gebhart/patrepeval huggingface dataset:
The IUSM‐Purdue Alzheimer’s Disease Drug Discovery Center: A member of the NIH‐funded TREAT‐AD consortium (2020)

Abstract Background The T a r get E nablement to A dvance T herapeutics for A lzheimer’s D isease (TREAT‐AD) Consortium is a newly formed NIA initiative designed to accelerate the discovery of new medicines for Alzheimer’s Disease. It is comprised of two drug discovery centers: OPEN‐AD and the Indiana University School of Medicine‐Purdue University Alzheimer’s Disease Drug Discovery Center (IUSM‐Purdue ADDD Center). The strategic goal of the consortium is to integrate sophisticated capability for early drug discovery and contribute to a broad study of emerging Alzheimer’s Disease target hypotheses to create new classes of potential therapeutics. Method The TREAT‐AD consortium will establish itself as a strategic and operational partner for the NIA‐Funded AMP‐AD, MODEL‐AD other AD directed translational research programs. By design, this will provide drug discovery capability to bridge the foundational work in target discovery (AMP‐AD) with newly discovered molecules characterized in next generation AD animal models based on human pathology, genetics and translational biomarkers (MODEL‐AD). Additionally, the TREAT‐AD consortium will make all data and research tools available to the scientific community to catalyze new research efforts. Result The IUSM‐Purdue ADDD Center has assembled a world‐class team of scientists and capabilities that will pursue a research strategy focusing on neuro‐immune pathways implicated in Alzheimer’s Disease with the following aims: Create a dynamic portfolio of well characterized AD drug discovery targets representing novel intervention hypotheses that capitalizes on significant investments in basic research and emerging disease understanding. Perform advanced pre‐clinical target validation and enablement studies to prioritize the best opportunities for therapeutic discovery. Create high quality and well characterized Lead molecules for prioritized targets that meet rigorous milestone criteria and are valued opportunities for further translational investment. Create a robust and flexible data sharing platform to enable global researchers with data and Target Enablement Packages to expand on the work of the Center. Conclusion This presentation will provide an overview of the TREAT‐AD Consortium and the scientific strategy and plans for the IUSM‐Purdue ADDD Center.
Matching a Wavelet to ECG Signal (2006)

In this paper we develop an approach to synthesize a wavelet that matches the ECG signal. Matching a wavelet to a signal of interest has potential advantages in extracting signal features with greater accuracy, particularly when the signal is contaminated with noise. The approach that we have taken is based on the theoretical work done by Chapa and Rao [10]. We have applied their technique to a noise-free ECG signal representing one cardiac cycle. Results indicate that a matched wavelet, that was able to capture the broad ECG features, could be obtained. Such a wavelet could be used to extract ECG features such as QRS complexes and P&T waves with greater accuracy.
Engineering Stress in Perovskite Solar Cells to Improve Stability (2018)

Abstract An overlooked factor affecting stability: the residual stresses in perovskite films, which are tensile and can exceed 50 MPa in magnitude, a value high enough to deform copper, is reported. These stresses provide a significant driving force for fracture. Films are shown to be more unstable under tensile stress—and conversely more stable under compressive stress—when exposed to heat or humidity. Increasing the formation temperature of perovskite films directly correlates with larger residual stresses, a result of the high thermal expansion coefficient of perovskites. Specifically, this tensile stress forms upon cooling to room temperature, as the substrate constrains the perovskite from shrinking. No evidence of stress relaxation is observed, with the purely elastic film stress attributed to the thermal expansion mismatch between the perovskite and substrate. Additionally, the authors demonstrate that using a bath conversion method to form the perovskite film at room temperature leads to low stress values that are unaffected by further annealing, indicating complete perovskite formation prior to annealing. It is concluded that reducing the film stress is a novel method for improving perovskite stability, which can be accomplished by lower formation temperatures, flexible substrates with high thermal expansion coefficients, and externally applied compressive stress after fabrication.
Set/reset statistics and kinetics in phase change memory arrays (2014)

