cssi/SciSciGPT-SciSciNet huggingface dataset:
Estimates and power counting in uniform nuclear matter with softened interactions

Modern softened nucleon-nucleon interactions are well suited for perturbative many-body calculations, but a many-body power counting scheme is lacking. Estimates of diagrammatic contributions at finite density are important ingredients in such a scheme. Here we show how to make quantitative estimates of the particle-particle and hole-hole channel in uniform nuclear matter for soft interactions. We also use estimates to assess the role of normal-ordered three-body forces for a pure contact interaction.
A new selective route towards benzoic acid and derivatives from biomass-derived coumalic acid

The selective production of aromatics from bio-based sources is an area of interest to expand the potential for greener alternatives to petroleum-derived chemicals. A scalable, efficient route to produce bio-based benzoates is demonstrated by carrying out heterogeneous catalytic reactions in non-toxic bio-based solvents at 180 °C obtaining yields of up to 100 mol%. This approach extends the 2-pyrone (coumalic acid/methyl coumalate) Diels–Alder platform by utilizing a bioavailable co-reactant ethylene. A detailed investigation using a combination of kinetic experiments, DFT calculations, and multi-dimensional NMR was carried out to determine the detailed reaction network, and the corresponding activation energies for critical steps. Additionally, a series of experiments were conducted to maximize the yields by comparing different solvents, for both coumalic acid and methyl coumalate. Our results show that the choice of solvent was a significant factor when coumalic acid was the reactant (yields 71–92 mol%), while methyl coumalate was only minimally affected by the solvent (yields 95–100 mol%). Interestingly, the reaction network and kinetic analysis showed that the Diels–Alder reactions were not significantly different between coumalic acid and methyl coumalate, with the rate limiting step for both being decarboxylation with an activation barrier of 141 kJ mol−1 compared to 77 kJ mol−1 for the formation of the bicyclic adduct. Finally, the reaction cascade was found to be highly susceptible to by-product formation when as little as 5 vol% water was present in the solvent, which demonstrates that the absence of water is essential for high yielding benzoate production.
Hearing crosstalk: the molecular conversation orchestrating inner ear dorsoventral patterning

The inner ear is a structurally and functionally complex organ that functions in balance and hearing. It originates during neurulation as a localized thickened region of rostral ectoderm termed the otic placode, which lies adjacent to the developing caudal hindbrain. Shortly after the otic placode forms, it invaginates to delineate the otic cup, which quickly pinches off of the surface ectoderm to form a hollow spherical vesicle called the otocyst; the latter gives rise dorsally to inner ear vestibular components and ventrally to its auditory component. Morphogenesis of the otocyst is regulated by secreted proteins, such as WNTs, BMPs, and SHH, which determine its dorsoventral polarity to define vestibular and cochlear structures and sensory and nonsensory cell fates. In this review, we focus on the crosstalk that occurs among three families of secreted molecules to progressively polarize and pattern the developing otocyst. WIREs Dev Biol 2018, 7:e302. doi: 10.1002/wdev.302 This article is categorized under: Establishment of Spatial and Temporal Patterns > Gradients Signaling Pathways > Cell Fate Signaling Vertebrate Organogenesis > From a Tubular Primordium: Non-Branched.
MicroRNAs and metastasis: small RNAs play big roles

MicroRNAs (miRNAs) are small non-coding RNAs regulating post-transcriptional gene expression. They play important roles in many biological processes under physiological or pathological conditions, including development, metabolism, tumorigenesis, metastasis, and immune response. Over the past 15 years, significant insights have been gained into the roles of miRNAs in cancer. Depending on the cancer type, miRNAs can act as oncogenes, tumor suppressors, or metastasis regulators. In this review, we focus on the role of miRNAs as components of molecular networks regulating metastasis. These miRNAs, termed metastamiRs, promote or inhibit metastasis through various mechanisms, including regulation of migration, invasion, colonization, cancer stem cell properties, epithelial-mesenchymal transition, and microenvironment. Some of these metastamiRs represent attractive therapeutic targets for cancer treatment.
Immune Reconstitution After Hematopoietic Stem Cell Transplantation

Immune reconstitution after hematopoietic stem cell transplantation (HSCT) is critical in order for HSCT recipients to recover their ability to fight all types of infections. Restoration of individual components of the immune system occurs with different timelines. Factors that influence this differential recovery include the type of HSCT, type of donor, donor histocompatibility, donor hematopoietic stem cell source, age of the donor and recipient, conditioning regimen used, the underlying disease or disorder, graft manipulation strategies, and the presence of graft-versus-host disease (GvHD). In general, innate immunity recovers much earlier post-HSCT as compared to adaptive immunity. Complete immune reconstitution may occur from several months to up to 2 years after HSCT. This chapter discusses the typical time course of immune reconstitution by cell type as well as methods to monitor immune reconstitution and an approach to revaccination post-HSCT.
Utilizing hot electrons

