gebhart/patrepeval huggingface dataset:
Portal vein stenosis preconditioning of living donor liver in swine: early mechanisms of liver regeneration and gain of hepatic functional mass (2018)

To reduce the morbidity and mortality risk for the donor in living donor liver transplantation (LDLT), we previously identified 20% left portal vein (LPV) stenosis as an effective preconditioning method to induce cell proliferation in the contralateral lobe without downstream ipsilateral atrophy. In this study, we report the pathways involved in the first hours after preconditioning and investigate the changes in liver volume and function. Fourteen pigs were used this study. Five pigs were used to study the genetic, cellular and molecular mechanisms set up in the early hours following the establishment of our preconditioning. The remaining nine pigs were equally divided into three groups: sham-operated animals, 20% LPV stenosis, and 100% LPV stenosis. Volumetric scanning and 99 mTc-Mebrofenin hepatobiliary scintigraphy were performed before preconditioning and 14 days after to study morphological and functional changes in the liver. We demonstrated that liver regeneration triggered by 20% LPV stenosis in the contralateral lobe involves TNF-α, IL-6, and inducible nitric oxide synthase 2 by means of STAT3 and hepatocyte growth factor. We confirmed that our preconditioning was responsible for an increase in the total liver volume. Finally, we demonstrated that this volumetric gain was associated with an increase in hepatic functional capacity. NEW & NOTEWORTHY We describe a new preconditioning method for major hepatectomy that is applicable to hepatectomy for donation. We identified 20% left portal vein stenosis as effective preconditioning that is capable of inducing cell proliferation in the contralateral lobe without the downstream ipsilateral atrophy. In this study, we report the pathways involved in the first hours following preconditioning, and we confirm that 20% left portal vein stenosis is responsible for an increase in the functional capacity and total liver volume in a porcine model.
Interactions between S4-S5 Linker and S6 Transmembrane Domain Modulate Gating of HERG K+ Channels (2002)

Outward movement of the voltage sensor is coupled to activation in voltage-gated ion channels; however, the precise mechanism and structural basis of this gating event are poorly understood. Potential insight into the coupling mechanism was provided by our previous finding that mutation to Lys of a single residue (Asp(540)) located in the S4-S5 linker endowed HERG (human ether-a-go-go-related gene) K(+) channels with the unusual ability to open in response to membrane depolarization and hyperpolarization in a voltage-dependent manner. We hypothesized that the unusual hyperpolarization-induced gating occurred through an interaction between Lys(540) and the C-terminal end of the S6 domain, the region proposed to form the activation gate. Therefore, we mutated six residues located in this region of S6 (Ile(662)-Tyr(667)) to Ala in D540K HERG channels. Mutation of Arg(665), but not the other five residues, prevented hyperpolarization-dependent reopening of D540K HERG channels. Mutation of Arg(665) to Gln or Asp also prevented reopening. In addition, D540R and D540K/R665K HERG reopened in response to hyperpolarization. Together these findings suggest that a single residue (Arg(665)) in the S6 domain interacts with Lys(540) by electrostatic repulsion to couple voltage sensing to hyperpolarization-dependent opening of D540K HERG K(+) channels. Moreover, our findings suggest that the C-terminal ends of S4 and S6 are in close proximity at hyperpolarized membrane potentials.
Cover Picture: Macromol. Theory Simul. 7∕2014 (2014)

Cover: A novel hybrid simulation approach combines the deterministic and stochastic modeling of complex polymerization networks, for all types of polymerization reactions in ideal and non-ideal reactors. The fast deterministic simulation solves the heat and pressure balances and generates position-dependent event frequency profiles. The detailed stochastic simulation offers insight into the polymeric microstructure of each macromolecule. Further details can be found in the article by E. Neuhaus, T. Herrmann, I. Vittorias, D. Lilge, G. Mannebach, A. Gonioukh, and M. Busch* on page 415.
All-Angle Broadband Negative Refraction of Metal Waveguide Arrays in the Visible Range: Theoretical Analysis and Numerical Demonstration (2006)

