gebhart/patrepeval huggingface dataset:
Local Synaptic Learning Rules Suffice to Maximize Mutual Information in a Linear Network (1992)

A network that develops to maximize the mutual information between its output and the signal portion of its input (which is admixed with noise) is useful for extracting salient input features, and may provide a model for aspects of biological neural network function. I describe a local synaptic Learning rule that performs stochastic gradient ascent in this information-theoretic quantity, for the case in which the input-output mapping is linear and the input signal and noise are multivariate gaussian. Feedforward connection strengths are modified by a Hebbian rule during a "learning" phase in which examples of input signal plus noise are presented to the network, and by an anti-Hebbian rule during an "unlearning" phase in which examples of noise alone are presented. Each recurrent lateral connection has two values of connection strength, one for each phase; these values are updated by an anti-Hebbian rule.
Overview of the Epidemiology of Immunodeficiency-Associated Cancers (1998)

Immunodeficiency, be it congenital, therapeutic, or infectious in origin, increases the risk of certain, but not all, types of cancer. A common feature of these cancers is that specific infectious agents appear to be important in their etiology, not only in immunodeficient subjects but also in the general population. People with acquired immunodeficiency syndrome (AIDS) are at an increased risk of Kaposi's sarcoma, non-Hodgkin's lymphoma, Hodgkin's disease, squamous cell carcinoma of the conjunctiva, and childhood leiomyosarcoma. It is striking that most of these cancers have been associated with specific human herpesvirus (HHV) infections: HHV-8 with Kaposi's sarcoma and the closely related Epstein-Barr virus with non-Hodgkin's lymphoma, Hodgkin's disease, and possibly also with childhood leiomyosarcoma. Moreover, similar associations between these viruses and cancer have been found, albeit inconsistently, in people who are not immunosuppressed. Further research is needed to establish whether the risk of other cancers is also increased in people with AIDS, although, if so, the cancers are likely to be rare or to have comparatively small associated relative risks. Existing evidence suggests that there may be no marked increase in the risk of two common cancers that are known to be caused by infectious agents--hepatocellular carcinoma and invasive carcinoma of the uterine cervix. The apparent lack of an increase in invasive cervical cancer is unexpected and needs further investigation, especially since the prevalence of cervical infection with human papillomaviruses and of low-grade preneoplastic changes in the cervical epithelium is increased in women with AIDS. With the prospect of improved survival in people with AIDS, the effect of immunosuppression on cancer is likely to become an increasingly important issue.
A Carbon-14 Tracer Study of the Alkaline Rearrangement of Chlorophenanthraquinones1,2 (1955)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA Carbon-14 Tracer Study of the Alkaline Rearrangement of Chlorophenanthraquinones1,2Donald G. Ott and Grant Gill SmithCite this: J. Am. Chem. Soc. 1955, 77, 8, 2325–2329Publication Date (Print):April 1, 1955Publication History Published online1 May 2002Published inissue 1 April 1955https://pubs.acs.org/doi/10.1021/ja01613a089https://doi.org/10.1021/ja01613a089research-articleACS PublicationsRequest reuse permissionsArticle Views90Altmetric-Citations13LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
All You Ever Wanted to Know about Dynamic Taint Analysis and Forward Symbolic Execution (but Might Have Been Afraid to Ask) (2010)

Dynamic taint analysis and forward symbolic execution are quickly becoming staple techniques in security analyses. Example applications of dynamic taint analysis and forward symbolic execution include malware analysis, input filter generation, test case generation, and vulnerability discovery. Despite the widespread usage of these two techniques, there has been little effort to formally define the algorithms and summarize the critical issues that arise when these techniques are used in typical security contexts. The contributions of this paper are two-fold. First, we precisely describe the algorithms for dynamic taint analysis and forward symbolic execution as extensions to the run-time semantics of a general language. Second, we highlight important implementation choices, common pitfalls, and considerations when using these techniques in a security context.
THE SYNERGISTIC ANTIOXIDANT EFFECT of ROSEMARY EXTRACT and ?-TOCOPHEROL IN SARDINE OIL MODEL SYSTEM and FROZEN-CRUSHED FISH MEAT (1992)

