gebhart/patrepeval huggingface dataset:
Epothilone and Paclitaxel:  Unexpected Differences in Promoting the Assembly and Stabilization of Yeast Microtubules (2002)

Paclitaxel (Taxol) and the epothilones are antimitotic agents that promote the assembly of mammalian tubulin and stabilization of microtubules. The epothilones competitively inhibit the binding of paclitaxel to mammalian brain tubulin, suggesting that the two types of compounds share a common binding site in tubulin, despite the lack of structural similarities. It is known that paclitaxel does not stabilize microtubules formed in vitro from Saccharomyces cerevisiae tubulin; thus, it would be expected that the epothilones would not affect yeast microtubules. However, we found that epothilone A and B do stimulate the formation of microtubules from purified yeast tubulin. In addition, epothilone B severely dampens the dynamics of yeast microtubules in vitro in a manner similar to the effect of paclitaxel on mammalian microtubules. We used current models describing paclitaxel and epothilone binding to mammalian beta-tubulin to explain why paclitaxel apparently fails to bind to yeast tubulin. We propose that three amino acid substitutions in the N-terminal region and at position 227 in yeast beta-tubulin weaken the interaction of the 3'-benzamido group of paclitaxel with the protein. These results also indicate that mutagenesis of yeast tubulin could help define the sites of interaction with paclitaxel and the epothilones.
The alliance of global navigation satellite systems and fuzzy logic in unmanned cars. (2001)

A clinical artificial intelligence (AI) system is often validated on data withheld during its development. This provides an estimate of its performance upon future deployment on data in the wild; those currently unseen but are expected to be encountered in a clinical setting. However, estimating performance on data in the wild is complicated by distribution shift between data in the wild and withheld data and the absence of ground-truth annotations. Here, we introduce SUDO, a framework for evaluating AI systems on data in the wild. Through experiments on AI systems developed for dermatology images, histopathology patches, and clinical notes, we show that SUDO can identify unreliable predictions, inform the selection of models, and allow for the previously out-of-reach assessment of algorithmic bias for data in the wild without ground-truth annotations. These capabilities can contribute to the deployment of trustworthy and ethical AI systems in medicine.
Genetic basis for altered idiotype expression in the hyperimmune response to (4-hydroxy-3-nitrophenyl)acetyl hapten. (1986)

To assess the significance of somatic point mutation in the hyperimmune response to the hapten NP, an in vivo enrichment procedure was followed. Mice that expressed high titers of B1-8 idiotopic determinants were selected as donors for serial transfer of small numbers of immune spleen cells into syngeneic irradiated recipient mice. Cells expressing B1-8 idiotopic determinants were chosen for enrichment because B1-8 cross-reactive determinants constitute a significant portion of the primary response. Furthermore, B1-8 is a monoclonal antibody derived from a primary response to NP, and its heavy and light chains are unmutated products of the germ-line genes VH186.2 and VL lambda 1, respectively. The germ-line sequence is thus available for comparison with the somatic mutants that arise during enrichment and hyperimmunization. The data show that serial transfer of spleen cells from mice with a high titer of idiotypic determinants results in a dramatic decrease in the titers of antibodies that bind antigen. Three lines of evidence indicate that progeny cells from the initial lambda-positive, idiotype-bearing, antigen-binding cells are successfully transferred and expanded during successive adoptive transfers. First, the proportion of lambda-bearing antibodies relative to NP-specific lambda-bearing antibodies increases with transfer, which is consistent with mutation away from antigen binding. Second, analysis of serum antibodies and hybridoma proteins derived from transfer-recipient mice confirm the presence of idiotype-positive antibodies that do not bind antigen. Third, RNA dot blot analysis of hybridomas constructed from a recipient mouse in the fourth transfer indicates a high frequency of expression of the VH gene predominantly used in the NP response. Many of the antibodies expressed by these hybridomas not only do not bind antigen, but have also lost the determinants recognized by the anti-idiotypic reagents. Most of these VH-positive hybridomas express lambda L chain. The most likely interpretation of the data is that somatic mutation is occurring during the hyperimmune response. Because we selected donor mice that expressed a high titer of idiotype-positive, antigen-specific antibody and immunized the recipient mice, we expected to observe a selective expansion of somatic variants that bound antigen. This was not the case. The observed loss of antigen binding suggests that the majority of mutations arising result in antibodies with lower affinity for the immunizing antigen.
Auditory Processing of Vowels by Normal-Hearing and Hearing-Impaired Listeners (1982)

