gebhart/patrepeval huggingface dataset:
Essential and Nonessential Elements in the 3′ Nontranslated Region of Bovine Viral Diarrhea Virus (2005)

The 3' nontranslated region (NTR) of the pestivirus Bovine viral diarrhea virus (BVDV), a close relative of human Hepatitis C virus, consists of three stem-loops which are separated by two single-stranded regions. As in other positive-stranded RNA viruses, the 3' NTR of pestiviruses is involved in crucial processes of the viral life cycle. While several studies characterized cis-acting elements within the 3' NTR of a BVDV replicon, there are no studies addressing the significance of these elements in the context of a replicating virus. To examine the functional importance of 3' NTR elements, a set of 4-base deletions and deletions of each of the three stem-loops were introduced into an infectious BVDV cDNA clone. Emerging mutant viruses were characterized with regard to plaque phenotype, growth kinetics, and synthesis of viral RNA. The results indicated that presence of stem-loop (SL) I and the 3'-terminal part of the single-stranded region between stem-loops I and II are indispensable for pestiviral replication. In contrast, deletions within SL II and SL III as well as absence of either SL II or SL III still allowed efficient viral replication; however, a mutant RNA lacking both SL II and SL III was not infectious. The results of this study provide a detailed map of the essential and nonessential elements within the 3' NTR of BVDV and contribute to our understanding of sequence and structural elements important for efficient viral replication of pestiviruses in natural host cells.
Micromechanical Analysis of the Binding of DNA-Bending Proteins HMGB1, NHP6A, and HU Reveals Their Ability To Form Highly Stable DNA−Protein Complexes (2004)

The mechanical response generated by binding of the nonspecific DNA-bending proteins HMGB1, NHP6A, and HU to single tethered 48.5 kb lambda-DNA molecules is investigated using DNA micromanipulation. As protein concentration is increased, the force needed to extend the DNA molecule increases, due to its compaction by protein-generated bending. Most significantly, we find that for each of HMGB1, NHP6A, and HU there is a well-defined protein concentration, not far above the binding threshold, above which the proteins do not spontaneously dissociate. In this regime, the amount of protein bound to the DNA, as assayed by the degree to which the DNA is compacted, is unperturbed either by replacing the surrounding protein solution with protein-free buffer or by straightening of the molecule by applied force. Thus, the stability of the protein-DNA complexes formed is dependent on the protein concentration during the binding. HU is distinguished by a switch to a DNA-stiffening function at the protein concentration where the formation of highly stable complexes occurs. Finally, introduction of competitor DNA fragments into the surrounding solution disassembles the stable DNA complexes with HMGB1, NHP6A, and HU within seconds. Since spontaneous dissociation of protein does not occur on a time scale of hours, we conclude that this rapid protein exchange in the presence of competitor DNA must occur only via "direct" DNA-DNA contact. We therefore observe that protein transport along DNA by direct transfers occurs even for proteins such as NHP6A and HU that have only one DNA-binding domain.
Induction of Antigen-Specific Tolerance in Multiple Sclerosis After Immunization With DNA Encoding Myelin Basic Protein in a Randomized, Placebo-Controlled Phase 1/2 Trial (2007)

In patients with MS, BHT-3009 is safe and induces antigen-specific immune tolerance with concordant reduction of inflammatory lesions on brain MRI.
The Long-Term Effect of Repeated Intravenous Lidocaine on Central Pain and Possible Correlation in Positron Emission Tomography Measurements (2004)

We present a case of persistent central pain after encephalitis in a patient who had long-term pain relief after a series of IV lidocaine infusions. A positron emission tomography scan study, done before and after treatment, suggested that lidocaine for the diagnosis of chronic neuropathic pain may have a specific site of action in the brain.
Nucleotide Sequencing of Psoriatic Arthritis Tissue before and during Methotrexate Administration Reveals a Complex Inflammatory T Cell Infiltrate with Very Few Clones Exhibiting Features That Suggest They Drive the Inflammatory Process by Recognizing Autoantigens (2004)

