gebhart/patrepeval huggingface dataset:
Selective intracellular retention of virally induced NKG2D ligands by the human cytomegalovirus UL16 glycoprotein (2002)

Human cytomegalovirus (HCMV) has evolved a multitude of molecular mechanisms to evade the antiviral immune defense of the host. Recently, using soluble recombinant molecules, the HCMV UL16 glycoprotein was shown to interact with some ligands of the activating immunoreceptor NKG2D and, therefore, may also function as a viral immunomodulator. However, the role of UL16 during the course of HCMV infection remained unclear. Here, we demonstrate that HCMV infection of fibroblasts induces expression of all known NKG2D ligands (NKG2DL). However, solely MICA and ULBP3 reach the cellular surface to engage NKG2D, whereas MICB, ULBP1 and ULBP2 are selectively retained in the endoplasmic reticulum by UL16. UL16-mediated reduction of NKG2DL cell surface density diminished NK cytotoxicity. Thus, UL16 functions by capturing activating ligands for cytotoxic lymphocytes that are synthesized in response to HCMV infection.
DNA sequencing on a chip (1997)

Today, interest in developing new technologies that can analyze DNA sequences quickly and cheaply is intense. The authors are pursuing an approach based on a combination of molecular biology with semiconductor manufacturing technology that takes advantage of the miniaturization and parallel processing inherent in modern semiconductor technologies. In this article, the authors review the basics of semi-conductor photolithography and DNA sequencing technology, describe how these can be combined to create tools for rapidly accessing genetic information on a large scale, and recount their recent work in this field.
Preparing DNA Libraries for Multiplexed Paired‐End Deep Sequencing for Illumina GA Sequencers (2011)

Whole-genome sequencing, also known as deep sequencing, is becoming a more affordable and efficient way to identify SNP mutations, deletions, and insertions in DNA sequences across several different strains. Two major obstacles preventing the widespread use of deep sequencers are the costs involved in services used to prepare DNA libraries for sequencing and the overall accuracy of the sequencing data. This unit describes the preparation of DNA libraries for multiplexed paired-end sequencing using the Illumina GA series sequencer. Self-preparation of DNA libraries can help reduce overall expenses, especially if optimization is required for the different samples, and use of the Illumina GA Sequencer can improve the quality of the data.
The Effect of Hypoxia/Reoxygenation on the Cellular Function of Intestinal Epithelial Cells (1999)

These results indicate that hypoxia/reoxygenation can directly impair cellular function as manifested by increased monolayer permeability to phenol red, increased E. coli bacterial translocation, and a decrease in TEER values.
A class of prefetch schemes for on-chip data caches (1992)

We introduce and evaluate a class of prefetch schemes for on-chip data caches in high-performance RISC processors. These schemes are conservative, initiating a prefetch only when a sequential pattern of references have been observed. Performance results based on traces of five programs in the SPEC suite on an IBM RS/6000 show that these schemes result in a significant reduction in miss ratio without the large increase in memory traffic associated with earlier schemes.
Squid Oil and Fat Production from Squid Wastes Using Subcritical Water Hydrolysis:  Free Fatty Acids and Transesterification (2006)

Application of subcritical water (sub-CW) treatment on the yield of oil and fat produced from squid waste entrails was studied experimentally in the temperature range of 443−653 K with a reaction time of 1−40 min. This process showed that the oil and the fat phases contain nine free fatty acids which were produced during hydrolysis of the triglyceride molecules and showed a maximum total yield at 513 K and 40 min (0.44 kg/kg oil). The order of the yields for the nine fatty acids, including omega-3 polyunsaturated fatty acids, eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA), was found to be DHA > palmitic > oleic > EPA > others. On the other hand, transesterification of the oil and the fat phases in the presence of trimethylsulfonium hydroxide (TMSH) which converted the free fatty acids to the corresponding fatty acid methyl esters (FAMEs) was studied. The total yield of FAMEs in the oil and the fat phases illustrated a peak at 473 and 493 K, respectively.
Inhibition of human tumor growth in nude mice by a conjugate of doxorubicin with monoclonal antibodies to epidermal growth factor receptor. (1989)

