cssi/SciSciGPT-SciSciNet huggingface dataset:
Mobile applications for breast cancer survivorship and self-management: A systematic review:

The use of mobile technology and mobile apps has become pervasive in our daily lives for completing a variety of daily tasks. Mobile health (mHealth) apps can provide an accessible platform for self-management among breast cancer (BC) survivors, as they recover from not just the intensive cancer treatments, but also their associated side-effects. They also offer a means to learn about survivorship topics and connect with peer survivors online, irrespective of their geographical location. This study is an attempt to assess the availability and characterize the self-management features of free mobile apps for breast cancer survivors on the Google Play (Android) and Apple App Store (iOS). Out of 249 such apps for the Android, only eight satisfied initial criteria, while only one of 174 iOS apps that met inclusion criteria was included for further analysis. A content analysis of the nine apps that met inclusion criteria was conducted to assess the inclusion of the following mHealth self-management features derived from the Chronic Care Model: symptom tracking; survivorship education; information-sharing with family and/or caregivers; scheduling follow-up visits; personal alerts and reminders; and social networking. Survivorship education was found to be the most common self-management feature among the apps reviewed, followed by social networking. The results of this study highlight the dearth of available mHealth resources for BC survivors. Future efforts in app development should involve survivors and healthcare providers to ensure comprehensive resources that address their unmet needs are made more accessible.
Changing the Face of Neuroimaging Research: Comparing a New MRI De-Facing Technique with Popular Alternatives.

Recent advances in automated face recognition algorithms have increased the risk that de-identified research MRI scans may be re-identifiable by matching them to identified photographs using face recognition. A variety of software exist to de-face (remove faces from) MRI, but their ability to prevent face recognition has never been measured and their image modifications can alter automated brain measurements. In this study, we compared three popular de-facing techniques and introduce our mri_reface technique designed to minimize effects on brain measurements by replacing the face with a population average, rather than removing it. For each technique, we measured 1) how well it prevented automated face recognition (i.e. effects on exceptionally-motivated individuals) and 2) how it altered brain measurements from SPM12, FreeSurfer, and FSL (i.e. effects on the average user of de-identified data). Before de-facing, 97% of scans from a sample of 157 volunteers were correctly matched to photographs using automated face recognition. After de-facing with popular software, 28-38% of scans still retained enough data for successful automated face matching. Our proposed mri_reface had similar performance with the best existing method (fsl_deface) at preventing face recognition (28-30%) and it had the smallest effects on brain measurements in more pipelines than any other, but these differences were modest.
Statistical Aspects of Target Setting for Attribute Data Monitoring

We consider early warning systems (EWS) for monitoring multi-stage data, in which downstream variables undergo changes associated with upstream process stages. In such applications, the EWS monitoring arm acts as a search engine that analyses a number of data streams for each monitored variable, as the problems of change detection and identification of the change-causing stage are handled jointly. Given massive amounts of data involved in analysis, it is important to achieve an acceptable balance between false alarms and sensitivity requirements, by focusing on changes of practical significance. The role of the target-setting arm of EWS is to ensure and maintain this balance via suitable selection of control scheme parameters. In this paper, we discuss principles of developing and managing targets, with examples from a supply chain operation.
Simplified tuning of long-range corrected density functionals for use in symmetry-adapted perturbation theory.

Long considered a failure, second-order symmetry-adapted perturbation theory (SAPT) based on Kohn–Sham orbitals, or SAPT0(KS), can be resurrected for semiquantitative purposes using long-range corrected density functionals whose asymptotic behavior is adjusted separately for each monomer. As in other contexts, correct asymptotic behavior can be enforced via “optimal tuning” based on the ionization energy theorem of density functional theory, but the tuning procedure is tedious, expensive for large systems, and comes with a troubling dependence on system size. Here, we show that essentially identical results are obtained using a fast, convenient, and automated tuning procedure based on the size of the exchange hole. In conjunction with “extended” (X)SAPT methods that improve the description of dispersion, this procedure achieves benchmark-quality interaction energies, along with the usual SAPT energy decomposition, without the hassle of system-specific tuning.
How two molecules self-assemble and what accelerates their assembly

Cram’s supramolecular capsule Octacid4 can irreversibly and noncovalently self-assemble with small- molecule guests at room temperature, but how they self-assemble and what accelerates their assembly are open questions that hold the key to developing noncovalent irreversible complexes. This article reports 72 distinct Octacid4•guest self-assembly pathways captured in unrestricted, unbiased, millisecond molecular dynamics simulations, revealing that the self-assembly process was initiated by the guest interaction with the cavity portal exterior of Octacid4 to increase the portal collisions that led to the portal expansion for guest ingress, accelerated by engaging populated host and guest conformations for the exterior interaction to increase the portal collision frequency, and completed by the portal contraction caused by the guest docking inside the cavity to impede guest egress. These revelations explain why the presence of a cryptic exterior binding site at the rim of the enzyme active site is a fundamental feature of fast enzymes such as acetylcholinesterase and why small molecules adopt local minimum conformations when binding to proteins. Furthermore, these revelations suggest that noncovalent irreversible complexes with fast assembly rates could be developed—by engaging populated host and guest conformations during the exterior interactions—for materials technology, data storage and processing, molecular sensing and tagging, and drug therapy.
Immune responses to two and three doses of the BNT162b2 mRNA vaccine in adults with solid tumors.

Vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have shown high efficacy, but immunocompromised participants were excluded from controlled clinical trials. In this study, we compared immune responses to the BNT162b2 mRNA Coronavirus Disease 2019 vaccine in patients with solid tumors (n = 53) who were on active cytotoxic anti-cancer therapy to a control cohort of participants without cancer (n = 50). Neutralizing antibodies were detected in 67% of patients with cancer after the first immunization, followed by a threefold increase in median titers after the second dose. Similar patterns were observed for spike protein-specific serum antibodies and T cells, but the magnitude of each of these responses was diminished relative to the control cohort. In most patients with cancer, we detected spike receptor-binding domain and other S1-specific memory B cell subsets as potential predictors of anamnestic responses to additional immunizations. We therefore initiated a phase 1 trial for 20 cancer cohort participants of a third vaccine dose of BNT162b2 ( NCT04936997 ); primary outcomes were immune responses, with a secondary outcome of safety. At 1 week after a third immunization, 16 participants demonstrated a median threefold increase in neutralizing antibody responses, but no improvement was observed in T cell responses. Adverse events were mild. These results suggest that a third dose of BNT162b2 is safe, improves humoral immunity against SARS-CoV-2 and could be immunologically beneficial for patients with cancer on active chemotherapy. After two doses of the BNT162b2 vaccine, virus-specific antibodies and T cells were reduced in patients with solid tumors as compared to individuals without cancer, but neutralizing antibodies increased in most patients who received a third vaccine dose.
Tribal Diversity, Political Patronage and the Yemeni Decentralization Experiment

Patronage is a tool used throughout the world to reward political allies. In this paper I create a dataset of Yemeni tribes to explore their role in an educational patronage network that accounts for upwards of 6% of the entire Yemeni government budget. My analysis has two key results. First, conditional on a rich set of controls, I find that the number of tribes has a significant impact on the quantity of patronage. This impact is negative between regions, though positive within regions, as regions with more tribes have less patronage while sub-regions with more tribes have more patronage. The contrast between these effects illustrates the differing influence of tribes in local and national politics. Second, I find no evidence that a recent decentralization reform affected this patronage network. The paper provides insight into how pre-Islamic institutions have an important role in the development outcomes of the Muslim Middle East and why decentralization reforms proposed for countries similar to Yemen, such as Afghanistan and Somalia, may be ineffective in weakening the power of local elites. ∗PhD Candidate, Department of Economics. E-mail: egel@econ.berkeley.edu. I thank Barry Eichengreen, Bryan Graham and Ted Miguel for their encouragement and support throughout this project. Robert Anderson, Fred Finan and Avner Greif provided valuable advice and helpful comments. I am deeply indebted to Lamis Aliryani, Betty Sadoulet and Alain de Janvry and the Social Fund for Development for supporting my fieldwork in Yemen. Nada Alhajjri, Mohammed Almawri, Mervat Al-Naimee, Ahmed Barakani, Ahmed Basharahi, Marta Colburn, Roberta Contin, Khalid Moheyddeen, Kunera Moore and Tareq Yeslam provided very helpful discussions during my stay in Yemen. I also thank Garret Christensen, Juan Sebastian Lleras, Guillermo Noguera, Jonathan Rose, Anna Spurlock, Chloe Thurston, Philippe Wingender and Lanwei Yang and participants in the Berkeley Development Lunch and the Stanford Labor and Development Reading Group for helpful discussions and comments. The data collection would not have been possible without Fayadh Alnageeb’s excellent research assistance and ability to coordinate my team of Yemeni researchers.
Rate distortion from planet to paper.

The overall data link commences with the lens of the spacecraft camera, followed by the telemetry format, and then the passing of the data onto a spacecraft tape recorder for later transmission at a slower rate. The properties of the individual pieces of information are described, and rate distortion theory is discussed. The video channel from the standpoint of information theory, and fidelity criteria for planetary video are considered. Areas for further research are indicated.
Near optimal output feedback control of nonlinear discrete-time systems based on reinforcement neural network learning

In this paper, the output feedback based finite-horizon near optimal regulation of nonlinear affine discrete-time systems with unknown system dynamics is considered by using neural networks (NNs) to approximate Hamilton-Jacobi-Bellman (HJB) equation solution. First, a NN-based Luenberger observer is proposed to reconstruct both the system states and the control coefficient matrix. Next, reinforcement learning methodology with actor-critic structure is utilized to approximate the time-varying solution, referred to as the value function, of the HJB equation by using a NN. To properly satisfy the terminal constraint, a new error term is defined and incorporated in the NN update law so that the terminal constraint error is also minimized over time. The NN with constant weights and time-dependent activation function is employed to approximate the time-varying value function which is subsequently utilized to generate the finite-horizon near optimal control policy due to NN reconstruction errors. The proposed scheme functions in a forward-in-time manner without offline training phase. Lyapunov analysis is used to investigate the stability of the overall closed-loop system. Simulation results are given to show the effectiveness and feasibility of the proposed method.
Chemical Vapor Deposition of Copper from Hexafluoroacetylacetonato Copper(I) Vinyltrimethylsilane Deposition Rates, Mechanism, Selectivity, Morphology, and Resistivity as a Function of Temperature and Pressure

