Miracle-dz/UniFAR-FTUs huggingface dataset:
New Ray-Driven System Matrix for Small-Animal Pinhole-SPECT with Detector Blur, Geometric Response and Edge Penetration Modeling

Iterative reconstruction of pinhole SPECT projection data acquired in preclinical animal imaging research benefits from modeling physical parameters of the imaging process. In this study, we developed a ray-driven system model that accounts for detector blur, the geometric response and edge penetration of the pinhole. GATE 2.2.0/GEANT 4 Monte Carlo simulations utilizing a tungsten knife-edge pinhole with an aperture diameter of 2 mm were applied to measure the pinhole point spread function (PSF) and to generate pinhole SPECT projection images of 2 different resolution phantoms (2.0 mm and 1.8 mm). The new Monte Carlo based PSF with edge penetration was compared to an ideal pinhole model without edge penetration. To conserve memory, the ray-driven system matrix was computed for one angle and rotation was performed by interpolating the radiotracer distribution within the object space. Detector symmetry and a bitwise incremental storage scheme were utilized for further reduction of memory requirements. Two system setups with a magnification of 7.2times and 2times were studied. Reconstruction results show an improvement in image quality and reconstruction resolution for the new pinhole PSF model. In the low magnification system operated at its resolution limits these improvements are more pronounced than in the high magnification system. The newly implemented ray-driven reconstruction method has great flexibility and offers to be a platform for further improvements such as non-uniform attenuation and scatter correction, and integration of detector misalignments in the system matrix.
Non spiral and spiral (helical) flow patterns in stenoses. In vitro observations using spin and gradient echo magnetic resonance imaging (MRI) and computational fluid dynamic modeling.

AIM Physiological blood flow patterns are themselves poorly understood despite their impact on arterial disease. Stable spiral (helical) laminar flow (SLF) has been observed in normal subjects. The purpose of the present study is to develop a method of magnetic resonance (MR) flow pattern visualization and to analyze spiral and non-spiral flow patterns with and without luminal narrowing in vitro. The flow conditions were then modeled using computational fluid dynamics (Star-CD). METHODS Laminar integrity was examined in a flow-rig using spin and gradient echo magnetic resonance imaging (MRI) in non-stenosed and stenosed conduits in the presence of non-spiral and spiral flow. RESULTS No difference was observed in a non-stenosed conduit between non-spiral and spiral flow. In the presence of a stenosis spiral flow preserves flow velocity coherence whereas non-spiral flow increasingly lost coherence beginning proximal to the stenosis. Computational fluid dynamic modeling of the in vitro experiment showed marked differences between the 2 flow patterns. Non-spiral flow produced greater inwardly directed forces just beyond the stenosis and greater outward pressures at more distal sites. The near wall turbulent energy was up to 700% less with spiral flow over non-spiral flow beyond the stenosis. CONCLUSIONS Spiral flow appears to offer clear flow profile stabilizing advantages over non-spiral flow, by significantly reducing the turbulence caused by a stenosis. Spiral flow also produces lower forces acting on the vessel wall.
Test Battery Designed to Quickly and Safely Assess Diverse Indices of Neuromuscular Function After Unweighting

