gebhart/patrepeval huggingface dataset:
Abstract 1153: Hypoxic microenvironments promote stemness and enhance the directed migration of glioma stem cells (2019)

Abstract Glioblastoma (GBM) is a highly malignant primary brain tumor and has a poor prognosis and is resistant to the most advanced therapies. The development of highly hypoxic centrally located necrotic regions is strongly associated with accelerated GBM progression, yet mechanistic explanations are not complete. Hypoxic regions within GBM are highly enriched for glioma stem cells (GSC), which are critical for tumor initiation, recurrence and therapeutic resistance due to their self-renewing capabilites. While most GBM cells migrate outward, away from hypoxia, GSCs accumulate there, forming a hypercellular border called pseudopalisades that promote their survival. Mechanisms that mediate GSC accumulation within pseudopalisades are unknown. We hypothesize that GSCs are enriched in the pseudopalisades due to the homing of a subpopulation towards the supportive hypoxic microenvironment. This in turn activates critical hypoxia-induced drivers to promote stemness, survival and migratory behavior encouraging the recruitment of more GSCs. Using two genetically distinct patient-derived GBM cell lines, we found that exposure to hypoxia in vitro led to enrichment of GSCs among a heterogeneous population of GSCs and non-GSCs. We found that hypoxia enhanced the expression of stem cell, pro-survival and pro-migratory factors in GSCs, such as the pro-migratory chemokine SDF-1α, and its cognate receptor CXCR4. Importantly, we found hypoxia also induced upregulation of OLIG2, one of four core transcription factors necessary and sufficient to induce stemness, in GSCs and non-GSCs exposed to hypoxia. We determined that OLIG2 was necessary for the expression of stem cell markers, and that its knockdown reduced cellular migration in hypoxia vs normoxia in GSCs. This suggests a critical role for OLIG2 in both hypoxia-induced stemness and homing behavior. We also generated a unique model of localized hypoxia in one brain hemisphere through vaso-cclusion and observed the homing of xenografted GBM cells towards hypoxia, regulated by OLIG2 in vivo. These data shed light on how hypoxic tumor microenvironments facilitate mechanisms vital to GBM progression and therapeutic resistance. Citation Format: Nitya V. Sharma, Monica Chau, Subhas Mukherjee, James Ross, Brandon Miller, Changming Zhang, Jun Kong, Carol Tucker-Burden, Emily Kaissi, John W. Reitnauer, Bilge Dundar, Cheryl L. Olson, Gregory Bix, Daniel J. Brat. Hypoxic microenvironments promote stemness and enhance the directed migration of glioma stem cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1153.
Abstract LB-264: Landscape of tumor-infiltrating T-cell repertoire of human cancers (2016)

Abstract T cells play a critical role in antitumor immunity and are the primary targets in many immunotherapies. However, the study of tumor-infiltrating T cells has been complicated by the extremely diverse repertoire of T cell receptors, characterized by the complementarity determining region 3 (CDR3). Here using our newly developed algorithm, we studied the CDR3 sequences of tumor infiltrating T cells in 9,142 RNA-seq samples across 29 diseases. In total, we assembled over 600 thousands CDR3 sequences, covering the α, β, γ, δ chains. TRBV genes usage, CDR3 sequence length and conservation of infiltrating T cells resembled those in the peripheral blood of healthy donors in many tumors, except brain and kidney cancers. About 20% of the CDR3 calls were shared in multiple individuals. T cell clonotypes carrying these CDR3 sequences are known as the ‘public T cells’. In this work, we found that public T cell CDR3 amino acid (AA) sequences are shorter compared to the private ones and the middle 3 positions of the private CDR3 sequences were enriched for hydrophobic AAs. This finding potentially suggests that private T cell clonotypes in the tumors have greater potential to recognize neoantigens. We defined clonotype per kilo-reads (CPK) to measure the diversity of T cell repertoire and identified a strong positive association between CPK and tumor mutation load, implying that neoantigens may diversify the infiltrating T cell population. In addition, we predicted SPAG5 and TSSK6 as putative immunogenic cancer/testis antigens in multiple cancers based on their strong associations with CPK. Finally, we identified 3 potential immunogenic somatic mutations based on their co-occurrence with CDR3 sequences. One of them, PRAMEF4 F300V, was predicted to bind strongly to both MHC-I and MHC-II, with matched HLA types in its carriers. Our analyses have the potential to simultaneously identify immunogenic neoantigen and the tumor-reactive T-cell clonotype. Citation Format: Bo Li, Taiwen Liu, Binbin Wang, Jinzeng Wang, Sachet Shukla, Ruoxu Dou, Stephen Hodi, Catherine Wu, Nir Hacohen, Jun Liu, X. Shirley Liu. Landscape of tumor-infiltrating T-cell repertoire of human cancers. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-264.
Internet predictions [Guest editor's introduction (2010)