"Masking" patterns were obtained in normal-hearing and hearing-impaired listeners using the pulsation-threshold procedure. Synthesized vowel maskers /a/ and /ae/ were presented at various sound pressure levels and alternated witha sinusoidal probe of a given frequency at a repetition rate of 4 Hz, T = 250 msec. Simultaneous-masking patterns also were obtained in one normal-hearing listener. The vowel pulsation patterns (VPPs) for the normal-hearing listeners closely resembled the acoustic spectra of the vowel maskers. Neither the pulsation patterns for the hearing-impaired listeners nor the simultaneous-masking patterns for the normal-hearing listener preserved the contour of the vowel spectra. These results are interpreted in terms of suppression effects, which have been observed only with nonsimultaneous-masking paradigms in normal-hearing listeners and have not been observed in listeners with a cochlear hearing loss. The effects of increased masker level were the same for both groups of listeners and are discussed in terms of upward spread of masking and a masking function with a slope less than 1.0.
Determining small refractive index contrast in chalcogenide-glass pairs at mid-infrared wavelengths (2019)

A two-composition thin film (Ge20Sb10Se70/Ge20Sb10Se67S3 atomic%core/cladding glasses) was fabricated using a hot-fibre-pressing technique in which both glasses follow the same post-fibre processing. A simple approach is proposed that uses normal incidence transmission spectra to determine their refractive index contrast over the wavelength range from 2 to 25 μm with an error of less than _ 0.002. Using an improved Swanepoel method, the calculated numerical aperture of these two compositions was within _ 0.011 of that obtained from prism minimum deviation measurements. Results show that introducing 3 atomic % S into the Ge-Sb-Se glass system lowered the refractive index and blue-shifted the visible optical bandgap, the far-infrared fundamental vibrational absorption bands and the zero-dispersion wavelength.
Accuracy/energy-flexible stochastic configurable 2D Gabor filter with instant-on capability (2017)

This paper introduces an accuracy/energy-flexible configurable 2D Gabor filter based on stochastic computation, where bit streams representing information are used. The Gabor filters show a powerful feature extraction capability, but the calculation based on binary computation is complicated. As opposed to traditional memory-based methods that use fixed Gabor coefficients calculated by software in advance, the proposed circuit dynamically generates the coefficients with small hardware, thanks to stochastic computation. The on-line coefficient-generation method leads to the “Instant-On” and hence the power-gating capabilities. For energy-efficient circuits, dynamic voltage-frequency-length scaling (DVFLS) is proposed to match the performance demands depending on situations. DVFLS controls the lengths of the stochastic bit streams with voltage and frequency, which can lower the energy dissipation and/or increase the throughput with a little accuracy loss. The proposed 64 parallel stochastic Gabor filter is fabricated using TSMC 65 nm CMOS technology with a size of 1.79 mm × 1.79 mm. The measurement results with DVFLS show a 200 Mpixel/s and a 0.510 μJ/pixel, exhibiting 16x higher and 3x lower than that using a conventional DVFS technique, respectively, with a 0.586% accuracy loss. Compared with a conventional configurable Gabor filter, the proposed chip achieves an order-of-magnitude higher throughput with more flexibility of the Gabor coefficients.
3D plasmonic hollow nanoantennas as tools for neuroscience applications (2014)

3D plasmonic nanoantennas were fabricated on active biodevices for in-vitro neuroscience experiments. The technique consents to realize nanoantennas patterns suitable for neurons culture and that can be used concurrently as intracellular nanoelectrodes and spectroscopic probes.
&lt;title&gt;Automated follicle analysis in ovarian ultrasound&lt;/title&gt; (1998)

