cssi/SciSciGPT-SciSciNet huggingface dataset:
Lymphoplasmacytic lymphoma and Waldenström macroglobulinaemia: clinicopathological features and differential diagnosis.

Summary Lymphoplasmacytic lymphoma (LPL) represents a distinct type of mature B-cell lymphoma with a substantial subset of cases being associated with Waldenstrom macroglobulinaemia (WM), defined as primarily bone marrow involvement and the presence of an IgM monoclonal paraprotein. MYD88 L265P mutation, although not specific, is present in the vast majority (>90%) of LPL cases and sheds light on the potential pathogenesis of this disease. This review offers an overview of current knowledge on the pathogenesis, clinical presentations, histological features and immunophenotype of LPL and WM. In addition, the differential diagnosis of LPL and WM from other mature B cell neoplasms is highlighted with a focus on distinction from marginal zone lymphoma and plasma cell neoplasms.
David Oliver: Racism in medicine—what ethnic minority doctors told me on Twitter

When my editor asked me to write a column for this issue, I was hesitant. As a white, male, middle class British doctor, what could I possibly say that was useful? I could emphasise that I work alongside doctors, nurses, and allied professionals from ethnic minority backgrounds and that, without their commitment, our health and care services would collapse. I could write about the data. For instance, 13.1% of the NHS workforce have non-British nationality,1 and 20.7% of NHS doctors are from ethnic minority backgrounds23—higher in general practice. Lower paid occupations such as social care rely even more on overseas and ethnic minority recruits. I could describe the mismatch between their numbers in the rank and file and the number of doctors in high profile leadership positions. They don’t reflect the balance of the workforce in terms of gender or ethnicity. Speaker and panel line-ups at medical conferences, and expert media talking heads on …
18 – GROUP COMMUNICATIONS

Publisher Summary Group communications are an important part of scientific presentations. Serving with closed groups to make plans for research projects, to decide policy, or to evaluate a fellow employee's progress are all included in group communication. This chapter describes different types of group communications, and suggests ways to excel in it. The round-table discussion, or buzz session, is informal. The purpose may be for brainstorming or for a professional sharing of ideas with no formal agenda and no decisive outcome expected. A board or a committee is a more formal, small group selected from a larger organization to assume a given responsibility. Whatever responsibilities are required and whatever format is used, professional ethics dictates to actively perform to the best of an individual ability to accomplish the group's goals. Decision making involves alternatives. Defining what the alternatives are may require research and discussion. In problem solving there may be no obvious alternatives. The best solutions can be reached with a step-by-step procedure. Whether it is a committee appointed to recommend a company policy or a panel of experts discussing an issue before an audience, the principles that take group communication to a desired goal are the same.
How Do Mothers’ and Fathers’ Work–Family Conflict Impact Children’s Problem Behaviors?:

Using 509 mother/father–child dyads drawn from Wave 8 of The German Family Panel (pairfam), this study examines the direct effects of mothers’ and fathers’ work–family conflict (WFC) on children’s ...
Accelerated Aging of the Brain: Neuroendocrine Studies in Huntingdon’s Disease

Neuropathological studies of Huntingdon’s disease reveal neuronal atrophy, lipofucsin accumulation and other findings characteristic of the aged brain. The pathology is limited to specific areas such as the caudate nucleus, cerebral cortex and hypothalamus.
Quality of Post-Acute Care in Skilled Nursing Facilities That Disproportionately Serve Hispanics With Dementia.

Abstract Objectives As the number of Hispanics with dementia continues to increase, greater use of post-acute care in nursing home settings will be required. Little is known about the quality of skilled nursing facilities (SNFs) that disproportionately serve Hispanic patients with dementia and whether the quality of SNF care varies by the concentration of Medicare Advantage (MA) patients with dementia admitted to these SNFs. Design Cross-sectional study using 2016 data from Medicare certified providers. Setting and Participants Our cohort included 177,396 beneficiaries with probable dementia from 8884 SNFs. Methods We examined facility-level quality of care among facilities with high and low proportions of Hispanic beneficiaries with probable dementia enrolled in MA and fee-for-service (FFS) using data from Medicare-certified providers. Three facility-level measures were used to assess quality of care: (1) 30-day rehospitalization rate; (2) successful discharge from the facility to the community; and (3) Medicare 5-star quality ratings. Results About 20% of residents were admitted to 1615 facilities with a resident population that was more than 15% Hispanic. Facilities with a higher share of Hispanic residents had a lower proportion of 4- or 5-star facilities by an average of 14% to 15% compared with facilities with little to no Hispanics. In addition, these facilities had a 1% higher readmission rate. There were also some differences in the quality of facilities with high (>26.5%) and low ( Conclusions and Implications Achieving better quality of care for people with dementia may require efforts to improve the quality of care among facilities with a high concentration of Hispanic residents.
Abstract 6590: Epigenetic suppression of transgenic T-cell receptor (TCR) expression in adoptive cell transfer (ACT) therapy

