gebhart/patrepeval huggingface dataset:
Photodynamic therapy mediates the oxygen-independent activation of hypoxia-inducible factor 1α (2006)

Photodynamic therapy (PDT) induces the expression of the hypoxia-inducible factor 1alpha (HIF-1alpha) subunit of the HIF-1 transcription factor and its target genes in vitro and in vivo. PDT also induces the expression of the enzyme cyclooxygenase-2 and its metabolite, prostaglandin E2 (PGE2). PGE2 and hypoxia act independently and synergistically to increase HIF-1alpha accumulation and nuclear translocation. To examine the expression of HIF-1 target genes in response to PDT-mediated oxidative stress and PGE2 under normoxic conditions, we established EMT6 cells transfected with a plasmid consisting of a hypoxia response element promoter and a downstream gene encoding for green fluorescent protein (GFP). To examine the temporal kinetics of HIF-1alpha nuclear translocation in response to PDT, we transfected a second line of EMT6 cells with a GFP-tagged HIF-1alpha fusion vector. Cell monolayers were incubated with 1 microg mL(-1) Photofrin for 24 h and irradiated with fluences of 1, 2.5, and 5 J cm(-2). Direct measurement of oxygen concentration during irradiation confirmed that cells remained well oxygenated. Cells were also exposed to 1 and 10 micromol/L PGE2 for 3 h. In normoxic conditions, Photofrin, PDT, and PGE2 treatment activated HIF-1alpha and induced its nuclear translocation. Maximal Photofrin-PDT-mediated HIF-1alpha activation was intermediate in magnitude between that induced by PGE2 and that by the hypoxia mimic cobalt chloride. This work establishes that PDT induces significant activation of the HIF-1alpha pathway in the absence of hypoxia and supports the interpretation that the induction of HIF-1 target genes by PDT may be mediated, at least in part, by the prostaglandin pathway.
An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce (2013)

We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F<sub>7:8</sub> recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species.
A New Initiative in Nephrology: ‘Kidney Disease: Improving Global Outcomes’ (2005)

The burden of kidney disease: Improving global outcomes. Chronic kidney disease (CKD) is a worldwide public health problem with an increasing incidence and prevalence of patients requiring replacement therapy. There is an even higher prevalence of patients in earlier stages of CKD, with adverse outcomes such as kidney failure, cardiovascular disease, and premature death. Patients at earlier stages of CKD can be detected through laboratory testing and their treatment is effective in slowing the progression to kidney failure and reducing cardiovascular events. The evidence-based care of these patients are universal and independent of their geographic location. This paper describes the need to develop a uniform and global public health approach to the worldwide epidemic of CKD. It is to this end that a new initiative Kidney Disease: Improving Global Outcomes' has been established. Some current and future activities of this initiative are described. They include among others modification of the classification of CKD, the development of guidelines on hepatitis C, the organisation of consensus conferences like on Renal Osteodystrophy, and the creation of a website allowing the comparison of the five main English language clinical practice guidelines in kidney disease worldwide.
Continuous flow synthesis of small silver nanoparticles involving hydrogen as the reducing agent (2010)

Two narrow-channel reactor designs have been developed and used in conjunction with gas–liquid segmented flow in order to intensify reactions and to effect synthesis under continuous flow conditions, incorporating single pass and recirculating capability, under high pressure and temperature. Silver nanoparticles approximately 3–5 nm in diameter are accessible with the average size depending on the reaction temperature and polyphosphate concentration, with smaller and more monodisperse nanoparticles produced at low polyphosphate concentrations and low temperatures. The use of continuous flow conditions leads to the possibility of simple scale-up to commercial production.
Synthesis and Characterization of Nanocomposites xLi2MnO3•(1-x)LiMO2(M = Cr, Mn, Co, Ni) for Li Secondary Batteries (2010)

Abstract not Available.
Complement in sepsis—when science meets clinics (2020)

Sepsis as life-threatening organ dysfunction caused by microorganisms represents a dreadful challenge for the immune system. The role of the complement system as major column of innate immunity has been extensively studied in various sepsis models, but its translational value remains in the dark. Complement activation products, such as C3a and C5a, and their corresponding receptors provide useful diagnostic tools and promising targets to improve organ function and outcome. However, a monotherapeutic complement intervention irrespective of the current immune function seems insufficient to reverse the complex sepsis mechanisms. Indeed, sepsis-induced disturbances of cross talking complement, coagulation, and fibrinolytic cascades lead to systemic 'thromboinflammation', ultimately followed by multiple-organ failure. We propose to reliably monitor the complement function in the patient and to re-establish the immune balance by patient-tailored combined therapies, such as complement and Toll-like receptor inhibition. Our working hypothesis aims at blocking the 'explosive' innate immune recognition systems early on before downstream mediators are released and the inflammatory response becomes irreversible, a strategy that we name 'upstream approach'.
Reporter gene imaging identifies intratumoral infection voids as a critical barrier to systemic oncolytic virus efficacy (2014)

