In that article, I proposed changes to police interrogation practices, including Miranda warnings, that encourage the rendering and reception of reliable confessions. Just as this earlier article suggests reforms to maximize truthful confessions, this Article proposes reforms to minimize false confessions. These complementary ends serve a larger goal, which is the defining purpose of a criminal trial: to search for the truth.
Regression Models of Atlas Appearance

Models of object appearance based on principal components analysis provide powerful and versatile tools in computer vision and medical image analysis. A major shortcoming is that they rely entirely on the training data to extract principal modes of appearance variation and ignore underlying variables (e.g., subject age, gender). This paper introduces an appearance modeling framework based instead on generalized multi-linear regression. The training of regression appearance models is controlled by independent variables. This makes it straightforward to create model instances for specific values of these variables, which is akin to model interpolation. We demonstrate the new framework by creating an appearance model of the human brain from MR images of 36 subjects. Instances of the model created for different ages are compared with average shape atlases created from age-matched sub-populations. Relative tissue volumes vs. age in models are also compared with tissue volumes vs. subject age in the original images. In both experiments, we found excellent agreement between the regression models and the comparison data. We conclude that regression appearance models are a promising new technique for image analysis, with one potential application being the representation of a continuum of mutually consistent, age-specific atlases of the human brain.
A Note on the Non-Existence of the Return Drag of a Cap-Weighted Portfolio Comparing to a Fair-Value-Weighted Portfolio

By expanding the calculation in Hsu (2006), I show that the return drag of a cap-weighted portfolio comparing to a fair-value-weighted portfolio is a result of miscalculation. As long as the number of stocks in the portfolio is large enough, a cap-weighted portfolio provides approximately the same return as a fair-value-weighted portfolio. However, this result does not imply the gain in non-cap-weighted portfolio will disappear. All the fundamental indexing gains thus should be attributed to the return advantage of non-capweighted portfolio.
PACT HDL: a compiler targeting ASICS and FPGAS with power and performance optimizations

Recently, there has been a focus on high-level languages, C/C++ in particular, for hardware synthesis. At the same time, power dissipation is becoming an important metric in hardware design. This work presents PACT HDL, a C to HDL Compiler with facilities for power and performance optimizations. PACT HDL is an attempt to merge together automated hardware synthesis optimizations for power and performance with the capability to leverage high-level algorithms written in C and target arbitrary hardware architectures. By making the compiler modular and flexible, optimizations may be executed in any order and at different levels in the compilation process. PACT HDL generates HDL codes, such as RTL Verilog and VHDL that can be synthesized and profiled for power using commercial tools.
Re-Mutualizing the Mutual fund Industry-The Alpha and the Omega

The mutual fund industry began in 1924 with the formation of a truly mutual mutual fund: one organized, operated, and managed, not by a separate management. company with its own commercial interests, but by its own trustees; compensated not on the basis of the trust's principal, but, under traditional fiduciary standards, its income. This model of the mutual fund (the Alpha model) has been replaced by the mutual fund complex of 2004 (the Omega model). Although most mutual funds utilize this model, this Essay argues it is contrary to the intent and language of the Investment Company Act of 1940 as it benefits managers and directors as opposed to shareholders. This Essay compares the actual benefit to shareholders from funds utilizing the Omega model versus those using the Alpha model and proposes it is time to return to the Alpha model of 1924.
The type 2 diabetic patient and cardiac mitochondrial dysfunction: a new perspective (688.10)

Cardiac complications are the leading cause of mortality among diabetic patients, with the mitochondrion being implicated in the etiology. We have previously observed enhanced dysfunction to cardiac subsarcolemmal mitochondria (SSM) in db/db mice as a result of type 2 diabetes mellitus. The goal of this study was to determine whether hyperglycemia or hemoglobin A1c (HbA1c) level correlates with the extent of SSM dysfunction observed in type 2 diabetic patients. Using linear spline models to assess correlative risks we determined that diabetic patients display dysfunctional SSM state 3 respiration rate and ETC complex I activity irrespective of the absolute blood glucose or HbA1c level. In addition, we found that SSM dysfunction observed in type 2 diabetic patients with comorbidities, such as coronary artery disease (CAD) and hypertension is not due to either CAD or hypertension independently. Further, a scatter plot analysis of patients’ body mass index (BMI) indicated that BMI is not an effective predict...
Engaging Experience: A New Perspective of User Experience with Physical Products

