gebhart/patrepeval huggingface dataset:
LPA3 receptor mediates chemotaxis of immature murine dendritic cells to unsaturated lysophosphatidic acid (LPA) (2007)

Increasing evidence supports roles for lipids in the biology of immune cells. In particular, bioactive lipids such as sphingosine-1-phosphate (S1P) bind to cognate G protein-coupled receptors (GPCRs) and modulate leukocyte trafficking and homeostasis. Lysophosphatidic acid (LPA) represents a family of bioactive lipids, which differ in the length and degree of saturation of the fatty acyl chain. LPA is structurally related to S1P and exerts cellular effects by binding to five known GPCRs (LPA(1-5)). Its function in the immune system is less clear, although it was shown to induce chemotaxis of human dendritic cells (DCs) and activated T cells. In this study, we show that LPA can induce chemotaxis of immature but not mature mouse DCs and that only unsaturated and not saturated LPA species are efficient chemoattractants. However, both LPA species do not alter DC maturation or chemotaxis to other chemokines. The loss of DC migration capability correlated with the down-regulation of expression of the receptors LPA(3) and LPA(5), and expression of LPA(1), LPA(2), and LPA(4) did not change. A LPA(3) antagonist reduced immature DC migration to LPA by 70%, suggesting that LPA(3) mediates immature DC chemotaxis to unsaturated species of LPA. Furthermore, isolated, immature DCs from mice lacking LPA(3) exhibited a 50% reduction in migration to LPA. In summary, our results indicate that immature mouse DCs migrate preferentially in response to unsaturated LPA and that LPA(3) is important in this response.
Branch history table optimization (1992)

To maintain peak execution rates, a pipeline processor must have a steady stream of instructions available. Taken branches in the instruction stream produce breaks in execution and drop performance to well below ideal. To attempt to eliminate these latencies, branch prediction mechanisms have been proposed that take advantage of past branching behavior.
A Branch History Table (BHT) stores past action and target for branches, and uses this history to predict future branch behavior. Although past behavior is a good indication of future behavior, many decision structures violate this simple prediction strategy. By studying the high-level language constructs that generate these low-level structures, mechanisms are developed that reduce the number of wrong predictions made by a BHT. A CALL/RETURN Stack Pair and a Case Block Table are combined with a BHT to significantly reduce the number of wrong branch predictions.
Although a BHT provides a reliable mechanism for predicting branches, the cost of a large BHT is high due to the size of a single BHT entry. By coupling a BHT with a Decode History Table (DHT), the overall table space can be reduced, while improving pipeline performance.
To investigate the merits of these new BHT designs, trace-driven modeling is used. The inputs to the models are traces taken from the SPEC benchmark suite. To characterize the branch content of the traces used in this research, renewal theory is used. Branches on the traces are treated as renewals, and the number of instructions between branches as inter-renewal times. By measuring the density function of the inter-renewal times, the stationary distribution of the number of branches in a finite-length pipeline can be derived. The model results differ from actual measurements by less than 5% in most cases.
Design of a dynamic optical tissue phantom to model extravasation pharmacokinetics (2010)

We describe an optical tissue phantom that enables the simulation of drug extravasation from microvessels and validates computational compartmental models of drug delivery. The phantom consists of a microdialysis tubing bundle to simulate the permeable blood vessels, immersed in either an aqueous suspension of titanium dioxide (TiO2) or a TiO2 mixed agarose scattering medium. Drug administration is represented by a dye circulated through this porous microdialysis tubing bundle. Optical pharmacokinetic (OP) methods are used to measure changes in the absorption coefficient of the scattering medium due to the arrival and diffusion of the dye. We have established particle sizedependent concentration profiles over time of phantom drug delivery by intravenous (IV) and intra-arterial (IA) routes. Additionally, pharmacokinetic compartmental models are implemented in computer simulations for the conditions studied within the phantom. The simulated concentration-time profiles agree well with measurements from the phantom. The results are encouraging for future optical pharmacokinetic method development, both physical and computational, to understand drug extravasation under various physiological conditions.
Experiment on cross relaxation in CO&amp;lt;inf&amp;gt;2&amp;lt;/inf&amp;gt; (1972)

