gebhart/patrepeval huggingface dataset:
Empirical aspects of strand displacement amplification. (1993)

The most attractive feature of SDA is its operation at a single temperature, which removes the need for instrumented temperature cycling as with PCR and the ligase chain reaction. Highly reproducible temperature profiles, over a large array of samples, can burden the accuracy and expense of an amplification technique. However, the expense of a temperature cycler is offset somewhat by the cost of additional enzymes used in isothermal techniques. In comparisons with isothermal, transcription-based techniques, SDA requires fewer enzymes and has a simpler mechanism. SDA may also be more robust than transcription-based processes because it is not susceptible to contaminating ribonuclease activity. This is generally more of a concern when using clinical samples. The most significant disadvantage of SDA is its inability to efficiently amplify long target sequences. Until this short-coming is eliminated, SDA will be assigned to the diagnostic laboratory along with the ligase chain reaction. Currently, SDA cannot compete with PCR in research applications such as the isolation of gene sequences. The second disadvantage of SDA is that it operates at relatively low (nonstringent) temperatures, which produces considerable background reactions. Consequently, SDA reaction products cannot be analyzed routinely by ethidium-stained gel electrophoresis, as is used commonly with PCR, unless the target sample contains a large number of initial targets.
Mismatch Negativity Event-Related Potential Elicited by Speech Stimuli (1992)

The mismatch negativity (MMN) is a passively elicited event-related potential that is extremely sensitive to acoustic stimulus properties. The MMN was characterized in normal adults and school-age children in response to speech stimuli differing minimally in the onset frequency of the second and third formant transitions. The speech-evoked MMN consists of a negative waveform at about 230 msec that occurs in response to the deviant stimulus when it is presented in an oddball paradigm. It is absent in response to that same stimulus when presented alone. The MMN was clearly present in all adults and children tested. Using the procedures developed in this study, this event-related potential was found to be robust enough in individual subjects to be considered a potential clinical measure for assessing central auditory function in school-age children and adults.
Rescue of dystrophic skeletal muscle by PGC-1α involves restored expression of dystrophin-associated protein complex components and satellite cell signaling (2013)

Duchenne muscular dystrophy is typically diagnosed in the preschool years because of locomotor defects, indicative of muscle damage. Thus, effective therapies must be able to rescue muscle from further decline. We have established that peroxisome proliferator-activated receptor gamma coactivator 1-alpha (Pgc-1α) gene transfer will prevent many aspects of dystrophic pathology, likely through upregulation of utrophin and increased oxidative capacity; however, the extent to which it will rescue muscle with disease manifestations has not been determined. Our hypothesis is that gene transfer of Pgc-1α into declining muscle will reduce muscle injury compared with control muscle. To test our hypothesis, adeno-associated virus 6 (AAV6) driving expression of Pgc-1α was injected into single hind limbs of 3-wk-old mdx mice, while the contralateral limb was given a sham injection. At 6 wk of age, treated solei had 37% less muscle injury compared with sham-treated muscles (P < 0.05). Resistance to contraction-induced injury was improved 10% (P < 0.05), likely driven by the five-fold (P < 0.05) increase in utrophin protein expression and increase in dystrophin-associated complex members. Treated muscles were more resistant to fatigue, which was likely caused by the corresponding increase in oxidative markers. Pgc-1α overexpressing limbs also exhibited increased expression of genes related to muscle repair and autophagy. These data indicate that the Pgc-1α pathway remains a good therapeutic target, as it reduced muscle injury and improved function using a rescue paradigm. Further, these data also indicate that the beneficial effects of Pgc-1α gene transfer are more complex than increased utrophin expression and oxidative gene expression.
Future of Gait Analysis (2005)

Despite the plethora of information on human gait analysis, its continued use as a clinical tool remains uncertain. Analysis of gait dysfunction has become integral to podiatric medical practice, and, like many specialized fields, it is rapidly changing to meet the needs of the future. Practice in the 21st century is predicated on the concept of multidisciplinary working approaches and a growing trend toward evidence-based practice, in which gait analysis could play a prominent role. This article provides a historical synopsis of instrumented gait analysis and its associated subcomponents and discusses the salient issues concerning its future role in podiatric medicine.
Characterization of the Genomic Promoter of the Prototypic Arenavirus Lymphocytic Choriomeningitis Virus (2002)

