gebhart/patrepeval huggingface dataset:
Quantifying chelonid herpesvirus 5 in symptomatic and asymptomatic rehabilitating green sea turtles (2015)

, an infectious disease of sea turtles, is characterized by tumors of the skin, eye(s) and/or internal organ(s), and is associated with chelonid herpesvirus 5 (ChHV5). Despite extensive research on FP, the pathogenesis of ChHV5 remains poorly understood, particularly regarding asymptomatic infections. Here, we provide evidence for detectable ChHV5 DNA in biological samples from symptomatic and asymptomatic green turtles Chelonia mydas. Using a probe-based quantitative PCR (qPCR) assay for ChHV5, we evaluated the relationship between ChHV5 DNA loads and FP disease status, and investigated potential routes of ChHV5 shedding. Samples of tissue, blood, urine, and feces were collected from 67 green turtles at 3 rehabilitation facilities in the southeastern USA. Turtles were divided into 3 study groups: clinical signs of FP (n = 23), history of FP but no clinical signs (n = 13), and no known history of FP (n = 31). Via qPCR, ChHV5 DNA was reliably detected in FP tumors, non-tumored skin, blood, urine, cloacal swabs, and plasma from green turtles in all 3 groups. Our results provide novel evidence for ChHV5 DNA in blood cells, which may represent a critical phase of the ChHV5 life cycle and provide a mechanism for viral transport, and documents that viral DNA can be detected in the urine of symptomatic and asymptomatic turtles. As molecular diagnostics become more affordable, sea turtle health experts can use qPCR to monitor ChHV5 gene copies and thereby detect early signs of viral presence in blood, urine, and tissue samples.
Altered Expression Pattern of Polycystin-2 in Acute and Chronic Renal Tubular Diseases (2002)

Polycystin-2 represents one of so far two proteins found to be mutated in patients with autosomal-dominant polycystic kidney disease. Evidence obtained from experiments carried out in cell lines and with native kidney tissue strongly suggests that polycystin-2 is located in the endoplasmic reticulum. In the kidney, polycystin-2 is highly expressed in cells of the distal and connecting tubules, where it is located in the basal compartment. It is not known whether the expression of polycystin-2 in the kidney changes or whether it can be manipulated under certain instances. Therefore, the distribution of polycystin-2 under conditions leading to acute and chronic renal failure was analyzed. During ischemic acute renal failure, which affects primarily the S3 segment of the proximal tubule, a pronounced upregulation of polycystin-2 and a predominantly combined homogeneous and punctate cytoplasmic distribution in damaged cells was observed. After thallium-induced acute injury to thick ascending limb cells, polycystin-2 staining assumed a chicken wire-like pattern in damaged cells. In the (cy/+) rat, a model for autosomal-dominant polycystic kidney disease in which cysts originate predominantly from the proximal tubule, polycystin-2 immunoreactivity was lost in some distal tubules. In kidneys from (pcy/pcy) mice, a model for autosomal-recessive polycystic kidney disease in which cyst formation primarily affects distal tubules and collecting ducts, a minor portion of cyst-lining cells cease to express polycystin-2, whereas in the remaining cells, polycystin-2 is retained in their basal compartment. Data show that the expression and cellular distribution of polycystin-2 in different kinds of renal injuries depends on the type of damage and on the nephron-specific response to the injury. After ischemia, polycystin-2 may be upregulated by the injured cells to protect themselves. It is unlikely that polycystin-2 plays a role in cyst formation in the (cy/+) rat and in the (pcy/pcy) mouse.
Characterization of a micro optical distance sensor (2003)

A micro optical distance sensor with a PSD receiver built in a modular set-up using two planar chips has been characterized. Results from spot size, measurement range, linearity, resolution, and repeatability are described.
Proximal Humerus and Ilium Are Reliable Sources of Bone Marrow Aspirates for Biologic Augmentation During Arthroscopic Surgery (2020)

Level II- prospective laboratorial study.
Distortion-Aware Linear Precoding for Massive MIMO Downlink Systems with Nonlinear Power Amplifiers (2020)