In current solar cells, any photon energy exceeding the semiconductor bandgap is lost before being collected, limiting the cell performance. Hot carrier solar cells could avoid these losses. Now, a detailed experimental study and analysis shows that this strategy could lead to an improvement of the photoconversion efficiency in practice.
Proceedings of the 2012 workshop on Developing competency in parallelism: techniques for education and training

With the increasing penetration of parallelism into computing, programmers of all stripes need to acquire competencies in concurrent programming. This workshop will concentrate on discussing and disseminating resources for gently introducing parallelism into programmers' skill sets. This workshop, Developing Competency in Parallelism: Techniques for Education and Training brings together two dozen researchers and instructors who have worked to find new ways of introducing programmers to the basics of parallel programming. We are pleased to have selected two papers from among those submitted, that offer new ways of teaching parallel-programming concepts. Our workshop also includes an unconference session, whose minutes can be accessed through this hyperlink. We will also view demos of multicore programming assignments, and WebMapReduce for CS1. We are happy that you are able to join us for this exciting workshop, and hope that the ideas you take home with you will enrich the experience of your students.
Information Visualization and the Semantic Web

The Semantic Web emphasizes that data should be machine-understandable, whereas information visualization aims to maximize our perceptional and cognitive abilities to make sense of visual-spatial representations of abstract information structures. One of the fundamental requirements of the Semantic Web is to annotate Web data with ontology to accomplish machine-understandable Web. Will they fit to work along with one another? Our illustrative example is intended to demonstrate that on the one hand, the Semantic Web can largely simplify some information visualization tasks today, and semantic annotation can be utilized for semantic visualization; on the other hand, the two fields differ from their philosophical groundings to tactical approaches to individual problems such as knowledge modeling and representation. A lot of theoretical and practical work remains to be done to find the right track for the two fields to work together harmoniously.
Solubilization of the Fusicoccin Receptor and a Protein Kinase from Highly Purified Plasma Membrane from Oat Roots

Fusicoccin (FC), a diterpine glucoside Phytotoxin, that stimulates electrogenic H+ extrusion in higher plants binds specifically to a plant plasma membrane (PM) protein. A highly purified preparation of plasma membrane vesicles has been prepared from oat roots and used to study the FC-binding protein (receptor). In these right-side out vesicles the FC-binding site is protected from trypsin degradation, but disruption of the vesicle integrity with Triton X-100 or solubilization of the receptor renders it susceptible to trypsin degradation. The receptor has been successfully solubilized with octyl-glucoside (90% recovery) and can be assayed effectively by binding to glass-fiber filters coated with 1% polyethylinimine.
High-lysine corn as a source of protein and energy for finishing calves.

Three trials evaluated the protein and energy value of high-lysine corn for finishing calves. In Trial 1, 60 finishing steer calves were used to evaluate corn source (high-lysine vs control) and protein source (urea, blood meal [BM], corn gluten meal [CGM]) and level (BM and CGM addition; low, medium, high). Calves were individually fed using Calan gates for 102 d, and then were pen-fed (two pens per corn treatment) the remaining 83 d. During the initial 102 d, calves fed high-lysine corn had similar gains but were 6% more efficient (P .10) among sources or levels of protein supplementation. Over the entire feeding period (185 d), calves fed high-lysine corn were 10% more efficient (P .10) between corn sources. Steers fed high-lysine corn tended to have greater ruminal (P = .23) and postruminal (P = .18) starch digestion, resulting in greater (P < .10) total tract starch digestibility.(ABSTRACT TRUNCATED AT 250 WORDS)
Abstract 4935: High-throughput immune-oncology screen identifies EGFR inhibitors as potent enhancers of CTL antigen-specific tumor cell killing

As immune checkpoint blocking antibodies increasing become foundational therapies for the treatment of cancer, there is a pressing need to identify compounds that synergize with checkpoint blockade as the basis of combinatorial treatment regimens. We have developed a screening assay in which a luciferized tumor cell line expressing a model antigen is co-cultured with a transgenic CD8+ T cell specifically recognizing the model antigen in a H-2b-restricted manner. The target tumor cell/T cell assay was screened with a small molecule library to identify compounds that inhibit or enhance T cell-mediated killing of tumor cells in an antigen-dependent manner. The EGFR inhibitor Erlotinib was the top hit that enhanced T cell killing of tumor cells. Subsequent experiments with Erlotinib and additional EGFR inhibitors validated the screen result. EGFR inhibitors increase both basal and IFN-γ-induced antigen processing and presentation of MHC class-I, which enhanced recognition and lysis by CD8+ cytotoxic T lymphocytes. The tumor cell line was also transduced to constitutively express Cas9, and a pooled CRISPR screen utilizing the same target tumor cell/T cell assay identified sgRNAs targeting EGFR as sensitizing tumor cells to T cell-mediated killing. Combination of PD-1 blockade with EGFR inhibition showed significant synergistic efficacy in the MC38 syngeneic colon cancer model that was superior to PD-1 blockade or EGFR inhibition alone, further validating EGFR inhibitors as immunomodulatory agents that enhance PD-1 checkpoint blockade. This novel target tumor cell/T cell assay can be screened in high-throughput with small molecule libraries and genome-wide CRISPR/Cas9 libraries to identify both compounds AND target genes, respectively, that enhance or inhibit T cell recognition and killing of tumor cells. Citation Format: Patrick H. Lizotte, Troy Luster, Megan E. Cavanaugh, Luke J. Taus, Abha Dhaneshwar, Naomi Mayman, Aaron Yang, Mark Bittinger, Paul Kirschmeier, Nathanael S. Gray, David A. Barbie, Pasi A. Janne. High-throughput immune-oncology screen identifies EGFR inhibitors as potent enhancers of CTL antigen-specific tumor cell killing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4935.
Pragmatic characteristics of security conversations: an exploratory linguistic analysis

