gebhart/patrepeval huggingface dataset:
Oil industry first field trial of inter-well reservoir nanoagent tracers (2015)

This short manuscript highlights the industry's first proven reservoir nanoagents' design and demonstrates a successful multi-well field trial using these agents. Our fundamental nanoparticles tracer template, A-Dots or Arab-D Dots, is intentionally geared towards the harsh but prolific Arab-D carbonate reservoir environment of 100<sup>+</sup>&deg;C temperature, 150,000<sup>+</sup>ppm salinity, and an abundant presence of divalent ions in the connate water. Preliminary analyses confirmed nanoparticles' breakthrough at a producer nearly 500m from the injector at the reservoir level; thus, proving the tracer nanoparticles' mobility and transport capability. This is considered industry-first and a breakthrough achievement complementing earlier accomplishments in regard to the nanoagents' reservoir stability with the first successful single well test and ease of scale up with the synthesis of one metric ton of this material. The importance of this accomplishment is not in how sophisticated is the sensing functionalities of this design but rather in its stability, mobility, scalability, and field application potentials. This renders the concept of having active, reactive, and even communicative, in-situ reservoir nanoagents for underground sensing and intervention a well anticipated near-future reality.
Mugshot: deterministic capture and replay for Javascript applications (2010)

Mugshot is a system that captures every event in an executing JavaScript program, allowing developers to deterministically replay past executions of web applications. Replay is useful for a variety of reasons: failure analysis using debugging tools, performance evaluation, and even usability analysis of a GUI. Because Mugshot can replay every execution step that led to a failure, it is far more useful for performing root-cause analysis than today's commonly deployed client-based error reporting systems--core dumps and stack traces can only give developers a snapshot of the system after a failure has occurred.Many logging systems require a specially instrumented execution environment like a virtual machine or a custom program interpreter. In contrast, Mugshot's client-side component is implemented entirely in standard JavaScript, providing event capture on unmodified client browsers. Mugshot imposes low overhead in terms of storage (20-80KB/minute) and computation (slowdowns of about 7% for games with high event rates). This combination of features--a low-overhead library that runs in unmodified browers--makes Mugshot one of the first capture systems that is practical to deploy to every client and run in the common case. With Mugshot, developers can collect widespread traces from programs in the field, gaining a visibility into application execution that is typically only available in a controlled development environment.
Localization of the Herpes Simplex Virus Type 1 Major Capsid Protein VP5 to the Cell Nucleus Requires the Abundant Scaffolding Protein VP22a (1994)

The intracellular distributions of three herpes simplex virus type 1 (HSV-1) capsid proteins, VP23, VP5 and VP22a, were examined using vaccinia virus and plasmid expression systems. During infection of cells with HSV-1 wild-type virus, all three proteins were predominantly located in the nucleus, which is the site of capsid assembly. However, when expressed in the absence of any other HSV-1 proteins, although VP22a was found exclusively in the nucleus as expected, VP5 and VP23 were distributed throughout the cell. Thus nuclear localization is not an intrinsic property of these proteins but must be mediated by one or more HSV-1-induced proteins. Co-expression experiments demonstrated that VP5 was efficiently transported to the nucleus in the presence of VP22a, but the distribution of VP23 was unaffected by the presence of either or both of the other two proteins.
La música prehispánica. Sonidos rituales a lo largo de la historia (2008)

Aunque en Mesoamerica, 
la musica y los sonidos rituales tenian una 
gran importancia, su reconstruccion apenas esta en proceso. Si bien 
la historia del mundo sonoro prehispanico 
aun no esta escrita, sabemos que ese mundo estaba muy desarrollado y que en el subyacian conceptos magico-religiosos.
The Genetic Regulation and Coordination of Biosynthetic Pathways in Yeast: Amino Acid and Phospholipid Synthesis (1984)

We have made rapid progress in recent years in identifying the genetic causes of many human diseases. However, despite this recent progress, our mechanistic understanding of these diseases is often incomplete. This is a problem because it limits our ...Read More
Biofilms in dairy manufacturing plant‐description, current concerns and methods of control (1997)