For women undergoing assisted reproductive therapy, ovarian ultrasound has become an invaluable tool for monitoring the growth and assessing the physiological status of individual follicles. Measurements of the size and shape of follicles are the primary means of evaluation by physicians. Currently, follicle wall segmentation is achieved by manual tracing which is time consuming and susceptible to inter- operator variation. We are introducing a completely automated method of follicle wall isolation which provides faster, more consistent analysis. Our automated method is a 4-step process which employs watershed segmentation and a knowledge-based graph search algorithm which utilizes a priori information about follicle structure for inner and outer wall detection. The automated technique was tested on 36 ultrasonographic images of woman's ovaries. Five images from this set were omitted due to poor image quality. Validation of the remaining 31 ultrasound images against manually traced borders has shown an average rms error of 0.61 +/- 0.40 mm for inner border and 0.61 +/- 0.31 mm for outer border detection. Quantitative comparison of the computer-defined borders and the user-defined borders advocates the accuracy of our automated method of follicle analysis.
Zn-Mn Alloy Electrodeposition on Steel (1997)

SummaryElectrodeposition of Zn-Mn (0÷50 w/o) onto carbon steel sheet and wire is discussed in the present paper. An original bath is proposed and effects of stabilisers are studied. Baths and deposits are studied from the electrochemical and structural points of view. Electrochemical investigations include galvanostatic and potentiodynamic studies carried out in laboratory cells under natural and forced (rotating disk electrode) convection and a wire-plating pilot plant. Structural and compositional investigations include X-ray diffraction analyses, scanning electron imaging and energy dispersive analyses on steel sheet and wire. Electrochemical data can be correlated with alloy composition (limiting currents and how they are affected by mass transport conditions), morphological results (lamellar low-Mn vs. globular high-Mn) and crystallographic (metastable € monophasic deposits in the high-Mn range, polyphasic low-Mn coatings) structure, the variables which have a bearing on functional properties of the coatings.
Pulmonary Microvascular Endothelial Cells Form a Tighter Monolayer when Grown in Chronic Hypoxia (2007)

Unique among the vascular beds, loss of endothelial integrity in the pulmonary microcirculation due to injury can lead to rapidly fatal hypoxemia. The ability to regain confluence and re-establish barrier function is central to restoring proper gas exchange. The adult respiratory distress syndrome (ARDS) is a heterogeneous disease, however, meaning that endothelial cells within different regions of the lung do not likely see the same oxygen tension as they attempt to proliferate and re-establish an intact endothelial monolayer; the effect of hypoxia on the integrity of this newly formed endothelial monolayer is not clear. Immortalized human pulmonary microvascular endothelial cells (PMVEC) (ST1.6R cells) were sparsely plated and grown to confluence over 4 days in either normoxia (21% oxygen) or hypoxia (5% oxygen). Confluence attained in a hypoxic environment resulted in a tighter, less permeable endothelial monolayer (as determined by an increase in transendothelial electrical resistance, decreased permeability to fluorescently labeled macromolecules, and decreased hydraulic conductance). PMVEC grown to confluence under hypoxia had decreased RhoA activity; consistent with this finding, inhibition of Rho kinase, a well-described downstream target of RhoA, markedly increased electrical resistance in normoxic, but not hypoxic, PMVEC. These results were confirmed in primary human and rat PMVEC. These data suggest that PMVEC grown to confluence under hypoxia form a tighter monolayer than similar cells grown under normoxia. This tighter barrier appears to be due, in part, to the inhibition of RhoA activity in hypoxic cells.
Systems-wide analyses of mucosal immune responses to<i>Helicobacter pylori</i>at the interface between pathogenicity and symbiosis (2016)

Helicobacter pylori is the dominant member of the gastric microbiota in over half of the human population of which 5-15% develop gastritis or gastric malignancies. Immune responses to H. pylori are characterized by mixed T helper cell, cytotoxic T cell and NK cell responses. The presence of Tregs is essential for the control of gastritis and together with regulatory CX3CR1+ mononuclear phagocytes and immune-evasion strategies they enable life-long persistence of H. pylori. This H. pylori-induced regulatory environment might contribute to its cross-protective effect in inflammatory bowel disease and obesity. Here we review host-microbe interactions, the development of pro- and anti-inflammatory immune responses and how the latter contribute to H. pylori's role as beneficial member of the gut microbiota. Furthermore, we present the integration of existing and new data into a computational/mathematical model and its use for the investigation of immunological mechanisms underlying initiation, progression and outcomes of H. pylori infection.
Gallium phosphide microlenses by mass transport (1989)