Psoriatic arthritis is an interesting MHC class I allele associated autoimmune disease where injury is likely mediated exclusively by T cells. We used TCR beta-chain nucleotide sequencing to gain insight into the adaptive immune events responsible for this injury and determine whether the numerous oligoclonal expansions of this disease represent extreme determinant spreading among driving clones that recognize autoantigen or were non-Ag-driven, inflammation-related expansions. Because methotrexate suppresses but does not eliminate this inflammation, we hypothesized that clones persisting during methotrexate treatment would likely drive the inflammation. Seventy-six percent of the T cell clones in active tissue were polyclonal and unexpanded, accounting for 31% of transcripts. They were decreased greatly by methotrexate. Strikingly, most expanded clones in the inflamed joint did not persist during methotrexate treatment, were found only in inflammatory sites, exhibited no structural homology to one another, and were either CD4 or CD8 in lineage, suggesting they were non-autoantigen-driven, inflammation-related expansions. Only 12% of the expanded clones could be grouped into clonal sets distinguished by structurally homologous CDR3 beta-chain amino acid motifs suggesting Ag drive. These were exclusively CD8 in lineage, persisted during methotrexate administration, and were present in both joint fluid and blood implying they were candidate driver clones that recognized an autoantigen. However, a major set of putative driver clones exhibited a previously described EBV-specific beta-chain motif, emphasizing that the dominant feature of the disease was activation of multiple clones apparently lacking specificity for an inciting autoantigen.
Effects of electronic current overflow and inhomogeneous carrier distribution on InGaN quantum-well laser performance (2004)

Laser performance of several InGaN quantum-well (QW) lasers with an emission wavelength of 392-461 nm are numerically studied with a LASTIP simulation program. Specifically, the effects of electronic current overflow and inhomogeneous carrier distribution on the laser performance of InGaN QW lasers operating at different wavelengths are investigated. Simulation results indicate that the use of an AlGaN blocking layer can help reduce the electronic current overflow and, in addition to the dissociation of the InGaN well layer at a high growth temperature during crystal growth, the inhomogeneous carrier distribution in the QWs also plays an important role in the laser performance. From the simulation results, we conclude that the lowest threshold current density is obtained when the number of InGaN well layers is two if the emission wavelength is shorter than 427 nm and one if the emission wavelength is longer than 427 nm, which are in good agreement with the results observed by Nakamura et al. in their experiments.
The Quality Investigation of 6H-SiC Crystals Grown by a Conventional PVT Method with Various SiC Powders (2010)

In this paper, we investigate the quality difference of SiC crystals grown by a conventional physical vapor transport method using various SiC powders. While the growth rate was revealed to be dependent upon the particle size of the SiC powder, the growth rate of SiC bulk crystals grown using SiC powder with a smaller particle size (20 nm) was definitely higher than those using lager particle sizes with <TEX>$0.1-0.2\;{\mu}m$</TEX> and <TEX>$1-10\;{\mu}m$</TEX>, respectively. All grown 2 inch SiC single crystals were proven to be the polytype of 6H-SiC and the carrier concentration levels of about <TEX>$10^{17}\;cm^3$</TEX> were determined from Hall measurements. It was revealed that the particle size and process method of SiC powder played an important role in obtaining a good quality, high growth rate, and to reduce growth temperature.
Fluoroalkylsilane-Modified Textile-Based Personal Energy Management Device for Multifunctional Wearable Applications (2016)

The rapid development of wearable electronics in recent years has brought increasing energy consumption, making it an urgent need to focus on personal energy harvesting, storage and management. Herein, a textile-based personal energy management device with multilayer-coating structure was fabricated by encapsulating commercial nylon cloth coated with silver nanowires into polydimethylsiloxane using continuous and facile dip-coating method. This multilayer-coating structure can not only harvest mechanical energy from human body motion to power wearable electronics but also save energy by keeping people warm without losing heat to surroundings and wasting energy to heat empty space and inanimate objects. Fluoroalkylsilanes (FAS) were grafted onto the surface of the film through one single dip-coating process to improve its energy harvesting performance, which has hardly adverse effect to heat insulation and Joule heating property. In the presence of FAS modification, the prepared film harvested mechanical energy to reach a maximum output power density of 2.8 W/m(2), charged commercial capacitors and lighted LEDs, showing its potential in powering wearable electronics. Furthermore, the film provided 8% more thermal insulation than normal cloth at 37 °C and efficiently heated to 40 °C within 4 min when applied the voltage of only 1.5 V due to Joule heating effect. The high flexibility and stability of the film ensures its wide and promising application in the wearable field.
The biotin‐streptavidin interaction can be reversibly broken using water at elevated temperatures (2005)

