gebhart/patrepeval huggingface dataset:
Learning To Simulate (2018)

Simulation is a useful tool in situations where training data for machine learning models is costly to annotate or even hard to acquire. In this work, we propose a reinforcement learning-based method for automatically adjusting the parameters of any (non-differentiable) simulator, thereby controlling the distribution of synthesized data in order to maximize the accuracy of a model trained on that data. In contrast to prior art that hand-crafts these simulation parameters or adjusts only parts of the available parameters, our approach fully controls the simulator with the actual underlying goal of maximizing accuracy, rather than mimicking the real data distribution or randomly generating a large volume of data. We find that our approach (i) quickly converges to the optimal simulation parameters in controlled experiments and (ii) can indeed discover good sets of parameters for an image rendering simulator in actual computer vision applications.
Assembly and mineralization processes in biomineralization: strategies for forming biological composite materials (2001)

Many organisms produce materials with mechanical properties that are better than those of comparable synthetically produced materials, built from the same or similar basic components [1, 2]. The key to biological material production is, of course, the genetically programmed activities of cells, that reflect the accumulated experience of evolving by trial and error field testing over tens, if not hundreds, of millions of years. It is highly unlikely that the synthetic processes that humans are capable of performing will ever be able to reproduce or even mimic these cellular functions. Detailed studies of the structure of the formed material and the formation processes involved in producing the material can, however, provide an understanding of the basic design and assembly principles incorporated into the structure. Materials scientists may then be able to use some of this knowledge to improve the fabrication processes and the performance of novel synthetic materials.
AHNAK-mediated Activation of Phospholipase C-γ1 through Protein Kinase C (2004)

We have recently shown that phospholipase C-gamma (PLC-gamma) is activated by the central repeated units (CRUs) of the AHNAK protein in the presence of arachidonic acid. Here we demonstrate that four central repeated units (4 CRUs) of AHNAK act as a scaffolding motif networking PLC-gamma and PKC-alpha. Specifically, 4 CRUs of AHNAK bind and activate PKC-alpha, which in turn stimulates the release of arachidonic acid near where PLC-gamma1 is localized. Moreover, 4 CRUs of AHNAK interacted with PLC-gamma and the concerted action of 4 CRUs with arachidonic acid stimulated PLC-gamma activity. Stimulation of NIH3T3 cells expressing 4 CRUs of AHNAK with phorbol 12-myristate 13-acetate resulted in the increased generation of total inositol phosphates (IP(T)) and mobilization of the intracellular calcium. Phorbol 12-myristate 13-acetate-dependent generation of IP(T) was completely blocked in NIH3T3 cells depleted of PLC-gamma1 by RNA interference. Furthermore, bradykinin, which normally stimulated the PLC-beta isozyme resulting in the generation of a monophasic IP(T) within 30 s in NIH3T3 cells, led to a biphasic pattern for generation of IP(T) in NIH3T3 cells expressing 4 CRUs of AHNAK. The secondary activation of PLC is likely because of the scaffolding activity of AHNAK, which is consistent with the role of 4 CRUs as a molecular linker between PLC-gamma and PKC-alpha.
A Comprehensive Population-Based Characterization of Heart Failure with Mid-Range Ejection Fraction (2017)

HFmrEF was an intermediate phenotype, except that CAD was more common in HFmrEF and HFrEF vs. HFpEF, crude all-cause mortality was lower in HFmrEF and HFrEF, adjusted all-cause mortality was lower in HFmrEF and HFpEF, and CAD portended a higher adjusted risk of death in HFmrEF and HFrEF.
Investigation of the Dynamics of Attached Cavitation on Hydrofoils (1998)

An electrical impedance probe is used to study the properties of partial attached cavitation. The method uses a series of electrodes mounted flush to the surface of a cavitating hydrofoil to obtain ti.me-dependent information about the presence of liquid or vapor in the region of interest. The impedance technique is used to measure the near-surface vapor-phase velocity and the shedding frequency of the cavity. The dependence of velocities upon cavity dimensions is discussed, and the measured frequencies are compared to current cavitation theory.
Stroma-regulated HMGA2 is an independent prognostic marker in PDAC and AAC (2017)