Spiering, BA, Lee, SMC, Mulavara, AP, Bentley, JR, Buxton, RE, Lawrence, EL, Sinka, J, Guilliams, ME, Ploutz-Snyder, LL, and Bloomberg, JJ. Test battery designed to quickly and safely assess diverse indices of neuromuscular function after unweighting. J Strength Cond Res 25(2): 545-555, 2011-Adequately describing the functional consequences of unweighting (e.g., bed rest, immobilization, spaceflight) requires assessing diverse indices of neuromuscular function (i.e., strength, power, endurance, central activation, force steadiness). Additionally, because unweighting increases the susceptibility of muscle to damage, testing should consider supplementary safety features. The purpose of this study was to develop a test battery for quickly assessing diverse indices of neuromuscular function. Commercially available exercise equipment was modified to include data acquisition hardware (e.g., force plates, position transducers) and auxiliary safety hardware (e.g., magnetic brakes). Ten healthy, ambulatory subjects (31 ± 5 years, 173 ± 11 cm, 73 ± 14 kg) completed a battery of lower- and upper-body neuromuscular function tests on 3 occasions separated by at least 48 hours. The battery consisted of the following tests, in order: (1) knee extension central activation, (2) knee extension force steadiness, (3) leg press maximal strength, (4) leg press maximal power, (5) leg press power endurance, (6) bench press maximal strength, (7) bench press force steadiness, (8) bench press maximal power, and (9) bench press power endurance. Central activation, strength, rate of force development, maximal power, and power endurance (total work) demonstrated good-to-excellent measurement reliability (SEM = 3-14%; intraclass correlation coefficient [ICC] = 0.87-0.99). The SEM of the force steadiness variables was 20-35% (ICC = 0.20-0.60). After familiarization, the test battery required 49 ± 6 minutes to complete. In conclusion, we successfully developed a test battery that could be used to quickly and reliably assess diverse indices of neuromuscular function. Because the test battery involves minimal eccentric muscle actions and impact forces, the potential for muscle injury has likely been reduced.
Clustering or Co-Agglomeration? A Love-for-Variety Approach

We develop a simple partial-equilibrium model of endogenous city structure formation. No production externalities are at work, the only two forces shaping the spatial configurations of the city being love for variety (on the consumer side) and seeking for a better access to the market (on the firm side). We show that, unlike in existing models of a similar nature, our model generates clustering rather than co-agglomeration. Namely, if there are few firms relative to the urban population size, then firms tend to cluster at the city center, while consumers choose to reside on the outskirts. Otherwise, the opposite holds. Although a continuum of equilibrium city structures may emerge, we show that all spatial equilibria are segregated. In addition, the market outcome features spatial price dispersion, even though our framework does not involve imperfect information and search costs on the consumer side.
N-(Adamantan-1-yl)-1,2,3,4-tetrahydroisoquinoline-2-carbothioamide

In the title compound, C20H26N2S, the N-containing six-membered ring adopts a boat conformation and the dihedral angle between the thiocarbamide group and the benzene ring is 49.67 (9)°. An intramolecular C—H⋯S hydrogen bond generates an S(6) ring motif. The N—H group is sterically hindered and there are no significant intermolecular interactions beyond van der Waals contacts.
Conformational flexibility of a model protein upon immobilization on self‐assembled monolayers

The present study reports on the retention of conformational flexibility of a model allosteric protein upon immobilization on self‐assembled monolayers (SAMs) on gold. Organothiolated SAMs of different compositions were utilized for adsorptive and covalent attachment of bovine liver glutamate dehydrogenase (GDH), a well‐characterized allosteric enzyme. Sensitive fluorimetric assays were developed to determine immobilization capacity, specific activity, and allosteric properties of the immobilized preparations as well as the potential for repeated use and continuous catalytic transformations. The allosteric response of the free and immobilized forms towards ADP, L‐leucine and high concentrations of NAD+, some of the well‐known activators for this enzyme, were determined and compared. The enzyme immobilized by adsorption or chemical binding responded similarly to the activators with a greater degree of activation, as compared to the free form. Also loss of activity involving the two immobilization procedures were similar, suggesting that residues essential for catalytic activity or allosteric properties of GDH remained unchanged in the course of chemical modification. A recently established method was used to predict GDH orientation upon immobilization, which was found to explain some of the experimental results presented. The general significance of these observations in connection with retention of native properties of protein structures upon immobilization on SAMs is discussed. Biotechnol. Bioeng. 2008;100: 19–27. © 2007 Wiley Periodicals, Inc.
Cognitive outcome and clinically silent thromboembolic events after coiling of asymptomatic unruptured intracranial aneurysms.