Biofilms on the surfaces of dairy manufacturing plant threaten the quality and safety of dairy products. Biofilms on dairy processing lines are characterised by rapid development (< 12 h) and the predominance of single species of bacteria (e.g. Streptococcus thermophilus or Bacillus spp.). Increased processing times, more complex processing systems and demands for higher quality products have contributed to the increased recognition of the problems posed by biofilms. The growth of biofilms on the surface of plate heat exchanger pasteurizers can contaminate the milk with > 106 bacteria ml‐1 and this affects the quality of products manufactured from this milk. Biofilm control currently relies on the effectiveness of clean‐in‐place systems. A shortage of information on the development and control of biofilms in dairy manufacturing plant means that to reduce biofilm problems, increasing the frequency of cleaning is currently the only option for dairy manufacturers.
Transforming Growth Factor Beta Induces Sensory Neuronal Hyperexcitability, and Contributes to Pancreatic Pain and Hyperalgesia in Rats with Chronic Pancreatitis (2012)

TGFβ1 is an important and complex modulator of sensory neuronal function in chronic inflammation, providing a link between fibrosis and nociception and is a potentially novel target for the treatment of persistent pain associated with chronic pancreatitis.
The innate immune receptor Dectin-2 mediates the phagocytosis of cancer cells by Kupffer cells for the suppression of liver metastasis (2016)

Tumor metastasis is the cause of most cancer deaths. Although metastases can form in multiple end organs, the liver is recognized as a highly permissive organ. Nevertheless, there is evidence for immune cell-mediated mechanisms that function to suppress liver metastasis by certain tumors, although the underlying mechanisms for the suppression of metastasis remain elusive. Here, we show that Dectin-2, a C-type lectin receptor (CLR) family of innate receptors, is critical for the suppression of liver metastasis of cancer cells. We provide evidence that Dectin-2 functions in resident macrophages in the liver, known as Kupffer cells, to mediate the uptake and clearance of cancer cells. Interestingly, Kupffer cells are selectively endowed with Dectin-2-dependent phagocytotic activity, with neither bone marrow-derived macrophages nor alveolar macrophages showing this potential. Concordantly, subcutaneous primary tumor growth and lung metastasis are not affected by the absence of Dectin-2. In addition, macrophage C-type lectin, a CLR known to be complex with Dectin-2, also contributes to the suppression of liver metastasis. Collectively, these results highlight the hitherto poorly understood mechanism of Kupffer cell-mediated control of metastasis that is mediated by the CLR innate receptor family, with implications for the development of anticancer therapy targeting CLRs.
Internal Ribosomal Entry Site-Mediated Translation Initiation in Equine Rhinitis A Virus: Similarities to and Differences from That of Foot-and-Mouth Disease Virus (2000)

Equine rhinitis A virus (ERAV) has recently been classified as an aphthovirus, a genus otherwise comprised of the different serotypes of Foot-and-mouth disease virus (FMDV). FMDV initiates translation via a type II internal ribosomal entry site (IRES) and utilizes two in-frame AUG codons to produce the leader proteinases Lab and Lb. Here we show that the ERAV 5' nontranslated region also possesses the core structures of a type II IRES. The functional activity of this region was characterized by transfection of bicistronic plasmids into BHK-21 cells. In this system the core type II structures, stem-loops D to L, in addition to a stem-loop (termed M) downstream of the first putative initiation codon, are required for translation of the second reporter gene. In FMDV, translation of Lb is more efficient than that of Lab despite the downstream location of the Lb AUG codon. The ERAV genome also has putative initiation sites in positions similar to those utilized in FMDV, except that in ERAV these are present as two AUG pairs (AUGAUG). Using the bicistronic expression system, we detected initiation from both AUG pairs, although in contrast to FMDV, the first site is strongly favored over the second. Mutational analysis of the AUG codons indicated that AUG2 is the major initiation site, although AUG1 can be accessed, albeit inefficiently, in the absence of AUG2. Further mutational analysis indicated that codons downstream of AUG2 appear to be accessed by a mechanism other than leaky scanning. Furthermore, we present preliminary evidence that it is possible for ribosomes to access downstream of the two AUG pairs. This study reveals important differences in IRES function between aphthoviruses.
Metal-catalyzed Oxidation of α-Synuclein (2004)

