gebhart/patrepeval huggingface dataset:
Liquid Injection MOCVD Grown Binary Oxides and Ternary Rare-Earth Oxide as Alternate Gate-Oxides for Logic Devices (2010)

ZrO2, HfO2 and DyScO3 thin films having thickness in the range 2-20 nm were grown on SiOx/Si(100) substrates in a multi-wafer planetary MOCVD reactor combined with a liquid delivery system using engineered precursors. Growth rate, surface morphology, crystal structure, crystal density of the as-deposited films were analysed as a function of deposition temperature. The influence of post deposition annealing on the densification and crystallization was studied. Electrical properties of MIS capacitor structures are also discussed. Results on the optimised gate stack of Pt/ZrO2/SiOx/Si, Pt/HfO2/SiOx/Si, Pt/DyScO3/SiOx/Si are finally compared; and DyScO3 seems to be promising high-k material candidate compared to Group-IVB oxides for the coming technology nodes.
Importance of Complete Pathology Reporting for Neuroendocrine Carcinoma: WHO Guidelines Are a Good Start but Not Enough (2020)

Implementation of the WHO 2010 guideline is associated with a significant increase in reporting parameters needed for classification. Stratification of patients is more reliable based on reports containing all parameters. Guidelines alone however are not enough to warrant complete reporting; synoptic reports might be needed.
Dynamic silencing of somatic L1 retrotransposon insertions reflects the developmental and cellular contexts of their genomic integration (2017)

We hypothesize that the <i>de novo</i> methylation marks at newly inserted sequences retrotransposed by L1 in early pre-implantation development are maintained or re-established in adult somatic tissues. By contrast, histone deacetylation reversibly silences L1 reporter insertions that had mobilized at later timepoints in somatic development and differentiation, e.g., in cancer cell lines. We conclude that the cellular contexts of L1 retrotransposition can determine expression or silencing of newly integrated sequences. We propose a model whereby reporter expression from somatic TE insertions reflects the timing, molecular mechanism, epigenetic controls and the genomic, cellular and developmental contexts of their integration.
Exploiting Chemical Toolboxes for the Expedited Generation of Tetracyclic Quinolines as a Novel Class of PXR Agonists (2018)

The discovery of lead compounds relies on the iterative generation of structure-activity relationship data resulting from the synthesis and biological evaluation of hit analogues. Using traditional approaches, a significant time delay may occur from compound design to results, leading to slow and expensive hit-to-lead explorations. Herein, we have exploited the use of chemical toolboxes to expedite lead discovery and optimization. In particular, the integration of flow synthesizers, automation, process analytical technologies, and computational chemistry has provided a prototype system enabling the multicomponent flow synthesis, in-line analysis, and characterization of chiral tetracyclic quinolines as a novel class of PXR agonists. Within 29 compounds, a novel template <b>19b</b> (3a<i>S</i>,11<i>R</i>,11a<i>S</i>) was identified with an EC<sub>50</sub> of 1.2 μM (efficacy 119%) at the PXR receptor.
Experimental characterization of mm-wave detection by a micro-array of Golay cells (2009)

We present experimental results for an uncooled imaging focal plane array technology that consists of a polymer/metal/polymer layered membrane suspended over a micro-fabricated array of cavities. The device operation is Golay-like (heating of air in the cavity causes a detectable deflection of the membrane proportional to incident EM power), but potentially offers both greater sensitivity and more read-out options (optical or electrical) than a traditional Golay cell through tailoring of the membrane properties. The membrane is formed from a layer-by-layer deposition of polymer with one or more monolayers of gold nanoparticles (or other metal) that help control the membrane's elasticity and deformation-dependent optical reflectivity/electrical conductivity. Baseline capabilities of the device have been established through optical measurements of membrane deflection due to incident mm-wave radiation modulated at 30 Hz (corresponding to a video refresh rate). The device demonstrates an NEP of 300 nW/&radic;Hz at 105 GHz for a 19-layer membrane (9 poly/1 Au/9 poly) suspended over an array of 80 &mu;m diameter cavities (depth = 100 &mu;m) etched in a 500 &mu;m thick substrate of Si. Calculations of membrane sensitivity show that this NEP could be reduced to ~ 100 pW/&radic;Hz with enlarged cavity diameters on the order of 600 &mu;m.
Discovery of a Neutral 40-PdII-Oxo Molecular Disk, [Pd40O24(OH)16{(CH3)2AsO2}16]: Synthesis, Structural Characterization, and Catalytic Studies (2021)