This study identifies HMGA2 expression in tumour cells as an independent prognostic marker in PDAC and AAC. Correlative data analysis gives novel tissue-based evidence for a heterotypic cross-talk with stroma cells as a possible mechanism for HMGA2 induction, which is further supported by experimental models.
Eat All You Can in an All-you-can-eat Buffet: A Case for Aggressive Resource Usage. (2008)

Abstract — In contrast to a focus on efficiency, we advocate aggressive usage of available resources. This view is embodied in what we call the Buffet principle: continue using more resources as long as the marginal cost can be driven lower than the marginal benefit. We illustrate through several examples how this seemingly obvious principle is not adhered to by many common designs and how its application produces better designs. We also discuss broadly the considerations in applying the Buffet principle in practice. 1.
Self-Assembly of Microscale Objects at a Liquid/Liquid Interface through Lateral Capillary Forces (2001)

Small (100−600 μm in width) hexagonal polymeric plates with faces patterned into hydrophobic and hydrophilic regions, and interacting through lateral capillary forces, were allowed to self-assemble at the perfluorodecalin/water interface. These plates were fabricated from photoresist and patterned by shadow evaporation of gold onto selected faces. The arrays that assembled from the 100 μm objects were similar in structure to those that assembled from millimeter-sized objects with analogous patterns of hydrophobic and hydrophilic faces, but with three important differences. (i) The contribution of buoyancy forces in establishing the level at which the 100 μm objects floated relative to the interface was small compared to the contribution of the vertical capillary forces. (ii) As a result, the designs of hydrophobic edges necessary to generate menisci useful in self-assembly were different for 100 μm objects than for millimeter-sized objects. (iii) The arrays that formed from the 100 μm objects had higher densities of defects than the arrays that formed from the millimeter-sized objects; these defects reflected the increase in the strength of the capillary forces (which favored assembly) relative to the shear forces (which disrupted assembly). This work adds two new elements to the study of mesoscale self-assembly: (i) It describes a new method of fabrication of plates with faces patterned into regions of different hydrophobicity that is applicable to small (perhaps <10 μm) objects, and (ii) it describes the self-assembly of 100 μm plates made by this method into ordered arrays. The work also established the contours of the menisci on the separate 100 μm and millimeter-sized plates. The scaling of the lateral and vertical capillary forces and buoyancy forces acting on millimeter-sized objects, relative to those acting on 100 μm objects, is described.
Caspase-mediated Cleavage of DNA Topoisomerase I at Unconventional Sites during Apoptosis (1999)

Previous studies have demonstrated that topoisomerase I is cleaved late during apoptosis, but have not identified the proteases responsible or examined the functional consequences of this cleavage. Here, we have shown that treatment of purified topoisomerase I with caspase-3 resulted in cleavage at DDVD146 downward arrowY and EEED170 downward arrowG, whereas treatment with caspase-6 resulted in cleavage at PEDD123 downward arrowG and EEED170 downward arrowG. After treatment of Jurkat T lymphocytic leukemia cells with anti-Fas antibody or A549 lung cancer cells with topotecan, etoposide, or paclitaxel, the topoisomerase I fragment comigrated with the product that resulted from caspase-3 cleavage at DDVD146 downward arrowY. In contrast, two discrete topoisomerase I fragments that appeared to result from cleavage at DDVD146 downward arrowY and EEED170 downward arrowG were observed after treatment of MDA-MB-468 breast cancer cells with paclitaxel. Topoisomerase I cleavage did not occur in apoptotic MCF-7 cells, which lack caspase-3. Cell fractionation and band depletion studies with the topoisomerase I poison topotecan revealed that the topoisomerase I fragment remains in proximity to the chromatin and retains the ability to bind to and cleave DNA. These observations indicate that topoisomerase I is a substrate of caspase-3 and possibly caspase-6, but is cleaved at sequences that differ from those ordinarily preferred by these enzymes, thereby providing a potential explanation why topoisomerase I cleavage lags behind that of classical caspase substrates such as poly(ADP-ribose) polymerase and lamin B1.
Abstract 5758: Generation and characterization of novel monoclonal antibodies against overexpressed CD109 on pancreatic cancer cells for use in diagnosis and therapy (2018)

