gebhart/patrepeval huggingface dataset:
Molecular targeting of prostate cancer with cytotoxins and radioisotopes linked to fully human monoclonal antibodies against prostate-specific membrane antigen (2005)

2560 Background: Prostate-specific membrane antigen (PSMA) is an attractive target for immunotherapy of prostate cancer due to its abundant expression on prostate cancer cells and its up-regulation on metastatic disease. The objectives of this study were to evaluate the ability of fully human anti-PSMA monoclonal antibodies (mAbs) to specifically deliver cytotoxic payloads to prostate cancer cells in vitro and in vivo. Methods: Using novel recombinant forms of PSMA and the XenoMouse™ technology, we previously generated a panel of fully human mAbs against PSMA. Characterization of these antibodies was conducted using Biacore, ELISA, flow cytometry, anti-PSMA Western blot and other functional assays. In this study, the therapeutic potential of radiolabeled mAbs and immunotoxins was comparatively evaluated in cell-based in vitro cytotoxicity assays and in vivo xenografted animals. Results: We demonstrated that these fully human mAbs specifically recognize conformational, dimer-specific epitopes on PSMA with subnanomolar affinity. The mAbs were modified with bifunctional chelates for radiolabeling or conjugated with potent cytotoxins. The binding of the mAbs to cell-surface PSMA was virtually unchanged following conjugation. The conjugated mAbs were internalized rapidly upon binding to PSMA on tumor cells (∼60% in 2 hours) which provides efficient delivery of cytotoxins. Immunotoxins killed PSMA-expressing tumor cells with pM potency and ∼1000-fold selectivity. In tumor-bearing animal models, mAbs radiolabeled with Lu-177, a beta-emitting isotope, selectively targeted PSMA-expressing tumors, with a high tumor uptake of 30% injected dose per gram of tumor. In an aggressive tumor model using 3T3-PSMA cells, a single 400 μCi dose of Lu-177 labeled antibody significantly delayed tumor growth and increased median survival time by 3.5-fold compared to untreated control animals (p<0.005). Additional xenograft studies have been initiated using the androgen-independent human prostate cancer cell line C4-2. Conclusions: Fully human PSMA mAbs can selectively deliver cytotoxic payloads to control prostate tumor growth in vitro and in vivo. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration PSMA Development Company, LLC
A sustainable revival process for defective LiFePO4 cathodes through the synergy of defect-targeted healing and in-situ construction of 3D-interconnected porous carbon networks (2023)

The reutilization of spent cathode materials plays a key role in the sustainable development of Li-ion battery technology. However, current recycling approaches generally based on hydro-/pyrometallurgy fail to cater to Co-free cathodes (e.g., LiFePO<sub>4</sub>, or LFP) owing to high consumption and secondary contamination. Here, a sustainable process is proposed for the revival of defective LFP cathodes through the synergy of defect-targeted healing and surface modification. Li deficiency and Fe oxidation of cathodes are precisely repaired by solution-based relithiation; meanwhile, 3D-interconnected porous carbon networks (3dC) are in-situ constructed with the intervention of salt template during annealing, which enhances the rate performance and electronic/ionic conductivity, by providing more convenient migration channels for Li ions and controlling carbon hybridization. Nitrogen is also doped via induction of urea to fabricate advanced nanohybrid rLFP@3dC-N. New cells using rLFP@3dC-N as cathode exhibit a reversible capacity of up to 169.74 and 141.79 mAh g<sup>-1</sup> at 0.1 and 1C, respectively, with an excellent retention rate of over 95.7% at 1C after 200 cycles. Impressively, a high capacity of 107.18 mAh g<sup>-1</sup> is retained at 5C. This novel concepts for Li replenishment and the construction of ion-transfer channels as well as conductive networks facilitate the regeneration of spent LFP and the optimization of its high-rate performance.
Characterization of the Complete Mitochondrial Genomes of Two Sibling Species of Parasitic Roundworms, Haemonchus contortus and Teladorsagia circumcincta (2020)