The biotin-streptavidin system is the strongest noncovalent biological interaction known, having a dissociation constant, K(d), in the order of 4x10(-14) M. The strength and specificity of the interaction has led it to be one of the most widely used affinity pairs in molecular, immunological, and cellular assays. However, it has previously been impossible to re-use any streptavidin solid support, since the conditions needed to break the interaction with biotin has led to the denaturation of the streptavidin. Here, we show that a short incubation in nonionic aqueous solutions at temperatures above 70 degrees C can efficiently break the interaction without denaturing the streptavidin tetramer. Both biotin and the streptavidin remain active after dissociation and both molecules can therefore be re-used. The efficiency of the regeneration allowed solid supports with streptavidin to be used many times, here exemplified with the multiple re-use of streptavidin beads used for sample preparation prior to automated DNA sequencing. The results suggest that streptavidin regeneration can be introduced as an improvement in existing methods and assays based on the streptavidin system as well as emerging solid phase applications in fields, such as microfluidics and nanotechnology.
Transposition of Tn904 encoding streptomycin resistance into the octopine Ti plasmid of Agrobacterium tumefaciens (1980)

A transfer-deficient derivative of plasmid RP1-pMG1 was isolated after insertion of Mu cts62. The Tra- R plasmid was used to donate Tn904, encoding streptomycin resistance, to Ti plasmid pAL102 harbored by Agrobacterium tumefaciens Ach5. Under conditions promoting high Ti transfer frequencies, 155 strains were isolated in which the streptomycin marker coupled with Ti plasmid in further transfer experiments. These isolates represent stable insertions of Tn904 into the Ti plasmid. In addition, 19 strains were isolated in which the insertion of Tn904 was apparently unstable. The frequency of stable Tn904 transpositions was estimated to be 3 x 10(4-) per transferred Ti plasmid. Evidence was obtained that Tn904 readily may transpose from the Ti plasmid into the bacterial chromosome. The strains carrying Ti plasmids with stable insertions were characterized with respect to virulence, octopine degradation, octopine synthesis in induced tumors, and Ti plasmid transfer. Thirteen of the strains were found to be affected in tumor-inducing ability.
Peer to peer content sharing on ad hoc networks of smartphones (2011)

Peer-to-peer networks offer advantages over traditional client-server networking models, such as the lack of a need for connectivity to trusted intermediary hosts or servers and the use of less costly communication links. While they have become popular in the wired broadband environment, they have not yet been effectively adapted to the resource-constrained mobile network environment. They promise significant potential in applications such as the sharing of files like multimedia and operating system updates between mobile devices. However, the peer-to-peer model faces unique challenges in the mobile context, such as limitations on processing power, on-board device memory, wireless data bandwidth, and available battery energy. We propose a high-level framework for a peer-to-peer protocol with these specific constraints addressed. In addition, we investigate the feasibility of a practical implementation of a peer-to-peer file sharing model on smartphones, including an analysis of how performance is impacted by various variables that can be dynamically controlled in the protocol. Through experimentation on leading smartphones, we have found various optimal strategies, including minimizing the upload-to-download ratio to conserve battery life, using larger file segments to increase throughput, and using sockets to decrease memory overhead.
SpamCop: A Spam Classification & Organisation Program (1998)

We present a simple, yet highly accurate, spam filtering program, called SpamCop, which is able to identify about 92% of the spams while misclassifying only about 1.16% of the nonspam e-mails. SpamCop treats an e-mail message as a multiset of words and employs a na’fve Bayes algorithm to determine whether or not a message is likely to be a spam. Compared with keyword-spotting rules, the probabilistic approach taken in SpamCop not only offers high accuracy, but also overcomes the brittleness suffered by the keyword spotting approach.
SHORTVEIN, A NEW COMPONENT OF THE DECAPENTAPLEGIC GENE COMPLEX IN DROSOPHILA MELANOGASTER (1985)