We introduce a framework for linear precoder design over a massive multiple-input multiple-output downlink system in the presence of nonlinear power amplifiers (PAs). By studying the spatial characteristics of the distortion, we demonstrate that conventional linear precoding techniques steer nonlinear distortions towards the users. We show that, by taking into account PA nonlinearity, one can design linear precoders that reduce, and in single-user scenarios, even completely remove the distortion transmitted in the direction of the users. This, however, is achieved at the price of a reduced array gain. To address this issue, we present precoder optimization algorithms that simultaneously take into account the effects of array gain, distortion, multiuser interference, and receiver noise. Specifically, we derive an expression for the achievable sum rate and propose an iterative algorithm that attempts to find the precoding matrix which maximizes this expression. Moreover, using a model for PA power consumption, we propose an algorithm that attempts to find the precoding matrix that minimizes the consumed power for a given minimum achievable sum rate. Our numerical results demonstrate that the proposed distortion-aware precoding techniques provide significant improvements in spectral and energy efficiency compared to conventional linear precoders.
RBF Volume Ray Casting on Multicore and Manycore CPUs (2014)

Abstract Modern supercomputers enable increasingly large N‐body simulations using unstructured point data. The structures implied by these points can be reconstructed implicitly. Direct volume rendering of radial basis function (RBF) kernels in domain‐space offers flexible classification and robust feature reconstruction, but achieving performant RBF volume rendering remains a challenge for existing methods on both CPUs and accelerators. In this paper, we present a fast CPU method for direct volume rendering of particle data with RBF kernels. We propose a novel two‐pass algorithm: first sampling the RBF field using coherent bounding hierarchy traversal, then subsequently integrating samples along ray segments. Our approach performs interactively for a range of data sets from molecular dynamics and astrophysics up to 82 million particles. It does not rely on level of detail or subsampling, and offers better reconstruction quality than structured volume rendering of the same data, exhibiting comparable performance and requiring no additional preprocessing or memory footprint other than the BVH. Lastly, our technique enables multi‐field, multi‐material classification of particle data, providing better insight and analysis.
Alkylation of Cysteine 468 in Stat3 Defines a Novel Site for Therapeutic Development (2011)

Stat3 is a latent transcription factor that promotes cell survival and proliferation and is often constitutively active in multiple cancers. Inhibition of Stat3 signaling pathways suppresses cell survival signals and leads to apoptosis in cancer cells, suggesting direct inhibition of Stat3 function is a viable therapeutic approach. Herein, we identify a small molecule, C48, as a selective Stat3-family member inhibitor. To determine its mechanism of action, we used site-directed mutagenesis and multiple biochemical techniques to show that C48 alkylates Cys468 in Stat3, a residue at the DNA-binding interface. We further demonstrate that C48 blocks accumulation of activated Stat3 in the nucleus in tumor cell lines that overexpress active Stat3, leading to impressive inhibition of tumor growth in mouse models. Collectively, these findings suggest Cys468 in Stat3 represents a novel site for therapeutic intervention and demonstrates the promise of alkylation as a potentially effective chemical approach for Stat3-dependent cancers.
Sustained Release of a Synthetic Autoinducing Peptide Mimetic Blocks Bacterial Communication and Virulence In Vivo. (2022)

A synthetic peptide was found to block cell-to-cell signalling, or quorum sensing, in bacteria and be highly bioavailable in mouse tissue. The controlled release of this agent from degradable polymeric microparticles strongly inhibited skin infection in a wound model at levels that far surpassed the potency of the peptide when delivered conventionally.
ChemInform Abstract: CHEMISTRY IN HYDROGEN FLUORIDE. 7. A NOVEL SYNTHESIS OF ARYL TRIFLUOROMETHYL ETHERS (1979)

Abstract Aus den Phenolen (I) erhält man mit Tetrachlorkohlenstoff und Fluorwasserstoff die Tritluormethylether (II).
Identification of an Orally Efficacious Matrix Metalloprotease 12 Inhibitor for Potential Treatment of Asthma (2009)

