cssi/SciSciGPT-SciSciNet huggingface dataset:
Common Problems and Solutions in Experiments

Abstract Although the development of procedures for experimental research and the implementation of the design often appear to be simple and straightforward projects, the steps involved are far more time-consuming and complicated than one may expect. This chapter discusses some of the common problems encountered when conducting laboratory research, including bias in experimental manipulations, possible contamination, issues with using and training confederates, recruiting and scheduling subjects, video ­recording, managing time, and maintaining records. We offer suggestions and a “hands-on” approach to setting up and running an experiment primarily in university settings using undergraduate subjects.
Leveraging Antenna Side-Lobe Information for Expedited Neighbor Discovery in Directional Terahertz Communication Networks

Terahertz (THz)-band (0.1-10 THz) communication is envisioned as a potentially key technology to satisfy the need for much higher wireless data rates. The THz-band provides a huge transmission bandwidth, which ranges from hundreds of GHz up to a few THz. Nevertheless, this bandwidth comes at the cost of a very high pass loss, and, as a result, highly directional antennas are needed simultaneously in transmission and reception to establish a communication link beyond a few meters. In directional communication networks, efficient neighbor discovery is needed to overcome the deafness problem. Existing neighbor discovery protocols for lower frequency bands cannot be directly utilized, because they do not capture the peculiarities of the THz band or the need to support multi Giga-bit-per-second and even Tera-bit-per- second links. In this paper, a neighbor discovery protocol for THz- band communication networks that leverages the directional antenna side-lobe information is presented. More specifically, the full antenna radiation pattern is utilized to detect a series of effective signals and map them to a universal detection standard and expedite the neighbor discovery process. A mathematical framework is developed to compare the neighbor discovery protocols with and without the antenna side-lobe information, and numerical results are provided to illustrate the performance of the proposed neighbor discovery protocol in terms of total time needed to complete the discovery process.
A Review of Nanoporous Metals in Interconnects

Interconnections in semiconductor devices need to provide a seamless electrical, thermal, and mechanical link to different parts of the circuit. Since the move away from lead-based solders due to toxicity concerns, the search has been on for materials that can provide desirable attributes before, during, and after bonding. While lead-free solders have been extensively used as a replacement, they are now reaching their limits in terms of pitch scaling, as well as, electrical and thermal properties, forcing the semiconductor industry to look for alternative material systems for the next interconnection node. This review provides an overview of key properties needed in metal interconnections and possible use of nanoporous metals due to ease of fabrication, nanostructured ligaments, and other key physical attributes.
From leave it to beaver to modern family: The influence of family structure on adoption attitudes

How do social and religious views influence attitudes of the capability and appropriateness of a prospective adoptive parent? The present experiment presents an investigation into the sources of attitudes and biases towards gay and lesbian couples and single parents in an adoption scenario. The author discusses existing theories of discrimination against LGBT populations and outgroups in general, including Social Dominance Orientation and Religious Fundamentalism, all highly predictive of LGBT bias. Current forms of adoption discrimination against nontraditional adopters from public policy makers and adoption agencies alike is explored and an empirical test of these discriminatory trends was created. Proposed adoption scenarios were presented and participant sentiments about the appropriateness of the adoption and prospective parent(s) were assessed. The direct and interactive effects of overt social and religious views were measured and these factors were clearly demonstrated to influence adoption attitudes. The present research aimed to uncover modern sources of prejudice towards gay and lesbian and single adoptive parents and offer new avenues of exploration into the foundation of such discrimination.
Increasing T stage is associated with the need for more extensive lymph node assessment in clinical stage I non-small cell lung cancer.

Lymph node assessment is an important determinant of stage in non-small cell lung cancer (NSCLC); the optimal number of nodes needed in a lymphadenectomy during pulmonary resection, however, remains unclear.
Hyperreal Instruments: Bridging VR and Digital Fabrication to Facilitate New Forms of Musical Expression

Virtual Reality (VR) and digital fabrication technologies today are ushering in a new wave of opportunities in instrument design; the marriage of these two domains, seemingly at odds with each othe...
Innovative Methods for Rare Disease Drug Development

In the United States, a rare disease is defined by the Orphan Drug Act as a disorder or condition that affects fewer than 200,000 persons. For the approval of "orphan" drug products for rare diseases, the traditional approach of power analysis for sample size calculation is not feasible because there are only limited number of subjects available for clinical trials. In this case, innovative approaches are needed for providing substantial evidence meeting the same standards for statistical assurance as drugs used to treat common conditions. Innovative Methods for Rare Disease Drug Development focuses on biostatistical applications in terms of design and analysis in pharmaceutical research and development from both regulatory and scientific (statistical) perspectives. Key Features: Reviews critical issues (e.g., endpoint/margin selection, sample size requirements, and complex innovative design). Provides better understanding of statistical concepts and methods which may be used in regulatory review and approval. Clarifies controversial statistical issues in regulatory review and approval accurately and reliably. Makes recommendations to evaluate rare diseases regulatory submissions. Proposes innovative study designs and statistical methods for rare diseases drug development, including n-of-1 trial design, adaptive trial design, and master protocols like platform trials. Provides insight regarding current regulatory guidance on rare diseases drug development like gene therapy.
Regulating Insider Trading

