gebhart/patrepeval huggingface dataset:
cell-related gene expression in 3D cancer spheroids induced by purified colon tumor-initiating cells (2010)

Background: Growing evidence suggests that the majority of tumors are organized hierarchically, comprising a population of tumor-initiating, or cancer stem cells (CSCs) responsible for tumor development, maintenance and resistance to drugs. Previously we have shown that the CD133high/CD44high fraction of colon cancer cells is different from their bulk counterparts at the functional, morphological and genomic levels. In contrast to the majority of colon cancer cells expressing moderate levels of CD133, CD44 and CD166, cells with a high combined expression of CD133 and CD44 possessed several characteristic stem cell features, including profound self-renewal capacity in vivo and in vitro, and the ability to give rise to different cell phenotypes. The present study was undertaken for two aims: a) to determine stem cell-related genomic characteristics of floating 3D multicellular spheroids induced by CD133 high / CD44high colon cancer cells; and b) to evaluate CSC-specific alterations induced by new-generation taxoid SB-T-1214. Results: Selected CSC phenotype was isolated from three independent invasive colon cancer cell lines, HCT116, HT29 and DLD-1. A stem cell-specific PCR array assay (SABiosciences) revealed that colonospheres induced by purified CD133 high /CD44 high expressing cells display profound up-regulation of stem cell-related genes in comparison with their bulk counterparts. The FACS analysis has shown that the 3D colonospheres contained some minority cell populations with high levels of expression of Oct4, Sox2, Nanog and c-Myc, which are essential for stem cell pluripotency and self-renewal. Single administration of the SB-T-1214 at concentration 100 nM-1 μM for 48 hr not only induced growth inhibition and apoptotic cell death in these three types of colon cancer spheroids in 3D culture, but also mediated massive inhibition of the stem cell-related genes and significant down-regulation of the pluripotency gene expression. PCR array and FACS data were confirmed with western blotting. Importantly, viable cells that survived this treatment regimen were no longer able to induce secondary floating spheroids and exhibited significant morphological abnormalities. Conclusions: We report here that a new-generation taxoid SB-T-1214 possesses significant activity against colon cancer spheroids induced by and enriched with drug resistant tumorigenic CD133high/CD44high cells and efficiently inhibited expression of the majority of stem cell-related genes. Our data indicates that the previously observed longterm efficacy of SB-T-1214 against drug resistant colon tumors in vivo may be explained by the down-regulation of multiple stem cell-related genes in the tumorigenic cell population, in addition to its known efficacy as a mitotic poison against proliferating cancer cells.
Partitioning Sparse Matrices with Eigenvectors of Graphs (1990)

The problem of computing a small vertex separator in a graph arises in the context of computing a good ordering for the parallel factorization of sparse, symmetric matrices. An algebraic approach for computing vertex separators is considered in this paper. It is, shown that lower bounds on separator sizes can be obtained in terms of the eigenvalues of the Laplacian matrix associated with a graph. The Laplacian eigenvectors of grid graphs can be computed from Kronecker products involving the eigenvectors of path graphs, and these eigenvectors can be used to compute good separators in grid graphs. A heuristic algorithm is designed to compute a vertex separator in a general graph by first computing an edge separator in the graph from an eigenvector of the Laplacian matrix, and then using a maximum matching in a subgraph to compute the vertex separator. Results on the quality of the separators computed by the spectral algorithm are presented, and these are compared with separators obtained from other algorithms for computing separators. Finally, the time required to compute the Laplacian eigenvector is reported, and the accuracy with which the eigenvector must be computed to obtain good separators is considered. The spectral algorithm has the advantage that it can be implemented on a medium-size multiprocessor in a straightforward manner.
Thermoplastic Molding of Regenerated Silk (2019)

