gebhart/patrepeval huggingface dataset:
Measuring T cell activation in T cell-APC conjugates using the ImageStream imaging flow cytometer (P5043) (2013)

Abstract Adaptive immune responses require antigen presentation to antigen-specific effector cells. Upon interaction between the antigen presenting cell (APC), specific antigen and T cell there is a reorganization of the cytoskeleton and recruitment of adhesive and signaling molecules to the site of intercellular contact forming an immunological synapse (IS). Upon formation of a functional IS, signaling molecules join the clusters and contribute to the signaling cascade leading to translocation of nuclear factors from the cytoplasm to the nucleus culminating in gene activation. Recruitment of these molecules is measured by imaging cell conjugates directly. To analyze a statistically significant number of specific conjugates we used the ImageStream imaging flow cytometer with a 60X objective, which objectively and rapidly collects large numbers of images and provides quantitative image analysis tools to evaluate subcellular localization of molecules. In this study we evaluate the specific location of the adhesion and signaling molecules LFA-1 and Lck within the IS complex in T cells when presented with SEB pulsed APC. In addition we measured the translocation of NFkB in the T cell from the cytoplasm to the nucleus showing the activation of the T cells when conjugated to APC.
Fig. S2 from Small-Molecule–Mediated Stabilization of PP2A Modulates the Homologous Recombination Pathway and Potentiates DNA Damage-Induced Cell Death (2023)

&lt;p&gt;Fig. S2&lt;/p&gt;
The chemistry of the fac-[Re(CO)2(NO)]2+ fragment in aqueous solution (2005)

The anions [ReX3(CO)2(NO)]- (with X = Cl, 1; X = Br, 2) have been prepared with different counterions. Complex 1 was found to lose its chloride ligands in water within 24 h. The [Re(H2O)3(CO)2(NO)]2+ cation obtained after hydrolysis is a strong acid, which consequently undergoes a slow condensation reaction in water to form the very stable [Re(mu3-O)(CO)2(NO)]4 cluster 4 at pH > 2, that precipitates from the aqueous solution and is insoluble also in organic solvents. Fast deprotonation of [Re(H2O)3(CO)2(NO)]2+ did not lead to 4 but rather to the mononuclear species [Re(OH)(H2O)2(CO)2(NO)]+. Subsequent attack of OH- at a CO group resulted in the formation of a rhenacarboxylic acid and its carboxylate anion. For solutions of even higher pH, IR spectroscopy provided evidence for the formation of a Re(C(O)ON(O)) species. These processes were found to be reversible on lowering the pH. Starting from cluster 4 it was possible to obtain complexes of the types [ReX(CO)2(NO)L2] or [Re(CO)2(NO)L3](L2 = 2-picolinate, 2,2'-bipyridine, L-phenylalanate; L3 = tris(pyrazolyl)methane, 1,4,7-trithiacyclononane) in the presence of an acid in protic solvents, but only in low yields. In further synthetic studies, complexes 1 and 2 were found to be superior starting materials for substitution reactions to form [ReX(CO)2(NO)L2] or [Re(CO)2(NO)L3] complexes.
Receptor‐mediated endocytosis of Neisseria gonorrhoeae into primary human urethral epithelial cells: the role of the asialoglycoprotein receptor (2001)