Abstract Pancreatic cancer is one of the most aggressive and lethal types of cancer, and more effective therapeutic agents are urgently needed. Overexpressed cell surface antigens are ideal targets for therapy with monoclonal antibody (mAb)-based drugs, and several have been approved for the treatment of human cancers; however, none have approval for pancreatic cancer. Our aim was to discover novel overexpressed cell surface antigens in human pancreatic cancer cells using mAb technology. We have generated two novel mouse mAbs, KU42.33C and KU43.13A, against the human pancreatic cancer cell line BxPC-3. Using ELISA, flow cytometry, competitive assay and mass spectrometry, we discover that these two mAbs target two distinct epitopes on the external domain of CD109 that are overexpressed by varying amounts in human pancreatic cancer cell lines. Treatment with these two naked antibodies alone did not affect tumor cell growth in vitro or cell migration. Of the two mAbs, only KU42.33C was useful in determining the expression of CD109 in tumor cells by Western blot and immunohistochemistry. Immunohistochemistry of human pancreatic carcinoma arrays with mAb KU42.33C showed that 94% of the 65 human pancreatic adenocarcinoma cases were CD109 positive, with no expression in normal pancreatic tissues. Our results suggest that these two novel mAbs are excellent tools for determining the expression level of CD109 in the tumor specimens and sera of patients with a wide range of cancers, in particular pancreatic cancer, and for investigating its diagnostic, prognostic and predictive value. Further research should unravel the therapeutic potential of the humanized forms or the conjugated versions of such antibodies in patients whose tumors overexpress CD109 antigen. Citation Format: Gustavo A. Arias-Pinilla, Angus Dalgleish, Satvinder Mudan, Izhar Bagwan, Tony Walker, Helmout Modjtahedi. Generation and characterization of novel monoclonal antibodies against overexpressed CD109 on pancreatic cancer cells for use in diagnosis and therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5758.
Automatic parallelization of simulink applications (2010)

The parallelization of Simulink applications is currently a responsibility of the system designer and the superscalar execution of the processors. State-of-the-art Simulink compilers excel at producing reliable and production-quality embedded code, but fail to exploit the natural concurrency available in the programs and to effectively use modern multi-core architectures. The reason may be that many Simulink applications are replete with loop-carried dependencies that inhibit most parallel computing techniques and compiler transformations.
Effect of ambient temperature on human skeletal muscle metabolism during fatiguing submaximal exercise (1999)

To examine the effect of ambient temperature on metabolism during fatiguing submaximal exercise, eight men cycled to exhaustion at a workload requiring 70% peak pulmonary oxygen uptake on three separate occasions, at least 1 wk apart. These trials were conducted in ambient temperatures of 3 degrees C (CT), 20 degrees C (NT), and 40 degrees C (HT). Although no differences in muscle or rectal temperature were observed before exercise, both muscle and rectal temperature were higher (P < 0.05) at fatigue in HT compared with CT and NT. Exercise time was longer in CT compared with NT, which, in turn, was longer compared with HT (85 +/- 8 vs. 60 +/- 11 vs. 30 +/- 3 min, respectively; P < 0.05). Plasma epinephrine concentration was not different at rest or at the point of fatigue when the three trials were compared, but concentrations of this hormone were higher (P < 0.05) when HT was compared with NT, which in turn was higher (P < 0.05) compared with CT after 20 min of exercise. Muscle glycogen concentration was not different at rest when the three trials were compared but was higher at fatigue in HT compared with NT and CT, which were not different (299 +/- 33 vs. 153 +/- 27 and 116 +/- 28 mmol/kg dry wt, respectively; P < 0.01). Intramuscular lactate concentration was not different at rest when the three trials were compared but was higher (P < 0.05) at fatigue in HT compared with CT. No differences in the concentration of the total intramuscular adenine nucleotide pool (ATP + ADP + AMP), phosphocreatine, or creatine were observed before or after exercise when the trials were compared. Although intramuscular IMP concentrations were not statistically different before or after exercise when the three trials were compared, there was an exercise-induced increase (P < 0.01) in IMP. These results demonstrate that fatigue during prolonged exercise in hot conditions is not related to carbohydrate availability. Furthermore, the increased endurance in CT compared with NT is probably due to a reduced glycogenolytic rate.
Scale-Free Brain Functional Networks (2005)

