gebhart/patrepeval huggingface dataset:
Behind the Fos and Jun leucine zipper. (1989)

The production of the nuclear oncoproteins Fos and Jun is rapidly induced in response to extracellular signals. In the nucleus, the two proteins combine to form a tight complex via leucine zipper domains. The resulting Fos-Jun heterodimer can bind to the TPA-responsive element (TRE) by way of a novel, highly basic motif and can activate the transcription of TPA-responsive genes. The existence of several Fos- and Jun-related proteins with dimerization and DNA binding properties similar to Fos and Jun suggests that these two oncoproteins may be part of a network of related but functionally distinct transcription factors.
Antibody isotypes mediating antigen retention in passively immunized mice. (1980)

Antibody isotypes vary in their capacity to mediate retention of a readily catabolized protein antigen, human serum albumin (HSA) in spleen, popliteal lymph node (PLN) and hind foot. Hyperimmune anti-HSA mouse sera were separated into fractions highly enriched for IgM, IgG1 and IgG2 via differential elution from protein A-Sepharose. These fractions were used to immunize normal mice passively. Twenty-four hours later the mice were injected with radio-iodinated HSA into the hind footpad. When the amount of HSA retained in the spleen 6 days later was determined, the potency of various antibody fractions to mediate retention could be ranked IgG2=IgG1 > IgM. The amount of HSA retention mediated by various fractions correlated well with autoradiographic evidence demonstrating localization of HSA in splenic follicles. The localization pattern in PLN was similar to the spleen except that the IgM-containing fraction mediated follicular localization of HSA to a considerable degree. In tendons of the hind foot, IgG1 mediated HSA retention five times better than IgG2 or IgM fractions. The amount of radioactivity found in the liver varied inversely with HSA retention in other locations. The results demonstrate differences in antibody isotype requirements for antigen localization in spleen, regional lymph node and collagenous sites of the hind foot.
Prolonged maintenance of 2,3-DPG in liquid blood storage: use of an internal CO2 trap to stabilize pH. (1977)

A close relationship exists between the decrease in concentration of 2,3-diphosphoglycerate (2,3-DPG) and a fall in the pH of stored blood. Buffering the stored red cells with bicarbonate is one solution to the problem of maintaining pH during storage. The effectiveness of this buffer depends upon loss from the stored blood of carbonic acid in the form of CO2. We describe a system in which the CO2 is trapped in a small internal package which contains calcium hydroxide, or calcium hydroxide embedded in Silastic. A medium containing bicarbonate, adenine, glucose, phosphate and mannitol (BAGPM) is added after initial packing of the erythrocytes. With this approach, it has been possible to maintain 2,3-DPG at 92 percent of original, and ATP was approximately 62 percent of initial levels at the end of 42 days of storage if an internal Silastic bag containing calcium was used in bags agitated once weekly. More frequent agitation (five times weekly) produced acceptable maintenance of both 2,3-DPG (78 percent of original) and ATP (44 percent of original) after 42 days of storage when a Silastic block impregnated with calcium hydroxide was utilized to absorb CO2.
A revised glossary of terms most commonly used by clinical electroencephalographers and updated proposal for the report format of the EEG findings. Revision 2017 (2017)

This glossary includes the terms most commonly used in clinical EEG. It is based on the previous proposals (Chatrian et al., 1974; Noachtar et al., 1999) and includes terms necessary to describe the EEG and to generate the EEG report. All EEG phenomena should be described as precisely as possible in terms of frequency, amplitude, phase relation, waveform, localization, quantity, and variability of these parameters (Brazier et al., 1961). The description should be independent of the recording parameters such as amplification, montages, and computer program/display.
Mitochondrial deafness alleles confer misreading of the genetic code (2008)

