gebhart/patrepeval huggingface dataset:
Labeling DNA Damage with Terminal Transferase (2002)

Apoptotic and programmed cell death are characterized by, and indeed were first discovered from observations of, remarkable morphological changes that occur in the nucleus (see 1 for a comprehensive review of apoptosis and programmed cell death). Thus, light and electron microscopy were the first tools for the detection of apoptosis. This characteristic collapse of chromatin and ultimately the structural organization of the nucleus is triggered by the degradation of DNA, which is an active process and occurs prior to death of the cell. The degradation of DNA was subsequently found to be mediated by endonucleolytic activity that generated a specific pattern of fragments (2). The fragment sizes were multiples of approx 200 bp, the amount of DNA wound around a single nucleosome, and the pattern became known as the DNA ladder (Fig. 1A). Later it became apparent that DNA fragmentation is quite variable within cells and some cell types produce only high molecular weight (HMW) fragments (Fig. 1B, 3). The latter observations formed the basis of a convenient in vitro biochemical technique for the routine detection of apoptosis by resolving the fragmented DNA by conventional or pulsed field agarose gel electrophoresis. However, this technique requires relatively large amounts of material and DNA extraction. Subsequently, a variety of techniques have emerged to detect apoptotic DNA fragmentation in situ by exploiting the fact that the hydroxyl group at the 5′ or 3′ ends of the small DNA fragments becomes exposed. Nucleotide analogues can be attached to the ends by several enzymes, with Terminal deoxynucleotide Transferase (TdT) being the most popular (4,5). The assays are typically fluorescence-based, either by the direct incorporation of a nucleotide to which a fluorochrome has been conjugated, or indirectly using fluorescent dye conjugated antibodies that recognize biotin- or digoxigenin-tagged nucleotides. Radioactively labeled nucleotides can also be used. Since several million fragments are generated during complete DNA fragmentation and low levels of fluorescence can be readily detected by photo-multipliers and CCD arrays, the assays are extremely sensitive. The assays have been formatted for light and confocal microscopy as well as flow cytometry, thereby greatly facilitating the detection and quantitation of apoptosis in situ. In addition, endlabeling techniques are employed in studies of the actual mechanism of DNA fragmentation, as well as the detection and characterization of endonucleases.
Bioaugmentation: An Emerging Strategy of Industrial Wastewater Treatment for Reuse and Discharge (2016)

A promising long-term and sustainable solution to the growing scarcity of water worldwide is to recycle and reuse wastewater. In wastewater treatment plants, the biodegradation of contaminants or pollutants by harnessing microorganisms present in activated sludge is one of the most important strategies to remove organic contaminants from wastewater. However, this approach has limitations because many pollutants are not efficiently eliminated. To counterbalance the limitations, bioaugmentation has been developed and consists of adding specific and efficient pollutant-biodegrading microorganisms into a microbial community in an effort to enhance the ability of this microbial community to biodegrade contaminants. This approach has been tested for wastewater cleaning with encouraging results, but failure has also been reported, especially during scale-up. In this review, work on the bioaugmentation in the context of removal of important pollutants from industrial wastewater is summarized, with an emphasis on recalcitrant compounds, and strategies that can be used to improve the efficiency of bioaugmentation are also discussed. This review also initiates a discussion regarding new research areas, such as nanotechnology and quorum sensing, that should be investigated to improve the efficiency of wastewater bioaugmentation.
Quasispecies Theory and the Behavior of RNA Viruses (2010)

A large number of medically important viruses, including HIV, hepatitis C virus, and influenza, have RNA genomes. These viruses replicate with extremely high mutation rates and exhibit significant genetic diversity. This diversity allows a viral population to rapidly adapt to dynamic environments and evolve resistance to vaccines and antiviral drugs. For the last 30 years, quasispecies theory has provided a population-based framework for understanding RNA viral evolution. A quasispecies is a cloud of diverse variants that are genetically linked through mutation, interact cooperatively on a functional level, and collectively contribute to the characteristics of the population. Many predictions of quasispecies theory run counter to traditional views of microbial behavior and evolution and have profound implications for our understanding of viral disease. Here, we discuss basic principles of quasispecies theory and describe its relevance for our understanding of viral fitness, virulence, and antiviral therapeutic strategy.
Vaccinate – don’t procrastinate (2010)