Functional magnetic resonance imaging is used to extract functional networks connecting correlated human brain sites. Analysis of the resulting networks in different tasks shows that (a) the distribution of functional connections, and the probability of finding a link versus distance are both scale-free, (b) the characteristic path length is small and comparable with those of equivalent random networks, and (c) the clustering coefficient is orders of magnitude larger than those of equivalent random networks. All these properties, typical of scale-free small-world networks, reflect important functional information about brain states.
Synthesis of primary hydroxyl functional poly(propylene oxide) of controlled molecular weight by direct polymerization (1991)

Abstract Utilization of aluminiumporphyrin catalyst/initiator structures was demonstrated to be highly capable of producing controlled molecular weight/narrow molecular weight distributions and in several cases good functionalities. Further extension of our studies to systems wherein benzyl alcohol is first reacted with the aluminiumporphyrin initiator have been conducted. The resulting aluminiumporphyrin benzyl alcohol alkoxide is capable of initiating propylene oxide in a controlled manner. After work‐up, the resulting material can be subjected to hydrogenolysis and this regenerates a very desirable primary hydroxyl group at the initiating site. Moreover, the hydrogenolysis disrupts the aromatic character of the porphyrin species and greatly diminishes any residual color which is usually attributed to the initiator fragments. Difunctional species can be generated by a coupling reaction with terephthaloyl chloride and star‐shaped macromolecules are possible via coupling with bisphenol‐A diglycidyl ether. Synthesis of these materials and characterization is discussed herein. In particular, fluorine‐19 NMR derivatization has been quite effective at distinguishing between the derived primary hydroxyl species and the usual secondary hydroxyl systems.
Activation of transcription by guanosine 5'-diphosphate,3'-diphosphate, transfer ribonucleic acid, and novel protein from Escherichia coli. (1975)

A protein factor TFms) that is required for ppGpp to stimulate RNA synthesis has been purified from an eluate of crude ribosomes. TFms also has the capacity to stimulate RNA synthesis without ppGpp present. Under standard conditions the action TFms and ppGpp requires uncharged tRNA. TFms and ppGpp act at inhibition to promote the formation of rifampicin-resistant or polytrI)-resistant preinitiation complexes. In the presence of rifampicin or poly(rI), tRNA is no longer required. With lambdah80dlacPs DNA as template, ppGpp together with TFms stimulated gal RNA synthesis to a much greater extent than total RNA synthesis. The stimulation of both lac and gel RNA synthesis was increased in the presence of cyclic AMP receptor and cyclic AMP.
Fast DBMS-Resident Machine Learning and Statistics: Extending the Sloan Digital Sky Survey SQL Server Database (2009)

is a step towards the goal of embedding machine learning (ML) in Microsoft products.We introduce the most successful spatial data algorithms in literature as extensions to Microsoft SQL Server.Our library is extensible and works in-place, side-stepping cost of data transfer and transformation.Our library runs within SQL CLR, and is thus immediately available to all existing SQL Server users.
Multi-Switch for Antenna Selection in Massive MIMO (2015)

Massive MIMO has been shown to greatly improve spectral and transmit-energy efficiency. When implementing a massive MIMO system, one challenge is high hardware complexity. A solution is to reduce the number of radio frequency (RF) transceiver chains by performing antenna selection. However, a full RF switch that connects the antennas and RF chains can be highly complex and incurs significant loss in output signal quality, especially when the number of antennas and RF chains are large. We therefore propose a simpler solution - binary switching architecture, which is suboptimal but provides better signal quality, as compared to the full switching network. To evaluate the proposed technique, we compare the sum-rate capacity when using several different configurations of binary switching with the performance of the full switching. Full MIMO performance obtained without antenna selection is also presented as a reference. The investigations in this paper are all based on measured channel data at 2.6 GHz, using a uniform linear array and a cylindrical array, both having 128 antenna elements. It is found that the proposed binary switching gives very competitive performance that are close to the full switching, for the measured channels. The results indicate a potential to simplify massive MIMO hardware by reducing the number of RF chains, and performing antenna selection with simple binary switching architecture.
Therapeutic antitumor immunity induced by combined intratumoral injection of dendritic cells (DCs) and systemic chemotherapy in murine lymphoma (2004)

