cssi/SciSciGPT-SciSciNet huggingface dataset:
Traps, Pitfalls and Misconceptions of Machine Learning applied to Scientific Disciplines

In the last decade, Machine Learning has experienced a dramatic increase in performance on a wide variety of tasks, including computer vision, speech recognition, text parsing, and language translation, just to name a few. This has corresponded to an understandable hype especially for the remarkable results achieved in some cases. Therefore, practitioners of Scientific Disciplines have become interested in utilizing new Machine Learning techniques, and have sometimes started doing so with mixed success.The purpose of this paper is to describe some of the common Traps, Pitfalls and Misconceptions of Machine Learning as relevant to the Scientific Discipline, and how to avoid them. In fact, Machine Learning and Deep Learning are fast evolving fields, and some of the astonishing results achieved recently sit on small but important details which have become the state of the art. Some of these details are not broadly known by the scientific community. No new scientific result is presented in this paper, which is a survey and a summary of the best of the field, for the benefit of researchers with limited experience.It is not the intention of the authors to provide any criticism to the work of experienced practitioners, particularly not to the ones working on the cutting edge of what is currently possible: in these cases expert researchers may well be doing exactly what we recommend here to avoid, and for a good reason. However we believe that the advice provided here will be useful, and perhaps even a reference, for the newcomers of the field.
Early Discontinuation of Infliximab in Pregnant Women with Inflammatory Bowel Disease

OBJECTIVES Early discontinuation of infliximab (IFX) in pregnant women with inflammatory bowel disease (IBD) decreases the intrauterine fetal exposure to the drug but may increase the risk of disease flaring leading to poor pregnancy outcomes. In this study, we assessed the impact of early IFX discontinuation on mother's disease activity and on their at-risk babies. METHODS In a retrospective study of the Truven Health Analytics MarketScan database from 2011 to 2015, we compared IBD patients who discontinued IFX more than 90 days ("early IFX") with those who discontinue IFX 90 days or less ("late IFX) before delivery. We evaluated the risk of flaring, defined by new steroid prescriptions, visits to emergency room and/or hospital admissions, the pregnancy outcomes, and the at-risk babies. RESULTS After IFX discontinuation, the early IFX group (68 deliveries) required significantly more steroid prescriptions than the late IFX group (318 deliveries) to control disease activity (P < 001). There were more preterm babies in the early IFX group (P < 049), but no difference within the 2 groups was noticed in the rate of intrauterine growth retardation, small for gestation, and stillborn babies. Similarly, there was no increase in acute respiratory infections, development delays, and congenital malformations in babies of the mothers from the late IFX vs early IFX groups. CONCLUSIONS Steroid-free remission IBD mothers are at risk for disease flares and preterm babies when IFX is discontinued early in pregnancy. Continuation of IFX seems to be safe at least for the first year of life.
The Effect of Preoperative Anemia on Complications After Total Hip Arthroplasty.

Abstract Background Current literature suggests that preoperative hematocrit levels may play an important role in determining risk for complications after total hip arthroplasty (THA). The purpose of this study was to determine the role of preoperative anemia status on 30-day complications after THA. Methods Using the National Surgical Quality Improvement Program registry from 2006 to 2016, we identified all patients who underwent primary THA. Patients were placed into 3 cohorts based on preoperative hematocrit levels (normal > 36% [N = 166,538], mild anemia 27%-36% [N = 13,214], and severe anemia Results Multivariate logistic regression analysis identified mild anemia compared with normal hematocrit as a significant risk factor for total complications (OR: 1.46, P Conclusion Preoperative anemia is a significant risk for perioperative complications after primary THA. Even mild anemia can lead to significantly increased risks of mortality, medical complications, and unplanned hospital readmissions in THA. This study further supports the need for screening and preoperative intervention for patients in this at-risk group.
Structured Reward Shaping using Signal Temporal Logic specifications

Deep reinforcement learning has become a popular technique to train autonomous agents to learn control policies that enable them to accomplish complex tasks in uncertain environments. A key component of an RL algorithm is the definition of a reward function that maps each state and an action that can be taken in that state to some real-valued reward. Typically, reward functions informally capture an implicit (albeit vague) specification on the desired behavior of the agent. In this paper, we propose the use of the logical formalism of Signal Temporal Logic(STL) as a formal specification for the desired behaviors of the agent. Furthermore, we propose algorithms to locally shape rewards in each state with the goal of satisfying the high-level STL specification. We demonstrate our technique on two case studies, a cart-pole balancing problem with a discrete action space, and controlling the actuation of a simulated quadrotor for point-to-point movement.The proposed framework is agnostic to any specific RL algorithm, as locally shaped rewards can be easily used in concert with any deep RL algorithm.
A 10nm SRAM Design using Gate-Modulated Self-Collapse Write Assist Enabling 175mV V MIN Reduction with Negligible Power Overhead

A 21Mb/mm2 SRAM design using 0.0367um2 HCC bitcell on a 10nm CMOS technology is presented. Gate-modulated self-collapse (GSC) write assist is utilized to enable 175mV reduction in V MIN with minimal energy overhead. Instance area overhead is limited to 3–5% by implementing the GSC circuitry in a row-based configuration with modified SRAM bitcells.
The Wisdom of Jane Eyre

Examines Bronte's beloved novel from the lens of personal discipline in the context of cultural influences.
Free-Breathing Abdominal Magnetic Resonance Fingerprinting Using a Pilot Tone Navigator.