Historically, early insights into the unique structure and properties of native silk indicate that thermal processing was not a good option for this material due to the stability of β-sheet nanocrystallites, resulting in thermal degradation prior to melting. Thus, canonical approaches developed over the past 65 years to fabricate silk-based materials for biomedical applications involve solution-derived processing methods that have advantages and limitations with regard to silk protein solubility, stability in solution, and time and cost efficiency. Here we report the first successful solid-state thermal processing of regenerated silk, resulting in the molding of solid silk directly into bulk ‘parts’ or devices with tunable mechanical properties, while retaining machinability, biocompatibility and degradability. At elevated temperature and pressure,regenerated amorphous silk nanomaterials (ASN) with ultralow β-sheet content undergo thermal fusion via molecular rearrangement and self-assembly assisted by bound waterto form a robust bulk material. This transformativethermal processing technique with silk reverses presumptions about the limitations of direct thermal processing of silk into functional devices, demonstrating new options in molding silk into a wide range of new material formats that align with more traditional thermal processing options for synthetic polymer. Furthermore, a variety of silk-based functional composite materials can be made for tailoring the properties of the devices.
A MICROFLUIDIC DEVICE FOR SORTING CANCER CELLS BASED ON (2011)

In this paper, we present a microfluidic device that allows for sorting of cancer cells based on their chemotactic migration speeds. We used breast cancer cell line cells to demonstrate cell seeding, migration and releasing in our microfluidic device. The ability of our device to provide subpopulations of chemotactically heterogeneous cancer cells should find useful applications in studying cancer and metastasis.
Constructing the context through goals and schemata: top-down processes in comprehension and beyond (2015)

My main purpose here is to provide an account of context selection in utterance understanding in terms of the role played by schemata and goals in top-down processing. The general idea is that information is organized hierarchically, with items iteratively organized in chunks-here called "schemata"-at multiple levels, so that the activation of any items spreads to schemata that are the most accessible due to previous experience. The activation of a schema, in turn, activates its other components, so as to predict a likely context for the original item. Since each input activates its own schemata, conflicting schemata compete with (and inhibit) each other, while multiple activations of a schema raise its likelihood to win the competition. There is therefore a double movement-with bottom-up activation of schemata enabling top-down prediction of other contextual components-triggered by multiple sources. Another claim of the paper is that goals are represented by schemata placed at the highest-levels of the executive hierarchy, in accordance with Fuster's model of the brain as a hierarchically organized perception-action cycle. This account can be considered, in part at least, a development of ideas contained in Relevance Theory, though it may imply that some other claims of the theory are in need of revision. Therefore, a secondary purpose of the paper is a contribution to the analysis of that theory.
Enantioselective Total Synthesis of the Cyclophilin-Binding Immunosuppressive Agent Sanglifehrin A This work was financially supported by Eli Lilly and Company and a Robert Mayer Graduate Fellowship (to M.D.). We thank Prof. K. C. Nicolaou for providing authentic spectra of 1. (2001)

Crafting of the building blocks 1–3 allows the convergent conjoining of 2–3 in advance of macrolactonization. The subsequent linkup of the eastern sector with 1 by Stille coupling enabled the convenient stereocontrolled assembly of the immunosuppressive agent (−)-sanglifehrin A (Boc=tert-butoxycarbonyl).
Observation of an Ionospheric Disturbance Caused by a Gamma-Ray Burst (1987)

A first observation of an ionospheric disturbance from a gamma-ray burst is reported. The burst, GB30801, occurred at 22:14:18 UT on August 1, 1983, and was one of the strongest ever observed. The total fluence was 0.002 erg/sq cm, most of which occurred in the first 4 s of the burst. Simultaneously, a change was observed in the amplitude of a VLF radio signal from a transmitter in Rugby, England indicative of an ionospheric disturbance. Weaker disturbances were also recorded at the same receiving site on signals from VLF stations in Annapolis, Maryland and Lualualei, Hawaii. The times of the burst and the disturbances are coincident within the 10-s resolution of the VLF recording system. No similar disturbances were observed within 60 hr around the time of the burst. In the future, a network of VLF burst monitors may provide measurements of the total ionizing energy fluence from a burst, as well as some limited directional information.
Highly Enantioselective Phase‐Transfer Catalytic α‐Alkylation of α‐tert‐Butoxycarbonyllactams: Construction of β‐Quaternary Chiral Pyrrolidine and Piperidine Systems (2011)

