gebhart/patrepeval huggingface dataset:
Verteporfin heterogeneity in pancreatic adenocarcinoma and the relationship to tumor vasculature and collagen distribution (2018)

Photodynamic therapy (PDT) has emerged as one promising treatment regimen for several cancer types, with a clinical trial ongoing in pancreatic adenocarcinoma (PDAC). PDT treatment efficacy mainly depends on the combination of light delivery, oxygen availability and photosensitizer uptake, each of which can be limited in pancreas cancer. Therefore, increasing drug uptake in the tumor would make an important impact on treatment outcome. This study was conducted to focus on the issue with drug resistance by examining the relationship between photosensitizer verteporfin and tissue parameters such as collagen and vascular patency. Verteporfin uptake in the tumors was assessed by fluorescence imaging while collagen content and patent vessel area fraction were quantified by evaluating Masson’s Trichrome and Lectin pathology staining images. Two tumor cell lines – AsPC-1 and BxPC-3 – were modeled in nude mice to investigate the impact of different tumor microenvironments. Experimental results highlighted the correlation between vascular patency and verteporfin uptake. Collagen content was found to be an independent factor within each tumor line, but a comparison across two tumor types suggested that collagen area of greater than 10% of tumor cross section reflected a lower verteporfin uptake. It was observed that whole-slice tumor quantifications have showcased some interesting trends which could be greatly enhanced and further supported by regional analysis.
Development of API 11D1 and API 19AC Validation Grade V0 Barrier-Qualified Gravel Pack System for Troll Phase 3 Big-Bore, High-Rate Gas Completions on the Norwegian Continental Shelf (2021)

Abstract The Troll Phase 3 (TP3) wells were designed to enable high gas rates and sand free production for an expected lifetime of 40 years with a minimum pressure drop. By taking reservoir and production properties into account, open-hole gravel pack (GP) sand screens in the lower completion and big bore tubing in the upper completion were selected. To further reduce the pressure loss in the well, reduce rig time and cost, and reduce deployment risks, eliminating the intermediate completion was proposed. Traditionally, an intermediate completion is required to serve as a gas-tight barrier for running of the upper completion, mainly due to historical limitations of the GP extension (GP sleeve) not being a barrier qualified to API 19AC Validation grade V0 (referred to as V0 hereafter) after pumping sand slurry through it (post-erosion). An extensive qualification program was completed to qualify the GP system to API 11D1 and API 19AC V0 for use as a gas-tight barrier post-erosion. This allows the GP system to serve as a primary barrier while installing the upper completion and temporarily abandoning the well. The GP packer was qualified to API 11D1 V0 with the additional requirement to perform entire qualification in as-rolled casing and including a plug-in-tailpipe load case. The GP sleeve provided the most technically challenging requirements: a full-scale erosion test, immediate closure of the sleeve after pumping operation, followed by API 19AC Annex A V0 validation. Challenges were encountered trying to meet the rigorous V0 (zero bubble) acceptance criteria post-erosion. A significantly different approach was developed to achieve gas-tight performance in debris-laden environments. The new design successfully passed the post-erosion API 19AC V0 qualification to the full rating of the GP sleeve. The GP system development and qualification enabled the industry-first V0 post-erosion GP system for Equinor, which eliminates the need for an intermediate completion. This state-of-the-art gravel pack system enabled the simplified high gas rate, big-bore well design, not previously possible given well barrier considerations. The reduced pressure drop across the lower completion is expected to yield a higher gas production rate for the 40 years expected well life, contributing significant value to the TP3 project.
Using compression to improve chip multiprocessor performance (2006)