Oxidative stress is implicated in a number of neuro-degenerative diseases and is associated with the selective loss of dopaminergic neurons of the substantia nigra in Parkinson's disease. The role of alpha-synuclein as a potential target of intracellular oxidants has been demonstrated by the identification of posttranslational modifications of synuclein within intracellular aggregates that accumulate in Parkinson's disease brains, as well as the ability of a number of oxidative insults to induce synuclein oligomerization. The relationship between these relatively small soluble oligomers, potentially neurotoxic synuclein protofibrils, and synuclein filaments remains unclear. We have found that metal-catalyzed oxidation of alpha-synuclein inhibited formation of synuclein filaments with a concomitant accumulation of beta sheet-rich oligomers that may represent synuclein protofibrils. Similar results with a number of oxidative and enzymatic treatments suggest that the covalent association of synuclein into higher molecular mass oligomers/protofibrils represents an alternate pathway from filament formation and renders synuclein less prone to proteasomal degradation.
Uncovering the Complexity of Transcriptomes with RNA-Seq (2010)

In recent years, the introduction of massively parallel sequencing platforms for Next Generation Sequencing (NGS) protocols, able to simultaneously sequence hundred thousand DNA fragments, dramatically changed the landscape of the genetics studies. RNA-Seq for transcriptome studies, Chip-Seq for DNA-proteins interaction, CNV-Seq for large genome nucleotide variations are only some of the intriguing new applications supported by these innovative platforms. Among them RNA-Seq is perhaps the most complex NGS application. Expression levels of specific genes, differential splicing, allele-specific expression of transcripts can be accurately determined by RNA-Seq experiments to address many biological-related issues. All these attributes are not readily achievable from previously widespread hybridization-based or tag sequence-based approaches. However, the unprecedented level of sensitivity and the large amount of available data produced by NGS platforms provide clear advantages as well as new challenges and issues. This technology brings the great power to make several new biological observations and discoveries, it also requires a considerable effort in the development of new bioinformatics tools to deal with these massive data files. The paper aims to give a survey of the RNA-Seq methodology, particularly focusing on the challenges that this application presents both from a biological and a bioinformatics point of view.
The electromagnetic response of human skin in the millimetre and submillimetre wave range (2009)

Recent studies of the minute morphology of the skin by optical coherence tomography revealed that the sweat ducts in human skin are helically shaped tubes, filled with a conductive aqueous solution. This, together with the fact that the dielectric permittivity of the dermis is higher than that of the epidermis, brings forward the supposition that as electromagnetic entities, the sweat ducts could be regarded as low Q helical antennas. The implications of this statement were further investigated by electromagnetic simulation and experiment of the in vivo reflectivity of the skin of subjects under varying physiological conditions (Feldman et al 2008 Phys. Rev. Lett. 100 128102). The simulation and experimental results are in a good agreement and both demonstrate that sweat ducts in the skin could indeed behave as low Q antennas. Thus, the skin spectral response in the sub-Terahertz region is governed by the level of activity of the perspiration system and shows the minimum of reflectivity at some frequencies in the frequency band of 75-110 GHz. It is also correlated to physiological stress as manifested by the pulse rate and the systolic blood pressure. As such, it has the potential to become the underlying principle for remote sensing of the physiological parameters and the mental state of the examined subject.
A humanized monovalent CD3 antibody which can activate homologous complement (1991)