More than a dozen leading experts give their opinions on where the Internet is headed and where it will be in the next decade in terms of technology, policy, and applications. They cover topics ranging from the Internet of Things to climate change to the digital storage of the future.
Baud-Rate-Adaptive OLT Integrated-Coherent Transceiver for Nyquist Spectral Shaped/Channel Spaced WDM-PON (2020)

We propose a rate-adaptive optical-line-terminal-side transceiver that changes capacity from 4 x 25-Gb/s per optical network unit (ONU) signal with the channel spacing of 6.25 GHz to 100-Gb/s per ONU signal by controlling the available number of sub-bands. A set of single laser diode and single coherent receiver collectively operates Nyquist spectral shaped WDM signals with Nyquist spacing to realize an integrated configuration with high spectral efficiency.
Critical Incidents Associated with Intraoperative Exchanges of Anesthesia Personnel (1982)

Bioengineering Unit, Department of Anesthesia, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts
Dietary effects on the presence of ulcers and urease producing organisms in the stomach of weaner pigs (1998)

Oesophagogastric ulceration (OGU) occurs frequently in swine, and numerous dietary factors have been incriminated in its aetiology (3). Helicobacter pylori and Helicobacter heilmannii are recognised as causative agents of gastritis and gastrointestinal ulcers in humans (2). Recently a strong association between the presence of Helicobacter heilmannii and the occurrence of OGU was demonstrated in pigs (1,5).&#13;\n&#13;\nHelicobacter species produce large quantities of the enzyme urease (2). As mammalian cells are unable to produce this enzyme, a positive urease activity in gastric biopsies can be interpreted as indicating the presence of urease producing microorganisms (UPM).&#13;\n&#13;\nIn this study a combined dietary and microbiological experiment was carried out to investigate the relationship between diet, the presence of UPM and the incidence of gastric lesions in weaner pigs.
T1 mapping and extracellular volume fraction measurement to evaluate the poor‐prognosis factors in patients with cervical squamous cell carcinoma (2023)

Both T<sub>1</sub> mapping and DWI could stratify the CSCC histologic grade. In addition, T<sub>1</sub> mapping and ECV measurement might provide more quantitative metrics for noninvasively predicting poor prognostic factors and aiding in preoperative risk assessment in CSCC patients.
Network visualization with Nam, the VINT network animator (2000)

Network protocol designers face many difficult tasks, including simultaneously monitoring state in a potentially large number of nodes, understanding and analyzing complex message exchanges, and characterizing dynamic interactions with competing traffic. Traditionally they have used packet traces to accomplish these tasks, but traces have two major drawbacks: they present an incredible amount of detail, which challenges the designer's ability to comprehend the data; and they are static, which hides an important dimension of protocol behavior. As a result, detailed analysis frequently becomes tedious and error-prone. Although network simulators such as the VINT project's ns can easily generate numerous detailed traces, they provide limited help for analyzing and understanding the data. Nam, the network animator that we developed in our work at the VINT project, provides packet-level animation, protocol graphs, traditional time-event plots of protocol actions, and scenario editing capabilities. Nam benefits from a close relationship with ns, which can collect detailed protocol information from a simulation. With some preprocessing. Nam can visualize data taken directly from real network traces.
Nanocrystalline gold catalysts: A reflection on catalyst discovery and the nature of active sites (2009)