The development of next-generation PCM arrays requires a better understanding of set/reset processes at statistical level. This work presents experimental programming characteristics on 45 nm arrays and analyzes the statistical distribution of set/reset program and read currents. Results show (i) a reset-voltage dependence for both the melt current and the crystallization kinetics and (ii) a reduced crystallization spread in the high-temperature (set) regime, compared to the low-temperature (retention) one.
Crystalline silicon core fibres from aluminium core preforms (2015)

Traditional fibre-optic drawing involves a thermally mediated geometric scaling where both the fibre materials and their relative positions are identical to those found in the fibre preform. To date, all thermally drawn fibres are limited to the preform composition and geometry. Here, we fabricate a metre-long crystalline silicon-core, silica-cladded fibre from a preform that does not contain any elemental silicon. An aluminium rod is inserted into a macroscopic silica tube and then thermally drawn. The aluminium atoms initially in the core reduce the silica, to produce silicon atoms and aluminium oxide molecules. The silicon atoms diffuse into the core, forming a large phase-separated molten silicon domain that is drawn into the crystalline silicon core fibre. The ability to produce crystalline silicon core fibre out of inexpensive aluminium and silica could pave the way for a simple and scalable method of incorporating silicon-based electronics and photonics into fibres.
Flexible and high-performance electrochromic devices enabled by self-assembled 2D TiO2/MXene heterostructures (2021)

Transition metal oxides (TMOs) are promising electrochromic (EC) materials for applications such as smart windows and displays, yet the challenge still exists to achieve good flexibility, high coloration efficiency and fast response simultaneously. MXenes (e.g. Ti<sub>3</sub>C<sub>2</sub>T<sub>x</sub>) and their derived TMOs (e.g. 2D TiO<sub>2</sub>) are good candidates for high-performance and flexible EC devices because of their 2D nature and the possibility of assembling them into loosely networked structures. Here we demonstrate flexible, fast, and high-coloration-efficiency EC devices based on self-assembled 2D TiO<sub>2</sub>/Ti<sub>3</sub>C<sub>2</sub>T<sub>x</sub> heterostructures, with the Ti<sub>3</sub>C<sub>2</sub>T<sub>x</sub> layer as the transparent electrode, and the 2D TiO<sub>2</sub> layer as the EC layer. Benefiting from the well-balanced porosity and connectivity of these assembled nanometer-thick heterostructures, they present fast and efficient ion and electron transport, as well as superior mechanical and electrochemical stability. We further demonstrate large-area flexible devices which could potentially be integrated onto curved and flexible surfaces for future ubiquitous electronics.
Two‐Phase (Bio)Catalytic Reactions in a Table‐Top Centrifugal Contact Separator (2008)

A new spin on catalysis: A table-top centrifugal contact separator allows for fast continuous two-phase reactions to be performed by intimately mixing two immiscible phases and then separating them. Such a device has been used to produce biodiesel from sunflower oil and MeOH/NaOMe. A lipase-catalyzed esterification of oleic acid with nBuOH (see picture) also proceeds with high conversion and can be run for up to 13 h.
Chemical Synthesis of Insulin Analogs through a Novel Precursor (2013)

Insulin remains a challenging synthetic target due in large part to its two-chain, disulfide-constrained structure. Biomimetic single chain precursors inspired by proinsulin that utilize short peptides to join the A and B chains can dramatically enhance folding efficiency. Systematic chemical analysis of insulin precursors using an optimized synthetic protocol identified a 49 amino acid peptide named DesDi, which folds with high efficiency by virtue of an optimized structure and could be proteolytically converted to bioactive two-chain insulin. In subsequent applications, we observed that the folding of the DesDi precursor was highly tolerant to amino acid substitution at various insulin residues. The versatility of DesDi as a synthetic insulin precursor was demonstrated through the preparation of several alanine mutants (A10, A16, A18, B12, B15), as well as ValA16, an analog that was unattainable in prior reports. In vitro bioanalysis highlighted the importance of the native, hydrophobic residues at A16 and B15 as part of the core structure of the hormone and revealed the significance of the A18 residue to receptor selectivity. We propose that the DesDi precursor is a versatile synthetic intermediate for the preparation of diverse insulin analogs. It should enable a more comprehensive analysis of function to insulin structure than might not be otherwise possible through conventional approaches.
Interleukin-4 counteracts pyrogen-induced downregulation of thrombomodulin in cultured human vascular endothelial cells (1991)