MMP-12 plays a significant role in airway inflammation and remodeling. Increased expression and production of MMP-12 have been observed in the lungs of asthmatic patients. Compound 27 was identified as a potent and selective MMP-12 inhibitor possessing good physicochemical properties. In pharmacological studies, the compound was orally efficacious in an MMP-12 induced ear-swelling inflammation model in the mouse with a good dose response. This compound also exhibited oral efficacy in a naturally Ascaris-sensitized sheep asthma model showing significant inhibition of the late phase response to allergen challenge. This compound has been considered for further development as a treatment therapy for asthma.
ChemInform Abstract: Dynamics of Interfacial Electron‐Transfer Processes in Colloidal Semiconductor Systems. (1982)

Abstract TiO 2 ‐ und CdS‐Sole, die transparente, wäßrige Dispersionen bilden, wurden hergestellt.
Dispersion control of near-infrared surface plasmon polariton using hyperbolic metamaterials (2013)

We demonstrate dispersion control of near-infrared surface plasmon polariton by tuning the filling fraction of a multilayer metallo-dielectric hyperbolic metamaterial. We show that effective medium approximation accurately provides the dispersion behavior for a structure with only 2.5 periods.
Data from Preferential Replication of Systemically Delivered Oncolytic Vaccinia Virus in Focally Irradiated Glioma Xenografts (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Radiotherapy is part of the standard of care in high-grade gliomas but its outcomes remain poor. Integrating oncolytic viruses with standard anticancer therapies is an area of active investigation. The aim of this study was to determine how tumor-targeted ionizing radiation (IR) could be combined with systemically delivered oncolytic vaccinia virus.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; U-87 glioma xenografts were grown subcutaneously or orthotopically. Oncolytic vaccinia viruses GLV-1h68 and LIVP 1.1.1 were injected systemically and IR was given focally to glioma xenografts. In a bilateral tumor model, glioma xenografts were grown in both flanks, oncolytic vaccinia was injected systemically and radiation was delivered specifically to the right flank tumor, whereas the left flank tumor was shielded. Viral replication and tumor regression, after systemic injection, was analyzed and compared in irradiated and nonirradiated glioma xenografts.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Systemically administered oncolytic vaccinia virus replicated to higher titers in preirradiated U-87 xenografts than in nonirradiated glioma xenografts. This increased oncolytic viral replication correlated with increased tumor xenograft regression and mouse survival in subcutaneous and orthotopic U-87 glioma models compared with monotherapies. The ability of focal IR to mediate selective replication of oncolytic vaccinia was shown in a bilateral glioma model in which systemically administered oncolytic vaccinia replicated preferentially in the irradiated tumor compared with the nonirradiated tumor in the same mouse.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusion:&lt;/b&gt; These findings show a potential clinical role of focal IR in sensitizing irradiated tumor sites for preferential vaccinia virus–mediated oncolysis. &lt;i&gt;Clin Cancer Res; 18(9); 2579–90. ©2012 AACR.&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
Regulation of 4F2 heavy-chain gene expression during normal human T-cell activation can be mediated by multiple distinct molecular mechanisms. (1988)

The 4F2 molecule belongs to the set of cell surface antigens which is induced following lectin- or antigen-mediated T-cell activation. The increase in 4F2 cell surface expression following lectin-mediated stimulation has been shown to be accompanied by a parallel increase in the steady-state levels of 4F2 heavy-chain (4F2HC) mRNA. The studies described in this report were designed to further elucidate the molecular mechanisms responsible for induction of 4F2HC gene expression following activation of normal resting human peripheral blood T cells. The low levels of mature 4F2HC mRNA in resting T cells were shown to be the result of a block to transcription elongation within the exon 1-intron 1 region of the 4F2HC gene rather than promoter inactivity. Phorbol myristate acetate stimulation of resting T cells resulted in a 20-fold increase in steady-state 4F2HC mRNA levels which was mediated by removal of this block to transcription elongation. The phorbol myristate acetate-induced increase in 4F2HC gene expression is distinct from previously described AP-1-mediated, phorbol ester-induced gene expression in that it requires new protein synthesis. Treatment of resting T cells with ionomycin plus PMA resulted in a 60-fold increase in 4F2HC mRNA levels. This induction was mediated by both an increase in promoter utilization and removal of the block to transcription elongation. Finally, by increasing the half-life of 4F2HC mRNA, cycloheximide treatment of resting T cells induced an approximately five fold increase in the levels of 4F2HC gene expression, although the physiologic significance of this mechanism remains unclear. These results demonstrate that the level of 4F2HC gene expression in normal peripheral blood T cells can be regulated by at least three distinct molecular pathways: (i) changes in promoter utilization, (ii) modulation of a block to transcription elongation, and (iii) alteration in mRNA stability.
A rapid radiochemical purity testing method for Tc-99m tetrofosmin (2009)

