cssi/SciSciGPT-SciSciNet huggingface dataset:
The PLOS Computational Biology Software Section

As a member of the PLOS family, PLOS Computational Biology promotes open and unrestricted access to scientific publications and the research products that support them. For PLOS Computational Biology, this specifically includes computational methods and the software that implements them. To foster a culture of open exchange and reuse of software, we created a new category of manuscripts called Software Articles. We have been accepting submissions in this category for over a year now, and all articles published in this category are now also available as an online collection (http://www.ploscollections.org/software). This is a collection of articles spanning a wide range of different topics in computational biology, starting from video image analysis in “Automated Tracking of Whiskers in Videos of Head Fixed Rodents” [1], over to simulation and analysis of biological system models in “Hybrid Models and Biological Model Reduction with PyDSTool” [2]. We have published articles describing genomic tools, such as “Podbat: Genomic Tool for Epigenetic Meta-Analysis” [3] and “Exploring Massive, Genome Scale Datasets with the GenometriCorr Package” [4], computational chemistry, in “AutoClickChem: Click Chemistry in Silico” [5], and protein science, in “ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein Origin” [6] and “CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures” [7]. As new Software Articles get published in this journal, they will be added to this collection.
Application of an invariant second-order closure model to compressible turbulent shear layers

A second-order closure model for two-dimensional, compressible shear flows is investigated using the invariant modeling technique developed by Donaldson. The invariant model parameters were originally selected by comparison of model predictions with critical experimental data on basic incompressible flows. Additional modeling for compressible flows has been introduced. A number of different shear flows such as the free shear layer, flat plate boundary layer and a simulation of the mixing region of a chemical laser are computed. The model is consistent with first-order closure turbulence models for equilibrium flows and is further capable of predicting nonequilibrium flows that cannot be correctly solved by eddy viscosity models. The results are in generally good agreement with experimental measurements but suggest the need for inclusion of a Mach number dependent model of the pressure diffusion terms in order to adequately represent high speed compressible flows.
Direct Observation of Isotopic Exchange in the Solid State

THE first report of isotopic exchange in a solid system was given by Kaucic and Vlatkovic1. They heated Ca(IO3)2 doped with 131I− at temperatures higher than 170° C and observed, by chemical analysis, incorporation of activity into the iodate. Apers et al.2 found that thermal treatment of K2CrO4 doped with 51Cr3+ results in the incorporation of chromium-51 activity into the chromate form. This overall process, which results in the incorporation of radio-species having a non-parent oxidation state into the parent chemical form, has been termed “transfer annealing”2—a process which may involve either an oxidation or a reduction of the tracer species and is not necessarily an isotopic exchange. In a subsequent article3, the same group of researchers considered several possible mechanisms for oxidation of the dopant 51O3+, resulting in the formation of species (in the solid state) which would form the parent chromate during subsequent dissolution. Incorporation of activity into the chromate by isotopic exchange was not considered. Later, Nath et al.4–6 showed that isotopic exchange exists in complex molecules; in this case, cobalt chelates doped with radio-Co2+. They considered that it was not possible to interpret the incorporation of cobalt activity in the chelate form by the oxidative mechanisms suggested for the K2CrO4–51Cr3+ system2,3, and they regarded “transfer annealing” as a genuine case of isotopic exchange. In some systems, for example tris-dipyridy Co(III) perchlorate trihydrate doped with 57Co++, the exchang occurs quite rapidly even at room temperatures. Nath et al. have suggested that the energy required to overcome the large potential barriers encountered in isotopic exchange in the solid state is derived from electrons detrapped from donors during thermal treatment. A free electron is captured by 57Co++ ion to form a highly excited 57Co+ ion which, in turn, interacts with a neighbouring chelate molecule and replaces the inactive cobalt atom. where *Co+ represents the highly excited ion.
Two-electron excitation to Rydberg levels in fast I6+ on hydrogen collisions

Abstract The emission of electrons in the forward direction in collisions of 0.3 MeV/u I 6+ with H 2 has been studied, and strong autoionization peaks are observed on the shoulder of the cusp peak. The energies of these autoionization lines in the projectile rest frame are determined by high-resolution electron spectroscopy. Using the electron projectile final charge state coincidence technique, we probe different collision mechanisms, which create continuum electrons that are slow in the projectile rest frame. We conclude that the observed autoionization lines are due to two electron excitation to projectile Rydberg levels.
Numerical Modeling of Geofoam Embankments