Utilizing a new understanding of firm compliance responses to regulation, I find that Sarbanes-Oxley helped both identify and reduce abnormal returns to informed insider trading. The number of forms insiders file post-SOX increased by 175% per year, causing an 84% increase in firm compliance policies to handle the implicit costs to filing by selecting staff to oversee and orchestrate the trading of insiders. Insiders sign their own insider trading forms identify deviation from firm policy, and signal informed insider trading reaping abnormal annualized returns to their purchases (sales) of 9.6% (-10.8%). Using this novel measure to identify informed insider trading, Sarbanes-Oxley cuts abnormal returns nearly in half. I find that SOX does so by limiting insiders’ ability to sequence smaller trades multiple times, a previously undisclosed strategy. Sarbanes-Oxley’s insider trading provisions work as intended—to limit insiders from using their informational advantages to lucratively trade—and it does so by increasing both the amount and speed of disclosure.
A performance portability framework for Python

Kokkos is a programming model for writing performance portable applications for all major high performance computing platforms. It provides abstractions for data management and common parallel operations, allowing developers to write portable high performance code with minimal knowledge of architecture-specific details. Kokkos is implemented as a heavily-templated C++ library. However, C++ is not ideal for rapid prototyping and quick algorithmic exploration. An increasing number of developers use Python for scientific computing, machine learning, and data analytics. In this paper, we present a new Python framework, dubbed PyKokkos, for writing performance portable applications entirely in Python. PyKokkos provides Kokkos-like abstractions that are easier to use and more concise than the C++ interface. We implemented PyKokkos by building a translator from a subset of Python to C++ Kokkos and bridging necessary function calls via automatically generated Python bindings. PyKokkos is also compatible with NumPy, a widely-used high performance Python library. By porting several existing Kokkos applications to PyKokkos, including ExaMiniMD (∼3k lines of code in C++), we show that the latter can achieve efficient execution with low performance overhead.
Volume ratios between the thermophilic and the mesophilic digesters of a temperature-phased anaerobic digestion system affect their performance and microbial communities

An experimental temperature-phased anaerobic digestion (TPAD) system, with the thermophilic digester operated at neutral pH and with a balanced acidogenesis and methanogenesis (referred to as NT-TPAD), was evaluated with respect to the microbial communities and population dynamics of methanogens when digesting dairy cattle manure at 15-day overall system hydraulic retention time (HRT). When fed a manure slurry of 10% total solid (TS), similar system performance, 36–38% volatile solid (VS) removal and 0.21–0.22 L methane g−1 VS fed, was achieved between a 5-day and 7.5-day HRT for the thermophilic digester. However, the thermophilic digester achieved a greater volumetric biogas yield when operated at a 5-day RT than at a 7.5-day HRT (6.3 vs. 4.7 L/L/d), while the mesophilic digester had a stable volumetric biogas yield (about 1.0 L/L/d). Each of the digesters harbored distinct yet dynamic microbial populations, and some of the methanogens were significantly correlated with methane productions. Methanosarcina and Methanosaeta were the most important methanogenic genera in the thermophilic and the mesophilic digesters, respectively. The microbiological findings may help understand the metabolism that underpins the anaerobic processes within each of the two digesters of TPAD systems when fed dairy manure.
Architectural Implications of Optical Computing

All-electronic computers need greater performance than can be achieved for many applications, and for this reason, optical processing technology is considered. Optical logic gates are not likely to perform faster than electronic logic gates in the foreseeable future, but the speed of the switching devices does not limit the overall performance of current digital computers. Computers have increased in performance by a factor of 10 every decade (Figure 1), for the same cost, since the 1950s (Hennessy and Patterson, 1990). The major contributor to this increase in performance for a fixed cost is the increase in density of active components on a single integrated circuit (IC). Density is achieved by shrinking the component sizes (the sizes of the transistors) and by packing components closer together. Smaller components translate to faster switching speeds for transistors, but faster transistors do not necessarily lead to faster computers.
Impaired Aβ clearance: a potential link between atherosclerosis and Alzheimer's disease.

Alzheimer’s Disease (AD) and atherosclerosis remain two of the largest public health burdens in the world today. Although traditionally considered distinct pathological entities, mounting epidemiologic, clinical and experimental evidence suggests that cerebrovascular atherosclerosis and AD interact reciprocally to disrupt brain structure and function. Whereas the hypoperfusion and hypoxia caused by atherosclerosis of cerebral vessels may enhance the production of amyloid-β peptide (Aβ), a peptide central to AD pathology, Aβ, in turn, may promote formation of atherosclerotic lesions through vascular oxidative stress and endothelial dysfunction leading to additional vascular damage. Here, we briefly review evidence suggesting that impaired clearance of Aβ is an additional, simultaneously occurring mechanism by which AD and cerebrovascular disease may be causally linked. We examine the literature supporting mechanisms by which flow-limiting large-artery stenosis, arterial stiffening and microvascular dysfunction could contribute to AD pathophysiology by impairing Aβ clearance and elevating brain levels of Aβ. Finally, we highlight the need for further research to improve our understanding of the complex interactions of AD and atherosclerosis with Aβ clearance, which may ultimately serve to guide the development of novel diagnostic and therapeutic approaches for this devastating and highly prevalent condition.
Contributions to our knowledge of the cranial morphology of some ranid genera of frogs.—Part II