Experts suggest that engineering secure software requires a defensive mindset to be ingrained in developer culture, which could be reflected in conversation. But what does a conversation about software security in a real project look like? Linguists analyze a wide array of characteristics: lexical, syntactic, semantic, and pragmatic. Pragmatics focus on identifying the style and tone of the author's language. If security requires a different mindset, then perhaps this would be reflected in the conversations' pragmatics. Our goal is to characterize the pragmatic features of conversations about security so that developers can be more informed about communication strategies regarding security concerns. We collected and annotated a corpus of conversations from 415,041 bug reports in the Chromium project. We examined five linguistic metrics related to pragmatics: formality, informativeness, implicature, politeness, and uncertainty. Our initial exploration into these data show that pragmatics plays a role, however small, in security conversations. These results indicate that the area of linguistic analysis shows promise in automatically identifying effective security communication strategies.
Dual-target hazard perception: Could identifying one hazard hinder a driver's capacity to find a second?

Abstract Low-level cognitive processes like visual search are crucial for hazard detection. In dual-target searches, subsequent search misses (SSMs) are known to occur when the identification of one target impedes detection of another that is concurrently presented. Despite the high likelihood of concurrent hazards in busy driving environments, SSMs have not been empirically investigated in driving. In three studies, participants were asked to identify safety-related target(s) in simulated traffic scenes that contained zero, one, or two target(s) of low or high perceptual saliency. These targets were defined as objects or events that would have prevented safe travel in the direction indicated by an arrow preceding the traffic scene. Findings from the pilot study (n = 20) and Experiment 1 (n = 29) demonstrated that detecting one target hindered drivers’ abilities to find a second from the same scene. In Experiment 2 (n = 30), explicit instructions regarding the level of risk were manipulated. It was found that search times were affected by the instructions, though SSMs persisted. Implications of SSMs in understanding the causes of some crashes are discussed, as well as future directions to improve ecological and criterion validity and to explore the roles of expertise and cognitive capabilities in multi-hazard detection.
A Proposed Definition and Structure of Counselor Dispositions

Dispositions have been identified as critical elements of counselor development and competency. Although there is currently no professional agreement regarding the definition or structure of counse...
Effect of acupressure on postpartum low back pain, salivary cortisol, physical limitations, and depression: a randomized controlled pilot study.

Objective To investigate the effect of acupressure on postpartum low back pain (LBP), salivary cortisol, physical limitations, and postpartum depression. Methods Participants were 70 postpartum women who were randomly assigned to either an intervention (n = 35) or a control (n = 35) group. The intervention group received 10 acupressure sessions (1 session per day, 5 d per week). The control group received 10 sham acupressure sessions. Outcomes were assessed using a visual analogue scale (LBP intensity), salivary cortisol values (LBP biomarker), and Chinese versions of the Roland-Morris Disability Questionnaire (daily activity limitations), Oswestry Disability Index (physical activity limitations), and the Edinburgh Postnatal Depression Scale (postpartum depression). Results Participants in the intervention group had significantly lower levels of LBP intensity, daily activity limitations, physical activity limitations, and postpartum depression than those in the control group. There was no significant between-group difference in salivary cortisol. Conclusion Acupressure may reduce postpartum LBP intensity and limitations in daily and physical activity, and alleviate postpartum depressive symptoms. Acupressure should be offered in postpartum care settings as an alternative treatment for postpartum women with LBP.
DeepTracer: Automated Protein Complex Structure Prediction from CoV-related Cryo-EM Density Maps

Abstract Information about the macromolecular structure of viral protein complexes such as SARS-CoV-2, and the related cellular and molecular mechanisms can assist the search for vaccines and drug development processes. To obtain such structural information, we present DeepTracer, a fully automatic deep learning-based method for de novo multi-chain protein complex structure prediction from high-resolution cryo-electron microscopy (cryo-EM) density maps. We applied DeepTracer on a set of 62 coronavirus-related raw experimental density maps, among them 10 with no existing deposited model structure. We observed an average residue match of 84% with the deposited structures and an average RMSD of 0.93A. Larger comparative tests further exemplify DeepTracer’s competitive accuracy and efficiency of multi-chain all atom complex structure prediction, with the ability of tracing around 60,000 residues within two hours. The web service and prediction results are globally accessible at https://deeptracer.uw.edu.
Sensitivity of 21st Century Ocean Carbon Export Flux Projections to the Choice of Export Depth Horizon

