gebhart/patrepeval huggingface dataset:
Algal-fungal symbiosis leads to photosynthetic mycelium (2019)

Mutualistic interactions between free-living algae and fungi are widespread in nature and are hypothesized to have facilitated the evolution of land plants and lichens. In all known algal-fungal mutualisms, including lichens, algal cells remain external to fungal cells. Here, we report on an algal-fungal interaction in which <i>Nannochloropsis oceanica</i> algal cells become internalized within the hyphae of the fungus <i>Mortierella elongata</i>. This apparent symbiosis begins with close physical contact and nutrient exchange, including carbon and nitrogen transfer between fungal and algal cells as demonstrated by isotope tracer experiments. This mutualism appears to be stable, as both partners remain physiologically active over months of co-cultivation, leading to the eventual internalization of photosynthetic algal cells, which persist to function, grow and divide within fungal hyphae. <i>Nannochloropsis</i> and <i>Mortierella</i> are biotechnologically important species for lipids and biofuel production, with available genomes and molecular tool kits. Based on the current observations, they provide unique opportunities for studying fungal-algal mutualisms including mechanisms leading to endosymbiosis.
Code clone detection experience at microsoft (2011)

Cloning source code is a common practice in the software development process. In general, the number of code clones increases in proportion to the growth of the code base. It is challenging to proactively keep clones consistent and remove unnecessary clones during the entire software development process of large-scale commercial software. In this position paper, we briefly share some typical usage scenarios of code clone detection that we collected from Microsoft engineers. We also discuss our experience on building XIAO, a code clone detection tool, and the feedback we have received from Microsoft engineers on using XIAO in real development settings.
Evaluation of a Recombinant Vaccine Candidate r56Lc-1 in a Chigger Challenge Mouse Model (2014)

Scrub typhus, an acute, febrile disease is transmitted by the bite of an Orientia infected chigger. We evaluated the protective potential of a recombinant 56 kDa antigen in a chigger challenge mouse model which mimics the natural transmission of Orientia. Chiggers from an L. chiangraiensis line 1 (Lc-1) was chosen for this challenge because the line produces chiggers with stable infectivity of 90-100% in several generations. The 56kD antigen gene of O. tsutsugamushi was cloned into an expression vector, expressed, purified, and refolded. All ICR mice were immunized 3 times at 4 weeks intervals and challenged by placing an individual chigger in the inner ear of each mouse 4 weeks after the last immunization. Mice were immunized with adjuvant Montanide+CpG or 25 g of r56Lc-1 emulsion with Montanide+CpG. Both groups were challenged by an individual Lc-1 chigger (un-infected or infected). There was no death in the groups of mice challenged by an uninfected chigger, with or without the vaccine candidate r56Lc-1. There was no survival in the groups of mice immunized with adjuvant only and challenged by an infected chigger. Our data demonstrated that r56Lc-1 provided 20-30% of protection consistently upon challenge by an infected chigger which carries the same Orientia strain based on the sequence of 56 kDa antigen. Time to mortality was delayed in mice immunized with the vaccine candidate then challenged with infected chiggers as compared to their adjuvant counterparts Since Orientia is an intracellular pathogen, the clearance of this pathogen may heavily depend on T-cell immune responses rather than B-cell immune responses and may require a vaccine candidate that mainly promotes T-cell immunity.
General preparative synthesis of 2′‐<i>O</i>‐methylpyrimidine ribonucleosides (1994)

Abstract A convergent and general approach to synthesizing 2′‐ O ‐Methylpyrimidine ribonucleosides 4a‐e, 6,7 on a multigram scale is described which begins with an improved procedure for making larger quantities of 2‐ O ‐methyl‐1,3,5‐tri‐ O ‐benzoyl‐α‐D‐ribose. The sugar was reacted with the desired silylated pyrimidines at room temperature under Vorbrüggen conditions. The crude products contained less than 10% of the α anomers and the desired β anomers were isolated by crystallization. The blocked nucleosides were then deprotected and isolated by standard methods.
A New Approach for the Treatment of Arthritis in Mice with a Novel Conjugate of an Anti-C5aR1 Antibody and C5 Small Interfering RNA (2015)