The details of the hole-burning process are studied experimentally and theoretically in a Doppler-broadened gain or absorption line in pure CO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> and in CO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> -N <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> mixtures contained in a test cell. The change of absorption or gain of the test cell when irradiated by a saturating laser in a <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">P</tex> transition is probed with another laser operating in one of many <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R</tex> transitions. In this way one may determine the rate of velocity cross relaxation within a single rotational-vibrational level and the rate of cross relaxation between different rotational levels of the upper and lower vibrational states. When the probing laser shares a common upper or lower level with the saturating laser, a pip is observed in the differential absorption or gain profile at total pressures of less than 0.5 torr. At higher pressures the relaxation across the velocity profile eliminates the pip. An analysis is presented of the population distribution in the multilevel system of CO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> . Three of the relaxation rates (describing the relaxation across the velocity profile of a single level, the relaxation among rotational levels of the vibrational state, and the phenomenological relaxation rate of entry into and departure from the upper and lower vibrational states) are determined. The last of the three rates is found to be dominated by diffusion at the pressures used in the experiment.
Abstract WP4: Which Characteristics Determine the Decision to Proceed With Endovascular Therapy in Acute Stroke Patients: Results From an International Multidisciplinary Study (2019)

Introduction: The current management of acute ischemic stroke has changed recently with the publication of randomized trials using endovascular therapy (EVT). Rationale/Hypothesis: Limited information is however available on how physicians make decisions regarding patient selection for endovascular therapy (EVT) in the real-world. Methods: We conducted an international web-based cross-sectional survey of stroke physicians and interventionalists to assess the decision to offer EVT. Part 1 of the survey used hierarchical Bayes’ disaggregate discrete choice modelling to analyze ten pairs of patient scenarios, randomly generated from ten key patient characteristics to have respondents choose which scenario was best suited for EVT in their practice. Part 2 of the survey used mixed effects logistic regression modelling to analyze 22 randomly chosen patient scenarios, again randomly generated from several key patient and hospital level characteristics. Results: 607 physicians [mean age of 44 (SD 8.5) years, 83.5% men, 53.6% neurologists, 28.7% neuro-interventionists, 13.3% neurosurgeons, 4.7% other], from 38 countries participated. Using disaggregate discrete choice analysis, the most influential characteristic in deciding about EVT was the extent of ischemic change (ASPECTS)/volume of infarct core (26-28% of the choice). Patient age, premorbid status, baseline NIHSS score, and occlusion location (13-15% each) were the other relevant characteristics. Using mixed effects logistic regression, baseline stroke severity (NIHSS&gt; 15 vs. NIHSS 0-5, OR 6.7; 95% CI 4.8-9.5), ASPECTS (5-7 vs. 0-4, OR 9.4; 95% CI7.4-11.9) and occlusion location (distal M2 vs. ICA/M1, OR 012; 95% CI 0.08-0.17) were the most relevant characteristics in deciding about EVT. Time from stroke onset, sex, comorbidities, time of day (off hours vs. day time) were all less relevant in deciding about EVT in both analyses. Conclusion: Severity of stroke assessed clinically, and extent of brain infarction and location of thrombus assessed on imaging are the dominant characteristics that treating physicians use in the real world when deciding about EVT for patients with an acute ischemic stroke.
Broadband marine CSEM: New benefits for subsalt and around salt exploration (2014)

Summary We present the results of a demonstration research long-offset, multi-component, broadband marine Controlled Source Electromagnetic (mCSEM) survey conducted over a complex salt diapirs ultra deep water domain in the Espirito Santo Basin (offshore Brazil). The Espirito Santo ultra-deep water area was chosen and the mCSEM acquisition strategy was set to proof the value of broadband mCSEM coupled with a new ‘hybrid’ seismic-EM interpretation workflow for enhanced subsalt and around salt imaging. We show that, while NAZ seismic leaves large uncertainties in the interpretation of the shape, size and base of salt (BOS) structures, requiring expensive advanced depth migration and decision to resort to wide azimuth or full azimuth data acquisition, the broadband mCSEM data and the seismic-EM interpretation workflow may be applied as a cost-effective alternative to deliver significant improvements of subsalt and around salt imaging suitable for prospect generation.
Lithium Iron Orthosilicate Cathode: Progress and Perspectives (2017)