2237 Objectives The standard radiochemical purity (RCP) testing method for 99mTc-tetrofosmin requires extensive time and considerable skill to achieve accurate results. Also, ITLC/SG paper (2 x 20 cm) used in the standard method may not be available. The purpose of this study was to evaluate whether a RCP testing method developed for 99mTc-sestamibi could also be used for 99mTc-tetrofosmin. Methods The alternative RCP testing system consisted of a paper strip (1 x 8.5 cm) from Solvent Saturation Pads as stationary phase with 1:1 CH3Cl:THF used as mobile phase. Comparisons were performed with kits reconstituted according to the package insert and 99mTc NaTcO4 was added to create trials with RCP values below 90% purity. Results 158 trials (77 were replicated trials) were run from 13 kit preparations. 53 (34%) of the trials were below 90% based on the standard method. The agreement between the two methods was 93%. Sensitivity of the alternative method for unacceptable RCP was 85% and specificity for acceptable RCP was 97%. The agreement between the replicated trials of alternative and standard methods were 99% and 91% respectively. For the standard method, sensitivity of unacceptable RCP ranged from 81-92%. Conclusions The alternative method is faster, easier, and can be used for RCP testing of 99mTc-tetrofosmin and 99mTc-sestamibi. The stationary phase is readily available, not moisture sensitive, and less susceptible to operation technique. Our method is accurate in determining the RCP value of 99mTc-tetrofosmin, and is a better RCP testing method.
An implementation study of a detection-based adaptive block replacement scheme (1999)

In this paper, we propose a new adaptive buffer management scheme called DEAR (DEtection based Adaptive Replacement) that automatically detects the block reference patterns of applications and applies different replacement policies to different applications based on the detected reference pattern. The proposed DEAR scheme uses a periodic process. Detection is made by associating block attribute values such as backward distance and frequency gathered at the (i - 1)-th invocation with forward distances of blocks referenced between the (i - 1)-th and i-th invocations. We implemented the DEAR scheme in FreeBSD 2.2.5 and measured its performance using several real applications. The results show that compared with the LRU buffer management scheme, the proposed scheme reduces the number of disk I/Os by up to 51% (with an average of 23%) and the response time by up to 35% (with an average of 12%) in the case of single application executions. For multiple applications, the proposed scheme reduces the number of disk I/Os by up to 20% (with an average of 12%) and the over-all response time by up to 18% (with an average of 8%).
Catecholamines stimulate MHC class I, class II, and invariant chain gene expression in brain endothelium through different mechanisms (1993)

Bovine brain microvessel endothelial cells in primary culture retain a differentiated phenotype reminiscent of the in vivo blood-brain barrier endothelium. The IFN-gamma-induced surface expression of MHC class II molecules on those cells is stimulated by catecholamines through a cAMP-independent mechanism. We report that both the induction of MHC class II molecule expression by IFN-gamma and its potentiation by isoproterenol, a catecholamine analog, are preceded by increases of steady-state levels of the corresponding mRNA. Similar results were obtained for the regulation of invariant chain expression. In addition, isoproterenol alone is able to increase class I mRNA levels, but, in contrast to what is observed for class II expression, this effect appears to be mainly mediated by cAMP. These studies demonstrate that, in bovine brain microvessel endothelial cells, catecholamines up-regulate MHC class I and class II Ag, as well as invariant chain with different kinetics and through different mechanisms and suggest that these regulatory effects occur at the transcriptional level.
Low power cryogenic RF ASICs for quantum computing (2023)