Systemically administered oncolytic viruses have the ability to cause tumor destruction through the expansion and coalescence of intratumoral infectious centers. Efficacy is therefore dependent upon both the density and intratumoral distribution of virus-infected cells achieved after initial virus infusion, and delivery methods are being developed to enhance these critical parameters. However, the three-dimensional (3D) mapping of intratumoral infectious centers is difficult using conventional immunohistochemical methodology, requiring painstaking 3D reconstruction of numerous sequential stained tumor sections, with no ability to study the temporal evolution of spreading infection in a single animal. We therefore developed a system using very high-resolution noninvasive in vivo micro single-photon emitted computed tomography/computed tomography (microSPECT/CT) imaging to determine the intratumoral distribution of thyroid radiotracers in tumors infected with an oncolytic virus encoding the thyroidal sodium-iodide symporter (NIS). This imaging system was used for longitudinal analysis of the density, distribution, and evolution of intratumoral infectious centers after systemic administration of oncolytic vesicular stomatitis virus in tumor-bearing mice and revealed heterogeneous delivery of virus particles both within and between tumors in animals receiving identical therapy. This study provides compelling validation of high resolution in vivo reporter gene mapping as a convenient method for serial monitoring of intratumoral virus spread that will be necessary to address critical barriers to systemic oncolytic virus efficacy such as intratumoral delivery.
Optimization of the surface morphologies and electron mobilities in GaN grown by plasma-assisted molecular beam epitaxy (2000)

The morphology and electrical properties of homoepitaxial GaN layers grown by molecular beam epitaxy at 720 °C were investigated as a function of Ga/N ratio. GaN films grown with low Ga/N ratios (N-stable regime) are semi-insulating and have heavily pitted morphologies. GaN films grown with higher Ga/N ratios (intermediate regime) have fewer pits with areas of atomically flat surface. The room-temperature electron mobilities in samples grown in the intermediate regime are greater than 800 cm2/V s and increase with Ga/N ratio. At the highest Ga/N ratios (Ga-droplet regime), Ga droplets formed on the surface during growth. Although the surface morphology is free of pits and atomically flat for films grown within the Ga-droplet regime, the mobility decreases significantly compared to films grown in the intermediate regime. Room-temperature electron mobilities as high as 1191 cm2/V s were measured in a GaN film grown with the highest Ga/N ratio within the intermediate regime.
Intraoperative Fractures of the Acetabulum During Primary Total Hip Arthroplasty (2006)

Therapeutic Level III.
Lipopolysaccharide stimulates the expression of pro-opiomelanocortin mRNA in chicken macrophages, as demonstrated with a competitive polymerase chain reaction (2002)

The goal of the present study was to develop a competitive PCR assay to measure changes in the expression of pro-opiomelanocortin (POMC) mRNA in myelomonocytic HD11 cells after Salmonella typhimurium lipopolysaccharide (LPS) stimulation. Pro-opiomelanocortin mRNA could be detected in HD11 cells by reverse transcription - polymerase chain reaction (RT-PCR). To our knowledge, this is the first observation of a POMC mRNA transcript in avian macrophages. Based on this observation, the effect of stimulation with bacterial LPS on the POMC expression in HD1 cells was investigated by means of a competitive PCR assay. For this purpose, the HD 11 cells received a one-hour LPS challenge with LPS concentrations ranging from 10 to 100 ng/ml. A PCR MIMIC (consisting of a heterologous DNA fragment flanked by templates for the gene-specific primers) was used as an internal control in the competitive PCR assay. A ten-fold dilution series of the MIMIC was co-amplified with a constant amount of experimental cDNA. While HD11 POMC mRNA expression showed an increase of one order of magnitude following treatment with 100 ng/ml LPS as compared with untreated controls, no significant differences could be observed after treatment with 50 and 10 ng/ml LPS. Quantitative measurement of POMC mRNA levels is a first step towards a better understanding of the physiological role of non-hypophysial POMC-derived peptides in the response to immune stress in birds.
GraphSAC: Detecting anomalies in large-scale graphs (2019)

