gebhart/patrepeval huggingface dataset:
Optimization of Polymerase Chain Reactions (2003)

The polymerase chain reaction (PCR) is a powerful method for fast in vitro enzymatic amplifications of specific DNA sequences. PCR amplifications can be grouped into three different categories: standard PCR, long PCR, and multiplex PCR. Standard PCR involves amplification of a single DNA sequence that is less than 5 kb in length and is useful for a variety of applications, such as cycle sequencing, cloning, mutation detection, etc. Long PCR is used for the amplification of a single sequence that is longer than 5 kb and up to 40 kb in length. Its applications include long-range sequencing; amplification of complete genes; PCR-based detection and diagnosis of medically important large-gene insertions or deletions; molecular cloning; and assembly and production of larger recombinant constructions for PCR-based mutagenesis (1,2). The third category, multiplex PCR, is used for the amplification of multiple sequences that are less than 5 kb in length. Its applications include forensic studies; pathogen identification; linkage analysis; template quantitation; genetic disease diagnosis; and population genetics (3–5). Unfortunately, there is no single set of conditions that is optimal for all PCR. Therefore, each PCR is likely to require specific optimization for the template/primer pairs chosen. Lack of optimization often results in problems, such as no detectable PCR product or low efficiency amplification of the chosen template; the presence of nonspecific bands or smeary background; the formation of “primer-dimers” that compete with the chosen template/primer set for amplification; or mutations caused by errors in nucleotide incorporation.
Parameterized Joint Reconstruction of the Initial Pressure and Sound Speed Distributions for Photoacoustic Computed Tomography (2018)

Accurate estimation of the initial pressure distribution in photoacoustic computed tomography (PACT) depends on knowledge of the sound speed distribution. However, the sound speed distribution is typically unknown. Further, the initial pressure and sound speed distributions cannot both, in general, be stably recovered from PACT measurements alone. In this work, a joint reconstruction (JR) method for the initial pressure distribution and a low-dimensional parameterized model of the sound speed distribution is proposed. By employing <i>a priori</i> information about the structure of the sound speed distribution, both the initial pressure and sound speed can be accurately recovered. The JR problem is solved by use of a proximal optimization method that allows constraints and non-smooth regularization functions for the initial pressure distribution. The gradients of the cost function with respect to the initial pressure and sound speed distributions are calculated by use of an adjoint state method that has the same per-iteration computational cost as calculating the gradient with respect to the initial pressure distribution alone. This approach is evaluated through 2D computer-simulation studies for a small animal imaging model and by application to experimental in vivo measurements of a mouse.
Surface plasmons enhance optical transmission through subwavelength holes (1998)

Optically thick metal films perforated with a periodic array of subwavelength holes show exceptional transmission properties. The zero-order transmission spectra exhibit well-defined maxima and minima of which the positions are determined by the geometry of the hole array. We show that the minima are the collection of loci for Wood's anomaly, which occurs when a diffracted beam becomes tangent to the film, and that the maxima are the result of a resonant excitation of surface plasmons (SP's). SP's from both surfaces of the metal film are apparent in the dispersion diagram, independent of which side of the film is illuminated, indicating an anomalously strong coupling between the two sides. This leads to wavelength-selective transmission with efficiencies that are about 1000 times higher than that expected for subwavelength holes.
Multi-tenant databases for software as a service (2008)

In the implementation of hosted business services, multiple tenants are often consolidated into the same database to reduce total cost of ownership. Common practice is to map multiple single-tenant logical schemas in the application to one multi-tenant physical schema in the database. Such mappings are challenging to create because enterprise applications allow tenants to extend the base schema, e.g., for vertical industries or geographic regions. Assuming the workload stays within bounds, the fundamental limitation on scalability for this approach is the number of tables the database can handle. To get good consolidation, certain tables must be shared among tenants and certain tables must be mapped into fixed generic structures such as Universal and Pivot Tables, which can degrade performance.
Active HSF1 Significantly Suppresses Polyglutamine Aggregate Formation in Cellular and Mouse Models (2005)

