gebhart/patrepeval huggingface dataset:
Single input state polarization sensitive swept source optical coherence tomography based on an all single mode fiber interferometer (2014)

We present a newly developed single mode fiber based swept source polarization sensitive optical coherence tomography system using a single input state at 1040 nm. Two non-polarizing fiber based beam splitters are combined to form a Mach-Zehnder interferometer, while two polarizing beam splitters are used to obtain a polarization sensitive detection. Both types of beam splitters solely feature conventional single mode fibers. Polarization control paddles are used to set and maintain the polarization states in the fibers of the interferometer and detection unit. By use of a special paddle alignment scheme we are able to eliminate any bulk optic wave plates and polarization maintaining fibers in the interferometer and detection paths while preserving the advantages of a single input state system that illuminates the sample with circularly polarized light. To demonstrate the capabilities of our system, we performed retinal measurements on healthy human volunteers.
Rewrite techniques for performance optimization of schema matching processes (2010)

A recurring manual task in data integration, ontology alignment or model management is finding mappings between complex meta data structures. In order to reduce the manual effort, many matching algorithms for semi-automatically computing mappings were introduced.Unfortunately, current matching systems severely lack performance when matching large schemas. Recently, some systems tried to tackle the performance problem within individual matching approaches. However, none of them developed solutions on the level of matching processes.In this paper we introduce a novel rewrite-based optimization technique that is generally applicable to different types of matching processes. We introduce filter-based rewrite rules similar to predicate push-down in query optimization. In addition we introduce a modeling tool and recommendation system for rewriting matching processes.Our evaluation on matching large web service message types shows significant performance improvements without losing the quality of automatically computed results.
Fibronectin and androgen receptor expression data in prostate cancer obtained from a RNA-sequencing bioinformatics analysis (2017)

Prostate cancer is the second most commonly diagnosed male cancer in the world. The molecular mechanisms underlying its development and progression are still unclear. Here we show analysis of a prostate cancer RNA-sequencing dataset that was originally generated by Ren et al. [3] from the prostate tumor and adjacent normal tissues of 14 patients. The data presented here was analyzed using our RNA-sequencing bioinformatics analysis pipeline implemented on the bioinformatics web platform, Galaxy. The relative expression of fibronectin (FN1) and the androgen receptor (AR) were calculated in fragments per kilobase of transcript per million mapped reads, and represented in FPKM unit. A subanalysis is also shown for data from three patients, that includes the relative expression of FN1 and AR and their fold change. For interpretation and discussion, please refer to the article, "miR-1207-3p regulates the androgen receptor in prostate cancer via FNDC1/fibronectin" [1] by Das et al.
Bias independent heavy- and light-hole degeneracy in InGaAs/InGaAsP quantum wells (1998)

We present a type of strained semiconductor quantum-well structure that exhibits bias-independent heavy- and light-hole degeneracy. This effect is achieved by inserting thin layers of highly strained material in an unstrained quantum well. By adjusting the thickness and the position of the highly tensile strained layers, the quantum confined Stark effect for the heavy and light holes can be engineered separately to control the bias dependent polarization properties. Experimental results on such a structure agree well with the theory. These unique bias-dependent polarization properties have important applications in optoelectronic devices when specific polarization properties are required.
Selective activation of the sacral anterior roots for induction of bladder voiding (2005)

Selective activation of sacral ventral roots combined with dorsal rhizotomy may provide a viable means of low-pressure continuous voiding in neurological impairment.
A Leo Satellite Navigation Algorithm Based on GPS and Magnetometer Data (2000)

The Global Positioning System (GPS) has become a standard method for low cost onboard satellite orbit determination. The use of a GPS receiver as an attitude and rate sensor has also been developed in the recent past. Additionally, focus has been given to attitude and orbit estimation using the magnetometer, a low cost, reliable sensor. Combining measurements from both GPS and a magnetometer can provide a robust navigation system that takes advantage of the estimation qualities of both measurements. Ultimately a low cost, accurate navigation system can result, potentially eliminating the need for more costly sensors, including gyroscopes.
VolturnUS 1:8-Scale FRP Floating Wind Turbine Tower: Analysis, Design, Testing and Performance (2014)

