gebhart/patrepeval huggingface dataset:
Learning deep features for dead and living breast cancer cell classification without staining (2021)

Automated cell classification in cancer biology is a challenging topic in computer vision and machine learning research. Breast cancer is the most common malignancy in women that usually involves phenotypically diverse populations of breast cancer cells and an heterogeneous stroma. In recent years, automated microscopy technologies are allowing the study of live cells over extended periods of time, simplifying the task of compiling large image databases. For instance, there have been several studies oriented towards building machine learning systems capable of automatically classifying images of different cell types (i.e. motor neurons, stem cells). In this work we were interested in classifying breast cancer cells as live or dead, based on a set of automatically retrieved morphological characteristics using image processing techniques. Our hypothesis is that live-dead classification can be performed without any staining and using only bright-field images as input. We tackled this problem using the JIMT-1 breast cancer cell line that grows as an adherent monolayer. First, a vast image set composed by JIMT-1 human breast cancer cells that had been exposed to a chemotherapeutic drug treatment (doxorubicin and paclitaxel) or vehicle control was compiled. Next, several classifiers were trained based on well-known convolutional neural networks (CNN) backbones to perform supervised classification using labels obtained from fluorescence microscopy images associated with each bright-field image. Model performances were evaluated and compared on a large number of bright-field images. The best model reached an AUC = 0.941 for classifying breast cancer cells without treatment. Furthermore, it reached AUC = 0.978 when classifying breast cancer cells under drug treatment. Our results highlight the potential of machine learning and computational image analysis to build new diagnosis tools that benefit the biomedical field by reducing cost, time, and stimulating work reproducibility. More importantly, we analyzed the way our classifiers clusterize bright-field images in the learned high-dimensional embedding and linked these groups to salient visual characteristics in live-dead cell biology observed by trained experts.
Pro‐inflammatory Maternal Cytokine Profile in Preterm Delivery (2003)

These data are suggestive of a maternal type 1 cytokine bias in PTD.
Projecting deep-subwavelength patterns from diffraction-limited masks using metal-dielectric multilayers (2008)

We utilize a metal-dielectric multilayer structure to generate deep-subwavelength one-dimensional and two-dimensional periodic patterns with diffraction-limited masks. The working wavelength and the pattern are set by the flexible design of the multilayer structure. This scheme is suitable to be applied to deep-subwavelength photolithography. As an example, we numerically demonstrate pattern periods down to 50nm under 405nm light illumination.
Dopamine receptors –<scp>IUPHAR R</scp>eview 13 (2014)

The variety of physiological functions controlled by dopamine in the brain and periphery is mediated by the D1, D2, D3, D4 and D5 dopamine GPCRs. Drugs acting on dopamine receptors are significant tools for the management of several neuropsychiatric disorders including schizophrenia, bipolar disorder, depression and Parkinson's disease. Recent investigations of dopamine receptor signalling have shown that dopamine receptors, apart from their canonical action on cAMP-mediated signalling, can regulate a myriad of cellular responses to fine-tune the expression of dopamine-associated behaviours and functions. Such signalling mechanisms may involve alternate G protein coupling or non-G protein mechanisms involving ion channels, receptor tyrosine kinases or proteins such as β-arrestins that are classically involved in GPCR desensitization. Another level of complexity is the growing appreciation of the physiological roles played by dopamine receptor heteromers. Applications of new in vivo techniques have significantly furthered the understanding of the physiological functions played by dopamine receptors. Here we provide an update of the current knowledge regarding the complex biology, signalling, physiology and pharmacology of dopamine receptors.
Implant platform switching concept: an updated review. (2009)

It was shown that platform switching helps to prevent crestal bone loss after implant placement and helps obtain satisfactory aesthetic results.
Preparation routes based on magnetron sputtering for tungsten disulfide (WS<sub>2</sub>) films for thin‐film solar cells (2008)