Monoclonal antibodies that recognize the extracellular domain of the epidermal growth factor receptor (mAb108) were conjugated with doxorubicin through a dextran bridge. Several antibody-drug conjugates, containing different amounts of doxorubicin, retained binding capacity to human epidermoid carcinoma (KB) cells overexpressing epidermal growth factor receptors. Slight decrease in drug cytotoxicity was seen in in vitro tests, as determined either by inhibition of thymidine incorporation into cells or by reduction in number and size of KB-cell colonies. Yet, when tested in vivo against KB tumor xenografted into nude mice, the anti-epidermal growth factor-receptor drug conjugates with high drug-substitution levels were significantly more effective than free doxorubicin, antibody alone, mixture of dextran-doxorubicin and antibody, or drug conjugated with irrelevant antibody. When the labile covalent bonds linking antibody to dextran bridge were stabilized by reduction, the therapeutic efficacy of the conjugate was markedly decreased. These results show that antibodies against the extracellular domain of the epidermal growth factor can deliver doxorubicin specifically and efficiently to tumor sites that express high receptor levels exerting a specific antitumor effect.
NH2-Terminal Sequences of Mammalian Plasminogens and Plasmin S-Carboxymethyl Heavy (A) and Light (B) Chain Derivatives (1973)

The NH?-terminal E-residue sequences of human and rabbit plasminogens were determined to be Glu-Pro-Leu-Asp-Asp-Tyr-Val-Asn-X-Gln-Gly-Ala-.The cat plasminogen 12-residue sequence differed only in the 1st residue, in which aspartic acid replaced glutamic acid.The bovine plasminogen NH?-terminal 7-residue sequence was determined to be Asp -Leu -Leu -Asp -Asp -Tyr -Val-.The NH2-terminal residue of dog plasminogen is blocked since the protein could not be sequenced.The NHZ-terminal 5-residue sequences of the isolated Scarboxymethyl heavy (A) chain derivatives of cat, dog, rabbit, and bovine plasmins (urokinase-activated)were determined and found to be homologous with each other and with the human S-carboxymethyl heavy (A) chain S-residue sequence.These NH2-terminal sequences were different from those found in the five mammalian zymogens studied, indicating a specific cleavage at the NHz-terminal end of each zymogen during activation at apparently the same position in the peptide chain.These sequences are also homologous with the human Lys-plasminogen NH&erminal sequence.The NH,-terminal Zl-residue sequences of the isolated Scarboxymethyl light (B) chain derivatives of cat, dog, rabbit, and bovine plasmins (urokinase-activated) were determined and found to be homologous with each other and with a previously reported human S-carboxymethyl light (B) chain ZOresidue sequence (ROBBINS,
[Increased expression of Abi1 in hepatocellular carcinoma and its correlation with poor prognosis of hepatocellular carcinoma]. (2009)

Expression level of Abi1 is up-regulated in HCC tissues compared with corresponding para carcinomatous liver tissue and the expression level of Abi1 is significantly correlated with the number of tumor, capsular formation, venous invasion, Edmondson-Steiner grade and prognosis of HCC.
Cancer Exosomes Express CD39 and CD73, Which Suppress T Cells through Adenosine Production (2011)

Extracellular adenosine is elevated in cancer tissue, and it negatively regulates local immune responses. Adenosine production from extracellular ATP has attracted attention as a mechanism of regulatory T cell-mediated immune regulation. In this study, we examined whether small vesicles secreted by cancer cells, called exosomes, contribute to extracellular adenosine production and hence modulate immune effector cells indirectly. We found exosomes from diverse cancer cell types exhibit potent ATP- and 5'AMP-phosphohydrolytic activity, partly attributed to exosomally expressed CD39 and CD73, respectively. Comparable levels of activity were seen with exosomes from pleural effusions of mesothelioma patients. In such fluids, exosomes accounted for 20% of the total ATP-hydrolytic activity. Exosomes can perform both hydrolytic steps sequentially to form adenosine from ATP. This exosome-generated adenosine can trigger a cAMP response in adenosine A(2A) receptor-positive but not A(2A) receptor-negative cells. Similarly, significantly elevated cAMP was also triggered in Jurkat cells by adding exosomes with ATP but not by adding exosomes or ATP alone. A proportion of healthy donor T cells constitutively express CD39 and/or CD73. Activation of T cells by CD3/CD28 cross-linking could be inhibited by exogenously added 5'AMP in a CD73-dependent manner. However, 5'AMP converted to adenosine by exosomes inhibits T cell activation independently of T cell CD73 expression. This T cell inhibition was mediated through the adenosine A(2A) receptor. In summary, the data highlight exosome enzymic activity in the production of extracellular adenosine, and this may play a contributory role in negative modulation of T cells in the tumor environment.
Biodistribution, metabolism, and excretion of radioiodinated phospholipid ether analogs in tumor-bearing rats. (1993)