Background: ACT of TCR transgenic T cells recognizing shared tumor antigens is associated with robust initial response rates, but frequent disease relapse. This usually occurs in the setting of poor long-term persistence of cells expressing the transgenic TCR, generated most frequently using a murine stem cell virus (MSCV) gamma retroviral vector. Patients and Methods: Between 2009 and 2016, 24 patients were treated at UCLA using transgenic TCR ACT directed against the tumor antigens MART-1 or NY-ESO-1 for the treatment of melanoma or sarcoma, respectively. We analyzed 16 of these patients9 cell therapy products for in vivo persistence and expression of the transgenic TCR at baseline and over time. Transgenic TCR DNA, RNA, and surface protein expression were assessed over time via TCR sequencing, qRT-PCR, and MHC dextramer analysis via FACS, respectively. DNA methylation status of the MSCV 59LTR promoter region was determined via targeted bisulfite sequencing. Custom biotinylated RNA probes that target the entire MSCV vector were utilized to assess whole vector methylation over time, as well as integration sites within the host genome. Results: Despite overall strong persistence of the transgenic TCR at the DNA level in all patients over time, its expression was profoundly decreased over time at the RNA and protein levels. In a subset of these patients (N=6), the degree of TCR surface expression at day +70 was Conclusions: Progressive acquisition of DNA methylation within the MSCV retroviral vector is associated with suppression of expression of the encoded transgenic TCR. These results have significant implications for the design of future transgenic cell therapies and their associated viral vectors. Citation Format: Theodore S. Nowicki, Colin Farrell, Marco Morselli, Liudmilla Rubbi, Katie Campbell, Beata Berent-Maoz, Begonya Comin-Anduix, Matteo Pellegrini, Antoni Ribas. Epigenetic suppression of transgenic T-cell receptor (TCR) expression in adoptive cell transfer (ACT) therapy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6590.
Amino Acids in Dog Nutrition and Health

The dog has assumed a prominent role in human society. Associated with that status, diet choices for companion dogs have begun to reflect the personal preferences of the owners, with greater emphasis on specialty diets such as organic, vegan/vegetarian, and omission or inclusion of specific ingredients. Despite consumer preferences and many marketing strategies employed, the diets must ensure nutritional adequacy for the dog; if not, health becomes compromised, sometimes severely. The most frequent consideration of consumers and dog food manufacturers is protein source and concentration with a growing emphasis on amino acid composition and bioavailability. Amino acids in general play diverse and critical roles in the dog, with specific amino acids being essential. This review covers what is known regarding amino acids in dog nutrition.
Initial Outcomes of CardioClick, a Telehealth Program for Preventive Cardiac Care: Observational Study.

Background: Telehealth use has increased in specialty clinics, but there is limited evidence on the outcomes of telehealth in primary cardiovascular disease (CVD) prevention. Objective: The objective of this study was to evaluate the initial outcomes of CardioClick, a telehealth primary CVD prevention program. Methods: In 2017, the Stanford South Asian Translational Heart Initiative (a preventive cardiology clinic focused on high-risk South Asian patients) introduced CardioClick, which is a clinical pathway replacing in-person follow-up visits with video visits. We assessed patient engagement and changes in CVD risk factors in CardioClick patients and in a historical in-person cohort from the same clinic. Results: In this study, 118 CardioClick patients and 441 patients who received in-person care were included. CardioClick patients were more likely to complete the clinic’s CVD prevention program (76/118, 64.4% vs 173/441, 39.2%, respectively; P<.001) and they did so in lesser time (mean, 250 days vs 307 days, respectively; P<.001) than the patients in the historical in-person cohort. Patients who completed the CardioClick program achieved reductions in CVD risk factors, including blood pressure, lipid concentrations, and BMI, which matched or exceeded those observed in the historical in-person cohort. Conclusions: Telehealth can be used to deliver care effectively in a preventive cardiology clinic setting and may result in increased patient engagement. Further studies on telehealth outcomes are needed to determine the optimal role of virtual care models across diverse preventive medicine clinics.
SU-E-J-31: Monitor Interfractional Variation of Tumor Respiratory Motion Using 4D KV Conebeam Computed Tomography for Stereotactic Body Radiation Therapy of Lung Cancer