The Indian firmisternous Anuran family Ranidae comprises a large number of genera, the examples of which exhibit a great diversity in life-habits. While some are aquatic, others are definitely semi-aquatic; arboreal and terrestrial forms are not uncommon. The body organisation, therefore, is also adapted to different environmental conditions in which they live.
Signal Transduction Pathways in Critical Illness and Injury

Cells respond to environmental stimuli using an elaborate process to propagate and amplify a signal from the cell surface to the nucleus leading to initiation of gene induction in a process termed “signal transduction”. The NFκB and MAPK pathways are two important pathways in the cellular responses during critical illness. Both pathways are composed of a series of kinases that utilize phosphorylation to activate downstream kinases. Once activated these pathways must be deactivated in order to reestablish homeostasis usually by a phosphatase. Additionally, intracellular inhibitors and epigenetic processes are important in regulating the activation of signal pathways.
Cladistic Concepts and the Species Problem in Hominoid Evolution

Over the past 20 years, since the initial application of Hennigian phylogenetic principles to the study of human evolution, the usage of cladistic concepts has become increasingly popular in paleoanthropology (Eldredge and Tattersall, 1975; Delson et al., 1977; Tattersall and Eldredge, 1977; Bonde, 1977; Olson, 1978; White et al., 1981; Skelton et al., 1986; Wood and Chamberlain, 1986; Stringer, 1987; Chamberlain and Wood, 1987; Kimbel et al., 1988; Tobias, 1988; Groves, 1989). The rigorous operational framework, in conjunction with its potential for the application of Popperian deductive reasoning in testing inferences about character states and morphocline polarities upon which phylogenetic hypotheses are based, has made cladistics an attractive methodological approach, even among some of its initial antagonists (Nelson, 1970, 197la,b); Bonde, 1977; Bock, 1977; Szalay, 1977; Platnick, 1977, 1978, 1979; Platnick and Gaffney, 1977; Patterson, 1978; Mayr, 1968, 1981; but see Cartmill, 1981 for a critique of the utility of Popper’s model of scientific enquiry for testing phylogenetic interpretations).
Unique normal forms and confluence of rewrite systems: persistence

Programming language interpreters, proving theorems of the form A = 2?, abstract data types, and program optimization can all be represented by a finite set of rules called a rewrite system. In this paper, we study two fundamental concepts, uniqueness of normal forms and confluence, for nonlinear systems in the absence of termination. This is a difficult topic with only a few results so far. Through a novel approach, we show that every persistent system has unique normal forms. This result is tight and a substantial generalization of previous work. In the process we derive a necessary and sufficient condition for persistence for the first time and give new classes of persistent systems. We also prove the confluence of the union (function symbols can be shared) of a nonlinear system with a left-linear system under fairly general conditions. Again persistence plays a key role in this proof. We are not aware of any confluence result that allows the same level of function symbol sharing.
Community Practice in the Bulldozer’s Shadow: The History and Legacy of Social Work in Urban Renewal

Social work has a long history of involvement in urban development policy, dating to the settlement house movement. This article explores a neglected part of this history by analyzing the role of social work in urban renewal programs. The functions of social work in urban renewal—including relocating families displaced by slum clearance and community organizing to foster resident input in planning—reflect enduring tensions in practice between social justice and social control. Implications for current practice are explored as the profession continues to define its part in urban redevelopment policies.
Investigation of Human Urogenital Tract Tumors for Papovavirus Etiology: Brief Communication

Cells cultured from human urogenital cancer and other cancers as well as cells from noncancerous tissues were examined by immunofluorescent staining with antibodies to T-antigens and capsid antigens of papovaviruses BK virus (BKV), JC virus, and simian virus 40(SV40), and to capsid antigens of herpes simplex virus types 1 and 2 and human cytomegalovirus (CMV). Cells from early passage cultures of 123 primary tissues and from 14 continuous lines derived from transitional or renal cell carcinoma were tested. None of the cell preparations was specifically stained with any of the antisera. A serologic comparison of patients with bladder cancer, patients with prostate cancer, and normal control groups of BKV hemagglutination-inhibiting and SV40-neutralizing antibodies showed no differences among the 3 groups. None of the sera in the 3 groups had SV40 or BKV T-antibodies. In tests of supernatants of 35 primary cultures for presence of virus, a single isolation, that of a cytomegalovirus, was made. The study revealed no evidence that infection with papovaviruses of the SV40-polyoma subgroup has any part in the production of bladder and prostate cancer.
Vascular Endothelial Growth Factor Expression, β-Catenin Tyrosine Phosphorylation, and Endothelial Proliferative Behavior: A Pathway for Transformation?