Arrays of high quality refractive microlenses have been formed in GaP substrates by mesa etching followed by a heat treatment in which the multistep mesas were smoothed due to surface energy minimization. A smooth lens surface and an accurately controlled lens profile have been obtained. Microlenses of 130 μm diameter and 200 μm focal length have been used to collimate the outputs of GaInAsP/InP and GaAs/GaAlAs diode lasers and have yielded a nearly diffraction-limited beam divergence of 0.68°.
Pathways Mediating Resistance to Vascular Endothelial Growth Factor–Targeted Therapy (2008)

Vascular endothelial growth factor (VEGF)-targeted therapy has become an important treatment option for the management of a number of human malignancies. Unfortunately, a significant number of patients do not respond to VEGF-targeted therapy when used as a single agent or in combination with chemotherapy. Furthermore, the duration of benefit from VEGF-targeted therapy can be relatively short (weeks to months). Ultimately, the vast majority of patients who initially respond to therapy will develop resistance. To date, the molecular and cellular mechanisms associated with resistance to VEGF-targeted agents are poorly understood. The mechanisms of action of anti-VEGF therapy are diverse, and it is entirely possible that resistance mechanisms are similarly diverse and depend on the tumor type. A better understanding of these mechanisms will help in the selection of those patients that are more likely to benefit from VEGF-targeted therapy and also provide for the rational development of therapies that circumvent or overcome resistance.
Exploiting device mismatch in neuromorphic VLSI systems to implement axonal delays (2012)

Axonal delays are used in neural computation to implement faithful models of biological neural systems, and in spiking neural networks models to solve computationally demanding tasks. While there is an increasing number of software simulations of spiking neural networks that make use of axonal delays, only a small fraction of currently existing hardware neuromorphic systems supports them. In this paper we demonstrate a strategy to implement temporal delays in hardware spiking neural networks distributed across multiple Very Large Scale Integration (VLSI) chips. This is achieved by exploiting the inherent device mismatch present in the analog circuits that implement silicon neurons and synapses inside the chips, and the digital communication infrastructure used to configure the network topology and transmit the spikes across chips. We present an example of a recurrent VLSI spiking neural network that employs axonal delays and demonstrate how the proposed strategy efficiently implements them in hardware.
Heat Transfer Performance of Axially Grooved Heat Pipes (1987)

This paper describes experiments and analysis of the heat transport capability of axially grooved heat pipes. The heat pipes were made of aluminum axially grooved extruded pipes and the working fluid was R11. The effects of fluid inventory and inclination angle on the capillary pumping limit were investigated. A theoretical model has been developed to predict the temperature rise in the evaporator and the heat transport capability. In this model, the puddling effect, liquid recession into the groove bottom and the heat conduction in the evaporator were taken into consideration and the prediction agreed well with the experimental data. It was found that the temperature at the evaporator end bagan to increase just after all the grooves dried out at the evaporator end. The flooding limit and the evaporator and condenser film coefficients in the case of the gravity-supported operation were also investigated and compared with the performance of closed two-phase thermosyphons.
Comparative gene expression analysis of NKT cell subpopulations (2006)