The rat monoclonal antibody (mAb) YTH12.5, specific for the CD3 antigen complex on human T cells has been modified in order to improve its efficacy in human therapy. With the aim of rendering it less immunogenic, it has been humanized using the method of framework grafting. During this process sequence analysis of the YTH12.5 VL gene indicated that it was of the lambda subclass, however, it was markedly dissimilar from previously published rat and mouse V lambda gene sequences and may represent a new V lambda gene family. The humanization of this light chain represents the first successful reshaping of a lambda light chain V region. To improve the effector function of the antibody we have created a monovalent form (1 Fab, 1 Fc) using a novel method involving the introduction of an N-terminally truncated human IgG1 heavy chain gene into cells producing the humanized CD3 mAb. Comparison of the mono- and bivalent humanized mAb in a complement-mediated cell lysis assay revealed that the monovalent antibody mediated lysis of human T cell blasts whereas the bivalent form did not. The availability of a humanized, complement-fixing CD3 mAb may improve opportunities for human therapy, in the management of organ rejection, autoimmunity and the treatment of T cell lymphoma.
Extreme Damping in Composite Materials with a Negative Stiffness Phase (2001)

Composites with negative stiffness inclusions in a viscoelastic matrix are shown to have higher stiffness and mechanical damping tandelta than that of either constituent and exceeding conventional bounds. The causal mechanism is a greater deformation in and near the inclusions than the composite as a whole. Though a block of negative stiffness is unstable, negative stiffness inclusions in a composite can be stabilized by the surrounding matrix. Such inclusions may be made from single domains of ferroelastic material below its phase transition temperature or from prebuckled lumped elements.
Efficient shadow computations in ray tracing (1993)

Two techniques to speed up shadow computations in ray tracing are examined. The first, atomic adaptive sampling, is intended for any light type, such as directional, spot, point, linear, and area lights, in antialiasing, while the second, plane-vertex checking, specifically accelerates shadow computation of linear and area lights. The basic ideas can be extended to other ray types and, for the plane-vertex check, to radiosity applications as well. Existing surveys explain the fundamentals and provide references to intersection culler and shadow algorithms.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
An approach to support a single service provider address image for wide area networks environment (2002)

Request dispatching mechanism is at the heart of any cluster-computing environment. The goal is to support a single service provider address image for a given cluster of workstations. That is to say a given cluster publicises a single IP address and client requests are addressed to that IP address. This means, from the client's viewpoint, there are no nodes in the cluster, only services and the network names through which they are accessible. As a result, the cluster becomes a single virtual node. We propose a simple and elegant scheme for making the cluster transparent to clients outside the cluster such that the clients can interact with the cluster as if it were a single high-performance and highly available resource.
Hypertext hands-on—an introduction to a new way of organizing and accessing information (1989)

Provides the first hands-on, non-technical introduction to hypertext. Hypertext is a new way of organizing and accessing information.
Construction of heterodimer tyrosyl-tRNA synthetase shows tRNATyr interacts with both subunits. (1986)

The tyrosyl-tRNA synthetase (EC 6.1.1.1) from Bacillus stearothermophilus is a dimer of two identical subunits. The dimer shows "half-of-the-sites" reactivity in that only one molecule of tyrosyladenylate is formed and one molecule of tRNATyr binds per dimer. To identify whether the tRNATyr binds to a single subunit in the dimer, or to both subunits, heterodimers were constructed by mixing two variant dimers together in 8 M urea. As the unfolded protein is electrophoresed into a native polyacrylamide gel, it refolds and reassociates, and heterodimers can be purified from the parental dimers. Kinetic analysis of heterodimers formed between variant enzymes with defective tyrosine activation or tRNA aminoacylation shows that a molecule of tRNATyr interacts with the N-terminal region of one subunit and the C-terminal region of the other subunit in the dimer.
Cloning, expression, and purification of UDP-3-O-acyl-GlcNAc deacetylase from Pseudomonas aeruginosa: a metalloamidase of the lipid A biosynthesis pathway (1997)