Engaging experience is a specific kind of experience that a user acquires when and after using a product frequently, intensively, actively, vividly, and completely, etc. For example, if the appearance of a toaster is completely transparent, a user can see how the bread changes from white to brown. The transparent sides stage the toasting process as a visually engaging performance. To expand on engaging experience, this paper presents the definition of engaging experience, example products that engage users, the classification and instinctiveness of engaging experience, and product properties that foster engaging experience.
Carcinogenic risk assessment

Carcinogenic risk assessment involves a mixture of statistical, scientific, and public policy considerations. Concepts in current use, such as "no observed effect levels" and "virtual safety," and the problems in implementing them by means of dose-response models, particularly the probit-log dose and linear models are reviewed. The upper limits to risk provided by some conservative procedures are inconsistent with coherent balancing of risks and benefits. A common basis to the dose-response curves describing both carcinogenic and noncarcinogenic effects is to be found in deactivating reactions. A simplified model in which a toxic substance is activated and deactivated in separate and simultaneous reactions is presented and the dose response curve implied by the model is deduced. This curve has the general form of a hockey stick, with the striking part flat or nearly flat until the dose administered saturates the deactivation system, after which the probability of a response rises rapidly. Such a curve describes the Bryan-Shimkin methylcholanthrene-tumor incidence dose response curve as well as the probit log-dose model. The concept of a saturation dose is relevant to risk assessments for carcinogenic and noncarcinogenic substances alike.
Consequences of wave-particle interactions on chaotic acceleration

The recent model of Ashour-Abdalla et al. (1991) has proposed that the earth's plasma sheet can be formed by chaotic acceleration in a magnetotail-like field configuration. The ion velocity distributions created by chaotic acceleration have unstable features and represent robust free energy sources for kinetic plasma waves that can modify the original distributions. In the plasma sheet boundary layer, field-aligned ion beamlets are formed which drive a host of instabilities creating a broadbanded noise spectrum and cause thermal spreading of the beamlets. In addition, there is strong heating of any cold background plasma that may be present. In the central plasma sheet, ion antiloss cone distributions are created which are unstable to very low frequency waves that saturate by filling the antiloss cone.
Paired comparison estimates of willingness to accept versus contingent valuation estimates of willingness to pay

Estimating empirical measures of an individual's willingness to accept that are consistent with conventional economic theory, has proven difficult. The method of paired comparison offers a promising approach to estimate willingness to accept. This method involves having individuals make binary choices between receiving a particular good or a sum of money. Willingness to accept can be inferred from the ranking of dollar amounts and the good of interest. Using the paired comparison approach, mean (median) willingness to accept for a private good is estimated at $59($52). Contingent valuation estimate of willingness to pay for the same good yields a mean (median) of $28($28). While these estimates are statistically different, the ratio of willingness to accept to willingness to pay is less than in most previous studies and closer to ratios found in actual cash experiments.
Effect of recombinant bovine IL-1 and IL-2 on B cell proliferation and differentiation

Abstract The roles of interleukin (IL)-1 and IL-2 in bovine B cell function were investigated by determining the ability of each cytokine to support proliferation and differentiation. Recombinant bovine (rb)IL-2, but not rbIL-1β, induced the proliferation of B cells. The effect of IL-2 was dependent on the state of B cell activation. Only low and medium density B cells, but not high density, proliferated in response to IL-2. IL-1 enhanced the IL-2-induced proliferation; this effect was maintained if addition of IL-2 was delayed 48 h. IL-1 did not induce the differentiation of B cells into immunoglobulin-secreting cells. IL-2 was an inducer of secretion in all classes of immunoglobulin. As with proliferative responses, only activated B cells were responsive and IL-2 could not induce immunoglobulin secretion by high density B cells. IL-1 acted as a modulator of IL-2-induced immunoglobulin secretion, an effect which was influenced by the timing of the addition of IL-1 and the target B cell population. Simultaneous addition of IL-1 and IL-2 resulted in the inhibition of IL-2-induced IgM secretion, whilst delayed addition of IL-2 inhibited the amount of IgG1 secreted by purified B cells but had no effect on IgM, IgG2 and IgA secretion. IL-1 had no effect on the ability of low- or high-density B cells to secrete immunoglobulins. However, simultaneous or delayed addition of IL-1 maintained or enhanced the production of immunoglobulins by medium-density B cells in response to IL-2.
Refining the submesh strategy in the two-level finite element method: application to the advection-diffusion equation

We introduce a new submesh strategy for the two-level finite element method. The numerical results show that the new submesh is able to better capture the boundary layer which is caused by the choice of bubble functions. The effect of an improved approximation of the residual free bubbles is studied for the advective–diffusive equation. Copyright © 2002 John Wiley & Sons, Ltd.
Decoding long nanopore sequencing reads of natural DNA