Inflammatory mediators such as tumor necrosis factor (TNF) or interleukin-1 (IL-1) and bacterial lipopolysaccharides (LPS) were shown to shift the hemostatic balance of the endothelial cell (EC) surface in favor of procoagulant activities by inducing tissue factor (TF) expression and downregulation of thrombomodulin (TM). In the present study, the effects of IL-4 on these regulatory mechanisms were investigated using cultured human umbilical vein EC. TM downregulation induced by the pyrogens IL-1 (100 U/mL), TNF (500 U/mL), and LPS (20 micrograms/mL) to less than 50% of TM activity of untreated cells during a 12-hour incubation period was completely neutralized when these mediators were coincubated with IL-4 (100 U/mL). In accordance with TM surface activity, TM messenger RNA was decreased by IL-1, TNF, and LPS to less than 40% of untreated cells; this effect was in part antagonized by IL-4. No influence of IL-4 on EC tissue factor induction by IL-1, TNF, and LPS was found. Binding studies using 125I-radiolabeled IL-4 suggest that EC express a single class of high-affinity binding sites (kd = 3.2 pmol/L; 2,000 to 2,500 receptors per cell). These results show that IL-4, in part, protects the EC surface against pyrogen-induced procoagulant changes. Transcriptional regulatory mechanisms seem to be involved in EC surface TM regulation.
Abstract 5440: Activity of mesothelin-targeted immunotoxin RG7787 against triple-negative breast cancer (2014)

Abstract Mesothelin (MSLN) is a cell surface glycoprotein normally expressed by mesothelial cells of the pleura, pericardium and peritoneum, but also highly expressed in mesothelioma, pancreatic and ovarian cancers. It was recently reported that many triple negative breast cancers (TNBCs) also express MSLN. RG7787 is a next generation, deimmunized recombinant immunotoxin (RIT) consisting of a high-affinity anti-MSLN Fab fragment for targeting, fused to a 24 kD fragment of Pseudomonas exotoxin A for cell killing. Here, we demonstrate using flow cytometry that the TNBC cell lines HCC70 and SUM149 express significant MSLN on the cell surface. HCC70 and SUM149 are sensitive to RG7787 and related RITs with IC50 values in the subnanomolar range. RG7787 has less off-target toxicity in mice than earlier mesothelin-targeted immunotoxins and could be safely administered to mice at six-fold higher doses. RG7787 shrinks HCC70 tumor xenografts grown in athymic nude mice by &amp;gt;40% and produces a 10 day delay in tumor progression compared to vehicle (p &amp;lt; 0.02). Tumor volume decreased by &amp;gt;85% when RG7787 was given following paclitaxel, a statistically significant improvement over paclitaxel alone. Together these data demonstrate that RG7787 has significant activity against TNBC and warrants further study as a treatment for this malignancy. Citation Format: Christine Alewine, Emily Maon-Osann, Ira Pastan. Activity of mesothelin-targeted immunotoxin RG7787 against triple-negative breast cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5440. doi:10.1158/1538-7445.AM2014-5440
FluorescentPlasmodium bergheisporozoites and pre-erythrocytic stages: a new tool to study mosquito and mammalian host interactions with malaria parasites (2001)