<i>Haemonchus contortus</i> and <i>Teladorsagia circumcincta</i> are among the two most pathogenic internal parasitic nematodes infecting small ruminants, such as sheep and goats, and are a global animal health issue. Accurate identification and delineation of Haemonchidae species is essential for development of diagnostic and control strategies with high resolution for Trichostrongyloidea infection in ruminants. Here, we describe in detail and compare the complete mitochondrial (mt) genomes of the New Zealand <i>H. contortus</i> and <i>T. circumcincta</i> field strains to improve our understanding of species- and strain-level evolution in these closely related roundworms. In the present study, we performed extensive comparative bioinformatics analyses on the recently sequenced complete mt genomes of the New Zealand <i>H. contortus</i> NZ_Hco_NP and <i>T. circumcincta</i> NZ_Teci_NP field strains. Amino acid sequences inferred from individual genes of each of the two mt genomes were compared, concatenated and subjected to phylogenetic analysis using Bayesian inference (BI), Maximum Likelihood (ML), and Maximum Parsimony (MP). The AT-rich mt genomes of <i>H. contortus</i> NZ_Hco_NP and <i>T. circumcincta</i> NZ_Teci_NP are 14,001 bp (A+T content of 77.4%) and 14,081 bp (A+T content of 77.3%) in size, respectively. All 36 of the typical nematode mt genes are transcribed in the forward direction in both species and comprise of 12 protein-encoding genes (PCGs), 2 ribosomal RNA (<i>rrn</i>) genes, and 22 transfer RNA (<i>trn</i>) genes. The secondary structures for the 22 <i>trn</i> genes and two <i>rrn</i> genes differ between <i>H. contortus</i> NZ_Hco_NP and <i>T. circumcincta</i> NZ_Teci_NP, however the gene arrangements of both are consistent with other Trichostrongylidea sequenced to date. Comparative analyses of the complete mitochondrial nucleotide sequences, PCGs, A+T rich and non-coding repeat regions of <i>H. contortus</i> NZ_Hco_NP and <i>T. circumcincta</i> NZ_Teci_NP further reinforces the high levels of diversity and gene flow observed among Trichostrongylidea, and supports their potential as ideal markers for strain-level identification from different hosts and geographical regions with high resolution for future studies. The complete mt genomes of <i>H. contortus</i> NZ_Hco_NP and <i>T. circumcincta</i> NZ_Teci_NP presented here provide useful novel markers for further studies of the meta-population connectivity and the genetic mechanisms driving evolution in nematode species.
Adsorption of ethylene on the Ge(100)-2×1 surface: Coverage and time-dependent behavior (1999)

Studies of the adsorption and thermal chemistry of ethylene on the Ge(100)-2×1 surface have been performed. The results of multiple internal reflection Fourier transform infrared (MIR-FTIR) spectroscopy and temperature programmed desorption (TPD) show that ethylene chemisorbs molecularly on the Ge(100)-(2×1) surface at room temperature. Infrared spectroscopy gives evidence for only one adsorbate configuration on this surface at room temperature, consistent with a structure in which ethylene bridges across a germanium dimer. However, TPD measurements show two molecular desorption features at almost all coverages, indicating that at least two adsorption states can be formed. Further shifts in one of the peaks with both coverage and time, paralleled by changes in the vibrational spectrum, suggest the presence of attractive intermolecular interactions or cooperative effects. The complex time- and coverage dependence of ethylene adsorption on Ge(100)-2×1 is analyzed using a two-state kinetic model.
Transforming Big Data into Cancer-Relevant Insight: An Initial, Multi-Tier Approach to Assess Reproducibility and Relevance (2016)

The Cancer Target Discovery and Development (CTD(2)) Network was established to accelerate the transformation of "Big Data" into novel pharmacologic targets, lead compounds, and biomarkers for rapid translation into improved patient outcomes. It rapidly became clear in this collaborative network that a key central issue was to define what constitutes sufficient computational or experimental evidence to support a biologically or clinically relevant finding. This article represents a first attempt to delineate the challenges of supporting and confirming discoveries arising from the systematic analysis of large-scale data resources in a collaborative work environment and to provide a framework that would begin a community discussion to resolve these challenges. The Network implemented a multi-tier framework designed to substantiate the biological and biomedical relevance as well as the reproducibility of data and insights resulting from its collaborative activities. The same approach can be used by the broad scientific community to drive development of novel therapeutic and biomarker strategies for cancer. Mol Cancer Res; 14(8); 675-82. ©2016 AACR.
Precise Control of Gas Concentration Ratio in Process Chamber (2001)