BACKGROUND Thromboembolic events are the most common complication after coiling of unruptured intracranial aneurysms (UIAs). However, it remains unclear whether these clinically silent ischemic lesions (CSILs) have any clinical significance. OBJECTIVE To evaluate cognitive outcome after coil embolization of asymptomatic UIAs and its relationship with CSILs after the procedure. METHODS We prospectively enrolled 40 UIA patients who showed no new focal neurological deficit after coil embolization. CSILs were assessed with diffusion-weighted imaging (DWI) within 1 day after the procedure. A battery of neuropsychological tests was performed 3 times: preoperatively and postoperatively at 1 and 4 weeks after coil embolization. RESULTS The incidence of cognitive impairment after coiling in patients with UIAs was 44% (17 of 39) at 1 week and 19% (7 of 37) at 4 weeks after coil embolization. DWI within 1 day after coil embolization revealed that 60% of patients (24 of 40) showed CSILs. However, no significant difference was found in any mean cognitive scores or in the number of cognitively impaired variables between patients with and without CSILs at weeks 1 and 4. Additional correlation analysis revealed no correlations between the number of CSILs on DWI and the cognitive sum z score at both 1 and 4 weeks. CONCLUSION Exhaustive neuropsychological evaluation of UIA patients who underwent coil embolization demonstrated recovery or improvements from baseline cognitive function after 4 weeks, although some patients still showed cognitive deficits at 4 weeks after the procedure. However, we found no statistically significant relationship between the presence and number of CSILs on DWI and cognitive changes after the procedure.
De Novo Purine Biosynthesis in Intact Cells of Cucurbita pepo.

The capacity of intact cells of roots excised from summer squash plants (Cucurbita pepo L. cv Early Prolific Straightneck) to synthesize purine nucleotides de novo was investigated. Evidence that purine nucleotides are synthesized de novo included: (a) demonstration of the incorporation of [1-(14)C]glycine, [2-(14)C]glycine, NaH(14)CO(3), and H(14)COONa into total adenine nucleotides; (b) observation that the addition of azaserine or aminopterin, known inhibitors of de novo purine synthesis in other organisms, blocked the incorporation of these precursors into adenine nucleotides; and (c) demonstration that the purine ring synthesized from these precursors was labeled in a manner consistent with the pathway for de novo purine biosynthesis found in microorganisms and animal tissues. Under optimal conditions, the activity of this pathway in roots excised from 2-day-old squash plants was 244 +/- 13 nanomoles (mean +/- standard error, n = 17) NaH(14)CO(3) incorporated into summation operatorAde (the sum of the adenine nucleotides, nucleoside and free base) per gram tissue during the 3-hour incubation period.The possible occurrence of alternative enzymic reactions for the first steps of de novo purine biosynthesis was also investigated. No conclusive evidence was obtained to support the operation of alternative enzymic reactions in the intact cell of C. pepo.
A method to measure cardiac autophagic flux in vivo

Autophagy, a highly conserved cellular mechanism wherein various cellular components are broken down and recycled through lysosomes, has been implicated in the development of heart failure. However, tools to measure autophagic flux in vivo have been limited. Here, we tested whether monodansylcadaverine (MDC) and the lysosomotropic drug chloroquine could be used to measure autophagic flux in both in vitro and in vivo model systems. Using HL-1 cardiac-derived myocytes transfected with GFP-tagged LC3 to track changes in autophagosome formation, autophagy was stimulated by mTOR inhibitor rapamycin. Administration of chloroquine to inhibit lysosomal activity enhanced the rapamycin-induced increase in the number of cells with numerous GFP-LC3-positive autophagosomes. The chloroquine-induced increase of autophagosomes occurred in a dose-dependent manner between 1 µM and 8 µM, and reached a maximum 2 hour after treatment. Chloroquine also enhanced the accumulation of autophagosomes in cells stimulated with hydrogen peroxide, while it attenuated that induced by Bafilomycin A1, an inhibitor of V-ATPase that interferes with fusion of autophagosomes with lysosomes. The accumulation of autophagosomes was inhibited by 3-methyladenine, which is known to inhibit the early phase of the autophagic process. Using transgenic mice expressing mCherry-LC3 exposed to rapamycin for 4 hr, we observed an increase in mCherry-LC3-labeled autophagosomes in myocardium, which was further increased by concurrent administration of chloroquine, thus allowing determination of flux as a more precise measure of autophagic activity in vivo. MDC injected 1 hr before sacrifice colocalized with mCherry-LC3 puncta, validating its use as a marker of autophagosomes. This study describes a method to measure autophagic flux in vivo even in non-transgenic animals, using MDC and chloroquine.
Applications of multislice computed tomography in coronary artery disease