The lpxC (envA) gene of Escherichia coli encodes UDP-3-O-acyl-GlcNAc deacetylase, the second and committed step of lipopolysaccharide biosynthesis. Although present in all gram-negative bacteria examined, the deacetylase from E. coli is the only example of this enzyme that has been expressed and purified. In order to examine other variants of this protein, we cloned the Pseudomonas aeruginosa deacetylase structural gene from a lambda library as a 5.1-kb EcoRI fragment. The LpxC reading frame encodes an inferred protein of 33,435 Da that is highly homologous to the E. coli protein and that possesses a nearly identical hydropathy profile. In order to verify function, we subcloned the P. aeruginosa lpxC gene into the T7-based expression vector pET11a. Upon induction at 30 degrees C, this construct yielded active protein to approximately 18% of the soluble fraction. We devised a novel, rapid, and reproducible assay for the deacetylase which facilitated purification of the enzyme in three steps. The purified recombinant protein was found to be highly sensitive to EDTA yet was reactivated by the addition of excess heavy metal, as was the case for crude extracts of P. aeruginosa. In contrast, deacetylase activity in crude extracts of E. coli was insensitive to EDTA, and the extracts of the envA1 mutant were sensitive in a time-dependent manner. The lpxC gene has no significant homology with amidase signature sequences. Therefore, we assign this protein to the metalloamidase family as a member with a novel structure.
Adding Fingers to an Engineered Zinc Finger Nuclease Can Reduce Activity (2011)

Zinc finger nucleases (ZFNs) have been used to direct precise modifications of the genetic information in living cells at high efficiency. An important consideration in the design of ZFNs is the number of zinc fingers that are required for efficient and specific cleavage. We examined dimeric ZFNs composed of [1]+[1], [2]+[2], [3]+[3], [4]+[4], [5]+[5], and [6]+[6] zinc fingers, targeting 6, 12, 18, 24, 30, and 36 bp, respectively. We found that [1]+[1] and [2]+[2] fingers supported neither in vitro cleavage nor single-strand annealing in a cell-based recombination assay. An optimal ZFN activity was observed for [3]+[3] and [4]+[4] fingers. Surprisingly, [5]+[5] and [6]+[6] fingers exhibited significantly reduced activity. While the extra fingers were not found to dramatically increase toxicity, directly inhibit recombination, or perturb the ZFN target site, we demonstrate the ability of subsets of three fingers in six-finger arrays to bind independently to regions of the target site, possibly explaining the decrease in activity. These results have important implications for the design of new ZFNs, as they show that in some cases an excess of fingers may actually negatively affect the performance of engineered multifinger proteins. Maximal ZFN activity will require an optimization of both DNA binding affinity and specificity.
An unusual structural motif of antimicrobial peptides containing end-to-end macrocycle and cystine-knot disulfides (1999)

Four macrocyclic cystine-knot peptides of 29-31 residues, kalata, circulin A and B (CirA and CirB), and cyclopsychotride, have been isolated from coffee plants but have undetermined physiological functions. These macrocycles and 10 of their analogs prepared by chemical synthesis were tested against nine strains of microbes. Kalata and CirA were specific for the Gram-positive Staphylococcus aureus with a minimum inhibition concentration of approximately 0.2 microM. They were relatively ineffective against Gram-negative bacteria such as Escherichia coli and Pseudomonas aeruginosa. However, CirB and cyclopsychotride were active against both Gram-positive and Gram-negative bacteria. In particular, CirB showed potent activity against E. coli with a minimum inhibitory concentration of 0.41 microM. All four cyclic peptides were moderately active against two strains of fungi, Candida kefyr and Candida tropicalis, but were inactive against Candida albicans. These macrocycles are cytotoxic and lysed human red blood cell with a lethal dose 50% of 400 microM. Modifying the Arg residue in kalata with a keto aldehyde significantly reduced its activity against S. aureus whereas blocking the arg in CirA produced no significant effect. The two-disulfide variants and their scrambled disulfide isomers exhibited antimicrobial profiles and potency similar to their native peptides. However, in high-salt assays (100 mM NaCl), few of these macrocyclic peptides, natives or analogs, retained antimicrobial activity. These results show that the macrocyclic peptides possess specific and potent antimicrobial activity that is salt-dependent and that their initial interactions with the microbial surfaces may be electrostatic, an effect commonly found in defensin antimicrobial peptides. Furthermore, their end-to-end cyclic structure with a cystine-knot motif represents a molecular structure of antimicrobials and may provide a useful template for the design of novel peptide antibiotics.