gebhart/patrepeval huggingface dataset:
Recognizing Pitfalls in Virtual Screening: A Critical Review (2012)

The aim of virtual screening (VS) is to identify bioactive compounds through computational means, by employing knowledge about the protein target (structure-based VS) or known bioactive ligands (ligand-based VS). In VS, a large number of molecules are ranked according to their likelihood to be bioactive compounds, with the aim to enrich the top fraction of the resulting list (which can be tested in bioassays afterward). At its core, VS attempts to improve the odds of identifying bioactive molecules by maximizing the true positive rate, that is, by ranking the truly active molecules as high as possible (and, correspondingly, the truly inactive ones as low as possible). In choosing the right approach, the researcher is faced with many questions: where does the optimal balance between efficiency and accuracy lie when evaluating a particular algorithm; do some methods perform better than others and in what particular situations; and what do retrospective results tell us about the prospective utility of a particular method? Given the multitude of settings, parameters, and data sets the practitioner can choose from, there are many pitfalls that lurk along the way which might render VS less efficient or downright useless. This review attempts to catalogue published and unpublished problems, shortcomings, failures, and technical traps of VS methods with the aim to avoid pitfalls by making the user aware of them in the first place.
Measurement of elastic properties in fluid using high bandwidth atomic force microscope probes (2013)

High bandwidth interdigitated probes have enabled high-speed mapping of elastic properties of various samples in air. To extend this capability to imaging in fluids, we implemented a signal processing scheme to calculate the tip-sample interaction force as well as elastic properties from high-frequency photodiode signals. Using this method, we imaged a styrene-(ethylene/butylene)-styrene copolymer sample submerged in water and obtained spatial maps of elastic properties as well as maps of higher harmonics of the motion of the tip. We observed that multiple physical quantities contribute to the contrast observed in the phase and higher harmonic images.
Application of statistical element selection to 3D integrated AlN MEMS filters for performance correction and yield enhancement (2015)

By 3D integration of an array of 12 nominally identical AlN MEMS sub-filters with a CMOS switching matrix and application of statistical element selection to the same system, we have built a self-healing filter offering 495 unique filter responses and a tuning range of 500 kHz for both center frequency and bandwidth. The demonstrated system enables correction of intrinsic, fabrication-induced variation in filter performance that would otherwise constitute a severe yield limitation to the manufacture of standalone filters.
Identification and Characterization of the Putative Fusion Peptide of the Severe Acute Respiratory Syndrome-Associated Coronavirus Spike Protein (2005)

Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) is a newly identified member of the family Coronaviridae and poses a serious public health threat. Recent studies indicated that the SARS-CoV viral spike glycoprotein is a class I viral fusion protein. A fusion peptide present at the N-terminal region of class I viral fusion proteins is believed to initiate viral and cell membrane interactions and subsequent fusion. Although the SARS-CoV fusion protein heptad repeats have been well characterized, the fusion peptide has yet to be identified. Based on the conserved features of known viral fusion peptides and using Wimley and White interfacial hydrophobicity plots, we have identified two putative fusion peptides (SARS(WW-I) and SARS(WW-II)) at the N terminus of the SARS-CoV S2 subunit. Both peptides are hydrophobic and rich in alanine, glycine, and/or phenylalanine residues and contain a canonical fusion tripeptide along with a central proline residue. Only the SARS(WW-I) peptide strongly partitioned into the membranes of large unilamellar vesicles (LUV), adopting a beta-sheet structure. Likewise, only SARS(WW-I) induced the fusion of LUV and caused membrane leakage of vesicle contents at peptide/lipid ratios of 1:50 and 1:100, respectively. The activity of this synthetic peptide appeared to be dependent on its amino acid (aa) sequence, as scrambling the peptide rendered it unable to partition into LUV, assume a defined secondary structure, or induce both fusion and leakage of LUV. Based on the activity of SARS(WW-I), we propose that the hydrophobic stretch of 19 aa corresponding to residues 770 to 788 is a fusion peptide of the SARS-CoV S2 subunit.
Seven-probe scintillator dosimeter for treatment verification in HDR-brachytherapy (2023)