Quantum computing is a promising new approach to computing that may allow the solution of certain problems that are very difficult to solve on classical computers. The field received its biggest impetus in 1994 when Shor [1] devised a quantum algorithm for finding the prime factors of large numbers and showed that this algorithm could greatly surpass the performance of known classical algorithms. Since that time, many additional applications have been proposed, and much effort has been devoted to developing hardware capable of running quantum algorithms.
A 60-ns 16-Mbit CMOS DRAM with a transposed data-line structure (1988)

Low-noise, high-speed circuit techniques for high-density DRAMs (dynamic random-access memories), as well as their application to a single 5-V 16-Mb CMOS DRAM with a 3.3-V internal operating voltage for a memory array, are described. It was found that data-line interference noise becomes unacceptably high (more than 25% of the signal) and causes a serious problem in 16-Mb DRAM memory arrays. A transposed data-line structure is proposed to eliminate the noise. Noise suppression below 5% is confirmed using this transposed data-line structure. A current sense amplifier is also proposed to maintain the data-transmission speed in common I/O lines, in spite of a reduced operating voltage and increased parasitic capacitance loading in the memory array. A speed improvement of 10 ns is achieved. Using these circuit techniques, a 16-Mb CMOS DRAM with a typical RAS access time of 60 ns was realized.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Union Bounds on the Bit Error Probability of Coded MRC in Nakagami-m Fading (2006)

In this letter new union bounds are derived for coded maximal ratio combining (MRC) over Nakagami-m fading channels. The union bounds are expressed in the product form, which makes them easily, evaluated using the transfer function of the code. The bounds are general to any diversity order and coding scheme with a known transfer function. Results show that the new bounds are tight to simulation results for wide ranges of diversity orders and Nakagami parameters
Proteomics of septicemic Escherichia coli (2016)

Virulent strains of Escherichia coli have become a major cause of infections, especially in hospitals and institutions, and result in high morbidity and mortality, due to the widespread antibiotic resistance. The infections usually start as complications of urinary tract infections or invasive medical procedures. Septicemic bacteria have to go through the blood stream, where they are exposed to a variety of stress conditions. The most difficult of these is the presence of the immune complement, which is strongly bactericidal. However, recently it has become clear that the nutritional immunity (metabolic stress) of serum is just as important. Thus, as shown by proteomic analyses, septicemic E. coli can cope with this latter stress condition by globally modifying the expression of a variety of metabolic genes. These include genes involved in amino acid metabolism and in metal homeostasis, whose robust regulation of expression appears to be critical for surviving the metabolic immunity of serum. Recognition of the nutritional immunity and the molecular mechanisms that enable septicemic bacteria to overcome it are the focus of this paper.
Environmental benefits of magnesium hydroxide-based peroxide bleaching of mechanical pulp – mill results (2013)

The use of a new, technical, high-purity magnesium hydroxide-based peroxide bleaching additive was evaluated in full mill-scale trial runs on two target brightness levels. Trial runs were conducted at a Finnish paper mill using Norwegian spruce (Picea abies) as the raw material in a conventional pressurized groundwood process, which includes a high-consistency peroxide bleaching stage. On high brightness grades, the use of sodium-based additives cause high environmental load from the peroxide bleaching stage. One proposed solution to this is to replace all or part of the sodium hydroxide with a weaker alkali, such as magnesium hydroxide. The replacement of traditional bleaching additives was carried out stepwise, ranging from 0% to 100%. Sodium silicate was dosed in proportion to sodium hydroxide, but with a minimum dose of 0.5% by weight on dry pulp. The environmental effluent load from bleaching of both low and high brightness pulps was significantly reduced. We observed a 35% to 48% reduction in total organic carbon (TOC), 37% to 40% reduction in chemical oxygen demand (COD), and 34% to 60% reduction in biological oxygen demand (BOD7) in the bleaching effluent. At the same time, the target brightness was attained with all replacement ratios. No interference from transition metal ions in the process was observed. The paper quality and paper machine runnability remained good during the trial. These benefits, in addition to the possibility of increasing production capacity, encourage the implementation of the magnesium hydroxide-based bleaching concept.