The treatment of α-tocopherol-rosemary mixture (0.05%+ 0.02%) had the strongest antioxidant activity among the antioxidants tested in sardine oil model system and frozen-crushed fish meat. In sardine oil, it delayed the onset of oxidation 5 days longer than either α-tocopherol or rosemary extract alone, and its antioxidant activity was comparable to that of BHA. It was found that the α-tocopherol in sample of mixture treatment remained 5 days longer than in sample of α-tocopherol. In frozen-crushed bonito meat, the thiobarbituric acid value (TBA) in sample of mixture treatment was the lowest among antioxidant treatments. the analysis of the ratio of EPA + DHA/16:0 during the storage also showed that the ratio in sample of mixture treatment was about 10% higher than that in sample of α-tocopherol. This suggested that oxidation of polyunsaturated fatty acid was inhibited. the treatment of α-tocopherol-rosemary mixture also caused less triglyceride hydrolysis than either a-tocopherol or rosemary extract alone. A synergistic effect between α-tocopherol and rosemary extract was observed.
Development of a Fluorescent Chemosensor for the Detection of Kynurenine (2012)

Kynurenine, a metabolite of tryptophan, is known to contribute to cancer progression when overproduced. A method for facile fluorescent sensing of kynurenine using sensor 1 has been developed. When bound at low pH, sensor 1 undergoes a very large bathochromic shift because kynurenine extends the conjugation of the fluorophore. This unusual mechanism of activation provides a 390-fold fluorescence enhancement that is very specific to kynurenine and a wavelength of fluorescence that extends into the red.
Molecular Mechanism of Scanning and Start Codon Selection in Eukaryotes (2011)

The correct translation of mRNA depends critically on the ability to initiate at the right AUG codon. For most mRNAs in eukaryotic cells, this is accomplished by the scanning mechanism, wherein the small (40S) ribosomal subunit attaches to the 5' end of the mRNA and then inspects the leader base by base for an AUG in a suitable context, using complementarity with the anticodon of methionyl initiator tRNA (Met-tRNAiMet) as the key means of identifying AUG. Over the past decade, a combination of yeast genetics, biochemical analysis in reconstituted systems, and structural biology has enabled great progress in deciphering the mechanism of ribosomal scanning. A robust molecular model now exists, describing the roles of initiation factors, notably eukaryotic initiation factor 1 (eIF1) and eIF1A, in stabilizing an "open" conformation of the 40S subunit with Met-tRNAiMet bound in a low-affinity state conducive to scanning and in triggering rearrangement into a "closed" conformation incompatible with scanning, which features Met-tRNAiMet more tightly bound to the "P" site and base paired with AUG. It has also emerged that multiple DEAD-box RNA helicases participate in producing a single-stranded "landing pad" for the 40S subunit and in removing the secondary structure to enable the mRNA to traverse the 40S mRNA-binding channel in the single-stranded form for base-by-base inspection in the P site.
Derivation of HLA types from shotgun sequence datasets (2012)

The human leukocyte antigen (HLA) is key to many aspects of human physiology and medicine. All current sequence-based HLA typing methodologies are targeted approaches requiring the amplification of specific HLA gene segments. Whole genome, exome and transcriptome shotgun sequencing can generate prodigious data but due to the complexity of HLA loci these data have not been immediately informative regarding HLA genotype. We describe HLAminer, a computational method for identifying HLA alleles directly from shotgun sequence datasets (http://www.bcgsc.ca/platform/bioinfo/software/hlaminer). This approach circumvents the additional time and cost of generating HLA-specific data and capitalizes on the increasing accessibility and affordability of massively parallel sequencing.
ULBP6/RAET1L is an additional human NKG2D ligand (2009)

To date five ULBP/RAET (UL16-binding protein, also known as retinoic acid early transcript) genes, encoded on human chromosome 6q24.2-q25.3, have been shown to encode ligands of the activating immunoreceptor NKG2D. Here, we show that a sixth gene, ULBP6/RAET1L, is a polymorphic locus that expresses a functional transcript. ULBP6 had a more restricted expression profile in cell lines and primary human tissues than other NKG2D ligands, but expression was detected in several human papillomavirus-positive cervical carcinoma cell lines and was inducible on infection with human CMV. ULBP6 bound to recombinant NKG2D as well as the human CMV immune evasion molecule UL16. By confocal microscopy we show that UL16 retains ULBP6 inside the cell, preventing it from reaching the cell surface. Expression of ULBP6 on target cells induced a significant increase in NK-cell killing. Comparison of ULBP6 with ULBP4 and ULBP5 indicated that differences in recombinant NKG2D binding correlated with differences in NK-cell activation.
Gene Expression Profile of Adult Human Olfactory Bulb and Embryonic Neural Stem Cell Suggests Distinct Signaling Pathways and Epigenetic Control (2012)