Prevention is better than cure, and vaccines play a vital role in the prevention of many infectious bacterial and viral diseases, especially the infectious childhood diseases. Not only do vaccines protect the vaccinee, but in many instances, they also protect the community by reducing the overall prevalence of the disease (i.e. the so-called ‘herd immunity’).
In vitro mutagenesis of biologically active transcripts of beet necrotic yellow vein virus RNA 2: evidence that a domain of the 75-kDa readthrough protein is important for efficient virus assembly. (1992)

RNA 2 of the multipartite genome of beet necrotic yellow vein virus carries the cistron for 21-kDa viral coat protein at its 5' extremity. The amber termination codon of the coat protein cistron undergoes suppression approximately 10% of the time so that translation continues into an adjacent 54-kDa open reading frame, yielding a 75-kDa readthrough protein. The roles of coat protein and the readthrough protein in infection were investigated with biologically active transcripts of RNA 2. Much of the coat protein cistron of the RNA 2 transcript could be deleted without interfering with viral replication and local lesion formation on leaves, although formation of the rod-shaped virions did not occur. Mutants in which the amber coat protein termination codon was replaced with an ochre codon or a tyrosine codon were also viable. The ochre codon was suppressed both in vitro and in planta. The mutant containing the tyrosine substitution produced only the 75-kDa read-through protein and was deficient in viral assembly. Deletions in the 54-kDa readthrough domain were also viable in planta but had different effects on virus assembly. A deletion in the C-terminal portion of the readthrough domain did not interfere with RNA packaging but, unexpectedly, deletions in the N-terminal portion were assembly deficient, although 21-kDa coat protein was produced in planta. Thus, the 75-kDa protein can apparently intervene in virion assembly even though it has not been detected in purified virions.
Grade 1 or “Ding” Concussions in High School Athletes (2004)

A reconsideration of current concussion grading systems appears to be warranted.
Matricellular Proteins in Cardiac Adaptation and Disease (2012)

The term matricellular proteins describes a family of structurally unrelated extracellular macromolecules that, unlike structural matrix proteins, do not play a primary role in tissue architecture, but are induced following injury and modulate cell-cell and cell-matrix interactions. When released to the matrix, matricellular proteins associate with growth factors, cytokines, and other bioactive effectors and bind to cell surface receptors transducing signaling cascades. Matricellular proteins are upregulated in the injured and remodeling heart and play an important role in regulation of inflammatory, reparative, fibrotic and angiogenic pathways. Thrombospondin (TSP)-1, -2, and -4 as well as tenascin-C and -X secreted protein acidic and rich in cysteine (SPARC), osteopontin, periostin, and members of the CCN family (including CCN1 and CCN2/connective tissue growth factor) are involved in a variety of cardiac pathophysiological conditions, including myocardial infarction, cardiac hypertrophy and fibrosis, aging-associated myocardial remodeling, myocarditis, diabetic cardiomyopathy, and valvular disease. This review discusses the properties and characteristics of the matricellular proteins and presents our current knowledge on their role in cardiac adaptation and disease. Understanding the role of matricellular proteins in myocardial pathophysiology and identification of the functional domains responsible for their actions may lead to design of peptides with therapeutic potential for patients with heart disease.
An adaptive weighted TDM scheduler for video transport in ATM networks (2002)

Describes a technique for exploiting scene level variations for multiplexing heterogeneous video streams into a video bundle to be transported by ATM under a CBR contract. The method combines a dynamic bandwidth allocation scheme operating at the time-scale of scene changes, with a weighted time division multiplexing (WTDM) scheduling discipline operating at the time scale of cell arrivals. The TDM weights are adapted at the time scale of scene changes according to the bandwidth requirements of each stream: measured backlogs and estimated traffic loads. Adaptation has the objective of equalizing the queue solutions of the multiplexed streams at the time scale of scene changes. The adaptive WTDM operates as a "piecewise" TDM scheduler, resulting in low computational cost.
Role of mixed metal oxides in catalysis science—versatile applications in organic synthesis (2012)