Global Earth system model simulations of ocean carbon export flux are commonly interpreted only at a fixed depth horizon of 100-m, despite the fact that the maximum annual mixed layer depth (MLD<su...
Reproductive biology of the introduced Mayan cichlid, Cichlasoma urophthalmus, within an estuarine mangrove habitat of southern Florida

We investigated the reproductive biology of the Mayan cichlid, Cichlasoma urophthalmus, for twenty consecutive months in a southern Florida mangrove creek and compared it to that of available published accounts where this species is native. Mayan cichlid reproduction occurred during a period of the year when physical conditions facilitated the best growth and survival of the young, and was influenced more by changes in water level and salinity than by temperature. Most nests were observed along mangrove shorelines in April. The majority of reproduction and parental care of the young followed in May, and was completed by June when rising water levels flooded shallow habitats and dispersed young-of-year fish. Mayan cichlids in Florida became reproductively mature at a greater size than in native regions, but produced roughly the same number of eggs at a given body mass. The similarity of environmental conditions between southern Florida and areas where Mayan cichlids naturally occur imparts a very favorable reproductive potential for this species in southern Florida, and facilitates their continued presence within the ichthyofauna of the region.
Seabed classification using localized forward modeling and deep learning

We use full wave solutions to generate synthetic high-frequency data for training seafloor classifiers with acoustic signals in the ocean. We expect to recover high level details that cannot be achieved by standard forward models that do not include seafloor roughness. By creating acoustic templates using micro local analysis of full-wave simulations on smaller domains, we avoid the high cost of solving the equations on large domains, the main obstacle in full wave inversion. To demonstrate the usefulness of this modeling, we generate a training library of templates and show how well these can be used in classifying seafloor parameters. We consider two-layer seafloors with varying material types and thicknesses. We address the geoacoustic inversion problem with standard machine learning techniques and more sophisticated deep learning methods. The standard classifiers provide results with worse accuracy that do not generalize well to other test environments; the deep learning classifiers are more costly to train but have higher accuracy, generalizing better. We compare the performance with simulations performed at lower frequencies using a normal mode approach with no roughness effects, where the classification problem becomes simpler. [Work supported by NSF, EOARD, and ONR.]
Promoting bone health in children and adolescents following solid organ transplantation.

Solid organ transplantation in children and adolescents provides many benefits through improving critical organ function, including better growth, development, cardiovascular status, and quality of life. Unfortunately, bone status may be adversely affected even when overall status is improving, due to issues with pre-existing bone disease as well as medications and nutritional challenges inherent post-transplantation. For all children and adolescents, bone status entering adulthood is a critical determinant of bone health through adulthood. The overall health and bone status of transplant recipients benefits from attention to regular physical activity, good nutrition, adequate calcium, phosphorous, magnesium and vitamin D intake and avoidance/minimization of soda, extra sodium, and obesity. Many immunosuppressive agents, especially glucocorticoids, can adversely affect bone function and development. Minimizing exposure to "bone-toxic" medications is an important part of promoting bone health in children post-transplantation. Existing guidelines detail how regular monitoring of bone status and biochemical markers can help detect bone abnormalities early and facilitate valuable bone-directed interventions. Attention to calcium and vitamin D supplementation, as well as tapering and withdrawing glucocorticoids as early as possible after transplant, can provide best bone outcomes for these children. Dual-energy X-ray absorptiometry can be useful to detect abnormal bone mass and fracture risk in this population and newer bone assessment methods are being evaluated in children at risk for poor bone outcomes. Newer bone therapies being explored in adults with transplants, particularly bisphosphonates and the RANKL inhibitor denosumab, may offer promise for children with low bone mass post-transplantation.
Understanding the genetic pathology of Stargardt disease: a review of current findings and challenges

Introduction: Stargardt macular dystrophy (STGD1), an autosomal recessive disorder, is caused by genetic mutations affecting ATP-Binding Cassette, subfamily A, member 4 (ABCA4). The genetic patholo...
Effects of Longer Seated Lunch Time on Food Consumption and Waste in Elementary and Middle School-age Children: A Randomized Clinical Trial.