Chemical vapor deposition (CVD) of copper from (hfac)copper(I)VTMS, where hfac = hexafluoroacetylacetonato and VTMS = vinyltrimethylsilane has been studied as a function of temperature and pressure. Analogous to other , (hfac)CuVTMS also deposits pure copper films via a quantitative thermally induced disproportionation reaction. The reaction kinetics of (hfac)CuVTMS were examined in a warm‐wall differential reactor over the temperature range of 130 to 200°C and pressure range of 10 to 500 mTorr. Deposition rates of up to ∼5000 A/min at 190°C and 500 mTorr were obtained. Apparent activation energies of 43(5) and 10(2) kcal/mol at 10 and 500 mTorr precursor pressure, respectively, were obtained. The deposition rate was nearly first order over precursor partial pressure of 10 to 30 mTorr and zero order over 50 to 500 mTorr at 160°C. The data are consistent with a mechanism of chemisorption of (hfac)CuVTMS, dissociation to form (hfac)Cu and VTMS, disproportionation of (hfac)Cu to form Cu metal and , and desorption of and VTMS. A strong dependence of film resistivity on precursor partial pressure was observed. Selectivity for tungsten (W) surfaces in the presence of PECVD was not observed under the conditions employed.
Carcinoma of the endometrium: stage I.

Abstract During the 10-year period ending December 1972, 577 patients with Stage I endometrial cancer received their primary treatment at the Mayo Clinic. The average age of the group was 60.8 years. The higher-grade lesions were found in older individuals. The data did not show that high grade was related to age at menopause. The initial therapy was total abdominal hysterectomy and bilateral salpingo-oophorectomy. The absolute survival at 5 years was 92.7% for Stage IAG1, 86.5% for IAG2, 68.2% for IAG3, 89.6% for IBG1, 76.4% for IBG2, and 62.9% for IBG3.
Distress Screening and the Integration of Psychosocial Care Into Routine Oncologic Care

Many patients being treated for cancer have significant distress and often do not receive the attention they require. The psychosocial concerns of these patients are now better recognized and treated through psycho-oncology, which has become a multidisciplinary subspecialty of oncology concerned with the emotional responses of patients at all stages of disease, their families, and staff. In her presentation at the NCCN 18th Annual Conference, Dr. Jimmie C. Holland briefly reviewed the early role played by the NCCN as well as other national and international organizations in improving the psychosocial care of patients with cancer.
Auth-SL: a system for the specification and enforcement of quality-based authentication policies

This paper develops a language and a reference architecture supporting the management and enforcement of authentication policies. Such language directly supports multi-factor authentication and the high level specification of authentication factors, in terms of conditions against the features of the various authentication mechanisms and modules. In addition the language supports a rich set of constraints; by using these constraints, one can specify for example that a subject must be authenticated by two credentials issued by different authorities. The paper presents a logical definition of the language and its corresponding XML encoding. It also reports an implementation of the proposed authentication system in the context of the FreeBSD Unix operating system (OS). Critical issues in the implementation are discussed and performance results are reported. These results show that the implementation is very efficient.
Comparison of Four Methods for Measuring Uric Acid: Copper-Chelate, Phosphotungstate, Manual Uricase, and Automated Kinetic Uricase

Glutathione, ascorbic acid and many commonly used antibiotics falsely elevate uric acid concentrations when measured with the Du Pont "aca," in which the copper-chelate method is used. L-Dopa interferes with both the copper-chelate method and the Technicon "SMA 12/60" phosphotungstate method. A new kinetic uricase method has been developed for use on the Du Pont aca. This kinetic uricase method has a coefficient of variation of 2.40% and gives values that are essentially identical to those obtained by a manual end-point uricase method.
Computed tomography of the heart: evaluation of anatomy and function.

Diseases of the heart and blood vessels represent one of the most challenging problems for advanced diagnostic imaging systems. Computed tomographic scanning is potentially an ideal cardiac imaging modality since it is a cross-sectional imaging method with very high resolution. Currently available computed tomographic scanners have exposure speeds of 1 to 5 seconds, which are inadequate for the majority of cardiovascular imaging applications. Nevertheless, a variety of limited computed tomographic scanning techniques have been successfully performed in selected patient subgroups. These methods require the administration of contrast medium injected or infused into a peripheral vein, combined with either dynamic computed tomographic scanning or some form of electrocardiographic gated computed tomography. The newer conventional computed tomographic scanners can display anatomic structures in the heart and great vessels with considerable fidelity and provide not only cross-sectional displays but also, by means of computer manipulation, any selected reconstructed images in oblique, coronal or sagittal projections. Feasibility studies indicate improved accuracy of computed tomographic measurements of cardiac chamber volumes. Physiologic measurements include estimation of shunt flows and cardiac output and analysis of myocardial wall thickening. The full potential of computed tomography should be reached once fast, multiple slice, computed tomographic scanners using scanning electron beam techniques become available. The prototype CVCT (cine computed tomographic C-100 scanner) designed at the University of California, San Francisco, is now undergoing evaluation. This instrument images up to eight contiguous slices at the rate of 16 to 24 images/so The computed tomographic scanner specifically designed for cardiac imaging should extend the utility of computed tomography in the evaluation of cardiac diseases and the study of cardiovascular physiology.
Imaging of fatigue cracks in cladded pressure vessels with the SLIC-50