Nanopore sequencing of DNA is a single-molecule technique that may achieve long reads, low cost and high speed with minimal sample preparation and instrumentation. Here, we build on recent progress with respect to nanopore resolution and DNA control to interpret the procession of ion current levels observed during the translocation of DNA through the pore MspA. As approximately four nucleotides affect the ion current of each level, we measured the ion current corresponding to all 256 four-nucleotide combinations (quadromers). This quadromer map is highly predictive of ion current levels of previously unmeasured sequences derived from the bacteriophage phi X 174 genome. Furthermore, we show nanopore sequencing reads of phi X 174 up to 4,500 bases in length, which can be unambiguously aligned to the phi X 174 reference genome, and demonstrate proof-of-concept utility with respect to hybrid genome assembly and polymorphism detection. This work provides a foundation for nanopore sequencing of long, natural DNA strands.
Constraint logic programming: Applications and implications

Abstract The main features of constraint logic programming (CLP) are presented. Examples of using CLP( R ) are given to demonstrate the power and limitation of the current implementation. Two application examples from model-based diagnosis and planning are discussed. Some implications of development in CLP on areas of research in artificial intelligence are outlined.
STAT3 attenuates EGFR-mediated ERK activation and cell survival during oxidant stress in mouse proximal tubular cells

We have shown that renal epithelial cell survival depends on the sustained activation of the extracellular signal-regulated protein kinase (ERK) and lack of this activation was associated with death during oxidative stress. ERK is activated via the canonical epidermal growth factor receptor (EGFR)–Ras–MEK pathway, which could be attenuated by oxidants. We now show that the failure to activate ERK in a sustained manner during severe oxidative stress is owing to the activation of the signal transducer and activator of transcription-3 (STAT3) rather than the failure to activate the EGFR. Tyrosine phosphorylation of the EGFR and STAT3 was studied in hydrogen peroxide (H2O2)-treated mouse proximal tubule (TKPTS) cells or in mouse kidney after ischemia/reperfusion (I/R) injury by Western blotting. STAT3 activation was inhibited by either pharmacologically (AG490) through its upstream janus kinase (JAK2) or by a dominant-negative STAT3 adenovirus. EGFR was inhibited by AG1478. Survival was determined by fluorescence-activated cell sorter analysis and trypan blue exclusion. We found that the EGFR was phosphorylated on its major autophosphorylation site (Tyr1173) regardless of the H2O2 dose. On the other hand, both I/R and severe oxidative stress – but not moderate stress – increased tyrosine phosphorylation of STAT3 in an EGFR and JAK2-dependent manner. Inhibition of JAK2 or STAT3 lead to increased ERK activation and survival of TKPTS cells during severe oxidative stress. Our data suggest a role of tyrosine-phosphorylated STAT3 in the suppression of ERK activation. These data suggest that the STAT3 pathway might represent a new target for improved survival of proximal tubule cells exposed to severe oxidant injury.
ASH2L Regulates Ubiquitylation Signaling to MLL: trans-Regulation of H3 K4 Methylation in Higher Eukaryotes

Crosstalk between H2B ubiquitylation (H2Bub) and H3 K4 methylation plays important roles in coordinating functions of diverse cofactors during transcription activation. The underlying mechanism for this trans-tail signaling pathway is poorly defined in higher eukaryotes. Here, we show the following: (1) ASH2L in the MLL complex is essential for H2Bub-dependent H3 K4 methylation. Deleting or mutating K99 of the N-terminal winged helix (WH) motif in ASH2L abrogates H2Bub-dependent regulation. (2) Crosstalk can occur in trans and does not require ubiquitin to be on nucleosomes or histones to exert regulatory effects. (3) trans-regulation by ubiquitin promotes MLL activity for all three methylation states. (4) MLL3, an MLL homolog, does not respond to H2Bub, highlighting regulatory specificity for MLL family histone methyltransferases. Altogether, our results potentially expand the classic histone crosstalk to nonhistone proteins, which broadens the scope of chromatin regulation by ubiquitylation signaling.
A two-component system that regulates an osmosensing MAP kinase cascade in yeast

In the prokaryotic two-component signal transduction systems, recognition of an environmental stimulus by a sensor molecule results in the activation of its histidine kinase domain and phosphorylation of a histidine residue within that domain. This phosphate group is then transferred to an aspartate residue in the receiver domain of a cognate response regulator molecule, resulting in the activation of its output function. Although a few eukaryotic proteins were identified recently that show sequence similarity to the prokaryotic sensors or response regulators, it has not been clear whether they constituted a part of a 'two-component' system. Here we describe a two-component system in Saccharomyces cerevisiae that regulates an osmosensing MAP kinase cascade.
Surface waves guided by a plane ungrounded magneto plasma slab