BACKGROUND Quantitative T1 and T2 mapping in the abdomen provides valuable information in tissue characterization but is technically challenging due to respiratory motions. The proposed technique integrates magnetic resonance fingerprinting (MRF) and pilot tone (PT) navigator with retrospective gating to provide simultaneous quantification of multiple tissue properties in a single acquisition without breath-holding or patient set-up. PURPOSE To develop a free-breathing abdominal MRF technique for quantitative mapping in the abdomen. STUDY TYPE Prospective. POPULATION Twelve healthy volunteers. FIELD STRENGTH/SEQUENCE A 3 T, two-dimensional (2D) and three-dimensional (3D) spiral MRF sequence with fast imaging with steady-state free precession (FISP) readout. ASSESSMENT The PT navigator was compared to standard respiratory belt performance. The T1 and T2 values acquired using 2D and 3D MRF with and without PT were obtained in a phantom and compared to reference values. Digital phantom simulation was performed to evaluate PT MRF reconstruction with varying breathing patterns. In the in vivo studies, T1 and T2 values derived from PT 2D MRF were compared to 2D breath-hold MRF. T1 and T2 values derived from PT 3D MRF were compared to published values. STATISTICAL TESTS Principal component analysis (PCA), linear regression, relative error, Pearson correlation, paired Student's t-test, Bland-Altman Analysis. RESULTS The phantom study showed PT MRF T1 values had a mean difference of 0.2% ± 0.1%, and T2 values had a mean difference of 0.1% ± 0.4% when compared to no-PT MRF values. The digital phantom experiment suggested the T1 and T2 maps at both end-exhalation and end-inhalation states resemble the corresponding ground-truth maps. DATA CONCLUSION The phantom study showed good agreement between MRF T1 and T2 values and with reference values. In vivo studies demonstrated that 2D and 3D quantitative imaging in the abdomen could be achieved with integration of PT navigation with MRF reconstruction using retrospective gating of respiratory motion. EVIDENCE LEVEL: 1 TECHNICAL EFFICACY: Stage 1.
Informal preparation and years of experience: Key correlates of dyslexia knowledge among Massachusetts early elementary teachers.

BACKGROUND Dyslexia is a neurobiological condition affecting phonological processing and characterized by reading and phonological awareness difficulties. We assessed correlations between dyslexia knowledge and five independent variables among early elementary teachers in Massachusetts. METHODS We designed a survey based on two published assessment tools and surveyed 92 early elementary teachers. Using univariate and multivariate linear regression models, we assessed the relationships among knowledge (dependent variable) and confidence, feelings of preparedness, years of teaching experience, informal education and professional development opportunities (independent variables). RESULTS The mean knowledge score was 68 ± 14%; teachers performed best on questions about perceptions of dyslexia, classroom management/teaching strategies and some dyslexia characteristics. Informal education and years of teaching experience were consistently positively associated with knowledge. DISCUSSION AND CONCLUSIONS Formal training and professional development opportunities may need to focus more specifically on learning disabilities and dyslexia. Teachers should also have input on professional development needs. Our findings suggest a need for additional studies on strategies to improve educator knowledge of dyslexia and assess outcomes.
FEASIBILITY STUDY OF A SYSTEM SAFETY MONITOR FOR HAZARDOUS MATERIAL TRUCKING

This paper gives a summary of a study which investigated the feasibility of applying a system safety monitor (SSM) to hazardous materials trucking. The focus of the study was to provide a continuous record of truck and safety system operation and to detect the onset of specific critical situations. In order to assess the feasibility of the SSM, a theoretical analysis of truck dynamics was performed and preliminary instrumentation and support electronics design was developed.
Ubiquitous germination among common perennial species in response to facilitated and unfacilitated microhabitats

Abstract We present results from a study that examines species-specific facilitation of germination in an arid perennial community. This system suffered 64% adult mortality and the local extinction of two common species as a consequence of drought that occurred between 1999 and 2004. Ambrosia dumosa, Larrea tridentata, and Tetracoccus hallii are included as candidate benefactor species based on their high abundance and broad distribution at the study site. Using complementary field and greenhouse experiments, we measured the effects of facilitation, light and nitrogen on germination of four species common to the region, L. tridentata, A. dumosa, Sphaeralcea ambigua and Eriogonum fasciculatum. Our results show that benefactor species do not uniquely influence germination. Species-specific effects among beneficiaries largely explained differences in percent germination in the field, and the interaction between beneficiary species and microhabitat was significant for only one species. E. fasciculatum consistently showed significantly higher germination than more abundant species and showed reduced germination in the interspace. In the greenhouse, germination responses differed at each light level, beneficiaries responding most uniquely at full light. These results refine expectations from previous studies of facilitation at this site by showing that facilitation does not strongly enhance germination.
Ribonucleic Acid Regulation in Permeabilized Cells of Escherichia coli Capable of Ribonucleic Acid and Protein Synthesis

