Miracle-dz/UniFAR-FTUs huggingface dataset:
Fine Needle Aspiration Cytology of Primary Pulmonary Meningioma Associated with Minute Meningotheliallike Nodules

BACKGROUND Pulmonary meningioma is an unusual tumor located in the lung. Minute pulmonary meningotheliallike nodules are also uncommon tumor-like lesions found at the pleuropulmonary level as solitary or multiple nodules. The association of both entities is described in a recent report. CASE A 58-year-old, male smoker without pathology underwent radiologic study before a surgical procedure. A peripheral nodule was found in the left lower lobe of the lung with benign characteristics. Fine needle aspiration cytology was performed under computed tomography guidance. Cytologic examination showed features of transitional meningioma and other lesions near the tumor. Minute pulmonary meningotheliallike nodules were also present. CONCLUSION A diagnosis of meningioma should be considered when there is a combination of scanty material, whorls composed of concentrically arranged cells and isolated cells with intranuclear inclusions. The simultaneous presence of meningioma and meningotheliallike nodules corroborates the unifying hypothesis of their common origin and the nature of these rare pulmonary lesions.
Ni–Au core–shell nanowires: synthesis, microstructures, biofunctionalization, and the toxicological effects on pancreatic cancer cells

The nickel (Ni)–gold (Au) core–shell nanowires (CSNWs) were synthesized by a combination of electrodeposition and electroless-plating methods. This template based, electroless-plating approach can control the size and shape of nanostructures by adjusting the experimental conditions. The X-ray diffraction, transmission electron microscopy (TEM), and TEM line-scanning and elemental mapping analyses were applied to investigate the formation and microstructure of the core–shell nanostructure. Also using a focused ion beam lift-out technique provides an important route to prove the inner microstructural details of the CSNWs. The optical characterization showed the surface plasmon absorption shifting with electroless-plating time, whereas the magnetic measurements revealed the shape anisotropy and soft ferromagnetic properties of the NWs. Using the strong interaction between biotin and streptavidin, streptavidin–fluorescent dyes were successfully conjugated on the biotinylated CSNWs. This was then analyzed for the surface plasmon resonance effect and Stokes' shifting viaultraviolet-visible and photoluminescence spectroscopy measurements and imaged by confocal scanning laser microscopy. Proliferating cancer cells (Panc-1) have been used to study the toxicological effects of both Ni–Au CSNWs and Ni NWs in a living cell system: the cellular responses to nanowire effects were observed. Ni–Au CSNWs appeared to be tolerated more by this cell line at the dose tested than Ni NWs.
Digging into Lipid Membrane Permeation for Cardiac Ion Channel Blocker d-Sotalol with All-Atom Simulations

Interactions of drug molecules with lipid membranes play crucial role in their accessibility of cellular targets and can be an important predictor of their therapeutic and safety profiles. Very little is known about spatial localization of various drugs in the lipid bilayers, their active form (ionization state) or translocation rates and therefore potency to bind to different sites in membrane proteins. All-atom molecular simulations may help to map drug partitioning kinetics and thermodynamics, thus providing in-depth assessment of drug lipophilicity. As a proof of principle, we evaluated extensively lipid membrane partitioning of d-sotalol, well-known blocker of a cardiac potassium channel Kv11.1 encoded by the hERG gene, with reported substantial proclivity for arrhythmogenesis. We developed the positively charged (cationic) and neutral d-sotalol models, compatible with the biomolecular CHARMM force field, and subjected them to all-atom molecular dynamics (MD) simulations of drug partitioning through hydrated lipid membranes, aiming to elucidate thermodynamics and kinetics of their translocation and thus putative propensities for hydrophobic and aqueous hERG access. We found that only a neutral form of d-sotalol accumulates in the membrane interior and can move across the bilayer within millisecond time scale, and can be relevant to a lipophilic channel access. The computed water-membrane partitioning coefficient for this form is in good agreement with experiment. There is a large energetic barrier for a cationic form of the drug, dominant in water, to cross the membrane, resulting in slow membrane translocation kinetics. However, this form of the drug can be important for an aqueous access pathway through the intracellular gate of hERG. This route will likely occur after a neutral form of a drug crosses the membrane and subsequently re-protonates. Our study serves to demonstrate a first step toward a framework for multi-scale in silico safety pharmacology, and identifies some of the challenges that lie therein.
Controlled reshaping and plasmon tuning mechanism of gold nanostars