A new system for controlling gas concentration in a process chamber was developed using a combination of a new flow controller and a gas pumping system. The new flow controller does not exhibit overshooting; thus, a stable gas flow rate can be realized in a process chamber after valve operation. Furthermore, very rapid gas displacement in the chamber can be realized by combined gas flow system and pumping system. As a result, it took only 2 s to stabilize chamber pressure and gas composition from purge gas to process gases using Fourier transform infrared spectroscopy (FT-IR) method. It is possible to control process parameters such as gas concentration and working pressure during the entire process using this system.
ELECTROPORATION: BIO-ELECTROCHEMICAL MASS TRANSFER AT THE NANO SCALE (2000)

This article provides a brief review of the field of electroporation and introduces a new microdevice that facilitates studies to test theories, gain understanding, and control this important biomedical technology. Electroporation, a bio-electrochemical process whose fundamentals are not yet understood, is a means of permeating the cell membrane by applying a voltage across the cell and forming nano-scale pores in the membrane. It has become an important field in biotechnology and medicine for the controlled introduction of macromolecules, such as gene constructs and drugs, into various cells. It is viewed as an engineering alternative to biological techniques for the genetic engineering of cells. To study and control electroporation, we have created a low-cost microelectroporation chip that incorporates a live biological cell with an electric circuit. The device revealed an important behavior of cells in electrical fields. They produce measurable electrical information about the electroporation state of the cell that may enable precise control of the process. The device can be used to facilitate fundamental studies of electroporation and can become useful in providing precise control over biotechnological processes.
Plow quantitation with echo‐planar phase‐contrast velocity mapping: In vitro and in vivo evaluation (1995)

We present a multishot echo-planar imaging (EPI) phase-contrast implementation for flow quantitation. The measurement accuracy of this technique was evaluated in vitro and in vivo. A gated eight-shot EPI phase-contrast sequence (TR/TE = 16/7.4, 45 degrees flip angle), with a flow-phase interval of 32 msec and an in-plane resolution of 2 x 2 mm was initially evaluated in a pulsatile flow phantom. Subsequently, EPI phase-contrast flow measurements of the ascending and descending aorta, obtained in 10 volunteers, were compared with flow volume data acquired with a conventional cine phase-contrast sequence (TR/TE = 24/7, 45 degrees flip angle, 48-msec flow-phase interval, 2 x 1 mm in-plane resolution). Comparisons between flow measurements were made using data obtained with the flow probe and cine phase contrast as the standard of reference for in vitro and in vivo measurements, respectively. EPI phase-contrast sequences reduced data acquisition times tenfold compared with cine phase-contrast sequences. EPI phase-contrast flow measurements correlated well with phantom flow (r = .98, slope = 1.1) as well as with aortic cine phase-contrast flow volume determinations (r = .98). A 95% confidence interval of measurement differences between echo-planar and cine phase-contrast imaging, ranging from 2.0 to -1058 mL/min was computed. Ultrafast phase-contrast flow measurements are possible. Multishot EPI phase-contrast imaging provides high measurement accuracy in pulsatile vessels while keeping the image acquisition interval short enough to be accomplished in a comfortable breath-hold.
Benastatins A and B, new inhibitors of glutathione S-transferase, produced by Streptomyces sp. MI384-DF12. II. Structure determination of benastatins A and B. (1992)

Benastatins A and B, new inhibitors of glutathione S-transferase, have been isolated from the culture broth of Streptomyces sp. MI384-DF12. By X-ray crystallography, benastatin A was determined to be 8,13-dihydro-1,7,9,11-tetrahydroxy-13-dimethyl-8-oxo-3-pentyl- benzo[a]naphthacene-2-carboxylic acid. The structure of benastatin B was elucidated by NMR studies.
Obsessive–compulsive symptomatology in female adolescent inpatients with restrictive compared with binge–purge eating disorders (2018)