Polyglutamine diseases are inherited neurodegenerative diseases characterized by misfolding and aggregation of proteins possessing expanded polyglutamine repeats. As overexpression of some heat shock protein (Hsp) suppresses polyglutamine aggregates and cell death, it is assumed that combined overexpression of Hsps will suppress that more effectively. Here, we examined the impact of active forms of heat shock transcription factor 1 (HSF1), which induces a set of Hsps, on polyglutamine inclusion formation and disease progression. We found that active HSF1 suppressed polyglutamine inclusion formation more significantly than any combination of Hsps in culture cells, possibly by regulating expression of unknown genes, as well as major Hsps. We crossed R6/2 Huntington disease mice with transgenic mice expressing an active HSF1 (HSF1Tg). Analysis of the skeletal muscle revealed that the polyglutamine inclusion formation and its weight loss were improved in R6/2/HSF1Tg mice. Unexpectedly, the life span of R6/2/HSF1Tg mice was significantly improved, although active HSF1 is not expressed in the brain. These results indicated that active HSF1 has a strong inhibitory effect on polyglutamine aggregate formation in vivo and in vitro.
Caspases and apoptosis (2002)

The ability of metazoan cells to undergo programmed cell death is vital to both the precise development and long-term survival of the mature adult. Cell deaths that result from engagement of this programme end in apoptosis, the ordered dismantling of the cell that results in its 'silent' demise, in which packaged cell fragments are removed by phagocytosis. This co-ordinated demise is mediated by members of a family of cysteine proteases known as caspases, whose activation follows characteristic apoptotic stimuli, and whose substrates include many proteins, the limited cleavage of which causes the characteristic morphology of apoptosis. In vertebrates, a subset of caspases has evolved to participate in the activation of pro-inflammatory cytokines, and thus members of the caspase family participate in one of two very distinct intracellular signalling pathways.
Operating system support for simultaneous multithreaded processors (2021)

Simultaneous multithreaded (SMT) processors are able to execute multiple application threads in parallel in order to improve the utilisation of the processor’s execution resources. The improved utilisation provides a higher processor-wide throughput at the expense of the performance of each individual thread. Simultaneous multithreading has recently been incorporated into the Intel Pentium 4 processor family as “Hyper-Threading”. While there is already basic support for it in popular operating systems, that support does not take advantage of any knowledge about the characteristics of SMT, and therefore does not fully exploit the processor. SMT presents a number of challenges to operating system designers. The threads’ dynamic sharing of processor resources means that there are complex performance interactions between threads. These interactions are often unknown, poorly understood, or hard to avoid. As a result such interactions tend to be ignored leading to a lower processor throughput. In this dissertation I start by describing simultaneous multithreading and the hardware implementations of it. I discuss areas of operating system support that are either necessary or desirable. I present a detailed study of a real SMT processor, the Intel Hyper-Threaded Pentium 4, and describe the performance interactions between threads. I analyse the results using information from the processor’s performance monitoring hardware. Building on the understanding of the processor’s operation gained from the analysis, I present a design for an operating system process scheduler that takes into account the characteristics of the processor and the workloads in order to improve the system-wide throughput. I evaluate designs exploiting various levels of processor-specific knowledge. I finish by discussing alternative ways to exploit SMT processors. These include the partitioning onto separate simultaneous threads of applications and hardware interrupt handling. I present preliminary experiments to evaluate the effectiveness of this technique.
Inflammatory Bowel Disease Genetics: Nod2 (2006)

The inflammatory bowel diseases (IBD) are comprised of two major subphenotypes, Crohn's disease (CD) and ulcerative colitis (UC). A significant role for genetic factors in IBD was established from epidemiologic studies and, more recently, the identification of well-established disease associations, notably the association of Nod2 (CARD15) polymorphisms with CD. The mapping to CD of Nod2 variants that alter protein function represents one of the earliest, most well-established, associations in complex genetic disorders. Since the initial discovery, genotype-phenotype correlations, definition of Nod2 expression and signaling pathways, association studies in other, related disorders, and features of Nod2 deficiency in murine models have been reported. Taken together, the Nod2 association to CD provides an illustrative model of the role of single gene variants in disease pathogenesis for common, complex multigenic disorders. Here we review general aspects of IBD genetics with particular focus on the role of Nod2 in CD.
Isolation and Characterization of the Alkaline Protease Gene of Aspergillus oryzae. (1991)