Anisotropic multi-branched gold nanoparticles exhibit intense localized electromagnetic fields at their tips/edges and hence have attracted significant attention in surface enhanced Raman scattering (SERS), as well as in bio-sensing applications. Our quest for such complex hyper-branching in gold nanostructures has revealed that even the addition of a simple base (like NaOH) to the precursor reaction mixture enhances the fine tuning/reshaping of the 3D star/flower-like gold nanostars with controlled precision right from the nucleation stage. With increasing the basicity of the reaction mixture, the two strongly localized surface plasmon resonance (LSPR) peaks of the gold nanostars essentially merge into a broad singular peak, effectively indicating the steady transition from (non)planar structures to conventional spheroidal nanostructures, as confirmed by the transmission electron microscopy (TEM) measurements. Such pH induced size/shape transitions of gold nanostructures were monitored kinetically in detail through correlated molecular spectroscopic measurements nuclear magnetic resonance, fourier transformation infrared spectroscopy and X-ray photoelectron spectroscopy (NMR, FTIR and XPS), for the first time to the best of our knowledge, which ascertains a rational paradigm in better understanding the complex polyvinylpyrrolidone (PVP) functionality for its simultaneous reducing, as well as stabilizing action, in precisely controlling the anisotropic gold nanostructure growth mechanism and further exploiting this functionality in utilizing these as-formed extremely stable colloidal gold dispersions for various specific plasmonic applications.
DYNAMIC KC TESTING OF STRUCTURAL STEEL

Fracture toughness \IK\N\Dc\N values were determined for structural steels in thickness and at loading rates and temperatures representative of service conditions for many civil structures, with particular interest centered on bridges. The measurements were made using notched-bend tests with specimens 3-in. deep, 12-in. long, the full plate thickness, and with notches fatigue precracked to a depth of 1 in. The \IK\N\Dc\N values were computed using the observed maximum load and a crack size plasticity adjustment. A cushioned drop-weight loading technique provided loading times of 0.5 x 10\u-³ sec to 2 x 10\u-³ sec. Strain gages on the loading tup of the free-falling weight permitted load-time recordings for the tests. The limitation on useful \IK\N\Dc\N determinations due to specimen size was approximately 1.25 (in.)¹\u/² in. times the applicable yield strength of the steel. The test results presented are for temperatures ranging from –120° to 60°F and include, for comparison, results obtained with loading times of 1 - 3 sec.
Alexithymia, immunity and cervical intraepithelial neoplasia: replication.

BACKGROUND In a previous study [Psychother Psychosom 1994;61:199-204] we investigated the relationship between alexithymia, carcinogenesis and immunity in a group of women who were unconscious sufferers from precancerous lesions of the cervix (CIN). The results of this study showed a high level of association between alexithymia and CIN and, an even more interesting fact, between alexithymia and reduced levels of immunity. METHODS The aim of the present study is to check the results of the previous one by testing a larger group (43 women affected by cervical dysplasia and 67 healthy women) and by the use of a self-administered test for detection of alexithymia, the well-validated Twenty-Item Toronto Alexithymia Scale (TAS-20). RESULTS The results confirm that women suffering from CIN have higher average TAS-20 ratings (55) than normal women (47.32) and that the level of alexithymia detected in the group of women suffering from dysplasia (42.5%) is higher than that of normal women (12.85%). Moreover, the present study confirms that alexithymic women have lower rates of a number of lymphocyte subsets than non-alexithymic women. CONCLUSIONS This study fully confirms the results of our previous work and those of a number of other studies: (1) personality might be one of the factors jointly responsible for the outbreak of cancer; (2) the immune system appears to play an important part as a mediator between personality and cancer.
Rapid estimate of solid volume in large tuff cores using a gas pycnometer