Obsessionality is more severe in acutely ill AN-B/P patients than in patients with AN-R and BN, whereas a greater improvement in obsessionality from the acutely ill to the stabilized ED condition is found in patients with binge/purge in comparison with restrictive pathology.
Life Cycle of a SLAM System: Implementation, Evaluation and Port to the Project Tango Device (2016)

Augmented Reality (AR) applications are becoming popular recently. Among other things, AR requires a precise real-time tracking to work properly. Simultaneous Localization and Mapping (SLAM) is one way to perform this task. Commonly used in robotics applications, SLAM creates a map of the environment to use it as input to compute the pose while uses the pose to increment the map. At the same time, mobile devices are evolving faster lately. Along with more processing power and memory capabilities, they are being embedded with several powerful resources, such as depth sensors. Taking this into account, this work introduces STAM, a Simple Tracking and Mapping system that was developed in desktop and evaluated in a challenging scenario. Additionally, STAM was ported to a mobile version, using the Android platform and Google's Tango tablet device. Finally, the system was evaluated concerning its desktop version. The desktop version presented better tracking performance in simple scenarios with respect to reprojection error, but it presented a few drawbacks when dealing with the most complex ones. Regarding the mobile version, it proved to be slower than its desktop counterpart. However, it was more precise.
18F-FDG PET/MRI in Chronic Sciatica: Early Results Revealing Spinal and Nonspinal Abnormalities (2017)

Chronic sciatica is a major cause of disability worldwide, but accurate diagnosis of the causative pathology remains challenging. In this report, the feasibility of an <sup>18</sup>F-FDG PET/MRI approach for improved diagnosis of chronic sciatica is presented. <b>Methods:</b><sup>18</sup>F-FDG PET/MRI was performed on 9 chronic sciatica patients and 5 healthy volunteers (healthy controls). Region-of-interest analysis using SUV<sub>max</sub> was performed, and <sup>18</sup>F-FDG uptake in lesions was compared with that in the corresponding areas in healthy controls. <b>Results:</b> Significantly increased <sup>18</sup>F-FDG uptake was observed in detected lesions in all patients and was correlated with pain symptoms. <sup>18</sup>F-FDG-avid lesions not only were found in impinged spinal nerves but also were associated with nonspinal causes of pain, such as facet joint degeneration, pars defect, or presumed scar neuroma. <b>Conclusion:</b> The feasibility of <sup>18</sup>F-FDG PET/MRI for diagnosing pain generators in chronic sciatica was demonstrated, revealing various possible etiologies.
Fluorescent Calixarene Scaffolds for NO Detection in Protic Media (2019)

Abstract We present the first fluorescent water‐soluble conjugated calixarene scaffolds that are capable of NO gas detection. Two different scaffolds, one based on a 5,5′‐bicalixarene structure and its isomer bearing two distantly conjugated calixarene moieties, were synthesized. While the fluorescence of both isomers is quenched upon either passing of NO gas or generating it in situ from diethylamine NONOate, the bicalixarene‐based scaffold showed a significantly stronger response. We also present an example of a dye encapsulation strategy to achieve the detection of NO at longer wavelengths than in the parent calixarene host. Finally, a conjugated polymer bearing a 5,5′‐bicalixarene scaffold has also been prepared and demonstrated enhanced sensitivity compared to the monomer due to the molecular wire effect.
Blocked recursive image composition with exclusion zones (2010)

Photo collages are a popular and powerful storytelling mechanism. They are often enhanced with background artwork that sets the theme for the story. However, layout algorithms for photo collage creation typically do not take this artwork into account, which can result in collages where photos overlay important artwork elements. To address this, we extend our previous Blocked Recursive Image Composition (BRIC) method to allow any number of photos to be automatically arranged around preexisting exclusion zones on a canvas (exBRIC). We first generate candidate binary splitting trees to partition the canvas into regions that accommodate both photos and exclusion zones. We use a Cassowary constraint solver to ensure that the desired exclusion zones are not covered by photos. Finally, photo areas, exclusion zones and layout symmetry are evaluated to select the best candidate. This method provides flexible, dynamic and integrated photo layout with background artwork.
CNS-derived extracellular vesicles from superoxide dismutase 1 (SOD1)G93A ALS mice originate from astrocytes and neurons and carry misfolded SOD1 (2019)