A graph-based sampling and consensus (GraphSAC) approach is introduced to effectively detect anomalous nodes in large-scale graphs. Existing approaches rely on connectivity and attributes of all nodes to assign an anomaly score per node. However, nodal attributes and network links might be compromised by adversaries, rendering these holistic approaches vulnerable. Alleviating this limitation, GraphSAC randomly draws subsets of nodes, and relies on graph-aware criteria to judiciously filter out sets contaminated by anomalous nodes, before employing a semi-supervised learning (SSL) module to estimate nominal label distributions per node. These learned nominal distributions are minimally affected by the anomalous nodes, and hence can be directly adopted for anomaly detection. Rigorous analysis provides performance guarantees for GraphSAC, by bounding the required number of draws. The per-draw complexity grows linearly with the number of edges, which implies efficient SSL, while draws can be run in parallel, thereby ensuring scalability to large graphs. GraphSAC is tested under different anomaly generation models based on random walks, clustered anomalies, as well as contemporary adversarial attacks for graph data. Experiments with real-world graphs showcase the advantage of GraphSAC relative to state-of-the-art alternatives.
MEMS-tunable polarization management in photonic integrated circuits (2023)

Optical fibers are generally polarization-insensitive while photonic integrated circuits (PICs) often exhibit a large polarization dependence due to the high-aspect-ratio and high-index-contrast of integrated waveguides. As PICs become more mature there is an increasing need for tunable polarization management on-chip. Although micro-electro-mechanical systems (MEMS) are increasingly finding application in PICs for optical switching and phase shifting, they have so far not found wide application for polarization management. In this work we propose two optical MEMS architectures for polarization management enabling tunable polarization splitting and rotation - key functions so far lacking in PICs. The first structure consists of a directional coupler with a MEMS-tunable gap enabling a continuously-variable polarization splitting ratio. A second architecture consists of a symmetry-breaking MEMS perturber suspended over an air-cladded waveguide enabling tunable polarization rotation. For both architectures we simulate a polarization extinction exceeding 25 dB, and the operating bandwidth can be as large as 100 nm. We conclude with a discussion of actuation schemes and examine fabrication considerations for implementation in PIC foundries.
Decomposing spiking neural networks with Graphical Neural Activity Threads (2023)

A satisfactory understanding of information processing in spiking neural networks requires appropriate computational abstractions of neural activity. Traditionally, the neural population state vector has been the most common abstraction applied to spiking neural networks, but this requires artificially partitioning time into bins that are not obviously relevant to the network itself. We introduce a distinct set of techniques for analyzing spiking neural networks that decomposes neural activity into multiple, disjoint, parallel threads of activity. We construct these threads by estimating the degree of causal relatedness between pairs of spikes, then use these estimates to construct a directed acyclic graph that traces how the network activity evolves through individual spikes. We find that this graph of spiking activity naturally decomposes into disjoint connected components that overlap in space and time, which we call Graphical Neural Activity Threads (GNATs). We provide an efficient algorithm for finding analogous threads that reoccur in large spiking datasets, revealing that seemingly distinct spike trains are composed of similar underlying threads of activity, a hallmark of compositionality. The picture of spiking neural networks provided by our GNAT analysis points to new abstractions for spiking neural computation that are naturally adapted to the spatiotemporally distributed dynamics of spiking neural networks.
Prodrugs of the Phosphoribosylated Forms of Hydroxypyrazinecarboxamide Pseudobase T-705 and Its De-Fluoro Analogue T-1105 as Potent Influenza Virus Inhibitors (2018)

We here disclose chemical synthesis of ribonucleoside 5'-monophosphate (RMP), -diphosphate (RDP), and -triphosphate (RTP) and cycloSal-, Di PPro-, and Tri PPPro nucleotide prodrugs of the antiviral pseudobase T-1105. Moreover, we include one nucleoside diphosphate prodrug of the chemically less stable T-705. We demonstrate efficient T-1105-RDP and -RTP release from the Di PPro and Tri PPPro compounds by esterase activation. Using crude enzyme extracts, we saw rapid phosphorylation of T-1105-RDP into T-1105-RTP. In sharp contrast, phosphorylation of T-1105-RMP was not seen, indicating a yet unrecognized bottleneck in T-1105's metabolic activation. Accordingly, Di PPro and Tri PPPro compounds displayed improved cell culture activity against influenza A and B virus, which they retained in a mutant cell line incapable of activating the nucleobase parent. T-1105-RTP had a strong inhibitory effect against isolated influenza polymerase, and Di PPro-T-1105-RDP showed 4-fold higher potency in suppressing one-cycle viral RNA synthesis versus T-1105. Hence, our T-1105-RDP and -RTP prodrugs improve antiviral potency and achieve efficient metabolic bypass.
Enhancing seed conservation in rural communities of Guatemala by implementing the dry chain concept (2020)