Importance Health experts recommend at least 20 minutes of seated lunch time for children, but no federal policy for lunch period duration exists in the United States. Additional strategies in the National School Lunch Program for mitigating food waste are needed to maintain the viability of the Healthy, Hunger-Free Kids Act. Objective To assess the effect of a longer seated lunch time on food consumption and waste among elementary and middle school–age children. Design, Setting, and Participants This randomized within-participant crossover trial was conducted from June 3 to June 28, 2019, for a total of 20 study days. All attendees of a summer camp held at the University of Illinois at Urbana-Champaign, were invited to participate in the study. Participants were elementary and middle school–age children and were provided every study day with lunch prepared according to the National School Lunch Program nutrition standards. Intervention Five menus were served throughout the study. A 20-minute or 10-minute seated lunch condition was randomly assigned to each day within the 5 menus. Main Outcomes and Measures The primary outcomes were food consumption, waste, and dietary intake, which were analyzed separately for each meal component (fruit, vegetable, entree [protein plus grain], beverage [both milk and water], and milk alone). Dietary intake was assessed for calories, fat, carbohydrates, fiber, protein, vitamin D, calcium, iron, and potassium. Participant behaviors were observed during the meal, including seated time as well as level of talking and phone use. Results A total of 38 children with 241 lunch trays were observed. The 38 children had a mean (SD) age of 11.86 (1.23) years and 23 were female participants (61%); 30 had a non-Hispanic/non-Latino ethnicity (79%) and 23 were White individuals (61%). During 10 minutes of seated lunch time, participants consumed significantly less fruit (−11.3 percentage points; 95% CI, −18.1 to −4.5) and vegetables (−14.1 percentage points; 95% CI, −22.7 to −5.7) compared with 20 minutes of seated lunch time. Entree and beverage consumption and waste did not differ between the 10-minute and 20-minute seated lunch conditions. Participants also consumed significantly more and wasted significantly less calories (−22.03 kcal; 95% CI, −39.47 to −4.61 kcal), carbohydrates (−3.81 g; 95% CI, −6.20 to −1.42 g), dietary fiber (−0.51 g; 95% CI, −0.81 to −0.19 g), protein (−1.11 g; 95% CI, −2.17 to −0.04 g), iron (−0.20 mg; 95% CI, −0.38 to −0.02 mg), and potassium (−53.49 mg; 95% CI, −84.67 to −22.32 mg) during the 20-minute seated lunch condition. Conclusions and Relevance This study found that fruit and vegetable consumption increased in school-age children during a 20-minute seated lunch condition. This finding supports policies that require children to receive at least 20 minutes of seated lunch time; such policies could have favorable implications for children’s dietary intake and food waste. Trial Registration ClinicalTrials.gov Identifier:NCT04191291
Enhanced Microalgae Harvesting in a Microfluidic Centrifugal Separator

Microalgal biofuels have the substantial potential to meet national energy demands. One challenge of the microalgae-derived biofuels is limited harvesting efficiency, prompting an urgent need for alternative harvesting methods that are cost-effective and viable. Centrifugation has been used as one such method of separation, but most centrifugation methods lie in the high operating costs as opposed to other mechanical or chemical methods. To maximize separation efficiency while also limiting costs, we hereby demonstrate a spiral microalgae separator consistent with the centrifugal method, along with manipulating selected parameters of the algal medium to achieve a degree of separation within a single experiment that yields significantly more concentrated algal slurry. Concentration, temperature, and pH manipulation were among the few selected parameters that we found to yield high concentrations within single, rapid separations in seconds. Initial concentration of algae solutions was found to relate proportionally to separation efficiency. Algae solutions at lower density experienced flocculation that aids in the separation and centrifugal effect whereas high density samples experienced flocculation of algal groups too large for efficient separation. Similarly, basic pH and higher temperature manipulations specifically targeted the flocculation of microalgae particles to form larger groups, with more efficient harvesting. These parameters enable the principle and benefits of microfluidic centrifugal separation to be demonstrated on the microalgae flow, with the ability to be scaled up using parallelization of multiple platforms: a viable alternative to the conventional centrifugal method.
The varied experience of undergraduate students learning chemistry in virtual reality laboratories

Abstract Over the past two decades, there has been increased interest in understanding the prospects of virtual reality laboratories (VR Labs) in science education. VR Labs are designed to emulate a physical teaching laboratory through an immersive computer experience that affords intimate and intuitive interaction. According to a recent literature review, there is a scantiness of varied theoretical and methodological approaches concerning the student learning experience with VR Labs. Most of the studies were evaluative, seeking to establish the efficacy of VR Labs for meeting specific needs under the expectation that the mere use of them would bring about predetermined student outcomes. A phenomenographic investigation, which assumes that a person's perception is informed by their broader environment and results in multiple perspectives of the same phenomena was employed to investigate the various ways undergraduate chemistry students' experience learning with VR Labs. The inquiry is situated in an undergraduate chemistry course, where the VR Labs aligned with the course curriculum. From a purposive sample of six diverse participants, four qualitatively different experiences were discovered, which included: a) VR Labs hindered my ability to learn b) the amount of content knowledge I have and/or my prior experience influenced my learning c) the affordances I perceived enhanced my learning and d) VR Labs removed barriers I perceived to learning. The more comprehensive understanding provided by this study informs the design and development of new pedagogical approaches and innovative forms of curriculum.
Thermodynamics of Hydrogels for Applications to Atmospheric Water Harvesting, Evaporation, and Desalination