A cell permeabilization procedure is described that reduces viability less than 10% and does not significantly reduce the rates of ribonucleic acid and protein synthesis when appropriately supplemented. Permeabilization abolishes the normal stringent coupling of protein and ribonucleic acid synthesis.
Light guiding by gauge field for photons

We propose a waveguiding mechanism based on the effective gauge potential for photons, where the core and cladding regions have the same dispersion relation but are subject to different gauge potentials. This can be realized in a dynamically modulated resonator lattice, and provides a dynamically reconfigurable mechanism for generating a one-way waveguide.
THE PHENOMENOLOGY OF MATHEMATICAL PROOF

Everybody knows what a mathematical proof is. A proof of a mathematical theorem is a sequence of steps which leads to the desired conclusion. The rules to be followed in this sequence of steps were made explicit when logic was formalized early in this century and they have not changed since. These rules can be used to disprove a putative proof by spotting logical errors; they cannot, however, be used to find the missing proof of a mathematical conjecture.
An RLS-based algorithm for estimation and demodulation of QS-CDMA signals

In order to construct the optimal decorrelator for a quasi-synchronous (QS) CDMA receiver, it is necessary to estimate the user delays. However since the system is quasi-synchronous, it is shown that delay estimation is equivalent to estimating a parameter vector which is related linearly to the received signal. A recursive least-squares (RLS) algorithm is developed that approximately computes the joint maximum-likelihood (ML) estimates of the delays and user amplitudes. It is shown that the optimal decorrelator and demodulated symbols are also generated by the RLS algorithm. Simulation and analytical results are presented for the bit-error rate (BER) performance of the adaptive receiver and the averaged squared error (ASE) of the estimated delay vectors is compared with the Cramer-Rao bound.
Thyroid hormone regulation of the rat glycoprotein hormone alpha-subunit gene promoter activity.

Abstract An important physiological control of the glycoprotein hormone alpha-subunit is the negative feedback by thyroid hormones in the thyrotrope. A region of the rat glycoprotein hormone alpha-subunit gene that is involved in transcriptional regulation by thyroid hormone has been identified by transient transfection studies, and sequence-specific binding of the thyroid hormone receptor to a site within this region has been demonstrated. Deletion-mutation studies using plasmid expression vectors containing either 246, 170, or 80 base pairs of the 5'-flanking region of the rat alpha-subunit gene fused to the coding region of the bacterial chloramphenicol acetyltransferase gene demonstrate 3,5,3'-triiodo-L-thyronine (T3)-regulated expression in GH3 cells, a T3-responsive somatotrophic cell line. In order to investigate the possibility of thyroid hormone receptor interaction with this segment of the rat alpha-subunit gene, the binding of the thyroid hormone receptor to synthetic oligodeoxynucleotides was analyzed using an avidin-biotin complex DNA binding assay. An oligodeoxyribonucleotide representing a fragment of the alpha-subunit gene from -74 to -38, relative to the transcriptional start site, shows significant binding to [125I]T3-receptor complex present in nuclear extracts of GH3 cells. This fragment binds receptor to a degree similar to that seen with a fragment of the rat growth hormone gene which contains a putative thyroid hormone-responsive element. In addition, this fragment of the rat alpha-subunit gene binds to the in vitro synthesized human c-erbA beta protein, which has been identified as a member of the family of putative T3 receptors. These data demonstrate that a cis-active thyroid hormone-responsive element resides in the 5'-flanking region of the rat alpha-subunit gene and that the mechanism involved in the suppression of expression of this gene by T3 could involve specific binding of the thyroid hormone receptor to this region of the gene.
Topology, spin, and light

Ocean waves form between air and water, and both winds and currents decay exponentially with distance from the water surface. Similar evanescent surface waves may occur whenever two substances with differing physical properties meet—but some are special cases because they must exist for topological reasons. Such mandated surface modes occur in the low-energy quasi-particle spectrum of p-wave superconductors and superfluids and constitute the defining feature of the electronic properties of topological insulators. On page 1448 of this issue, Bliokh et al. ( 1 ) suggest that we add evanescent solutions of Maxwell's equations to this list of special cases, and in particular, the coupled oscillations of the electromagnetic field and the near-surface electrons in a metal that are known as surface plasmon-polaritons.
Abstract 215: The Redox Activation of DUSP4 by N-Acetyl Cysteine Protects Endothelial Cells and the Myocardium against Oxidative Damage

Background: Redox imbalance is the primary cause for endothelial dysfunction (ED), obstructed blood flow, and subsequent heart attack and failure. Under oxidant stress, many critical proteins regulating endothelial function undergo oxidative modifications that lead to ED. Cellular levels of glutathione (GSH), the primary reducing source, can significantly regulate cell function via reversible protein thiol modification. N-Acetyl cysteine (NAC), a precursor for GSH biosynthesis, is beneficial for many vascular diseases; however, the detailed mechanism of these benefits is still not clear. Methods: We employed EPR spin-trapping, HPLC, fluorescent microscopy, immunoblotting, and qPCR of both in vitro and ex vivo experiments using either cultured cells or the Langendorff heart preparation. Results: NAC treatment increases NO generation from endothelial cells, as well as the enzyme and cofactor responsible for its production, ie eNOS and BH4. Interestingly, NAC treatment also increased the expression of DUSP4,...
Extreme Ultraviolet Quantum Efficiency Of Opaque Alkali Halide Photocathodes On Microchannel Plates