Despite the fact that important genetic diseases are caused by mutant mitochondrial ribosomes, the molecular mechanisms by which such ribosomes result in a clinical phenotype remain largely unknown. The absence of experimental models for mitochondrial diseases has also prevented the rational search for therapeutic interventions. Here, we report on the construction of bacterial hybrid ribosomes that contain various versions of the mitochondrial decoding region of ribosomal RNA. We show that the pathogenic mutations A1555G and C1494T decrease the accuracy of translation and render the ribosomal decoding site hypersusceptible to aminoglycoside antibiotics. This finding suggests misreading of the genetic code as an important molecular mechanism in disease pathogenesis.
Selective generation of single-walled carbon nanotubes with metallic, semiconducting and other unique electronic properties (2009)

As-synthesized single-walled carbon nanotubes (SWNTs) are mixtures of semiconducting and metallic species and separation of the two is of crucial importance for many applications. In this article, the methods employed for the enrichment of semiconducting and metallic SWNTs are presented, along with possible procedures to prepare either of the species selectively. Equally important are the methods for chirality selection. The discovery of metal-semiconductor transitions in SWNTs induced by interaction with electron donor and acceptor molecules is not only of academic interest, but may also find applications. Synthesis of Y-junction SWNTs with unique electronic properties at the junction is yet to be fully accomplished.
A one‐step conversion of N‐acylaminoketones into 5‐alkylidene‐3‐pyrrolin‐2‐ones (1983)

Abstract A simple and efficient one‐pot synthesis of 5‐alkylidene‐3‐pyrrolin‐2‐ones 3a,e‐g from N ‐acylaminoketones is described. A mechanism is proposed and it is substantiated by synthethising and converting the proposed intermediates into the pyrrolinones 3a,e‐g .
Diversifying search results (2009)

We study the problem of answering ambiguous web queries in a setting where there exists a taxonomy of information, and that both queries and documents may belong to more than one category according to this taxonomy. We present a systematic approach to diversifying results that aims to minimize the risk of dissatisfaction of the average user. We propose an algorithm that well approximates this objective in general, and is provably optimal for a natural special case. Furthermore, we generalize several classical IR metrics, including NDCG, MRR, and MAP, to explicitly account for the value of diversification. We demonstrate empirically that our algorithm scores higher in these generalized metrics compared to results produced by commercial search engines.
Large-scale IP traceback in high-speed internet: practical techniques and theoretical foundation (2004)

Tracing attack packets to their sources, known as IP traceback, is an important step to counter distributed denial-of-service (DDoS) attacks. In this paper, we propose a novel packet logging based (i.e., hash-based) traceback scheme that requires an order of magnitude smaller processing and storage cost than the hash-based scheme proposed by Snoeren, et al. (2001), thereby being able to scalable to much higher link speed (e.g., OC-768). The baseline idea of our approach is to sample and log a small percentage (e.g., 3.3%) of packets. The challenge of this low sampling rate is that much more sophisticated techniques need to be used for traceback. Our solution is to construct the attack tree using the correlation between the attack packets sampled by neighboring routers. The scheme using naive independent random sampling does not perform well due to the low correlation between the packets sampled by neighboring routers. We invent a sampling scheme that improves this correlation and the overall efficiency significantly. Another major contribution of this work is that we introduce a novel information-theoretic framework for our traceback scheme to answer important questions on system parameter tuning and the fundamental trade-off between the resource used for traceback and the traceback accuracy. Simulation results based on real-world network topologies (e.g. Skitter) match very well with results from the information-theoretic analysis. The simulation results also demonstrate that our traceback scheme can achieve high accuracy, and scale very well to a large number of attackers (e.g., 5000+).
Adhesion of Pt Nanoparticles Supported on γ-Al2O3 Single Crystal (2013)

A model catalyst system of Pt nanoparticles (2–5 nm) dispersed on γ-Al2O3 (111) was prepared to study the support effects on nanoparticles shape and structure by cross-sectional high-resolution electron microscopy. A dewetting equilibrium shape of Pt nanoparticles was observed with a low-index plane orientation relation: Pt(111)[211]∥γ-Al2O3(111)[211] and Pt(100)[011]∥γ-Al2O3(111)[211]. Lattice-matching epitaxy of Pt(110)∥γ-Al2O3(110) was found across their interface to maintain a minimum interface strain during particle growth. To quantitatively interpret the interfacial energy and adhesion energy of the nanoparticles, the Wulff–Kaischew theorem was applied by taking into account the γ-Al2O3 support modifications to the equilibrium shape of nanoparticles. The present approach quantitatively solved the adhesion energy of the particle/support and could help to interpret nanoparticles equilibrium shape and stability.
Designing amino acid sequences to fold with good hydrophobic cores (1995)