A variety of mixed metal oxides (MMOs), containing alkali, alkaline, rare earth and noble metals, and their applications are presented. In this mini review, we summarize versatile applications of mixed metal oxides in organic synthesis. A variety of reactions such as reduction, oxidation, multicomponent, Mannich, alkylation, condensation, deprotection, cycloaddition, hydroxylation, dehydration, dehydrogenation, transesterification, reactions involving biomimetic oxygen-evolving catalysts and other important C–C bond forming reactions are well presented on the surface of mixed metal oxides under a variety of reaction conditions. The scope of MMOs in important organic reactions, industrial applications, and green chemistry and recent applications of MMOs are well presented in this review.
Human immunodeficiency virus proteins induce the inhibitory cAMP/protein kinase A pathway in normal lymphocytes. (1993)

Proliferation of normal T lymphocytes is impaired by human immunodeficiency virus (HIV) proteins. In this paper, we demonstrate important parts of this mechanism. Initially, HIV-induced impairment of proliferation was shown to be an active process involving induction of protein tyrosine kinases in both CD4 and CD8 T cells. Furthermore, the impairment of cell proliferation was demonstrated to be linked to induction of the inhibitory protein kinase A (PKA) pathway by HIV proteins. This induction of PKA was accompanied by an increase in intracellular cAMP, which is necessary for the activation of PKA. Finally, increases in cAMP/PKA activity were shown to induce biochemical changes that impaired proliferation when cells were stimulated with phytohemagglutinin. This was demonstrated by showing that (i) agents, other than HIV proteins, that increase cAMP/PKA activity (cholera toxoid and 8-bromo-cAMP) also decreased T-lymphocyte proliferation; (ii) exposure of lymphocytes to HIV or cholera toxoid led to decreased membrane activity of the proliferation promoter protein kinase C upon stimulation; and (iii) agents that reduced cAMP generation neutralized the effect of HIV proteins and restored lymphocyte proliferation. These studies show that the HIV-induced augmentation of cAMP/PKA activity may be a key part of the mechanism responsible for all or part of the HIV-induced anergy of T lymphocytes.
The Hippo pathway target, YAP, promotes metastasis through its TEAD-interaction domain (2012)

The transcriptional coactivator Yes-associated protein (YAP) is a major regulator of organ size and proliferation in vertebrates. As such, YAP can act as an oncogene in several tissue types if its activity is increased aberrantly. Although no activating mutations in the yap1 gene have been identified in human cancer, yap1 is located on the 11q22 amplicon, which is amplified in several human tumors. In addition, mutations or epigenetic silencing of members of the Hippo pathway, which represses YAP function, have been identified in human cancers. Here we demonstrate that, in addition to increasing tumor growth, increased YAP activity is potently prometastatic in breast cancer and melanoma cells. Using a Luminex-based approach to multiplex in vivo assays, we determined that the domain of YAP that interacts with the TEAD/TEF family of transcription factors but not the WW domains or PDZ-binding motif, is essential for YAP-mediated tumor growth and metastasis. We further demonstrate that, through its TEAD-interaction domain, YAP enhances multiple processes known to be important for tumor progression and metastasis, including cellular proliferation, transformation, migration, and invasion. Finally, we found that the metastatic potential of breast cancer and melanoma cells is strongly correlated with increased TEAD transcriptional activity. Together, our results suggest that increased YAP/TEAD activity plays a causal role in cancer progression and metastasis.
Influence of human wet cerumen on the growth of common and pathogenic bacteria of the ear (2000)