Purpose: 4DCT has been widely used to generate internal tumor volume (ITV) for a lung tumor for treatment planning. However, lung tumors may show different respiratory motion on the treatment day. The purpose of this study is to evaluate 4D KV conebeam computed tomography (CBCT) for monitoring tumor interfractional motion variation between simulation and each fraction of stereotactic body radiation therapy (SBRT) for lung cancer. Methods: 4D KV CBCT was acquired with the Elekta XVI system. The accuracy of 4D KV CBCT for image-guided radiation therapy (IGRT) was tested with a dynamic thorax motion phantom (CIRS, Virginia) with a linear amplitude of 2 cm. In addition, an adult anthropomorphic phantom (Alderson, Rando) with optically stimulated luminescence (OSL) dosimeters embedded at the center and periphery of a slab of solid water was used to measure the dose of 4D KV CBCT and to compare it with the dose with 3D KV CBCT. The image registration was performed by aligning\ each phase images of 4D KV CBCT to the planning images and the final couch shifts were calculated as a mean of all these individual shifts along each direction.A workflow was established based on these quality assurance tests for lung cancer patients.more » Results: 4D KV CBCT does not increase imaging dose in comparison to 3D KV CBCT. Acquisition of 4D KV CBCT is 4 minutes as compared to 2 minutes for 3D KV CBCT. Most of patients showed a small daily variation of tumor respiratory motion about 2 mm. However, some patients may have more than 5 mm variations of tumor respiratory motion. Conclusion: The radiation dose does not increase with 4D KV CBCT. 4D KV CBCT is a useful tool for monitoring interfractional variations of tumor respiratory motion before SBRT of lung cancer patients.« less
Automated design of assemblable, modular, synthetic chromosomes

The goal of the Saccharomyces cerevisiae v2.0 project is the complete synthesis of a re-designed genome for baker's yeast. The resulting organism will permit systematic studies of eukaryotic chromosome structure that have been impossible to explore with traditional gene-ata-time experiments. The efficiency of chemical synthesis of DNA does not yet permit direct synthesis of an entire chromosome, although it is now feasible to synthesize multi-kilobase pieces of DNA that can be combined into larger molecules. Designing a chromosome-sized sequence that can be assembled from smaller pieces has to date been accomplished by biological experts in a laborious and error-prone fashion. Here we pose DNA design as an optimization problem and obtain optimal solutions with a parallelizable dynamic programming algorithm.
Regulation of tyrosine-hydroxylase (TH) gene expression by hypoxia and von Hippel-Lindau tumor suppressor complex

Loss of von Hippel-Lindau (VHL) gene function leads to a familial cancer syndrome, VHL disease, characterized by CNS and retinal hemangioblastomas, renal clear cell carcinomas, and pheochromocytomas. Pheochromocytomas, tumors of the chromaffin cells of the adrenal medulla, secrete large amounts of catecholamines. This results from enhanced expression of TH, the rate-limiting enzyme in catecholamine biosynthesis. Overexpression of exogenous pVHL in PC12 cells lead to a substantial repression of TH protein and mRNA [1]. Here we examined the role of endogenous pVHL in the regulation of TH gene expression. We developed PC12 clonal cell lines that stably express VHL antisense RNA and have reduced levels of endogenous pVHL by 5–10 fold. In these cells, TH protein and mRNA were increased 2–3 fold as compared to control cells. Nuclear run-on analysis revealed an increase in the overall TH gene transcription. In addition, we measured augmented efficiency of the TH transcript elongation in the distal part of the gene. Transient co-transfections of -773 kb TH-CAT promoter-reporter constructs with the VHL antisense RNA resulted in an approximately 2–3 fold increase in reporter gene activity. TH is a hypoxia-inducible gene. The overall accumulation of THmRNA and the rate of TH gene transcription were substantially enhanced in cells with decreased levels of pVhl exposed to 1% O2 for 16 h. These results indicate that endogenous pVhl constitutively represses TH gene expression in PC12 cells. TH promoter contains a functional hypoxia-responsive element (HRE) - like sequence. Transient co-transfections of the HIF1α and HIF2α expression vectors with the wild type, but not mutated TH promoter revealed significant 3–4 fold induction of the reporter gene activity. Gel-shift analysis showed presence of the hypoxia-inducible complexes associated with the wild type but not mutated THHRE. Electroelution of protein complexes from the hypoxia-inducible complex showed presence of the HIF2α, and to lesser extent of the HIF1 subunit. pVHL is part of the E3 ubiquitin ligase complex that targets the HIF alphas for ubiquitination and degradation. Changes in the levels of the pVHL in PC12 cells by either overexpression of pVHL or expression of VHL antisense RNA resulted in respectively decreased and increased HIF-and hypoxia-mediated activation of the TH promoter. Stable changes in the pVHL levels in PC12 cells resulted in accumulation of HIF alphas during normoxia in cells with decreased amounts of pVHL, and in decreased expression of HIF alphas during hypoxia in cells overex-pressing pVHL. The changes in HIFα protein accumulation induced by pVHL resulted from ubiquitination of HIF alphas by pVHL.
Nonlinear Programming: Theory and Algorithms, 3rd Edition by M.S. Bazarra, H.D. Sherali, and C.M. Shetty

This book is a third edition that deals with the subject of optimizing a nonlinear objective function in the presence of equality and inequality constraints. The development of highly efficient and...
Evaluation of a wireless cardio respiratory monitor for neonates