Extracellular vesicles (EVs) are secreted by myriad cells in culture and also by unicellular organisms, and their identification in mammalian fluids suggests that EV release also occurs at the organism level. However, although it is clearly important to better understand EVs' roles in organismal biology, EVs in solid tissues have received little attention. Here, we modified a protocol for EV isolation from primary neural cell culture to collect EVs from frozen whole murine and human neural tissues by serial centrifugation and purification on a sucrose gradient. Quantitative proteomics comparing brain-derived EVs from nontransgenic (NTg) and a transgenic amyotrophic lateral sclerosis (ALS) mouse model, superoxide dismutase 1 (SOD1)<sup>G93A</sup>, revealed that these EVs contain canonical exosomal markers and are enriched in synaptic and RNA-binding proteins. The compiled brain EV proteome contained numerous proteins implicated in ALS, and EVs from SOD1<sup>G93A</sup> mice were significantly depleted in myelin-oligodendrocyte glycoprotein compared with those from NTg animals. We observed that brain- and spinal cord-derived EVs, from NTg and SOD1<sup>G93A</sup> mice, are positive for the astrocyte marker GLAST and the synaptic marker SNAP25, whereas CD11b, a microglial marker, was largely absent. EVs from brains and spinal cords of the SOD1<sup>G93A</sup> ALS mouse model, as well as from human SOD1 familial ALS patient spinal cord, contained abundant misfolded and nonnative disulfide-cross-linked aggregated SOD1. Our results indicate that CNS-derived EVs from an ALS animal model contain pathogenic disease-causing proteins and suggest that brain astrocytes and neurons, but not microglia, are the main EV source.
e#: Sharper Expertise Detection from Microblogs (2016)

Microblogging platforms such as Twitter provide low cost access to an immense reserve of authoritative professionals, opinion leaders and hobbyists for a wide range of topics. Yet, as microposts are short and incredibly diverse, many of these experts are hidden. In this paper, we present e#, a system to retrieve experts automatically for a given set of keywords. Our design targets exhaustivity: e# can detect previously undetectable experts. The core idea is to enhance a state-ofthe-art expert detection algorithm with a graph of expertise domains. Our system produces this graph from hundreds of Gigabytes of Web search query logs and behavioral data, processed in a distributed, parallel fashion. We provide a detailed description of our architecture, including an original SQL-based community detection algorithm. We then benchmark our system with 750 queries, using crowdsourcing. We observe that e# finds many more experts than a state-of-the-art baseline.
Chromatic aberration-based phase and fluorescence microscope for cell cycle study (Conference Presentation) (2020)

We designed a particularly simple, compact and robust microscope for phase and fluorescent imaging. The phase-contrast image is reconstructed from a single, approximately 100 µm defocused image with an algorithm based on a constrained optimization of Fresnel diffraction model. Fluorescence image is recorded in-focus. No mechanical movement of neither sample nor objective or any other part of the system is needed to change between the phase-contrast and fluorescence modality. The change of focus between phase (out-of-focus) and fluorescence (in-focus) imaging is achieved with chromatic aberration specifically enhanced by the optical design of our system. Our microscope is sufficiently compact (10x10x10 cm^3) to fit into a standard biological incubator. The simple and robust design reduces the vibration and the drift of the sample. The absence of motorized components makes the system robust and resistant to the humid conditions inside the biological incubator. These aspects greatly facilitate the long-time observation of cell cultures. We can observe a thousand of cells in parallel in a single field of view (1mm^2) with resolution down to 2 µm. We show FUCCI marked HeLa cell culture observed over three days directly in the incubator. FUCCI (fluorescence ubiquitination cell-cycle indicator), is a genetically encoded, two-colour (red and green), indicator of the progression through the cell cycle: the cells in G1 phase show red fluorescence nuclei while the cells in S, G2 and M phase display green fluorescence within the nuclei. We use phase images for segmentation and tracking of the individual cells which allows us to determine the level of fluorescence in each cell in the green and red fluorescence channel. We compare the obtained statistics with the data from flow cytometer acquired at the end of the observation. We show that we can produce a statistically relevant time-resolved measurement of a cell population while keeping access to the individual cells.