The pursuit of cathodes with a high capacity is remarkably driven by the ever increasing demand of high-energy lithium ion batteries in electronics and transportation. In this regard, polyanionic lithium iron orthosilicate (Li2FeSiO4) offers a promising opportunity because it affords a high theoretical capacity of 331 mAh g–1. However, such a high theoretical capacity of Li2FeSiO4 has frequently been compromised in practice because of the extremely low electronic and ionic conductivity. To address this issue, material engineering strategies to boost the Li storage kinetics in Li2FeSiO4 have proven indispensable. In this Perspective, we will briefly present the structural characteristics, intrinsic physicochemical properties, and electrochemical behavior of Li2FeSiO4. We particularly focus on recent materials engineering of silicates, which is implemented mainly through advanced synthetic techniques and elaborate controls. This Perspective highlights the importance of integrating theoretical analysis into experimental implementation to further advance the Li2FeSiO4 materials.
[A Case of Bladder Adenocarcinoma with Rectal Metastasis]. (2015)

A 77 year-old man with asymptomatic microscopic hematuria underwent a cystoscopic examination, which identified a broad-based papillary tumor at the cervix of the bladder. Adenocarcinoma was detected in the biopsy specimen. MRI and CT examination showed a huge papillary tumor of the bladder invading the inner lobe of the prostate. In addition, the wall of the lower rectum exhibited thickening with enlargement of the regional lymph nodes. Endoscopy disclosed a hemi-circular rectal tumor and pathological examination revealed adenocarcinoma, the profile of which was similar to the bladder tumor. The levels of CEA and CA19-9 were 5.3 ng/mL and 39 U/mL, respectively. A differential diagnosis considering bladder cancer, rectal cancer, or both was necessary before planning a treatment strategy. Since both tumors were judged to be resectable, total pelvic exenteration was carried out. Through detailed postoperative pathological examinations, it was concluded that this tumor was of bladder origin and it invaded the prostate along with metastasis to the rectum. Adenocarcinoma of the bladder is extremely rare and exhibits aggressive behavior.
LP-based pivoting algorithm for higher-order correlation clustering (2018)

Correlation clustering is an approach for clustering a set of objects from given pairwise information. In this approach, the given pairwise information is usually represented by an undirected graph with nodes corresponding to the objects, where each edge in the graph is assigned a nonnegative weight, and either the positive or negative label. Then, a clustering is obtained by solving an optimization problem of finding a partition of the node set that minimizes the disagreement or maximizes the agreement with the pairwise information. In this paper, we extend correlation clustering with disagreement minimization to deal with higher-order relationships represented by hypergraphs. We give two pivoting algorithms based on a linear programming relaxation of the problem. One achieves an $$O(k \log n)$$ -approximation, where n is the number of nodes and k is the maximum size of hyperedges with the negative labels. This algorithm can be applied to any hyperedges with arbitrary weights. The other is an O(r)-approximation for complete r-partite hypergraphs with uniform weights. This type of hypergraphs arise from the coclustering setting of correlation clustering.
RBIO-02. PERSONALIZED SCREENING OF RADIOSENSITIZATION BY A TGF-β SMALL MOLECULE INHIBITOR USING CULTURED EXPLANTS OF HIGH GRADE GLIOMA (HGG) PATIENT SPECIMENS (2016)