In 2001, the Utah Department of Transportation completed a 4-year $1.4 billion I-15 reconstruction project in Salt Lake City, Utah. This project included widespread use of expanded polystyrene geofoam as lightweight embankment at important utility crossings and where close proximity to existing buildings necessitated minimizing consolidation settlement. This paper presents construction and long-term monitoring results for some of these embankments with numerical modeling of the field measurements. Fast Lagrangian Analysis of Continua, a finite-difference program, was used to estimate the complex stress distribution and the displacements (i.e., strain) that developed in select geofoam embankments. The writers used a bilinear elastic model to produce reasonable estimates of gap closure, block seating, and the subsequent elastic compression of the geofoam embankment at higher stress levels. Such estimations are important for modeling and designing geofoam embankments and potential connections with other systems. The calculation of the complex stress distribution and displacements that develops in a geofoam embankment has application to settlement, lateral earth pressure against retaining and buried walls, slope stability, and seismic design of geofoam embankments.
Topology Stability Analysis and Its Application in Hierarchical Mobile Ad Hoc Networks

The hierarchical architecture has been proven effective for solving the scalability problems in large-scale ad hoc networks. The stability of the hierarchical architecture is a key factor in determining the network performance. Although many solutions have been proposed to construct stable clusters, the maximum stability achievable in mobile environments is still unknown. In this paper, we define three metrics for measuring network stability: (1) the cluster lifetime;(2) the intercluster link lifetime; and (3) the end-to-end path lifetime. We model and analyze the maximum of these lifetimes under the constraint of random node mobility. Analytical results provide the fundamental understanding of the bounds on network stability. Inspired by this understanding, we propose a clustering algorithm and a hierarchical routing protocol that work together to achieve the maximum network stability. The analytical results are verified by simulations.
Enhanced mobility protocol for wireless networks

The purpose of this research was to improve the communication technology for mobile computing devices. It focused on increasing the speed and reliability of data, voice, and video transmissions while away from a home or office and mobile. A new mobility protocol is proposed building on the existing mobile Internet protocol (Mobile IP). This new protocol used the concept of port redirection to route traffic to a mobile node and eliminated the need for tunneling. The enhanced protocol was designed to more efficiently use network resources, improve performance, and increase scalability. The analysis shows that with the exception of the first packet exchanged, the delay of the proposed protocol was similar to that of the current mobile IP protocol, and the amount of overhead required was decreased when compared to mobile IP as the number of packets exchanged increased. This occurred because of a one-time overhead in the new protocol compared to an overhead with every tunneled packet in mobile IP.
A simple model for spatial rainfall fields

Spatial rainfall amounts accumulated over short to medium periods of time, say a few days, tend to have a probabilistic structure with very distinctive features. Some of these that are specially relevant for the purpose of spatial modeling are the presence of mixed sampling distributions, right skewed distributions conditional on rainfall occurrence, and a complex spatial association structure. The goal of this work is to construct a family for the bivariate distributions of spatial rainfall fields that incorporates these distinctive features. It is based on the separate modeling of spatial occurrence of rainfall and the spatial distribution of positive rainfalls. The main properties of the bivariate distributions are derived, and some properties of the random field realizations are illustrated through simulation. Some limitations of the proposed model are also discussed.
Delayed chest closure after lung transplantation: Techniques, outcomes, and strategies

Background Delayed chest closure (DCC) after lung transplantation is a viable option to be taken in the cases of prolonged cardiopulmonary bypass time, prolonged ischemic time, coagulopathic problems or oversized donor lung grafts. Decision-making for DCC in the operating room remains challenging to surgeons, because the impact of DCC on outcomes after lung transplantation has not yet been fully elucidated. Methods We performed a retrospective review of 90 lung transplantations with DCC and 783 cases with primary chest closure to clarify the reasons for DCC, complications of DCC, and the risk factors for adverse outcomes. Results The 30- and 90-day mortality in the DCC group was 7.8% and 9.9%, respectively. Early post-operative bleeding and severe primary graft dysfunction (PGD) were higher in the DCC group ( p 4 hours), post-operative extracorporeal oxygen requirement and use of a DCC technique with open skin and retracted ribs were significantly associated with mortality ( p p Conclusions Our technical approaches to prevent possible problems in DCC cases are described. DCC can be safely performed with acceptable procedure-related risks. DCC should not be considered a sub-optimal option after lung transplantation.
IMPORTANCE OF NEIGHBORING GROUP PARTICIPATION IN THE REMARKABLY RAPID PHOTOREDUCTION OF 1,1,4,4-TETRAMETHYL-l,4-DIHYDRO-2,3-NAPHTHALENEDIONE#

— The photochemistry of 1,1,4,4-tetramethyl-1,4-dihydro-2,3-naphthalenedione (I) in the presence of hydrogen donors has been examined in solution at room temperature by laser flash photolysis. The triplet state of I shows a remarkable reactivity towards hydrogen abstraction, exceeding that of biacetyl by ca. three orders of magnitude, and being comparable, and occasionally exceeding that of triplet benzophenone. This remarkable behavior is attributed to a considerable degree of stabilization of the transition state due to intramolecular hydrogen bonding.
A truncated Cauchy distribution