Abstract A two-step multibeam-multimode approach to ultrasonic in-service inspection of cladded reactor pressure vessels for near-surface fatigue cracks is presented. Detection of cracks is achieved with the SLIC-40 multibeam transducer, which yields a strong reflected-diffracted signal from the upper crack extremity (pulse 1). Sizing is accomplished with the SLIC-50 multimode transducer, which also yields a mode-converted (hence, well-separated) diffracted signal from the lower crack extremity (pulse 2). These SLIC transducers were used by the manual MBSP team (employing multiple beams and satellite pulses) in the PISC II international round-robin exercise and were qualified on the eight near-surface cracks in plate 2. Data from this exercise are discussed. The first sizing results obtained with a mechanized SLIC-50 and a computer-aided doublet acquisition and imaging system (DAISY) for three semi-elliptical underclad fatigue cracks are also compared with results reported by manual ultrasonic examiners as well as with the known crack depths.
Constant-Time Pattern Matching For Real-Time Production Systems

Many intelligent systems must respond to sensory data or critical environmental conditions in fixed, predictable time. Rule-based systems, including those based on the efficient Rete matching algorithm, cannot guarantee this result. Improvement in execution-time efficiency is not all that is needed here; it is important to ensure constant, 0(1) time limits for portions of the matching process. Our approach is inspired by two observations about human performance. First, cognitive psychologists distinguish between automatic and controlled processing. Analogously, we partition the matching process across two networks. The first is the automatic partition; it is characterized by predictable 0(1) time and space complexity, lack of persistent memory, and is reactive in nature. The second is the controlled partition; it includes the search-based goal-driven and data-driven processing typical of most production system programming. The former is responsible for recognition and response to critical environmental conditions. The latter is responsible for the more flexible problem-solving behaviors consistent with the notion of intelligence. Support for learning and refining the automatic partition can be placed in the controlled partition. Our second observation is that people are able to attend to more critical stimuli or requirements selectively. Our match algorithm uses priorities to focus matching. It compares priority of information during matching, rather than deferring this comparison until conflict resolution. Messages from the automatic partition are able to interrupt the controlled partition, enhancing system responsiveness. Our algorithm has numerous applications for systems that must exhibit time-constrained behavior.
Effects of attentional focusing on pain perception

Two experiments were conducted to examine the hypothesized differential effectiveness of two attentional focusing strategies in pain perception. In the first experiment, subjects (72 male college students) rated their levels of pain after being exposed to either low- or high-intensity pressure stimulation for 75 s. Subjects were instructed to use either an external or internal focus of attention during the pain induction. Results revealed that external focusing was more effective for coping than internal focusing across both levels of stimulus intensity. The second experiment was a replication of the first, and featured bolstered internal focusing and stimulus intensity manipulations. Results showed that high-intensity stimulation produced higher pain ratings than did low-intensity stimulation for subjects in the internal focusing conditions, but not for those in the external focusing conditions. The findings support the power of distraction strategies for dealing with short-term pain with a rapid onset. Theoretical implications are discussed.
The nature of consistency motivation: Consistency, aconsistency, and anticonsistency in a dissonance paradigm

The attitudinal consequences of acute and chronic activation of a motive for consistency were examined in two studies. In the first, only participants whose consistency motives had been temporarily activated showed a traditional dissonance effect—greater attitude change following a counterattitudinal statement made with perceived free choice. In the second, consistency‐activated participants with chronic high, middle, or low preferences for consistency showed strong, weak, and reverse dissonance effects, respectively. The results support a bivalent model of consistency motivation and account for prior difficulties in obtaining and replicating dissonance effects. Renee J. Bator is now at the Department of Psychology at the State University of New York, Plattsburgh. Thanks are due to Terri Asher, Allison Deacon, Jon Finkl, and Joe Vogler for their help in the collection of data in Study 2.
cAMP Activates MAP Kinase and Elk-1 through a B-Raf- and Rap1-Dependent Pathway

Cyclic adenosine monophosphate (cAMP) has tissue-specific effects on growth, differentiation, and gene expression. We show here that cAMP can activate the transcription factor Elk-1 and induce neuronal differentiation of PC12 cells via its activation of the MAP kinase cascade. These cell type-specific actions of cAMP require the expression of the serine/threonine kinase B-Raf and activation of the small G protein Rap1. Rap1, activated by mutation or by the cAMP-dependent protein kinase PKA, is a selective activator of B-Raf and an inhibitor of Raf-1. Therefore, in B-Raf-expressing cells, the activation of Rap1 provides a mechanism for tissue-specific regulation of cell growth and differentiation via MAP kinase.
Screens, iron, and leukemia.