Our laboratory has been concerned with the structure and function of the decapentaplegic gene complex (DPP-C) in Drosophila melanogaster. To define the boundaries of the complex, we have studied the genetics of mutations allelic to a previously discovered mutation shortvein (shv), known to reside near decapentaplegic. We found that shortvein resides distal to Hin-d and dpp within the same polytene chromosome doublet, 22F1-2. Lesions in shv can affect not only the formation of the wing veins but also can interfere with normal development of parts of the adult and/or be lethal. Like those of dpp mutants, the shv-associated adult abnormalities affect distal epidermal structures. Some shv lesions cause a larval lethal syndrome which is associated with an unusually long larval stage (ca. five to six times its normal duration). Lesions in shv exhibit an involved pattern of complementation with dpp mutations, indicating that both shv and dpp are parts of a single gene complex. A subset of the array of mutant phenotypes displayed by shv/dpp trans-heterozygotes appear to be dpp-specific phenotypes; we interpret these as reflecting an inactivation effect of certain shv alleles on dpp functions. The other abnormalities displayed by these trans-heterozygotes appear to be shv-specific defects; we view these as indicating an inactivation effect of certain dpp mutations on shv functions. Furthermore, embryonic lethal (EL) mutations within the DPP-C exhibit allelic interactions with all shv mutations. We conclude that the shortvein region represents a newly identified integrated portion of the DPP-C.
Site-Directed Mutagenesis of the Catalytic Base Glutamic Acid 400 in Glucoamylase from Aspergillus niger and of Tyrosine 48 and Glutamine 401, Both Hydrogen-Bonded to the .gamma.-Carboxylate Group of Glutamic Acid 400 (1994)

Replacement of the catalytic base Glu400 by glutamine in glucoamylase from Aspergillus niger affects both substrates ground-state binding and transition-state stabilization. Compared to those of the wild-type enzyme, Km values for maltose and maltoheptaose are 12- and 3-fold higher for the Glu400-->Gln mutant, with kcat values 35- and 60-fold lower, respectively, for the same substrates. This unusually high residual activity for a glycosylase mutant at a putative catalytic group is tentatively explained by a reorganization of the hydrogen bond network, using the crystal structure of the related Aspergillus awamori var. X100 glucoamylase in complex with 1-deoxynojirimycin [Harris, E. M. S., Aleshin, A. E., Firsov, L. M., & Honzatko, R. B. (1993) Biochemistry 32, 1618-1626]. Supposedly Gln400 in the mutant hydrogen bonds to the invariant Tyr48, as does Glu400 in the wild-type enzyme. For Tyr48-->Trp A. niger glucoamylase kcat is reduced 80-100-fold, while Km is increased only 2-3-fold. Gln401 also hydrogen bonds to Glu400, but its mutation to glutamic acid has only a minor effect on activity. The Tyr48-->Trp and Glu400-->Gln glucoamylases share particular features in displaying unusually high activity below pH 4.0-which reflects lack of the wild-type catalytic base function- and unusually low binding affinity at subsite 2. Both mutants have lost 13-16 kJ mol-1 in transition-state stabilization energy.(ABSTRACT TRUNCATED AT 250 WORDS)
Quadriceps Weakness After Single-Shot Adductor Canal Block (2020)

Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.
Soybean Aphid Resistance in Soybean Jackson Is Controlled by a Single Dominant Gene (2006)

The soybean aphid, Aphis glycines Matsumura, has become established as a serious pest of soybean, Glycine max (L.) Merr., since it was first found in North America in 2000 and has caused millions of dollars in economic losses. While the application of chemical insecticides is the only means to control the soybean aphid at present, genetic resistance to the aphid was recently discovered in soybean. A single dominant gene named Rag1 that controls resistance to the soybean aphid was found in the cultivar Dowling. Another cultivar found to have strong antibiosis‐type resistance to the soybean aphid was Jackson. The primary objective of this study was to determine the inheritance of resistance to the soybean aphid in Jackson. Segregation of resistance was analyzed in F 2 and among F 2 –derived F 3 (F 2:3 ) families produced from crosses between Jackson and the susceptible soybean cultivar Loda. Segregation of F 2 plants was 247 resistant to 97 susceptible and fit a 3:1 genetic ratio ( P = 0.17). Segregation among F 2:3 families was not clear because a number of susceptible F 2 plants did not produce a sufficient amount of seed for progeny testing. Ignoring the susceptible class, the segregation of F 2:3 families fit a 1:2 (all resistant/segregating) ratio. These results indicated that a single dominant gene controlled resistance in Jackson. There is no known genetic relationship between Jackson and Dowling. The genetic relationship between Rag1 in Dowling and the gene in Jackson is unknown.
Review of Skin‐Lightening Agents (2005)