A truncated version of the Cauchy distribution is introduced. Unlike the Cauchy distribution, this possesses finite moments of all orders and could therefore be a better model for certain practical situations. One such situation in finance is discussed. Explicit expressions for the moments of the truncated distribution are also derived.
Slow Leakage of Ca-Dipicolinic Acid from Individual Bacillus Spores during Initiation of Spore Germination

ABSTRACT When exposed to nutrient or nonnutrient germinants, individual Bacillus spores can return to life through germination followed by outgrowth. Laser tweezers, Raman spectroscopy, and either differential interference contrast or phase-contrast microscopy were used to analyze the slow dipicolinic acid (DPA) leakage (normally ∼20% of spore DPA) from individual spores that takes place prior to the lag time, T lag , when spores begin rapid release of remaining DPA. Major conclusions from this work with Bacillus subtilis spores were as follows: (i) slow DPA leakage from wild-type spores germinating with nutrients did not begin immediately after nutrient exposure but only at a later heterogeneous time T 1 ; (ii) the period of slow DPA leakage (Δ T leakage = T lag − T 1 ) was heterogeneous among individual spores, although the amount of DPA released in this period was relatively constant; (iii) increases in germination temperature significantly decreased T 1 times but increased values of Δ T leakage ; (iv) upon germination with l-valine for 10 min followed by addition of d-alanine to block further germination, all germinated spores had T 1 times of less than 10 min, suggesting that T 1 is the time when spores become committed to germinate; (v) elevated levels of SpoVA proteins involved in DPA movement in spore germination decreased T 1 and T lag times but not the amount of DPA released in Δ T leakage ; (vi) lack of the cortex-lytic enzyme CwlJ increased DPA leakage during germination due to longer Δ T leakage times in which more DPA was released; and (vii) there was slow DPA leakage early in germination of B. subtilis spores by the nonnutrients CaDPA and dodecylamine and in nutrient germination of Bacillus cereus and Bacillus megaterium spores. Overall, these findings have identified and characterized a new early event in Bacillus spore germination.
Aging and dying: medical and ethical considerations

The idea of writing a chapter on aging seems particularly appropriate. I'm at the right age to address this topic. As I did the preparatory reading and research, I had an unusual experience. For the first time in my life, I felt like an expert. I could judge what people were saying about aging by my own experience. Besides facing aging myself, I work mainly with rural hospitals and nursing homes and hospice organizations where most of the patients are elderly. Both in my personal life and in my work, I am surrounded by the realities of aging and dying. In a recent book entitled Gray Dawn (1) on the economics and politics of aging, the author, Peter Peterson used a gripping metaphor to describe the challenge of an increasing aging population. Global aging, he said, is like a massive iceberg which very well could destroy even the most powerful economic vessels in the world. The aging population worldwide, according to this author, threatens human survival and is the most important challenge we face in the 21st century. His iceberg metaphor highlights the danger of global aging and the fact the all human beings are exposed to this danger.
Career Maturity and Foreclosure in Student Athletes, Fine Arts Students, and General College Students

Three groups of undergraduate students, fine arts students (n = 121), general college students (n = 104), and student athletes (n = 101), were compared on career maturity attitudes, identity foreclosure, and career foreclosure. Findings indicated that student athletes, but not fine arts students, scored lower on career maturity as compared to general college students. Findings also revealed that student athletes reported greater identity foreclosure as compared to general college students and fine arts students. No significant group difference was found for career foreclosure.
Privacy-Preserving Data Mining

Privacy-preserving data mining (PPDM) refers to the area of data mining that seeks to safeguard sensitive information from unsolicited or unsanctioned disclosure. Most traditional data mining techniques analyze and model the data set statistically, in aggregation, while privacy preservation is primarily concerned with protecting against disclosure individual data records. This domain separation points to the technical feasibility of PPDM. Historically, issues related to PPDM were first studied by the national statistical agencies interested in collecting private social and economical data, such as census and tax records, and making it available for analysis by public servants, companies, and researchers. Building accurate socioeconomical models is vital for business planning and public policy. Yet, there is no way of knowing in advance what models may be needed, nor is it feasible for the statistical agency to perform all data processing for everyone, playing the role of a trusted third party. Instead, the agency provides the data in a sanitized form that allows statistical processing and protects the privacy of individual records, solving a problem known as privacy-preserving data publishing. For a survey of work in statistical databases, see Adam and Wortmann (1989) and Willenborg and de Waal (2001). The term privacy-preserving data mining was introduced in the papers Agrawal and Srikant (2000) and Lindell and Pinkas (2000). These papers considered two fundamental problems of PPDM: privacy-preserving data collection and mining a data set partitioned across several private enterprises. Agrawal and Srikant devised a randomization algorithm that allows a large number of users to contribute their private records for efficient centralized data mining while limiting the disclosure of their values; Lindell and Pinkas invented a cryptographic protocol for decision tree construction over a data set horizontally partitioned between two parties. These methods were subsequently refined and extended by many researchers worldwide. Other areas that influence the development of PPDM include cryptography and secure multiparty computation (Goldreich, 2004; Stinson, 2006), database query auditing for disclosure detection and prevention (Dinur & Nissim, 2003; Kenthapadi, Mishra, & Nissim, 2005; Kleinberg, Papadimitriou, & Raghavan, 2000), database privacy and policy enforcement (Aggarwal et al., 2004; Agrawal, Kiernan, Srikant, & Xu 2002), database security (Castano, Fugini, Martella, & Samarati, 1995), and of course, specific application domains.
The influence of inhibitory control and episodic memory on the risky sexual behavior of young adult cannabis users.