Objective: Each year thousands of preterm and sick infants are admitted to neonatal intensive care units (NICU) requiring continuous cardio respiratory monitoring. A new and innovative wireless monitor was evaluated which incorporates two unique non invasive electrodeless sensors for the detection of respiration and cardiac waveforms. The objective of the study was to determine if the sensors used by the wireless monitor (PGS Medical Research and Electronic Design, LLC, Fairfield, CT) provide equal performance for data acquisition compared to reference monitors. A further objective was to evaluate the potential ease of application and lack of wires offered by this technology in the NICU. Methods: After approval from the Institutional Review Board (IRB) and obtaining parental consent, 25 patients were enrolled in the study. The wireless sensor belt was then placed around the abdomen. Breathing and heart rate waveform were recorded from the wireless research monitor and from the existing NICU equipment (reference monitor) for a total of 90 minutes. Results: Waveform data was recorded on a 4 channel analog Windaq system. Each file was then reviewed and 5 selections of at least 3 minutes duration wherein both monitors were displaying stable waveforms were compared for parity of peaks representing a beat. Manually counting the peaks showed a 96% correspondence with standard deviation of ±2 beats discrepancy between
Studies in spectral line formation II. Linear coupling in multilevel atom problems

Abstract The transfer of line radiation through an atmosphere of three-level model sodium atoms and four-level model oxygen atoms is studied. The physical significance of the source functions and the net radiative brackets of the spectral lines is considered, with particular emphasis on the conditions for the multiplet line source functions to have a common depth dependence.
Libel, Freedom of the Press, and the New Yorker

Abstract An American icon and important press institution, the New Yorker magazine has actively protected its freedoms of expression against the chilling effect of libel law since its inception in 1925. This history examines how the magazine and the law firm Greenbaum, Wolff & Ernst created editorial and legal procedures and strategies to combat libel complaints in the New Yorker's first forty years of existence. During these years, libel threats influenced the New Yorker's editorial decision-making and processes, content, and use of human and financial resources. Although the history of American libel law is well documented, the social effects of libel law on particular publications are not. This study helps to fill the gap.
Application of electromagnetic propagation logging in the interpretation of fresh water neogene sands of upper Assam tertiary basin (India)

The θEPT and θND overlay technique has been tried and found to be quite succesful in distinguishing between hydrocarbon and water zones in fresh water Tipam and Girujan sands, some of which could have been easily overlooked other wise, in a number of Upper Assam oilfields. The EPT-MSEL combination offers reliable values of m which could be utilized for estimation of more accurate values of water saturation. EPT measurement has also proved to be particularly useful in resolution of thin beds in the wells of Upper Assam basin.
Publishing in China and India: Opportunities and Challenges

With the rapid growth in the Chinese and Indian economies, the opportunities for publishers have dramatically expanded. The paper discusses the regulatory, political, economic and cultural factors to be considered in entering these markets. Finally, the paper discusses three key tradeoffs to be considered in these markets: standardization/localization, volume/margin and the relative importance of digital/paper publications.
High-order harmonic cutoff extension of the O 2 molecule due to ionization suppression

High-order harmonic generation has been observed experimentally from ${\mathrm{O}}_{2}$ molecules at the saturation ionization intensity. The harmonic cutoff extends far beyond the cutoff of Xe despite both have nearly equal ionization potentials. In contrast, the harmonic spectra for ${\mathrm{N}}_{2}$ and Ar, which have almost the same ionization potentials, are essentially close to each other. We show the extension of harmonic cutoff in ${\mathrm{O}}_{2}$ is a consequence of ionization suppression. Using a simple modified tunneling ionization model for molecules, we predict both the harmonic cutoff extension and the ionization suppression semiquantitatively.
Automatic Control Chart for Micropipet

The control chart is defined and exemplified, and the importance of controlling the volume delivered by a micropipet is discussed. A LabVIEW VI is described, which automates control chart generation and routine use based on the gravimetric calibration of a micropipette, using a Sartorius balance. A user selects between creating a new control chart and adding a data point to the control chart. File storage and retrieval, and construction of the control chart are automated. A sample control chart for a micropipet is presented.
Model Predictive Control of Organic Rankine Cycle for Waste Heat Recovery in Heavy-Duty Diesel Powertrain

This paper continues the development of a previous conference paper that introduces advanced controllers for an Organic Rankine Cycle (ORC) in a heavy-duty diesel powertrain. The ORC’s heat exchangers are modeled as control-oriented, nonlinear Moving Boundary models. The pump and expander, which are coupled to the engine crankshaft, have relatively faster dynamics than the heat exchangers and are modeled as static components. The driving cycle produces transient heat source and engine conditions for the ORC whose goal is to maximize waste heat recovery under specified operating constraints. This paper describes a Model Predictive Controller (MPC) and compares it to Proportional Integral (PI) and Linear Quadratic Integral (LQI) controllers. The three controllers attempts to regulate heat exchanger pressures while satisfying specified operating constraints. Extended Kalman Filters (EKFs) are designed and implemented for state estimation feedback for MPC and LQI requiring full state feedback. The simulation results show the advantage of the advanced controllers in reducing pressure regulation error, with MPC having the lowest pressure regulation error among the three controllers and able to incorporate the operating constraints into its control law.Copyright © 2014 by ASME
Memory and psychoanalysis : a new look at infantile amnesia and transference

