gebhart/patrepeval huggingface dataset:
AI-MIX: Using Automated Planning to Steer Human Workers Towards Better Crowdsourced Plans (2014)

One subclass of human computation applications are those directed at tasks that involve planning (e.g. tour planning) and scheduling (e.g. conference scheduling). Interestingly, work on these systems shows that even primitive forms of automated oversight on the human contributors helps in significantly improving the effectiveness of the humans/crowd. In this paper, we argue that the automated oversight used in these systems can be viewed as a primitive automated planner, and that there are several opportunities for more sophisticated automated planning in effectively steering the crowd. Straightforward adaptation of current planning technology is however hampered by the mismatch between the capabilities of human workers and automated planners. We identify and partially address two important challenges that need to be overcome before such adaptation of planning technology can occur: (i) interpreting inputs of the human workers (and the requester) and (ii) steering or critiquing plans produced by the human workers, armed only with incomplete domain and preference models. To these ends, we describe the implementation of AI-MIX, a tour plan generation system that uses automated checks and alerts to improve the quality of plans created by human workers; and present a preliminary evaluation of the effectiveness of steering provided by automated planning.
Pittkit And The Breadboard Laboratory Interface Processor (Blip): An Educational Apparatus Centered On The Individual Student (2020)

We describe a kit of electronics tools, components, and equipment developed for the required one-semester instrumentation course in the Bioengineering Department at the University of Pittsburgh. The kit is owned by each student and includes a microprocessor-based apparatus that communicates to any standard computer (PC/Linux/Mac) without special software, acting as a variety of basic laboratory instruments that no longer must be purchased and maintained by the department. Fundamental electronics and bioengineering principals are taught using a hands-on approach that serves students in all branches of bioengineering. We report results after four years and more than 200 students, as we prepare to make the kits available to other universities.
Role of Myocardial Extracellular Volume Fraction Measured with Magnetic Resonance Imaging in the Prediction of Left Ventricular Functional Outcome after Revascularization of Chronic Total Occlusion of Coronary Arteries (2018)

Extracellular volume fraction obtained by CMR may provide incremental value for the prediction of functional recovery both at the segmental and global levels in CTO patients, and may facilitate the identification of patients who can benefit from revascularization.
Submilliwatt Operation of AlInGaN Based Multifinger-Design 315 nm Light Emitting Diode (LED) over Sapphire Substrate (2002)

We report on sub-milliwatt operation of ultra-violet light emitting diodes on sapphire with a peak emission wavelength of 315 nm having quaternary AlInGaN multiple quantum well (MQW) active region. A significant increase in the device-emitted power was achieved using an interdigitated finger geometry design, which reduces the differential resistance and eliminates current crowding. The flip-chip mounting of the diced chips with sapphire substrates improves thermal management and increases the light extraction efficiency from the device active area. For 315 nm emission an optical power as high as 0.23 mW was obtained with 800 mA pulsed pumping current.
4,5,6‐Trisubstituted Piperidinones as Conformationally Restricted Ceramide Analogues: Synthesis and Evaluation as Inhibitors of Sphingosine and Ceramide Kinases and as NKT Cell‐Stimulatory Antigens (2009)

The conformationally based piperidinone sphingosine analogues 7, 8, 15, and 16 were synthesized from allylic alcohol 34 via lactams 31 and 32. The L-arabino diol 7 and the L-ribo diol 8 were transformed into the amino alcohols 17-24. The L-gluco ceramide analogues 43, 46a, and 47, and the L-altro ceramide analogues 51a and 52 were synthesized from either 31 or 32. The L-ribo diols 8 and 16, and the amino alcohols 19 and 20 inhibit sphingosine kinase 1 (SPHK1), while the L-arabino analogues 7, 15, 17, and 18 are inactive. The L-arabino and the L-ribo dimethylamines 21-24, the L-gluco ceramide analogues 43, 46a, and 47, and the L-altro ceramide analogues 51a and 52 did not block SPHK1. Neither the L-arabino diol 7 nor the L-ribo diol 8 inhibited SPHK2 or ceramide kinase. The L-arabino diols 7 and 15 stimulate invariant natural killer T (iNKT) cells when presented by living antigen-presenting cells (APC) and also by plate-bound human CD1d, whereas the L-ribo diols 8 and 16, the L-arabino amino alcohols 17-18, and the dimethylamines 21-22 did not activate iNKT cells. The L-gluco ceramide analogues 43, 46a, and 47 had strongly stimulatory effects on iNKT cells when presented by living APC and also by plate-bound human CD1d, whereas the L-altro ceramide analogue 52 activated only weakly. All activatory compounds induced preferentially the release of pro-inflammatory cytokines, indicating the formation of a stable CD1d--lipid--T-cell receptor complex.
Intercellular coupling amplifies fate segregation during Caenorhabditis elegans vulval development (2006)