Urethral epithelial cells are invaded by Neisseria gonorrhoeae during gonococcal infection in men. To understand further the mechanisms of gonococcal entry into host cells, we used the primary human urethral epithelial cells (PHUECs) tissue culture system recently developed by our laboratory. These studies showed that human asialoglycoprotein receptor (ASGP-R) and the terminal lactosamine of lacto-N-neotetraose-expressing gonococcal lipooligosaccharide (LOS) play an important role in invasion of PHUECs. Microscopy studies showed that ASGP-R traffics to the cell surface after gonococcal challenge. Co-localization of ASGP-R with gonococci was observed. As ASGP-R-mediated endocytosis is clathrin dependent, clathrin localization in PHUECs was examined after infection. Infected PHUECs showed increased clathrin recruitment and co-localization of clathrin and gonococci. Preincubating PHUECs in 0.3 M sucrose or monodansylcadaverine (MDC), which both inhibit clathrin-coated pit formation, resulted in decreased invasion. N. gonorrhoeae strain 1291 produces a single LOS glycoform that terminates with Gal(beta1-4)GlcNac(beta1-3)Gal(beta1-4)Glc (lacto-N-neotetraose). Invasion assays showed that strain 1291 invades significantly more than four isogenic mutants expressing truncated LOS. Sialylation of strain 1291 LOS inhibited invasion significantly. Preincubation of PHUECs in asialofetuin (ASF), an ASGP-R ligand, significantly reduced invasion. A dose-response reduction in invasion was observed in PHUECs preincubated with increasing concentrations of NaOH-deacylated 1291 LOS. These studies indicated that an interaction between lacto-N-neotetraose-terminal LOS and ASGP-R allows gonococcal entry into PHUECs.
Long-Term Follow-Up of BEACOPPescalated Chemotherapy in Patients with Advanced-Stage Hodgkin Lymphoma on Behalf of the German Hodgkin Study Group. (2007)

Abstract The HD9 trial of the German Hodgkin Study Group (GHSG) compared two different doses (baseline and escalated) of the novel chemotherapy regimen BEACOPP (bleomycin, etoposide, doxorubicin, cyclophosphamide, vincristine, procarbazine, and prednisone) in patients with advanced-stage Hodgkin lymphoma (HL). The previous analysis with a median follow-up of 5 years showed improved tumor control (FFTF) and overall survival (OS) for BEACOPPescalated. Since BEACOPPescalated had been associated with more toxicity as compared with ABVD we report the results of long-term follow-up of 1196 patients enrolled and randomized in that study. The median follow-up was 112 months; a total of 370 centres contributed. Patients received one of three chemotherapy regimens: 8 cycles of COPP (cyclophosphamide, vincristine, procarbazine, and prednisone) alternating with ABVD (doxorubicin, bleomycin, vinblastin, and dacarbazine), 8 cycles of standard-dose BEACOPP or 8 cycles of escalated-dose BEACOPP. At 10 years, FFTF rates were 64%, 70% and 82%, OS rates were 75%, 80%, and 86 for COPP-ABVD (arm A), BEACOPPbaseline (arm B), and BEACOPPescalated, respectively (p &amp;lt; 0,001). Importantly, BEACOPPescalated was also significantly better than BEACOPPbaseline in terms of FFTF (p &amp;lt; 0.0001) and OS (p = 0.0053). Death due to HL occurred in 11.5%, 8.1% and 2.8% in arms A, B, and C, respectively. 74 second malignancies were documented, including secondary acute myeloid leukaemias (1,7,14), Non-Hodgkin lymphoma (7,8,5), and solid tumors (7,16,9) in arms A, B, and C respectively. The corresponding overall secondary malignancy rates were 6.7%, 8.9% and 6.8%. Importantly, the risk of secondary AML (sAML), although increased in this study after BEACOPPescalated, amounts to 0.9% in our follow-up study with BEACOPPescalated (HD12) in 1502 advanced-stage HL patients randomized and four years median follow-up. Although the higher rate of secondary AML after BEACOPPescalated in HD9 most likely occurred by chance, interestingly, 70% of patients in this group had additional radiotherapy whereas only 39% were radiated in HD12. Taken together, the 10 years follow-up of BEACOPPescalated chemotherapy demonstrates a stabilized significant improvement in long-term FFTF and OS for advanced-stage HL. Although for formal prove the results of ongoing prospective randomized comparisons with 8 cycles of ABVD might be required, these results clearly challenge ABVD as standard of care for this patient population.
Data from Pharmacologic Unmasking of Epigenetically Silenced Genes in Breast Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Aberrant promoter hypermethylation of several known or putative tumor suppressor genes occurs frequently during the pathogenesis of various cancers including breast cancer. Many epigenetically inactivated genes involved in breast cancer development remain to be identified. Therefore, in this study we used a pharmacologic unmasking approach in breast cancer cell lines with 5-aza-2′-deoxycytidine (5-aza-dC) followed by microarray expression analysis to identify epigenetically inactivated genes in breast cancer.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Breast cancer cell lines were treated with 5-aza-dC followed by microarray analysis to identify epigenetically inactivated genes in breast cancer. We then used bisulfite DNA sequencing, conventional methylation-specific PCR, and quantitative fluorogenic real-time methylation-specific PCR to confirm cancer-specific methylation in novel genes.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Forty-nine genes were up-regulated in breast cancer cells lines after 5-aza-dC treatment, as determined by microarray analysis. Five genes (&lt;i&gt;MAL, FKBP4, VGF, OGDHL&lt;/i&gt;, and &lt;i&gt;KIF1A&lt;/i&gt;) showed cancer-specific methylation in breast tissues. Methylation of at least two was found at high frequency only in breast cancers (40 of 40) as compared with normal breast tissue (0 of 10; &lt;i&gt;P&lt;/i&gt; &lt; 0.0001, Fisher's exact test).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; This study identified new cancer-specific methylated genes to help elucidate the biology of breast cancer and as candidate diagnostic markers for the disease.&lt;/p&gt;&lt;/div&gt;
A Flight-Rated Petri Dish Apparatus Providing Two Stage Fluid Injection for Aseptic Biological Investigations in Space (2001)