Abstract The semiconductor tungsten disulfide (WS 2 ) exhibits van der Waals bonding, crystallizes in a layer‐type structure and is of interest as an absorber layer for thin‐film solar cells. In this review article different preparation routes for WS 2 thin films, based on magnetron sputtering, are reviewed. Films prepared by direct magnetron sputtering, though exhibiting quite a good structural quality, are not or only poorly photoactive. This can be attributed to the generation of recombination centers, especially sulfur vacancies, during the ion bombardment of the films, due to the low defect‐formation energy of tungsten disulfide, an intrinsic property of transition metal dichalcogenides. A promising preparation route, which leads to photoactive WS 2 films, is a two‐step process, where, in a first step, a sulfur‐rich, X‐ray amorphous tungsten sulfide is deposited at low substrate temperatures onto a thin metal film (Ni, Co). This film sandwich is after wards annealed in an ampoule in a sulfur atmosphere or in flowing gas with a sufficient H 2 S partial pressure. From in‐situ transmission electron microscopy and energy‐dispersive X‐ray diffraction, it was found that the WS 2 film crystallization with a pronounced (001) texture is closely related to the formation of the liquid (eutectic) metal–sulfur phase. Based on these in‐situ investigations the growth of the 2‐dimensional WS 2 nanosheets from an amorphous WS 3+ x precursor can be described as an amorphous solid‐liquid‐crystalline solid process (SLS), somewhat similar to the well‐known vapor‐liquid‐solid (VLS) process for the growth of whiskers or nanorods and nanotubes. Research opportunities, to overcome current limitations for a broad use of WS 2 (and MoS 2 ) as thin‐film solar cell absorbers are given. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Resolvase-like recombination performed by the TP901-1 integrase The GenBank accession number for the sequence reported in this paper is Y15043. (2001)

The site-specific recombination system of temperate lactococcal bacteriophage TP901-1 is unusual in several respects. First, the integrase belongs to the family of extended resolvases rather than to the lambda integrase family and second, in the presence of this integrase, a 56 bp attP fragment is sufficient for efficient recombination with the chromosomal attB site in the host Lactococcus lactis subsp. cremoris MG1363. In the present work, this attB site was analysed and a 43 bp attB region was found to be the smallest fragment able to participate fully in recombination. In vitro studies showed that the TP901-1 integrase binds this 43 bp attB fragment, the 56 bp attP and a larger attP fragment with equal affinity. Mutational analysis of the 5 bp common core region (TCAAT) showed that the TC dinucleotide is essential for recombination, but not for binding of the integrase, whereas none of the last three bases are important for recombination. When a number of attL sites, obtained by recombination between an attB site containing a mutation in this TC dinucleotide and a wild-type attP site, were sequenced, a mix of sites with the wild-type or the mutated sequence was obtained. These results are consistent with the hypothesis that the TC dinucleotide constitutes the TP901-1 overlap region. A 2 bp overlap region has been observed in recombination reactions catalysed by all other members of the resolvase/invertase family tested so far. By selecting for attB sites with a decreased ability to participate in recombination, two bases located outside the core region of attB were shown to be involved in the in vitro binding of the TP901-1 integrase.
Backtesting (2015)

When evaluating a trading strategy, it is routine to discount the Sharpe ratio from a historical backtest. The reason is simple according to the authors: there is inevitable data mining by both the researcher and by other researchers in the past. In this article, the authors provide a statistical framework that systematically accounts for these multiple tests. They propose a method to determine the appropriate haircut for any given reported Sharpe ratio. They also provide a profit hurdle that any strategy needs to achieve in order to be deemed “significant.” <bold>TOPICS:</bold> <ext-link>Statistical methods</ext-link>, <ext-link>portfolio management/multi-asset allocation</ext-link>
A Novel Preparation of Degradable Scaffolds Using BSA Microbubbles as Porogen (2007)