Cannabis use is associated with risky sexual behavior (RSB) and sex-related negative health consequences. This investigation examined the role of inhibitory control and episodic memory in predicting RSB and sex-related negative consequences among current cannabis users. Findings indicated that the relationships among cannabis, neurocognition, and sexual-risk varied according to the dimension of neurocognition and the parameter of RSB in question. Specifically, more risk-taking was associated with more RSB. Furthermore, amount of recent cannabis use was associated with more RSB and sex-related negative consequences, but only among those with worse performances on a measure of decision-making and of risk-taking. Contrary to hypotheses, worse episodic memory also significantly predicted higher overall sexual-risk and decreased safe-sex practices. Results indicate that worse neurocognitive performance in the areas of risk-taking, decision-making, and episodic memory may influence the degree to which cannabis users engage in RSB and experience negative health consequences as a result. (JINS, 2012, 18, 1–7)
PET brain imaging with [11C](+)McN5652 shows increased serotonin transporter availability in major depression.

Abstract Background : Alterations in the brain serotonin (5-HT) system have been found in patients with depression. We used the selective 5-HT transporter site ligand [ 11 C](+)McN5652 and positron emission tomography (PET) to examine the hypothesis that alterations in 5-HT transporter levels may be present in selected regions of the brain in depressed patients. Methods : Four drug free depressed patients and four healthy control subjects were studied using [ 11 C](+)McN5652 and PET. The distribution volume (DV) ratio of the PET ligand in selected regions of interest (ROIs) compared to cerebellum were calculated for the ROIs. Results : Patients showed significantly larger DV ratios in the left frontal cortex ( P =0.013) and right cingulate cortex ( P =0.043) compared to control subjects. Limitation : The sample size was modest with gender differences between the subject groups. The PET agent, [ 11 C](+)McN5652, may have a lower binding affinity for the 5-HT transporter in the cortical regions compared to other brain regions. Conclusion : These findings suggest that 5-HT transporter sites may be increased in the frontal and cingulate cortices of depressed patients. These alterations in 5-HT transporter sites may be of pathophysiologic significance in the etiology of depression and its treatment.
The Effects of Double Fault Bends on Rupture Propagation: A Geometrical Parameter Study

We use the 2D finite element method to determine how geometrical parameters determine whether rupture will propagate across a linked stepover in a strike-slip fault. The end segments of the fault system are aligned in the direction of maximum shear, and the length and angle of the linking segment are allowed to vary. We observe that ruptures propagate through extensional stepovers with steeper angles and longer linking segments than otherwise equivalent compressional step- overs. These different rupture behaviors form distinct regions in angle-stepover-length parameter space; the boundary between these regions takes the shape of an asymptotic curve in both the extensional and compressional cases. Models in which the size of the entire fault system was made larger or smaller revealed that the location of the bound- aries between regions of different rupture behavior do not scale linearly with the system size; it was easier to rupture steeper and relatively longer stepovers in fault systems that were larger overall. A separate set of models in which the stress field is rotated so that the parallel end segments were optimally aligned for rupture significantly altered the rupture behavior curves; in this stress field, it was easier to rupture compressional stepovers with steeper angles and longer linking segments than it was to rupture equivalent extensional stepovers. In both the case in which the end segments are aligned with the direction of maximum shear and the case in which the end segments are optimally oriented for rupture, the angles at which rupture could no longer propagate through the entire fault corresponded with peaks in the fault's S value.
Alveolar macrophage content of isoferritins and transferrin. Comparison of nonsmokers and smokers with and without chronic airflow obstruction.