Nanocrystalline gold catalysts:A reflection on catalyst discovery and the nature of active sites
TU-AB-303-08: GPU-Based Software Platform for Efficient Image-Guided Adaptive Radiation Therapy (2015)

Purpose: In this study, we develop an integrated software platform for adaptive radiation therapy (ART) that combines fast and accurate image registration, segmentation, and dose computation/accumulation methods. Methods: The proposed system consists of three key components; 1) deformable image registration (DIR), 2) automatic segmentation, and 3) dose computation/accumulation. The computationally intensive modules including DIR and dose computation have been implemented on a graphics processing unit (GPU). All required patient-specific data including the planning CT (pCT) with contours, daily cone-beam CTs, and treatment plan are automatically queried and retrieved from their own databases. To improve the accuracy of DIR between pCT and CBCTs, we use the double force demons DIR algorithm in combination with iterative CBCT intensity correction by local intensity histogram matching. Segmentation of daily CBCT is then obtained by propagating contours from the pCT. Daily dose delivered to the patient is computed on the registered pCT by a GPU-accelerated superposition/convolution algorithm. Finally, computed daily doses are accumulated to show the total delivered dose to date. Results: Since the accuracy of DIR critically affects the quality of the other processes, we first evaluated our DIR method on eight head-and-neck cancer cases and compared its performance. Normalized mutual-information (NMI) and normalized cross-correlation (NCC) computed as similarity measures, and our method produced overall NMI of 0.663 and NCC of 0.987, outperforming conventional methods by 3.8% and 1.9%, respectively. Experimental results show that our registration method is more consistent and roust than existing algorithms, and also computationally efficient. Computation time at each fraction took around one minute (30–50 seconds for registration and 15–25 seconds for dose computation). Conclusion: We developed an integrated GPU-accelerated software platform that enables accurate and efficient DIR, auto-segmentation, and dose computation, thus supporting an efficient ART workflow. This work was supported by NIH/NCI under grant R42CA137886.
Gravity induced flow cell (2023)

The flow cell includes first and second reservoirs having a selected volume containing a flowable redox electrode. A membrane separates charged and discharged material. An energy-extraction region includes electronically conductive porous current collectors through or adjacent to which the flowable redox electrodes flow and to which charge transfer occurs. Structure is provided for altering orientation of the flow cell whereby gravity induces flow of the flowable redox electrode between the first and second reservoirs to deliver power. By varying the angle of the cell, flow rate and power delivered on discharge or the charge rate on charge may be varied.
Pre-Incubation of Cell-Free HIV-1 Group M Isolates with Non-Nucleoside Reverse Transcriptase Inhibitors Blocks Subsequent Viral Replication in Co-Cultures of Dendritic Cells and T Cells (2005)

In order to study the inhibitory effect of various reverse transcriptase inhibitors (RTIs) on cell-free HIV, we adapted a recently described in vitro system, based on co-cultures of dendritic cells and resting CD4 T cells, modelling early target cells during sexual transmission. The compounds tested included the second-generation non-nucleoside RTI (NNRTI) TMC-120 (R147681, dapivirine) and TMC-125 (R165335, travertine), as well as the reference nucleoside RTI AZT (zidovudine), the nucleotide RTI PMPA (tenofovir) and the NNRTI UC-781. The virus strains included the reference strain HIV-1Ba-L and six primary isolates, representative of the HIV-1 group M pandemic. They all display the non-syncytium-inducing and CCR5 receptor-using (NSI/R5) phenotype, important in transmission. Cell-free virus was immobilized on a poly-L-lysine (PLL)-treated microwell plate and incubated with compound for 1 h. Afterwards, the compound was thoroughly washed away; target cells were added and cultured for 2 weeks, followed by an extended culture with highly susceptible mitogen-activated T cells. Viral production in the cultures was measured on supernatant with HIV antigen ELISA. Negative results were confirmed by showing absence of proviral DNA in the cells. TMC-120 and TMC-125 inhibited replication of HIV-1Ba-L with average EC50 values of 38 nM and 117 nM, respectively, whereas the EC50 of UC-781 was 517 nM. Complete suppression of virus and provirus was observed at compound concentrations of 100, 300 and 1000 nM, respectively. Inhibition of all primary isolates followed the same pattern as HIV-1Ba-L. In contrast, pre-treating the virus with the nucleotide RTI PMPA and AZT failed to inhibit infection even at a concentration of 100000 nM. These data clearly suggest that NNRTIs inactivate RT enzymatic activity of different viral clades (predominant in the epidemic) and might be proposed for further testing as a sterilizing microbicide worldwide.
Language modeling by variable length sequences: theoretical formulation and evaluation of multigrams (2002)