The characteristics of the plane surface waves supported by a plane ungrounded magnetoplasma slab are investigated for the case in which the magnetostatic field is oriented parallel to the two parallel interfaces but perpendicular to the direction of propagation. The dependence of the characteristics of the surface waves on the thickness of the plasma slab is discussed. For sufficiently small thickness of the plasma slab, backward surface waves arc found to exist. The group velocity as well as the amplitude characteristics of the surface waves are studied.
Particle filter with state permutations for solving image jigsaw puzzles

We deal with an image jigsaw puzzle problem, which is defined as reconstructing an image from a set of square and non-overlapping image patches. It is known that a general instance of this problem is NP-complete, and it is also challenging for humans, since in the considered setting the original image is not given. Recently a graphical model has been proposed to solve this and related problems. The target label probability function is then maximized using loopy belief propagation. We also formulate the problem as maximizing a label probability function and use exactly the same pairwise potentials. Our main contribution is a novel inference approach in the sampling framework of Particle Filter (PF). Usually in the PF framework it is assumed that the observations arrive sequentially, e.g., the observations are naturally ordered by their time stamps in the tracking scenario. Based on this assumption, the posterior density over the corresponding hidden states is estimated. In the jigsaw puzzle problem all observations (puzzle pieces) are given at once without any particular order. Therefore, we relax the assumption of having ordered observations and extend the PF framework to estimate the posterior density by exploring different orders of observations and selecting the most informative permutations of observations. This significantly broadens the scope of applications of the PF inference. Our experimental results demonstrate that the proposed inference framework significantly outperforms the loopy belief propagation in solving the image jigsaw puzzle problem. In particular, the extended PF inference triples the accuracy of the label assignment compared to that using loopy belief propagation.
Exploring online social activities for adaptive search personalization

The web has largely become a very social environment and will continue to become even more so. People are not only enjoying their social visibility on the Web but also increasingly participating in various social activities delivered through the Web. In this paper, we propose to explore a user's public social activities, such as blogging and social bookmarking, to personalize Internet services. We believe that public social data provides a more acceptable way to derive user interests than more private data such as search histories and desktop data. We propose a framework that learns about users' preferences from their activities on a variety of online social systems. As an example, we illustrate how to apply the user interests derived by our system to personalize search results. Furthermore, our system is adaptive; it observes users' choices on search results and automatically adjusts the weights of different social systems during the information integration process, so as to refine its interest profile for each user. We have implemented our approach and performed experiments on real-world data collected from three large-scale online social systems. Over two hundred users from worldwide who are active on the three social systems have been tested. Our experimental results demonstrate the effectiveness of our personalized search approach. Our results also show that integrating information from multiple social systems usually leads to better personalized results than relying on the information from a single social system, and our adaptive approach further improves the performance of the personalization solution.
Reconciliations: Prevention of and Recovery from School Violence

After some three decades in education as student, teacher, or administrator, the author was widowed when a distressed graduate student murdered her husband in his university office. The author's self-designed recovery process included training in the principles of nonviolence and conflict resolution. In this essay, it is suggested that these principles and methods offer crucial curricular material for both analytical study and violence prevention in schools. These same principles also offer a balanced way to live. With respect to balanced living and the twin dilemmas of school violence and recovery, the author suggests that rational and emotional mental processes, private and public selves, individual and community goals, and microcommunity and macrocommunity structures be rethought. In addition to the principles of nonviolence, the author relies on a race relations scholar for notions of community and several feminist thinkers for analyses of ethics.
Changes in transmembrane helix alignment by arginine residues revealed by solid-state NMR experiments and coarse-grained MD simulations

Independent experimental and computational approaches show agreement concerning arginine/membrane interactions when a single arginine is introduced at selected positions within the membrane-spanning region of acetyl-GGALW(5)LALALAL(12)AL(14)ALALW(19)LAGA-ethanolamide, designated GWALP23. Peptide sequence isomers having Arg in position 12 or position 14 display markedly different behaviors, as deduced by both solid-state NMR experiments and coarse-grained molecular dynamics (CG-MD) simulations. With respect to the membrane normal of DOPC or DPPC lipid bilayer membranes, GWALP23-R14 shows one major state whose apparent average tilt is approximately 10 degrees greater than that of GWALP23. The presence of R14 furthermore induces bilayer thinning and peptide displacement to "lift" the charged guanidinium toward the bilayer surface. By contrast, GWALP23-R12 exhibits multiple states that are in slow exchange on the NMR time scale, with CG-MD simulations indicating two distinct positions with different screw rotation angles in the membrane, along with an increased tendency to exit the lipid bilayer.
Studies of bovine seminal fluid nucleotide pyrophosphatase.