The genome of the prototypic arenavirus lymphocytic choriomeningitis virus (LCMV) consists of two negative-sense, single-strand RNA segments designated L and S. Arenavirus genomes exhibit high sequence conservation at their 3' ends. All arenavirus genomes examined to date have a conserved terminal sequence element (3'-terminal 20 nucleotides [nt]) thought to be a highly conserved viral promoter. Terminal complementarity between the 5' and 3' ends of the L and S RNAs predicts the formation of a thermodynamically stable panhandle structure that could contribute to the control of RNA synthesis. We investigated these issues by using a transcription- and replication-competent minireplicon system. A series of overlapping deletions spanning the 3'-terminal 20-nt region of an LCMV minigenome (MG) was generated, and the mutant MGs were analyzed for their activity as templates for RNA synthesis by the LCMV polymerase. The minimal LCMV genomic promoter was found to be contained within the 3'-terminal 19 nt. Substitution of C for G at the last 3'-end nucleotide position in the MG resulted in nondetection of RNA transcription or replication, whereas the addition of a C at the 3' end did not have any significant affect on RNA synthesis mediated by the LCMV polymerase. All other mutations introduced within the 3'-terminal 19 nt of the MG resulted in undetectable levels of promoter activity. Deletions and nucleotide substitutions within the MG 5' end that disrupted terminal complementarity abolished chloramphenicol acetyltransferase expression and RNA synthesis mediated by the LCMV polymerase. These findings indicate that both sequence specificity within the 3'-terminal 19 nt and the integrity of the predicted panhandle structure appear to be required for efficient RNA synthesis mediated by the LCMV polymerase.
Do we really need long-term hepatitis B hyperimmune globulin? What are the alternatives? (2008)

1. The outcomes of liver transplantation for patients with hepatitis are the best for any diagnosis. 2. Prevention of HBV re-infection is the key to excellent outcomes after liver transplantation. 3. The use of hepatitis B immunoglobulin to prevent HBV re-infection is effective, but costly and with side effects. 4. Effective prophylaxis against HBV re-infection can now be accomplished with combination nucleoside/nucleotide anti-virals.
Cautionary tale of using 16S rRNA gene sequence similarity values in identification of human-associated bacterial species (2015)

Modern bacterial taxonomy is based on a polyphasic approach that combines phenotypic and genotypic characteristics, including 16S rRNA sequence similarity. However, the 95 % (for genus) and 98.7 % (for species) sequence similarity thresholds that are currently recommended to classify bacterial isolates were defined by comparison of a limited number of bacterial species, and may not apply to many genera that contain human-associated species. For each of 158 bacterial genera containing human-associated species, we computed pairwise sequence similarities between all species that have names with standing in nomenclature and then analysed the results, considering as abnormal any similarity value lower than 95 % or greater than 98.7 %. Many of the current bacterial species with validly published names do not respect the 95 and 98.7 % thresholds, with 57.1 % of species exhibiting 16S rRNA gene sequence similarity rates ≥98.7 %, and 60.1 % of genera containing species exhibiting a 16S rRNA gene sequence similarity rate <95 %. In only 17 of the 158 genera studied (10.8 %), all species respected the 95 and 98.7 % thresholds. As we need powerful and reliable taxonomical tools, and as potential new tools such as pan-genomics have not yet been fully evaluated for taxonomic purposes, we propose to use as thresholds, genus by genus, the minimum and maximum similarity values observed among species.
Purification of DMT-On Oligonucleotide by Simulated Moving-Bed (SMB) Chromatography (2005)

Recent clinical advances in the development of oligonucleotides as therapeutics have triggered a significant demand for these molecules in large quantities. To facilitate their development, purification of full-length oligonucleotide from various synthesis related byproducts is an important endeavour. Herein, we report for the first time an application of simulated moving-bed (SMB) chromatography as a purification tool for DMT-protected oligonucleotides. An efficient separation has been accomplished with polystyrene/divinyl benzene copolymer as the stationary phase and 0.05 M NH4HCO3 buffer (pH 8)/MeOH (6:4, v/v) as the mobile phase. A DMT-protected product purity of >99% with 77% yield for a 20-mer phosphorothioate oligonucleotide is reported.
Towards the treatment of saphenous vein bypass graft failure – a perspective of the Bristol Heart Institute (2002)