The multigram model assumes that language can be described as the output of a memoryless source that emits variable-length sequences of words. The estimation of the model parameters can be formulated as a maximum likelihood estimation problem from incomplete data. We show that estimates of the model parameters can be computed through an iterative expectation-maximization algorithm and we describe a forward-backward procedure for its implementation. We report the results of a systematical evaluation of multigrams for language modeling on the ATIS database. The objective performance measure is the test set perplexity. Our results show that multigrams outperform conventional n-grams for this task.
Efficient algorithms for maximum likelihood decoding in the surface code (2014)

We describe two implementations of the optimal error correction algorithm known as the maximum likelihood decoder (MLD) for the 2D surface code with a noiseless syndrome extraction. First, we show how to implement MLD exactly in time $O(n^2)$, where $n$ is the number of code qubits. Our implementation uses a reduction from MLD to simulation of matchgate quantum circuits. This reduction however requires a special noise model with independent bit-flip and phase-flip errors. Secondly, we show how to implement MLD approximately for more general noise models using matrix product states (MPS). Our implementation has running time $O(n\chi^3)$ where $\chi$ is a parameter that controls the approximation precision. The key step of our algorithm, borrowed from the DMRG method, is a subroutine for contracting a tensor network on the two-dimensional grid. The subroutine uses MPS with a bond dimension $\chi$ to approximate the sequence of tensors arising in the course of contraction. We benchmark the MPS-based decoder against the standard minimum weight matching decoder observing a significant reduction of the logical error probability for $\chi\ge 4$.
Imaging layers for 50 kV electron beam lithography: Selective displacement of noncovalently bound amine ligands from a siloxane host film (2001)

We report the development of an imaging layer technology for 50 kV electron-beam lithography based upon the displacement of noncovalently bound amine ligands from a siloxane host film. The patterned films were used as templates for the selective deposition of an electroless nickel film resulting in a positive tone imaging mechanism. The deposited nickel was sufficiently robust to function as an etch mask for pattern transfer by reactive ion etching. Metallized and etched patterns with linewidths to approximately 40 nm are demonstrated using an exposure dose of 500 μC/cm2.
Hyaluronan for knee osteoarthritis: an updated meta-analysis of trials with low risk of bias (2015)

This meta-analysis of high-quality trials of IAHA versus placebo shows that IAHA provides a moderate but real benefit for patients with KOA.
Lithium Salt Distribution and Thermodynamics in Electrolytes Based on Short Perfluoropolyether-block-Poly(ethylene oxide) Copolymers (2020)

Wide-angle X-ray scattering (WAXS) was used to study the distribution of salt in short-chain disordered block copolymer electrolytes with concentration fluctuations on the length scale of 1 nm. The electrolytes were binary mixtures of lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) salt and a short block copolymer comprising perfluoroether (PFE) segments covalently bonded to ethylene oxide (EO) segments. We develop a method to analyze scattering data from mixtures of block copolymers and salt where salt distribution is not known beforehand, using a minimal number of adjustable parameters. The WAXS peak due to scattering from disordered concentration fluctuations is fit to a random phase approximation (RPA) model that includes a parameter to describe the partitioning of salt between the perfluoropolyether (PFPE)-rich and poly(ethylene oxide) (PEO)-rich concentration fluctuations. This method enables quantification of the salt distribution and the effective Flory–Huggins interaction parameter between polymer segments. We posit that attractive interactions between the TFSI– anion and PFPE (fluorous effect) drive some of the salt into the PFPE-rich fluctuations. On the other hand, the attractive interactions between Li+ and EO segments drive the remaining salt molecules into the PEO-rich fluctuations. We use WAXS to quantify LiTFSI partitioning between the PFE and EO segments in the block copolymer. The segregation between blocks, quantified by an effective Flory–Huggins interaction parameter between polymer segments, decreases with increasing salt concentration, behavior that is atypical for block copolymer electrolytes.
Development of high spatial resolution detector for characterization of X-ray optics (2011)