Most thermodynamic modeling of hydrogels focused on predicting their final volumes in equilibrium with water, built on Flory's theories for the entropy of mixing and rubber elasticity, and Donnan's equilibrium conditions if polyelectrolyte polymer and mobile ions are involved. This work will focus on water and ions in and outside hydrogels, which are of interests in solar interfacial water evaporation for desalination and waste water treatment, atmospheric water harvesting, and forward osmosis. Via a reformulation of Flory's classical hydrogel thermodynamic model by considering a combined system consisting of the hydrogel and its ambient, some confusions in previous work will be clarified. The reformulated thermodynamic model shows clearly the high pressure state of water in hydrogels and the coupling between the osmotic pressure and the Donnan potential. The model is applied to study thermodynamic properties of both pure and salty water in non-electrolyte and electrolyte hydrogels such as (1) the latent heat of evaporation, (2) the ability of hydrogels to retain water and to absorb water from the atmosphere, (3) the use of hydrogels for desalination via solar or forward osmosis, (4) the antifouling characteristics of hydrogels, and (5) melting point suppression and boiling point elevation, and solubility of salts in hydrogels. The reformulated thermodynamic framework will also be useful for understanding polymer electrolytes and ion transport in electrochemical and biological systems.
NEW APPROACH TO PREDICT LIME REACTIVITY OF SOILS

The purpose of this paper is to provide a nondestructive technique that can be used to evaluate the lime reactivity of a soil from the long-term strength developed in lime stabilized soils in a short-term test. The method proposed is based on the dielectric dispersion properties of clay-water electrolyte system. The properties of treated and untreated soil samples were compared and the difference between them was found to correlate with lime reactivity, i.e. the greater the difference after 1 day cure, the higher the strength after 7 and 28-day cure.
Epidemiology and Natural History

This chapter discusses the epidemiology and the natural history of invasive penile cancers, which for the majority involve the squamous mucosal epithelium of the glans, coronal sulcus, and inner preputial surfaces. Epidemiologic data and age-standardized incidence rates of penile cancer in different geographical areas of the world are presented. The etiologic role of phimosis, human papillomavirus infection, lichen sclerosus, psoralen and ultraviolet A photochemotherapy, and penile trauma is reviewed. The impact of risk factors such as socioeconomic status, religion, sexual practices, and other habits, including poor genital hygiene of different racial and ethnic groups on the incidence of penile cancer, is discussed. Factors resulting in diagnostic delay and the stepwise development of penile cancer from a penile lesion to regional lymph nodes involvement and distant metastatic spread are described in the natural history section of the chapter. A critical review of the most significant currently available literature is presented.
Cloning of a rat adipocyte membrane protein implicated in binding or transport of long-chain fatty acids that is induced during preadipocyte differentiation. Homology with human CD36.

A cDNA for an adipocyte membrane protein, implicated in the transport of long-chain fatty acids, was isolated by screening with a synthetic oligonucleotide derived from the amino terminal sequence of the protein. The 88-kDa adipocyte membrane protein was previously identified by covalent labeling with N-sulfosuccinimidyl esters of long-chain fatty acids which irreversibly inhibited fatty acid transport by 75% (Harmon, C. M., and Abumrad, N.A. (1993) J. Membr. Biol. 124, 261-268). The cDNA (FAT, 2432 base pairs (bp)) contained 70 bp of 5‘-untranslated sequence, an open reading frame encoding a 472-amino acid protein with a predicted molecular mass of 52466, and 940 bp of 3‘-untranslated sequence with two polyadenylation signal sequences but with no polyadenylation tail. The deduced protein sequence predicted two transmembrane segments and 10 potential N-linked glycosylation sites. Extensive glycosylation most likely explains why the molecular mass of the isolated protein (88 kDa) is different from that deduced from the cDNA sequence (53 kDa). The sequence of FAT is 85% homologous with that of glycoprotein IV (CD36) identified in human platelets and in lactating mammary epithelium. Consistent with this, a polyclonal antibody against CD36 reacted with adipocyte plasma membranes and detected a single band at 88 kDa. Northern blot analysis of RNA obtained from rat adipose tissue and probed with the cDNA identified two major transcripts of 4.8 and 2.9 kilobases which were abundant in heart, intestine, fat, muscle, and testis. The mRNAs were not detectable in cultured adipose cell lines (Ob1771, 3T3F442A) at the fibroblastic stage but were strongly induced during the differentiation process and by treatment of preadipocytes with dexamethasone, conditions that were also associated with an increase in oleate transport. In contrast, the fibroblastic cell lines 3T3-C2 and L929, which do not differentiate, did not express the mRNAs at all stages of culture. The data suggest that FAT and CD36 belong to a family of proteins that bind/transport long-chain fatty acids or function as regulators of these processes.
Amino acid transport in bone. II. Regulation of collagen synthesis by perturbation of proline transport.