In this Letter, we introduce a simple metal waveguide array for realizing all-angle wide frequency bandwidth negative refraction from the visible to infrared frequencies. Theoretical analysis from the rigorous coupled-wave theory reveals that the negative coupling constant resulting from the anomalous coupling of guided surface plasmon polariton modes contributes to the negative refraction. The analytical results are confirmed by finite-difference time-domain numerical simulations. Our result provides an alternative way to construct robust all-angle negative refractive materials operating in a wide range of frequency from the near-infrared to the visible range.
Comparing the Effects of Different Prostate Cancer Treatments on Quality of Life and Cancer Recurrence—NC ProCESS (2020)

Background: Prostate cancer is the most common cancer in men, with more than 240,000 men diagnosed and 30,000 dying from it each year. Many treatment options exist for patients with early prostate cancer, but few studies have directly compared the different treatments in terms of their effectiveness in curing the cancer and their impact on patient quality of life. In addition, recent advances in technology have introduced more costly treatments such as minimally invasive radical prostatectomy (MIRP), intensity-modulated radiation therapy (IMRT), and proton therapy (PT). The rapid adoption of these new technologies resulted in an estimated $350 million increase in US healthcare expenditures in 2005 alone. Yet, the clinical benefit from these newer treatments is unproven. Few studies have directly compared patient outcomes from older versus newer techniques for radiation therapy (IMRT versus PT) and surgery (open prostatectomy versus MIRP). In fact, two recently published studies suggest that newer surgical and radiation treatments may cause worse outcomes than older treatments. Objective: To examine comparative outcomes after four to five years among different prostate cancer treatment options. Method: NC ProCESS is a cohort of 1,700 patients from diverse backgrounds diagnosed with early prostate cancer and who were enrolled from January 2011 to June 2013. This observational study collects information on quality of life, cancer control, and health care received, inclusive of treatment and management of subsequent effects including complications and recurrence. We will use several statistical techniques to minimize the chance that differences between patients receiving different treatments will lead to misleading results about the effect of the treatments on quality of life, disease-free survival, and use of healthcare resources. Patient and Stakeholder Engagement: We have collaborated with patients and other stakeholders from initial study design through data collection. Stakeholders will continue to be closely involved in interpretation of study findings and dissemination of findings to patients who can directly benefit from them. Anticipated Impact: Study results can help patients and physicians make treatment decisions and inform policy makers and other stakeholders about the comparative effectiveness of different modern treatment options. These results will provide new, timely and urgently needed information to help patients and clinicians in the decision-making process.
Cortical activation during optokinetic stimulation – an fMRI study (2009)

BOLD signal increases were observed in the visual association area of both hemispheres (BA19) (MT/V5), primary visual cortex (BA17) of the right hemisphere, bilateral superior parietal lobules (BA7), and bilateral frontal eye fields (BA6). Decreases of BOLD signals were observed in the PIVC bilaterally.
mPlane (2009)

Customers are increasingly demanding service-level guarantees from ISPs. Unfortunately, ISPs today have limited ability to measure and monitor their own networks. ISPs use active probes for monitoring network health and use tomographic approaches to localize any end-to-end problems observed, which are typically postulated as underconstrained problems, and hence, often limited in accuracy. Active probes are also fundamentally unscalable; operators cannot afford to inject them at high frequencies. We present an architecture, mPlane, that addresses these problems. The key idea in mPlane is to break paths into segments consisting of router forwarding paths and links, and conduct measurements on a per-segment basis. Node measurements are obtained through scalable high-fidelity hardware primitives, while the link measurements are conducted using segment-level active probes at low frequencies. Unfortunately, upgrading all routers with these primitives faces significant deployment hurdles; we propose an incremental deployment strategy that picks the most important routers to upgrade. Our simulations with RocketFuel topologies indicate a partial deployment on 15% of an ISP's routers can yield two orders of magnitude decrease in measurement overhead, and reduce the average localization granularity from 4 hops to about 1.5.
All-Solid-State Diode-Pumped Fluorescence Lifetime Imaging System for Biomedicaine and Microscopy (1999)