Coronary artery bypass graft surgery (CABG) is widely used for the treatment of atheromatous stenosis of coronary arteries. However, as many as 50% of grafts fail within 10 years after CABG due to neointima (NI) formation, a process involving the proliferation and migration of vascular smooth muscle cells (VSMCs). Superimposed on neointima formation is accelerated atherogenesis which ultimately results in late vein graft failure. To date no therapeutic intervention has proved successful in treating late vein graft failure and as such is a matter of some urgency. However, in recent years, several diverse approaches aimed at preventing neointimal formation have been devised which have yielded promising results. These include the use of external stents, gene therapy as well as conventional pharmacological interventions. The objective of this article, therefore, is to review these recent approaches and their potential clinical applications in the treatment of vein graft disease.
Prefetching in segmented disk cache for multi-disk systems (1996)

Article Free Access Share on Prefetching in segmented disk cache for multi-disk systems Author: Valery Soloviev Computer Science Department, North Dakota State University Computer Science Department, North Dakota State UniversityView Profile Authors Info & Claims IOPADS '96: Proceedings of the fourth workshop on I/O in parallel and distributed systems: part of the federated computing research conferenceMay 1996 Pages 69–82https://doi.org/10.1145/236017.236037Published:27 May 1996Publication History 11citation446DownloadsMetricsTotal Citations11Total Downloads446Last 12 Months14Last 6 weeks1 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Optical biosensor provides insights for bradykinin B2receptor signaling in A431 cells (2005)

The spatial and temporal targeting of proteins or protein assemblies to appropriate sites is crucial to regulate the specificity and efficiency of protein-protein interactions, thus dictating the timing and intensity of cell signaling and responses. The resultant dynamic mass redistribution could be manifested by label free optical biosensor, and lead to a novel and functional optical signature for studying cell signaling. Here we applied this technology, termed as mass redistribution cell assay technology (MRCAT), to study the signaling networks of bradykinin B(2) receptor in A431 cells. Using MRCAT, the spatial and temporal relocation of proteins and protein assemblies mediated by bradykinin was quantitatively monitored in microplate format and in live cells. The saturability to bradykinin, together with the specific and dose-dependent inhibition by a B(2) specific antagonist HOE140, suggested that the optical signature is a direct result of B(2) receptor activation. The sensitivity of the optical signature to cholesterol depletion by methyl-beta-cyclodextrin argued that B(2) receptor signaling is dependent on the integrity of lipid rafts; disruption of these microdomains hinders the B(2) signaling. Modulations of several important intracellular targets with specific inhibitors suggested that B(2) receptor activation results in signaling via at least dual pathways - G(s)- and G(q)-mediated signaling. Remarkably, the two signaling pathways counter-regulate each other. Several critical downstream targets including protein kinase C, protein kinase A, and epidermal growth factor receptor had been identified to involve in B(2) signaling. The roles of endocytosis and cytoskeleton modulation in B(2) signaling were also demonstrated.
The Art of Computer Programming: Volume 3: Sorting and Searching (1973)

This book is in the Addison-Wesley series in Computer Science and Information Processing
A programmable optical interconnection system using an amorphous silicon ferroelectric spatial light modulator (1990)

The authors describe a programmable optical interconnect device for use in 2D optical information processing systems. They have concentrated on the moderately rapidly reconfigurable type as this approach is likely to yield a useful and flexible interconnection system with present available optical technology. The type of system considered uses a device which consists of a 2-D array of independent electrooptically induced diffraction gratings. This approach is novel in that it combines the highly parallel 2-D array capabilities of a static holographic interconnect approach with the ability to reconfigure the interconnection pattern. The induced diffraction gratings are used to diffract information carrying beams of light to any desired output location. As all the gratings in the 2-D array are completely independent the device can support all possible interconnection patterns between the input and output locations.<
 >
Distinct functions for integrins alpha 3 beta 1 in focal adhesions and alpha 6 beta 4/bullous pemphigoid antigen in a new stable anchoring contact (SAC) of keratinocytes: relation to hemidesmosomes. (1990)