&lt;div class="htmlview paragraph"&gt;The BRIC-LED (Biological Research In Canisters-Light Emitting Diode) PDFU (Petri Dish Fixation Unit) apparatus was originally developed to support the on-orbit growth and subsequent fixation of any biological material amenable to petri dish culture in space. The PDFU component has been modified to support a two-stage fluid provision option so that investigations can incorporate an initial injection of a biologically active solution followed by a subsequent fixative injection to terminate the experiment in space. Crew-operated actuator tools initiate the delivery of the liquid treatments. Aseptic protocols have been developed which permit the entire experiment to be conducted under sterile conditions.&lt;/div&gt;
Semiconductor mode-locked laser intracavity gain dynamics measurements under three wavelength operation (2006)

The intracavity gain dynamics of an external cavity semiconductor hybrid mode-locked laser are measured under three wavelength operation. The results show a partial coherence and a temporal skew among pulses corresponding to different wavelength channels. The temporal skew broadens the temporal pulse profile and the partial coherence decreases the temporal beating between wavelength channels. A measurement of the temporal evolution of the gain reveals a slow gain depletion, avoiding nonlinearities, and gain competition between wavelength channels, making multiwavelength operation feasible.
Supplementary Figure 5 from AMG 757, a Half-Life Extended, DLL3-Targeted Bispecific T-Cell Engager, Shows High Potency and Sensitivity in Preclinical Models of Small-Cell Lung Cancer (2023)

&lt;p&gt;Supplementary Figure 5 A, DLL3 RNA expression levels in a panel of SCLC patient-derived xenograft (PDX) models compared with positive (NCI-H82) and negative (NCI-H460) control SCLC cell lines. Data are reported as relative quantification normalized to NCI-H460 cell line expression. B, DLL3 protein expression levels in a panel of SCLC PDX models compared with positive (NCI-H82) and negative (NCI-H460) control SCLC cell lines. GAPDH, glyceraldehyde 3-phosphate dehydrogenase.&lt;/p&gt;
How Could a Flash Cache Degrade Database Performance Rather Than Improve It? Lessons to be Learnt from Multi-Tiered Storage (2014)

Contrary to intuition, host-side flash caches can degrade performance rather than improve it. With flash write operations being expensive, cache hit-rates need to be relatively high to offset the overhead of writes. Otherwise, the end-to-end performance could be worse with flash cache. We believe that some lessons learnt from multi-tiered storage systems can be applied to flash cache management. Multi-tiered storage systems migrate data based on long-term I/O monitoring, carefully ensuring that the background data migration does not adversely affect foreground I/O performance. To test our hypothesis, we designed and implemented a new flash cache, named Scalable Cache Engine (SCE). In SCE, cache populations occur in the background in 1 MiB sized fragment units rather than the typical storage I/O size (4 KiB). By doing so, we warm-up the flash cache much faster while also benefiting from a prefetching effect that is very effective for improving cache hitrates when the workload demonstrates strong spatial locality. Additionally, large, aligned writes to flash are much more efficient than small random ones and therefore reduce the cache population overhead. We show that our approach successfully tackles several issues of existing flash cache management approaches and works well for OLTP database workloads. For instance, the throughput under a TPC-E workload actually degraded by 79.1% with flashcache, a popular open-source solution, compared to the baseline performance. For the same conditions, SCE could achieve a 301.7% improved throughput.
Perceptual loudness compensation in interactive object-based audio coding systems (2015)