Alveolar macrophages (AM) contain iron and ferritin, and concentrations of both are increased in AM of smokers compared with nonsmokers. Ferritin stores iron in a nontoxic form but can release iron in the presence of reducing agents and thereby catalyze the generation of toxic hydroxyl radicals via the Haber-Weiss reaction. Two distinct isoferritins are found in peripheral monocytes, L ferritin and H ferritin. H ferritin is the predominant isoferritin in human monocytes and is more effective than L ferritin in detoxifying iron in vitro. In this study we quantitated content of H and L ferritins, transferrin, and iron in AM recovered by bronchoalveolar lavage (BAL) of 24 subjects, including eight nonsmokers, eight smokers with normal spirometry, and eight smokers with chronic airflow obstruction (CAO). Of total AM ferritin in nonsmokers 95% was composed of L ferritin. Smokers without CAO demonstrated a 6.5-fold increase in the AM content of L ferritin (1,886 ± 266 versus 290 ± 51 ng, mean ± SEM; p < 0.0001)...
Visual exploration and analysis of historic hotel visits

Understanding the spatial and temporal characteristics of individual and group behavior in social networks is a critical component of visual tools for intelligence analysis, emergency management, consumer analysis, and human geography. Identification and analysis of patterns of recurring events is an essential feature of such tools. In this paper, we describe an interactive visual tool for exploring the visitation patterns of guests at two hotels in central Pennsylvania from 1894 to 1900. The centerpiece of the tool is a wrapping spreadsheet technique, called reruns, that reveals regular and irregular periodic patterns of events in multiple overlapping artificial and natural calendars. Implemented as a coordinated multiple view visualization in Improvise, the tool is in ongoing development through an iterative process of data collection, transcription, hypothesis, design, discovery, analysis, and evaluation in close collaboration with historical geographers. Numerous discoveries have driven additional data collection from archival newspaper and census sources, as well as plans to enhance analysis of spatial patterns using historic weather records and railroad schedules. Distributed online evaluations of usability and usefulness have resulted in feature and design recommendations that are being incorporated into the tool.
Gonadal Regression Induced by Caloric Restriction Is Not Mediated by the Pineal Gland in Deer Mice (Peromyscus maniculatus)

The role of the pineal gland in mediating reproductive regression in response to nonphotoperiodic cues was assessed. A proportion of deer mice (Peromyscus maniculatus) undergo gonadal regression subsequent to moderate food restriction. The reproductive regression after inanition qualitatively and quantitatively resembles short-day-induced regression. The physiological mechanisms responsible for gonadal regression after food restriction are unknown. The hypothesis that the mechanisms underlying photoperiodic responsiveness also mediate testicular regression caused by reduced food consumption was tested. Males were pinealectomized or received sham operations. Upon recovery, food availability was restricted to 70% of ad libitum intake. After 8 weeks, the reproductive condition was examined. Pinealectomy did not prevent gonadal regression, suggesting that the pineal gland does not mediate caloric information in this species.
TIM selection criteria for silicon validation environment

Thermal interface materials (TIMs) are widely used as heat conductive medium between a heat source and a heat dissipating device. A high thermal performance TIM can provide a low thermal resistance path and thus improve the thermal management of the heat source. This paper presents various criteria for TIMs used in silicon validation environment in addition to the well-known criteria for high performance TIMs. Seven commercially available greases and eight different thermal pads were evaluated based on the requirements for use in the silicon validation environment. These criteria include thermal performance before and after subjected to elevated temperature, adhesiveness of the grease before and after subjected to elevated temperature, adhesiveness of the grease over multiple usages, compliance of the thermal pad, reusability of the thermal pad for multiple loading and unloading cycles, and severity of silicone bleed from the thermal pad under elevated temperature and pressure. In addition to these validation requirements of TIMs, there is an additional requirement of high cycle of reusability in the robotic testing environment to minimize human interface. Indium TIM, a metallic TIM, provides well over 500 reusability cycles. Adhesion issue with high Indium content becomes dominant at high temperature and needs to be well addressed to take advantage of the reusability characteristics of Indium TIM.
Effect of Modified Metal/Passivation Interfaces on Stress Voiding in Interconnects +

Stress and electromigration voids are believed to nucleate at the metal/passivation interface. In this study, modified interfaces were synthesized to experimentally elucidate the role of the interface on stress voiding for comparison with theoretical predictions. Interfaces were modified by depositing photoresist in a controlled manner on Ti/Algfi lines prior to passivation deposition. Stress voiding susceptibility was assessed in as-received lines as well as those subjected to storage anneals for 1, 5, and 25 days at 190°C to accelerate void formation. The global textures of all the lines were fiber and were not significantly affected by the interface modification. Differences in stress voiding were attributed to the different interfaces. Higher ratios of voids in modified regions to voids in unmodified regions were observed both in as-received lines and those given a 1 day storage anneal due to the heterogeneous nucleation sites provided by the photoresist contamination in the modified regions. However, the void ratio appears to decrease exponentially with longer time anneals. Lowered driving force for void formation in the modified regions leads to less voiding with time, while higher driving force and a limited number of nucleation sites in the unmodified regions leads to more voiding with time. Local textures at a limited number of voided sites in modified and unmodified regions were identical to the global texture of the line. In our limited sampling, voids did not form in local regions of weaker texture.
Enzyme replacement therapy results in substantial improvements in early clinical phenotype in a mouse model of globoid cell leukodystrophy