ABSTRACT Objective This article reexamines the psychoanalytic concepts of infantile amnesia and transference in the light of certain findings derived from neurobiological research, information-processing theory, child development research, cognitive-developmental theory, and, more speculatively, evolutionary theory concerning memory. Method Relevant developments from recent research in the neurosciences, and psychopathological phenomena in two psychiatric disorders—posttraumatic stress disorder and child abuse—in which memory changes are of critical importance, are first reviewed briefly. Four alternative hypotheses for infantile amnesia and three for transference are then derived from this review. Results The hypotheses discussed provide plausible alternative explanations for at least part of the phenomena classically subsumed in the psychoanalytic concepts of infantile amnesia and transference. Conclusions Neurobiological, information-processing, developmental shifts, cognitive-developmental, and evolutionary findings and theories provide alternative hypotheses for infantile amnesia and transference that suggest a need for revisions and redefinitions for these two psychoanalytic concepts.
Dynamic analysis for two-dimensional multiple crack division

Abstract Based on the concept of linear-elastic fracture mechanics, two dynamic adjustments are made upon the static form of the crack-extension force ζ for the problem of evenly spaced radial cracks spreading out from a point and terminating on a circular locus. The first adjustment is concerned with the magnitude of the local dynamic stress tending to open the crack. This dynamic stress can be approximated by the circumferential stress near a circular locus of stress relief expanding at a constant speed provided that the arc length between adjacent crack ends is sufficiently small in comparison with the circle radius. The second adjustment is concerned with the influence of crack speed on the crack-opening displacement and on the rate of release of stress field energy, ζ. This can be determined by application of the crack closure method for a traveling crack. These two dynamic adjustments are found to be opposite in direction. The degree of compensation depends on the speed of crack propagation and the Poisson's ratio of the material.
Automorphism groups of designs

From a geometric point of view, the most interesting designs (see w 2 for definitions) are generally those admitting fairly large automorphism groups. The methods of finite permutation groups may be applied to such designs, and vice versa, as in [5, 6, 8, 11, 13 and 143. We shall prove several general results which are useful in the study of automorphism groups of designs, and then use some of these to characterize some designs admitting large automorphism groups. Further applications are found in [11]. A Hadamard design is a symmetric design with k = (v- 1)/2 (see [3] or [17] for the connection with Hadamard determinants). The best known examples of such designs - other than the Desarguesian projective spaces over GF(2) - are the Paley designs ([15]; cf. [183 and [11]). The points of a Paley design are the elements ofF = GF(v), where v > 3 is a prime power -=- 3 (rood 4), while the blocks are the translates under F + of the set Q of non-zero squares of F. This design admits an automorphism group of odd order {x --+ x ~ t + a[t E Q, a ~ F, ~Aut(F)} which is transitive on incident point-block pairs; this group is not always the full automorphism group (cf. [11]). Theorem 1.1. Paley designs are the only Hadamard designs admitting automorphism groups which are transitive on incident point-block pairs but which are not 2-transitive on points, A larger class of designs will also be considered, all related to F. Our characterizations of some of these designs generalize many of the results of Liineburg [13], whose approach is different.
Acetone emission from conifer buds

Abstract Acetone was detected in the headspace of excised vegetative buds of all seven conifers examined. Acetone emission rates of 7.4 ± 1.5 μg hr −1 g −1 fr. wt were measured from intact buds of Abies concolor during a growth chamber experiment. Little or no acetone emission was observed from the leaves of conifers or from any angiosperm vegetative tissue tested. Acetone headspace concentrations from buds of three conifer species were measured over two growing seasons at a forest site. Acetone concentrations were highest in winter and dropped precipitously with the onset of budbreak, suggesting that acetone may play a role in cold tolerance in gymnosperms.
Synthesis and accumulation of mannose-containing glycopeptides in human fibroblast cells: possible separate pathways for neutral and acidic glycopeptides.

Abstract The normal human fibroblast, WI-38, was labelled with radioactive mannose and its incorporation, as well as the accumulation of acidic and neutral glycopeptides on the cell surface, was followed as a function of time. The transit time of newly made Pronase-released cell surface glycopeptides from their intracellular site of synthesis to the cell surface was slower in nongrowing cells than in a rapidly growing culture. When the surface glycopeptides were separated by high-voltage paper electrophoresis into neutral and acidic species, it was observed that the cell surface material was initially enriched with neutral glycopeptides. However, with time the relative proportion of acidic species increased so that by 3 h the ratio between the acidica and neutral species approached a constant value. Our data are consistent with the hypothesis that multiple pathways for asparagine-linked glycoprotein biosynthesis are possible.
Cellular Metabolism Fluidizes the Glassy Bacterial Cytoplasm