A thermally insulated, rigid-volume gas pycnometer system has been developed. The pycnometer chambers have been machined from solid PVC cylinders. Two chambers confine dry high-purity helium at different pressures. A thick-walled design ensures minimal heat exchange with the surrounding environment and a constant volume system, while expansion takes place between the chambers. The internal energy of the gas is assumed constant over the expansion. The ideal gas law is used to estimate the volume of solid material sealed in one of the chambers. Temperature is monitored continuously and incorporated into the calculation of solid volume. Temperature variation between measurements is less than 0.1{degrees}C. The data are used to compute grain density for oven-dried Apache Leap tuff core samples. The measured volume of solid and the sample bulk volume are used to estimate porosity and bulk density. Intrinsic permeability was estimated from the porosity and measured pore surface area and is compared to in-situ measurements by the air permeability method. The gas pycnometer accommodates large core samples (0.25 m length x 0.11 m diameter) and can measure solid volume greater than 2.20 cm{sup 3} with less than 1% error.
CytoRich Liquid-Based Cervical Cytologic Test

OBJECTIVE To eliminate the disadvantages and inherent bias of split-sample studies by evaluating the relative performance of monolayers and conventional cervical cytologic smears in a single laboratory through evaluation of two large and similar, randomly derived patient groups from the same geographical and demographically similar population. STUDY DESIGN Two randomly created large patient groups from the same population were evaluated using conventional microscopic screening. One group was tested using the conventional smear. The other was evaluated using only the new liquid-preservative-based CytoRich preparation (AutoCyte, Inc., Elon College, North Carolina, U.S.A.) with the intended direct-tovial cell collection method. Results were then compared statistically as to disease detection and sample adequacy. RESULTS Age comparisons between the two groups demonstrated equivalency. Specimen adequacy was greatly improved in the group tested with the CytoRich monolayer preparation. The monolayer group also demonstrated a significant reduction in ambiguous atypical squamous cells of undetermined significance/atypical glandular cells of undetermined significance diagnoses and a threefold increase in the detection of squamous intraepithelial lesion and cancer. CONCLUSION Routine use of homogeneous monolayer preparations as a total replacement for the conventional smear can be expected to dramatically improve specimen adequacy and sensitivity of the conventional smear alone. Direct-to-vial use of the new monolayer preparation generated significantly better results than those shown in any of the earlier split-sample trials.
Synthesis and Densification of Transparent Magnesium Aluminate Spinel by SPS Processing

Mixtures of elementary oxides, MgO-Al 2 O 3 , were used to fabricate transparent polycrystalline magnesium aluminate spinel specimens by means of the spark plasma sintering technique. A sintering aid, 1 wt% of LiF, was added to the mixed powder. The presence of the additive promotes the synthesis of spinel that starts at 900°C and is completed at 1100°C. The LiF additive wets spinel on its melting and promotes densification, which is completed at 1600°C. LiF vapor plays a cardinal role in eliminating residual carbon contamination and in the fully dense state, allows attaining a 78% level of optical transmittance. The optimal conditions for achieving adequate transparency were determined and the role of the LiF addition in the various stages of the process is discussed.
Recent development of push–pull conjugated polymers for bulk-heterojunction photovoltaics: rational design and fine tailoring of molecular structures

Bulk-heterojunction polymer solar cells have emerged as an attractive type of cost-effective solar energy–electrical power transforming device. Recently, great progress in the development of new photo-harvesting materials and device optimizations have been achieved in this field, resulting in the significant improvement of the power conversion efficiencies of polymer solar cells from around 1% to higher than 8.0%. The rational design and fine tailoring of the molecular structures of donor polymers significantly contributed to these prominent advances. Among all kinds of donor polymers, push–pull conjugated polymers, which consist of alternating electron-rich and electron-deficient units have been most extensively developed and have dominated the library of donor materials for polymer solar cells, because their intrinsic optical and electronic properties can be readily tuned to the desired situation by controlling the intramolecular charge transfer from donor unit to acceptor unit. This review provides a brief overview of the recent development of push–pull conjugated polymers and their application in solar cells. The relationships between the materials' chemical structures and properties, such as absorption spectra, energy levels, mobilities and photovoltaic behaviors, were also discussed.
Variations Among Medicare Beneficiaries Living in Different Settings