Changing the rendering through interactivity in object-based audio coding may change the overall signal loudness. This paper proposes a method for estimating the change in the overall loudness using loudness information of the partial mixes and the rendering description. The method has been designed for a dialogue enhancement application scenario. The results of the method are compared with reference values from measurements, and the results match well with the mean absolute error of 0.11 LU. A subjective listening test is conducted for studying the amount of amplification applied by the test participants on a probe signal simulating the result of an interactive rendering when comparing it with a reference signal of the default mix. The average level adjustment reflects the change in the signal loudness through the modification.
Vehicle/Driver Monitoring for Enhanced Safety of Transit Buses (2007)

This report documents the findings of the study “Vehicle/Driver Monitoring for Enhanced Safety of Transit Buses” conducted as part of the PATH project TO5400. The goal of study TO5400 is todesign and implementation of a reliable vehicle/driver monitoring system with aim to enhance driving safety of transit buses.The main objectives of the project are: (1) to identify a simply model that best describes the driving patterns of human drivers, and (2) to develop an algorithm which can generate warning messages when there is a provision of danger.In this study, it is assumed that the driver sets the angle of the steering wheel in response to the lateral deviation of the vehicle from the center line of the road and/or the road curvature ahead of the vehicle which he/she infers from the visual perception. It is also assumed that the dynamic relationship between the lateral deviation and the road curvature (i.e. the inputs to the driver) and the steering angle (i.e. the output from the driver) may be represented by a linear model with Auto Regressive Moving Average with eXogeneous (ARMAX) structure. The order of the ARMAX model is determined by off-line analysis of experimental data collected from actual driving tests. Once the order of the model is determined, the parameters of the model can be estimated by processing the input and output data in real time during actual driving.The on-line data processing and prediction can also estimate three critical parameters for driving safety: the driver’s response time (tr), the time-to-collision (TTC) and the time-to-lane-crossing (TLC) TLC. A timely warning message scheme, which incorporates all the three parameters, is designed to determine whether an alarm should be issued.
Composite Code Sparse Autoencoders for First Stage Retrieval (2021)

We present a Composite Code Sparse Autoencoder (CCSA) approach for Approximate Nearest Neighbor (ANN) search of document representations based on Siamese-BERT models. In Information Retrieval (IR), the ranking pipeline is generally decomposed in two stages: the first stage focuses on retrieving a candidate set from the whole collection. The second stage re-ranks the candidates by relying on more complex models. Recently, Siamese-BERT models have been used as first stage rankers to replace or complement the traditional bag-of-words models. However, indexing and searching a large document collection requires efficient similarity search on dense vectors and this is why ANN techniques come into play. Since composite codes are naturally sparse, we show how CCSA can learn efficient parallel inverted index thanks to an uniformity regularizer. Our experiments on MS MARCO reveal that for the same quantization budget and [email protected] targets, CCSA is able to outperform IVF (inverted-index file) with product quantization on both
On the dynamic range improvement and robustness against branch imbalance of mode- multiplexing LINC amplifiers (2007)

In this paper a comparative study of LINC based amplifiers and LINC-like amplifiers designated herein as Mode- Multiplexing amplifiers is briefly reported. The latter technique uses a novel signal decomposition algorithm to enhance the power efficiency of the system. In addition it offers greater robustness to branch’s imbalance, which results into an extension of the dynamic range of the system. Computer simulation based on an analytical formulation as well experimental validation were carried out to demonstrate the superiority of the proposed method in comparison to standard LINC technique.
Supplementary Movie 2 from <i>In Vivo</i> Imaging of Drug-Induced Mitochondrial Outer Membrane Permeabilization at Single-Cell Resolution (2023)