The phospholipid ether analog, [125I]-1-O-[12-(m-iodophenyl)dodecyl]propanediol-3-phosphocholine (NM-295) was synthesized and evaluated for its ability to visualize tumors. Preliminary studies were performed in rats bearing the Walker 256 carcinosarcoma. Most of the radioactivity was cleared from the animals during the first 24 hours. However, the tumor showed a decreased rate of clearance of radioactivity when compared with non-target tissue. This difference in the clearance rate allowed for excellent images of the tumor at 24 hours. Scintigraphic images compared favorably with other radioiodinated phospholipid ether analogs such as [125I-rac-1-O-[12-(m-iodophenyl)dodecyl]-2-O-methylglycero-3- phosphocholine (NM-294) and [125I]-12-(m-iodophenyl)dodecyl phosphocholine (NM-324). In contrast with the latter two compounds, however, tissue distribution studies revealed that NM-295 cleared at a much faster rate from all tissues, including tumor. In addition, within 24 hours following administration of NM-295, over 70% of the radioactivity was excreted as compared to 50% and 20% for NM-294 and NM-324, respectively. The majority of excreted radioactivity appeared in the urine for all three compounds. Thin-layer chromatography of urine and fecal extracts showed the presence of metabolites only. In contrast, lipid extracts of either liver or tumor demonstrated only the presence of the parent compound. Therefore, these data suggest that in each case it was the parent phospholipid analog that was taken up and retained by the tissues, while the metabolic product(s) was cleared and excreted from the animal.
An adaptive fuzzy control traffic shaping scheme over wireless networks (2007)

In this paper, we propose an adaptive fuzzy control traffic shaping scheme based on leaky bucket in order to solve the traffic congestion problem over wireless networks. It is found that backpressure algorithm is suitable for low traffic and, it prevents buffer overflows. When buffer exceeds the upper threshold, the source receives a backpressure signal and, it pauses sending frames until it receives a signal from the same server. In backoff time using leaky bucket over traffic shaping mechanism, it is suitable for high traffic, Backoff time computations are widely used in order to avoid the impact on the network performance whenever the increment of the offered load arises. The fluctuation of offered load will cause the congestion at waiting room. We propose a fuzzy control backpressure and backoff time in traffic shaping that aims at detecting violations in parameter negotiation. We evaluate and compare the performance of fuzzy backpressure and backoff time in traffic shaping schemes. The studied approaches are fuzzy backpressure and exponential backoff time (FBE), backpressure in leaky bucket (BP), and exponential backoff time (EB). The performance of fuzzy control backpressure and backoff time has been investigated through fluctuations in telecommunication traffic streams (burst/silent type). Simulation results show that on wireless frames, the fuzzy logic control scheme helps to improve the performance in traffic shaping schemes much better than conventional backpressure algorithm and exponential backoff time. This has been verified by testing various types of burst/silence traffic.
Frequency selection demosaicking: a review and a look ahead (2008)

In this paper, we restate the model of spatio-chromatic sampling in single-chip digital cameras covered by Color Filter Array (CFA)<sup>1</sup>. The model shows that a periodic arrangement of chromatic samples in the CFA gives luminance and chromatic information that is localized in the Fourier domain. This representation allows defining a space invariant uniform demosaicking method which is based on the frequency selection of the luminance and chrominance information. We then show two extended methods which used the frequency representation of the Bayer CFA<sup>2,3</sup> to derive adaptive demosaicking. Finally, we will show the application of the model for CFA with random arrangement of chromatic samples, either using a linear method based on Wiener estimation<sup>4</sup> or with an adaptive method<sup>5</sup>.
New Wars, Old Laws: Part 2 (2013)