The available data on the effect of human wet cerumen on bacterial growth are not conclusive. Nevertheless it is widely accepted that cerumen has a bactericidal effect. In this study the activity of human wet cerumen on bacterial growth was assessed by applying cerumen suspensions to bacterial cultures. Bacterial counts were performed before and after application of cerumen suspensions. A total of 383 assays was carried out with 73 pools of cerumen that were tested against cultures of Staphylococcus aureus, Staphylococcus epidermidis, Corynebacterium spp., Escherichia coli, Proteus mirabilis, Pseudomonas aeruginosa and Serratia marcescens. An increase in growth occurred much more frequently than a decrease in growth in almost every microrganism tested, with the mean increase percentage being much higher than the mean decrease percentage, except in the case of S. aureus. The largest average growth increase was obtained with E. coli. The largest average decrease in bacterial growth was recorded with S. marcescens. Our study does not support the conception of a decrease in bacterial growth produced by humen wet cerumen. In vitro, the most observable effect was in fact an increase in microbial growth.
Xylose utilization in ethanol production: a patent landscape (2016)

Bioethanol is considered as one of the best alternatives to fossil fuels as unwanted biomass is converted into fuel ethanol. As there is increasing demand for fuel ethanol, researchers have started looking for some better ways to produce ethanol. In light of the present scenario, we have attempted to develop a global patent landscape view of xylose utilization in ethanol production. Our country‐specific patent analysis has revealed that most of the research on xylose‐utilizing ethanol production is carried out in the USA followed by China and Sweden. Moreover, it has been found that more patent applications/grants have been claimed for processes, followed by recombinant strains. Patent publication trends for genes and enzymes have shown that most of the research is focused on the xylA gene and xylulokinase. Assignee patenting trends suggest that Du Pont is the major player in xylose‐utilizing ethanol production research. Additionally, analysis based on micro‐organisms used in xylose‐utilizing ethanol production revealed that most of the research has been performed using Saccharomyces cerevisiae to enhance the ethanol yields. © 2016 Society of Chemical Industry and John Wiley & Sons, Ltd
Analyzing memory access intensity in parallel programs on multicore (2008)

As the shared memory bus becomes a major performance bottleneck for many numerical applications on multicore chips, understanding how the increased parallelism on chip strains the memory bandwidth and hence affects the efficiency of parallel codes becomes a critical issue. This paper introduces the notion of memory access intensity to facilitate quantitative analysis of program's memory behavior on multicores which employ state-of-the-art prefetching hardware. Three numerical solvers for large scale sparse linear systems are used to demonstrate the estimation of memory access intensity and its effect on program performance.
Regioselective Synthesis of Highly Functionalized Furans Through the Ru<sup>II</sup>‐Catalyzed [3+2] Cycloaddition of Diazodicarbonyl Compounds (2014)

Abstract A novel method for the Ru II ‐catalyzed regioselective synthesis of highly functionalized furans from readily available cyclic and acyclic diazodicarbonyl compounds and terminal alkynes is described. The devised protocol offers a straightforward means to the construction of a variety of diverse furan derivatives through powerful cascade processes, including the formation of ruthenium carbenoid, cyclopropenation, ring‐opening metathesis, and cyclization.
Identification of Novel Pathways That Control Farnesoid X Receptor-mediated Hypocholesterolemia (2009)

Farnesoid X receptor (FXR) plays important regulatory roles in bile acid, lipoprotein, and glucose homeostasis. Here, we have utilized Fxr(-/-) mice and mice deficient in scavenger receptor class B type I (SR-BI), together with an FXR-specific agonist and adenovirus expressing hepatocyte nuclear factor 4alpha or constitutively active FXR, to identify the mechanisms by which activation of FXR results in hypocholesterolemia. We identify a novel pathway linking FXR to changes in hepatic p-JNK, hepatocyte nuclear factor 4alpha, and finally SR-BI. Importantly, we demonstrate that the FXR-dependent increase in SR-BI results in both hypocholesterolemia and an increase in reverse cholesterol transport, a process involving the transport of cholesterol from peripheral macrophages to the liver for excretion into the feces. In addition, we demonstrate that FXR activation also induces an SR-BI-independent increase in reverse cholesterol transport and reduces intestinal cholesterol absorption. Together, these data indicate that FXR is a promising therapeutic target for treatment of hypercholesterolemia and coronary heart disease.
Tissue segmentation of the brain in Alzheimer disease. (1997)