The hypothesis that tumor growth is angiogenesis dependent has been documented by a considerable body of direct and indirect experimental data and has generated intense basic and pharmaceutical-related interest. In contrast, the study of endothelial cell tumors has been modest by comparison. Hemangioma is the most common tumor of any kind seen in infancy and also, perhaps, the least understood. We compared a mouse hemangioma-derived cell line (EOMA) and primary human endothelial cells (HUVEC) for their proliferative behavior and molecular alterations. EOMA cells intrinsically expressed vascular endothelial growth factor (VEGF), which acts in an autocrine manner, resulting in an increase in CD1 expression and cell proliferation, both of which were inhibited by anti-VEGF neutralizing antibodies. Such an autocrine loop is supported by constitutive VEGF receptor (Flk-1) tyrosine phosphorylation, Flk-1 and Flt-1 nuclear localization, and mitogen-activated protein kinase activation. β-catenin was also found to exhibit significant nuclear localization and constitutively associate with Flk-1 and Flt-1 in EOMA cells but much less so in HUVEC, and immunoprecipitated Flk-1 was able to phosphorylate purified β-catenin in an immune complex kinase assay. EOMA cells were also noted to express reduced levels of N-cadherin and γ-catenin compared with HUVEC. Interestingly, sequestration of endogenous VEGF in EOMA cultures resulted in a dramatic decrease in nuclear β-catenin and a reduction in CD1 levels, whereas addition of exogenous VEGF elicited increased nuclear β-catenin localization and increased CD1 levels in HUVEC. The possible contributions of VEGF signaling pathways, cell junction component expression levels, and phosphorylation states to endothelial cell transformation and proliferation are discussed.
Use of RIFLE Criteria to Predict the Severity and Prognosis of Acute Kidney Injury in Emergency Department Patients with Rhabdomyolysis

Abstract Background RIFLE criteria (Risk, Injury, Failure, Loss, End-stage) have not been evaluated in Emergency Department (ED) patients at risk of acute kidney injury (AKI). AKI occurs in rhabdomyolysis. Study Objectives To use RIFLE criteria to stratify the severity of AKI and predict prognosis in ED patients with acute rhabdomyolysis. Methods This is a retrospective study of consecutive patients with rhabdomyolysis over a 44-month period. Data included ED admission anion gap, blood urea nitrogen (BUN), calcium, phosphate, potassium, urinalysis, toxicology screen, and hematocrit. Creatine kinase, creatinines, and hematocrits were followed serially. Hospital length of stay (LOS) and need for dialysis were also recorded. Results RIFLE categories were calculated for 135 patients. At admission, 60 (44%) had no AKI, 20 (15%) had Risk, 32 (24%) had Injury, and 23 (17%) had Failure. These categories were significantly associated with increasing magnitude of volume depletion, potassium, phosphate, BUN, and the anion gap. They predicted differences in LOS, dialysis, discharge creatinine, and the rate of normalization of the admission creatinine. Mortality was low (2%), as was morbidity. Only 8/132 surviving patients (6%) were discharged with a creatinine >2 mg/dL. Conclusions The RIFLE categories correlated significantly with known markers of rhabdomyolysis and AKI. They also predicted LOS, dialysis, renal morbidity, and the timing of recovery. RIFLE criteria could be used to predict the outcome of ED patients and facilitate admission and discharge decisions.
Value of the bronchodilator response in assessing controller naïve asthmatic children.

Objective To define the bronchodilator response (BDR) cutoff point that best identified asthma to determine the frequency of abnormal spirometry results across severity. Study design Controller naive children were evaluated with clinical criteria alone to establish a diagnosis of asthma and severity classification, then compared with the BDR, which was calculated as the percent change from the initial forced expiratory volume in 1 second. Receiver operator characteristic analysis determined the cutoff point for asthma diagnosis that gave the best combination of sensitivity and specificity. Results Children with asthma (n = 346) and 51 children without asthma, aged 4 to 17 years, who met entry criteria for spirometry were identified. The mean BDR in asthmatics was 8.6% (95% CI, 7.5-9.8), compared with 2.2% (95% CI, 0.2-4.3) for non-asthmatics (P Conclusion Spirometric criteria that include BDR can potentially identify children who have clinically mild asthma and might benefit from controller therapy.
Comparison of two self-directed weight loss interventions: Limited weekly support vs. no outside support

Summary Objective The purpose of this study was to compare the efficacy of two home-based weight loss interventions that differ only in the amount of outside support provided. Methods This was a 12-week, randomized, controlled trial. One group received limited support (LWS, n =35) via a single 10min phone call each week while another group received no weekly support (NWS, n =28). Both the LWS and NWS received pre-packaged meals (PM) and shakes. A third group served as control (CON, n =30) and received no components of the intervention. Weight loss at 12 weeks was the primary outcome. Diet (PM, shake, and fruit/vegetable (F/V) intake) and physical activity (PA) were self-monitored, recorded daily and reported weekly. An exit survey was completed by participants in the intervention groups upon completion of the study. Results Weight loss and percent weight loss in the LWS, NWS, and CON groups were 7.7±4.4kg (8.5±4.2%), 5.9±4.1kg (6.0±4.2%), and 0.3±1.9kg (0.4±1.2%), respectively. The decrease in body weight and percent weight loss was significantly greater in the LWS and NWS groups when compared to the CON group and the percent weight loss was significantly greater in the LWS when compared to both the NWS and CON groups. Conclusion A home-based weight loss program utilizing PM and shakes results in clinically significant percent weight loss and the addition of a brief weekly call promotes additional percent weight loss.
The association of depressive symptoms and urinary incontinence among older adults