We present two methods for designing amino acid sequences of proteins that will fold to have good hydrophobic cores. Given the coordinates of the desired target protein or polymer structure, the methods generate sequences of hydrophobic (H) and polar (P) monomers that are intended to fold to these structures. One method designs hydrophobic inside, polar outside; the other minimizes an energy function in a sequence evolution process. The sequences generated by these methods agree at the level of 60-80% of the sequence positions in 20 proteins in the Protein Data Bank. A major challenge in protein design is to create sequences that can fold uniquely, i.e. to a single conformation rather than to many. While an earlier lattice-based sequence evolution method was shown not to design unique folders, our method generates unique folders in lattice model tests. These methods may also be useful in designing other types of foldable polymer not based on amino acids.
Programmable materials and the nature of the DNA bond (2015)

For over half a century, the biological roles of nucleic acids as catalytic enzymes, intracellular regulatory molecules, and the carriers of genetic information have been studied extensively. More recently, the sequence-specific binding properties of DNA have been exploited to direct the assembly of materials at the nanoscale. Integral to any methodology focused on assembling matter from smaller pieces is the idea that final structures have well-defined spacings, orientations, and stereo-relationships. This requirement can be met by using DNA-based constructs that present oriented nanoscale bonding elements from rigid core units. Here, we draw analogy between such building blocks and the familiar chemical concepts of "bonds" and "valency" and review two distinct but related strategies that have used this design principle in constructing new configurations of matter.
Heat shock proteins: new keys to the development of cytoprotective therapies (2001)

All cells, from bacterial to human, have a common, intricate response to stress that protects them from injury. Heat shock proteins (Hsps), also known as stress proteins and molecular chaperones, play a central role in protecting cellular homeostatic processes from environmental and physiologic insult by preserving the structure of normal proteins and repairing or removing damaged ones. An understanding of the interplay between Hsps and cell stress tolerance will provide new tools for treatment and drug design that maximise preservation or restoration of health. For example, the increased vulnerability of tissues to injury in some conditions, such as ageing, diabetes mellitus and menopause, or with the use of certain drugs,, such as some antihypertensive medications, is associated with an impaired Hsp response. Additionally, diseases that are associated with tissue oxidation, free radical formation, disorders of protein folding, or inflammation, may be improved therapeutically by elevated expression of Hsps. The accumulation of Hsps, whether induced physiologically, pharmacologically, genetically, or by direct administration of the proteins, is known to protect the organism from a great variety of pathological conditions, including myocardial infarction, stroke, sepsis, viral infection, trauma, neurodegenerative diseases, retinal damage, congestive heart failure, arthritis, sunburn, colitis, gastric ulcer, diabetic complications and transplanted organ failure. Conversely, lowering Hsps in cancer tissues can amplify the effectiveness of chemo- or radiotherapy. Treatments and agents that induce Hsps include hyperthermia, heavy metals (zinc and tin), salicylates, dexamethasone, cocaine, nicotine, alcohol, alpha-adrenergic agonists, PPAR-gamma agonists, bimoclomol, geldanamycin, geranylgeranylacetone and cyclopentenone prostanoids. Compounds that suppress Hsps include quercetin (a bioflavinoid), 15-deoxyspergualin (an immunosuppressive agent) and retinoic acid. Researchers who are cognisant of the Hsp-related effects of these and other agents will be able to use them to develop new therapeutic paradigms.
PHAGE T4 INTRONS: SELF-SPLICING AND MOBILITY (1990)