In eukaryotes, active transport involves motor proteins and cytoskeletal filaments. In contrast, bacteria (which lack cytoskeletal motor proteins) are thought to primarily rely on diffusion for molecular transport and cytoplasmic mixing. However, the physical nature of the bacterial cytoplasm remains poorly understood. Through single particle tracking of protein filaments, plasmids, storage granules and foreign particles of different sizes, we have found that the bacterial cytoplasm exhibits striking similarities to glass-forming liquids. Glass-forming liquids are noted for their metastability near the glass transition where their behavior changes from liquid-like to amorphous solid with even small perturbations. We find that particles of different sizes exhibit distinct dynamics and their mobility changes from fluid-like to glassy with increasing particle size. This size dependency provides an explanation for previous reports of both normal and anomalous diffusion in the bacterial cytoplasm. Moreover, we find that cellular metabolism attenuates the glassy properties of the bacterial cytoplasm. As a result, components that would otherwise be caged in narrow regions of confinement are able to explore the cytoplasmic space under metabolically active conditions. Cytoplasmic dynamics are directly impacted by environmental conditions that impact cellular metabolism. These findings have broad implications for our understanding of bacterial physiology as the glassy behavior of the cytoplasm impacts all intracellular processes involving large cellular components.
Optimization of k-space sampling in atomic imaging by electron emission holography

Abstract Two limiting-case algorithms have previously been proposed for holographically imaging atoms near surfaces using photoelectron diffraction data and other diffraction data associated with electron emission: (i) a phased sum of Fourier transforms of scanned-angle data taken at several energies from Barton, (ii) and a phased sum of Fourier transforms of scanned-energy data taken along several directions due to Tong et al. We first point out that both methods are equivalent three-dimensional transforms in the wave vector k of the emitted electron, differing only in the way they sample k-space. A continuum of different sampling densities in the direction and magnitude of k exists in such holography, spanning the two limits previously discussed. An additional variant on these methods involves using only a small cone of data in k-space for each transform. Using model diffraction calculations for localized electron emission (e.g., core photoelectron emission) from Cu(001) clusters, we have explored the full range of k-space sampling possible, and find that optimum image quality is expected for choices intermediate between the extreme limits of scanned-angle or scanned-energy. General rules for optimizing image quality for a given data-set range are also discussed, and used to evaluate the sampling choices made in some prior experimental studies.
Seeing beneath the farmland, steppe and desert soil: magnetic prospecting and soil magnetism

Geophysical science offers a large range of methods that have been adapted for the detection of archaeological structures beneath the surface. Magnetometry is among others the most successful, and with respect to large survey areas, the most widely-used scientific toolkit that is used by archaeologists. New developments in instrument techniques and real-time GPS enlarged the role of magnetometer prospecting for archaeological science considerably and allow even the detailed prospecting and analysis of landscapes. An integral part of this method however should be the archaeological interpretation of the geophysical result. In this paper the rock magnetic and soil magnetic background will be discussed, which is necessary for a comprehensive understanding of survey results. The diversity of the magnetic anomalies is exemplified on the basis of selected survey results, and explains the role of magnetic prospecting in the field of archaeological science.
Hydrophobic Aided Replica Exchange: an Efficient Algorithm for Protein Folding in Explicit Solvent

A hydrophobic aided replica exchange method (HAREM) is introduced to accelerate the simulation of all-atom protein folding in explicit solvent. This method is based on exaggerating the hydrophobic effect of various protein amino acids in water by attenuating the protein-water attractive interactions (mimicking the Chaperon effect) while leaving other interactions among protein atoms and water molecules unchanged. The method is applied to a small representative protein, the alpha-helix 3K(I), and it is found that the HAREM method successfully folds the protein within 4 ns, while the regular replica exchange method does not fold the same protein within 5 ns, even with many more replicas.
Resistance to the Mexican Rice Borer (Lepidoptera: Crambidae) Among Louisiana and Texas Sugarcane Cultivars

Abstract A 2-yr study to evaluate Louisiana and Texas sugarcane, Saccharum spp., cultivars for resistance to the Mexican rice borer, Eoreuma loftini (Dyar), was conducted in two locations in Texas, chosen for having different infestation levels. Criteria for assessment of resistance included percentage of bored internodes and adult emergence holes, the latter used to determine the relative impact of each cultivar on the potential areawide buildup or reduction of adult E. loftini populations. A recently released cultivar, HoCP 85-845, seemed to lose a portion of its resistance under heavy E. loftini infestation pressure, suggesting its value only in moderate-to-low infestation conditions. Cultivar CP 70-321 was the most resistant. Results indicated that cultivar LCP 85-384 was significantly (P < 0.05) more susceptible than NCo 310, traditionally the most susceptible cultivar commercially produced in Texas. In 2001, LCP 85-384, which now represents 85% of the production area in Louisiana, had the greatest m...
Optimal actuator placement in adaptive precision trusses

Precision structures, used in space, are usually fabricated from truss concepts and support precision equipment/objects that require a high degree of accuracy for reasonable performance. Maintaining this precision, in the face of disturbances that displace the positions of these precision points, can be achieved by the use of highly sensitive actuators, such as the JPL Active Member (Fanson et al., 1989, Anderson et al., 1990). These actuators are attached at their vertices (i.e., end points) to the nodes of the precision truss structure and are capable of length extension/contraction.
Performance Evaluation and Optimization Mechanisms for Inter-operable Graphics and Computation on GPUs