OBJECTIVES: To examine the relationship of urinary incontinence (UI) and depressive symptoms (DS) in older adults. DESIGN: A randomized, controlled trial to determine the effects of clinical practice guideline implementation on provider attitudes and behavior, and patients' UI, health status, quality of life, and satisfaction with care. Baseline and endpoint data were collected from patients via computer-assisted telephone interviewing. SETTING: Forty-one nonacademic primary care practices (PCP) in North Carolina. PARTICIPANTS: A total of 668 community-dwelling adults (age > 60) who had visited the one of the selected PCPs. INTERVENTION: PCPs in the intervention group were given instruction in the detection and management of UI, educational materials for providers and patients, office system supports, and academic detailing. MEASUREMENTS: The dependent measure was assessed using an eight-item screener for DS. UI (status, frequency, amount), health (physical, mental), and demographic (age, gender, marital status) and self-report information about bladder control served as predictors. RESULTS: Wilcoxon rank sum tests showed that UI status was associated with moderate to severe DS (43% vs 30%, P = .05). Multivariate analyses showed that UI status, physical and mental health, and gender were significant predictors of DS. Among UI adults (n = 230), physical and mental health, life satisfaction, and the perception that UI interfered with daily life were significant predictors of DS. CONCLUSIONS: This study provides clear evidence that UI is related to DS in older adults. J Am Geriatr Soc 48: 413–416, 2000.
Neuroprotective effects of N-acetylaspartylglutamate in a neonatal rat model of hypoxia-ischemia.

Abstract Neuroprotective effects of N-acetylaspartylglutamate (NAAG), the precursor of glutamate and a selective agonist at the Group II metabotropic glutamate (mGlu) receptor, against hypoxic-ischemic brain injury were examined in a neonatal rat model of cerebral hypoxia-ischemia. The neonatal hypoxia-ischemia procedure (unilateral carotid artery ligation followed by exposure to an 8% oxygen hypoxic condition for 1.5 h) was performed in 7-day-old rat pups. Following unilateral carotid artery ligation, NAAG (0.5 to 20 mg/kg, i.p.) was administered before or after the hypoxic exposure. Brain injury was examined 1-week later by weight reduction in the ipsilateral brain and by neuron density in the hippocampal CA1 area. In the saline-treated rat, neonatal hypoxia-ischemia resulted in severe brain injury as indicated by a 24% reduction in the ipsilateral brain weight. Low doses of NAAG (2–10 mg/kg, but not 0.5 mg/kg), administered before or even if 1 h after the hypoxic exposure, greatly reduced hypoxia-ischemia-induced brain injury (3.8–14.2% reduction in the ipsilateral brain weight). A high dose of NAAG (20 mg/kg) was ineffective. While l (+)-2-Amino-4-phosphonobutyric acid ( l -AP4) and trans-[1S,3R]-1-Amino-cyclopentane-1, 3-dicarboxylic acid (t-ACPD) were unable to provide protection against hypoxic-ischemic brain injury, 2-(phosphonomethyl) pentanedioic acid (2-PMPA), an inhibitor of N-acetylated alpha-linked acidic dipeptidase (NAALADase), which hydrolyzes endogenous NAAG into N-acetyl-aspartate and glutamate, significantly reduced neonatal hypoxia-ischemia-induced brain injury. (αS)-α-Amino-α-[(1S, 2S)-2-carboxycyclopropyl]-9H-xanthine-9-propanoic acid (LY341495), a selective antagonist at the mGlu2/3 receptor, prevented the neuroprotective effect of NAAG. Neuron density data measured in the hippocampal CA1 area confirmed that ipsilateral brain weight reduction was a valid measure for hypoxic-ischemic brain injury. Neonatal hypoxia-ischemia stimulated an elevation of cyclic AMP (cAMP) concentration in the saline-treated rat brain. NAAG, l -AP4 and t-ACPD all significantly decreased hypoxia-ischemia-induced elevation of cAMP. LY341495 blocked the effect of NAAG, but not of l -AP4 or t-ACPD, on hypoxia-ischemia-stimulated cAMP elevation. The overall results suggest that the neuroprotective effect of NAAG is largely associated with activation of mGlu2/3 receptor.
Binary Interaction of Liquid Capsules in a Shear Flow