Purpose: We introduce a novel concept of a compact multiprobe scintillator detector and demonstrate its applicability in HDR-brachytherapy. Our fabricated seven-probe system is sufficiently narrow to be inserted in a brachytherapy needle or in a catheter. Methods: Our multiprobe detection system results from the parallel implementation of a miniaturized scintillator detector at the end of a bundle of seven fibers. The resulting system, which is narrower than 320 microns, is tested with a MicroSelectron 9.1 Ci Ir-192 HDR afterloader, in a water phantom. The detection signals from all seven probes are simultaneously read with an sCMOS camera (at a rate of 0.06 s). The camera is coupled to a chromatic filter to cancel Cerenkov signal induced within the fibers upon exposure. By implementing an aperiodic array of six scintillating cells along the bundle axis (one probe is kept bare to assess the stem effect), we first determine the range of inter-probe spacings leading to optimal source tracking accuracy. Then, three different source tracking algorithms involving sequentially or simultaneously all the scintillating probes are tested and compared. In each case, dwell positions are assessed from dose measurements and compared to the treatment plan. Dwell time is also determined and compared to the treatment plan. Results: The optimum inter-probe spacing for an accurate source tracking ranges from 15 mm to 35 mm. The optimum detection algorithm consists of adding the readout signals from all detector probes. In that case, the error to the planned dwell positions is of 0.01+/-0.14 mm and 0.02+/-0.29 mm at spacings between the source and detector axes of 5.5 and 40 mm, respectively. Using this approach, the average deviations to the expected dwell time are of -0.006+/-0.009 s and -0.008+/-0.058 s, at spacings between source and probe axes of 5.5 mm and 20 mm, respectively.
Contrast-to-noise ratio optimization for a prototype phase-contrast computed tomography scanner (2015)

In the field of biomedical X-ray imaging, novel techniques, such as phase-contrast and dark-field imaging, have the potential to enhance the contrast and provide complementary structural information about a specimen. In this paper, a first prototype of a preclinical X-ray phase-contrast CT scanner based on a Talbot-Lau interferometer is characterized. We present a study of the contrast-to-noise ratios for attenuation and phase-contrast images acquired with the prototype scanner. The shown results are based on a series of projection images and tomographic data sets of a plastic phantom in phase and attenuation-contrast recorded with varying acquisition settings. Subsequently, the signal and noise distribution of different regions in the phantom were determined. We present a novel method for estimation of contrast-to-noise ratios for projection images based on the cylindrical geometry of the phantom. Analytical functions, representing the expected signal in phase and attenuation-contrast for a circular object, are fitted to individual line profiles of the projection data. The free parameter of the fit function is used to estimate the contrast and the goodness of the fit is determined to assess the noise in the respective signal. The results depict the dependence of the contrast-to-noise ratios on the applied source voltages, the number of steps of the phase stepping routine, and the exposure times for an individual step. Moreover, the influence of the number of projection angles on the image quality of CT slices is investigated. Finally, the implications for future imaging purposes with the scanner are discussed.
Voids and vacancy-type defects in SiO2/GaN structures probed by monoenergetic positron beams (2020)

Voids in SiO2 films deposited on GaN were probed by using monoenergetic positron beams. The films were fabricated on GaN substrates by using plasma-enhanced chemical vapor deposition. The size and density of the voids in the films increased up to an annealing temperature of 800 °C and then decreased at 1000 °C. The observed annealing behaviors of the voids were attributed to the desorption of impurities incorporated during the deposition process and the shrinkage of the Si–O matrix by high-temperature annealing. Vacancy-type defects were introduced into the GaN substrate after 1000 °C annealing in O2 atmosphere due to the diffusion of Ga from the substrate to the SiO2 film. No out-diffusion of Ga into the SiO2 film was observed for the annealing in N2 atmosphere. Thus, the observed out-diffusion of Ga was attributed to the enhanced oxidation of GaN during the annealing in O2 atmosphere. The diffusion of positrons implanted into the GaN substrate toward the SiO2 film was suppressed by annealing, suggesting a decrease in the negative charges in the SiO2 film or near the SiO2/GaN interface.
Dense Depth Posterior (DDP) from Single Image and Sparse Range (2019)

We present a deep learning system to infer the posterior distribution of a dense depth map associated with an image, by exploiting sparse range measurements, for instance from a lidar. While the lidar may provide a depth value for a small percentage of the pixels, we exploit regularities reflected in the training set to complete the map so as to have a probability over depth for each pixel in the image. We exploit a Conditional Prior Network, that allows associating a probability to each depth value given an image, and combine it with a likelihood term that uses the sparse measurements. Optionally we can also exploit the availability of stereo during training, but in any case only require a single image and a sparse point cloud at run-time. We test our approach on both unsupervised and supervised depth completion using the KITTI benchmark, and improve the state-of-the-art in both.
Performance Comparison Between Cyclic Shift and Block Spreading CDMA Using MLD with Channel Coding Information for Uplink Control Signals (2009)