Amsterdam Law Forum (ALF) is the student-run 'International Law Journal' of VU University. Every year ALF publishes a winter, spring, and summer issue. The journal consists of three sections; scientific articles, opinion articles, and commentaries. As of this year, ALF also creates a section for inaugural speeches. In addition, ALF hosts a conference in spring with a relevant legal theme, where renowned speakers are invited to share their perspectives. Overall, ALF is a topical journal that provides a platform for established scholars and young academics to share knowledge, opinions and experiences and to make contributions to the international law discourse. Staff, PhD students and master students who have written a very good thesis are invited to submit an article to ALF. What is learned in the cradle is carried to the tomb: we are looking forward to sharing your articles on our website!
Fixing cystic fibrosis CFTR with correctors and potentiators. Off to a good start (2011)

Since the cloning of the cystic fibrosis transmembrane regulator (CFTR) protein in the late 1980s and subsequent significant advances in understanding the pathophysiology of cystic fibrosis (CF) there have been high expectations that transformative, disease-modifying therapies could be developed.1 2 Dysfunction of the CFTR protein results in significant reduction or absence of chloride transport and dysregulation of sodium transport.3–5 Other cationic ions such as bicarbonate may also be transported by CFTR and the interaction with the epithelial sodium channel ENaC still remains to be elucidated.6 7 However, a significant number of in vitro and animal studies strongly support the premise that correction of CFTR function is possible and will make a significant impact on the CF phenotype, particularly in the lung, which accounts for most of the morbidity and mortality from this condition.7 Two approaches to correction of CFTR function are currently being pursued: one based on gene transfer therapy and the other on small molecule modulators.

Gene therapy attempts to correct CFTR dysfunction in CF by transfection of airway cells with the wild-type CFTR gene to enable cells to express functional CFTR.8 Progress with this approach has been slow and methodical. Early studies suggest that it is possible to transfect nasal and bronchial epithelial cells and this results in a modest electrophysiological improvement.9 10 To date, there are no clinical studies in humans to determine if sufficient gene transfer can be achieved to result in a clinically meaningful benefit. A two-centre, double-blind, placebo-controlled trial of CF gene therapy is due to commence in the UK in 2012 using a specifically designed plasmid and a GL67 liposome complex. The results of this proof of concept study will help determine if gene therapy has the potential to provide a treatment which will benefit all mutation …
Perstimulatory Suprathreshold Auditory Adaptation (1976)

The decrease in loudness level of a pure tone was used as a criterion of suprathreshold auditory adaptation. The measuring technique is based on continuous binaural balancing of a steady adapting tone with an interrupted comparison tone of equal frequency, the pulse and pulse intervals being of 200 msec duration. This comparison tone eliminates the source of error caused by adaptation in the control ear, as was common in earlier test methods. Three adaptation types were found in normally hearing adult persons, for which values at 20–80 dB SL for frequencies between 250 and 6000 Hz are given. In children the test generally failed to reveal adaptation. In conductive deafness, adaptation was equal to that found in normal adult group. Very pronounced values were found in retrocochlear deafness. In primary hair cell lesions adaptation was slighter than in normal-hearing ears.
TRIM5 and the Regulation of HIV-1 Infectivity (2012)

The past ten years have seen an explosion of information concerning host restriction factors that inhibit the replication of HIV-1 and other retroviruses. Among these factors is TRIM5, an innate immune signaling molecule that recognizes the capsid lattice as soon as the retrovirion core is released into the cytoplasm of otherwise susceptible target cells. Recognition of the capsid lattice has several consequences that include multimerization of TRIM5 into a complementary lattice, premature uncoating of the virion core, and activation of TRIM5 E3 ubiquitin ligase activity. Unattached, K63-linked ubiquitin chains are generated that activate the TAK1 kinase complex and downstream inflammatory mediators. Polymorphisms in the capsid recognition domain of TRIM5 explain the observed species-specific differences among orthologues and the relatively weak anti-HIV-1 activity of human TRIM5. Better understanding of the complex interaction between TRIM5 and the retrovirus capsid lattice may someday lead to exploitation of this interaction for the development of potent HIV-1 inhibitors.
Integrated Analysis of Multiple Gene Expression Profiling Datasets Revealed Novel Gene Signatures and Molecular Markers in Nasopharyngeal Carcinoma (2012)