We report on the synthesis and structural characterization of a giant, discrete, and neutral molecular disk, [Pd<sub>40</sub>O<sub>24</sub>(OH)<sub>16</sub>{(CH<sub>3</sub>)<sub>2</sub>AsO<sub>2</sub>}<sub>16</sub>] (<b>Pd</b><sub><b>40</b></sub>), comprising a 40-palladium-oxo core that is capped by 16 dimethylarsinate moieties, resulting in a palladium-oxo cluster (POC) with a diameter of ∼2 nm. <b>Pd</b><sub><b>40</b></sub>, which is the largest known neutral Pd-based oxo cluster, can be isolated either as a discrete species or constituting a 3D H-bonded organic-inorganic framework (HOIF) with a 12-tungstate Keggin ion, [SiW<sub>12</sub>O<sub>40</sub>]<sup>4-</sup> or [GeW<sub>12</sub>O<sub>40</sub>]<sup>4-</sup>. <sup>1</sup>H and <sup>13</sup>C NMR as well as <sup>1</sup>H-DOSY NMR studies indicate that <b>Pd</b><sub><b>40</b></sub> is stable in aqueous solution, which is also confirmed by ESI-MS studies. <b>Pd</b><sub><b>40</b></sub> was also immobilized on a mesoporous support (SBA15) followed by the generation of size-controlled Pd nanoparticles (diameter ∼2-6 nm, as based on HR-TEM), leading to an effective heterogeneous hydrogenation catalyst for the transformation of various arenes to saturated carbocycles.
Asymptotically Optimal Delay-aware Scheduling in Queueing Systems (2018)

In this paper, we investigate a general delay-aware channel allocation problem where the number of channels is less than that of users. Due to the proliferation of delay sensitive applications, the objective of our problem is chosen to be the minimization of the total average backlog queues of the network in question. First, we show that our problem falls in the framework of Restless Bandit Problems (RBP), for which obtaining the optimal solution is known to be out of reach. To circumvent this difficulty, we tackle the problem by adopting a Whittle index approach. To that extent, we employ a Lagrangian relaxation of the original problem and prove it to be decomposable into multiple one-dimensional independent subproblems. Afterwards, we provide structural results on the optimal policy of each of the subproblems. More specifically, we prove that a threshold policy is able to achieve the optimal operating point of the considered subproblem. Armed with that, we show the indexability of the subproblems and characterize the Whittle's indices which are the basis of our proposed heuristic. We then provide a rigorous mathematical proof that our policy is optimal in the infinitely many users regime. Finally, we provide numerical results that showcase the remarkable good performance of our proposed policy and that corroborate the theoretical findings.
An unusual presentation of a urethral diverticulum as a vaginal wall mass: a case report (2013)

The diagnosis of urethral diverticula based on the vast array of presenting symptoms, is difficult. This original case report may benefit both gynecologic oncologists and female pelvic surgeons and reconstructive surgeons to keep urethral diverticulum in the differential diagnosis when faced with a bleeding midline anterior vaginal mass. This unusual presentation of a urethral diverticulum demonstrates how similarly it may present to a vaginal cancerous mass.
Association (2016)

In the past, aggregation and self-assembly have been associated principally with micellar and colloidal systems of molecules; however, with the advent of supramolecular chemistry, molecular self-assembly has been opened to a much wider understanding that has facilitated access to a variety of different shapes and sizes, along with the construction of new and fascinating molecular topologies. This document aims at defining more than 150 terms related to aggregation and self-assembly in the particular case of macromolecules. The list is restricted to the most commonly encountered terms.
AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data (2021)

Detecting multiplets in single nucleus (sn)ATAC-seq data is challenging due to data sparsity and limited dynamic range. AMULET (ATAC-seq MULtiplet Estimation Tool) enumerates regions with greater than two uniquely aligned reads across the genome to effectively detect multiplets. We evaluate the method by generating snATAC-seq data in the human blood and pancreatic islet samples. AMULET has high precision, estimated via donor-based multiplexing, and high recall, estimated via simulated multiplets, compared to alternatives and identifies multiplets most effectively when a certain read depth of 25K median valid reads per nucleus is achieved.
Fabrication of Lead-Free (Na0.5K0.5)NbO3–BaZrO3–(Bi0.5Li0.5)TiO3Ferroelectric Thin Films on (111)Pt/Ti/SiO2/(100)Si Substrate by Pulsed Laser Deposition (2011)