Biodegradable scaffolds play a key role in contemporary medicine for tissue replacement as well as regeneration. Many degradable scaffold fabrication techniques have been developed. However, these scaffolds often hamper the growth of cells due to material hydrophobicity and/or lack of biocompatible protein coating. To overcome the common problems, in this study, the use of protein microbubbles as a porogen and drug/protein carrier to produce polymeric scaffolds with good porosity was conceptualized. Albumin bubbles were produced by sonicating bovine serum albumin in the presence of nitrogen gas. PLGA scaffolds were then prepared by thermally induced phase separation with the incorporation of protein microbubbles as porogens. SEM and cryosectioning of scaffold revealed the presence of open interconnected pores measuring around 100 to 150 mum size, which is suitable for cell migration into scaffold. This novel technique provides two distinct advantages. First, microbubbles are made of biological materials which can provide biocompatible protein coating on the pores throughout the scaffold. Second, apart from having produced scaffolds with larger pores compared to conventional methods, our novel scaffold also has the potential to function as a delivery mechanism for delivering chemokines and drugs into the polymeric matrix.
Prospective Biological Control Agents of Varroa destructor n. sp., an Important Pest of the European Honeybee, Apis mellifera (2001)

This paper reviews prospective biological control agents of the varroa mite, Varroa destructor n. sp. (Acari, Mesostigmata). This ectoparasite has caused severe damage to populations of the European honeybee, Apis mellifera , world-wide in recent years. To date, no promising natural enemies of varroa species have been identified on A. mellifera or its original host, Apis cerana . Therefore, biological control will probably require natural enemies from other hosts. The following groups of organisms were reviewed as potential biological control agents: predatory mites, parasitoids and entomopathogens (nematodes, protozoa, viruses, Bacillus thuringiensis , rickettsiae, and fungi). The candidate groups were ranked according to their lethality to Acari, likely ability to operate under the physical conditions of honeybee colonies, ease of targeting, and ease of mass-production. Preferential consideration was given to the natural enemies of Acari that occupy taxonomic groups close to varroa. Entomopathogenic fungi, which kill a wide range of acarine species, were identified as prime candidates for screening against varroa. Bacillus thuringiensi s also requires study, particularly strains producing novel toxins active against non-insect hosts. Entomopathogenic protozoa and nematodes show less potential for varroa control, but nonetheless warrant preliminary investigation. We consider predators, parasitoids, viruses and rickettsiae to have little potential to control varroa. Because the physical conditions within honeybee colonies are similar everywhere, it is very likely that a biological control agent of varroa could be used successfully throughout the world.
Method for Screening and MALDI-TOF MS Sequencing of Encoded Combinatorial Libraries (2007)

We describe a new method for encoded synthesis, efficient on-resin screening, and rapid unambiguous sequencing of combinatorial peptide libraries. An improved binary tag system for encoding peptide libraries during synthesis was designed to facilitate unequivocal assignment of isobaric residues by MALDI-TOF MS analysis. The improved method for encoded library synthesis was combined with a new versatile on-resin screening strategy that permitted multiple stages and types of screening to be employed successively on one library under mild conditions. The new method facilitated a combinatorial study of transglutaminase (TGase) enzyme substrate peptides, revealing new details of the effect of amino acid composition on TGase substrates. The approach was first demonstrated for an encoded library (130,321 compounds) of lysine pentapeptide substrates of TGase, synthesized using the "split-mix" method. The library was reacted on-resin with TGase enzyme and a soluble desthiobiotin labeled glutamine substrate. Initial screening was performed by adsorbing streptavidin-coated magnetic microparticles onto library beads, followed by magnetic separation. The differential binding affinities of desthiobiotin and biotin for streptavidin were exploited to release the magnetic microparticles and regenerate the desthiobiotin-labeled resin beads for further screening by flow-cytometry-based automated bead sorting, resulting in 345 beads that were sequenced by MALDI-TOF MS analysis. A second library consisted of encoded glutamine hexapeptide substrates, which was reacted on-resin with TGase enzyme and a soluble desthiobiotin-labeled cadaverine. Two-stage screening identified 267 glutamine peptides as TGase-reactive, of which 21 were further analyzed by solution-phase enzyme kinetics. Kinetic results indicated that the peptide PQQQYV from the library has a 68-fold greater substrate specificity than the best known glutamine substrate QQIV. The new encoding and screening strategies described here are expected to be broadly applicable to synthesis and screening of combinatorial peptide libraries in the future.
Lamb wave–based quantitative crack detection using a focusing array algorithm (2012)