The genomic DNA for the alkaline protease (Alp) of the fungus Aspergillus oryzae was isolated using synthetic oligonucleotides as hydridization probes, and the complete nucleotide sequence was identified. The Alp gene is 1374 nucleotides long and contains three introns, one of which is in the pro region and two in the mature coding region. Sequences related to the TATA box (TATAAAT) and the CAAT box (CCAAAT) were found in the 5'-noncoding region. Primer extension analysis showed that three transcriptional start points are present.
Spatial transformations for rapid scan-line surface shadowing (1989)

A novel approach to surface shadowing is presented that is based on a parallel solution to the hidden-surface (visibility) problem. The approach computes visibility along scan lines of a spatial transformation of the surface height data. The transformation aligns in scan lines all potentially occluding points on the surface, allowing rapid 1-D determination of whether a point can be seen by the light source. Using this approach, arbitrarily defined surfaces can be shadowed very much more quickly than by conventional methods; a 512*512 surface image can be shadowed in less than 30 s on a MicroVAX II. The method also provides an efficient preprocessor for realistic 3-D scene synthesis, allowing the marking of shadowed pixels to eliminate unnecessary diffuse and specular reflection computations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Immunohistochemical overexpression of p16 protein associated with intact retinoblastoma protein expression in cervical cancer and cervical intraepithelial neoplasia (1998)

Both p16 and retinoblastoma (Rb) proteins are important tumor suppressors that regulate the cell cycle. The status of both proteins in invasive cervical cancer and cervical intraepithelial neoplasia (CIN) has not yet been examined. The aim of this study was to investigate the expression of p16 and Rb proteins by immunohistochemistry using 98 formalin-fixed and paraffin-embedded samples of various cervical neoplastic lesions. Strong immunoreactivity for the p16 protein was observed in both the nuclei and cytoplasm of all CIN and invasive cancer cases except several low-grade CIN lesions. Expression of Rb protein was also demonstrated in the scattered nuclei of neoplastic and normal cells in all cases investigated. The results suggest that the deletion or mutational inactivity of both p16 and Rb proteins may be a rare event in cervical carcinogenesis. Moreover, overexpression of the p16 protein may be a useful diagnostic marker for cervical neoplastic lesions on routine laboratory screening.
3D-corrective osteotomy using surgical guides for posttraumatic distal humeral deformity. (2012)

An original technique was developed to correct distal humerus malunion using a three-dimensional computer-assisted planning and a custom-made surgical guide. The technique was used in three cases (two with cubitus varus and one with cubitus valgus).A CT-scan of the distal humerus was obtained. The correction was simulated by software. A three-dimensional model of the patient's affected humerus was created by rapid prototyping, allowing creation of a surgical guide and premoulding of the osteosynthesis plate. At the time of surgery, the sterilised guide was placed on the surface of the bone to guide the saw blade. Osteosynthesis was performed using the moulded plate. At the latest follow-up, all three patients were asymptomatic and had regained full elbow mobility. Satisfying correction was obtained in all three cases. One complication was encountered: a postoperative infection that healed with plate removal and systemic antibiotic administration. Using an osteotomy guide facilitates three-dimensional humeral correction. This technique presents several benefits: it decreases the operating time and minimizes the surgical incision. Fluoroscopy is unnecessary during the procedure and accuracy is increased. Disadvantages are the time for planning and guide confection, the need of a CT-scanner and the increased cost.
Pulsed Ultrasound Differentially Stimulates Somatosensory Circuits in Humans as Indicated by EEG and fMRI (2012)