0.92(Na 0.5 K 0.5 )NbO 3 –0.06BaZrO 3 –0.02(Bi 0.5 Li 0.5 )TiO 3 (NKN–BZ–BLT) thin films were fabricated on a (111)Pt/Ti/SiO 2 /(100)Si substrate by pulsed laser deposition (PLD). The quality of the NKN–BZ–BLT thin films was improved by introducing an NKN–BZ–BLT buffer layer, which was deposited at a high substrate temperature of 850 °C. An X-ray diffraction pattern (XRD) showed that the 100 pt preferential-oriented NKN–BZ–BLT thin films [on the basis of a pseudotetragonal perovskite (pt) structure] were obtained without and with buffer layers. From the rocking curves, the crystallinity of the film was slightly improved by introducing the buffer layer. SEM images showed that the grain size was increased and cracks were eliminated by introducing the buffer layer. The dielectric constant of the films was comparable to that of NKN–BZ–BLT ceramics. The P – E hysteresis loops showed that the remanent polarization and spontaneous polarization of the films increased with the increase in the thickness of the buffer layer. The NKN–BZ–BLT film with a 0.8-µm-thick buffer layer exhibited a remanent polarization of 6.7 µC/cm 2 and a spontaneous polarization of 28.0 µC/cm 2 . This improvement of the ferroelectric properties would be due to the relaxation of the tensile stress in the presence of the buffer layer.
Amyloid-β toxicity modulates tau phosphorylation through the PAX6 signalling pathway (2021)

The molecular link between amyloid-β plaques and neurofibrillary tangles, the two pathological hallmarks of Alzheimer's disease, is still unclear. Increasing evidence suggests that amyloid-β peptide activates multiple regulators of cell cycle pathways, including transcription factors CDKs and E2F1, leading to hyperphosphorylation of tau protein. However, the exact pathways downstream of amyloid-β-induced cell cycle imbalance are unknown. Here, we show that PAX6, a transcription factor essential for eye and brain development which is quiescent in adults, is increased in the brains of patients with Alzheimer's disease and in APP transgenic mice, and plays a key role between amyloid-β and tau hyperphosphorylation. Downregulation of PAX6 protects against amyloid-β peptide-induced neuronal death, suggesting that PAX6 is a key executor of the amyloid-β toxicity pathway. Mechanistically, amyloid-β upregulates E2F1, followed by the induction of PAX6 and c-Myb, while Pax6 is a direct target for both E2F1 and its downstream target c-Myb. Furthermore, PAX6 directly regulates transcription of GSK-3β, a kinase involved in tau hyperphosphorylation and neurofibrillary tangles formation, and its phosphorylation of tau at Ser356, Ser396 and Ser404. In conclusion, we show that signalling pathways that include CDK/pRB/E2F1 modulate neuronal death signals by activating downstream transcription factors c-Myb and PAX6, leading to GSK-3β activation and tau pathology, providing novel potential targets for pharmaceutical intervention.
On Term Selection Techniques for Patent Prior Art Search (2015)

In this paper, we investigate the influence of term selection on retrieval performance on the CLEF-IP prior art test collection, using the Description section of the patent query with Language Model (LM) and BM25 scoring functions. We find that an oracular relevance feedback system that extracts terms from the judged relevant documents far outperforms the baseline and performs twice as well on MAP as the best competitor in CLEF-IP 2010. We find a very clear term selection value threshold for use when choosing terms. We also noticed that most of the useful feedback terms are actually present in the original query and hypothesized that the baseline system could be substantially improved by removing negative query terms. We tried four simple automated approaches to identify negative terms for query reduction but we were unable to notably improve on the baseline performance with any of them. However, we show that a simple, minimal interactive relevance feedback approach where terms are selected from only the first retrieved relevant document outperforms the best result from CLEF-IP 2010 suggesting the promise of interactive methods for term selection in patent prior art search.
Supplementary Figure 4 from Reducing TNF Receptor 2<sup>+</sup> Regulatory T Cells via the Combined Action of Azacitidine and the HDAC Inhibitor, Panobinostat for Clinical Benefit in Acute Myeloid Leukemia Patients (2023)