In this issue of Blood , Eberhard and colleagues screen a large library of off-patent agents for down-regulation of the survivin promoter in HeLa cells. Their most specific “hit” was ciclopirox, formerly developed as an antifungal, which was found to have preclinical antileukemic activity
Quenching of singlet oxygen by alkaloids and related nitrogen heterocycles

Abstract Fifteen plant alkaloids and related heterocyclic compounds were tested for their ability to quench singlet oxygen. Most of the compounds showed high activity; brucine and strychnine were especially efficient quenchers. Brucine, at a concentration of ca 2.6 x 10 −5 M, is capable of inactivating half the singlet oxygen molecules it encounters. This quenching may serve in nature to protect plants from the deleterious effects of singlet oxygen or other reactive oxidants.
A review of the feasibility of lightening structural polymeric composites with voids without compromising mechanical properties

High performance polymer-fiber composites are high strength, low weight materials that have many applications, many of which would benefit from a decrease in weight, without a decrease in material properties. Generally, the fibers serve as the main load carriers, while the matrix serves to distribute load and protect the fibers from the environment. Thus, it is postulated that if the volume fraction of matrix is reduced, while still ensuring complete wetting of the fibers by the matrix, the per unit weight, i.e., specific, mechanical properties could be improved. This can be done by introducing small, spherical bubbles. Given the small average inter-fiber distance and assuming that the bubbles must not interact with the surface of the reinforcements the bubble diameter would need to be less than 1 μm. Introducing bubbles this small and ensuring that they do not form, or become attached, on the surface of the reinforcement are significant challenges. Two methods to produce such bubbles and the effect of these bubbles on mechanical properties of neat resins are reviewed: the addition of hollow spherical fillers, called microballoons, and the creation of bubbles from blowing agents. Microballoons in resins are a class of materials called syntactic foams. Although commercial microballoons are too large, smaller diameters can be made and could be used to reduce the weight of a reinforced composite on the order of 10%. The use of a physical blowing agent to produce bubbles in a composite is also considered. However, traditional polymer foaming techniques may be inadequate, as nucleation on the reinforcing phase is likely, and the bubbles formed are generally too large, so the use of blowing agent wells is considered. Blowing agent wells are discontinuous regions made from copolymer micelles or immiscible polymers that act as reservoirs of blowing agent. Additionally, the use of nano-sized materials for use as heterogeneous nucleation sites and secondary reinforcement of the matrix is also considered. Bubbles made from blowing agent could reduce the weight slightly more than using hollow spheres, but the reduction would also be of the order of 10%.
Exploring the Medical Applications of the Internet: A Guide for Beginning Users

Various techniques for accessing informational resources of interest to physicians and other medical professionals currently are available on Internet, a global internetworking of computer systems. The basic strategies for sending electronic mail, transferring files, and logging on to distant computers, as well as newer and more user-friendly indexing and interface systems for accomplishing these tasks are discussed.
Joint impacts of Bus Rapid Transit and urban form on vehicle ownership: New evidence from a quasi-longitudinal analysis in Bogotá, Colombia

Abstract Bus Rapid Transit (BRT) has become popular as a means to provide non-automobile-based mobility and alleviate the impacts of rising traffic congestion in cities around the world. However, there is little empirical evidence supporting BRT’s potential to meet these objectives. This research improves our knowledge of BRT’s potential as an alternative to vehicle ownership at the household level and provides new evidence of the role of urban form in supporting transit investment. We use a difference-in-differences research design to examine the change in vehicle ownership from before to after implementation of Bogota, Colombia’s TransMilenio BRT system. Our results indicate access to TransMilenio’s main trunk system is significantly and negatively associated with vehicle ownership for higher wealth households. Among lower wealth households, access to the trunk system and the complementary feeder system (designed to bring passengers from peripheral neighborhoods into the main trunk system) are both associated with an unexpected increase in the odds of vehicle ownership; however, that increase appears to be reversed in neighborhoods where the built environment supports transit and non-motorized travel. This research contributes a methodology for joint analysis of urban form and transit availability on vehicle ownership, and demonstrates that urban form and transit access can have a synergistic effect. Neglecting this synergy would be a missed opportunity to further leverage the benefits of BRT investments. Our findings also suggest that, in the case of Bogota, the vehicle ownership impacts of BRT investment may not accrue to lower income households unless that investment is coordinated with policies to promote supportive urban form.
Kinetics of the reaction Cl + O3 → ClO + O2