Orthologs and paralogs are two fundamentally different types of homologous genes that evolved, respectively, by vertical descent from a single ancestral gene and by duplication. Orthology and paralogy are key concepts of evolutionary genomics. A ...Read More
Some Aryl Substituted 2-(4-Nitrophenyl)-4-oxo-4-phenylbutanoates and 3-(4-Nitrophenyl)-1-phenyl-1,4-butanediols and Related Compounds as Inhibitors of Rat Liver Microsomal Retinoic Acid Metabolising Enzymes (2003)

Some aryl substituted methyl 2-(4-nitrophenyl)-4-oxo-4-phenylbutanoates generally had poor to moderate inhibitory potency (4-73%) towards rat liver microsomal retinoic acid metabolising enzymes compared with ketoconazole (80%). Conversion to the corresponding 3-(4-nitrophenyl)-1-aryl-1,4-butanediols considerably increased potency (29-78%). The 4-iodophenyl analogue, (30) and the 4-iodo- (45) and 4-methoxyphenyl (46) analogues, were the most potent in both series respectively. The corresponding 5-membered lactones, in the three instances examined, were also potent (52%, 67%, 69%) as were the cis- and trans-isomers of the 5-membered tetrahydrofuran (77%, 65% respectively). Beckmann rearrangement of the oxime methyl 4-(2,4-dichlorophenyl)-4-hydroxyimino-2-(4-nitrophenyl)butanoate (54) gave the expected products (55) and (56), which were potent inhibitors (75%, 74% respectively) of the enzyme whereas the oxime was an activator.
De novo balanced chromosome rearrangements and extra marker chromosomes identified at prenatal diagnosis: clinical significance and distribution of breakpoints. (1991)

A questionnaire sent to major cytogenetics laboratories in the United States and Canada over a 10-year period collected data on the frequency and outcome of cases with either apparently balanced de novo rearrangements or de novo supernumerary marker chromosomes detected at amniocentesis. Of 377,357 reported amniocenteses, approximately 1/2,000 had a de novo reciprocal translocation, 1/9,000 a Robertsonian translocation, 1/10,000 a de novo inversion, and 1/2,500 an extra structurally abnormal chromosome of unidentifiable origin. The risk of a serious congenital anomaly was estimated to be 6.1% (n = 163) for de novo reciprocal translocations, 3.7% (n = 51) for Robertsonian translocations, and 9.4% (n = 32) for inversions. The combined risk for reciprocal translocations and inversions was 6.7% (95% confidence limits 3.1%-10.3%). The risk of abnormality for extra nonsatellited marker chromosomes was 14.7% (n = 68), and that for satellited marker chromosomes was 10.9% (n = 55). In non-Robertsonian rearrangements, distribution of breakpoints among chromosomes was not as would be expected strictly on the basis of length. Most breaks were stated to occur within G-negative bands, but there was little evidence of particular hot spots among these bands. Nevertheless, there did appear to be a correlation between those bands in which breakage was observed most often and those bands where common or rare fragile sites have been described.
Plasma extracellular RNA profiles in healthy and cancer patients (2016)

Extracellular vesicles are selectively enriched in RNA that has potential as disease biomarkers. To systemically characterize circulating extracellular RNA (exRNA) profiles, we performed RNA sequencing analysis on plasma extracellular vesicles derived from 50 healthy individuals and 142 cancer patients. Of ~12.6 million raw reads for each individual, the number of mappable reads aligned to RNA references was ~5.4 million including miRNAs (~40.4%), piwiRNAs (~40.0%), pseudo-genes (~3.7%), lncRNAs (~2.4%), tRNAs (~2.1%), and mRNAs (~2.1%). By expression stability testing, we identified a set of miRNAs showing relatively consistent expression, which may serve as reference control for exRNA quantification. By performing multivariate analysis of covariance, we identified significant associations of these exRNAs with age, sex and different types of cancers. In particular, down-regulation of miR-125a-5p and miR-1343-3p showed an association with all cancer types tested (false discovery rate <0.05). We developed multivariate statistical models to predict cancer status with an area under the curve from 0.68 to 0.92 depending cancer type and staging. This is the largest RNA-seq study to date for profiling exRNA species, which has not only provided a baseline reference profile for circulating exRNA, but also revealed a set of RNA candidates for reference controls and disease biomarkers.
Ray-tracing analysis of crosstalk in multi-core polymer optical fibers (2010)