&lt;p&gt;PDF file - 1561K, The expression levels of CD25 on TNFR2-FOXP3- and TNFR2+FOXP3+ T cells within healthy and AML patients.&lt;/p&gt;
Sorption behavior of polyaramides in relation to isolation of nucleic acids and proteins B Biointerfaces (2016)

The effect of chemical composition and morphology of the surface layers of new polyaramide-containing sorbents on the mechanism of selective sorption of nucleic acids and proteins was investigated as compared to the previously studied sorbents modified with fluoropolymers and polyaniline (high-throughput materials providing one-step isolation of DNA from biological mixtures). A series of silica-based sorbents modified with polyaramides having consistently varying structure and containing the set of “key” structural elements (aromatic units and nitrogen atoms in the backbone, fluorinated groups), and various donor and acceptor moieties was prepared. The chemical composition of the polymer coatings was evaluated by X-ray photoelectron spectroscopy. The surface morphology was studied by scanning probe microscopy. The sorption properties were investigated by passing the mixtures containing DNA, RNA and proteins of different nature through the cartridges containing the obtained sorbents. All the investigated materials weakly retain double-stranded DNA but effectively retain RNA and proteins. The sorption capacity of the sorbents depends on the protein nature. The observed sorption behavior was shown to be determined by the chemical structure and not by the morphology of the polymer coating. It was proposed that similarity of the sorption properties of the series of chemically different polymers could be determined by similar total input of different sorption mechanisms.
DSM economic marginal demand bidding (2010)

Asymmetric information in the electricity market creates incentive for customer aggregators (ESCOs, EMCOs, LSEs, etc.) to bid strategically as new information arrives. Such companies are pooling demand to provide enhanced services to customers. Since such demand pooling companies are not defined generically, all types of demand pooling companies will be termed demand serving company (DSC) to not confuse these with the existing company products and services. This paper considers strategic interaction between demand companies and the markets where energy is traded simultaneously in two or more markets. With information about the type of supplier bids in each market, a DSC's cost can be implied from the market prices, demand timing, and quantity of demand. The complexity comes into play when one market is more transparent and liquid than another. Smart Grid equipment is a facilitator for such market play by DSCs. The question then is to determine how a DSC would bid given the expectations of its competitors and the suppliers on each market as well as the knowledge on physical characteristics of each system.
Supplementary Table S3 from Genomic Features of Exceptional Response in Vemurafenib ± Cobimetinib–treated Patients with <i>BRAF</i><sup>V600</sup>-mutated Metastatic Melanoma (2023)

Supplementary Table S3 from Genomic Features of Exceptional Response in Vemurafenib ± Cobimetinib–treated Patients with &lt;i&gt;BRAF&lt;/i&gt;&lt;sup&gt;V600&lt;/sup&gt;-mutated Metastatic Melanoma
WearWrite (2015)

Smartwatches are becoming increasingly powerful, but limited input makes completing complex tasks impractical. Our WearWrite system introduces a new paradigm for enabling a watch user to contribute to complex tasks, not through new hardware or input methods, but by directing a crowd to work on their behalf from their wearable device. WearWrite lets authors give writing instructions and provide bits of expertise and big picture directions from their smartwatch, while crowd workers actually write the document on more powerful devices. We used this approach to write three academic papers, and found it was effective at producing reasonable drafts.
Revisiting the impact of synthetic ORF sequences on engineered LINE-1 retrotransposition (2022)