This paper presents a comparison based on the block error rate (BLER) performance of cyclic shift (CS) and block spreading (BS) CDMA using codeword maximum likelihood detection (MLD) and joint MLD that take advantage of the channel coding information for the Physical Uplink Control Channel (PUCCH) in the Evolved UTRA uplink. We first present the BLER performance of CSand that for BS-CDMA using codeword MLD and joint MLD in the GSM Typical Urban, ITU-R Vehicular-A, and Pedestrian-B channel models. Then, we compare the BLER performance between CS-and BS-CDMA in an exponentially decayed power delay profile model to focus on large delay spread environments in a macrocell. Simulation results show that although BS-CDMA is superior to CS-CDMA due to a lower required received signal-to-noise power ratio (SNR) in small delay spread environments, CS-CDMA using joint MLD is more appropriate than BS-CDMA to support small-to-large delay spread environments in a unified manner.
Towards high-power XUV generation using an Yb-Based enhancement cavity (2009)

A common method of producing extreme-ultraviolet (XUV) radiation relies on nonlinear processes in gas atoms. Focusing intense femtosecond laser pulses on a gas target leads to the generation of high-order harmonics (HHG) of the fundamental radiation, reaching into the XUV or even X-ray range. External enhancement cavities constitute a highly efficient approach to HHG [1–3]. A MHz repetition rate laser system feeds its pulses into a passive resonator containing the focus for the gas target. After each pass through the focus, the non-converted portion of the light pulse is coherently overlapped with the successive pulse from the laser. This way, a power enhancement of several hundreds and intensities of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">13</sup> W/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> or more, which are necessary for HHG, can be reached in the cavity focus. As opposed to traditional HHG schemes based on low repetition rate amplifiers, in the case of MHz passive cavities the frequency comb structure of the seeding laser is expected to be transferred to and usable in the XUV range. So far, XUV generation enhancement cavities based on Ti:Sapphire [1,2] and Yb [3] lasers have been demonstrated.
Table S3 from Phase I Dose-Escalation and -Expansion Study of Telisotuzumab (ABT-700), an Anti–c-Met Antibody, in Patients with Advanced Solid Tumors (2023)

&lt;p&gt;FISH analysis or ctDNA analysis for MET amplification was performed on enrolled patients (N=45).&lt;/p&gt;
Relativistic description of quark-antiquark bound states. Spin-independent treatment (1989)

We present the results of a detailed study of light- and heavy-quark-antiquark bound states in the context of the reduced Bethe-Salpeter equation with static vector and scalar interactions. In the present paper, we consider the spin-averaged spectra. Spin effects are considered in a separate paper. We find that this approach, although apparently successful for the heavy-quark $b\overline{b}$ and $c\overline{c}$ states, fails for the $s\overline{s}$, $l\overline{l}$, and light-heavy states. The reasons for the failure are intrinsic to the method, as we discuss. Difficulties are already evident for the $c\overline{c}$ states.
Optical emission‐based phantom to verify coincidence of radiotherapy and imaging isocenters on an MR‐linac (2021)

The phantom was capable of measuring both the MRI and radiotherapy treatment isocenters. This method has the potential to be of use in MR-linac commissioning, and could be streamlined to be valuable in daily constancy checks of isocenter coincidence.
Molecular Determinants of the Bittersweet Janus Head of Steviol Glycosides fromStevia rebaudiana(Bert.) Bertoni (2015)

To identify the structural requirements for the organoleptic properties of steviol glycosides from Stevia rebaudiana, we correlated in vivo data obtained from human psychophysical experiments with in vitro data from cell-based taste receptor assays. While sensory evaluation demonstrated the structural features causing the sweet and bitter taste of these sweeteners, screening experiments with the 25 human bitter taste receptors revealed hTAS2R4 and hTAS2R14 to be the general sensors for bitter taste elicited by steviol glycosides. These results help to navigate breeding of Stevia rebaudiana and improve postharvest downstream processing toward the production of preferentially sweet and least bitter tasting Stevia extracts.
Fabrication and characterization of CMOS-compatible integrated tungsten heaters for thermo-optic tuning in silicon photonics devices (2014)

We present fabrication and characterization of tungsten (W) heaters for thermo-optic tuning on silicon-on-insulator (SOI).The waferscale fabrication of these thermal tuners was done using standard complementary metal-oxide-semiconductor (CMOS) back-end fabrication materials and processes.Static and transient characterizations of heaters are presented.
Cutting Edge: Loss of T Cell RIAM Precludes Conjugate Formation with APC and Prevents Immune-Mediated Diabetes (2017)