Chip multiprocessors (CMPs) combine multiple processors on a single die, typically with private level-one caches and a shared level-two cache. The increasing number of processors cores in a CMP increases the demand on two critical resources: the shared L2 cache capacity and the off-chip pin bandwidth. Such demand is further exacerbated by latency-hiding techniques such as hardware prefetching. In this dissertation, we explore using compression to effectively increase cache and pin bandwidth resources and ultimately CMP performance. 
We identify two distinct and complementary designs where compression can help improve CMP performance: Cache Compression and Link Compression. Cache compression stores compressed lines in the cache, potentially increasing the effective cache size, reducing off-chip misses and improving performance. Unfortunately, decompression overhead can slow down cache hit latencies, possibly degrading performance. Link (i.e., off-chip interconnect) compression compresses communication messages before sending to or receiving from off-chip system components, thereby increasing the effective pin bandwidth and improving performance for bandwidth-limited configurations. 
While compression can have a positive impact on CMP performance, practical implementations of compression raise a few concerns. In this dissertation, we make five contributions that address these concerns. We propose a compressed L2 cache design based on a simple compression algorithm with a low decompression overhead. We develop an adaptive compression scheme that dynamically adapts to the costs and benefits of cache compression, and employs compression only when it helps performance. We show that cache and link compression both combine to improve CMP performance for commercial and (some) scientific workloads. We show that compression interacts in a strong positive way with hardware prefetching, whereby a system that implements both compression and hardware prefetching can have a higher speedup than the product of speedups of each scheme alone. We provide a simple analytical model that helps provide qualitative intuition into the trade-off between cores, caches, communication and compression, and use full-system simulation to quantify this trade-off for a set of commercial workloads.
Mapping Multiplexers onto Hard Multipliers in-FPGAs (2005)

Modern FPGAs now contain a selection of "hard" digital structures such as memory blocks and multipliers (Altera, 2003, Xilinx, 2003, QuickLogic, 2003, Actel, Lattice, 2004) in addition to the usual "soft" programmable logic typically consisting of lookup tables (LUTs) and flip-flops. These hard structures are a major benefit (in area and speed) for those applications that need them, but are completely wasted if an application circuit docs not require them. Finding other ways to use these structures will benefit these applications. In this paper, the authors presented a technique to map multiplexers to unused hard multipliers on an FPGA. An RTL synthesis tool flow that implements this technique over a set of benchmarks was created. While some circuits see no reduction in LUT count at all, others show meaningful improvements ranging from 10% to 70%. On average across the whole set of circuits the technique achieves a 7.3% reduction on the number of LUTs used. In some cases, however, the operating frequency of the circuit is reduced significantly.
Cysteamine Gliopathy in situ (1993)

In cultured astroglia, cysteamine induces the accumulation of peroxidase-positive cytoplasmic inclusions in the context of a generalized cellular stress response. In the present study, systemic cysteamine administration over a 3 week period induced HSP27, 72, 90, and GRP94 (stress proteins) in astrocytes and significantly increased numbers of peroxidase-positive astrocytic inclusions in the various brain regions relative to controls. Similar patterns of HSP expression were also observed at 24 hours following cysteamine treatment indicating that cellular stress may be a very proximal event in the biogenesis of the astrocytic inclusions. The topography of glial peroxidase activity may provide a "map" of central nervous system regions particularly prone to oxidative stress during normal aging and under pathologic conditions.
Videoendoscopia via posterior para cirurgia de hérnia de disco lombar (1999)

Resumo Os autores apresentam a técnica de abordagem videoendoscópica posterior da coluna lombar em 63 casos operados com seguimento médio de 1 ano e 8 meses. A técnica videoendoscópica, via posterior, da coluna lombar, conhecida como MED (Microendoscopic Discectomy) foi idealizada com a finalidade de transformar a cirurgia convencional, já bem estabelecida e padronizada, em uma cirurgia minimamente invasiva sob os princípios da cirurgia videoendoscópica. Portanto, por essa via de acesso, podem-se realizar todos os procedimentos efetuados a céu aberto, tais como hemilaminectomia, facetectomia medial, foraminotomia, retração da raiz nervosa e a discectomia. Os resultados iniciais em 63 cirurgias apontam para a tendência à recuperação mais rápida do paciente, que obtém alta hospitalar no mesmo dia da cirurgia e retorno ao trabalho em 15 dias, ou menos, em 50% dos nossos casos. A incisão cirúrgica é bastante reduzida (1,6 cm). Não houve infecção em nossos casos. Como principais desvantagens, citamos o aumento do tempo cirúrgico e a dificuldade da técnica cirúrgica que impõe treinamento específico. Em um futuro próximo, será possível a realização dessa cirurgia em nível ambulatorial e sob anestesia local, permitindo, inclusive, a realização em pacientes idosos e de alto risco.
Electrochemical Aptasensors for Biological and Chemical Analyte Detection (2020)