Comprehensive measurements are presented for the quantum detection efficiency (QDE) of the microchannel plate materials CsI, KBr, KCl, and MgF2, over the 44-1800 A wavelength range. QDEs in excess of 40 percent are achieved by several materials in specific wavelength regions of the EUV. Structure is noted in the wavelength dependence of the QDE that is directly related to the valence-band/conduction-band gap energy and the onset of atomic-like resonant transitions. A simple photocathode model allows interpretation of these features, together with the QDE efficiency variation, as a function of illumination angle.
The effects of interferon-α and acyclovir on herpes simplex virus type-1 ribonucleotide reductase

Herpes simplex virus-type 1 (HSV-1) encodes both the small (UL40) and large (UL39) subunits of the enzyme, ribonucleotide reductase. Treatment of HSV-1-infected cells with interferon-alpha (IFN-alpha) reduced the levels of both enzyme subunits. Reduced steady state levels of the large subunit were demonstrated by immunoblot using polyclonal antibody specific for the viral enzyme. Reduction in the amount of small subunit was shown by a reduction in the electron spin resonance signal derived from the iron-containing tyrosyl free-radical present in this subunit. Treatment of cells with 100 IU/ml of IFN-alpha decreased levels of both subunits resulting in a reduction in enzyme activity as measured by conversion of CDP to dCDP. The decrease in the amount of the large subunit was not due to a reduction in the level of its mRNA. The combination of IFN-alpha and ACV treatment of human cornea stromal cells did not result in a further reduction in amounts of ribonucleotide reductase relative to that detected with IFN-alpha alone. The IFN-alpha-induced reduction in ribonucleotide reductase activity is the likely cause of decreased levels of dGTP which we have previously demonstrated in IFN-alpha-treated, infected cells.
Complexation, crystallography, and electrochemistry of new chelating nicotinyl and thiazolyl anthraquinone ligands

Chelating anthraquinone ligands that contain nicotinyl and thiazolyl binding units have been synthesized. The complexation chemistry of these new ligands has also been explored using cadmium(II), lead(II), and ruthenium(II). The nicotinic substituted anthraquinone acts as a bidentate ligand, while the thiazolyl substituted anthraquinone binds in a tetradentate arrangement, not previously observed. Due to steric limitations, the number of these ligands that can coordinate to metal centers appears limited to bis-substituted products. Crystallographic data for both the free ligands and the cadmium and lead complexes are reported. Electrochemical data indicate that interaction does not take place between the intraannular carbonyl group and the neighboring metal centers within these complexes.
Decarbonization reactions between sodium metaborate and sodium carbonate

Autocausticizing, used for the recovery of kraft pulping chemicals, is nearing commercialization. This technology produces sodium hydroxide directly on dissolving the molten salts produced in the kraft recovery furnace in water. Thus, the dependence on the lime cycle for sodium hydroxide is reduced. Ongoing trials in several kraft mills are in progress to implement this technology. In this study, the reactions between sodium metaborate (NaBO2) and sodium carbonate (Na2CO3)the anticipated reactantswere studied in a tubular reactor heated in an electric furnace. It was found that the reaction begins in the solid phase, followed by a liquid phase reaction. The reaction rate is extremely rapid once the system melts. It was proposed that these reactions could proceed through the intermediate formation of sodium diborate (Na4B2O5).
CU-SeeMe VR immersive desktop teleconferencing

Current video-conferencing systems provide a “video-ina-window” user interface. This paper presents a distributed video-conferencing system called CU-SeeMe VR that embeds live video and audio conferencing in a virtual space. This paper describes a prototype implementation of CU-SeeMe VR, including the user interface, system architecture, and a detailed look at the enabling technologies. Future directions and the implications of the virtual reality meta phor are discussed.
Pharmacokinetics of bupropion and its major basic metabolites in normal subjects after a single dose

The pharmacokinetics of bupropion (BUP) and its three major basic metabolites (the erythroamino alcohol [EB], the threoamino alcohol [TB], and the hydroxy [HB] metabolites) were characterized after a single, oral, 200 mg dose of BUP in six healthy men. Twenty-one sequential plasma samples for analysis by HPLC were drawn from each subject over the 56-hour period after dosing. Pharmacokinetic analyses were by noncompartmental methods. The mean elimination t½ values of BUP, TB, EB, and HB were 9.8, 19.8, 26.8, and 22.2 hours, respectively. The mean plasma AUCs of TB and HB were 2.4 and 10.3 times greater, respectively, than that for BUP. Because of the substantial presence of these metabolites in systemic circulation, further studies are recommended to understand further their roles in the clinical profile of this new antidepressant. Clinical Pharmacology and Therapeutics (1985) 38, 586–589; doi:10.1038/clpt.1985.228
Demonstration of antral inhibitory hormone by cross-transfusion