Multislice computed tomography (MSCT) provides high accuracy for noninvasive assessment of coronary artery disease (CAD). The introduction of the latest computed tomography (CT) technology allows comprehensive evaluation of various aspects of CAD, including the coronary calcium score, coronary artery stenoses, bypass patency, and myocardial function. Other applications, such as plaque characterization, first‐pass perfusion imaging, and viability imaging using delayed contrast enhancement, are still under development and may demonstrate clinical utility in the future. Further improvements in CT hardware and imaging protocols are expected that may result in improved coronary artery imaging, new applications, and a significant reduction of radiation dose. J. Magn. Reson. Imaging 2007;26:14–22. © 2007 Wiley‐Liss, Inc.
Selective modulation of motor cortical plasticity during voluntary contraction of the antagonist muscle

A fundamental approach for resolving motor deficits in patients suffering from various neurological diseases is to improve the impaired cortical function through the modulation of plasticity. In order to advance clinical practice in this regard, it is necessary to better understand the interactions that occur between functional neuromuscular activity and the resulting cortical plasticity. This study tested whether the voluntary contraction of an antagonist muscle modulates the plasticity‐like effect of continuous theta burst stimulation (cTBS) recorded from the agonist. The effects of various opposing torques produced by the antagonist were also measured. As a result, the suppressing effect of cTBS was enhanced by mild antagonist contraction, whereas effortful antagonist contraction suspended the plasticity caused by cTBS. In contrast, the antagonist contractions right after cTBS did not significantly influence the effect of cTBS. The results indicate that the antagonist activity alters the effect of cTBS, especially in protocols with synchronous magnetic stimulation and antagonist contraction. Such modulation on cTBS may be through a reciprocal mechanism within the motor cortex, although the spinal regulation of the motoneuronal pool cannot be fully excluded. The present findings are beneficial for elucidating the mechanism of neuromuscular control and for resolving related neurological disorders.
Consideration of Kaolinite Interference Correction for Quartz Measurements in Coal Mine Dust

Kaolinite interferes with the infrared analysis of quartz. Improper correction can cause over- or underestimation of silica concentration. The standard sampling method for quartz in coal mine dust is size selective, and, since infrared spectrometry is sensitive to particle size, it is intuitively better to use the same size fractions for quantification of quartz and kaolinite. Standard infrared spectrometric methods for quartz measurement in coal mine dust correct interference from the kaolinite, but they do not specify a particle size for the material used for correction. This study compares calibration curves using as-received and respirable size fractions of nine different examples of kaolinite in the different correction methods from the National Institute for Occupational Safety and Health Manual of Analytical Methods (NMAM) 7603 and the Mine Safety and Health Administration (MSHA) P-7. Four kaolinites showed significant differences between calibration curves with as-received and respirable size fractions for NMAM 7603 and seven for MSHA P-7. The quartz mass measured in 48 samples spiked with respirable fraction silica and kaolinite ranged between 0.28 and 23% (NMAM 7603) and 0.18 and 26% (MSHA P-7) of the expected applied mass when the kaolinite interference was corrected with respirable size fraction kaolinite. This is termed “deviation,” not bias, because the applied mass is also subject to unknown variance. Generally, the deviations in the spiked samples are larger when corrected with the as-received size fraction of kaolinite than with the respirable size fraction. Results indicate that if a kaolinite correction with reference material of respirable size fraction is applied in current standard methods for quartz measurement in coal mine dust, the quartz result would be somewhat closer to the true exposure, although the actual mass difference would be small. Most kinds of kaolinite can be used for laboratory calibration, but preferably, the size fraction should be the same as the coal dust being collected.
Occipital nerve stimulation in the treatment of medically intractable SUNCT and SUNA.