Abstract A new enantioselective α‐alkylation of α‐ tert ‐butoxycarbonyllactams for the construction of β‐quaternary chiral pyrrolidine and piperidine core systems is reported. α‐Alkylations of N ‐methyl‐α‐ tert ‐butoxycarbonylbutyrolactam and N ‐diphenylmethyl‐α‐ tert ‐butoxycarbonylvalerolactam under phase‐transfer catalytic conditions (solid potassium hydroxide, toluene, −40 °C) in the presence of ( S , S )‐3,4,5‐trifluorophenyl‐3,3′,5,5′‐tetrahydro‐2,6‐bis(3,4,5‐trifluorophenyl)‐4,4′‐spirobi[4 H ‐dinaphth[2,1‐ c :1′,2′‐ e ]azepinium] bromide [( S , S )‐NAS Br] (5 mol%) afforded the corresponding α‐alkyl‐α‐ tert ‐butoxycarbonyllactams in very high chemical (up to 99%) and optical yields (up to 98% ee ). Our new catalytic systems provide attractive synthetic methods for pyrrolidine‐ and piperidine‐based alkaloids and chiral intermediates with β‐quaternary carbon centers.
Factors influencing options in primary breast cancer treatment. (1987)

Primary breast cancer treatment is determined by tumor factors and by patient preference. Breast cancer treatments that preserve the cosmetic appearance of the breast are appealing and effective for appropriately selected patients; long-term survival following tumor excision and breast irradiation appears to be comparable to that for mastectomy. Since April 1981, when a protocol was developed and treatment options were offered, factors influencing treatment selection have been analyzed in 206 consecutive primary breast cancer patients. Mastectomy was dictated by tumor-related factors in 96 patients (47%); 110 patients (53%) had the option of mastectomy or conservation--tumor excision plus radiotherapy to the breast. Among these 110 eligible patients, 54 chose conservation (49%) and 56 chose mastectomy (51%). Intraoperative findings for ten patients electing conservation necessitated mastectomy, so conservation was accomplished for 44 (21%) of those treated for breast cancer. Beginning in July 1982, breast cancer patients took a battery of psychosexual assessments before any operation (Profile of Mood States [POMS], Health Locus of Control Scale [HLCS] Locke-Wallace Marital Adjustment Test [MAT], Psychosocial Adjustment to Illness Scale [PAIS], Derogatis Sexual Function Inventory [DSFI], Millon Clinical Multiaxial Inventory [MCMI], and a Breast Cancer Information Test [BCIT]). Comparisons of psychologic and demographic variables were made between patients who chose mastectomy and those who chose conservation. No demographic variable was statistically significantly related to choice, although older women tended to select mastectomy more than younger women. Compared with those who elected conservation, women who elected mastectomy were more tense and anxious (P less than .01), more introverted (P less than .01), felt more depressed and dejected (P less than .05), and reported more sexual problems (P less than .05). Those who elected conservation valued their physical appearance more highly (P less than .01) and were generally more self-interested (P less than .05). Mastectomy was dictated by medical considerations for approximately half of patients with breast cancer. Among candidates for breast conservation, the importance of retaining the breast appeared to be determined to a significant degree by measurable psychological factors.
Tracking People by Predicting 3D Appearance, Location and Pose (2022)

We present an approach for tracking people in monocular videos by predicting their future 3D representations. To achieve this, we first lift people to 3D from a single frame in a robust manner. This lifting includes information about the 3D pose of the person, their location in the 3D space, and the 3D appearance. As we track a person, we collect 3D observations over time in a tracklet representation. Given the 3D nature of our observations, we build temporal models for each one of the previous attributes. We use these models to predict the future state of the tracklet, including 3D appearance, 3D location, and 3D pose. For a future frame, we compute the similarity between the predicted state of a tracklet and the single frame observations in a probabilistic manner. Association is solved with simple Hungarian matching, and the matches are used to update the respective tracklets. We evaluate our approach on various benchmarks and report state-of-the-art results. Code and models are available at: https://brjathu.github.io/PHALP.
CORRELATED MORPHOMETRIC AND BIOCHEMICAL STUDIES ON THE LIVER CELL (1969)