Basal cells of stratified epidermis are anchored to the basement membrane zone (BMZ) of skin via hemidesmosomes. We previously identified integrin alpha 3 beta 1, in focal adhesions (FAs), of cultured human keratinocytes (HFKs) as a mediator of HFK adhesion to secreted BMZ-like extracellular matrix (ECM; Carter, W.G., E.A. Wayner, T.S. Bouchard, and P. Kaur. 1990. J. Cell Biol. 110: 1387-1404). Here, we have examined the relation of integrins alpha 6 beta 4 and alpha 3 beta 1, to bullous pemphigoid antigen (BPA), a component of hemidesmosomes. We conclude that alpha 6 beta 4 in HFKs localizes in a new stable anchoring contact (SAC) that cooperates with alpha 3 beta 1-FAs to mediate adhesion to ECM, based on the following. (a) Comparison of secreted ECM, with exogenous laminin, fibronectin and collagen identified ECM as the preferred ligand for HFK adhesion and spreading and for formation of both alpha 6 beta 4-SACs and alpha 3 beta 1-FAs. (b) Inhibition of HFK adhesion with combined anti-alpha 3 beta 1 (P1B5) and anti-alpha 6 beta 4 (GoH3) antibodies indicated that both receptors were functional in adhesion to ECM while alpha 3 beta 1 played a dominant role in spreading. (c) alpha 6 beta 4 colocalized with BPA in SACs that were proximal to but excluded from FAs. Both alpha 6 beta 4-SACs and alpha 3 beta 1-FAs were in contact with the adhesion surface as indicated by antibody exclusion and interference reflection microscopy. (d) In contrast to alpha 3 beta 1-FAs, alpha 6 beta 4-SACs were present only in nonmotile cells, not associated with stress fibers, and were relatively stable to detergents and urea, suggesting a nonmotile, or anchoring function for SACs and motility functions for alpha 3 beta 1-FAs. (e) alpha 6 beta 4 formed a detergent-insoluble complex with exogenous ECM in an affinity isolation procedure, confirming the ability of an unidentified ECM ligand to interact with alpha 6 beta 4. (f) We suggest that alpha 6 beta 4/BPA-SACs in culture restrict migration of HFKs on ECM while alpha 3 beta 1-FAs form dynamic adhesions in spreading and migrating cells. alpha 6 beta 4/BPA-SACs in culture bear functional and compositional similarities to hemidesmosomes in skin.
Comparison of Monovalent and Trivalent Live Attenuated Influenza Vaccines in Young Children (1993)

Fifty children, 6 months to 2 years of age, were vaccinated intranasally with a trivalent preparation containing 10(6) TCID50 each of H1N1 and H3N2 and 10(4) (n = 14) or 10(6) (n = 36) TCID50 of B live, attenuated, cold-adapted (ca) influenza strains. The same doses were administered as monovalent vaccines to 69 comparably aged children. Forty-five controls were given placebo. No clinically significant adverse reactions to vaccines were observed. Of children seronegative to H1N1 or H3N2, > or = 90% were infected by these vaccine strains. Trivalent vaccine containing 10(4) TCID50 of B infected only 27% of children seronegative to B (3/11), which was markedly reduced from the 88% infection rate (7/8) following monovalent B vaccine of the same dose (P = .02); increasing the B dose to 10(6) TCID50 increased the infection rate to 81% (21/26). Replication of ca influenza viruses in tissue culture matched vaccine responses. Trivalent ca influenza vaccines can be formulated that are safe and immunogenic in young children.
Do Changing Times Mean a Change in Agendas for the Elderly? (1993)

No abstract available for this article.
[Lysosomal glycogen storage disease with normal acid maltase (Danon) without apparent cardiomyopathy and mental retardation]. (2000)