Rap1-interacting adaptor molecule (RIAM) is a Rap1 effector that mediates the recruitment of talin to integrins, thereby supporting their activation. In this study, we investigated the role of RIAM in an adoptive transfer model for type I diabetes and report that RIAM expression in T cells is necessary for diabetes development. Loss of RIAM did not prevent lymphocyte recruitment to draining lymph nodes 24 h after transfer, but it was required for Ag-driven proliferation and cytotoxic killing. RIAM is recruited to immune synapses along with talin and LFA-1, and loss of RIAM profoundly suppresses Ag-dependent conjugate formation in primary naive and effector T cells. These data identify the requirement of RIAM for formation of immunological synapses and in resulting T cell functions in autoimmunity. Moreover, because RIAM-null mice are healthy, fertile, and display no bleeding abnormalities, our results identify RIAM and its regulators as potential targets for therapies of T cell-mediated autoimmunity.
Power-aware microarchitectures: Design, modeling and metrics (2005)

Presents a collection of slides covering the following: power breakdown data; power-performance efficiency metrics; and hierarchical power modeling (levels of abstraction).
Hint-based acceleration of Web proxy caches (2002)

Numerous studies show that proxy cache miss ratios are typically at least 40%-50%. This paper proposes and evaluates a new approach for improving the throughput of proxy caches by reducing cache miss overheads. An embedded system able to achieve significantly better communications performance than a traditional proxy filters the requests directed to a proxy cache, forwarding the hits to the proxy and processing the misses itself. This system, called a Proxy Accelerator, uses hints of the proxy cache content and may include a main memory cache for the hottest objects. Scalability with the Web proxy cluster size is achieved by using several accelerators. We use analytical models and trace-based simulations to study the benefits and the implementation tradeoffs of this new approach. A single proxy accelerator node in front of a four-node Web proxy improves the cost-performance ratio by about 40%. Implementation choices that do not affect the overall hit ratio are available.
Follicular Dendritic Cell Sarcoma: Ultrastructural and Immunohistochemical Studies. (2000)

A rare case of follicular dendritic cell (FDC) sarcoma is reported. A 71-year-old woman was admitted for evaluation of constipation. Computerized tomography showed cervical, supraclavicular, retroperitoneal, and paraaortic lymphadenopathies. Histological findings from a cervical lymph node revealed Hodgkin's disease at first. But tumors that arose both in the cervical and the left interscapular regions during the chemotherapy were immunohistochemically confirmed to be of follicular dendritic cell origin. The ultrastructural findings were consistent with those of FDC sarcoma. FDC sarcoma is a rare nonlymphoid cell-derived malignant tumor originating from the lymphoid tissue. The diagnosis of FDC sarcoma is most accurately established by immunohistochemical methods, using its specific markers.
Robust initialization of 2D-3D image registration using the projection-slice theorem and phase correlation (2010)

The authors have shown that the initialization method based on the projection-slice theorem and phase correlation yields adequate initializations for existing registration methods, thereby substantially enlarging the capture range of these methods.
Wurtzite phase control for self-assisted GaAs nanowires grown by molecular beam epitaxy (2021)

The accurate control of the crystal phase in III-V semiconductor nanowires (NWs) is an important milestone for device applications. Although cubic zinc-blende (ZB) GaAs is a well-established material in microelectronics, the controlled growth of hexagonal wurtzite (WZ) GaAs has thus far not been achieved successfully. Specifically, the prospect of growing defect-free and gold catalyst-free wurtzite GaAs would pave the way towards integration on silicon substrate and new device applications. In this article, we present a method to select and maintain the WZ crystal phase in self-assisted NWs by molecular beam epitaxy. By choosing a specific regime where the NW growth process is a self-regulated system, the main experimental parameter to select the ZB or WZ phase is the V/III flux ratio. Using an analytical growth model, we show that the V/III flux ratio can be finely tuned by changing the As flux, thus driving the system toward a stationary regime where the wetting angle of the Ga droplet can be maintained in the range of values allowing the formation of pure WZ phase. The analysis of the in situ reflection high energy electron diffraction evolution, combined with high-resolution scanning transmission electron microscopy (TEM), dark field TEM, and photoluminescence all confirm the control of an extended pure WZ segment, more than a micrometer long, obtained by molecular beam epitaxy growth of self- assisted GaAs NWs with a V/III flux ratio of 4.0. This successful controlled growth of WZ GaAs suggests potential benefits for electronics and opto-electronics applications.
Functional imaging of the brain using computed tomography. (1981)

Data from rapid-sequence CT scans of the same cross section, obtained following bolus injection of contrast material, were analyzed by functional imaging. The information contained in a large number of images can be compressed into one or two gray-scale images which can be evaluated both qualitatively and quantitatively. The computational techniques are described and applied to the generation of images depicting bolus transit time, arrival time, peak time, and effective width.