The aim of this paper is to present a new ray-tracing model which describes the propagation of light in multi-core polymer optical fibers (MCPOFs), taking into account the crosstalk among their cores. The new model overcomes many of the limitations of previous approaches allowing us to simulate MCPOFs of arbitrary designs. Additionally, it provides us with the output ray distribution at the end of the fiber, making it possible to calculate useful parameters related to the fiber performance such as the Near-Field Pattern, the Far-Field Pattern or the bandwidth. We also present experimental measurements in order to validate the computational model and we analyze the importance of crosstalk in different MCPOF configurations.
A synthetic system for expression of components of a bacterial microcompartment (2013)

In general, prokaryotes are considered to be single-celled organisms that lack internal membrane-bound organelles. However, many bacteria produce proteinaceous microcompartments that serve a similar purpose, i.e. to concentrate specific enzymic reactions together or to shield the wider cytoplasm from toxic metabolic intermediates. In this paper, a synthetic operon encoding the key structural components of a microcompartment was designed based on the genes for the Salmonella propanediol utilization (Pdu) microcompartment. The genes chosen included pduA, -B, -J, -K, -N, -T and -U, and each was shown to produce protein in an Escherichia coli chassis. In parallel, a set of compatible vectors designed to express non-native cargo proteins was also designed and tested. Engineered hexa-His tags allowed isolation of the components of the microcompartments together with co-expressed, untagged, cargo proteins. Finally, an in vivo protease accessibility assay suggested that a PduD-GFP fusion could be protected from proteolysis when co-expressed with the synthetic microcompartment operon. This work gives encouragement that it may be possible to harness the genes encoding a non-native microcompartment for future biotechnological applications.
Double-layered monolithic silicon photonic crystals (2008)

Double-layered, self-aligned, silicon photonic crystals are fabricated using directional and isotropic etches - a potential step towards 3D PCs. One structure shows sharper resonances compared to corresponding single layer structure. Another shows high, broadband reflectivity.
Translocated c-myc oncogene of Burkitt lymphoma is transcribed in plasma cells and repressed in lymphoblastoid cells. (1984)

We examined somatic cell hybrids between Burkitt lymphoma cells and either human lymphoblastoid cells or mouse plasmacytoma cells for the expression of the translocated c-myc oncogene. The results of this study indicate that the translocated c-myc oncogene is transcribed in plasma cells but is repressed in lymphoblastoid cells. Thus, the factors necessary for translocated c-myc transcription are present in plasma cells and Burkitt lymphoma cells but are absent or inactive in lymphoblastoid cells. Since the distance between the rearranged immunoglobulin loci and the c-myc oncogene can even exceed 30-50 kilobases, we speculate that the translocated c-myc oncogene is under the transcriptional control of enhancer-like elements capable of acting over long distances. The activity of this long-range enhancer may depend on the interaction with transacting factors that are active in plasma cells and in Burkitt lymphoma cells but are not active in lymphoblastoid cells. We also examined the transcription of the first exon of the c-myc oncogene, which becomes separated from the second and third exon because of the chromosomal break involving the first intron. This exon is transcribed at high levels in ST486 Burkitt lymphoma cells with the t(8;14) chromosome translocation. Hybrids between lymphoblastoid and ST486 cells expressed high levels of transcripts of the first exon, whereas hybrids between plasma cells and ST486 cells did not. Thus, transcription of the separated first exon can be enhanced in lymphoblastoid and Burkitt lymphoma cells because of its close proximity to the heavy chain enhancer that is normally located between the joining and the switch region of the C mu gene. Such enhancement, however, does not occur in plasma cells, possibly because these cells are able to suppress completely the c-myc oncogene, unless it has been placed in the proximity of a rearranged immunoglobulin constant region gene.