Global gene expression profiling was performed using RNA from human embryonic neural stem cells (hENSC), and adult human olfactory bulb-derived neural stem cells (OBNSCs), to define a gene expression pattern and signaling pathways that are specific for each cell lineage. We have demonstrated large differences in the gene expression profile of human embryonic NSC, and adult human OBNSCs, but less variability between parallel cultures. Transcripts of genes involved in neural tube development and patterning (ALDH1A2, FOXA2), progenitor marker genes (LMX1a, ALDH1A1, SOX10), proliferation of neural progenitors (WNT1 and WNT3a), neuroplastin (NPTN), POU3F1 (OCT6), neuroligin (NLGN4X), MEIS2, and NPAS1 were up-regulated in both cell populations. By Gene Ontology, 325 out of 3875 investigated gene sets were scientifically different. 41 out of the 307 investigated Cellular Component (CC) categories, 45 out of the 620 investigated Molecular Function (MF) categories, and 239 out of the 2948 investigated Biological Process (BP) categories were significant. KEGG Pathway Class Comparison had revealed that 75 out of 171 investigated gene sets passed the 0.005 significance threshold. Levels of gene expression were explored in three signaling pathways, Notch, Wnt, and mTOR that are known to be involved in NS cell fates determination. The transcriptional signature also deciphers the role of genes involved in epigenetic modifications. SWI/SNF DNA chromatin remodeling complex family, including SMARCC1 and SMARCE1, were found specifically up-regulated in our OBNSC but not in hENSC. Differences in gene expression profile of transcripts controlling epigenetic modifications, and signaling pathways might indicate differences in the therapeutic potential of our examined two cell populations in relation to in cell survival, proliferation, migration, and differentiation following engraftments in different CNS insults.
Nanofabrication of a two-dimensional array using laser-focused atomic deposition (1995)

Fabrication of a two-dimensional array of nanometer-scale chromium features on a silicon substrate by laser-focused atomic deposition is described. Features 13±1 nm high and having a full-width at half maximum of 80±10 nm are fabricated in a square array with lattice constant 212.78 nm, determined by the laser wavelength. The array covers an area of approximately 100 μm×200 μm. Issues associated with laser-focusing of atoms in a two-dimensional standing wave are discussed, and potential applications and improvements of the process are mentioned.
Orienteering design through data: The data-driven design model (2018)

Until recently, the processes and methods used by designers have been rather traditional. As times have changed, so too have the tools used by designers to bring their inspirations into reality and develop their concepts. Now, the majority of results of the design process can be attributed to intelligent products or services. We are rapidly advancing towards an era of Industry 4.0, which is radically transforming the creative process. Data can now be part of the creative process in new and innovative ways. Many businesses in a wide range of fields are already using data to provide personalised experiences to millions of people through their products. The ever- growing influence of data management has not yet been fully appreciated in the field of design. Information derived from data allows the designer to understand context, learn and evolve with the consumer and create unique experiences. In this research paper, a new way of working is defined and new models to follow are developed.
Rishi: identify bot contaminated hosts by IRC nickname evaluation (2007)

In this paper, we describe a simple, yet effective method to detect bot-infected machines within a given network that relies on detection of the communication channel between bot and Command &amp;amp; Control server (C&amp;amp;C server). The presented techniques are mainly based on passively monitoring network traffic for unusual or suspicious IRC nicknames, IRC servers, and uncommon server ports. By using n-gram analysis and a scoring system, we are able to detect bots that use uncommon communication channels, which are commonly not detected by classical intrusion detection systems. Upon detection, it is possible to determine the IP address of the C&amp;amp;C server, as well as, the channels a bot joined and the additional parameters which were set. The software Rishi implements the mentioned features and is able to automatically generate warning emails to report infected machines to an administrator. Within the 10 GBit network of RWTH Aachen university, we detected 82 botinfected machines within two weeks, some of them using communication channels not picked up by other intrusion detection systems. 1
Calibrated real-time control of lesion size based on reflectance images (1993)

Lesion size induced by laser photocoagulation is controlled in real time based on a two-dimensional reflectance image recorded by a CCD array during lesion formation. A feedback system using components of the reflectance image achieves uniform lesions by compensating for light absorption variability in biological media. Lesions are formed in a phantom by an argon laser to simulate retinal photocoagulation. The tissue model consists of a thin absorptive layer covered by a clear albumin protein layer. Results show a low variance in the sizes of the lesions (diameter or depth) produced in different irradiation conditions and the ability to produce lesions of a predefined size in varying illumination conditions.
Physics and Applications of Microfluidics in Biology (2002)