Three-dimensional numerical simulations using front-tracking method are presented on the hydrodynamic interaction between two deformable particles suspended in simple shear flow. Particles are modeled as liquid capsules, that is, liquid drops surrounded by elastic membranes. Small and finite inertia are considered. Two sets of simulations are presented. In the first set, interaction between two identical capsules are considered. In the limit of zero inertia, it has been known from past research that the hydrodynamic interaction between two deformable particles results in an irreversible shift in the trajectories of the particles as one particle rolls over the other. We show that the presence of inertia can significantly alter the capsule trajectories, and the capsules engage in a symmetric spiraling motions. In the second set of simulations, we consider the interaction between two non-identical capsules which differ from each other in terms of capillary number. The interaction between them results in greater lateral separation as compared to that of an identical pair. This result suggests that the shear-induced diffusion mechanism may play an even greater role in mixing in suspension of bidisperse particles. The long-time trajectory of the non-identical capsules at finite Re shows that they move in spirals with different radii while translating along the streamwise direction. The more deformable capsule moves with smaller radius, and vice versa.Copyright © 2008 by ASME
Characterization of the F plasmid mating aggregation gene traN and of a new F transfer region locus trbE.

Abstract The product of the F plasmid transfer gene, traN, is thought to be required for the formation of stable mating aggregates during F-directed conjugation. By testing chimeric plasmids that express F transfer region segments for complementation of F lac traN mutant transfer, we mapped traN to the F transfer region between trbC and traF. Both protein and DNA sequence analysis determined the traN product to be a large, 66,000-Mr, polypeptide that undergoes signal sequence processing. The mature polypeptide was associated with outer membrane protein fractions, and a protease accessivity test confirmed that at least one portion of TraN is exposed on the cell surface. Our DNA sequence analysis also revealed that another gene, trbE, is located between traN and traF. The product of trbE was identified and shown to be a small, integral, inner membrane protein. The mating efficiency and pilus-specific phage susceptibility of a trbE::Kan insertion mutant suggested that trbE is not essential for F transfer from Escherichia coli K-12 under standard mating conditions.
A generalized Oseen theory of two-dimensional Brownian motion

Abstract A generalization of the Oseen arguments to a quasi-two-dimensional system of a nonuniformly moving Brownian cylinder yields a remarkable “long time” behavior o(t) ∼ {1 + 2t/τ} − 3 2 t −1 for the velocity autocorrelation function o(t). The characteristic time τ = 16mbv/(kBT) is generally much greater than the initial relaxation time tR and “long times” means after a few tR. Previous theories have predicted o(t) ∼ t−1 after a few tR and our result is consistent with this for times much less than τ. On a longer time scale ∼τ our result predicts an ususual behavior o(t) ∼ t − 5 2 which is sufficient to yield a finite diffusion coefficient from the Green-Kubo formula.
Affine Invariant Surface Evolutions for 3D Image Segmentation

In this paper we present an algorithm for 3D medical image segmentation based on an affine invariant flow. The algorithm is simple to implement and semi-automatic. The technique is based on active contours evolving in time according to intrinsic geometric measures of the image. The surface flow is obtained by minimizing a global energy with respect to an affine invariant metric. Affine invariant edge detectors for 3-dimensional objects are also computed which have the same qualitative behavior as the Euclidean edge detectors. Results on artificial and real MRI images show that the algorithm performs well, both in terms of accuracy and robustness to noise.
'Programming language paradigms' instruction through designing a new paradigm

Undergraduate and master's students enrolled in a programming language paradigms class are given the assignment to design a new programming language paradigm. The students are asked to develop a paradigm concept, demonstrate the utility of the paradigm for programmed solutions, and outline a sample programming language. Resulting student-designed paradigms from this class fall into three loosely defined categories: connection with a physical item, modeling a process, and representing program structure. The resulting class experience demonstrates that students can think and create beyond existing paradigms and features of languages to the level of abstraction that defines a new paradigm.
Thermochemistry and diffusion of nitrogen in solid molybdenum

The solubility of nitrogen in pure molybdenum was measured over the temperature range of 2173 to 2473 K and up to one atmosphere (101 kPa) of nitrogen gas pressure. Both thermochemical and kinetic aspects of this phenomenon were considered in this study. The solution of nitrogen in molybdenum may be expressed by the reaction $$1/2N_2 \left( g \right) = \underset{\raise0.3em\hbox{$\smash{\scriptscriptstyle-}$}}{N} \left( {Mo, s} \right)$$ , for which the standard Gibbs energy is given by the expression ΔGo = 78,500 + 27.367T Joules/g atom N. The formation of molybdenum nitrides, specifically, Mo2N, was considered. Attention was also focused on the mechanism of nitrogen solution in molybdenum. Estimates of the diffusivity of nitrogen atoms in solid molybdenum were derived from the kinetic data.
HBV plus HCV, HCV plus HIV, HBV plus HIV

Coinfection of hepatitis C virus (HCV), hepatitis B virus (HBV), and HIV is common due to shared modes of transmission. These coinfections accelerate the course of chronic liver disease and facilitate progression to cirrhosis and hepatocellular carcinoma. The viral interactions between these viruses are complex, and their treatment may be challenging for clinicians.
Computational Experience with Applications of Bilinear Cutting Planes

This work analyzes the effectiveness of cutting planes applied during the global optimization of nonconvex nonlinear and mixed-integer nonlinear programming problems arising from process synthesis and process operations. In a previous publication, we introduced algorithms for bilinear substructure detection, cutting plane identification, cut filtering, and cut selection. Our implementation embeds reformulation–linearization, lift-and-project, and advanced convex envelope construction techniques that exploit underlying bilinear substructures and tighten factorable programming reformulations at every node in the branch-and-bound tree. In this work, we utilize industrial examples to demonstrate a variety of relaxation tightening strategies afforded by these bilinear cutting plane algorithms. A detailed description and associated computational experience are presented for applied cutting planes.
Determination of dynamic moduli of soy doughs using an orthogonal rheometer.