The speed of efficacy and type and extent of side effects vary greatly among depigmenting agents. Knowing the properties associated with each agent enables a physician to choose a product that will best meet a patient's expectations and minimize adverse reactions.
User Interface Design: A Software Engineering Perspective (2004)

Preface Part A: Best of the Classics 1.Usability 2. Prototyping and iterative design 3. Data presentation 4. Mental models and interface design Part B: Systematic Interface Design 5. Analysis, visions and domain description 6. Virtual windows design 7. Function design 8. Prototypes and defect correction 9. Reflections on user interface design Part C: Supplementary Design Issues 10. Web-based course rating 11. Designing an e-mail system 12. User documentation and support 13. More on usability testing 14. Heuristic evaluation 15. Systems development 16. Data modelling 17. Exercises 18. References Index
<title>Fast proximity correction with zone sampling</title> (1994)

Proximity effects cause integrated circuit features to be distorted when compared to the original mask pattern. These effects are becoming widely recognized as serious barriers to achieving effective half-micrometer and smaller wafer lithography processes. A promising remedy for proximity effects is to adjust mask feature shapes to compensate for predictable distortions in the wafer lithography process. We present a general method for computing proximity-corrected shapes. A technique we call `zone sampling' provides accurate models of proximity behaviors with optimum computational efficiency. Proximity behavior for arbitrary layout configurations is derived from 2-D density measurements (zone samples) computed from IC layout pattern data. Zone sampling provides a complete `behavior model' of combined, non-linear proximity effects, including optical, process, and underlying substrate mechanisms.
An Unusual Side Reaction in the Rearrangement of 3,4,6-Tri-O-Acetyl-1,2-O-(Allyloxyethylidene)-β-D-Mannopyranose with TMS-Triflate: Formation of an α(1→2)-Linked Disaccharide (1997)

Sugar 1,2-orthoesters are versatile intermediates in carbohydrate synthesis. They are stable in neutral and basic medium but are readily hydrolysed under acidic conditions to form the corresponding 2-O-acetyl-protected reducing sugars.1 The formation of the 2-OH-unprotected glycosyl actetates with trifluoroacetic acid has also been reported.2 Furthermore 1,2-orthoacetates are known as glycosylating agents after activation by protic or Lewis acids.3
Organic Field-Effect Transistors (1998)

Organic field-effect transistors (OFETs) were first described in 1987. Their characteristics have undergone spectacular improvements during the last two or three years. At the same time, several models have been developed to rationalize their operating mode. In this review, we examine the performance of OFETs as revealed by recently published data, mainly in terms of field-effect mobility and on–off current ratio. We compare the various compounds that have been used as the active component, and describe the most prominent fabrication techniques. Finally, we analyze the charge transport mechanisms in organic solids, and the resulting models of OFETs.
Bioimpedance of soft tissue under compression (2012)

In this paper compression-dependent bioimpedance measurements of porcine spleen tissue are presented. Using a Cole-Cole model, nonlinear compositional changes in extracellular and intracellular makeup; related to a loss of fluid from the tissue, are identified during compression. Bioimpedance measurements were made using a custom tetrapolar probe and bioimpedance circuitry. As the tissue is increasingly compressed up to 50%, both intracellular and extracellular resistances increase while bulk membrane capacitance decreases. Increasing compression to 80% results in an increase in intracellular resistance and bulk membrane capacitance while extracellular resistance decreases. Tissues compressed incrementally to 80% show a decreased extracellular resistance of 32%, an increased intracellular resistance of 107%, and an increased bulk membrane capacitance of 64% compared to their uncompressed values. Intracellular resistance exhibits double asymptotic curves when plotted against the peak tissue pressure during compression, possibly indicating two distinct phases of mechanical change in the tissue during compression. Based on these findings, differing theories as to what is happening at a cellular level during high tissue compression are discussed, including the possibility of cell rupture and mass exudation of cellular material.