Semiautomated segmentation of MR images of the brains of patients with Alzheimer disease reveals significant brain atrophy attributable to loss of cortical gray matter, which is compatible with the pathologic features of Alzheimer disease. There is also a significant increase in white matter signal hyperintensities. Tissue segmentation may increase our understanding of dementia but, as yet, when used alone, it does not play a role in the premorbid diagnosis of Alzheimer disease.
A Case of Unilateral Single Vaginal Ectopic Ureter with Ipsilateral Hypoplastic Pelvic Kidney and Bicornuate Uterus (2002)

A case of a female subject with a unilateral vaginal ectopic ureter associated with a single system, ipsilateral hypoplastic pelvic kidney and bicornuate uterus is reported. Although there are many reports of concomitant urinary and reproductive system malformations, a review of the literature shows these unique associations in the same patient to be extremely rare. This malformation is not limited to any combination of abnormal development of the mesonephric(wolffian) and paramesonephric(mllerian) ducts in the development of the urogenital system. Embryological aspects as well as clinical presentation, diagndstic approach and treatment applicable to this case are discussed.
Taxi : defeating code reuse attacks with tagged memory (2015)

Thesis: M. Eng., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2015.
Sub-micron resolution surface plasmon resonance imaging enabled by nanohole arrays with surrounding Bragg mirrors for enhanced sensitivity and isolation (2008)

We present nanohole arrays in thin gold films as sub-micron resolution surface plasmon resonance (SPR) imaging pixels in a microarray format. With SPR imaging, the resolution is not limited by diffraction, but by the propagation of surface plasmon waves to adjacent sensing areas, or nanohole arrays, causing unwanted interference. For ultimate scalability, several issues need to be addressed, including: (1) as several nanohole arrays are brought close to each other, surface plasmon interference introduces large sources of error; and (2) as the size of the nanohole array is reduced, i.e. fewer holes, detection sensitivity suffers. To address these scalability issues, we surround each biosensing pixel (a 3-by-3 nanohole array) with plasmonic Bragg mirrors, blocking interference between adjacent SPR sensing pixels for high-density packing, while maintaining the sensitivity of a 50 x larger footprint pixel (a 16-by-16 nanohole array). We measure real-time, label-free streptavidin-biotin binding kinetics with a microarray of 600 sub-micron biosensing pixels at a packing density of more than 10(7) per cm(2).
Iterative CT Reconstruction Using Shearlet-Based Regularization (2013)

Total variation (TV) methods have been proposed to improve the image quality in count-reduced images, by reducing the variation between neighboring pixels. Although very easy to implement and fast to compute, TV-based methods may lead to a loss of texture information when applied to images with complex textures, such as high-resolution abdominal CT images. Here, we investigate the use of another regularization approach in the context of medical images based on multiresolution transformations. One such transformation is the shearlet transform, which is optimally sparse for images that are C <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> except for discontinuities along C <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> curves, and has better directional sensitivity than most other, related, wavelet transform approaches. We propose to solve the convex problem using the split-Bregman (augmented Lagrangian) approach. One of the primary advantages of the split-Bregman approach, is that the shearlet transform can easily be incorporated into the sparse-view CT reconstruction. The required sparsity prior is the l1 norm of the shearlet coefficients. Results are shown for this method in comparison to the same framework with TV as the regularization term on simulated data. The noise-resolution performance is investigated at different contrast levels. At equal image noise, TV-based regularization outperforms shearlet-based regularization. However, when image texture is analyzed on measured mouse data, shearlets outperform TV, which suffers from staircasing effects. Our results show that there are benefits in using shearlets in CT imaging: texture is reconstructed more accurately compared to when TV is used, without biasing the image towards a piecewise constant image model. However, due to the larger support of the basis functions, our results suggest that uncareful usage of shearlets may lead to wavy artifacts, which can be equally unwanted as staircasing effects.