Abstract Nucleotide pyrophosphatase of bovine seminal plasma was demonstrated to catalyze effectively the hydrolysis of NAD, FAD, etheno-NAD, adenosine diphosphoribose, 3-aminopyridine adenine dinucleotide, and bis-p-nitrophenylphosphate. The enzyme was purified 80-fold resulting in a partial separation from 5′-nucleotidase and alkaline phosphatase activities. The 80-fold purified nucleotide pyrophoshatase had a pH optimum of 9.0 and was competitively inhibited by adenosine, AMP, and sodium pyrophosphate. Time-dependent inactivation of the enzyme was observed by thermal denaturation at 62 °C and by incubation with EDTA at 4 °C. The activity of the enzyme was increased with increasing ionic strength and specific stimulation by Mg2+ was not observed. In the absence of NAD glycohydrolase, the hydrolysis of NAD in bovine seminal plasma was demonstrated through timed product studies to proceed initially through the hydrolysis of the pyrophosphate linkage catalyzed by nucleotide pyrophosphatase. The resulting product, AMP, was further hydrolyzed to adenosine in a reaction catalyzed by 5′-nucleotidase. The observed functioning of adenosine diphosphoribose as a substrate for the nucleotide pyrophosphatase provided evidence in support of a second conversion of NAD to adenosine in seminal plasma through an initial hydrolytic reaction catalyzed by NAD glycohydrolase.
An automatic visual inspection system for integrated circuit chips

Abstract A formulation of an automatic visual inspection and final packaging system is presented in this paper. An integrated system on the basis of such a formulation is then proposed for the automatic visual inspection and wire-bonding of integrated circuit (IC) chips. An input chip image is first segmented so that the IC image can be extracted. The image registration is then carried out in two steps. The macroregistration is achieved by locating the mask frame first, and each mask subpattern is microregistered independently by means of the proposed unnormalized cross correlation of contrast method. A task-dependent, context-dependent image filter is designed to transform the IC image into another image so that at any moment only relevant information is emphasized while irrelevant information is suppressed. Such a transformed or coded image is then examined to detect existent IC defects. Each IC chip under inspection is then classified into one of three categories: accept, or reject, or to be reworked. Finally, each accepted IC chip is soldered to a package substrate for wire-bonding.
Molecular recognition and processing of periodic signals in cells: study of activation of membrane ATPases by alternating electric fields

A molecule which is immobilized, oriented or tumbling more slowly than the frequency of a periodic field, may interact with the field to produce chemical effects that are uncommon in a homogeneous solution. Among these effects are the alteration of the rate of a chemical reaction and the exchange of energy between the oscillating field and the conformation of the molecule. When certain conditions are satisfied, this exchange allows the molecule to absorb and couple the energy of the field to drive an endergonic reaction. The efficiency of energy coupling depends on field strength and frequency and on the ligand concentration. There are windows of these parameters to achieve efficient coupling. These windows can be expressed in terms of the rate constants and equilibrium constants of the catalytic reactions, and the amplitude and frequency of the periodic field. This mechanism allows cells to receive, process and transmit energy of high and medium level periodic potentials by means of membrane enzymes or receptors. A theory for the transduction of electric energy, electroconformational coupling (ECC) will be discussed. The electric field induced cation pumping activities of Na,K-ATPase and Ca-ATPase of human erythrocytes and the ATP synthetic activity of beef heart mitochondrial ATPase will then be used to test an ECC membrane transport model. For the processing of low level periodic signals, a theory of an oscillatory activation barrier (OAB), which considers resonance transduction between an oscillating field and the activation barrier of the rate limiting step in an enzymic reaction, will be discussed. The OAB mechanism successfully interprets the AC stimulated ATP hydrolysis activity of Ecto-ATPase from chicken oviduct and F0F1-ATPase from beef heart. We propose that mechanisms similar to an OAB model are adopted by cells to sense weak electric, acoustic, mechanical, concentration (i.e., chemical potential) and other types of signals, and to communicate with other cells by these signals. The experimental data and mechanistic information presented in this communication give us a glimpse of the molecular electronic designs in living cells. This information is also relevant with respect to environmental issues. Environmental electromagnetic fields and sonic pollutants may interfere with normal communications of cells and organisms. Their benefit, if any, and detrimental effects can be assessed and dealt with only if we fully understand mechanisms of cellular interactions with these fields and pollutants, at the molecular level.