Older people with complex health issues and needs for functional support are increasingly living in different types of residential care environments as alternatives to nursing homes. This study aims to compare the demographics and health-care expenditures of Medicare beneficiaries by the setting in which they live: nursing homes, residential care settings, and at home using data from the 2002 to 2010 Medicare Current Beneficiary Study (MCBS), a nationally representative survey of the Medicare population. All Medicare beneficiaries aged 65 years or older who participated in the fall MCBS interview (years 2002–2010) and were alive for the full year (N = 83,507) were included in the sample. We found that there is a gradient in health status, physical and cognitive functioning, and health-care use and spending across settings. Minority elderly are overrepresented in facilities and underrepresented in alternative living settings.
Discovery of pan autophagy inhibitors through a high-throughput screen highlights macroautophagy as an evolutionarily conserved process across 3 eukaryotic kingdoms

ABSTRACT Due to the involvement of macroautophagy/autophagy in different pathophysiological conditions such as infections, neurodegeneration and cancer, identification of novel small molecules that modulate the process is of current research and clinical interest. In this work, we developed a luciferase-based sensitive and robust kinetic high-throughput screen (HTS) of small molecules that modulate autophagic degradation of peroxisomes in the budding yeast Saccharomyces cerevisiae. Being a pathway-specific rather than a target-driven assay, we identified small molecule modulators that acted at key steps of autophagic flux. Two of the inhibitors, Bay11 and ZPCK, obtained from the screen were further characterized using secondary assays in yeast. Bay11 inhibited autophagy at a step before fusion with the vacuole whereas ZPCK inhibited the cargo degradation inside the vacuole. Furthermore, we demonstrated that these molecules altered the process of autophagy in mammalian cells as well. Strikingly, these molecules also modulated autophagic flux in a novel model plant, Aponogeton madagascariensis. Thus, using small molecule modulators identified by using a newly developed HTS autophagy assay, our results support that macroautophagy is a conserved process across fungal, animal and plant kingdoms.
Porous polymeric scaffolds for bone regeneration

Abstract Solvent casting/particulate leaching has been used to synthesize highly porous polymeric scaffolds of controlled pore size, based on poly(methyl methacrylate) (PMMA) and poly(ε-caprolactone) (PCL). Obtained structures have a total porosity of c. 60%, with good interconnections between the pores. Porous scaffolds prepared using the greatest size of NaCl particles have the best mechanical properties. Both PMMA- and PCL-based materials can be sterilized by ionizing radiation. In the case of PCL-based scaffolds, irradiation causes cross-linking of polymer chains, which leads to an improvement of the mechanical properties of the scaffold. The compressive elastic modulus for non-porous samples increases with irradiation dose from 1.5 MPa for 0 kGy to 1.9 MPa for 280 kGy. Preliminary in vitro studies indicate good biocompatibility of both materials.
Real-time analysis of the role of Ca2+ in flagellar movement and motility in single sea urchin sperm

Eggs of many marine and mammalian species attract sperm by releasing chemoattractants that modify the bending properties of flagella to redirect sperm paths toward the egg. This process, called chemotaxis, is dependent on extracellular Ca2+. We used stroboscopic fluorescence imaging to measure intracellular Ca2+ concentration ([Ca2+]i) in the flagella of swimming sea urchin sperm. Uncaging of cyclic GMP induced Ca2+ entry via at least two distinct pathways, and we identified a nimodipine-sensitive pathway, compartmentalized in the flagella, as a key regulator of flagellar bending and directed motility changes. We found that, contrary to current models, the degree of flagellar bending does not vary in proportion to the overall [Ca2+]i. Instead we propose a new model whereby flagella bending is increased by Ca2+ flux through the nimodipine-sensitive pathway, and is unaffected by [Ca2+]i increases through alternative pathways.
Frequency of Microplastics in Mesopelagic Fishes from the Northwest Atlantic