Further studies of the CSD genes as gene signatures and molecular markers of NPC might improve the understanding of the disease and identify new therapeutic targets.
Molecular structure and enzymatic function of lycopene cyclase from the cyanobacterium Synechococcus sp strain PCC7942. (1994)

A gene encoding the enzyme lycopene cyclase in the cyanobacterium Synechococcus sp strain PCC7942 was mapped by genetic complementation, cloned, and sequenced. This gene, which we have named crtL, was expressed in strains of Escherichia coli that were genetically engineered to accumulate the carotenoid precursors lycopene, neurosporene, and zeta-carotene. The crtL gene product converts the acyclic hydrocarbon lycopene into the bicyclic beta-carotene, an essential component of the photosynthetic apparatus in oxygen-evolving organisms and a source of vitamin A in human and animal nutrition. The enzyme also converts neurosporene to the monocyclic beta-zeacarotene but does not cyclize zeta-carotene, indicating that desaturation of the 7-8 or 7'-8' carbon-carbon bond is required for cyclization. The bleaching herbicide 2-(4-methylphenoxy)triethylamine hydrochloride (MPTA) effectively inhibits both cyclization reactions. A mutation that confers resistance to MPTA in Synechococcus sp PCC7942 was identified as a point mutation in the promoter region of crtL. The deduced amino acid sequence of lycopene cyclase specifies a polypeptide of 411 amino acids with a molecular weight of 46,125 and a pI of 6.0. An amino acid sequence motif indicative of FAD utilization is located at the N terminus of the polypeptide. DNA gel blot hybridization analysis indicated a single copy of crtL in Synechococcus sp PCC7942. Other than the FAD binding motif, the predicted amino acid sequence of the cyanobacterial lycopene cyclase bears little resemblance to the two known lycopene cyclase enzymes from nonphotosynthetic bacteria. Preliminary results from DNA gel blot hybridization experiments suggest that, like two earlier genes in the pathway, the Synechococcus gene encoding lycopene cyclase is homologous to plant and algal genes encoding this enzyme.
The Biomolecular Interaction Network Database and related tools 2005 update (2004)

The Biomolecular Interaction Network Database (BIND) (http://bind.ca) archives biomolecular interaction, reaction, complex and pathway information. Our aim is to curate the details about molecular interactions that arise from published experimental research and to provide this information, as well as tools to enable data analysis, freely to researchers worldwide. BIND data are curated into a comprehensive machine-readable archive of computable information and provides users with methods to discover interactions and molecular mechanisms. BIND has worked to develop new methods for visualization that amplify the underlying annotation of genes and proteins to facilitate the study of molecular interaction networks. BIND has maintained an open database policy since its inception in 1999. Data growth has proceeded at a tremendous rate, approaching over 100 000 records. New services provided include a new BIND Query and Submission interface, a Standard Object Access Protocol service and the Small Molecule Interaction Database (http://smid.blueprint.org) that allows users to determine probable small molecule binding sites of new sequences and examine conserved binding residues.
Epi-third and second harmonic generation microscopic imaging of abnormal enamel (2008)

Enamel covers the tooth crown and is responsible for protecting the inner tissues of the teeth. It is thus clinically important to diagnose the anomalies in tooth enamel structures in the early stage for prevention and treatment. In this article, we report the epi-harmonic-generation-microscopic study of various abnormal enamel from the nature surface of human teeth. With a 1230 nm light source and with an epi-collection scheme, an imaging depth greater than 300 microm can be achieved. The contrast sources of THG and SHG in the abnormal enamel have been identified and verified by comparing the images from the sound enamel with those from white spot lesions, cracks, and the irradiated enamel. Besides the previously reported interprismatic space, THG is found to be contributed from cracks or the material inhomogeneities inside the enamel prisms; while SHG is attributed to the strain-induced breakage of the 6/m point group symmetry. Combined with the high 3D spatial resolution and no energy release during imaging, our study shows that the infrared-laser-based epi-harmonic generation microscopy can provide different contrasts to differentiate the abnormal enamel from sound enamel and could provide a valuable tool for in vivo monitoring of both morphological changes and strain status of hydroxyapatite crystals in the enamel without sectioning and staining.