Rheumatoid arthritis (RA) is an inflammatory autoimmune joint disease in which the complement system plays an important role. Of the several components of complement, current evidence points to C5 as the most important inducer of inflammation. Several groups generated Abs or small interfering RNAs (siRNAs) or small molecule inhibitors against C5 and C5aR1 (CD88) that have showed some efficacy in RA in animal models. However, none of these candidate therapeutics has moved from bench to bedside. In this study, we test in collagen Ab-induced arthritis (CAIA) a new therapeutic strategy using a novel anti-C5ab-C5 siRNA conjugate. We first demonstrate that although C5aR2 or C5L2 (GPR77) plays no role in CAIA, C5aR1 contributes to pathogenesis. We demonstrate that injection of siRNAs blocking C5, C5aR1, or the combination decreased clinical disease activity in mice with CAIA by 45%, 51%, and 58%, respectively. Anti-C5 Ab (BB5.1) has only limited efficacy, but significantly reduced arthritis up to 66%. We then generated a novel anti-C5aR1 Ab-protamine-C5 siRNA conjugate. To our knowledge, we show for the first time that whereas unconjugated Ab plus siRNAs reduce arthritis by 19%, our anti-C5aR1 Ab-protamine-C5 siRNA conjugate was effective in reducing arthritis by 83% along with a parallel decrease in histopathology, C3 deposition, neutrophils, and macrophages in the joints of mice with CAIA. These data suggest that by targeting anti-C5 siRNAs to the receptor for its C5a activation fragment (C5aR1), a striking clinical effect can be realized.
Combining air filtration with ultra-fine particle sensing for an enhanced energy-efficient indoor air quality optimization (2007)

SUMMARY A satisfactory indoor air quality (IAQ) relies, amongst other things, on the availability of clean ventilation air. The outdoor air cleanliness in many urban environments is far from optimum. Fine particles (FPs ≤ 2.5 µm) and certainly ultra-fine particles (UFPs ≤ 0.3 µm) feature prominently as hazardous constituents of common urban air pollution. Installed filters in ventilation units of buildings and cars can clean mechanically supplied ventilation air. However, because affordable particle sensors of sufficient reliability and robustness are not commercially available, the degree to which the applied ventilation and filtration strategy is able to control the absolute indoor pollution level at any time remains usually unknown. This paper introduces a UFP sensor capable of recording the ambient UFP pollution level, yielding a sensor signal that relates to the relative inhalation-induced health hazard of airborne UFPs. The monitoring functionality of this sensor can be used for creating awareness with regard to the ambient UFP pollution level. For control purposes, UFP sensors can be used in addition to common T, RH and CO2 sensors. Furthermore, a new type of electrostatically-enhanced particle filter is presented that accomplishes its air cleaning functionality in a more energyefficient way than a comparable mechanical filter. Providing air handling units with particle filters as well as with UFP sensors downstream of these filters and/or in indoor spaces allows for a versatile control of air handling units that explicitly takes the indoor UFP pollution level into account as a decision factor for the ventilation strategy. This enables an enhanced sensorcontrolled fine-tuning of the IAQ with anticipated savings in power consumption.
Bilingual Semantic Role Labeling Inference via Dual Decomposition (2016)