Abstract The determination of fluorescence lifetime requires only relative measurements of intensity and so is especially useful for biomedical samples in which the heterogeneous nature of tissue and autofluorescence cause significant problems. Since fluorescence lifetime is dependent upon both radiative and non-radiative decay rates, it may be used to distinguish between different fluorophore molecules (with different radiative decay rates) and to monitor local environmental perturbations that affect the non-radiative decay rate. Fluorescence lifetime probes have been demonstrated for many biologically significant analytes including [O2], [Ca2+] and pH. Fluorescence lifetime imaging (FLIM) can be applied to almost any optical imaging modality, including microscopy and potentially to non-invasive optical biopsy. Fluorescence lifetime data may be acquired in the frequency or time domain. The recent development of user-friendly and relatively portable ultrafast laser technology and the availability of ultrafast gated optical image intensifiers (GOI’s) enable the development of potentially inexpensive time domain FLIM instruments that may be deployed outside specialist laser laboratories.
Visual analytics for the exploration of multiparametric cancer imaging (2014)

Tumor tissue characterization can play an important role in the diagnosis and design of effective treatment strategies. In order to gather and combine the necessary tissue information, multi-modal imaging is used to derive a number of parameters indicative of tissue properties. The exploration and analysis of relationships between parameters and, especially, of differences among distinct intra-tumor regions is particularly interesting for clinical researchers to individualize tumor treatment. However, due to high data dimensionality and complexity, the current clinical workflow is time demanding and does not provide the necessary intra-tumor insight. We implemented a new application for the exploration of the relationships between parameters and heterogeneity within tumors. In our approach, we employ a well-known dimensionality reduction technique [5] to map the high-dimensional space of tissue properties into a 2D information space that can be interactively explored with integrated information visualization techniques. We conducted several usage scenarios with real-patient data, of which we present a case of advanced cervical cancer. First indications show that our application introduces new features and functionalities that are not available within the current clinical approach.
Quality of Service-enabled Management of Database Workloads. (2008)

Database administrators struggle when managing workloads that have widely different performance requirements. For example, the same database may support short-running OLTP queries and batch jobs containing multitudes of queries with varying complexity. Different workloads may have different performance requirements, expressed in terms of service level objectives (SLOs) that must be fulfilled in order to keep the issuing database users satisfied. In this paper, we identify basic query classes and describe the challenges they pose for SLO-aware workload management. Additionally, we propose a generic architecture for an SLO-aware DBMS. We give an overview of workload management techniques already implemented in today’s DBMS and outline future research directions for as yet unsupported concepts. 1
L-Ascorbic Acid Biosensor Based on Immobilized Enzyme on ZnO (2011)

In this present research, we have grown the well aligned, perpendicular to the substrate and highly dense ZnO nanorods on the gold coated substrate by using the hydrothermal growth method. The ZnO nanorods were functionalized by immobilizing the ascorbate oxidase enzyme with cross linking molecule 3-glycidoxypropy1trimethoxysilane (GPTS).The electrochemical measurements were carried out through using potentiometric technique, we observed that the output response exhibited by the biosensor to the wide linear dynamic range concentration of L-ascorbic acid from 1×10-6 to 5×10-2 M with good sensitivity of 32 mV/decade. Moreover the biosensor showed excellent fast response time less than 10 seconds, better selectivity, repeatability, reproducibility and no significant interference to the common interfering ions such as potassium K+1, sodium ions Na+1, calcium ions Ca+2, glucose, fructose, and zinc ions Zn +2 etc. except slight interference with copper Cu +2 ions.
Regulation of SR-BI-mediated high-density lipoprotein metabolism by the tissue-specific adaptor protein PDZK1 (2005)

The functions of ARH and PDZK1 suggest that other adaptor proteins may be found to control the activities of other cell-surface receptors in a similar tissue-specific fashion. Manipulation of the expression and/or activities of such adaptors might provide new insights into receptor physiology and these adaptors may prove to be attractive targets for pharmaceutical intervention in cholesterol metabolism-related disease processes.
Array‐CGH predicts prognosis in plasma cell post‐transplantation lymphoproliferative disorders (2016)