2509 Background: DCs are potent antigen presenting cells that can induce both immune responses and self-tolerance. Immune tolerance to tumors and the lack of defined tumor antigens are the two major hurdles for immunotherapy. To overcome this, a novel immunotherapy approach was developed to induce systemic antitumor immunity by combining of intratumoral injection of naïve DCs and systemic chemotherapy in a murine tumor model. Methods: Using a murine A20 B cell lymphoma model, syngeneic mice with established subcutaneous tumors and systemic spread were treated first with chemotherapy (cyclophosphamide or CTX, 50–200mg/kg body wt) and then by direct intratumoral injection of bone marrow-derived DCs (on day 2 and 4 post chemotherapy). The mechanisms of tumor regression was also dissected. Results: Intratumoral DC injection alone had a minimal effect. The systemic chemotherapy alone resulted in only transient tumor regression with prolonged survival, but the majority of treated mice having tumor re-growth and eventually succumbing to systemic lymphoma. Strikingly, the addition of local intratumoral injection of DCs combined with systemic chemotherapy led to complete, long-term regression in the majority of treated mice. Thawed frozen DCs are equally effective as the freshly prepared DCs. This therapeutic effect of intratumoral DC injection was dose dependent and also dependent on injection of the DCs directly into the tumor site rather than a regional or distant site. Furthermore, this DC-mediated antitumor effect was systemic because distant tumor inoculated in the contra-lateral flank of the mice were also made to regress. In vivo T cell depletion studies indicated both CD4+ and CD8+ T cells are involved in the tumor regression. Interestingly, tumor re-challenge in those long term surviving mice revealed broad cross protection which was also mirrored by the in vitro cytotoxic T lymphocyte assay. Conclusion: The combination of chemotherapy induced tumor death and DC loading of tumor antigens in situ may provide a convenient mode of inducing systemic antitumor immunity and may be relevent to the clinical setting. No significant financial relationships to disclose.
β1 Receptors Protect the Renal Afferent Arteriole of Angiotensin-Infused Rabbits from Norepinephrine-Induced Oxidative Stress (2006)

Renal afferent arterioles (Aff) from angiotensin II (AngII)-infused rabbits have enhanced contractions to AngII that are normalized by tempol (superoxide dismutase mimetic), whereas contractions to norepinephrine (NE) are normal and unaffected by tempol. Tested was the hypothesis that beta-receptor stimulation with NE prevents enhanced reactivity and superoxide generation. Preconstricted Aff from AngII- or vehicle-infused rabbits were perfused at physiologic pressure. Aff from vehicle-infused rabbits had strong, endothelium-independent relaxations to dobutamine (beta(1)-receptor agonist; 78 +/- 6%; P < 0.0001; mean +/- SD) but only weak relaxations to salbutamol (beta(2)-receptor agonist; 13 +/- 3%; P < 0.05) or BRL-37,344 (beta(3)-receptor agonist; 14 +/- 3%; P < 0.05). Contractions to NE were similar in Aff from vehicle- and AngII-infused rabbits (-36 +/- 5 versus -34 +/- 3%; NS) and were unaffected by tempol (-32 +/- 4%; NS). In contrast, phenylephrine contractions (alpha(1) agonist) were enhanced in Aff from AngII-infused rabbits (-59 +/- 6 versus -46 +/- 4%; P < 0.05) and normalized by tempol. NE contractions in Aff from AngII-infused rabbits (-34 +/- 4%) were enhanced (P < 0.01) by propranolol (nonselective beta antagonist; -53 +/- 6%), CGP-20,712A (selective beta(1)-receptor antagonist; -61 +/- 9%), or Rp-cAMP (competitive inhibitor of cAMP; -56 +/- 4%); were normalized by tempol; but were unaffected by ICI-118,551 (selective beta(2)-receptor antagonist) or SR-59,230A (selective beta(3)-receptor antagonist). Superoxide generation in Aff from AngII-infused rabbits that were assessed from ethidium:dihydroethidium was enhanced by addition of CGP-20,712A to NE but was normalized by tempol. Aff have robust alpha(1)-receptor contraction and beta(1)-receptor dilation. NE elicits beta(1) signaling via cAMP that moderates oxidative stress and contractions in Aff from AngII-infused rabbits.