In May of 2013 the VolturnUS 1:8 floating semi-submersible wind turbine was successfully deployed off the coast of Castine, Maine, making the unit the first grid connected offshore turbine in the United States. The VolturnUS 1:8 structure features a 20 kW turbine, a post-tensioned and reinforced concrete semi-submersible base and a fiber reinforced plastic (FRP) tower (E-glass and polyester resin). The VolturnUS 1:8 structure is a geometrically 1:8-scale of a 6 MW floating turbine design and is used to demonstrate the feasibility of both the concrete base and FRP tower and validate the performance of the structure in a scaled environment. Data collected from the deployed 1:8-scale structure will be used for modeling and simulating the behavior of the system at full-scale. The effort was led by the University of Maine’s Advanced Structures and Composites Center (UMaine) and a consortium of industry partners, including FRP manufacturer Ershigs, Inc. An overview of the process and methodology used in the analysis, design and testing of the 1:8 scale FRP floating wind turbine tower is presented. The use of an FRP tower on a floating wind turbine platform offers the benefits of reduced tower mass and maintenance requirements and has the potential to further reduce hull mass by lowering the global center of gravity of the structure. An FRP tower for use on the UMaine semi-submersible concrete VolturnUS 1:8 platform was developed that meets all strength and serviceability criteria and is robust enough to withstand the loading from both wind and waves. An overview of the tower loads analysis and FAST modeling, tower structural design, structural proof testing and preliminary analysis of performance are presented. The VolturnUS 1:8 wind turbine tower is the first time FRP materials have been used in an offshore wind tower application. Further, the methodologies and procedures that were developed in the design of the pilot-scale tower are directly applicable to the design and analysis of composite wind turbine towers at the full-scale level. These “lessons learned” are already in use as Ershigs and UMaine work to design a full-scale composite tower over 80 meters tall for use on the VolturnUS platform with a 6MW wind turbine. The results of the 1:8-scale program demonstrate the successful use of an FRP wind turbine tower on a floating platform and highlights the potential for the use of an FRP tower at the full-scale (6 MW) level.
Soluble, Exfoliated Hexagonal Boron Nitride Nanosheets (2009)

Hexagonal boron nitride (h-BN), the isoelectric analogue of graphite, was functionalized using lipophilic and hydrophilic amine molecules. The functionalization induced the exfoliation of the layered structure of h-BN, resulting in few-layered and monolayered nanosheets soluble in common organic solvents and/or water. The soluble h-BN nanosheets were characterized using various solution-phase and solid-state techniques. For example, the optical extinction coefficients of the h-BN nanosheets in homogeneous dispersions were estimated to be much lower than those of graphene sheets, confirming their low-colored nature. Solution-phase NMR spectroscopy supported the mechanism that the amino groups of the functional molecules complex to the electron-deficient boron atoms on the h-BN nanosheet surfaces in terms of Lewis acid−base interactions. Results from other microscopic and spectroscopic characterizations of these functionalized two-dimensional nanomaterials are also presented, and the implications of the reported versatile and effective functionalization strategy are discussed.
Effect of solute atoms on grain boundary sliding in magnesium alloys (2014)