Plasma-cell post-transplantation lymphoproliferative disorder (PC-PTLD) is a rare monomorphic PTLD entity divided into plasma cell myeloma (PCM) and plasmacytoma-like lesion (PLL) PTLD. To date, there are no exhaustive published cytogenetic data on PC-PTLD. We report array-based comparative genomic hybridization (aCGH) of 10 cases of PCM and PLL-PTLD. Patients had received kidney (n = 6), heart (n = 2), lung (n = 1) or bone marrow (n = 1) transplantation. There were six men and median age at time of PTLD was 56.5 years (3-74). We identified two different cytological features, plasmacytic and plasmablastic, among six PLL and three PCM PTLD. Eight cases were associated with EBV. First line treatment was heterogeneous: rituximab alone (n = 5), CHOP-like (n = 3) and multiple myeloma-like (n = 1). One patient died before any treatment. After a median follow-up of 19.5 months (0-150), five patients died (four from PTLD) and five were alive without evidence of disease. By aCGH, 5/10 demonstrated a complex profile. The most frequent abnormalities were +7q (5/10), +16q (5/10), +17q (5/10), +17p (4/10), +5q (4/10), t7 (4/10), t9 (3/10), del1p (3/10). No del17p13 (TP53) were observed. Del1p32.3 (CDKN2C) was observed in 2 cases. On univariate prognostic analysis, a complex aCGH was associated with a shorter OS. Thus, cytogenetic abnormalities seem to be closely related to those reported in multiple myeloma or diffuse large B cell lymphoma. Complex aCGH constitutes an unfavorable prognostic marker and aCGH should be integrated in the evaluation of patients with PLL/PCM-PTLD. © 2016 Wiley Periodicals, Inc.
Non-redundant Roles of Phosphoinositide 3-Kinase Isoforms α and β in Glycoprotein VI-induced Platelet Signaling and Thrombus Formation (2009)

Platelets are activated by adhesion to vascular collagen via the immunoglobulin receptor, glycoprotein VI (GPVI). This causes potent signaling toward activation of phospholipase Cgamma2, which bears similarity to the signaling pathway evoked by T- and B-cell receptors. Phosphoinositide 3-kinase (PI3K) plays an important role in collagen-induced platelet activation, because this activity modulates the autocrine effects of secreted ADP. Here, we identified the PI3K isoforms directly downstream of GPVI in human and mouse platelets and determined their role in GPVI-dependent thrombus formation. The targeting of platelet PI3Kalpha or -beta strongly and selectively suppressed GPVI-induced Ca(2+) mobilization and inositol 1,4,5-triphosphate production, thus demonstrating enhancement of phospholipase Cgamma2 by PI3Kalpha/beta. That PI3Kalpha and -beta have a non-redundant function in GPVI-induced platelet activation and thrombus formation was concluded from measurements of: (i) serine phosphorylation of Akt, (ii) dense granule secretion, (iii) intracellular Ca(2+) increases and surface expression of phosphatidylserine under flow, and (iv) thrombus formation, under conditions where PI3Kalpha/beta was blocked or p85alpha was deficient. In contrast, GPVI-induced platelet activation was insensitive to inhibition or deficiency of PI3Kdelta or -gamma. Furthermore, PI3Kalpha/beta, but not PI3Kgamma, contributed to GPVI-induced Rap1b activation and, surprisingly, also to Rap1b-independent platelet activation via GPVI. Together, these findings demonstrate that both PI3Kalpha and -beta isoforms are required for full GPVI-dependent platelet Ca(2+) signaling and thrombus formation, partly independently of Rap1b. This provides a new mechanistic explanation for the anti-thrombotic effect of PI3K inhibition and makes PI3Kalpha an interesting new target for anti-platelet therapy.
Performance Trade-Off Of File System Between Overwriting And Dynamic Relocation On A Solid State Drive (2008)

Most file systems overwrite modified file data and metadata in their original locations, while the Log-structured File System (LFS) dynamically relocates them to other locations. We design and implement the Evergreen file system that can select between overwriting or relocation for each block of a file or metadata. Therefore, the Evergreen file system can achieve superior write performance by sequentializing write requests (similar to LFS-style relocation) when space utilization is low and overwriting when utilization is high. Another challenging issue is identifying performance benefits of LFS-style relocation over overwriting on a newly introduced SSD (Solid State Drive) which has only Flash-memory chips and control circuits without mechanical parts. Our experimental results measured on a SSD show that relocation outperforms overwriting when space utilization is below 80% and vice versa.
Mediation of noradrenaline‐induced contractions of rat aorta by the (α1B‐adrenoceptor subtype (1995)