Summary Early studies are reported which demonstrate a humoral substance, presumably a hormone, liberated from the gastric antrum irrigated with acid, which acts to suppress acid production by the denervated fundic pouch.
Pursuit-evasion games in the presence of a line segment obstacle

This paper studies planar pursuit-evasion games in the presence of line segment obstacles that inhibit the motions of the players. The key achievement of the paper is to provide the dominance regions, where a point in the plane is said to be dominated by one of the players if that player is able to reach the point before the opposing player, regardless of the opposing player's actions. This paper also presents a study of the effects of introducing line segment obstacles by comparing the dominance regions in the presence of obstacles with the dominance regions in the absence of obstacles.
Analysis of Pallidotomy Lesion Positions Using Three-dimensional Reconstruction of Pallidal Lesions, the Basal Ganglia, and the Optic Tract

OBJECTIVE: To assess the position of radiofrequency pallidotomy lesions placed using microelectrode stimulation and cellular recordings in relation to a stereotactically defined starting point. Radiofrequency lesion locations were also evaluated in relation to the putamen, posterior limb of the internal capsule, and optic tract. METHODS: Magnetic resonance images obtained from 23 patients with Parkinson's disease who underwent pallidotomy at the University of Kansas Medical Center were analyzed. Using computerized techniques, lesion positions in relation to the midcommissural point and a hypothetical starting point were determined. Data segmentation and three-dimensional reconstruction of pallidal lesions, the internal capsule, and the optic tract allowed assessment of lesion position in relation to internal anatomy. Clinical outcome of pallidotomy was assessed using both the Unified Parkinson's Disease Rating Scale and the Dementia Rating Scale. RESULTS: Pallidal lesions were usually placed anterior and dorsal to the stereotactically defined starting point. The position of pallidal lesions in the men were observed, in four trials, to be significantly more dorsal than the lesions in the women. The outer zone of the lesion was usually adjacent to the internal capsule and the putamen and relatively close to the optic tract. The inner zone of the lesion was usually several millimeters removed from anatomic boundaries of the putamen, internal capsule, and optic tract. Patients achieved favorable outcomes, with reduced dyskinesias and off time and improvement of their Parkinsonian symptoms, as evidenced by clinical assessment, the Unified Parkinson's Disease Rating Scale, and the Dementia Rating Scale. CONCLUSION: Microelectrode stimulation and cellular recordings usually led to a final pallidotomy lesion position that deviated from the stereotactically defined starting point. The pallidotomy lesions in the men were observed to be more dorsal than the lesions in the women. Clinical outcomes were not correlated with either lesion location relative to the starting point or distances between the pallidal lesion and the putamen, internal capsule, or optic tract. Kinesthetically responsive cells may be localized generally more anterior and dorsal to the starting point (within the globus pallidus) and may be grouped variably from patient to patient in relation to other basal ganglia structures. Although the primary lesion site is most likely within the sensorimotor region of the globus pallidus internus, the more dorsal locations of responsive cell groups may indicate that some lesion sites may be localized within the globus pallidus externus.
Composition and variability of mountain gorilla diets in the Central Virungas

Data are presented here on the feeding ecology of wild mountain gorillas (Gorilla gorilla beringei) which were observed for approximately 2,400 hours over a 17-month period in the Parc National des Volcans, Rwanda. Aspects of the relationship between the composition, diversity, and temporal consistency of the gorillas' diet and spatial and temporal variability in food distribution patterns are described. Mountain gorillas are folivores that show considerable specialization on plant parts, species and families. This pattern is facilitated by the general richness of their habitat. Their environment is heterogeneous, and spatial variability in food distribution is more pronounced than temporal variability. The gorillas rely almost completely on perennially available foliage of herbs and vines. Their diet varies little in association with seasonal factors but varies markedly in space in association with variability in the vegetational composition of the habitat. Individuals in the main study group shared basically similar patterns of food choice. Different groups also shared a similar general pattern, although there were differences in detail that apparently resulted largely from vegetational contrasts between home ranges. The gorillas' behavioral responses to environmental complexity lend general support to recent ideas concerning the evolution of their social system.
Energy-Momentum Stability of Icosahedral Configurations of Point Vortices on a Sphere