To track malaria parasites for biological studies within the mosquito and mammalian hosts, we constructed a stably transformed clonal line of Plasmodium berghei, PbFluspo, in which sporogonic and pre-erythrocytic liver-stage parasites are autonomously fluorescent. A cassette containing the structural gene for the FACS-adapted green fluorescent protein mutant 2 (GFPmut2), expressed from the 5' and 3' flanking sequences of the circumsporozoite (CS) protein gene, was integrated and expressed at the endogenous CS locus. Recombinant parasites, which bear a wild-type copy of CS, generated highly fluorescent oocysts and sporozoites that invaded mosquito salivary glands and were transmitted normally to rodent hosts. The parasites infected cultured hepatocytes in vitro, where they developed into fluorescent pre-erythrocytic forms. Mammalian cells infected by these parasites can be separated from non-infected cells by fluorescence activated cell sorter (FACS) analysis. These fluorescent insect and mammalian stages of P. berghei should be useful for phenotypic studies in their respective hosts, as well as for identification of new genes expressed in these parasite stages.
TILGen: A Program to Investigate Immune Targets in Breast Cancer Patients - First Results on the Influence of Tumor-Infiltrating Lymphocytes (2018)

TILs are a strong predictor of pCR in TNBC and HER2-positive breast cancer patients. Implications for the use of this information including the effect on prognosis might help to identify patients most likely to benefit from a neoepitope-based therapy approach.
Plant genome engineering from lab to field—a Keystone Symposia report (2021)

Facing the challenges of the world's food sources posed by a growing global population and a warming climate will require improvements in plant breeding and technology. Enhancing crop resiliency and yield via genome engineering will undoubtedly be a key part of the solution. The advent of new tools, such as CRIPSR/Cas, has ushered in significant advances in plant genome engineering. However, several serious challenges remain in achieving this goal. Among them are efficient transformation and plant regeneration for most crop species, low frequency of some editing applications, and high attrition rates. On March 8 and 9, 2021, experts in plant genome engineering and breeding from academia and industry met virtually for the Keystone eSymposium "Plant Genome Engineering: From Lab to Field" to discuss advances in genome editing tools, plant transformation, plant breeding, and crop trait development, all vital for transferring the benefits of novel technologies to the field.
Development of the Fischer-Tropsch Process: From the Reaction Concept to the Process Book (2016)

The process development by IFP Energies nouvelles (IFPEN)/ENI/Axens of a Fischer-Tropsch process is described. This development is based on upstream process studies to choose the process scheme, reactor technology and operating conditions, and downstream to summarize all development work in a process guide. A large amount of work was devoted to the catalyst performances on one hand and the scale-up of the slurry bubble reactor with dedicated complementary tools on the other hand. Finally, an original approach was implemented to validate both the process and catalyst on an industrial scale by combining a 20 bpd unit in ENI’s Sannazzaro refinery, with cold mock-ups equivalent to 20 and 1 000 bpd at IFPEN and a special “Large Validation Tool” (LVT) which reproduces the combined effect of chemical reaction condition stress and mechanical stress equivalent to a 15 000 bpd industrial unit. Dedicated analytical techniques and a dedicated model were developed to simulate the whole process (reactor and separation train), integrating a high level of complexity and phenomena coupling to scale-up the process in a robust reliable base on an industrial scale.
Insulin Action in the Hypothalamus Increases Second-Phase Insulin Secretion in Humans (2019)

In participants with high hypothalamic insulin sensitivity, insulin action in the brain enhanced second-phase insulin secretion from pancreatic beta cells. This reaction could, for example, contribute to late postprandial glucose regulation by suppressing hepatic glucose production by portal venous insulin.
Max-cover in map-reduce (2010)

The NP-hard Max-k-cover problem requires selecting k sets from a collection so as to maximize the size of the union. This classic problem occurs commonly in many settings in web search and advertising. For moderately-sized instances, a greedy algorithm gives an approximation of (1-1/e). However, the greedy algorithm requires updating scores of arbitrary elements after each step, and hence becomes intractable for large datasets.
Towards Passive Haptic Learning of piano songs (2015)

Passive Haptic Learning (PHL) enables users to acquire motor skills by receiving tactile stimulation while no perceived attention is given to learning. Initial work used gloves with embedded vibration motors to passively teach users how to play simple, one-handed, one-note-at-a-time piano melodies. In an effort to create a practical system for learning full piano pieces, we have developed a method of passively teaching two-handed chorded skills, initially focusing on Braille typing. Here, we extend this effort to piano and show that passive stimulation is more effective at teaching piano pieces when presented on both hands simultaneously as opposed to training the left hand and then the right, as is common in many active teaching methods. We also demonstrate that accompanying audio is not needed for passive learning of piano melodies, which allows mobile PHL gloves to be used in more everyday situations.
Record RF performance of sub-46 nm L/sub gate/ NFETs in microprocessor SOI CMOS technologies (2006)