Abstract The bimolecular rate constant for the reaction Cl + O3 → ClO + O2 is measured over the temperature range 210 to 360 K in a discharge flow system using Cl atom resonance fluorescence at 134.72 nm to monitor the decay of Cl under pseudo first order conditions. Results, expressed in the form k1 = (2.35 ± 0.5) × 10−11 exp[−(171 ± 30)/T], are compared with other recent studies of this reaction. Stratospheric implications are discussed briefly including the possibility of a concurrent three-body mechanism with O2 forming ClO3.
Crystallization of Old Yellow Enzyme Illustrates an Effective Strategy for Increasing Protein Crystal Size

Abstract Old Yellow Enzyme (OYE) was the first flavoenzyme discovered, and has been widely used as a model flavoenzyme. Three crystal forms have been grown from natural protease-nicked OYE and one has been grown from intact recombinant OYE. The recombinant OYE crystals are best suited for structure determination and grow from a solution containing polyethylene glycol and MgCl2. They belong to space group P43212 with unit cell dimensions a=b=142·88 A, c=43·01 A and have a single OYE chain per asymmetric unit. In order to optimize the production of large single crystals, we have carried out a systematic study of crystal size versus drop volume. Crystallographic lore holds that the volume of the medium in which the crystals are grown should have a significant effect on the final size of the crystals produced. However, a systematic investigation of the degree to which the volume of the crystallization sample affects the final size of the crystals has not been reported. In order to investigate this phenomenon, drops were set up in both hanging and sandwich geometry at a variety of drop volumes, but otherwise identical crystallization conditions. A 60-fold increase in drop volume produced a 730-fold increase in crystal volume, and a simultaneous increase in the effective diffraction limit of the crystals from near 2·5 A to well beyond 2·0 A resolution. The dramatic crystal volume increase appears to be due both to the increased amount of protein and the slower equilibration rates associated with larger drops. Our results also emphasize that the quality of diffraction data may often be limited by crystal size rather than intrinsic crystal order even in the case of reasonably sized (200 to 400 μm) crystals.
Defect clusters in wustite, Fe1-xO

Abstract A quantum chemical approach based on predominantly covalent “normalized ion energies” has been developed for estimating structures and energies for defect clusters in quenched nonstoichiometric wustite (Fe 1− x O). Small defect clusters of zinc blende structure show special stability over other clusters considered. Of these, either a 13:5 or a 16:7 defect cluster (13 or 16 Fe 3+ vacancies and 5 or 7 tetrahedral Fe 3+ interstitials) have the proper structure and composition to account for the observed P′ and P″ phases in wustite.
Quadrupole-based mass spectrometric evaluation of isotope ratios of carbon dioxide in expired air from mice and men following the administration of 13C-methyl methionine

A method is described for the measurement of the isotopic ratio of 13CO2/12CO2 in expired air from individual mice and from humans by means of a quadrupole-based mass spectrometer system. Following the administration of 13C-methyl methionine or another appropriately labeled substrate, the 13C portion of the molecule is converted to 13CO2. The 13CO2 enters the carbonate pool(s) and is ultimately eliminated in the expired air where it is available for analysis. The expired air is transported by a small pump from the subject to a digital valve which provides for the alternate influx of expired air and standard into the mass spectrometer for 30 or 60 seconds each, respectively. The inlet consists of a control valve connected to a microbore stainless steel tube, and can be adjusted manually to achieve a source pressure of 4 X 10−5 torr. The correction factors for drift in sensitivity and in the mass axis are generated by repeated, automatic analysis of the running standard and relating those measurements to values generated for the standard during the first minutes of the experiment. Each measurement of an isotopic ratio in expired air is corrected by an amount determined by the standard immediately preceding it. Precision for the measurements of both sample and standard ratios is ±0.2%. The technique should prove useful in assessing the metabolism, of substrates that are converted to CO2 and may find utility as a diagnostic tool for certain diseases and metabolic disorders.
Complicated urinary tract infections

The distinction between complicated and uncomplicated urinary tract infections is usually based on the presence or absence of some abnormality in the path of urine flow. Other differences include characteristic patient profiles, usual setting, likely pathogens and their antimicrobial susceptibility, and treatment options. Complicated infections are most common in older patients, usually men with prostatic enlargement. Gram-negative bacilli are the most frequent pathogens, but Escherichia coli plays a less dominant role. Isolates from patients with complicated infections are more likely to be resistant to older antibiotics, and therapy is usually parenteral. Many complicated urinary tract infections are hospital-acquired, and are often due to indwelling urinary catheters. Resistance to antimicrobials among isolates is common in this setting. Nosocomial urinary tract infections contribute substantially to morbidity, mortality, and health care costs. Numerous effective treatment options are available for uncomplicated infections. The types of patients, predisposing factors, and organisms limit antimicrobial choices for complicated infections. Although new antibiotics offer certain advantages, final therapeutic success usually depends on resolving the disorder that predisposes the patient to infection.
Characterizing Wheel-Soil Interaction Loads Using Meshfree Finite Element Methods: A Sensitivity Analysis for Design Trade Studies