Graphics Processing Units (GPUs) have gained recognition as the primary form of accelerators for graphics rendering in the gaming domain. They have also been widely accepted as the computing platform of choice in many scientific and high performance computing domains. The parallelism offered by the GPUs is used for simultaneous processing of compute and graphics by applications belonging to a range of domains. The availability of programming standards such as OpenCL and OpenGL has been leveraged to achieve the compute-graphics interoperability in the same application.However, given the increasing demands in both compute and graphics for emerging scientific visualization and immersive gaming applications, degradation in efficiency can be seen due to the continual switching between compute/graphics, swapping in and out of their associated runtime environments. We need to better understand how to tune this interoperable environment in order to allow compute and graphics to run both efficiently and simultaneously. Presently we evaluate each of these domains in isolation.In this paper, we evaluate the performance and efficiency of the OpenCL-OpenGL(CL-GL) interoperability(interop) mode. We explore different methods to improve the execution performance of the CL-GL interop-based applications. We propose a slot-based rendering mechanism for CL-GL interop to increase the efficiency of the application.To evaluate CL-GL and our slot-based scheme, we study five scientific applications using OpenCL and OpenGL for compute and graphics rendering. Our study covers two AMD Radeon discrete GPUs and one shared memory AMD APU as test platforms. We demonstrate that leveraging the CL-GL interop interface results in a 2.2X performance increase, and our slot-based rendering provides 60% increase in performance by providing a 24% improvement in L2 cache hit rate on GPUs and APUs.
The pathology of magnetic-resonance-imaging-negative epilepsy.

Patients with magnetic-resonance-imaging (MRI)-negative (or ‘nonlesional’) pharmacoresistant focal epilepsy are the most challenging group undergoing presurgical evaluation. Few large-scale studies have systematically reviewed the pathological substrates underlying MRI-negative epilepsies. In the current study, histopathological specimens were retrospectively reviewed from MRI-negative epilepsy patients (n=95, mean age=30 years, 50% female subjects). Focal cortical dysplasia cases were classified according to the International League Against Epilepsy (ILAE) and Palmini et al classifications. The most common pathologies found in this MRI-negative cohort included: focal cortical dysplasia (n=43, 45%), gliosis (n=21, 22%), hamartia+gliosis (n=12, 13%), and hippocampal sclerosis (n=9, 9%). The majority of focal cortical dysplasia were ILAE type I (n=37) or Palmini type I (n=39). Seven patients had no identifiable pathological abnormalities. The existence of positive pathology was not significantly associated with age or temporal/extratemporal resection. Follow-up data post surgery was available in 90 patients; 63 (70%) and 57 (63%) attained seizure freedom at 6 and 12 months, respectively. The finding of positive pathology was significantly associated with seizure-free outcome at 6 months (P=0.035), but not at 12 months. In subgroup analysis, the focal cortical dysplasia group was not significantly correlated with seizure-free outcome, as compared with the negative-pathology groups at either 6 or 12 months. Of note, the finding of hippocampal sclerosis had a significant positive correlation with seizure-free outcome when compared with the negative-pathology group (P=0.009 and 0.004 for 6- and 12-month outcome, respectively). Absence of a significant histopathology in the resected surgical specimen did not preclude seizure freedom. In conclusion, our study highlights the heterogeneity of epileptic pathologies in MRI-negative epilepsies, with focal cortical dysplasia being the most common finding. The existence of positive pathology in surgical specimen may be a good indication for short-term good seizure outcome. There is a small subset of cases in which no pathological abnormalities are identified.
Solution structure and phospholipid interactions of the isolated voltage-sensor domain from KvAP.

Abstract Voltage-sensor domains (VSDs) are specialized transmembrane segments that confer voltage sensitivity to many proteins such as ion channels and enzymes. The activities of these domains are highly dependent on both the chemical properties and the physical properties of the surrounding membrane environment. To learn about VSD–lipid interactions, we used nuclear magnetic resonance spectroscopy to determine the structure and phospholipid interface of the VSD from the voltage-dependent K + channel KvAP (prokaryotic Kv from Aeropyrum pernix ). The solution structure of the KvAP VSD solubilized within phospholipid micelles is similar to a previously determined crystal structure solubilized by a nonionic detergent and complexed with an antibody fragment. The differences observed include a previously unidentified short amphipathic α-helix that precedes the first transmembrane helix and a subtle rigid-body repositioning of the S3–S4 voltage-sensor paddle. Using 15 N relaxation experiments, we show that much of the VSD, including the pronounced kink in S3 and the S3–S4 paddle, is relatively rigid on the picosecond-to-nanosecond timescale. In contrast, the kink in S3 is mobile on the microsecond-to-millisecond timescale and may act as a hinge in the movement of the paddle during channel gating. We characterized the VSD–phospholipid micelle interactions using nuclear Overhauser effect spectroscopy and showed that the micelle uniformly coats the KvAP VSD and approximates the chemical environment of a phospholipid bilayer. Using paramagnetically labeled phospholipids, we show that bilayer-forming lipids interact with the S3 and S4 helices more strongly than with S1 and S2.
An analytical approach to performance/cost modeling of parallel computers