Cracks are common defects in aluminum plate-like components that are in widespread use in aerospace, shipbuilding, and other industries. Ultrasonic detection using Lamb waves has proven to be an efficient method for crack detection and localization. However, quantitative information regarding crack size or orientation is of paramount importance for damage diagnosis and life prediction. In this article, employing a sparsely arranged piezoelectric sensor array, a quantitative crack detection and imaging approach using a Lamb wave–focusing array algorithm is developed and presented. Additionally, Lamb wave propagation on thin-wall plates and wave interaction with crack damage was studied using three-dimensional elastodynamic finite integration technique. The focusing array imaging algorithm was then developed and applied to both simulation and experimental data to generate intensity images of the structure under interrogation. Experimentally, wafer-type piezoelectric actuators/sensors are permanently installed on the testing structure to generate Lamb waves as well as to measure the waves propagating through the structures. Our results show that when applied to either experimental or simulated data, the focusing array algorithms yield images containing quantitative damage information. The results also demonstrate that three-dimensional elastodynamic finite integration technique can be used for future simulation-based investigations of sensing optimization for various damage scenarios.
First-principles study of Li ion diffusion in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">LiFePO</mml:mi></mml:mrow><mml:mrow><mml:mn>4</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math> (2004)

The diffusion mechanism of Li ions in the olivine ${\mathrm{LiFePO}}_{4}$ is investigated from first-principles calculations. The energy barriers for possible spatial hopping pathways are calculated with the adiabatic trajectory method. The calculations show that the energy barriers running along the $c$ axis are about 0.6, 1.2, and 1.5 eV for ${\mathrm{LiFePO}}_{4},$ ${\mathrm{FePO}}_{4},$ and ${\mathrm{Li}}_{0.5}{\mathrm{FePO}}_{4},$ respectively. However, the other migration pathways have much higher energy barriers resulting in very low probability of Li-ion migration. This means that the diffusion in ${\mathrm{LiFePO}}_{4}$ is one dimensional. The one-dimensional diffusion behavior has also been shown with full ab initio molecular dynamics simulation, through which the diffusion behavior is directly observed.
C3-OH of Amphotericin B Plays an Important Role in Ion Conductance (2015)

Amphotericin B (AmB) is the archetype for small molecules that form ion channels in living systems and has recently been shown to replace a missing protein ion transporter and thereby restore physiology in yeast. Molecular modeling studies predict that AmB self-assembles in lipid membranes with the polyol region lining a channel interior that funnels to its narrowest region at the C3-hydroxyl group. This model predicts that modification of this functional group would alter conductance of the AmB ion channel. To test this hypothesis, the C3-hydroxyl group was synthetically deleted, and the resulting derivative, C3deoxyAmB (C3deOAmB), was characterized using multidimensional NMR experiments and single ion channel electrophysiology recordings. C3deOAmB possesses the same macrocycle conformation as AmB and retains the capacity to form transmembrane ion channels, yet the conductance of the C3deOAmB channels is 3-fold lower than that of AmB channels. Thus, the C3-hydroxyl group plays an important role in AmB ion channel conductance, and synthetic modifications at this position may provide an opportunity for further tuning of channel functions.
Wind noise at microphones within and across hearing aids at wind speeds below and above microphone saturation (2011)

The variation of wind noise at hearing-aid microphones with wind speed, wind azimuth, and hearing-aid style was investigated. Comparisons were made across behind-the-ear (BTE) and completely-in-canal (CIC) devices, and between microphones within BTE devices. One CIC device and two BTE devices were placed on a Knowles Electronics Manikin for Acoustic Research. The smaller BTE device had vented plastic windshields around its microphone ports while the larger BTE device had none. The microphone output signals were digitally recorded in wind generated at 0, 3, 6, and 12 m/s at 8 wind azimuths. The microphone output signals were saturated at 12 m/s with wind-noise levels of up to 116 dB SPL at the microphone output. Wind-noise levels differed by up to 12 dB between microphones within the same BTE device, and across BTE devices by up to 6 or 8 dB for front or rear microphones, respectively. On average, wind-noise levels were lowest with the CIC device and highest at the rear microphone of the smaller BTE device. Engineering and clinical implications are discussed.
Design of efficient, broadband single-element (20-80 MHz) ultrasonic transducers for medical imaging applications (2003)