Abstract Aptamers are short length, single‐stranded DNA or RNA affinity molecules which interact with any desired targets such as biomarkers, cells, biological molecules, drugs or chemicals with high sensitivity. They have been extensively employed for medical applications due to having more advantages than the antibodies such as easier preparation and modification, higher stability, lower batch‐to‐batch variability and cost. Moreover, aptamers can be easily integrated efficiently with sensors, biosensors, actuators and other devices. In this review article, different applications of aptamers for biological and chemical molecules detection within the scope of electrochemical methods were presented with recent studies. In addition, the present status and future perspectives for highly‐effective aptasensors for specific and selective analyte detection were discussed. As in stated throughout the review, combining of extraordinary properties of aptamers with the electrochemical‐based biosensors could have improved the sensitivity of the assay and reduced limit of detection.
Genomic heterogeneity of circulating tumor cells in castration-resistant prostate cancer (CRPC) revealed by single-cell sequencing. (2013)

5030 Background: Circulating tumor cells (CTC) provide an opportunity to sample multiple metastatic tumor sites through a single blood draw – a ”fluid biopsy.” NextGen DNA sequencing provides the means to obtain detailed genetic information from captured cells prior to and during treatment. Here we demonstrate the use of DNA sequencing to interrogate genome-wide copy number variations (CNV) at the single-cell level in CTC isolated from pts with CRPC. Methods: Pre- and post-treatment blood samples were obtained from pts treated at MSKCC. EpCAM+ events were collected singly and in groups by cytometric flow sorting and were subjected to DNA amplification and Illumina NextGeneration sequencing. Parallel samples were assayed using the Veridex CellSearch method to ensure the presence of malignant cells. Results: Samples with up to 50 EpCAM+ events analyzed in bulk displayed CNV patterns expected from published CRPC data. Subsequent single cell analyses showed that the method could reliably detect common genomic markers in CRPC, including AR amplification, PTEN and RB1 loss, and the TMPRSS-ERG fusion. Individual genomic CNV profiles obtained from 125 single cells isolated from 15 patients were then analyzed. Using unsupervised clustering, cells from each pt showed a closely related lineage structure, consistent with an evolution from a common ancestor. The degree of genomic heterogeneity within CTC from an individual pt was highly variable, with R 2 correlation coefficients ranging from &gt;0.92 (nearly homogeneous) to &lt;0.75 (mixed populations). Two pts harbored separate subpopulations with both amplified AR and non-amplified AR cells and another displayed mixtures of genetic markers that changed over the course of treatment. Conclusions: The observed variation in complexity of CTC populations in CRPC pts underscores the importance of being able to sample and analyze multiple cells from an individual pt on multiple occasions and with real time analytics. Doing so is essential to understand and identify mechanisms of resistance so that they can be targeted effectively. Supported by STARR Cancer Consortium, NCI SPORE in Prostate Cancer; Department of Defense; Prostate Cancer Foundation.
Data from <i>TMPRSS2-ERG</i> Gene Fusion Is Not Associated with Outcome in Patients Treated by Prostatectomy (2023)