A 29-year-old male who had a past history of mild ECG abnormality of arrhythmia at the age of 14 years, was referred to our hospital because of elevated serum creatine kinase (CK) level. He had never been aware of muscular weakness nor cardiac symptoms. Neurological examination revealed normal muscle strength of all extremities except marked back muscle weakness. He had normal intelligence. On laboratory examination, serum AST, ALT, LDH, aldolase, CK and myoglobin levels were elevated. Both lactate and pyruvate levels were normally responded after an ischemic exercises test. Acid maltase activity was normal in white blood cells. A muscle biopsy obtained from rectus femoris muscle revealed vacuolar myopathy with mildly increased PAS positive material. On electron microscopy, there were autophagic vacuoles scavenging glycogen particles and cytoplasmic debris, and sarcolemmal indentation, compatible with the findings of lysosomal glycogen storage disease with normal acid maltase. This patient had unusual clinical features of absent mental retardation and no apparent cardiomyopathy. Accordingly, mental retardation is probably not necessary to see later onset of cardiac muscle involvement.
Recent advances in postoperative pain management. (2010)

Good pain control after surgery is important to prevent negative outcomes such as tachycardia, hypertension, myocardial ischemia, decrease in alveolar ventilation, and poor wound healing. Exacerbations of acute pain can lead to neural sensitization and release of mediators both peripherally and centrally. Clinical wind up occurs from the processes of N-Methyl D-Aspartate (NMDA) activation, wind up central sensitization, long-term potentiation of pain (LTP), and transcription-dependent sensitization. Advances in the knowledge of molecular mechanisms have led to the development of multimodal analgesia and new pharmaceutical products to treat postoperative pain. The new pharmacological products to treat postoperative pain include extended-release epidural morphine and analgesic adjuvants such as capsaicin, ketamine, gabapentin, pregabalin dexmetomidine, and tapentadol. Newer postoperative patient-controlled analgesia (PCA) in modes such as intranasal, regional, transdermal, and pulmonary presents another interesting avenue of development.
Biosensor Detection Systems: Engineering Stable, High-Affinity Bioreceptors by Yeast Surface Display (2009)

Over the past two decades, the field of biosensors has been developing fast, portable, and convenient detection tools for various molecules of interest, both biological and environmental. Although much attention is paid to the transduction portion of the sensor, the actual bioreceptor that binds the ligand is equally critical. Tight, specific binding by the bioreceptor is required to detect low levels of the relevant ligand, and the bioreceptor must be stable enough to survive immobilization, storage, and in ideal cases, regeneration on the biosensing device. Often, naturally-occurring bioreceptors or antibodies that are specific for a ligand either express affinities that may be too low to detect useful levels, or the proteins are too unstable to be used and reused as a biosensor. Further engineering of these receptors can improve their utility. Here, we describe in detail the use of yeast surface display techniques to carry out directed evolution of bioreceptors to increase both the stability of the molecules and their affinity for the ligands. This powerful technique has enabled the production of stabilized, single-chain antibodies, T cell receptors, and other binding molecules that exhibit affinity increases for their ligands of up to 1 million-fold and expression of stable molecules in E. coli.
Biodegradation and bioabsorption innovation of the functionally graded bovine bone–originated apatite with blood permeability (2005)

Bioabsorbable and functionally graded apatite (fg-HAp) ceramics were designed using bovine bone by the calcination and partial dissolution-precipitation methods. The fg-HAp ceramics that were developed had gradual distributions of the degree of crystallinity and the grain size of single-phase hydroxyapatite from the surface layer of the pore wall to the bulk structure region. Calcination at 1073 K gave a specific surface area of 30 m2 x g-1 and porosities of 60-80%. The pore structure of the fg-HAp was classified into two regions: a macro-pore region (100-600 microm) originating from spongy bone and a micro-pore region (10-160 nm) related to body fluid permeation and blood permeability. By implantation in subcutaneous tissue of rat, it was confirmed that body fluid permeated the bulk region of the fg-HAp ceramics through the micro-pores. The volumetric populations occupied by body fluid were 60% at 4 weeks and 68% at 8 weeks in the ceramics explants, indicating drastic bioabsorption, although the body fluid was found to be immunopositive for an albumin as the main serum protein in blood. On the fg-HAp ceramics developed here, the bioabsorption rate could be controlled by careful selection of the calcination temperature. These ceramics can be applied as new biomimetic ceramics exhibiting surface and bulk degradations and cellular absorption by giant cells.