This paper discusses the design, fabrication, and testing of sensitive broadband lithium niobate (LiNbO3) single-element ultrasonic transducers in the 20-80 MHz frequency range. Transducers of varying dimensions were built for an f# range of 2.0-3.1. The desired focal depths were achieved by either casting an acoustic lens on the transducer face or press-focusing the piezoelectric into a spherical curvature. For designs that required electrical impedance matching, a low impedance transmission line coaxial cable was used. All transducers were tested in a pulse-echo arrangement, whereby the center frequency, bandwidth, insertion loss, and focal depth were measured. Several transducers were fabricated with center frequencies in the 20-80 MHz range with the measured -6 dB bandwidths and two-way insertion loss values ranging from 57 to 74% and 9.6 to 21.3 dB, respectively. Both transducer focusing techniques proved successful in producing highly sensitive, high-frequency, single-element, ultrasonic-imaging transducers. In vivo and in vitro ultrasonic backscatter microscope (UBM) images of human eyes were obtained with the 50 MHz transducers. The high sensitivity of these devices could possibly allow for an increase in depth of penetration, higher image signal-to-noise ratio (SNR), and improved image contrast at high frequencies when compared to previously reported results.
FIELD SYNTHESIS IN INHOMOGENEOUS MEDIA: JOINT CONTROL OF POLARIZATION, UNIFORMITY AND SAR IN MRI B<sub>1</sub>-FIELD (2011)

The homogeneity of the amplitude of one of the polarizations of the RF field B 1 is a crucial issue in Magnetic Resonance Imaging (MRI), and several methods have been proposed for enhancing this uniformity ("Shimming"). The existing approaches aim at controlling the homogeneity of B + 1 and limiting the Specific Absorption Rate (SAR) of the RF field by independently controlling magnitude and phase of individual excitation currents in MRI scanners, either birdcage or TEM coil system. A novel approach is presented here which allows a joint control of B + 1 uniformity, SAR, and purity of polarization of the total RF B 1 field. We propose a convex optimization procedure with convex constraints, and special attention has been devoted to the issue of convexity of the proposed functional. The method is applied to MRI brain imaging; numerical tests have been performed on a realistic head model at low, medium, and high RF field in order to assess the effectiveness of the proposed method. We found that maintaining a specific polarization plays an important role also in maintaining the homogeneity of B + 1 amplitude.
Recommended procedures for the safety performance evaluation of highway appurtenances (1981)

Procedures are presented for conducting vehicle crash tests and in-service evaluation of roadside appurtenances. Appurtenances covered by these procedures are (1) longitudinal barriers such as bridge rails, guardrails, median barriers, transitions, and terminals; (2) crash cushions; and (3) breakaway or yielding supports for signs and luminaires. The purpose of the procedures is to promote the uniform testing and in-service evaluation of roadside appurtenances so that highway engineers may confidently compare safety performance of two or more designs that are tested and evaluated by different agencies. These procedures are guidelines that describe how an appurtenance should be tested and evaluated; the selection of specific new, existing, or modified appurtenances for testing and evaluation, the establishment of acceptable performance criteria are policy decisions that are beyond the purview of this document. These procedures are devised to subject highway appurtenances to severe vehicle impact conditions rather than to typical or the more predominant highway situations. For vehicle crash testing, specific impact conditions are presented for vehicle mass, speed, approach angle, and point on appurtenance to be hit. Vehicle types considered are mini-compact, subcompact, and standard size passenger sedans, intercity and utility type buses, and tractor-trailer cargo trucks. Impact speeds range from 20 to 60 mph (32 to 97 kph), and approach angles vary from 0 to 25 deg. Three appraisal factors are presented for evaluating the crash test performance: structural adequacy, occupant risk, and vehicle after-collision trajectory. Depending on the appurtenance's function, it should contain, redirect, or permit controlled penetration of the impacting vehicle in a predictable manner to satisfy structural adequacy requirements.