We report record RF FET performance in 65 and 90-nm silicon-on-insulator (SOI) CMOS technologies featuring measured gate lengths from 27 to 43 nm and analyze factors contributing to that performance. The effect of layout and geometry optimization as well as channel length scaling is investigated to improve RF performance, namely f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> , and f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">MAX</sub> . A peak f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> of 330 GHz is measured in a fully-wired 65-nm NFET. A complete de-embedding method to accurately determine RF characteristics of the intrinsic 90-nm SOI NFET results in a peak f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> of 290 GHz and an f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">MAX</sub> of 450 GHz
Evaluation of the Preservative Properties of Origanum elongatum Essential Oil in a Topically Applied Formulation Under a Challenge Test (2018)

The aim of this study is to evaluate the preservative efficacy of Origanum elongatum essential oil in topical cream under a challenge test that was performed following the standard procedure proposed by the European Pharmacopoeia, using standardized microorganisms. Essential oil was analyzed by GC–MS (gas chromatography–mass spectrometry). The antimicrobial activity of this essential oil was investigated by agar diffusion methods and broth microdilution assay to determine the minimum inhibitory concentration of essential oil required for preservation. The results demonstrated that the preservation effect was effective at 2% (v/w) of Origanum elongatum essential oil in topical cream, satisfying criterion A against S taphylococcus aureus , Escherichia coli and Aspergillus brasiliensis . However, the essential oil was ineffective against Pseudomonas aeruginosa with a reduction of 10 2 within 7 days of challenge and no increase up to the 28th day and against Candida albicans in the challenge test. Carvacrol predominated (63.06%), followed by the two monoterpenes hydrocarbons: γ-terpinene (15.99%) and p-cymene (9.51%). Our study highlighted the preservative power of Origanum elongatum essential oil as an alternative solution to chemical preservatives.
Targetfinder.org: a resource for systematic discovery of transcription factor target genes (2010)

Targetfinder.org (http://targetfinder.org/) provides a web-based resource for finding genes that show a similar expression pattern to a group of user-selected genes. It is based on a large-scale gene expression compendium (>1200 experiments, >13,000 genes). The primary application of Targetfinder.org is to expand a list of known transcription factor targets by new candidate target genes. The user submits a group of genes (the 'seed'), and as a result the web site provides a list of other genes ranked by similarity of their expression to the expression of the seed genes. Additionally, the web site provides information on a recovery/cross-validation test to check for consistency of the provided seed and the quality of the ranking. Furthermore, the web site allows to analyse affinities of a selected transcription factor to the promoter regions of the top-ranked genes in order to select the best new candidate target genes for further experimental analysis.
Correction of discontinuities in measurements of complex permittivity with the aid of a coaxial probe (2002)

In such measurements, discontinuities between the planes of reference and of measurement cause parasitic reflections which introduce oscillations into the measurements. Various techniques are presented for cancelling the effect of these discontinuities in permittivity measurements with a six-port reflectometer.
A Middleware Platform for Integrating Devices and Developing Applications in E-Health (2015)

In the Internet of Things (IoT) vision, any physical or virtual object can be identified, addressable, controlled, and monitored via Internet. In the e-health scenario, these smart objects can be body sensors allowing the continuous monitoring of vital signs of patients. Due to the inherent heterogeneity of such devices, it is necessary to enable interoperability among them and to facilitate the development of applications that make use of the provided data. In this context, this paper introduces EcoHealth (Ecosystem of Health Care Devices), a middleware platform that integrates heterogeneous body sensors for enabling the remote monitoring of patients and improving medical diagnosis. In this paper, we present the EcoHealth architecture and a performance evaluation with an e-health application developed as proof of concept.