Fluid flow at the microscale exhibits unique phenomena that can be leveraged to fabricate devices and components capable of performing functions useful for biological studies. The physics of importance to microfluidics are reviewed. Common methods of fabricating microfluidic devices and systems are described. Components, including valves, mixers, and pumps, capable of controlling fluid flow by utilizing the physics of the microscale are presented. Techniques for sensing flow characteristics are described and examples of devices and systems that perform bioanalysis are presented. The focus of this review is microscale phenomena and the use of the physics of the scale to create devices and systems that provide functionality useful to the life sciences.
Genomics via optical mapping. III: Contiging genomic DNA. (1999)

In this paper, we describe our algorithmic approach to constructing an alignment of (contiging) a set of restriction maps created from the images of individual genomic (uncloned) DNA molecules digested by restriction enzymes. Generally, these DNA segments are sized in the range of 1-4 Mb. The goal is to devise contiging algorithms capable of producing high-quality composite maps rapidly and in a scaleable manner. The resulting software is a key component of our physical mapping automation tools and has been used to create complete maps of various microorganisms (E. coli, P. falciparum and D. radiodurans). Experimental results match known sequence data.
Immunoelectron microscopic findings in cicatricial pemphigoid: their significance in relation to epidermolysis bullosa acquisita (1982)

Immunoelectron microscopic studies in a patient with cicatricial pemphigoid revealed the deposition of IgG above the basal lamina. This location is distinctive for pemphigoid and differs from that found in epidermolysis bullosa acquisita.
Incomplete Elongation of the Chondroitin Sulfate Linkage Region on Aggrecan and Response to Interleukin-1β (2012)

Aggrecan is the prominent proteoglycan in cartilage and is modified with approximately 100 chondroitin sulfate (CS) chains through a tetrasaccharide linkage structure. In osteoarthritis (OA), the viscoelastic properties of cartilage are compromised on both the quantity and integrity of aggrecan core protein expressed as well as reduced overall CS chain length. Herein, we postulated that chronic low-level inflammation may also contribute to OA progression by promoting regulatory mechanisms in early CS biosynthesis that yield incomplete linkage structures on aggrecan. To test this idea, chondrocytes extracted from human tali were cultured in alginate beads and challenged with 5 ng/mL IL-1β as a model for chronic inflammation leading to OA progression. Novel mass spectrometry-based methods were devised to detect and quantify partially elongated linkage structures relative to control cultures. The total mole fraction of unelongated xylose residues per aggrecan was significantly less (p = 0.03) after IL-1β treatment compared to control cultures, with unelongated xylose residues constituting between 6% and 12% of the fraction of total CS measured. A portion (<1%) of the partially elongated linkage structures was found to be either phosphorylated or sulfated. These results establish quantitative mass spectrometry as a very sensitive and effective platform for evaluating truncated proteoglycan linkage structures. Our observations using this method suggest a possible role for aberrant linkage structure elongation in OA progression.
Endothelial focal adhesion kinase mediates cancer cell homing to discrete regions of the lungs via E-selectin up-regulation (2011)

Primary tumors secrete factors that alter the microenvironment of distant organs, rendering those organs as fertile soil for subsequent metastatic cancer cell colonization. Although the lungs are exposed to these factors ubiquitously, lung metastases usually develop as a series of discrete lesions. The underlining molecular mechanisms of the formation of these discrete lesions are not understood. Here we show that primary tumors induce formation of discrete foci of vascular hyperpermeability in premetastatic lungs. This is mediated by endothelial cell-focal adhesion kinase (FAK), which up-regulates E-selectin, leading to preferential homing of metastatic cancer cells to these foci. Suppression of endothelial-FAK or E-selectin activity attenuates the number of cancer cells homing to these foci. Thus, localized activation of endothelial FAK and E-selectin in the lung vasculature mediates the initial homing of metastatic cancer cells to specific foci in the lungs.
High speed search and memory efficient Huffman coding HDTV (2002)

Code compression is a key element in high speed digital data transport. A major compression is performed by converting the fixed-length codes to variable-length codes through a (semi-)entropy coding scheme. Huffman coding combined with run-length coding is shown to be a very efficient coding scheme. To speed up the process of search for a symbol in a Huffman tree and to reduce the memory size, a tree clustering algorithm is proposed to avoid high sparsity of the tree. The method is shown to be very efficient in memory size, and fast in searching for the symbol. For an experimental video data with Huffman codes extended up to 13 bits in length, the entire memory space is shown to be 126 words, compared to normal 2/sup 13/ = 8192 words.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Mammalian Cells in Culture Frequently Release Type C Viruses (1973)

Cell cultures commonly used in animal cell research, both cell strains and continuous cell lines from various mammalian species, spontaneously produce type C RNA viruses.
Crystal structure refinement withSHELXL (2014)

The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as `a CIF') containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.