The basic morphological properties of liver cells are defined in the form of a morphometric model to permit integrated quantitative characterization of functionally important parameters. Stereologic methods which allow efficient and reliable quantitative evaluation of sectioned liver tissue are presented. Material, obtained by a rigorous three-stage sampling procedure from five normal rat livers, is systematically subjected to this analysis at four levels of magnification. This yields quantitative data which are expressed as "densities," i.e. content per 1 ml of tissue, as "specific dimensions" related to 100 g body weight, and as absolute dimensions per average "mononuclear" hepatocyte. Base line data relating to the normal rat liver are presented for the entire spectrum of parameters. As examples, 1 ml of liver tissue contains 169 x 10(6) hepatocyte nuclei, some 90 x 10(6) nuclei of other cells, and 280 x 10(9) mitochondria. Hepatocyte cytoplasm accounts for 77% of liver volume, and the mitochondria for 18%. The surface area of endoplasmic reticulum membranes in 1 ml of liver tissue measures 11 m(2) of which are (2/3) of the rough form carrying some 2 x 10(13) ribosomes. The surface area of mitochondrial cristae in the unit volume is estimated at 6 m(2). The validity and applicability of the method are discussed, and the data are compared with available information from other studies.
On the Problem of Optimal Path Encoding for Software-Defined Networks (2016)

Packet networks need to maintain the state in the form of forwarding tables at each switch. The cost of this state increases as networks support ever more sophisticated per-flow routing, traffic engineering, and service chaining. Per-flow or per-path state at the switches can be eliminated by encoding each packet's desired path in its header. A key component of such a method is an efficient encoding of paths through the network. We introduce a mathematical formulation of this optimal path-encoding problem. We prove that the problem is APX-hard, by showing that approximating it to within a factor less than 8/7 is NP-hard. Thus, at best, we can hope for a constant-factor approximation algorithm. We then present such an algorithm, approximating the optimal path-encoding problem to within a factor 2. Finally, we provide the empirical results illustrating the effectiveness of the proposed algorithm.
Efficient and safe correction of hemophilia A by lentiviral vector-transduced BOECs in an implantable device (2021)

Hemophilia A (HA) is a rare bleeding disorder caused by deficiency/dysfunction of the FVIII protein. As current therapies based on frequent FVIII infusions are not a definitive cure, long-term expression of FVIII in endothelial cells through lentiviral vector (LV)-mediated gene transfer holds the promise of a one-time treatment. Thus, here we sought to determine whether LV-corrected blood outgrowth endothelial cells (BOECs) implanted through a prevascularized medical device (Cell Pouch) would rescue the bleeding phenotype of HA mice. To this end, BOECs from HA patients and healthy donors were isolated, expanded, and transduced with an LV carrying FVIII driven by an endothelial-specific promoter employing GMP-like procedures. FVIII-corrected HA BOECs were either directly transplanted into the peritoneal cavity or injected into a Cell Pouch implanted subcutaneously in NSG-HA mice. In both cases, FVIII secretion was sufficient to improve the mouse bleeding phenotype. Indeed, FVIII-corrected HA BOECs reached a relatively short-term clinically relevant engraftment being detected up to 16 weeks after transplantation, and their genomic integration profile did not show enrichment for oncogenes, confirming the process safety. Overall, this is the first preclinical study showing the safety and feasibility of transplantation of GMP-like produced LV-corrected BOECs within an implantable device for the long-term treatment of HA.
Enhancement of gel properties of Scomberomorus niphonius myofibrillar protein using phlorotannin extracts under UVA irradiation (2020)

The effect of phlorotannin extracts (PTE) (from sporophyll of Undaria pinnatifida) added at different levels (0, 25, 125, 625 µmol/g protein) on the gel properties of mackerel (Scomberomorus niphonius) myofibrillar protein (MP) was studied with and without ultraviolet A (UVA) irradiation. The results showed that the gel strength and cooking yield increased in a PTE dose-dependent manner, and at the level of 625 µmol/g protein PTE, the highest gel strength of 308.43 ± 8.12 (mN·cm) and cooking yield of 76.16 ± 1.40% were obtained in the samples treated with UVA irradiation. The same samples also showed increased carbonyl content, decreased total sulfhydryl, unwinding of α-helix, and quenching of fluorescence intensity of endogenous tryptophan, all of which indicated that elevated protein oxidation in these samples led to enhanced protein cross-linking. Results of sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) indicated aggregation of myosin heavy chains (MHCs) in the UVA-treated gels with PTE, also evidenced by the dense three-dimensional network structure in these samples visualized by scanning electron microscopy (SEM). Electron spin resonance (ESR) and spin trapping results indicated that free radicals were produced during the gelation process, possibly originated from UVA-treated PTE, which played a critical role of oxidizing fish MPs, and eventually led to the improvement of the textural properties of the mackerel MP gel. PRACTICAL APPLICATION: Brown algae are a family of high-yield marine algae. Phlorotannin extracts are highly active natural substances extracted from brown algae that can have many applications. Ultraviolet A (UVA) as a green and environmentally friendly physical processing method has been widely used in food processing in recent years. The method proposed in this study could be utilized to improve properties of fish protein gel made from poorly performing low-priced fishes, and provide workable guidance for industry to expand the application of brown algae in food processing to better meet consumer's demand for high-quality marine foods.
Implementation of a MIMO OFDM-Based Wireless LAN System (2004)