The orthogonal rheometer in principle provides a relatively simple means of applying a dynamic strain to polymers to determine the dynamic storage and loss moduli (G′, G″) as functions of frequency and strain. In applying this technique to soy doughs, surface evaporation of water from the samples was found to be a serious problem, but when evaporation was controlled, good reproducibility for G′ and G″, was obtained. The moduli were very sensitive to dough moisture level, with G’ changing by a factor of 10 over the moisture range 40 to 50%. Plate diameter and percent strain both affected the absolute values of G′ and G″, though the effects were relatively small. Log G′ and log G″ increased linearly with decreasing nitrogen solubility index. The two major advantages of the orthogonal rheometer for such food systems are the ease of operation and the fact that sample thickness can be chosen to obviate problems associated with sample heterogeneity. Nevertheless, the effects of plate diameter and percent strain need more extensive study.
Properties of a thermostable 4Fe-ferredoxin from the hyperthermophilic bacterium Thermotoga maritima

A ferredoxin has been purified from one of the most ancient and the most thermophilic bacteria known, Thermotoga maritima, which grous up to 90°C. The reduced protein (Mr approx. 6300) contains a single S = 12 [4Fe4S]1+ cluster with complete cysteinyl ligation, and was unaffected after incubation at 95°C for 12 h. It functioned as an electron carrier for T. maritima pyruvate oxidoreductase. Remarkably, the properties and amino acid sequence of this hyperthermophilic bacterial protein are much more similar to those of ferredoxins from hyperthermophilic archaea, rather than ferredoxins from mesophilic and moderately thermophilic bacteria.
Observational drawing biases are predicted by biases in perception: Empirical support of the misperception hypothesis of drawing accuracy with respect to two angle illusions

We tested the misperception hypothesis of drawing errors, which states that drawing accuracy is strongly influenced by the perceptual encoding of a to-be-drawn stimulus. We used a highly controlled experimental paradigm in which nonartist participants made perceptual judgements and drawings of angles under identical stimulus exposure conditions. Experiment 1 examined the isosceles/scalene triangle angle illusion; congruent patterns of bias in the perception and drawing tasks were found for 40 and 60° angles, but not for 20 or 80° angles, providing mixed support for the misperception hypothesis. Experiment 2 examined shape constancy effects with respect to reproductions of single acute or obtuse angles; congruent patterns of bias in the perception and drawing tasks were found across a range of angles from 29 to 151°, providing strong support for the misperception hypothesis. In both experiments, perceptual and drawing biases were positively correlated. These results are largely consistent with the misperce...
A novel lipid hydroperoxide-derived modification to arginine.

The guanidine group present in the amino acid arginine was found to react with the lipid hydroperoxide-derived bifunctional electrophile, 4-oxo-2-nonenal. The reaction between Nα-tert-butoxycarbony-l-arginine and 4-oxo-2-nonenal resulted in the formation of an adduct (adduct A) that subsequently dehydrated on heating to adduct B. Liquid chromatography/mass spectrometry and nuclear magnetic resonance spectroscopy were used to assign the structure of adduct B as (Nδ,Nω‘-etheno-2‘-heptanon-2‘ ‘-one)-Nα-t-Boc-arginine. The reaction proceeded from initial reaction of the primary Nω-amino group at the C-1 aldehyde of 4-oxo-2-nonenal. Subsequently, an intramolecular Michael addition of a secondary Nδ-amino group occurring at C-3 resulted in formation of the cyclic carbinolamine adduct A. Dehydration and rearrangement of the exocyclic imine resulted in the formation of adduct B, which contained a stable imidazole ring. The tetra peptide LRDE reacted with 4-oxo-2-nonenal primarily at arginine rather than at the am...
Influence of Base Clearance on Subgrade Resilient Modulus of Florida Roadway Pavements

The resilient modulus of pavement subgrade materials is an essential parameter for mechanistically based flexible pavement design procedures. "Base clearance" is defined as the clearance between the groundwater level and the pavement base layer within a pavement system. A high pavement moisture content, which is strongly influenced by the base clearance, causes detrimental effects on the resilient modulus of pavement subgrades. The determination of a pavement base clearance is one of the most important steps toward setting up grade lines in a roadway design. This paper presents an experimental study to evaluate the effects of base clearance on the resilient modulus of pavement subgrades. Full-scale dynamic pavement tests were conducted in test pits to simulate vehicle dynamic impact on field pavements. The level of base clearance was adjusted by raising or lowering the water level within the pavement layer in the pit. Ten types of Florida subgrade material were tested at different base clearances for this...
Correlates of suicidal ideation among HIV-positive persons.