We investigate the nonlinear stability of the icosahedral relative equilibrium configuration of point vortices on a sphere. The relative equilibrium problem is formulated as a problem of finding the nullspace of the configuration matrix that encodes the geometry of the icosahedron, as in Jamaloodeen and Newton (Proc. Royal Soc. A, Math. Phys. Eng. Sci. 462(2075):3277, 2006). The seven-dimensional nullspace of the configuration matrix, A, associated with the icosahedral geometry gives rise to a basis set of vortex strengths for which the icosahedron stays in relative formation, and we use these values to form the augmented Hamiltonian governing the stability. We choose the basis set made up of (i) one element with equal strength vortices on every vertex of the icosahedron (the uniform icosahedron); (ii) six elements made up of equal and opposite antipodal pairs. We start by proving nonlinear stability of the antipodal vortex pair (by direct methods). Following the methods laid out in Simo et al. (Arch. Ration. Mech. Anal. 115(1):15–59, 1991) and Pekarsky and Marsden (J. Math. Phys. 39(11):5894–5907, 1998) and more generally in Marsden and Ratiu (Introduction to Mechanics and Symmetry, 1999), we then combine our knowledge of the nullspace structure of A with the structure of the underlying Hamiltonian, and analyze the stability of the icosahedron using the energy-momentum method. Because the parameter space is large, we focus on the physically motivated and important case obtained by combining the basis elements into (i) the uniform icosahedron; (ii) a von Karman vortex street configuration of equal and opposite staggered, evenly spaced latitudinal rows equidistant from the equator (Chamoun et al. in Phys. Fluids 21:116603, 2009), and (iii) the North Pole–South Pole equal and opposite vortex pair. Stability boundaries in a three-parameter space are calculated for linear combinations of these grouped basis configurations.
Low-angle Vascular Access for Neurovascular Procedures Using the Arstasis AXERA Access Device

Abstract Purpose To evaluate the safety and efficacy of the Arstasis AXERA access device in patients undergoing neuroendovascular procedures. Materials and Methods A single-center retrospective study of 94 patients undergoing neurovascular procedures with the use of an AXERA arterial access device was performed. The procedures were performed with 5–6-F vascular sheaths, and hemostasis was obtained with manual compression. Results A total of 104 neurovascular procedures (81 diagnostic, 23 interventional) were performed in 94 subjects. Eighty-seven procedures (83%) were performed with a 5-F sheath, and 17 procedures (16%) used a 6-F sheath. Intravenous heparin was administered in 64 procedures (61%), and 32 patients (30%) were taking antiplatelet medications at the time of the procedure. Median time to hemostasis was 4 minutes with manual compression, and outpatients undergoing diagnostic angiography were permitted to ambulate at 1 hour. Complications occurred in a total of 3% of cases; these included one local hematoma (1%) and two failed procedures (2%). Conclusions The new AXERA arterial access device modifies the arterial puncture angle in an attempt to reduce manual compression and ambulation times.
Zone electrophoresis in silica gel and silica paste.

Abstract Silica gel and silica paste have been used as anticonvection media in zone electrophoresis. Rapid methods for preparing gels and pastes containing the appropriate electrophoretic buffer, and their use in zone electrophoresis, are given.
Electromagnetic field computation of open boundary problems by a semi-analytic approach

Field computation of electromagnetic devices involves the modeling of the exterior open boundary region. Discretization of the exterior region by finite differences or finite elements is cumbersome, uneconomical and computationally inefficient. A semi-analytic approach is described in this paper which combines closed form solution for the exterior region with a finite element T-Omega discretization of the interior region for axisymmetric geometries.
Future Trends in the Study and Treatment of Depression in Young Children

Abstract The controversy over the existence of depression in children has abated and the maturation process of further delineation of the disorder has begun. Future advances in understanding, identifying and treating young dysphoric children will be based on the ongoing work described in this journal issue. Suggested areas where these thrusts will appear include the early identification of depressed young children, delineation of the frequency and situations where the depression occurs, primary mental health prevention, more comprehensive therapeutic interventions and determination of biological correlates. Samplings of these “goodies” are provided.
Global gene expression profiling in PAI-1 knockout murine heart and kidney: molecular basis of cardiac-selective fibrosis.

Fibrosis is defined as an abnormal matrix remodeling due to excessive synthesis and accumulation of extracellular matrix proteins in tissues during wound healing or in response to chemical, mechanical and immunological stresses. At present, there is no effective therapy for organ fibrosis. Previous studies demonstrated that aged plasminogen activator inhibitor-1(PAI-1) knockout mice develop spontaneously cardiac-selective fibrosis without affecting any other organs. We hypothesized that differential expressions of profibrotic and antifibrotic genes in PAI-1 knockout hearts and unaffected organs lead to cardiac selective fibrosis. In order to address this prediction, we have used a genome-wide gene expression profiling of transcripts derived from aged PAI-1 knockout hearts and kidneys. The variations of global gene expression profiling were compared within four groups: wildtype heart vs. knockout heart; wildtype kidney vs. knockout kidney; knockout heart vs. knockout kidney and wildtype heart vs. wildtype kidney. Analysis of illumina-based microarray data revealed that several genes involved in different biological processes such as immune system processing, response to stress, cytokine signaling, cell proliferation, adhesion, migration, matrix organization and transcriptional regulation were affected in hearts and kidneys by the absence of PAI-1, a potent inhibitor of urokinase and tissue-type plasminogen activator. Importantly, the expressions of a number of genes, involved in profibrotic pathways including Ankrd1, Pi16, Egr1, Scx, Timp1, Timp2, Klf6, Loxl1 and Klotho, were deregulated in PAI-1 knockout hearts compared to wildtype hearts and PAI-1 knockout kidneys. While the levels of Ankrd1, Pi16 and Timp1 proteins were elevated during EndMT, the level of Timp4 protein was decreased. To our knowledge, this is the first comprehensive report on the influence of PAI-1 on global gene expression profiling in the heart and kidney and its implication in fibrogenesis and several other biological processes. The significance of these observations in the light of heart-specific profibrotic signaling and fibrogenesis are discussed.
Decision analysis in animal health programs: Merits and limitations