During vulval development in Caenorhabditis elegans, six precursor cells acquire a spatial pattern of distinct cell fates. This process is guided by a gradient in the soluble factor, LIN-3, and by direct interactions between neighboring cells mediated by the Notch-like receptor, LIN-12. Genetic evidence has revealed that these two extracellular signals are coupled: lateral cell-cell interactions inhibit LIN-3-mediated signaling, whereas LIN-3 regulates the extent of lateral signaling. To elucidate the quantitative implications of this coupled network topology for cell patterning during vulval development, we developed a mathematical model of LIN-3/LIN-12-mediated signaling in the vulval precursor cell array. Our analysis reveals that coupling LIN-3 and LIN-12 amplifies cellular perception of the LIN-3 gradient and polarizes lateral signaling, both of which enhance fate segregation beyond that achievable by an uncoupled system.
Thermal Atomic Layer Etching of Al2O3 Using Sequential HF and BCl3 Exposures: Evidence for Combined Ligand-Exchange and Conversion Mechanisms (2022)

The atomic layer etching (ALE) of Al2O3 was demonstrated using sequential HF and BCl3 exposures. BCl3 is a new precursor for thermal Al2O3 ALE that can provide pathways for both ligand-exchange and conversion etching mechanisms. Fourier transfer infrared (FTIR) spectroscopy was utilized to observe the growth of Al2O3 ALD films using Al(CH3)3 (trimethylaluminum) and H2O and the subsequent etching of the Al2O3 ALD films using HF and BCl3. To confirm the conversion reaction, FTIR difference spectra revealed that initial BCl3 exposures on the Al2O3 ALD film converted the Al2O3 surface to a B2O3 layer. Surprisingly, larger BCl3 exposures on the B2O3 layer could also etch the B2O3 layer. Quadrupole mass spectrometry (QMS) measurements revealed that BCl3 produced ion intensities for AlCl3+ from AlCl3 during the conversion of the Al2O3 surface to a B2O3 layer. Concurrently, the BCl3 also etched the converted B2O3 layer and ion intensities for B3O3Cl3+ were observed from B3O3Cl3 boroxine rings. After the conversion of the Al2O3 surface to a B2O3 layer, the initial HF exposure then removed the B2O3 layer and fluorinated the underlying Al2O3 film. Following the initial BCl3 and HF exposures, the FTIR difference spectra showed that Al2O3 ALE proceeded primarily by a reaction pathway where HF fluorinates the Al2O3 and then BCl3 removes the surface fluoride layer by a ligand-exchange reaction. However, there was still evidence for some conversion of Al2O3 to a B2O3 layer during the subsequent BCl3 exposures and then removal of the B2O3 layer by the HF exposures. Spectroscopic ellipsometry measurements determined the etch rates during thermal Al2O3 ALE during sequential HF and BCl3 exposures. The etch rates were 0.03, 0.31, 0.65, and 0.92 Å/cycle at temperatures of 230, 255, 280, and 290 °C, respectively. QMS analysis also investigated the volatile etch products during the sequential HF and BCl3 exposures on Al2O3 at 270 °C. During the BCl3 exposures after the initial cycle, the QMS measurements observed ion intensities for BFCl2+ and AlCl2+. BFCl2 was the major ligand-exchange product, and AlCl3 was the main metal chloride etching product. In addition, small ion intensities for B3O3Cl3+ were also present from the conversion of Al2O3 to B2O3 and subsequent etching of B2O3 by BCl3 to yield boroxine ring products. These results indicate that thermal Al2O3 ALE using sequential HF and BCl3 exposures occurs by combined ligand-exchange and conversion mechanisms.
Structural studies on oncornavirus-related sequences in chicken genomic DNA: two-step analyses of EcoRI and Bgl I restriction digests and tentative mapping of a ubiquitous endogenous provirus digests and tentative mapping of a ubiquitous endogenous provirus. (1979)