This article focuses on bilingual Semantic Role Labeling (SRL); its goal is to annotate semantic roles on both sides of the parallel bilingual texts (bi-texts). Since rich bilingual information is encoded, bilingual SRL has been applied in many natural-language processing (NLP) tasks such as machine translation (MT), cross-lingual information retrieval (IR), and the like. A feasible way of performing bilingual SRL is using monolingual SRL systems to perform SRL on each side of bi-texts separately. However, it is difficult to obtain consistent SRL results on both sides of bi-texts in this way. Some works have tried to jointly infer bilingual SRL because there are many complementary language cues on both sides of bi-texts and they reported better performance than monolingual systems. However, there are two limits in the existing methods. First, the existing methods often require high inference costs due to the complex objective function. Second, the existing methods fully adopt the candidates generated by monolingual SRL systems, but many candidates are discarded in the argument pruning or identification stage of monolingual systems. In this article, we propose two strategies to overcome these limits. We utilize a simple but efficient technique: Dual Decomposition to search for consistent results for both sides of bi-texts. On the other hand, we propose a method called Bi-Directional Projection (BDP) to recover arguments discarded in monolingual SRL systems. We evaluate our method on a standard parallel benchmark: the OntoNotes dataset. The experimental results show that our method yields significant improvements over the state-of-the-art monolingual systems. In addition, our approach is also better and faster than existing methods due to BDP and Dual Decomposition.
Code Acquisition at Low SINR in Spread Spectrum Communications (2006)

We consider the problem of code acquisition at low signal to interference and noise ratio (SINR) in packet-based spread spectrum communications, where a centralized "pilot" synchronization signal and high-precision oscillators are not available. Such problems arise in the context of ad-hoc networks, for example, which require fast code acquisition times and gradual degradation of the network with decreasing SINR. We motivate the use of the "postdetection integration" approach, which utilizes the energy of multiple bits in a packet, for code acquisition at low SINR. We present the implementation of a fully parallel architecture which simultaneously looks at all possible code alignments over multiple bits. This leads to a drastic reduction in acquisition time compared to serial search based methods. We report some preliminary simulation and experimental results from a hardware prototype of a transceiver on which the code acquisition algorithm was implemented
Tissue Classification as a Potential Approach for Attenuation Correction in Whole-Body PET/MRI: Evaluation with PET/CT Data (2009)

A segmented attenuation map with 4 classes derived from CT data had only a small effect on the SUVs of (18)F-FDG-avid lesions and did not change the interpretation for any patient. This approach appears to be practical and valid for MRI-based AC.
Role of E-cadherin in the Pathogenesis of Gastroesophageal Reflux Disease (2011)

The EE in GERD has increased junctional permeability and this is in association with proteolytic cleavage of e-cadherin. As loss of e-cadherin can, alone, account for the increase in junctional permeability, cleavage of e-cadherin likely represents a critical molecular event in the pathogenesis of GERD, and identification of cleaved fragments may, if confirmed in larger studies, be valuable as a biomarker of GERD.
A novel interface for on-line coupling of liquid capillary chromatography with matrix-assisted laser desorption/ionization detection (1999)

A novel interface has been developed which should allow the direct on-line coupling of liquid capillary chromatography with matrix-assisted laser desorption/ionization (MALDI) mass spectrometry detection. The interface employs continuous analyte/matrix co-crystallization onto a porous frit installed at a capillary end which is used as the target for MALDI. After separation, the analyte effluent is premixed with the MALDI matrix solution and introduced into the interface. The analyte/matrix mixture is co-crystallized onto the frit surface in the vacuum environment of the mass spectrometer. Continuous matrix/analyte crystallization and interface regeneration is accomplished by a combination of solvent flushing and laser ablation. The memory effect is negligible over a dynamic range of ca. 200. Several applications, including analysis of small peptides and combination with gel permeation chromatography (GPC), have indicated that the on-line MALDI interface does not sacrifice chromatographic or mass spectral resolution, and have demonstrated the possibility of a reliable LC-MALDI system. Copyright 1999 John Wiley & Sons, Ltd.
High‐speed low‐power and low‐power supply voltage dynamic comparator (2015)

A structure of a dynamic comparator with high‐speed low‐power and a low‐power supply voltage is proposed. The proposed comparator is compared with previous dynamic comparators. For the same size of input/output transistors and latch as well as load capacitance, it is more than 1.3 times faster with <85% power consumption. The proposed structure exhibits faster speed and lower power consumption at the same time. Moreover, it provides better performance regarding low‐power supply voltage, it also brings moderate input‐referred noise and offset among these structures.
Regulation of Transcript Levels of the Arabidopsis Cytochrome P450 Genes Involved in Brassinosteroid Biosynthesis (2002)