Abstract The retrotransposon Long Interspersed Element 1 (L1) contains adenosine rich ORFs, a characteristic that limits its expression in mammalian cells. A synthetic mouse L1 (smL1) with ORF adenosine content decreased from 40% to 26% showed increased mRNA expression and retrotransposed far more efficiently than the native parental element, L1spa (1). Here, we observe two nonsynonymous substitutions between the L1spa and smL1 ORF1 sequences, and note that the smL1 3’UTR lacks a conserved guanosine-rich region (GRR) which could potentially take on a G-quadruplex secondary structure. We find that the combined effect of a single amino acid change and the GRR 3’UTR deletion, rather than synthetic ORF sequences, accounts for the increase in smL1 retrotransposition efficiency over L1spa. Furthermore, we demonstrate that the position of the GRR within the L1 reporter construct impacts retrotransposition efficiency. Our results prompt a reevaluation of synthetic L1 activity and suggest native mouse L1 mobility has in some cases been underestimated in engineered retrotransposition assays. Author Summary L1 retrotransposons are mobile DNA elements or “jumping genes” that can copy- and-paste their sequences to new locations in the host genome. The jumping ability, or retrotransposition efficiency, of individual L1 elements can be evaluated using a cultured cell assay in which the L1 is tagged in its 3’ untranslated region (3’UTR) with a reporter gene that becomes expressed upon successful retrotransposition. In a previous study, authors Han and Boeke reported that the retrotransposition efficiency of a mouse L1 element could be enhanced dramatically by synthetically increasing the GC content of the L1 ORFs without changing their amino acid sequence. Curiously, a similarly constructed synthetic human L1 achieved only a modest increase in retrotransposition efficiency over the native element. Here, we find that two coding changes and partial deletion of the mouse L1 3’UTR sequence which occurred during construction of the synthetic mouse L1 reporter actually are responsible for the increased jumping of this construct. We also find that changing the placement as well as the presence of this deleted 3’UTR region within the reporter construct determines its impact on engineered retrotransposition efficiency. Together, our study reconciles the disparate impacts of synthetic sequences upon human and mouse L1 retrotransposition efficiency, prompts a reconsideration of numerous studies using synthetic L1 constructs, and will inform the ongoing use of synthetic and natural mouse L1 reporter constructs in vivo and in vitro.
Source-mask optimization (SMO): from theory to practice (2010)

Source Mask Optimization techniques are gaining increasing attention as RET computational lithography techniques in sub-32nm design nodes. However, practical use of this technique requires careful considerations in the use of the obtained pixilated or composite source and mask solutions, along with accurate modeling of mask, resist, and optics, including scanner scalar and vector aberrations as part of the optimization process. We present here a theory-to-practice case of applying ILT-based SMO on 22nm design patterns.
FAR: an end-user language to support cottage e-services (2002)

E-commerce has begun to evolve beyond simple web pages to more sophisticated ways of conducting e-business transactions, such as through electronic advertising, negotiation, and delivery. However, to participate in these advances requires the skills of professional programmers, and end-user owners of small businesses often cannot justify this expense. In this paper, we present FAR, an end-user language to offer and deliver e-services. The novel aspects of FAR are its support of small e-services and its multiparadigm approach to combining ideas from spreadsheets and rule-based programming with drag-and-drop web page layout devices.
Enzymatically generated hydrogen peroxide reduces the number of acne lesions in acne vulgaris. (2013)

A major component to the etiology of acne is the growth and invasion by Propionibacterium acnes. Hydrogen peroxide is an excellent antimicrobial agent but is unstable in most formulations. We have developed a hydrogen peroxide generation system using the enzyme glucose oxidase and glucose. This system is stable in a simple formulation and nonirritating. In a short-term clinical study (4 days), this formulation was effective in reducing the individual lesion size and total number of inflammatory acne lesions. There was a 68% reduction in acne-induced inflammation and 61% reduction in acne size within 4 days of treatment. A long-term clinical study (6 weeks in use) displayed 56% reduction in total number of inflamed lesions and a 45% reduction in noninflamed lesions after 6 weeks. This suggests that topical enzymatically generated hydrogen peroxide may help alleviate acne.
Ordering Heuristics for Parallel Graph Coloring (2022)

This chapter introduces the largest-log-degree-first and smallest-log-degree-last ordering heuristics for parallel greedy graph-coloring algorithms, which are inspired by the largest-degree-first and smallest-degree-last serial heuristics, respectively. There is a historical tension between coloring quality and the parallel scalability of greedy graph coloring. The chapter reviews the asynchronous parallel greedy coloring algorithm first proposed by Jones and Plassmann. The parallel performance of JP was measured by computing the speedup it achieved on 12 cores and by comparing the 1-core runtimes of JP to an optimized serial implementation of Greedy. To color vertices more efficiently, the implementation of JP uses vertex-local bit vectors to store information about the availability of low-numbered colors. Parallel coloring algorithms have been explored extensively in the distributed computing domain. Several greedy coloring algorithms have been described in synchronous PRAM models.