Microplastics are a ubiquitous pollutant in our seas today and are known to have detrimental effects on a variety of organisms. Over the past decade numerous studies have documented microplastic ingestion by marine species with more recent investigations focussing on the secondary impacts of microplastic ingestion on ecosystem processes. However, few studies so far have examined microplastic ingestion by mesopelagic fish which are one of the most abundant pelagic groups in our oceans and through their vertical migrations are known to contribute significantly to the rapid transport of carbon and nutrients to the deep sea. Therefore, any ingestion of microplastics by mesopelagic fish may adversely affect this cycling and may aid in transport of microplastics from surface waters to the deep-sea benthos. In this study microplastics were extracted from mesopelagic fish under forensic conditions and analysed for polymer type utilising micro-Fourier Transform Infrared Spectroscopy (micro-FTIR) analysis. Fish specimens were collected from depth (300 - 600 m) in a warm-core eddy located in the Northwest Atlantic, 1200 km due west of Newfoundland during April and May 2015. In total, 233 fish gut contents from seven different species of mesopelagic fish were examined. An alkaline dissolution of organic materials from extracted stomach contents was performed and the solution filtered over a 0.7 µm borosilicate filter. Filters were examined for microplastics and a subsample originating from 35 fish was further analysed for polymer type through micro-FTIR analysis. 73% of all fish contained plastics in their gut contents with Gonostoma denudatum having the highest ingestion rate (100 %) followed by Serrivomer beanii (93 %) and Lampanyctus macdonaldi (75 %). Overall, we found a much higher occurrence of microplastic fragments, mainly polyethylene fibres, in the gut contents of mesopelagic fish than previously reported. Stomach fullness, species and the depth at which fish were caught at, were found to have no effect on the amount of microplastics found in the gut contents. However, these plastics were similar to those sampled from the surface water. Additionally, using forensic techniques we were able to highlight that fibres are a real concern rather than an artefact of airborne contamination.
Synthesizing programs that expose performance bottlenecks

Software often suffers from performance bottlenecks, e.g., because some code has a higher computational complexity than expected or because a code change introduces a performance regression. Finding such bottlenecks is challenging for developers and for profiling techniques because both rely on performance tests to execute the software, which are often not available in practice. This paper presents PerfSyn, an approach for synthesizing test programs that expose performance bottlenecks in a given method under test. The basic idea is to repeatedly mutate a program that uses the method to systematically increase the amount of work done by the method. We formulate the problem of synthesizing a bottleneck-exposing program as a combinatorial search and show that it can be effectively and efficiently addressed using well known graph search algorithms. We evaluate the approach with 147 methods from seven Java code bases. PerfSyn automatically synthesizes test programs that expose 22 bottlenecks. The bottlenecks are due to unexpectedly high computational complexity and due to performance differences between different versions of the same code.
Semantic locality and context-based prefetching using reinforcement learning

Most modern memory prefetchers rely on spatio-temporal locality to predict the memory addresses likely to be accessed by a program in the near future. Emerging workloads, however, make increasing use of irregular data structures, and thus exhibit a lower degree of spatial locality. This makes them less amenable to spatio-temporal prefetchers. In this paper, we introduce the concept of Semantic Locality, which uses inherent program semantics to characterize access relations. We show how, in principle, semantic locality can capture the relationship between data elements in a manner agnostic to the actual data layout, and we argue that semantic locality transcends spatio-temporal concerns. We further introduce the context-based memory prefetcher, which approximates semantic locality using reinforcement learning. The prefetcher identifies access patterns by applying reinforcement learning methods over machine and code attributes, that provide hints on memory access semantics. We test our prefetcher on a variety of benchmarks that employ both regular and irregular patterns. For the SPEC 2006 suite, it delivers speedups as high as 2.8× (20% on average) over a baseline with no prefetching, and outperforms leading spatio-temporal prefetchers. Finally, we show that the context-based prefetcher makes it possible for naive, pointer-based implementations of irregular algorithms to achieve performance comparable to that of spatially optimized code.