Globoid cell leukodystrophy (GLD) or Krabbe disease is a devastating, degenerative neurological disorder caused by mutations in the galactosylceramidase (GALC) gene that severely affect enzyme activity. Currently, treatment options for this disorder are very limited. Enzyme replacement therapy (ERT) has been shown to be effective in lysosomal storage disorders with predominantly peripheral manifestations such as type I Gaucher's and Fabry's disease. Little however is known about the possible benefit of ERT in GLD, which has a substantial central nervous system component. In this study, we examined the effect of peripheral GALC injections in the twitcher mouse model of the disease. Although we were unable to block the precipitous decline that normally occurs just before death, we did observe significant early improvements in motor performance, a substantial attenuation in the initial failure to thrive, and an increase in life span. Immunohistochemical and activity analyses demonstrated GALC uptake in multiple tissues, including the brain. This was associated with a decrease in the abnormal accumulation of the GALC substrate psychosine, which is thought to play a pivotal role in disease pathology. These results indicate that peripheral ERT is likely to be beneficial in GLD.
Adult responsiveness to ultrasonic signals from gerbils of varying ages: Parity, gender, and housing effects

Groups of adult gerbils differing by gender, parity, and presence or absence of young in the nest were exposed to taped ultrasonic distress calls of male and female pups on postnatal Days 3, 8, and 13. Frequency and time spent performing several behavioral items as well as frequency and time spent in the compartment housing the recorded tapes were assessed in the adult groups. Adult groups differed in rates and durations of certain behavioral items only during playback, with females with young in the home nest exhibiting the highest frequency of nest building in the test apparatus. However, all groups spent more time in the arm from which calls of Day-8 pups were played. Calls of Day-3 and Day-13 pups did not produce significant differences in adult responsiveness. These results reveal significant characteristics of the ultrasounds for each group which parallel certain morphological and behavioral changes.
Inexact visualization: qualitative object representation for recognizable reconstruction

The use of qualitative models as opposed to quantitative models for object recognition and reconstruction is discussed. Central to the author's model is an attempt to identify a minimal subset of attributes relevant to visualization. Each object is decomposed into simpler components, with each component described as a qualitative generalized cylinder and the joining operations specified by a three-dimensional qualitative spatial reasoning scheme. The spatial reasoning used is systematically derived and provides a complete description under considerations of tangency, nocontact, and overlap. The representation must be compact, yet contain sufficient information to be 'recognizable'-a term that is defined in terms of human perception and constitutes a measure of the goodness of the model. >
Equity and justice in environmental decision making: A proposed research agenda

The substantial health, social, and economic costs borne by rural, low‐income, and minority communities because of their differential exposure to environmental hazards is being increasingly acknowledged. For decades, these groups have been the the victims of a variety of activities and policies that have placed them at a substantial risk to their health and quality of life. Recently, many of these policies have come under increasing criticism by an emerging environmental justice movement—a movement that promises to be one of the strongest forces for environmental reform to appear in recent years. It is argued that questions of justice and equity in environmental decision making are deserving of increased attention by the research community. A number of questions that can guide such a research agenda are identified.
Communication patterns [message-passing patterns]

Parallel applications have message-passing patterns that are important to understand. Network topology, routing decisions, and connection and buffer management need to match the communication patterns of an application for it to run efficiently and scale well. These patterns are not easily discerned from the source code of an application, and even when the data is available it is not easy to categorize it appropriately such that meaningful knowledge emerges. We describe a novel system to gather the information we need to discover an application's communication pattern. We create five categories that help us analyze that data and explain how information from each category can be useful in the design of networking hardware and software. We use the NAS parallel benchmarks as examples on how to apply our techniques.
On the Predictability of Tropical Cyclone Tracks in the Northwest Pacific Basin

Abstract A new Northwest Pacific climatology and persistence (CLIPER) model is derived with historical tropical cyclone tracks during the satellite and aircraft reconnaissance era (1970–95). The new CLIPER extends the forecasts from 3 to 5 days and exhibits smaller forecast biases than the previous CLIPER, although forecast errors are comparable. The new model is based on more accurate historical tropical cyclone track data, and a simpler derivation of the regression equations, than is the old model. Nonlinear systems analysis shows that the predictability timescale in which the average errors increase by a factor e is just over 15 h, which is about the same as that calculated by similar methods near Australia and in the North Atlantic. This suggests that 5-day tropical cyclone track forecasts may be beneficial, assuming small initial errors; therefore, a CLIPER model extended to 5 days is needed as a baseline to measure the forecast skill.
Competition for actin between two distinct F-actin networks defines a bistable switch for cell polarization