Abstract Although parallel processing has been a focal point of computer architecture research for many years, fundamental questions and trade-offs still remain puzzling, not necessarily because of complexity but because of the multitude of possible answers (e.g., shared vs distributed memory, centralized vs distributed control, vector vs scalar). This paper addresses one such issue, namely heterogeneous vs homogeneous parallel machine organizations. Using simple performance and cost models, we argue that multiprocessors based on a fast global control unit capable of fast execution of serial code, and capable of managing an ensemble of slower processors, offer a performance/ cost ratio significantly better than any comparable homogeneous multiprocessor with distributed control. Although the issue of “deliverable” performance is an open question, it appears that such systems can achieve faster execution and higher program speedups at a much lower cost.
Phase variation of the lpf operon is a mechanism to evade cross-immunity between Salmonella serotypes

Conventional wisdom holds that phase variation is a mechanism for immune evasion. However, despite fimbrial phase variation, mice previously exposed to Salmonella typhimurium are protected against a subsequent challenge. We evaluated whether lpf phase variation instead may be a mechanism to evade cross-immunity between Salmonella serotypes. Mice were immunized orally with S. typhimurium aroA mutants either that expressed the lpf operon (phase-on variant) or in which the entire lpf operon had been removed by deletion. During a subsequent challenge with virulent Salmonella enteritidis a selection against lpf phase-on variants was observed in mice previously exposed to S. typhimurium long polar fimbriae. Vaccination with S. typhimurium did not confer protection against challenge with S. enteritidis, presumably because lpf phase-off variants were able to evade cross-immunity. We propose that lpf phase variation is a mechanism to evade cross-immunity between Salmonella serotypes, thereby allowing their coexistence in a host population.
Thyrotropin-releasing hormone: stimulation of colonic activity following intracerebroventricular administration

Intraventricularly administered thyrotropin-releasing hormone in rabbits elicited an increase in intraluminal pressure changes, a response commonly associated with muscular activity of the colon. The response appears to be central in origin with peripheral expression relying primarily on cholinergic receptors.
Location, location, location: stripe position effects on female sword preference

The evolution of complex signals via sexual selection is becoming a primary focus in mate choice studies. Male swordtail fish, Xiphophorus helleri, have a secondary sexual trait, the sword, which is a composite trait consisting of four components favoured by sexual selection via female mate choice. The components include three coloured stripes and size. Although a complete sword is most attractive to female green swordtails, females prefer partial swords containing complete black stripes to incomplete swords lacking black coloration. Female swordtails also prefer longer swords. We addressed how subcomponents of the sword affect female mate choice. Digitally altered videos were used to investigate whether females respond differently to swords with proximal black stripes than to swords with distal black stripes. Although females preferred complete swords to both of the stimuli with partial stripes, they preferred males with distally striped swords to males with proximally striped swords. These results are discussed in light of hypotheses concerning the evolution of mating preferences for multicomponent traits. This study contributes to the growing body of information regarding the response of females to multicomponent visual traits.
Event-driven data acquisition and continuous-time digital signal processing

This paper reviews research in event-driven data acquisition and associated digital signal processing. The approaches considered can potentially offer significant energy and bandwidth savings with certain important classes of signals, in which activity varies significantly with time. An extensive bibliography is provided.
Challenges in the design and analysis of non-inferiority trials: a case study

Background The literature on the design, conduct, and analysis of non-inferiority trials is continuously evolving. Several design issues continue to be researched including the choice of active con...
Modulation of zebrafish pitx3 expression in the primordia of the pituitary, lens, olfactory epithelium and cranial ganglia by hedgehog and nodal signaling

In this article we report the isolation of a novel zebrafish gene, pitx3, which plays an important role in the formation of several placode-derived structures. In wildtype embryos, pitx3 is first expressed in a crescent-shaped area in the anterior end of the embryo. At later stages, the primordia of the anterior pituitary, the lens, the olfactory sensory epithelium, and cranial ganglia express this gene. Pitx3 is not expressed in the more posterior preplacodal region that gives rise to the epibranchial, otic, and lateral line placodes. The dynamics of pitx3 in the anterior region of wildtype embryos suggests that pitx3 expression marks a common step in the formation of the pituitary, lens, olfactory placode as well as the trigeminal placode. Analysis of pitx3 expression in mutants lacking the hedgehog or nodal function demonstrates the differential dependence of pitx3 expression in these structures on nodal and hedgehog signaling. While the lens and trigeminal placodes express pitx3 in the absence of hedgehog and nodal signaling, there is no expression of pitx3 in the anteriormost ectoderm adjacent to the neural plate from which the anterior pituitary would derive. In mutants with impaired hedgehog signaling, the lens placode frequently extends into more anterior ventral regions of the embryo. genesis 41:33–40, 2005. © 2005 Wiley-Liss, Inc.