&lt;p&gt;AVI file, 169KB, Time lapse image sequence of MDA-MB-231 breast cancer cells treated with ABT-263, showing the fluorescent IMS-RP MOMP reporter. The cell with the asterisk undergoes MOMP during this image sequence.&lt;/p&gt;
Well Test Rate Conversion to Compositional Wellstream (2013)

Abstract Well test rates are measured with test separators operating at varying pressure and temperature during initial production tests for a new well and during periodic tests used to monitor well performance and allocate multi-well production separator rates. Converting test separator gas and oil volumetric rates to a common (fixed) set of surface separator conditions is useful to ensure consistent history matching and rate allocation, development of valid inflow performance relations, and correlating well performance changes over time. This paper provides a method to convert reported test rates to a molar compositional wellstream rate. This compositional wellstream will exactly reproduce the reported test rates at the separator conditions prevailing when rates were measured. The compositional wellstream rate can then be re-processed through a fixed set of separator conditions to provide total surface gas and stock-tank oil rates. The requirements for converting test rates to a compositional wellstream include: (1) an appropriate EOS model, (2) an estimate of the wellstream composition – the "seed feed", (3) test separator volumetric rates, and (4) test separator conditions of pressure and temperature. The seed feed is usually the previously-determined wellstream composition from an earlier test. The seed feed is flashed at test separator pressure and temperature, resulting in equilibrium gas and equilibrium oil compositions. These equilibrium compositions are recombined in a ratio that yields exactly the test separator gas-oil ratio with the EOS model, thereby yielding wellstream composition. Properties of the separator phases are used to convert separator volumes to moles and thereby wellstream molar rate. Sometimes a similar conversion is needed for volumetric gas and oil rates resulting from a multi-stage separation process. An important example is conversion of black-oil rates to compositional wellstreams, where the black-oil PVT tables have been generated from a multi-stage separation process. Finally, we discuss the processing of compositional wellstreams through a higher-level (group, field, or asset) process facility that takes into account the total feed composition of the process facility, and how to back-allocate well contributions of total product rates.
Configuring topologies of distributed semantic concept classifiers for continuous multimedia stream processing (2008)

Real-time multimedia semantic concept detection requires instant identification of a set of concepts in streaming video or images. However, the potentially high data volumes of multimedia content, and high complexity associated with individual concept detectors, have hindered its practical deployment. In this paper, we present a new online concept detection system deployed on top of a distributed stream mining system. It uses a tree-topology of classifiers that are constructed on a semantic hierarchy of concepts of interest. We introduce a novel methodology for configuring such cascaded classifier topologies under constraints on the available resources. In our approach, we configure individual classifiers with optimized operating points after jointly and explicitly considering the misclassification cost of each end-to-end class of interest in the tree, the system imposed resource constraints, and the confidence level of each object that is classified. We describe the implemented application, system, and optimization algorithms, and verify that significant improvement in terms of accuracy of classification can be achieved through our approach.
Retinal Vascular Caliber and the Long‐Term Risk of Diabetes and Impaired Fasting Glucose: The Blue Mountains Eye Study (2008)

This study suggests that wider retinal venular caliber was associated with higher risk of IFG in middle-aged persons.
Differences in apoptosis induced by anticancer drugs in sublines (SKG-3a, SKG-3b) from a human uterine cervical epidermoid carcinoma. (1999)

SKG-3a and SKG-3b are two distinct human uterine cervical epidermoid carcinoma cell lines derived from a single donor. We studied these two closely related cell lines from the standpoint of drug susceptibility. The growth inhibitory effects of cisplatin (CDDP), doxorubicin (ADM), etoposide (VP-16), and paclitaxel (taxol) on SKG-3a and SKG-3b cells assessed by crystalviolet dye uptake assay were almost the same. SKG-3b cells treated with CDDP, ADM, VP-16, and taxol showed the apoptotic cell death, whereas apoptosis in SKG-3a cells was not induced by these anticancer drugs. Caspase-3 activity was increased only in the SKG-3b cell lysate after treatment with CDDP, ADM, and VP-16 but was not found in the SKG-3a cell lysate. These results indicate that despite growth inhibitory effects of anticancer drugs being almost the same, there may be differences in the common signaling pathways involved in the apoptotic process between SKG-3a and SKG-3b obtained from the same tumor.