High-grade gliomas (HGG) manifest profound radioresistance via cell-intrinsic and microenvironmental mechanisms. Transforming growth factor-β (TGF-β) is a key component of the HGG microenvironment, which we have shown enables radioresistance directly by enforcing an effective DNA damage response (DDR), and indirectly by promoting glioma stem cell self-renewal. Heterogeneity of HGG subtypes and patient differences raise the question of general utility of TGF-β inhibition for radiosensitization. Given the impact of microenvironment, we reasoned that personalized radiation biology could be attained by maintaining critical cell interactions. Here, we used HGG explant cultures as a patient-specific platform to test whether a prototypic small molecule inhibitor of the TGF-β type I receptor kinase, LY364947, compromises the DDR. Radiation induced γ-H2AX foci formation was used to assess the molecular recognition of DNA damage, and Sox2 and Notch1 intracellular domain (NICD) were evaluated as glioma stem cell self-renewal signals. Primary HGG (n=7) explants were established on raft inserts for 4 days, treated for 24 hr with LY364947 before irradiating with 2 Gy on day 5. Specimens were fixed 60 min later for immunofluorescence detection of markers. Collectively, radiation-induced γ-H2AX foci were reduced by 37% in LY364947-treated specimens compared to controls. Individual patient specimens ranged from showing no effect of LY364947 to a complete abrogation of radiation-induced foci (2 non-responders and 5 responders), which suggest that cultured HGG explants might be useful for predicting patient-specific radiosensitization with TGF-β antagonists, which are currently in clinical trials. Compared to control explants, self-renewal signal Sox2 increased 2.4 ± 0.3-fold (p<0.01) and NICD1 increased 1.3 ± 0.1-fold (p<0.005) in irradiated explants. Neither marker increased in irradiated HGG specimens treated with LY364947. Our study demonstrates the utility of implementing explants for patient screening, while the apparent benefit of TGF-β inhibition in most irradiated HGG specimens provides further support for clinical trials of TGF-β inhibition during radiotherapy.
Synthesis of Macrocyclic Poly(3-hexylthiophene) and Poly(3-heptylselenophene) by Alkyne Homocoupling (2016)

Here we report the synthesis of cyclic samples of poly(3-hexylthiophene) (P3HT, degrees of polymerization = 25, 40, and 75) and poly(3-heptylselenophene) (P37S, DP = 30). Cyclization was accomplished using a mild alkyne-alkyne homocoupling procedure. Alkyne-terminated poly(ethylene glycol) was then coupled to residual uncyclized polymers, which were subsequently removed by column chromatography, enabling isolation and characterization of pure cyclic polymers. Cyclization was confirmed by the disappearance of terminal alkyne protons, the decrease in hydrodynamic radius [measured by size exclusion chromatography (SEC)], and the observed identical molecular weight distribution [measured by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry]. The lower weight macrocyclic polymers have decreased self-assembly as measured by optical absorption and transmission electron microscopy. The highest weight macrocycles were imaged using scanning tunneling microscopy. Cyclic polymers adopted a tightly bent conformation, while their linear analogues assembled as fully extended chains. Our method of cyclization and purification is broadly applicable to conjugated polymers (CPs) and will enable the development of novel optoelectronic materials.
Gonadal cell apoptosis: hormone-regulated cell demise (1996)

It has become evident that apoptosis, an active form of cell 'suicide', plays an important role in the normal function of all tissues. A balance of cell proliferation and apoptosis is maintained in a healthy individual and any imbalance of the two processes could lead to pathological changes. In both sexes, massive apoptosis accounts for the demise of a majority of gonadal cells (ovarian granulosa cells and male germ cells) during reproductive life. Recent studies have indicated the important role of gonadotrophins as survival factors in both the ovary and the testis. Furthermore, intra-gonadal survival. factors in the ovary (oestrogens, insulin-like growth factor I, epidermal growth factor, basic fibroblast growth factor, interleukin-1 beta, nitric oxide, etc.) and testis (androgens) have been shown to act in concert with the gonadotrophins. In contrast, several apoptotic factors (androgens, gonadotrophin-releasing hormone-like peptide and interleukin-6) may be important in inducing the demise of ovarian follicles. Understanding of the hormonal and cellular mechanisms responsible for gonadal cell apoptosis will provide new approaches for the treatment of gonadal degenerative conditions such as premature ovarian failure and cryptorchidism, as well as for the design of new contraceptive approaches.
Countercurrent tangential chromatography for large‐scale protein purification (2010)