OBJECTIVES:: The present investigation sought to determine the extent to which demographic characteristics, illness-related burdens, alcohol and other substance use, and psychosocial factors are independently associated with suicidal ideation in HIV-positive individuals. DESIGN:: HIV-positive individuals in four US cities (San Francisco, Los Angeles, Milwaukee, and New York City) were screened between July 2000 and January 2002 for recruitment into a randomized behavioral prevention trial. Utilizing data from this screening visit, rates and correlates of suicidal ideation were examined in a diverse sample of 2909 HIV-positive individuals. METHODS:: Using binary logistic regression study sites, demographic characteristics, illness-related burdens, alcohol and substance use, and psychosocial factors were entered as predictors of suicidal ideation. This cross-sectional model thus examined the independent effects of each factor. RESULTS:: Approximately one-fifth (19%) of participants reported thoughts of suicide in the past week. We observed that participants who were not heterosexual, rated HIV-related symptoms and medication side effects as more severe, reported regular marijuana use, and described elevated affective symptoms of depression were those who were more likely to report suicidal ideation. Conversely, participants who identified as Hispanic/Latino, individuals in a primary romantic relationship, and those who reported greater self-efficacy for coping were less likely to report suicidal ideation. CONCLUSION:: Suicidal ideation among HIV-positive individuals is relatively common and is associated with multiple factors. These independent correlates may assist with identifying HIV-positive individuals who are at increased risk of suicidal ideation so that they may be assessed regularly and referred for psychological treatment when appropriate. Language: en
Failure of familiar size to determine a metric for visually perceived distance

The use of knowledge of the familiar sizes of objects in determining the apparent distances of those objects is known as the familiar size cue to distance. If effective, this cue might be one of the factors responsible for supplying the metric (scalar) characteristics of perceptions of spatial extent within a visual display in which other information concerning scalar extents has been reduced to a minimum. Two groups of observers were presented with realistic objects of the same angular, but different assumed, sizes presented in such a cue-restricted display. Perceptions of size and distance within the display did not differ significantly as a function of the type of object initially presented. This result was consistent with the notion that scalar perceptions under these conditions probably are determined by a factor known as the specific distance tendency, rather than by the experiential factor of familiar size.
The art of producing consumers: A critical textual analysis of post-communist Polish advertising

This article offers a critical textual analysis of hundreds of advertisements that appeared in Polish magazines at a pivotal historical juncture: following the collapse of communism and at the rise of a capitalist market economy in the early 1990s. It draws out from the visual and rhetorical data emblematic themes and sociocultural undercurrents concerning entrepreneurial opportunism and financial reassurance, status envy and post-rationing excess and interconnected solidarity with the West through brands and the English language itself. By studying the anxieties and aspirations represented in this symbolic material, we might better understand how new consumers were ideologically shepherded through a moment of profound political transition. The study represents a starting point for future investigation into how advertising produces its subjects in the aftermath of communism.
Laser cooling of lithium using relay chirp cooling.

We demonstrate a chirp-cooling technique that uses a laser with multiple FM sidebands to slow lithium atoms from initial velocities of as much as 1880 m/s to final velocities near zero. Compared with the use of a single sideband, this multisideband technique significantly reduces FM bandwidth requirements and provides a greater flux of slowed atoms.
METHYLENE BLUE-SENSITIZED PHOTOOXIDATION OF HEMOGLOBIN: EVIDENCE FOR CROSS-LINK FORMATION*

— When exposed to light of wavelengths >520nm, human hemoglobin (Hb; I mg/m/ at pH X, 10°C) in the presence of methylene blue (MB) undergoes inter-subunit cross-linking, as visualized by sodium dodecyl sulfate (SDS)-gel electrophoresis. With 10μM MB and a light dose of ˜700kJ/m2, a prominent ‘dimer’ band (28,00–30,000 daltons) appears, with traces of higher mol wt components. This effect (also observed by SDS-Sepharose chromatography) is seen with dialyzed hemolysates and with chromatographically purified Hb. The sedimentation coefficient of photooxidized Hb in 6 M guanidine hydrochloride (2.3 S) is significantly larger than that of unirradiated Hb (1.3 S), which supports the above conclusion that stable cross-links are generated in the photoreaction. The bonds formed are presumably not disulfides, since they resist cleavage by dithiothreitol. The rate of cross-linking is diminished by N3, histidine, and bilirubin, but enhanced by D2O, indicating that 1O2 plays a role in the reaction. Cross-linking is minimal when photooxidation is carried out at pH 6.0. but increases steadily with pH up to 9.0, suggesting that the reaction involves residues which titrate over this pH range.
An Alternative to Marginal Myotomy

Retroequatorial myopexy (Fadenoperation, posterior fixation sutures) was performed on both previously recessed medial recti muscles in 12 patients with a persistent convergence excess-type esotropia. The operation reduced the deviation in all but one patient and was more effective at near than at distance fixation. This surgical approach has several advantages and no known disadvantages over the marginal myotomy.