DNA from a variety of uninfected chicken cell types has been analyzed by using restriction endonuclease digestion and RPC-5 ion-exchange chromatography followed by agarose gel electrophoresis. Endogenous retrovirus sequences were detected by using a 32P-labeled avian leukosis viral RNA probe. One simple pattern was identified in an individual containing unexpressed endogenous proviral genes (gs-chf-phenotype for group-specific antigens and chicken helper factor) that was common to all individuals studied. A tentative restriction has been derived for this and one other gs-chf-endogenous provirus. Other gs-chf-individuals and individuals with other phenotypes (e.g., gs+ chf+ and gsl chlfhE) showed more complicated patterns that often included additional bands and thus probably additional proviruses. RNA from an avian sarcoma virus was used to detect cellular sequences (sarc) homologous to the viral transforming gene (src). Results have revealed that a single restriction endonuclease EcoRI fragment of 13 x 10(6) daltons contains the majority of these sequences and confirm that they are not adjacent to the endogenous provirus.
Molecular cloning and sequence analysis of the gene coding for the 57-kDa major soluble antigen of the salmonid fish pathogen Renibacterium salmoninarum (1992)

The complete sequence coding for the 57-kDa major soluble antigen of the salmonid fish pathogen, Renibacterium salmoninarum, was determined. The gene contained an opening reading frame of 1671 nucleotides coding for a protein of 557 amino acids with a calculated M(r) value of 57,190. The first 26 amino acids constituted a signal peptide. The deduced sequence for amino acid residues 27-61 was in agreement with the 35 N-terminal amino acid residues determined by microsequencing, suggesting the protein is synthesized as a 557-amino acid precursor and processed to produce a mature protein of M(r) 54,505. Two regions of the protein contained imperfect direct repeats. The first region contained two copies of an 81-residue repeat, the second contained five copies of an unrelated 25-residue repeat. Also, a perfect inverted repeat (including three in-frame UAA stop codons) was observed at the carboxyl-terminus of the gene.
Identification of L1CAM, Jagged2 and Neuromedin U as ovarian cancer-associated antigens (2005)

In order to identify tumor-associated genes of ovarian carcinoma, we have investigated the transcriptional profile of 11 ovarian tumor cell lines and 2 immortalized ovarian surface epithelial cell lines (IOSE) derived from normal ovarian epithelium with Affymetrix GeneChip technology. We have analyzed the expression profile of 12652 genes. A total of 136 genes were up-regulated and 165 were down-regulated in at least 7 out of 11 ovarian tumor cell lines in comparison to the transcriptional profile of the IOSE cell lines with a change factor of +/-2 as the threshold level. We have focused on up-regulated genes encoding for transmembrane receptors and secreted proteins as possible markers for diagnosis and targets for therapy of ovarian carcinoma. We have identified the transmembrane Notch ligand Jagged2, cell adhesion molecule L1CAM and the secreted polypeptide Neuromedin U as possible candidates. Immunohistochemical analysis revealed expression of L1CAM predominantly in ovarian carcinomas, in borderline tumors to a lesser extent, and very rarely in ovarian non-epithelial types of cancer. Further analysis of L1CAM revealed that a splice variant lacking exons 2 and 27 is predominantly expressed in ovarian carcinoma cell lines DW and GG. Functional investigation of stable Delta(2,27)L1CAM transfectants of the ovarian tumor cell line OV-MZ-2 revealed significantly stronger adhesion to laminin in comparison to mock transfectants.
On Demand Distributed Public Key Management without Considering Routing Tables for Wireless Ad Hoc Networks (2005)

A wireless ad hoc network that has no connection to the Internet can not use a public key infrastructure (PKI). Although an on demand distributed public key management to construct the PKI has been proposed, it cannot work without considering routing tables, since nodes broadcast a packet which contains routing tables. In this paper, we propose an on demand distributed public key management which can separate the routing and authentication layers. In the proposed scheme, each node sends a packet which does not contain routing tables by unicasting. The proposed scheme can be applied to various communication protocols and simple terminals because the scheme does not need to consider routing tables in the authentication layer. By a computer simulation, we evaluate average traffic and show the adaptive flexibility of the proposed scheme in the ad hoc network
W-band imager without mechanical scanning based on an echelle spectrometer (2014)