The combination of multiple-input multiple-output (MIMO) signal processing with orthogonal frequency division multiplexing (OFDM) is regarded as a promising solution for enhancing the data rates of next-generation wireless communication systems operating in frequency-selective fading environments. To realize this extension of OFDM with MIMO, a number of changes are required in the baseband signal processing. An overview is given of the necessary changes, including time and frequency synchronization, channel estimation, synchronization tracking, and MIMO detection. As a test case, the OFDM-based wireless local area network (WLAN) standard IEEE 802.11a is considered, but the results are applicable more generally. The complete MIMO OFDM processing is implemented in a system with three transmit and three receive antennas, and its performance is evaluated with both simulations and experimental test results. Results from measurements with this MIMO OFDM system in a typical office environment show, on average, a doubling of the system throughput, compared with a single antenna OFDM system. An average expected tripling of the throughput was most likely not achieved due to coupling between the transmitter and receiver branches.
Cross-sectional imaging of pendeo-epitaxial GaN using continuous-wave two-photon microphotoluminescence (2002)

A technique utilizing continuous-wave two-photon absorption has been developed for optically sectioning and imaging deep into GaN structures. Imaging at depths greater than 20 μm below the surface of a coalesced pendeo-epitaxial GaN sample is demonstrated. Free and donor-bound excitonic emission in this sample appears to originate at the surface, acceptor-bound exciton transitions are strongest in the top bulk portion of the sample, and subgap luminescence is most intense deep in the sample. The depth resolution of the imaging system is measured to be 1.75 μm near the GaN surface.
Free-breathing motion compensated 4D (3D+respiration) T2-weighted turbo spin-echo MRI for body imaging (2022)

Purpose: To develop and evaluate a free-breathing respiratory motion compensated 4D (3D+respiration) $T_2$-weighted turbo spin echo sequence with application to radiology and MR-guided radiotherapy. Methods: k-space data are continuously acquired using a rewound Cartesian acquisition with spiral profile ordering (rCASPR) to provide matching contrast to the conventional linear phase encode ordering and to sort data into multiple respiratory phases. Low-resolution respiratory-correlated 4D images were reconstructed with compressed sensing and used to estimate non-rigid deformation vector fields, which were subsequently used for a motion compensated image reconstruction. rCASPR sampling was compared to linear and CASPR sampling in terms of point-spread-function (PSF) and image contrast with in silico, phantom and in vivo experiments. Reconstruction parameters for low-resolution 4D-MRI (spatial resolution and temporal regularization) were determined using a grid search. The proposed motion compensated rCASPR was evaluated in eight healthy volunteers and compared to free-breathing scans with linear sampling. Image quality was compared based on visual inspection and quantitatively by means of the gradient entropy. Results: rCASPR provided a superior PSF (similar in ky and narrower in kz) and showed no considerable differences in images contrast compared to linear sampling. The optimal 4D-MRI reconstruction parameters were spatial resolution=$4.5 mm^3$ and $λ_t=10^{-4}$. The groupwise average gradient entropy was 22.31 for linear, 22.20 for rCASPR, 22.14 for soft-gated rCASPR and 22.02 for motion compensated rCASPR. Conclusion: The proposed motion compensated rCASPR enables high quality free-breathing T2-TSE with minimal changes in image contrast and scan time. The proposed method therefore enables direct transfer of clinically used 3D TSE sequences to free-breathing.