BACKGROUND Short-lasting unilateral neuralgiform headache attacks with conjunctival injection and tearing (SUNCT) or with cranial autonomic symptoms (SUNA) are primary headaches characterized by frequent attacks of severe headaches in association with cranial autonomic features. Patients with chronic SUNCT or SUNA have unremitting symptoms that necessitate prolonged use of medical preventive treatments, many of which are prone to causing side effects. They can be medically intractable, in which case neurally destructive or cranially invasive surgical treatments can be offered, though these have hitherto yielded conflicting results. Occipital nerve stimulation (ONS) offers a nondestructive and relatively low risk surgical alternative. OBJECTIVE To assess the efficacy and safety of ONS in chronic, medically intractable SUNCT and SUNA patients. STUDY DESIGN Prospective open-label study. METHODS Nine medically intractable, chronic SUNCT and SUNA patients were implanted with electrodes for bilateral occipital nerve stimulation. Data were collected prospectively for pre- and postimplantation headache characteristics, including frequency, intensity and duration of attacks. Diaries were used to assess headache improvement. RESULTS At a median follow-up of 38 months (range 24-55 months), all but one patient reported substantial improvement. Four patients became pain-free, 3 were almost pain-free (96 - 98% improvement), and one had a marked reduction in attack frequency and severity (81% improvement). After an initial rapid improvement, the maximum benefit of ONS was attained after a lag of a few months. Device malfunction was followed by recurrence or worsening of the attacks within a few days in most patients. Adverse events included lead migration, exposure of the electrode, and pain due to muscle recruitment over the leads. One patient developed hemicrania continua one month after implantation and was successfully treated with indomethacin. CONCLUSION ONS appears to offer an effective and safe treatment option, without significant morbidity, for medically intractable SUNCT and SUNA. Given the variable results with cranially invasive or neurally destructive surgery, ONS might be considered the surgical treatment of choice for medically intractable SUNCT and SUNA.
Sensitivity to Reflection and Translation is Modulated by Objectness

The salience of a transformation between a pair of contours depends on the type of transformation (eg a reflection or a translation) and also on figure – ground organisation. Reflection is most salient when both contours belong to the same surface, and translation is most salient when they do not connect a surface. These findings are based on reaction time (RT). Here I replicate and extend them by measuring both RT and sensitivity. The figure – ground relations were changed unambiguously by using stereograms. I compared reflection and translation when they were present within a surface or across surfaces (experiment 1), and within an object or a hole (experiments 2 – 4). Holes are interesting because they are not objects, but their presence does not increase the number of total objects in the scene. The within-surface advantage for reflection was present in all experiments. There was a between-surface advantage for translation in experiment 1 but there was no hole advantage for translation in experiments 2 – 4. Thus the effect of context, ie objectness, on detection of regularity is a robust and general phenomenon present in every experiment, but the type of interaction differs for reflection and translation.
Exploring the perspective of midwives involved in offering serum screening for Down's syndrome in Northern Ireland.

AIMS To explore the perspective of midwives offering serum screening for Down's syndrome. BACKGROUND Previous literature has indicated that the offer and discussion of prenatal serum screening tests with women is complex, and health professionals may influence women's decisions to accept or decline screening. Midwives are usually the key professional to offer serum screening for Down's syndrome in the UK but their perspective is relatively neglected in the literature. DESIGN An explorative qualitative interview study with 15 midwives employed in a maternity unit in Northern Ireland involved in offering prenatal screening to pregnant women. Data were collected from 1 July 2005-31 October 2005. METHODS A focused ethnographic approach was used to explore the perspective of midwives. RESULTS Midwives reported difficulty in explaining the test to women and felt unable to provide the necessary information to adequately inform women within their appointment time. The test offered (the triple test) and potential pathway of subsequent care, were identified as sources of professional and personal conflict by midwives. The expectation that midwives would provide a universal offer of Down's syndrome serum screening but be unable to support women regarding termination of pregnancy also created dissonance. CONCLUSIONS The feasibility of proceeding with a universal serum screening programme for Down's syndrome is questionable in countries which legally or culturally oppose termination of pregnancy. Professionals practising within environments such as this experience conflict in their role, which affects communication with women when discussing screening tests. RELEVANCE TO CLINICAL PRACTICE As midwives are often, the primary health professional providing information to women, it is important that midwives are key participants in ongoing planning and discussions about screening policy to ensure programmes are implemented successfully.