We describe a two-dimensional imager in W-band using a single heterodyne transceiver and no mechanical scanning. By using an echelle grating spectrometer, frequencies are mapped onto a 2-D surface in space, so that spectral analysis of the signals provides a two-dimensional image.
Self-Interference of Coherent and Incoherent Signals for Sub-Nanometer Localization of Single Emitters (2015)

Localization precision of single emitters can be fundamentally improved by imposing interference fringes on the Point-Spread-Function. We show that this interference effect can be used for coherent and incoherent signals for sub nanometer localization.
Playful Experiences as Targets in Concept Design (2012)

User experience (UX) has been recognized as an important success factor of interactive products. However, concrete approaches of designing for certain types of experiences are scarce. This paper presents a study where categories of playful experience were utilized as design targets in a practical design assignment of a post-graduate seminar course. The students were given 3-4 PLEX Cards (with playful experience categories) to facilitate designing innovative product or service concepts for the design problem of “how to support moving and navigating during winter?” The seminar outcomes and learning experiences support the postulation that such general-level experience targets can serve well as design inspiration and guidance. The students experienced the PLEX-cards as fruitful starting points for brainstorming as well as constant reminders of the rationale of the design, i.e., serving as concrete targets for design.
International Neuroscience Initiatives through the Lens of High-Performance Computing (2018)

Neuroscience initiatives aim to develop new technologies and tools to measure and manipulate neuronal circuits. To deal with the massive amounts of data generated by these tools, the authors envision the co-location of open data repositories in standardized formats together with high-performance computing hardware utilizing open source optimized analysis codes.
Automated Heparin-Delivery System to Control Activated Partial Thromboplastin Time (1999)

These results suggest that the AutoHep system has the potential to significantly improve aPTT control of intravenous heparin compared with current clinical practice.
Longitudinal Optical Imaging of Tumor Metabolism and Hemodynamics (2010)

Fluorescence redox ratio imaging of metabolic demand, absorption microscopy of hemoglobin oxygen saturation and Doppler optical coherence tomography of blood flow were combined to monitor oxygen supply and demand in a tumor model in vivo.
Imaging CD19<sup>+</sup> B Cells in an Experimental Autoimmune Encephalomyelitis Mouse Model using Positron Emission Tomography (2023)

Multiple sclerosis (MS) is the most common demyelinating central nervous system (CNS) disease affecting young adults, often resulting in neurological deficits and disability as the disease progresses. B lymphocytes play a complex and critical role in MS pathology and are the target of several therapeutics in clinical trials. Currently, there is no way to accurately select patients for specific anti-B cell therapies or to non-invasively quantify the effects of these treatments on B cell load in the CNS and peripheral organs. Positron emission tomography (PET) imaging has enormous potential to provide highly specific, quantitative information regarding the in vivo spatiotemporal distribution and burden of B cells in living subjects. This paper reports methods to synthesize and employ a PET tracer specific for human CD19<sup>+</sup> B cells in a well-established B cell-driven mouse model of MS, experimental autoimmune encephalomyelitis (EAE), which is induced with human recombinant myelin oligodendrocyte glycoprotein 1-125. Described here are optimized techniques to detect and quantify CD19<sup>+</sup> B cells in the brain and spinal cord using in vivo PET imaging. Additionally, this paper reports streamlined methods for ex vivo gamma counting of disease-relevant organs, including bone marrow, spinal cord, and spleen, together with high-resolution autoradiography of CD19 tracer binding in CNS tissues.
Abstract 473: miR-135b mediates gemcitabine sensitivity in breast cancer cells by modulating epithelial-to-mesenchymal transition and mTOR-signaling (2018)