The effect of solid-solution alloying on grain boundary sliding (GBS) was investigated using pure magnesium and six kinds of Mg–X (X = Ag, Al, Li, Pb, Y and Zn) dilute binary solid solutions with an average grain size of 10 µm. A sharp increase in damping capacity caused by GBS was observed above a certain temperature. The temperature at which a sharp increase in damping capacity occurred depended on the alloying element. The addition of Y and Ag markedly increased the onset temperature (more than 100 K) for a sharp increase in damping capacity, whereas the addition of Zn, Al and Li slightly increased the onset temperature (less than 50 K) as compared with that for pure magnesium. Tensile tests at a temperature of 423 K revealed that the higher the onset temperature, the lower the strain rate sensitivity of the flow stress. It is suggested that the former elements (Y and Ag) are more effective in suppressing GBS in magnesium alloys than the latter ones (Zn, Al and Li). The suppression of GBS was associated with low grain boundary energy, and the extent to which the energy is reduced depended on the alloying element. It was suggested that the change in the lattice parameter (the so-called c/a ratio) affects the grain boundary energy, and thus, the occurrence of GBS.
Dynamic Materialization of Query Views for Data Warehouse Workloads (2008)

A materialized view, or Materialized Query Table (MQT), is an auxiliary table with precomputed data that can be used to significantly improve the performance of a database query. Previous research efforts have focused on finding the best candidate MQT set, with a common static heuristic being to greedily pre-materialize the MQTs prior to executing the workload. While this approach is sound when the size of the MQT set on disk is small, it will not be able to pre-materialize all MQTs and indexes when faced with real-world disk limits and view maintenance costs, and thus a static heuristic will fail to exploit the potentially large benefits of those MQTs not selected for materialization. In this paper we present an automated, dynamic MQT management scheme that materializes views and creates indexes in an on-demand fashion as a workload executes and manages them with an LRU cache. In order to maximize the benefit of executing queries with MQTs, the scheme makes an adaptive tradeoff between the MQT materializations, the base table accesses, and the benefit of MQT hits in the cache. To find the workload permutation that produces the overall highest net benefit, we use a genetic algorithm to search the N! solution space, and to avoid materializing seldom-used MQTs, we prune the set of MQT candidates. We ran our dynamic management on a TPC-H workload and found that our scheme produces higher benefit across a variety of scenarios; we demonstrate over 60% improvement in MQT benefit under harsh conditions when the size of available MQTs with indexes is larger than the cache.
Passive-state preparation for continuous-variable quantum key distribution (2020)

We conduct an experimental study of continuous-variable quantum key distribution using a passive-state preparation scheme. Using an off-the-shelf amplified spontaneous emission source, we show that a secure key can be generated over metro-area distances.
Multichannel detectors for profile measurements in clinical proton fields (2007)

Two beam profile measurement detectors have been developed at Indiana University Cyclotron Facility to address the need for a tool to efficiently verify dose distributions created with active methods of clinical proton beam delivery. The multipad ionization chamber (MPIC) has 128 ionization chambers arranged in one plane and is designed to measure lateral profiles in fields up to 38 cm in diameter. The MPIC pads have a 5 mm pitch for fields up to 20 cm in diameter and a 7 mm pitch for larger fields, providing the accuracy of field size determination about 0.5 mm. The multilayer ionization chamber (MLIC) detector contains 122 small-volume ionization chambers stacked at a 1.82 mm step (water-equivalent) for depth-dose profile measurements. The MLIC detector can measure profiles up to 20 cm in depth, and determine the 80% distal dose fall-off with about 0.1 mm precision. Both detectors can be connected to the same set of electronics modules, which comprise the detectors' data acquisition system. The detectors have been tested in clinical proton fields produced with active methods of beam delivery such as uniform scanning and energy stacking. This article describes detector performance tests and discusses their results. The test results indicate that the MPIC and MLIC detectors can be used for dosimetric characterization of clinical proton fields. The detectors offer significant time savings during measurements in actively delivered beams compared with traditional measurements using a water phantom.
Topological Insulator Lasers (2017)

We present, in theory and experiments, the first Topological Insulator Lasers: lasers where the cavity acts as a “superconductor for light”, maintaining slope high efficiency even in the presence of defects and disorder.
MUSCA: An Algorithm for Constrained Alignment of Multiple Data Sequences. (1998)