Abstract Seed conservation in rural communities of low- and middle-income countries located in tropical areas is particularly problematic, due to high relative humidity that promotes insect and fungal infestations and leads to rapid losses in seed viability. Seed conservation in those areas is affected by unreliable power supplies that do not allow the use of dehumidifying and refrigeration systems recommended for the long-term storage of seeds. We tested the dry chain, i.e., initial seed drying with a reusable desiccant in the form of zeolite beads followed by seed conservation in hermetic containers, in rural communities of Guatemala (Huehuetenango Department). In this region, a network of community seed reserves (CSRs) has been established to provide a safety backup for seed and to conserve local agrobiodiversity. Using a local maize variety in three communities, we compared the dry chain with the seed conservation methodology employed in the CSRs (i.e., undried seeds in hermetic flasks) as well as with seed conservation in open storage, both in the local CSR and in a farmer’s granary. Seed conserved using the dry chain treatment maintained very high seed viability (&gt; 80%) throughout the whole experiment (6 months) and reduced fungal and insect infestations (&lt; 3%). In the other treatments, the viability declined significantly to an average of 52% non-viable and 19% infested seeds after 6 months of storage. The dry chain was demonstrated to be an excellent solution for enhancing seed conservation in biodiversity hotspots of tropical areas as well as for improving seed security for farmers.
An Algorithm for Detection and Correction of Pelvic Tilt in Total Hip Replacement. (2019)

Successful joint replacement surgery requires precise preoperative planning and intraoperative placement of implants such that the function of the joint is optimized biomechanically and biologically. The five-step "pelvic tilt algorithm" will enhance the outcome of hip replacement surgery as a result of improved acetabular component alignment. It will solve the problem of pelvic tilt as an unknown variable during hip replacement surgery, and will allow for more consistent and accurate acetabular component placement.
Optimization of bilinear systems using higher-order method (1999)

This paper derives some optimization results for bilinear systems using higher-order method by characterizing them over matrix Lie groups. In the derivation of the results, a bilinear system is first transformed to a left-invariant system on matrix Lie groups. The product of exponential representation is then used to express this system in a canonical form. The conditions for optimality are then obtained by the principles of variational calculus. It is demonstrated that closed-form analytical solutions exist for classes of bilinear systems whose Lie algebra is nilpotent.
Chip Package Interaction: An Experiment Study on White Bump Mitigation Using Flat Laminates (2014)

Chip-Package Interaction (CPI) related failure risk has increased in organic laminate-based electronic packages fueled in part by certain industry-segments' requirements for larger silicon die size and signal performance. CPI-related stresses increase directly with radial distance from the center of the die, known as distance from the neutral-point (DNP). The resulting risk of local delamination (White Bumps, WBs) in the silicon back-end-of-line (BEOL), fracture of C4 interconnections and failure of underfill and chip ultimately impact electronic package reliability. Named from the notable visible white halo or circle around a C4 in a CSAM (C-Mode Scanning Acoustic Microscopy) image, WBs are the prime indicator of a CPI-related failure event in an organic laminate-based electronic package. Laminate and BEOL design, specifically wiring proximal to the C4 interconnection, are known to influence WB reliability. In this paper we specifically study the effect of laminate and BEOL design on the generation of white bumps. Four different chip designs, some of which are more susceptible to WBs than others are mated with both product-design and "flat" laminates, or laminates consisting of only a core and single copper layer on each side. Our ultimate goal is to highlight the silicon & laminate designs' ability to modulate WB occurrences, to create design ground-rules thereby relaxing the cost and facilitating the development of package assembly solutions. A comprehensive experiment was carried out to achieve these goals. As companion test vehicles to product laminates, four different flat laminate (0-2-0) designs were fabricated with several different core materials to both segregate the effect of laminate wiring design and modulate the overall laminate coefficient of thermal expansion (CTE). Four separate chip designs were used to study the effect of the back end of line design. Thermal stress was induced in the experiment using a high-cooling rate or "hammer" chip-join (HCJ) reflow profile which drives a higher C4 shearing stress than with the nominal profile. The occurrence of WBs was then monitored while the test vehicles were repeatedly subjected to the hammer profile in a controlled hammer thermal cycling (HTC) process. Diagnostic measurements including 3D Surface Metrology and CSAM were performed after each HTC cycle to monitor both laminate warpage and WB occurrence respectively. White Bump evolution was statistically analyzed and correlated to each die design, laminate cross-sectional design and CTE. Results demonstrated the importance of laminate design in that the flat laminates consistently lead to fewer WBs than product laminates. Lower-CTE laminates also result in fewer WBs than product laminates.