Abstract Background: We previously identified miR-135b as a possible biomarker for gemcitabine sensitivity in metastatic breast cancer patients. Here we aimed to better understand the role of this microRNA in breast cancer cells in order to identify new clinically relevant approaches to revert gemcitabine resistance. Methods: miR-135b KO MDA-MB-231 breast cancer cells were generated through CRISPR-Cas9 technology and tested for gemcitabine sensitivity by cell survival and apoptosis activation assays. Gene expression profile was performed by GeneChip® Human Transcriptome Array 2.0 (HTA 2.0 - Affymetrix). The One-Way between-subject ANOVA algorithm was used to calculate statistical significance of pairwise comparisons. The validation of different gene expression was assessed by qRT-PCR. The mesenchymal phenotype of miR-135b KO cells was tested by wound-healing and migration assay. mTOR pathway has been tested by Western blot analysis. Results: miR-135b KO MDA-MB-231 showed increased resistance to gemcitabine than WT cells. Gene expression profiling of miR-135b WT and KO cells revealed the upregulation of several genes, including miR-21 and gene involved in the epithelial-to-mesenchymal transition (EMT) in the absence of the microRNA. Functional enrichment analysis indicated the deregulation of multiple tumor-associated pathways, including focal adhesion, senescence and autophagy. Accordingly, miR-135b KO cells showed higher migrating properties and expression of mesenchymal genes. Moreover, miR-135b KO cells showed deregulation of the mTOR-signaling pathway upon starvation or treatment with gemcitabine. Based on these observations, we assessed whether inhibition of mTOR activation using a clinically approved inhibitor (everolimus) could enhance gemcitabine sensitivity in the absence of miR-135b. Our data indicate that blocking mTOR pathway could represent a valid approach to revert resistance to gemcitabine even in cancer cells with low levels of miR-135b. Conclusions: We identified several deregulated genes and pathways in the absence of miR-135b in breast cancer cells, in particular related to the EMT and mTOR pathway. These results confirm the role of miR-135b in breast cancer and pave the way for new studies for the combination of gemcitabine and mTOR inhibitors in a specific subset of metastatic breast cancer patients that could largely benefit from it. Citation Format: Anna Tessari, Meghan Pawlikowski, Kareesma Parbhoo, Olivia Willetts, Marianna Hernandez, Giovanni Nigita, Ashley Braddom, Joseph J. Mills, Dario Palmieri, Carlo M. Croce. miR-135b mediates gemcitabine sensitivity in breast cancer cells by modulating epithelial-to-mesenchymal transition and mTOR-signaling [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 473.
Congestive kidney failure in cardiac surgery: the relationship between central venous pressure and acute kidney injury (2016)

Acute kidney injury (AKI) in cardiac surgery has traditionally been linked to reduced arterial perfusion. There is ongoing evidence that central venous pressure (CVP) has a pivotal role in precipitating acute renal dysfunction in cardiac medical and surgical settings. We can regard this AKI driven by systemic venous hypertension as 'kidney congestive failure'. In the cardiac surgery population as a whole, when the CVP value reaches the threshold of 14 mmHg in postoperative period, the risk of AKI increases 2-fold with an odds ratio (OR) of 1.99, 95% confidence interval (95% CI) of 1.16-3.40. In cardiac surgery subsets where venous hypertension is a hallmark feature, the incidence of AKI is higher (tricuspid disease 30%, carcinoid valve disease 22%). Even in the non-chronically congested coronary artery bypass population, CVP measured 6 h postoperatively showed significant association to renal failure: risk-adjusted OR for AKI was 5.5 (95% CI 1.93-15.5; P = 0.001) with every 5 mmHg rise in CVP for patients with CVP <9 mmHg; for CVP increments of 5 mmHg above the threshold of 9 mmHg, the risk-adjusted OR for AKI was 1.3 (95% CI 1.01-1.65; P = 0.045). This and other clinical evidence are discussed along with the underlying pathophysiological mechanisms, involving the supremacy of volume receptors in regulating the autonomic output in hypervolaemia, and the regional effect of venous congestion on the nephron. The effect of CVP on renal function was found to be modulated by ventricular function class, aetiology and acuity of venous congestion. Evidence suggests that acute increases of CVP should be actively treated to avoid a deterioration of the renal function, particularly in patients with poor ventricular fraction. Besides, the practice of treating right heart failure with fluid loading should be avoided in favour of other ways to optimize haemodynamics in this setting, because of the detrimental effects on the kidney function.
DNA-Dependent Protein Kinase Drives Prostate Cancer Progression through Transcriptional Regulation of the Wnt Signaling Pathway (2019)

Our data show that <i>DNAPK</i> drives prostate cancer progression through transcriptional regulation of Wnt signaling and is an attractive therapeutic target in aggressive prostate cancer.