Given a set of N sequences, the Multiple Sequence Alignment problem is to align these N sequences, possibly with gaps, that brings out the best commonality of the N sequences. MUSCA is a two-stage approach to the alignment problem by identifying two relatively simpler sub-problems whose solutions are used to obtain the alignment of the sequences. We first discover motifs in the N sequences and then extract an appropriate subset of compatible motifs to obtain a good alignment. The motifs of interest to us are the irredundant motifs which are only polynomial in the input size. In practice, however, the number is much smaller (sub-linear). Notice that this step aids in a direct N-wise alignment, as opposed to composing the alignments from lower order (say pairwise) alignments and the solution is also independent of the order of the input sequences; hence the algorithm works very well while dealing with a large number of sequences. The second part of the problem that deals with obtaining a good alignment is solved using a graph-theoretic approach that computes an induced subgraph satisfying certain simple constraints. We reduce a version of this problem to that of solving an instance of a set covering problem, thus offer the best possible approximate solution to the problem (provided P not equalNP). Our experimental results, while being preliminary, indicate that this approach is efficient, particularly on large numbers of long sequences, and, gives good alignments when tested on biological data such as DNA and protein sequences. We introduce the the notion of an alignment number K (2 </= K </= N), a user-controlled parameter, that lends a useful flexibility to the aligning program: this additional requirement constrains the alignment to have at least K sequences agree on a character, whenever possible, in the alignment. The usefulness of the alignment number is corroborated by the users who view this as a natural constraint while dealing with a large number of sequences.
Accelerating Concurrent Workloads with CPU Cache Partitioning (2018)

Modern microprocessors include a sophisticated hierarchy of caches to hide the latency of memory access and thereby speed up data processing. However, multiple cores within a processor usually share the same last-level cache. This can hurt performance, especially in concurrent workloads whenever a query suffers from cache pollution caused by another query running on the same socket. In this work, we confirm that this particularly holds true for the different operators of an in-memory DBMS: The throughput of cache-sensitive operators degrades by more than 50%. To remedy this issue, we devise a cache allocation scheme from an empirical analysis of different operators and integrate a cache partitioning mechanism into the execution engine of a commercial DBMS. Finally, we demonstrate that our approach improves the overall system performance by up to 38%.
884. Patient Adherence to Long-Acting Injectable Cabotegravir + Rilpivirine Through 48 Weeks of Maintenance Therapy in the Phase 3 ATLAS and FLAIR Studies (2019)

Abstract Background Cabotegravir (CAB) and rilpivirine (RPV) are under development as a novel long-acting (LA) regimen for maintenance of HIV virologic suppression. Pooled Week 48 data from pivotal Phase 3 trials demonstrated noninferiority of CAB LA + RPV LA vs. current antiretroviral regimen (CAR) on the primary endpoint, proportion of subjects with HIV-1 RNA ≥50 c/mL (1.9% and 1.7%, respectively). Adherence to dosing visits, use of oral dosing (bridging) to cover planned missed injections and injection tolerability were examined for subjects in the ATLAS and FLAIR studies. Methods Virologically suppressed subjects (HIV-1 RNA < 50 c/mL) were randomized to switch to CAB LA + RPV LA or to continue CAR. On-time injections occurred Q4 weeks within a +7-day dosing window of the projected dosing date. Adherence to LA therapy was calculated as the number of on-time injection visits divided by the number of expected dosing visits through Week 48. Injection visits outside the pre-specified window and missed injection visits with/without the use of oral dosing were quantified. Injection tolerability was assessed via adverse event reporting. Results A total of 14,682 injections of CAB and RPV were administered to 581 subjects during 6,920 injection visits. 98% of injection visits took place within the allowed ±7-day dosing window with 3,194 (46%) on the projected dosing date. Forty-six (<1%) injection visits were early and 106 (2%) were late. Oral bridging was used in 16 subjects overall; 8 planned missed injection visits were successfully covered, with no change to virologic suppression status. No subject with HIV-1 RNA ≥ 50 c/mL at Week 48 had missed/late injection visits. 25% (3,663/14,682) of injections were associated with local injection site reactions (ISRs). The most common ISR was pain (3,087/3,663 = 84%). Most ISRs were grade 1–2 (99%), short duration (median 3 days), with few associated discontinuations (<1%). Conclusion Subjects receiving CAB LA + RPV LA demonstrated high rates of adherence to injection visits through week 48, with 98% of injections occurring within the ±7-day dosing window. Oral bridging with CAB and RPV was an effective strategy for maintaining viral load suppression to cover missed injection visits. Injections were well-tolerated with few associated discontinuations. Disclosures All Authors: No reported Disclosures.
Genomic structure and promoter analysis of the human  1,6-fucosyltransferase gene (FUT8) (2000)