&lt;div&gt;Abstract&lt;p&gt;A significant number of prostate cancers have been shown to have recurrent chromosomal rearrangements resulting in the fusion of the androgen-regulated &lt;i&gt;TMPRSS2&lt;/i&gt; promoter to a member of the &lt;i&gt;ETS&lt;/i&gt; transcription factor family, most commonly &lt;i&gt;ERG&lt;/i&gt;. This results in &lt;i&gt;ERG&lt;/i&gt; overexpression, which may have a direct causal role in prostate tumorigenesis or progression. However, the clinical significance of the rearrangement is unclear, and in particular, relationship to outcome has been inconsistent in recent reports. We analyzed &lt;i&gt;TMPRSS2-ERG&lt;/i&gt; gene rearrangement status by fluorescence &lt;i&gt;in situ&lt;/i&gt; hybridization in 521 cases of clinically localized surgically treated prostate cancer with 95 months of median follow-up and also in 40 unmatched metastases. Forty-two percent of primary tumors and 40% of metastases had rearrangements. Eleven percent had copy number increase (CNI) of the &lt;i&gt;TMPRRS2-ERG&lt;/i&gt; region. Rearrangement alone was associated with lower grade, but not with stage, biochemical recurrence, metastases, or death. CNI with and without rearrangement was associated with high grade and advanced stage. Further, a subgroup of cancers with CNI and rearrangement by deletion, with two or more copies of the deleted locus, tended to be more clinically aggressive. DNA index assessment revealed that the majority of tumors with CNI of &lt;i&gt;TMPRSS2-ERG&lt;/i&gt; had generalized aneuploidy/tetraploidy in contrast to tumors without &lt;i&gt;TMPRSS2-ERG&lt;/i&gt; CNI, which were predominantly diploid. We therefore conclude that translocation of &lt;i&gt;TMPRSS2-ERG&lt;/i&gt; is not associated with outcome, and the aggressive clinical features associated with CNI of chromosome 21 reflect generalized aneuploidy and are not due to CNI specifically of rearranged &lt;i&gt;TMPRSS2-ERG&lt;/i&gt;. [Cancer Res 2009;69(4):1400–6]&lt;/p&gt;&lt;/div&gt;
Genetics of a Second Locus Determining Pungency in Chili Peppers (<italic>Capsicum</italic>) (1988)

Lack of pungency has been shown to be controlled by a single recessive gene (C) in pepper (Capsicum annuum L.). We describe the discovery of a second independent gene (C2) conditioning absence of pungency. The source of this gene is the accession BG3547 (C. annuum var. glabriusculum). F1 progeny derived from a cross BG3547 (C2/C2 and ‘Deux des Landes’ (C annuum var. annuum) (c/c) were all pungent, whereas the F2 progeny segregated 9 pungent:7 nonpungent, consistent with the two-gene hypothesis. Progeny were scored for five isozyme loci—Aco-2, Pgm-1, Pgm-2, 6Pgdh-1, and 6Pgdh-2— none of which showed linkage with the C2 gene.
Tribocorrosion under galvanic interaction of Ti6Al4V and NiCr implant alloys (2020)

Micromovements that occur in the joint between dental prostheses and implants can lead to wear-induced degradation. This process can be enhanced by corrosion in the oral environment influenced by the presence of solutions containing fluoride. Moreover, the eventual galvanic interactions between NiCr and Ti alloys can accelerate the wear-corrosion process. In this work, the tribocorrosion process of Ti6Al4V and NiCr alloys used in dental implant rehabilitations immersed in fluoride solutions at different pH values was investigated. The galvanic interaction effect between the alloys was also assessed. Tribocorrosion tests in corrosive media were performed with isolated Ti6Al4V and NiCr alloys, followed by testing with both alloys in contact. The media selected were based on fluoride concentrations and pH values that are possible to be found in oral environments. Analysis of the surfaces after the tribocorrosion tests was carried out using confocal laser microscopy. The wear profile and volume losses were determined by confocal measurements. It was concluded that the galvanic interaction between the alloys increased the tribocorrosion resistance of Ti6Al4V, compared with that of the isolated Ti6Al4V alloy. Ti6Al4V coupled with NiCr reduced the electrochemical potential decay during sliding. The increased resistance was explained by the electrochemical shift of the Ti6Al4V potential from active dissolution to the passive domain.
Multiwavelength-channel header recognition for reconfigurable WDM networks using optical correlators based on sampled fiber Bragg gratings (2003)

We demonstrate a tunable, multiwavelength optical correlator that uses an array of sampled fiber Bragg gratings (FBGs) as the correlating element. The incoming wavelength-division-multiplexing (WDM) data streams are tapped off and the packet headers on each 10-Gb/s channel are simultaneously recognized and correlated to a reconfigurable header code. The correlation output for each channel is compared to a threshold level, and simple decision electronics are used to drive a set of switches to route the individual WDM packets accordingly. Using this technique, we recognize two WDM 10-Gb/s packet headers simultaneously, with a negligible power penalty when switching packets to the appropriate output port. Moreover, we tune the gratings for reconfigurable routing.
Transjugular intrahepatic portosystemic shunt for treatment of portal hypertension due to extramedullary hematopoiesis in idiopathic myelofibrosis (2002)