A wheel experiencing sinkage and slippage events poses a high risk to planetary rover missions as evidenced by the mobility challenges endured by the Mars Exploration Rover (MER) project. Current wheel design practice utilizes loads derived from a series of events in the life cycle of the rover which do not include (1) failure metrics related to wheel sinkage and slippage and (2) performance trade-offs based on grouser placement/orientation. Wheel designs are rigorously tested experimentally through a variety of drive scenarios and simulated soil environments; however, a robust simulation capability is still in development due to myriad of complex interaction phenomena that contribute to wheel sinkage and slippage conditions such as soil composition, large deformation soil behavior, wheel geometry, nonlinear contact forces, terrain irregularity, etc. For the purposes of modeling wheel sinkage and slippage at an engineering scale, meshfree nite element approaches enable simulations that capture su cient detail of wheel-soil interaction while remaining computationally feasible. This study implements the JPL wheel-soil benchmark problem in the commercial code environment utilizing the large deformation modeling capability of Smooth Particle Hydrodynamics (SPH) meshfree methods. The nominal, benchmark wheel-soil interaction model that produces numerically stable and physically realistic results is presented and simulations are shown for both wheel traverse and wheel sinkage cases. A sensitivity analysis developing the capability and framework for future ight applications is conducted to illustrate the importance of perturbations to critical material properties and parameters. Implementation of the proposed soil-wheel interaction simulation capability and associated sensitivity framework has the potential to reduce experimentation cost and improve the early stage wheel design proce
Building maps from maps in primary visual cortex

Neurons in the visual system respond to more complex and holistic features at each new stage of processing. Often, these features are organized into continuous maps. Could there be a fundamental link between continuous maps and functional hierarchies? Here, we review recent studies regarding V1 maps providing some of the most noteworthy advances in our understanding of how and why maps exist. In particular, we focus on the common theme that some maps are inherited from the input of parallel pathways, which are then intimately linked to the emergence of new functional properties and their corresponding maps. These results on V1 maps may prove to be a unifying framework for hierarchical representations in the visual cortex.
Surface Shear Rheology of β-Casein Layers at the Air/Solution Interface: Formation of a Two-Dimensional Physical Gel

A magnetic rod interfacial shear rheometer was used to measure the properties of β-casein adsorbed at the air/solution interface as a function of aging time. Over a wide range of concentrations (1 × 10-6 to 2 × 10-2 wt % β-casein) the initial rheology of the adsorbed surface layer is dominated by a viscous response of the interface. For solutions in the range 5 × 10-3 to 2 × 10-2 wt %, interfacial gelation is observed after ∼15 h of aging, long after the surface tension has stabilized. In particular, although both components of the complex interfacial shear modulus (i.e., the storage and loss moduli) gradually increase with aging time, the ratio of the loss to the storage modulusthe loss tangentdecreases and drops below unity. The frequency dependence of the shear modulus is consistent with sol−gel transitions observed in bulk systems and described within the context of percolation theory.
Degradation of ethylene thiourea (ETU) with three Fenton treatment processes

Anodic Fenton treatment (AFT), an electrochemical, hydroxyl radical oxidation treatment system, was developed for the degradation of aqueous pesticides and other aqueous organic wastes. AFT of ethylene thiourea (ETU) was optimized and compared with electrochemical Fenton treatment (EFT) and classic Fenton treatment (CFT). ETU is a known carcinogen and is an impurity and degradation product of the widely used ethylenebisdithiocarbamate (EBDC) fungicide group. ETU was degraded effectively in all treatment methods, with CFT being the most rapid; however, significant differences in degradation product profiles were noted over the course of treatments. AFT displayed the most efficient degradation of primary degradation products of ETU. Keywords: Ethylene thiourea; ETU; Fenton; hydroxyl; oxidation; radical
Effects of acetazolamide on tissue cations.

SummaryEvidence has been presented that potassium depletion occurs in the skeletal muscle, heart, kidney, and plasma of pregnant rats and in the skeletal muscle and plasma of the nonpregnant rat following chronic administration of 0.6% acetazolamide in the diet for 20 days. A similar pattern of depletion followed two injections of drug spaced 18 hr apart. Sodium recompensation was observed in both pregnant and nonpregnant rat tissue that was partially depleted of potassium. A rise in liver potassium was observed in the pregnant and nonpregnant animal following the injection of 500 mg/kg of acetazolamide on days 10 and 11 of gestation. A similar rise was observed only in the pregnant rat on the 0.6% diet for 20 days.
Scattering of fractons, the Ioffe-Regel criterion, and the (4/3) conjecture.