GDP-L-Fuc:N-acetyl-beta-D-glucosaminide alpha1,6-fucosyltransferase (alpha1,6FucT) catalyzes the transfer of a fucosyl moiety from GDP-fucose to the asparagine-linked GlcNAc residue of complex N-glycans via alpha1,6-linkage. We have cloned the genomic DNA which encodes the human alpha1,6FucT gene ( FUT8 ) and analyzed its structure. It was found that the gene consists of at least nine exons spanning more than a 50 kbp genomic region, and the coding sequence is divided into eight exons. The translation initiation codon was located at exon 2, and thus exon 1 encodes only 5'-untranslated sequences. Transcription initiation site of FUT8 was determined by 5'-rapid amplification of the cDNA end and a primer-extension analysis using the total RNA isolated from SK-OV-3 cells, which have a high level of alpha1,6FucT activity. We then characterized the FUT8 promoter region by a reporter gene assay. The luciferase reporter assay indicated that the 5'-flanking region of exon 1, which covered about 1 kbp, conferred the promoter activity in SK-OV-3 cells. This region contains potential binding sites for some transcription factors, such as bHLH, cMyb, GATA-1, as well as a TATA-box, but not a CCAAT motif. 5'-Untranslated sequences found in ESTs and the cDNA for the FUT8 suggest the presence of an additional exon(s) at the upstream of the first exon identified in this study, and therefore, the transcription of the gene would be regulated by multiple promoters.
Class-Aware Adversarial Lung Nodule Synthesis in CT Images (2018)

Though large-scale datasets are essential for training deep learning systems, it is expensive to scale up the collection of medical imaging datasets. Synthesizing the objects of interests, such as lung nodules, in medical images based on the distribution of annotated datasets can be helpful for improving the supervised learning tasks, especially when the datasets are limited by size and class balance. In this paper, we propose the class-aware adversarial synthesis framework to synthesize lung nodules in CT images. The framework is built with a coarse-to-fine patch in-painter (generator) and two class-aware discriminators. By conditioning on the random latent variables and the target nodule labels, the trained networks are able to generate diverse nodules given the same context. By evaluating on the public LIDC-IDRI dataset, we demonstrate an example application of the proposed framework for improving the accuracy of the lung nodule malignancy estimation as a binary classification problem, which is important in the lung screening scenario. We show that combining the real image patches and the synthetic lung nodules in the training set can improve the mean AUC classification score across different network architectures by 2%.
Coronavirus Main Proteinase (3CL <sup>pro</sup> ) Structure: Basis for Design of Anti-SARS Drugs (2003)

A novel coronavirus has been identified as the causative agent of severe acute respiratory syndrome (SARS). The viral main proteinase (Mpro, also called 3CLpro), which controls the activities of the coronavirus replication complex, is an attractive target for therapy. We determined crystal structures for human coronavirus (strain 229E) Mpro and for an inhibitor complex of porcine coronavirus [transmissible gastroenteritis virus (TGEV)] Mpro, and we constructed a homology model for SARS coronavirus (SARS-CoV) Mpro. The structures reveal a remarkable degree of conservation of the substrate-binding sites, which is further supported by recombinant SARS-CoV Mpro-mediated cleavage of a TGEV Mpro substrate. Molecular modeling suggests that available rhinovirus 3Cpro inhibitors may be modified to make them useful for treating SARS.