1. The subtypes of alpha 1-adrenoceptor mediating contractions to exogenous noradrenaline (NA) in rat aorta have been examined in both biochemical and functional studies. 2. Incubation of rat aortic membranes with the irreversible alpha 1B-adrenoceptor antagonist, chloroethylclonidine (CEC: 10 microM) did not change the KD of [3H]-prazosin binding in comparison to untreated membranes, but reduced by 88% the total number of binding sites (Bmax). 3. Contractions of rat aortic strips to NA after CEC (50 microM for 30 min) incubation followed by repetitive washing, showed a marked shift in the potency of NA and a partial reduction in the maximum response. The residual contractions to NA after CEC incubation were not affected by prazosin (10 nM). 4. The competitive antagonists prazosin, terazosin, (R)-YM-12617, phentolamine, 5-methylurapidil and spiperone inhibited contractions to NA with estimated pA2 values of 9.85, 8.54, 9.34, 7.71, 7.64 and 8.41, respectively. 5. The affinity of the same antagonists for the alpha 1A- and alpha 1B- adrenoceptors was evaluated by utilizing membranes from rat hippocampus pretreated with CEC, and rat liver, respectively. 5-Methylurapidil and phentolamine were confirmed as selective for the alpha 1A-adrenoceptors, whereas spiperone was alpha 1B-selective. 6. A significant correlation was found between the pA2 values of the alpha 1-adrenoceptor antagonists tested and their affinity for the alpha 1B-adrenoceptor subtype, but not for the alpha 1A-subtype. 7. In conclusion, these findings indicate that in rat aorta most of the contraction is mediated by alpha 1B-adrenoceptors, and that the potency (pA2) of an antagonist in this tissue should be related to its antagonistic effect on this subtype of the alpha 1-adrenoceptor population.
Rapid synthesis of aligned zinc oxide nanowires (2008)

A solution growth approach for zinc oxide (ZnO) nanowires is highly appealing because of the low growth temperature and possibility for large area synthesis. Reported reaction times for ZnO nanowire synthesis, however, are long, spanning from several hours to days. In this work, we report on the rapid synthesis of ZnO nanowires on various substrates (such as poly(ethylene terephthalate) (PET), silicon and glass) using a commercially available microwave oven. The average growth rate of our nanowires is determined to be as high as 100 nm min(-1), depending on the microwave power. Transmission electron microscopy analysis revealed a defect-free single-crystalline lattice of the nanowires. A detailed analysis of the growth characteristics of ZnO nanowires as functions of growth time and microwave power is reported. Our work demonstrates the possibility of a fast synthesis route using microwave heating for nanomaterials synthesis.
An improved enhancement layer for octree based point cloud compression with plane projection approximation (2016)

Recent advances in point cloud capture and applications in VR/AR sparked new interests in the point cloud data compression. Point Clouds are often organized and compressed with octree based structures. The octree subdivision sequence is often serialized in a sequence of bytes that are subsequently entropy encoded using range coding, arithmetic coding or other methods. Such octree based algorithms are efficient only up to a certain level of detail as they have an exponential run-time in the number of subdivision levels. In addition, the compression efficiency diminishes when the number of subdivision levels increases. Therefore, in this work we present an alternative enhancement layer to the coarse octree coded point cloud. In this case, the base layer of the point cloud is coded in known octree based fashion, but the higher level of details are coded in a different way in an enhancement layer bit-stream. The enhancement layer coding method takes the distribution of the points into account and projects points to geometric primitives, i.e. planes. It then stores residuals and applies entropy encoding with a learning based technique. The plane projection method is used for both geometry compression and color attribute compression. For color coding the method is used to enable efficient raster scanning of the color attributes on the plane to map them to an image grid. Results show that both improved compression performance and faster run-times are achieved for geometry and color attribute compression in point clouds.