Patients with idiopathic myelofibrosis (IMF) present with variable clinical, as well histomorphologic, features. In the fibrotic stage of the disease, bone marrow fibrosis causes ineffective erythropoiesis, which leads to extramedullary hematopoiesis, mainly in the spleen and the liver.[1][1] [2][2
Pseudo Content Delivery Protocol (CDP) for Protecting Multiple Source Flows in FEC Framework (2008)

This document provides a pseudo Content Delivery Protocol (CDP) to
protect multiple source flows with one or more repair flows based on
the FEC Framework document and the Session Description Protocol (SDP)
elements defined for the framework. The purpose of the document is not
to provide a full-pledged protocol, but to show how the defined
framework and SDP elements can be combined together to design a CDP.
UMARK: paper VOD system using figure code recognition (2005)

This paper discusses the paper VOD system using figure code recognition that can choose the target channel easily and quickly by carrying out simultaneous distribution of the IP movie and music of 200 channels, and carrying out the image recognition of the figure code given to the paper media using 100 M base HUB. We show the basic working principle based on the patent (P2003-26527) and explain the expected market with business model.
Duodenal calcium absorption in vitamin D receptor–knockout mice: Functional and molecular aspects (2001)

Rickets and hyperparathyroidism caused by a defective vitamin D receptor (VDR) can be prevented in humans and animals by high calcium intake, suggesting that intestinal calcium absorption is critical for 1,25(OH)(2) vitamin D [1,25(OH)(2)D(3)] action on calcium homeostasis. We assessed the rate of serum (45)Ca accumulation within 10 min of oral gavage in two strains of VDR-knockout (KO) mice (Leuven and Tokyo KO) and observed a 3-fold lower area under the curve in both KO strains. Moreover, we evaluated the expression of intestinal candidate genes involved in transcellular calcium transport. The calcium transport protein1 (CaT1) was more abundantly expressed at mRNA level than the epithelial calcium channel (ECaC) in duodenum, but both were considerably reduced (CaT1>90%, ECaC>60%) in the two VDR-KO strains on a normal calcium diet. Calbindin-D(9K) expression was decreased only in the Tokyo KO, whereas plasma membrane calcium ATPase (PMCA(1b)) expression was normal in both VDR-KOs. In Leuven wild-type mice, a high calcium diet inhibited (>90%) and 1,25(OH)(2)D(3) injection or low calcium diet induced (6-fold) duodenal CaT1 expression and, to a lesser degree, ECaC and calbindin-D(9K) expression. In Leuven KO mice, however, high or low calcium intake decreased calbindin-D(9K) and PMCA(1b) expression, whereas CaT1 and ECaC expression remained consistently low on any diet. These results suggest that the expression of the novel duodenal epithelial calcium channels (in particular CaT1) is strongly vitamin D-dependent, and that calcium influx, probably interacting with calbindin-D(9K), should be considered as a rate-limiting step in the process of vitamin D-dependent active calcium absorption.
Development of a first-in-class unimolecular dual GIP/GLP-2 analogue, GL-0001, for the treatment of bone fragility (2022)

ABSTRACT Due to ageing of the population, bone frailty is dramatically increasing worldwide. Although some therapeutic options exist, they do not fully protect or prevent against the occurrence of new fractures. All current drugs approved for the treatment of bone fragility target bone mass. However, bone resistance to fracture is not solely due to bone mass but relies also on bone ECM material properties, i.e. the quality of the bone matrix component. Here, we introduce the first-in-class unimolecular dual GIP/GLP-2 analogues, GL-0001, that activate simultaneously the glucose-dependent insulinotropic polypeptide receptor (GIPr) and the glucagon-like peptide-2 receptor (GLP-2r). GL-0001 acts synergistically through a cAMP-LOX pathway to enhance collagen maturity. Furthermore, in mice with ovariectomy-induced bone fragility, GL-0001 prevented excess trabecular bone degradation at the appendicular skeleton and also enhanced bone ECM material properties through reduction of the degree of mineralization and augmentation in enzymatic collagen crosslinking. These results demonstrate that targeting bone ECM material properties is a viable option to enhance bone strength and opens an innovative pathway for the treatment of patients suffering of bone fragility.