The relaxation time for scattering of vibrational modes by structural irregularities in d-dimensional random systems is shown to cross over from 1/\ensuremath{\tau}\ensuremath{\sim}${\mathrm{\ensuremath{\omega}}}^{\mathrm{d}+1}$${\mathrm{\ensuremath{\omega}}}_{\mathrm{c}}^{\mathrm{\ensuremath{-}}\mathrm{d}}$ for phonons (\ensuremath{\omega}${\mathrm{\ensuremath{\omega}}}_{\mathrm{c}}$, the crossover frequency between phonon and fracton vibrational excitations) to 1/\ensuremath{\tau}\ensuremath{\sim}${\mathrm{\ensuremath{\omega}}}^{5\mathrm{\ensuremath{-}}3\mathrm{d}\mathrm{\ifmmode \tilde{}\else \~{}\fi{}}}$ for fractons (d\ifmmode \tilde{}\else \~{}\fi{} is the fracton dimensionality). The Ioffe-Regel criterion for localization, \ensuremath{\omega}\ensuremath{\tau}\ensuremath{\sim}1, and a scaling Ansatz, then lead to the Alexander-Orbach value, d\ifmmode \tilde{}\else \~{}\fi{}=(4/3), and 1/\ensuremath{\tau}\ensuremath{\sim}\ensuremath{\omega} for all \ensuremath{\omega}g${\mathrm{\ensuremath{\omega}}}_{\mathrm{c}}$. .AE
Mesomorphic Complexes of Poly(amidoamine) Dendrimer with DNA

The self-assembly behavior of the complexes of DNA with fully surface-protonated poly(amidoamine) (PAMAM) dendrimer of generation four has been studied as a function of the overall complex composition. The complex composition (x) was expressed by the molar ratio of the positively charged ammonium groups in the dendrimer to the DNA base pairs. The complexation was found to result in DNA condensation through which the dendrimer-bound DNA chains aggregated significantly to form ordered structures. A condensed nematic phase in which the locally oriented DNA chains did not exhibit coherent positional order formed at x = 2. Although the numbers of positive and negative charges were identical at this composition, the charge matching was frustrated by the DNA−DNA repulsion which limited the number of DNA chains surrounding each dendrimer molecule. Therefore, the nematic mesophase was built up by the irregularly packed square columnar cells (with each dendrimer molecule surrounded by four DNA chains in each cell),...
Mutagenesis of a highly conserved lysine 340 of the PRD1 DNA polymerase

All known family B DNA polymerases contain a conserved region of amino acids, KX6-7YG, which appears to be correspond to the 'finger' alpha helix O of the Klenow fragment of E. coli DNA polymerase I, a family A DNA polymerase. Toward the goal of establishing the evolutionary relationship between the family A and B DNA polymerases, we have employed site-directed mutagenesis to access the functional role of the invariant amino acid lysine-340 of the PRD1 DNA polymerase. We have replaced the lysine-340 with three amino acids: histidine, asparagine and glutamic acid, respectively. Mutant DNA polymerases were overexpressed and purified to near homogeneity. Our results showed that the modification of the lysine-340 of the PRD1 DNA polymerase abolishes the polymerase activity without affecting the 3' to 5' exonuclease activity. These results support the proposal that the KX6-7YG motif of the family B DNA polymerases may be analogous to the KX7YG motif of the family A DNA polymerases, suggesting that two family DNA polymerases share a common ancestor.
Radial paper chromatography and columnar chromatography of the chloroplast pigments of leaves.

Abstract 1. 1. Analysis by radial paper chromatography indicates that the principal pigments of the leaves of cocklebur, wheat, oats, barley, violet and Elodea are chlorophylls a and b , lutein with or without zeaxanthin, violaxanthin, neoxanthin and carotene. Additional xanthophylls such as neozeaxanthin, lutein epoxide and eloxanthin were not detectable. These results were confirmed by column chromatography using a variety of adsorbents such as powdered sugar, cellulose, starch, ZnCO 3 and activated magnesia. The separability of the pigments and the chromatographic sequence varied with the adsorbent as well as with the solvent. Inseparability of neoxanthin and violaxanthin mixtures in columns of ZnCO 3 with benzene as the wash liquid may account for some reports that leaves contain lutein epoxide but not neoxanthin and violaxanthin. 2. 2. The chromatographic behavior of the epoxy carotenoid pigments varies with the adsorbent. With magnesia as the absorbent, the epoxy carotenoids were less sorbed than the parent pigments, consequently the epoxy groups are less sorbed than the double bonds that they replace. Conversely, with sugar as the adsorbent, the epoxy carotenoids are more sorbed than the parent pigments, hence, on sugar, the epoxy groups are more sorbed than the double bonds that they replace. When treated with acids, the epoxides were not reconverted to the parent carotenoid pigments. 3. 3. The postulation that O 2 evolution in photosynthetic organisms results from deoxygenation of xanthophyll epoxides is not supported by chemical experience and by the that fact epoxides do not occur in some autotrophic organisms. Accummulating evidence suggests a non-chemical role for the chloroplast pigments in photoxynthesis.
Two-loop calculations with vertex corrections in the Walecka model.

Two-loop corrections with scalar and vector form factors are calculated for nuclear matter in the Walecka model. The on-shell form factors are derived from vertex corrections within the framework of the model and are highly damped at large spacelike momenta. The two-loop corrections are evaluated first by using the one-loop parameters and mean fields and then by refitting the total energy/baryon to empirical nuclear matter saturation properties. The modified two-loop corrections are significantly smaller than those computed with bare vertices. Contributions from the anomalous isoscalar form factor of the nucleon are included for the first time. The effects of the implicit density dependence of the form factors, which arise from the shift in the baryon mass, are also considered. Finally, necessary extensions of these calculations are discussed.