Cytochrome P450 enzymes of the closely related CYP90 and CYP85 families catalyze essential oxidative reactions in the biosynthesis of brassinosteroid (BR) hormones. Arabidopsis CYP90B1/DWF4 and CYP90A1/CPD are responsible for respective C-22 and C-23 hydroxylation of the steroid side chain and CYP85A1 catalyzes C-6 oxidation of 6-deoxo intermediates, whereas the functions of CYP90C1/ROT3, CYP90D1, and CYP85A2 are still unknown. Semiquantitative reverse transcriptase-polymerase chain reaction analyses show that transcript levels of CYP85 and CYP90 genes are down-regulated by brassinolide, the end product of the BR biosynthesis pathway. Feedback control of the CYP90C1, CYP90D1, and CYP85A2 genes by brassinolide suggests that the corresponding enzymes might also participate in BR synthesis. CYP85 and CYP90 mRNAs show strong and transient accumulation during the 1st week of seedling development, as well as characteristic organ-specific distribution. Transcripts of CYP90A1 and CYP85A2 are preferentially represented in shoots and CYP90C1, CYP90D1, and CYP85A1 mRNAs are more abundant in roots, whereas CYP90B1 is ubiquitously expressed. Remarkably, the spatial pattern of CYP90A1 expression is maintained in the BR-insensitive cbb2 mutant, indicating the independence of organ-specific and BR-dependent regulation. Quantitative gas chromatography-mass spectrometry analysis of endogenous BRs in shoots and roots of Arabidopsis, pea (Pisum sativum), and tomato (Lycopersicon esculentum) reveal similar partitioning patterns of BR intermediates in these species. Inverse correlation between CYP90A1/CPD transcript levels and the amounts of the CYP90A1 substrate 6-deoxocathasterone in shoots and roots suggests that transcriptional regulation plays an important role in controlling BR biosynthesis.
Cell-bound complement activation products as lupus biomarkers: diagnosis, monitoring and stratification (2017)

Cell-bound complement activation products (CB-CAPs) were first reported in 2004, since which time multiple laboratories have demonstrated their value as biomarkers for diagnosis, monitoring, and stratification of patients with systemic lupus erythematosus. Areas covered: This review summarizes the highlights of these 14 years of CB-CAPs discovery and validation, concluding with a view toward their future potential for precision medicine. Expert commentary: The practice of medicine is both art and science and each physician can be considered both artist and scientist with a variable blend of the two skill sets. There is arguably no disease that presents a greater challenge, nor a greater opportunity, for implementation of precision medicine, as does lupus. The physician who is presented with diagnosis and/or management of a patient suspected of having lupus will need to augment artistic skills with scientific guidance, and that science will be delivered in the form of biomarkers. Ultimately, we will likely have a 'lupus liquid biopsy' that will be 100% sensitive and 100% specific for a diagnosis of lupus. This will undoubtedly be a panel of biomarkers rather than an individual laboratory test. Such a liquid biopsy could transform lupus diagnosis to an entirely scientific process.
4D vessel segmentation and tracking in Ultrasound (2012)

In this paper we describe a fast method to segment and track a vessel of interest in 4D (i.e. 3D + time) Ultrasound images. An initial 2D seed is used to initialize a single spatial Kalman-Filter tracker which tracks the vessel center-line in 3D. The 3D vessel is then segmented using a fast area weighted active contour method. This segmented 3D vessel is then tracked across multiple time-points using a set of temporal Kalman- Filters which track the movement of the center of the vessel in each 2D slice. The vessel boundaries are estimated by growing an area weighted active contour outward from the centerline. Based on qualitative as well as quantitative performance measures, the proposed method shows promising tracking results on numerous phantom as well as patient datasets.
Identification of Novel Compounds That Increase SMN Protein Levels Using an Improved SMN2 Reporter Cell Assay (2012)