Symmetry-breaking polarization enables functional plasticity of cells and tissues and is yet not well understood. Here we show that epithelial cells, hard-wired to maintain a static morphology and to preserve tissue organization, can spontaneously switch to a migratory polarized phenotype after relaxation of the actomyosin cytoskeleton. We find that myosin II engages actin in the formation of cortical actomyosin bundles and thus makes it unavailable for deployment in the process of dendritic growth normally driving cell motility. Under low-contractility regimes, epithelial cells polarize in a front-back manner owing to the emergence of actin retrograde flows powered by dendritic polymerization of actin. Coupled to cell movement, the flows transport myosin II from the front to the back of the cell, where the motor locally 'locks' actin in contractile bundles. This polarization mechanism could be employed by embryonic and cancer epithelial cells in microenvironments where high-contractility-driven cell motion is inefficient.
Effect of aftershock intensity on seismic collapse fragilities

This paper presents a procedure to compute the sensitivity of a mainshock (MS)-damaged building's collapse probability to earthquake intensity as a function of magnitude or site-to-source distance. Specifically, the effect of earthquake magnitude and spatial distribution of aftershocks on collapse fragilities is investigated. Aftershock (AS) fragilities for different site-to-source distances are examined by performing incremental dynamic analysis (IDA) using a sequence of MS+AS ground motions. The effect of MS damage is to alter the fragilities which can be quantified for the building investigated. It is observed that the collapse fragilities have a reasonable variation in collapse probabilities with changing AS magnitude and/or site-to-source distance.
Genic Variation of the Rock Vole, Microtus chrotorrhinus

Genic variation and genic structure of three populations of Microtus chrotorrhinus and two of Microtus pennsylvanicus were analyzed using horizontal starch gel electrophoresis. The mean heterozygosity ( H = 0.145) for 18 proteins encoded by 25 structural loci in M. pennsylvanicus was higher than that reported for most mammals. The mean heterozygosity observed in M. chrotorrhinus ( H = 0.049) was consistent with the mean value reported for rodents, but not with values reported for isolated populations of mammals. Although the difference in the level of genic variation maintained in M. chrotorrhinus and M. pennsylvanicus may reflect different rates of gene flow among populations, the differences in reproductive potential, effective population size, and frequency of bottleneck may account for the observed difference.
Dust mite allergy: its clinical significance.

Allergy to these arthropods is responsible for a goodly percentage of cases of asthma, rhinitis, and atopic dermatitis. There is also substantial evidence that it causes nonspecific bronchial hyperreactivity, so that symptoms may be triggered by tobacco smoke, cold air, emotion, and exercise. Sensitivity to the organisms should be ruled out in all allergic patients.
Creatine monohydrate supplementation and the quality of fresh pork in normal and halothane carrier pigs.

The objective of this research was to examine the impact of supplementation with creatine monohydrate (CMH) on the quality of various muscles from normal and heterozygous halothane carrier pigs. Twenty-nine crossbred pigs, 16 normal (NN) and 13 halothane carrier (Nn) genotypes, were supplemented with 0 or 25 g x pig(-1) x d(-1) of CMH for 5 d before slaughter. Supplemented pigs gained 2.26 kg more weight (P 0.05) drip loss or muscle composition. Supplementation with CMH also resulted in lower L* values in two ham muscles, semitendinosus (5.15 units) (P < 0.05) and semimembranosus (1.95 units) (P < 0.10) for Nn carcasses. Genotype had significant effects on most quality indicators, with Nn carcasses producing lower-quality lean as evidenced by less desirable subjective and objective color and higher drip losses. Genotype also affected the composition of several muscles, with the NN carcasses having more fat and less moisture.
The Use of Time Dependent Covariates in Modelling Data from an Occupational Cohort Study

In a retrospective cohort study of 768 textile workers, a model‐based approach is used to determine the effect of cumulative exposure to chrysotile asbestos on the hazard of death from lung cancer. Age at death is the outcome variable, and the effects of cumulative exposure, calendar year, and number of years since initial employment are modelled as time dependent covariates. This work quantifies and tests formally the dose‐response effect observed in a standardized mortality ratio analysis by Dement et al. (1982). An extended definition of the proportional hazards model is presented for time dependent covariates defined as step functions of the repeated measurements over time. A complete parametric modelling approach is employed here in addition to the use of Cox's model. Specifically, an underlying failure time distribution is assumed, and the model parameters are expressed as simple linear functions of the covariates. Nonparametric estimation of the cumulative hazard as a function of covariate strata is used to select an appropriate parametric form for the underlying hazard. These procedures are generalized to allow for changing covariate values over time. The Gompertz distribution is chosen for this particular data, and a departure from the proportional hazards model is suggested.
Unusual Vertebrate Microfaunas From the Willwood Formation, Early Eocene of the Bighorn Basin, Wyoming