Recent advances in cell culture technology have created significant pressure on the downstream purification process, leading to a "downstream bottleneck" in the production of recombinant therapeutic proteins for the treatment of cancer, genetic disorders, and cardiovascular disease. Countercurrent tangential chromatography overcomes many of the limitations of conventional column chromatography by having the resin (in the form of a slurry) flow through a series of static mixers and hollow fiber membrane modules. The buffers used in the binding, washing, and elution steps flow countercurrent to the resin, enabling high-resolution separations while reducing the amount of buffer needed for protein purification. The results obtained in this study provide the first experimental demonstration of the feasibility of using countercurrent tangential chromatography for the separation of a model protein mixture containing bovine serum albumin and myoglobin using a commercially available anion exchange resin. Batch uptake/desorption experiments were used in combination with critical flux data for the hollow fiber filters to design the countercurrent tangential chromatography system. A two-stage batch separation yielded the purified target protein at >99% purity with 94% recovery. The results clearly demonstrate the potential of using countercurrent tangential chromatography for the large-scale purification of therapeutic proteins.
The Electronics Revolution: From E-Wonderland to E-Wasteland (2009)

Discarded electronics present serious threats to health and ecosystems, making e-waste regulations a policy priority.
In‐Situ Formation of Silver Nanoparticles in PEI (2009)

Abstract Nanocomposites consisting of spherical particles of Ag were prepared using a single step in situ method whereby Ag is introduced into the dissolved polymer via dissolution as the organometallic complex Ag TFA in the same solvent as the polymer. The kinetic rate of formation of the particles is determined using WAXS and SAXS measurements. Nanoparticle formation is found to depend on reducing the solvent/polymer ratio, which leads to de‐solvating the metal complex. This destabilizes the metal precursor complex, causing it to degrade and the metal particles to phase separate by a thermodynamic driving force. The size of the nanoparticles varies with the cure temperature and the conditions affecting molecular mobility.
Identification of fibroblast growth factors in bovine cheese whey (1995)

Acidic and basic fibroblast growth factors (FGF) were identified in bovine cheese whey after partial purification using a two step procedure. Cation-exchange chromatography produced a mitogen-rich extract which was loaded on to a heparin-sepharose column and eluted stepwise with 0.8, 1.2 and 2.0 M-NH4HCO3. Mitogenic activity was found in all three fractions by cell growth assays using Balb/c-3T3 fibroblasts. Immunoblotting identified acidic FGF in the 1.2 M-eluate and basic FGF in the 2.0 M-eluate, but neither acidic nor basic FGF was detected in the 0.8 M-fraction. Quantitative radioreceptor assays indicated 5.8 ng of acidic FGF-like activity and 19.8 ng of basic FGF-like activity per 1 whey in the appropriate eluates. This study represents the first direct demonstration of FGF in milk.
Hodgkin Lymphoma (2020)

An excisional biopsy of a suspicious enlarged lymph node or from another affected organ should be performed to establish the diagnosis of Hodgkin lymphoma (HL). Differential diagnoses of HL include all types of benign or malignant lymph node swelling owing to infectious or reactive disease, other types of lymphoma, or solid tumors. HL patients are allocated to risk groups based on the clinical stage according to the Ann Arbor classification and the presence of clinical risk factors. Clinical, biological, and serological parameters also influence the risk group allocation. Younger patients with HL recurrence after first-line treatment are candidates for high-dose chemotherapy followed by autologous stem cell transplantation in the majority of cases. Patients diagnosed with early or intermediate stages, are usually treated with brief chemotherapy followed by consolidation radiotherapy whereas patients with advanced HL receive chemotherapy alone in most cases.
Hard-Potato routing (2000)

We present the first hot-potato routing algorithm for the n x n mesh whose running time on any hard (i.e., f~(n)) many-to-one batch routing problem is, with high probability, within a polylogarithmic factor of optimal. For any instance I of a batch routing problem, there exists a wellknown lower bound LBI based on maximum path length and maximum congestion. If LBt is f~(n), our algorithm solves I with high probability in time O(LBI. log ~ n). The algorithm is distributed and greedy, and it makes use of a new routing technique based on multi-bend paths, a departure from paths using a constant number of bends used in prior hot-potato algorithms.
Emerging Targets for the Treatment of Non-Alcoholic Steatohepatitis (NASH) (2018)

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