Abstract This paper reviews decision analysis as a method in animal health management programs. Because there are many possible management approaches to the solution of animal health problems, decision analysis is useful in making choices and delineating between them. It is flexible, easily understood and helpful in situations where outcomes cannot be predicted with certainty. The main limitations of this technique are the time involved in using it and the uncertainty about decision criteria, as well as the difficulty in establishing the value of model inputs and outputs and in deriving probabilities. These limitations, particularly the uncertainty about the decision criteria, are discussed in detail using a hypothetical example.
Arterial Blood Pressure Management during Carotid Endarterectomy and Early Cognitive Dysfunction

Background A common practice during cross-clamp of carotid endarterectomy (CEA) is to manage mean arterial pressure (MAP) above baseline to optimize collateral cerebral blood flow and reduce risk of ischemic stroke.
Oxygen radicals alter the cell membrane potential in a renal cell line (LLC-PK1) with differentiated characteristics of proximal tubular cells.

We employed a carbocyanine dye (1,1′,3,3,3′,3′-hexamethylindocarbocyanine iodide) to measure the plasma membrane potential of LLC-PK1 renal epithelial cells exposed to either xanthine oxidase-generated oxygen radicals or to hydrogen peroxide. Measurements were performed using a fluorescent-activated cell sorter to record fluorescence on a cell by cell basis. Initial exposure of cells to low concentrations of either H2O2 or xanthine oxidase resulted in a transient increase in membrane potential relative to control cells (P < 0.001), followed by an exponential decline in potential (P < 0.001). The addition of extracellular catalase diminished the H2O2-related decline in potential, consistent with a role for hydrogen peroxide in producing this effect. Pretreatment of cells with inhibitors of intracellular catalase and superoxide dismutase prior to exposure to xanthine oxidase caused an even larger decline in potential (P < 0.001). Cells could be partially protected from the radical-mediated loss of potential by incubating them in a hypertonic (400 mosmolal) environment during radical exposure. Similarly, the loss of membrane potential was increased after incubation of cells in a hypotonic (200 mosmolal) environment during radical exposure. These observations are consistent with a reduction in membrane potential effected by exposure to oxygen radicals (including superoxide anion and hydrogen peroxide). This reduction may be prevented, in part, by radical scavenging enzymes and by reducing the degree of cellular swelling in response to oxygen radical exposure.
Phase 1 study of tipifarnib in combination with imatinib for patients with chronic myelogenous leukemia in chronic phase after imatinib failure

BACKGROUND. The tolerability and efficacy of the combination of tipifarnib, an orally bioavailable nonpeptidomimetic farnesyl transferase inhibitor, and imatinib was investigated in patients with chronic myelogenous leukemia in chronic phase who had failed imatinib. METHODS. Twenty-six patients (13 [50%] with Abl kinase domain mutations) were treated. The initial dose level was tipifarnib at a dose of 300 mg twice daily and imatinib at a dose of 300 mg daily. Therapy was escalated following a ‘3 + 3’ phase 1 design and the maximum tolerated dose was defined as tipifarnib at a dose of 400 mg twice daily and imatinib at a dose of 400 mg daily. Therapy was administered for a median of 26 weeks (range, 3–150 weeks). RESULTS. Adverse events included diarrhea in 21 patients (81%) and nausea in 18 patients (69%), but were generally grade 2 or less (using the revised National Cancer Institute Common Toxicity Criteria). Grade 3–4 neutropenia and thrombocytopenia occurred in 11 patients (42%) and 8 patients (31%), respectively. Sixteen patients discontinued therapy (5 due to toxicity and 11 due to lack of response or disease progression). Hematologic responses were attained by 17 (68%) of 25 assessable patients. Nine patients (36%) also achieved a cytogenetic response (3 complete responses, 4 partial responses, and 2 minimal responses), including 4 patients harboring mutant Bcr-Abl tyrosine kinases. One patient bearing the highly imatinib-resistant T315I mutant achieved a partial cytogenetic response. The median response duration was 3 months (range, 2–30+ months). CONCLUSIONS. The combination of tipifarnib and imatinib is well tolerated and has activity against several Abl kinase domain mutants. Combinations of tipifarnib with more potent tyrosine kinase inhibitors warrant further investigation. © 2007 American Cancer Society.
A Conserved Mechanism of RNA Substrate Recognition and Cleavage by Fungal Dicers