Spinal muscular atrophy (SMA) is a neurodegenerative disorder that is characterized by progressive loss of motor neuron function. It is caused by the homozygous loss of the SMN1 (survival of motor neuron 1) gene and a decrease in full-length SMN protein. SMN2 is a nearly identical homolog of SMN1 that, due to alternative splicing, expresses predominantly truncated SMN protein. SMN2 represents an enticing therapeutic target. Increasing expression of full-length SMN from the SMN2 gene might represent a treatment for SMA. We describe a newly designed cell-based reporter assay that faithfully and reproducibly measures full-length SMN expression from the SMN2 gene. This reporter can detect increases of SMN protein by an array of compounds previously shown to regulate SMN2 expression and by the overexpression of proteins that modulate SMN2 splicing. It also can be used to evaluate changes at both the transcriptional and splicing level. This assay can be a valuable tool for the identification of novel compounds that increase SMN2 protein levels and the optimization of compounds already known to modulate SMN2 expression. We present here preliminary data from a high-throughput screen using this assay to identify novel compounds that increase expression of SMN2.
Fundamental Design Issues of Brush Seals for Industrial Applications (2002)

Abstract Advanced seals have been applied to numerous turbine machines over the last decade to improve the performance and output. Industrial experiences have shown that significant benefits can be attained if the seals are designed and applied properly. On the other hand, penalties can be expected if brush seals are not designed correctly. In recent years, attempts have been made to apply brush seals to more challenging locations with high speed (&gt;400 m/s), high temperature (&gt;650 °C), and discontinuous contact surfaces, such as blade tips in a turbine. Various failure modes of a brush seal can be activated under these conditions. It becomes crucial to understand the physical behavior of a brush seal under the operating conditions, and to be capable of quantifying seal life and performance as functions of both operating parameters and seal design parameters. Design criteria are required for different failure modes such as stress, fatigue, creep, wear, oxidation etc. This paper illustrates some of the most important brush seal design criteria and the trade-off of different design approaches.
Design of a block replicate gate for ion-implanted bubble devices (1982)

A block replicate gate has been designed for 4 μm period ion-implanted bubble devices. The gate consists of a conductor lying across a V-shaped unimplanted pattern between the minor loop end and the major line. Replication is accomplished by stretching the bubble with a stretch pulse through the conductor, cutting the domain by means of the charged wall formed at the edge of the V-shaped pattern together with a pulse of short duration, then restoring the bubble to the original condition by means of another stretch pulse. A bias field margin of 20 Oe was obtained with an error rate of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-5</sup> for a 100 kHz, 80 Oe peak triangular drive field.
Leveraging local image redundancy for efficient virtual machine provisioning (2012)

Virtualized data centers became ubiquitous and led to invention of new delivery model called Cloud computing. Cloud service providers pursue high degree of automation for the management processes in order to make their services responsive and inexpensive. One of such critical processes is virtual machine provisioning. This article proposes and evaluates a provisioning model that leverages virtual machine image similarity to reduce the data volume transferred from the storage server to the hypervisor on which the virtual machine is being instantiated. We also present an analytical model of such a provisioning process for a single hypervisor shedding light on the impact of degree of image similarity, system utilization, and hypervisor capacity on the performance of the system. The model is validated using discrete event simulator. The algorithm has been implemented on a testbed system and also extensive simulations of virtualized server clusters were conducted. The proposed provisioning scheme can offer significant (up to 80%) reduction in data transfer between storage server and hypervisors thus significantly reducing provisioning time while also decreasing cost.
Experimental results and numerical simulation of mode partition noise suppression in multiwavelength modelocked semiconductor lasers (2004)

We report experimental data and a simple numerical model which accurately explain multiwavelength modelocked semiconductor laser behavior with and without a saturable absorber used for mode partition noise suppression.