Abstract 1. 1. This report describes a system for the determination of tissue free proline, proline incorporation into protein and hydroxyproline formation in fetal rat calvaria. 2. 2. The magnitude of the tissue free proline pool, and the rates of proline incorporation into net protein and collagen varied directly with extracellular proline concentrations less than 0.15 mM. Above 0.15 mM, protein and collagen synthesis were unaffected by further increments in the medium concentration of proline. 3. 3. Addition of α-aminoisobutyric acid, hydroxyproline and l -azetidine-2-carboxylic acid to the incubation medium decreased the intracellular free proline and the rates of proline incorporation into protein and collagen. 4. 4. We conclude that alterations in intracellular proline concentration produced either by varying extracellular proline concentration or by inhibition the uptake of proline into the intracellular pool, may contribute to the regulation of collagen synthesis.
Management of resistant mucocutaneous herpes simplex infections in AIDS patients: a clinical and virological challenge

Background The use of highly active antiretroviral therapy (HAART) has been associated with a marked decrease in the prevalence of opportunistic infections in HIV-infected patients. However, chronic mucocutaneous herpes simplex virus (HSV) infection remains a difficult clinical challenge. Objective The aim of the study was to optimize the diagnosis and follow-up of chronic HSV-2 infection in HIV-infected patients and to correlate clinical data with CD4 cell count, in vitro HSV virological resistance and histology. Methods A retrospective case series was collected from a specialist out-patient clinic providing consultations to patients with infectious skin diseases. Clinical, biological, virological and histological data were analysed. Results Seven HIV-infected patients with genital and perianal herpes simplex infection were followed over 10 years. Ulcerative and pseudo-tumoral forms were observed. Lesions occurred at various stages of immune suppression (CD4 counts from 1 to 449 cells/μL). Clinical resistance to conventional anti-herpetic drugs was correlated with the in vitro resistance of HSV in 70% of cases. Conclusions Chronic mucocutaneous HSV infection in AIDS patients remains a rare but regularly observed infection in very immunosuppressed patients or those with unstable immunity during HAART. Virological results obtained from mucocutaneous samples were in most cases found to be correlated with clinical evolution and should therefore be used in making decisions on treatment. Despite efficient antiviral therapy, mucocutaneous healing is slow in the majority of cases.
Towards Patient-Centered Care for Depression

Background: Although antidepressants and counseling have been shown to be effective in treating patients with depression, non-treatment or under-treatment for depression is common, especially among the elderly and minorities. Previous work on patient preferences has focused on medication versus counseling, but less is known about the value that patients place on attributes of medication and counseling. Objective: To examine, using conjoint analysis, the relative importance of various attributes of depression treatment at the group level as well as to determine the range of individual-level relative preference weights for specific depression treatment attributes. In addition, to predict what modifications in treatment characteristics are associated with a change in the stated preferred alternative. Methods: A total of 86 adults who participated in an internet-based panel responded to an online discrete-choice task about depression treatment. Participants chose between medication and counseling based on choice sets presented first for a ‘mild depression’ scenario and then for a ‘severe depression’ scenario. Participants were given 18 choice sets that varied for medication based on type of side effect (nausea, dizziness, and sexual dysfunction) and severity of side effect (mild, moderate, and severe); and for counseling based on frequency of counseling sessions (once per week or every other week) and location of the sessions (mental health professional’s office, primary-care doctor’s office, or office of a spiritual counselor). Results: Treatment type (counseling vs medication) appeared to be more important in driving treatment choice than any specific attribute that was studied; specifically, counseling was preferred by most of the respondents. After treatment type, location and frequency of treatment were important considerations. Preferred attributes were similar in both the mild and severe depression scenarios. Side effect severity appeared to be most important in driving treatment choice compared with the other attributes studied. Individual-level relative preferences for treatment type revealed a distribution that was roughly bimodal; 27 participants had a strong preference for counseling and 14 had a strong preference for medication. Conclusions: Estimating individual-level preferences for treatment type allowed us to see the variability in preferences and determine which participants had a strong affinity for medication or counseling. We found that participants preferred counseling over medication, avoided options with severe side effects, and wanted to be seen in the primary-care doctor’s office as opposed to other venues.
Insulin-sensitive glucose transport.

Publisher Summary This chapter discusses the effects and classification of insulin-sensitive glucose transport across the plasma membrane. The effects of insulin on cellular metabolism are diverse; some effects are chronic, others acute and complete within five–twenty minutes. The chronic effects of insulin include many complex processes, such as the stimulation of protein synthesis, cell growth and mitosis. The acute effects are also complex but may be classified into subgroups, presented in the chapter. The effects of insulin on these enzymes are consistent with the interpretation that the hormone promotes dephosphorylation of the enzymes. The effects of insulin on Type A enzymes are reversed by phosphorylation mediated by either cyclic adenosine monophosphate (cAMP)-dependent protein kinase or protein kinase C. The insulin-dependent stimulation of cAMP phosphodiesterase (Type B) is observable only in the presence of adenosine triphosphate (ATP), and the effect of the hormone on this enzyme is reversed in the absence of ATP. The effect of insulin on this enzyme is mimicked, rather than reversed, by the action of agents that increase the cellular concentration of cAMP. ATP is involved in both the insulin-dependent translocation of the glucose transport system and the reversal of the hormonal effect on the system in adipocytes.
Ocular pathogenicity of types 1 and 2 Herpesvirus hominis in rabbits.