The Bighorn Basin of northwestern Wyoming is well known for its extensive and richly fossiliferous Paleocene and Eocene alluvial deposits, which have preserved events in the early Cenozoic history of mammals in unusually fine detail (e.g., Bown and Rose, 1987; Rose, 1990; Bown et al., 1994a, b; Silcox and Rose, 1997; Gingerich, 1989; O’Leary, 1996). Fieldwork in this region dates back to 1880, when Jacob Wortman uncovered the first fossilized mammalian remains (Gingerich, 1980). Since that time, field crews headed by Sinclair, Granger, Jepsen, Gilmore, Simons, Gingerich, and Bown and Rose have built extensive collections of early Tertiary vertebrate fossils. Tens of thousands of jaws and hundreds of skeletons provide a detailed record of the morphology of early mammalian taxa, and of the faunal composition of the region as a whole (e.g., Bown et al., 1994b).
Abstract 14392: Endothelial Endoplasmic Reticulum Stress and Insulin Resistance in Patients With Diabetes Mellitus are Reduced by Liraglutide

Prior studies have shown that nutrient excess induces endoplasmic reticulum (ER) stress in nonvascular tissues in patients with diabetes mellitus (DM). Initially, ER stress and the subsequent unfol...
Uremic Advanced Glycation End Products and Protein‐Bound Solutes Induce Endothelial Dysfunction Through Suppression of Krüppel‐Like Factor 2

BackgroundCardiovascular disease is the leading cause of morbidity and mortality in patients with end‐stage renal disease. The accumulation of uremic solutes in this patient population is associate...
Altered Cortical Gamma-Amino Butyric Acid in Female Veterans With Suicidal Behavior: Sex Differences and Clinical Correlates:

BackgroundSuicide is a public health concern in the civilian and veteran populations. Stressful life events are precipitating factors for suicide. The neurochemical underpinnings of the association...
Fluorescence Studies of Concentrated Mn2+ Systems

This article presents a review of some of the basic optical properties of concentrated Mn2+ systems and includes some recent experimental observations on the system KMnF3. The first three sections describe the general features of the well-known systems MnF2 and RbMnF3. The emphasis is on the spectral and thermal characteristics of the broad bands seen in emission in the 5800–7000 A res ion. These sections serve as an introduction to the fourth and last section, which deals with our current studies of the crystal KMnF3. This last system is of interest because it presents absorption and excitation properties which are very similar to those of MnF2 and RbMnF3 and yet displays emission properties which are rather different from those of the other systems. Finally, a phenomenological model is given to explain the observations.
Timolol reduces IOP in normal NZW rabbits during the dark only.

The role of beta-adrenergic receptors in mediating the circadian rhythm of intraocular pressure was examined by determining the effect on intraocular pressure of timolol applied topically at different times during the circadian cycle to New Zealand White rabbits entrained to alternating 12 hr periods of light and dark. Timolol lowered intraocular pressure when applied during the dark but not during the light phase of the circadian cycle. Timolol did not lower intraocular pressure when applied during the dark to animals after cervical ganglionectomy. These results are consistent with the idea that beta-adrenergic receptors participate in mediating the circadian rhythm of intraocular pressure, and suggest that endogenous agonists released by adrenergic nerves in the eye during the dark stimulate ocular beta-adrenergic receptors to increase intraocular pressure in rabbits. Invest Ophthalmol Vis Sci 31:715-721,1990 There is a circadian rhythm of intraocular pressure (IOP) in rabbits; IOP is low during the light phase and high during the dark phase. 1 " 3 A circadian rhythm of aqueous flow in phase with the rhythm of IOP makes a major contribution to the rhythm of IOP. 14 " 9 Adrenergic input to the eye is required for complete expression of the rhythm of IOP; cervical ganglionectomy (CGX) or decentralization (DX) decrease the dark phase increase of IOP. 310 The experiments reported here were designed to determine whether beta-adrenergic receptors participate in mediating the rhythm of IOP. To do this the effect on IOP of topical application of timolol, a nonselective beta-adrenergic antagonist which decreases aqueous flow,"" 19 was examined at different times during the circadian cycle in New Zealand White (NZW) rabbits.
On the Chemical and Environmental Modulation of Pheromone Release from Vertebrate Scent Marks

An equilibrium model of pheromone release from scent marks is developed employing equations from physical chemistry and chromatography. Experimental evaporation curves of phenylacetic acid, an odorous component of gerbil scent marks are given for a variety of conditions treated in the model. It is shown that the chemical nature of the pheromone, the non-pheromonal component of the scent mark, the type of surface to which the mark is applied and relative humidity have pronounced effects on the temporal pattern of pheromone release.
Preprints and the implications for subsequent peer review and publishing.

For most of us in biomedical fields, the idea of a preprint server is novel. Such servers, and there are many, are open access repositories of manuscripts that have yet to be published in traditional peer-reviewed journals; they exist to further research by getting results out quickly and allowing feedback from those interested in that work.