Technological innovations in grazing incidence X-ray optics have been crucial to the advancement of the field of X-ray astronomy. Improvements in X-ray focusing optics translate to higher sensitivity for X-ray telescopes operating in the energy range above 10 keV. Full characterization of the X-ray optics involves measurement of the point spread function, scattering, and reflectivity properties of substrate coatings. This requires a very high spatial resolution, high sensitivity, photon counting and energy discriminating large area detector. In this paper we describe the construction of a detector that is well suited to meet these requirements. A prototype version of this camera was used to calibrate the X-ray focusing optics for the Nuclear Spectroscopic Telescope Array (NuSTAR) mission. Analysis of the data obtained during the ground calibration of the NuSTAR telescopes demonstrated the advantages of such a high resolution 2D detector for hard X-rays (30+ keV); however it showed some limitations for medium energy X-rays (8–30 keV). We present here, alternative methods under investigation to improve performance of the detector for medium energy X-rays such as changing the morphology of the CsI:Tl scintillator, improving light transport from scintillator to EMCCD and using a novel bright scintillator, Ba2CsI5:Eu.
DVAE#: Discrete Variational Autoencoders with Relaxed Boltzmann Priors (2018)

Boltzmann machines are powerful distributions that have been shown to be an effective prior over binary latent variables in variational autoencoders (VAEs). However, previous methods for training discrete VAEs have used the evidence lower bound and not the tighter importance-weighted bound. We propose two approaches for relaxing Boltzmann machines to continuous distributions that permit training with importance-weighted bounds. These relaxations are based on generalized overlapping transformations and the Gaussian integral trick. Experiments on the MNIST and OMNIGLOT datasets show that these relaxations outperform previous discrete VAEs with Boltzmann priors. An implementation which reproduces these results is available at https://github.com/QuadrantAI/dvae .
Optimizing Bandwidth Density and Power Efficiency with Silicon Photonic Interconnections (2011)

We motivate the need for energy-efficient silicon-based optical interconnects to the chip and review recent progress in the development of ultra-low-power, high-density silicon photonic wavelength-division multiplexed link components. Article not available.
Surface Functionalized Carbon Nanofiber Supports for Alkaline ORR Catalysts (2015)

Fuel cells are attractive because they provide clean and efficient energy for stationary and portable applications. Among the various types of fuel cells, the proton-exchange membrane fuel cells (PEMFC) have a high energy density and a fast start-up, but the cost of noble-metal catalysts and perfluorinated membranes is high. Anion-exchange membrane fuel cells (AEMFC) are attractive because they have enhanced the oxygen reduction and methanol oxidation kinetics at high pH, which makes the use of non-noble catalysts possible. Carbon nanofibers (CNFs) have outstanding structural, mechanical and electrical properties, and are widely used as catalyst supports in fuel cells. CNFs are also considered to be good material for the oxygen reduction reaction catalysts in alkaline fuel cells because of their high surface area, thermal stability and electrical conductivity. In this work, we use CNFs as the support for fuel cell catalysts in hybrid fuel cells, which combine alkaline and acidic conditions at the different electrodes. Functional groups were added onto the CNFs, including carboxyl groups (CNF-OX), carbonyl groups (CNF-CO), hydroxyl groups (CNF-OH) and nitrogen-containing groups (CNF-ON). In previous studies, they were tested them in half-cell experiments and it was found that the catalysts supported on CNF-ON have high ORR activity. The CNF-ON electrodes can change the ORR from the two-electron pathway to the four-electron pathway. Pt/CNFs have been tested in hybrid fuel cell and compared with Pt/C.