Type 2 strains of Herpesvirus hominis produced more severe lesions in rabbit corneas than type 1 strains.
High Performance Fortran interface to the parallel C

Describes the design of a High Performance Fortran (HPF) interface to the parallel C++ (pC++) programming language. The pC++/HPF interface provides a mechanism for users to link pC++ programs with Fortran subroutines so that they can take advantage of both the fast computing speed of Fortran and the object-oriented programming paradigm of C++. We discuss the design of the Fortran interface and illustrate it with a galactic dynamics application. Our interface implementation is efficient. The galactic dynamics application can achieve a 14.4 GFLOPS sustained speed on a 512-node CM-5 massively parallel supercomputer. >
Postdefault Interest Rates in Bankruptcy

This Article shows that as Bankruptcy Code section 506(b) is currently written, postdefault interest rates are prohibited when the default is an “ipso facto event” — a filing for bankruptcy or insolvency as the event of a default. Yet some courts have insisted on postdefault interest in situations reinstating a loan agreement and have been ignoring restrictions on pendency interest to permit oversecured creditors from obtaining penalty rates of interest. This Article argues that those holdings violate section 506(b) and Supreme Court precedent. It begins with an analysis of ipso facto defaults, showing that the Bankruptcy Code prohibits ipso facto clauses even in nonexecutory contracts. The Article then examines regular monetary defaults. Noting that the Supreme Court only allows compensatory market rates to oversecured creditors, high default interest rates will never be a proxy for the market rate as they constitute penalties. Similarly, the Article argues that the “cure” of loan agreements allowed by reorganization chapters is a compensatory concept, also requiring the market rate of interest. Finally, the Article concludes by arguing that the Bankruptcy Code applies to solvent and insolvent debtors, and thus ipso facto clauses are prohibited and section 506(b) requires compensatory, not punitive, rates even in solvent bankruptcy cases.
Obtaining Functionally Relevant Protein Structural Transitions Using a Combined Physics/Structure-Based Coarse-Grained Model

The function of proteins is intimately tied to their dynamics and their ability to undergo structural transitions. These transitions are rare events, difficult to model computationally. Recently, we have developed ELNEDIN, a modeling approach that combines an elastic network with a physics based coarse-grained force field. We have shown that ELNEDIN can reproduce reliably the equilibrium dynamics of proteins. Here evaluate the ability of ELNEDIN to identify directions of conformational change that are functionally relevant, and to produce fully reversible transitions during the course of a simulation. To this end we selected a set of 15 protein systems known to exist in at least two conformational states (open/closed). ELNEDIN models of the open and closed state were simulated via molecular dynamics. The directions of the low frequency motions extracted from the trajectories were compared to the direction of the experimentally known conformational change. The main findings of these computational experiments are that: (1) ELNEDIN models based on the open(unliganded/apo) state of a protein system are more likely to identify correctly the direction of conformational change induced by the binding of the ligand than models based on the holo (liganded) state; (2) the degree of collectivity of the functional transition is the single most important predictor of the ability to identify computationally the direction of conformational change; (3) this is best achieved when the functional transition is of the hinge type, followed by shear type and worst for the unclassified type; (4) finally, in some cases, e.g. HIV-1 protease, fully reversible structural transitions can be observed during the course of a single simulation. These findings suggest that ELNEDIN models could be used towards understanding of the mechanistic processes associated with ligand-binding by allowing real-time simulations of such events.
Mass-induced crystalline color superconductivity

We demonstrate that crystalline color superconductivity may arise as a result of pairing between massless quarks and quarks with nonzero mass m_s. Previous analyses of this phase of cold dense quark matter have all utilized a chemical potential difference \delta\mu to favor crystalline color superconductivity over ordinary BCS pairing. In any context in which crystalline color superconductivity occurs in nature, however, it will be m_s-induced. The effect of m_s is qualitatively different from that of \delta\mu in one crucial respect: m_s depresses the value of the BCS gap \Delta_0 whereas \delta\mu leaves \Delta_0 unchanged. This effect in the BCS phase must be taken into account before m_s-induced and \delta\mu-induced crystalline color superconductivity can sensibly be compared.
Formation of sharp eccentric rings in debris disks with gas but without planets

'Debris disks' around young stars (analogues of the Kuiper Belt in our Solar System) show a variety of non-trivial structures attributed to planetary perturbations and used to constrain the properties of those planets. However, these analyses have largely ignored the fact that some debris disks are found to contain small quantities of gas, a component that all such disks should contain at some level. Several debris disks have been measured with a dust-to-gas ratio of about unity, at which the effect of hydrodynamics on the structure of the disk cannot be ignored. Here we report linear and nonlinear modelling that shows that dust-gas interactions can produce some of the key patterns attributed to planets. We find a robust clumping instability that organizes the dust into narrow, eccentric rings, similar to the Fomalhaut debris disk. The conclusion that such disks might contain planets is not necessarily required to explain these systems.