Natural killer T (NKT) cells are a lymphocyte lineage, which has diverse immune regulatory activities in many disease settings. Most previous studies have investigated the functions of this family of cells as a single entity, but more recent evidence highlights the distinct functional and phenotypic properties of NKT cell subpopulations. It is likely that the diverse functions of NKT cells are regulated and coordinated by these different NKT subsets. Little is known about how NKT subsets differ in their interactions with the host. We have undertaken the first microarray analysis comparing the gene expression profiles of activated human NKT cell subpopulations, including CD8(+) NKT cells, which have often been overlooked. We describe the significant gene expression differences among NKT cell subpopulations and some of the molecules likely to confer their distinct functional roles. Several genes not associated previously with NKT cells were shown to be expressed differentially in specific NKT cell subpopulations. Our findings provide new insights into the NKT cell family, which may direct further research toward better manipulation of NKT cells for therapeutic applications.
Data from Applications of ImmunoPET: Using &lt;sup&gt;124&lt;/sup&gt;I-Anti-PSCA A11 Minibody for Imaging Disease Progression and Response to Therapy in Mouse Xenograft Models of Prostate Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Prostate stem cell antigen (PSCA) is highly expressed in local prostate cancers and prostate cancer bone metastases and its expression correlates with androgen receptor activation and a poor prognosis. In this study, we investigate the potential clinical applications of immunoPET with the anti-PSCA A11 minibody, an antibody fragment optimized for use as an imaging agent. We compare A11 minibody immunoPET to &lt;sup&gt;18&lt;/sup&gt;F-Fluoride PET bone scans for detecting prostate cancer bone tumors and evaluate the ability of the A11 minibody to image tumor response to androgen deprivation.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Osteoblastic, PSCA-expressing, LAPC-9 intratibial xenografts were imaged with serial &lt;sup&gt;124&lt;/sup&gt;I-anti-PSCA A11 minibody immunoPET and &lt;sup&gt;18&lt;/sup&gt;F-Fluoride bone scans. Mice bearing LAPC-9 subcutaneous xenografts were treated with either vehicle or MDV-3100 and imaged with A11 minibody immunoPET/CT scans pre- and posttreatment. &lt;i&gt;Ex vivo&lt;/i&gt; flow cytometry measured the change in PSCA expression in response to androgen deprivation.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; A11 minibody demonstrated improved sensitivity and specificity over &lt;sup&gt;18&lt;/sup&gt;F-Fluoride bone scans for detecting LAPC-9 intratibial xenografts at all time points. LAPC-9 subcutaneous xenografts showed downregulation of PSCA when treated with MDV-3100 which A11 minibody immunoPET was able to detect &lt;i&gt;in vivo&lt;/i&gt;.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; A11 minibody immunoPET has the potential to improve the sensitivity and specificity of clinical prostate cancer metastasis detection over bone scans, which are the current clinical standard-of-care. A11 minibody immunoPET additionally has the potential to image the activity of the androgen signaling axis &lt;i&gt;in vivo&lt;/i&gt; which may help evaluate the clinical response to androgen deprivation and the development of castration resistance. &lt;i&gt;Clin Cancer Res; 20(24); 6367–78. ©2014 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
High capacity MnO<sub>x</sub>:ZrO<sub>2</sub> sorbent for elementary mercury capture: preparation, characterization and comparison to other sorbents (2017)

Manganese oxide-zirconia type (MnOx:ZrO2) sorbents were prepared using the sol-gel technique by co precipitation ZrO(NO3)2.xH2O and Mn(NO3)2 xH2O. The heat treatment below 500°C resulted a high surface area solid structure which consists of amorphous Mn2O3 (Bixbyite) and amorphous ZrO2 phases. This material was found a high capacity oxidative sorbent for mercury removal from gas streams.
Bioinspired Nanotubes from Self‐Assembly of a Linear <scp>l</scp>,<scp>d</scp>‐Oligopeptide‐Poly(ethylene glycol) Conjugate (2014)

The preparation and structural organization of a new bioinspired nanomaterial are investigated. A hybrid conjugate is obtained by end‐linking a linear octapeptide with regular alternating enantiomeric sequence to poly(ethylene glycol). This conjugate is able to self‐assemble, forming well‐defined nanorods having core/shell morphology with an internal peptide single channel that has, for the first time, been clearly visualized by transmission electron microscopy (TEM) images. It is remarkable that well‐defined cylindrical nanoparticles can be formed starting from a linear oligopeptide, the synthesis of which is significantly easier than that of the homologous cycles. In addition, the synthetic strategy and the structure of the conjugate ensure a controlled and regular pegylation of the aggregates and high density PEG blocks in the corona, making the nanoparticles more resistant to phagocytosis and able to prevent biofouling. Such features, along with biocompatibility and stability, make these nanoparticles promising candidates for drug delivery. image