Dicer is a central enzyme for processing small RNAs in RNA interference. It is able to cleave both hairpin and long double-stranded RNA precursors into microRNAs and small interfering RNAs respectively. While humans have one Dicer that is able to process both substrates, many organisms have multiple copies. Understanding how organisms with two Dicers chose specific RNAs for cleavage could give insight into how the human protein functions.We have turned to the thermophilic fungus Sporotrichum thermophile as a model system to purify stable Dicers for biochemical dissection. While the function of these two Dicers was thought to be partially redundant, our results show that they cleave different RNA substrates, similar to what is observed in the Drosophila melanogaster system. S. thermophile Dicer-1 dices hairpin precursor microRNAs faster than long double-stranded RNAs while S. thermophile Dicer-2 can only cleave perfect RNA duplexes accurately with the requirement for ATP. Removal of the helicase domain from Dicer-2 relieves the requirement of ATP for cleavage and allows the enzyme to process hairpin substrates. In addition, only Dicer-2 shows robust ATP hydrolysis in the presence of dsRNA and partial stimulation in the presence of single-stranded RNA or an RNA/DNA hybrid. The conserved function of these two Dicers may indicate a common mechanism used by eukaryotes to process small RNAs.
The activity of ribonuclease after digestion with carboxypeptidase

Abstract On incubating ribonuclease (RNase) with a crystalline carboxypeptides preparation, a number of amino acids were liberated. Of the 17 amino acids in the RNase molecule, all except cystine and proline have thus far been quantitatively determined as products of this hydrolytic reaction with no loss in the original activity of the RNase. During the early phases of the digestion, the activity of the RNase was increased. A separation of the digested from the undigested RNase molecules has been achieved by chromatography of the digests in secondary-butyl alcohol: water (3:1) at 3° C for 15 hours. The native RNase molecules did not migrate under these conditions and were quite stable, whereas the digested RNase molecules migrated and were less stable. The data obtained with this procedure correlates reasonably well with the amino acid determinations as a measure of the per cent of the RNase molecules digested. The extent of digestion thus far achieved approximates 80% of the RNase molecules present, with no loss in enzymic activity. It is calculated that approximately 15% of the amino acid residues which constitute RNase are not essential for the enzymic activity, but appear to be necessary for the stability of the molecule.
Associative and non-associative fentanyl tolerance in the rat: evaluation of cross tolerance with mu-and kappa-specific opioids.

Rationale: Associative tolerance to the analgesic effects of morphine is most pronounced when morphine is paired with a distinctive context at a long inter-dose interval (IDI). In contrast, morphine administered at a short IDI promotes the development of non-associative tolerance and disrupts the acquisition of associative tolerance. The impact of IDI on the development of associative tolerance to opioids other than morphine has not been investigated previously. Objectives: This research examined associative and non-associative tolerance to the analgesic effects of fentanyl in rats. Cross tolerance for these two forms of tolerance with morphine (mu- receptor agonist) and U50,488H (kappa-receptor agonist) analgesia was also investigated. Methods: Animals were given eight fentanyl injections (0.10 mg/kg) paired or unpaired with a distinctive context at either a 3-h (short) or 96-h (long) IDI. Subjects were then tested for tolerance in the distinctive context using the tail-flick procedure and dose–response curve methodology. Results: At the short IDI, animals developed non-associative tolerance to fentanyl that was receptor specific, i.e., cross tolerant with morphine analgesia but not with U50,488H analgesia. At the long IDI, fentanyl-tested animals displayed tolerance that appeared to be controlled primarily by associative processes. This associative form of tolerance was also receptor specific, displaying cross tolerance with morphine but not with U50,488H. Conclusions: The impact of IDI on the development of non- associative and associative fentanyl tolerance is consistent with findings obtained with morphine showing that conditions conducive to the development of non-associative tolerance disrupt the acquisition of associative tolerance. The cross-tolerance data, however, did not parallel previous research examining the cross-tolerance profiles of associative and non-associative morphine tolerance.
Neutron scattering study of Ar 36 monolayer films adsorbed on graphite

Diffraction of neutrons from $^{36}\mathrm{Ar}$ monolayers adsorbed on graphite basal planes indicates that an ordered, two-dimensional (2D) triangular lattice is formed at low temperature. The lattice constant is found to be slightly larger than that of the bulk 3D solid but significantly smaller than that of a registered $\sqrt{3}\ifmmode\times\else\texttimes\fi{}\sqrt{3}$ overlayer. Thermal expansion of the monolayer is anomalously large; up to 60 K the linear expansion is 4.5 times greater than in the 3D solid. There is no evidence of a sharp melting transition. Instead, the positional correlations (which extend to the full dimensions of the crystallite surfaces at low temperatures) are observed to decrease smoothly above 40 K, falling from 100 to 15 \AA{} at 80 K. Little if any positional order remains at temperatures where the nearest-neighbor distance in the monolayer matches that of a registered $\sqrt{3}\ifmmode\times\else\texttimes\fi{}\sqrt{3}$ phase. The spectrum of neutrons inelastically scattered from $^{36}\mathrm{Ar}$ monolayers in the nominally in-plane configuration can be reasonably well described at low temperatures by a 2D harmonic-phonon model while the scattering in the out-of-plane configuration seems to be best represented in terms of a resonant coupling of the monolayer film to out-of-plane collective motions of the graphite substrate. There is some evidence of renormalization of the in-plane transverse modes of the monolayer at higher temperatures; however, the in-plane longitudinal modes and the out-of-plane modes do not appear to be similarly affected.