Peripheral somatosensory circuits are known to respond to diverse stimulus modalities. The energy modalities capable of eliciting somatosensory responses traditionally belong to mechanical, thermal, electromagnetic, and photonic domains. Ultrasound (US) applied to the periphery has also been reported to evoke diverse somatosensations. These observations however have been based primarily on subjective reports and lack neurophysiological descriptions. To investigate the effects of peripherally applied US on human somatosensory brain circuit activity we recorded evoked potentials using electroencephalography and conducted functional magnetic resonance imaging of blood oxygen level-dependent (BOLD) responses to fingertip stimulation with pulsed US. We found a pulsed US waveform designed to elicit a mild vibration sensation reliably triggered evoked potentials having distinct waveform morphologies including a large double-peaked vertex potential. Fingertip stimulation with this pulsed US waveform also led to the appearance of BOLD signals in brain regions responsible for somatosensory discrimination including the primary somatosensory cortex and parietal operculum, as well as brain regions involved in hierarchical somatosensory processing, such as the insula, anterior middle cingulate cortex, and supramarginal gyrus. By changing the energy profile of the pulsed US stimulus waveform we observed pulsed US can differentially activate somatosensory circuits and alter subjective reports that are concomitant with changes in evoked potential morphology and BOLD response patterns. Based on these observations we conclude pulsed US can functionally stimulate different somatosensory fibers and receptors, which may permit new approaches to the study and diagnosis of peripheral nerve injury, dysfunction, and disease.
Carbon Dioxide Capture by Superbase‐Derived Protic Ionic Liquids (2010)

CO2 capture: Protic ionic liquids (PILs) from a superbase and fluorinated alcohol, imidazole, pyrrolinone, or phenol were designed to capture CO2 based on the reactivity of their anions to CO2. These PILs are capable of rapid and reversible capture of about one equivalent of CO2, which is superior to those sorption systems based on traditional aprotic ILs. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Production of granulocyte colony stimulating factor in decidual tissue and its significance in pregnancy. (1990)

The increase of the number of polymorphonuclear leukocytes (PMN) in peripheral blood during pregnancy is well known. Granulocyte colony stimulating factor (G-CSF) has been found to act as a hemopoietic factor for PMN. This study analyzed G-CSF concentrations in the peripheral blood of pregnant women and examined whether decidual tissue acted as source of G-CSF production. The proliferation of chorionic cells measured by [3H]-thymidine uptake and its association with G-CSF were also examined. The results revealed that the concentration of G-CSF increased during the course of pregnancy and was positively correlated with the number of PMN. Large amounts of G-CSF was produced in cultures of decidual cells. We also found that G-CSF stimulates the proliferation of the chorionic cells. It was concluded that the decidual cells have a G-CSF producing activity associated with the elevation of PMN and play some role in the proliferation of chorionic cells during pregnancy.
An instrument to measure the heat convection coefficient on the endocardial surface (2003)

This work describes the fundamentals and calibration procedure of an instrument for in vivo evaluation of the heat convection coefficient between the endocardium and the circulating blood flow. The instrument is to be used immediately before radio-frequency cardiac ablation is performed. Thus, this instrument provides researchers with a valuable parameter to predict lesion size to be achieved by the procedure. The probe is a thermistor mounted in a Swan-Ganz catheter, and it is driven by a constant-temperature anemometer circuit. A 1D model of the sensor behaviour in a convective medium, the calibration procedure and the apparatus are explained in detail. Finally, a performance analysis of the instrument in the range of 200-3500 W m(-2) K(-1) shows that the average absolute error of full scale is 7.4%.
The ideal tissue adhesive in facial plastic and reconstructive surgery. (1990)

In this paper we have reviewed cutaneous wound closure in facial plastic and reconstructive surgery using two different tissue adhesives: (1) Fibrin glue (Tisseel), and (2) N-butyl-2-Cyanoacrylate (Histoacryl Blue). Fibrin glue was used on 23 patients: eight lower blepharoplasties, eight hemi-facelifts, five mid browlifts and seven facial reconstructive procedures. Histoacryl glue was used in 108 blepharoplasty incisions, 30 facelift incisions, 21 submental incisions for liposuction, and 19 local flaps for facial reconstructive procedures. Comparison was made of the adequacy of bonding, cosmetic result of the incision, ease of use and cost. The results of our experience with tissue adhesives indicate the use of fibrin glue mainly on the undersurface of flaps. We think histoacryl glue is the ideal tissue adhesive for surface cutaneous wound closure in regards to safety, reliability, tensile strength and cost effectiveness.
Quinoline as a Privileged Scaffold in Cancer Drug Discovery (2011)

Quinoline (1-azanaphthalene) is a heterocyclic aromatic nitrogen compound characterized by a double-ring structure that contains a benzene ring fused to pyridine at two adjacent carbon atoms. Quinoline compounds are widely used as "parental" compounds to synthesize molecules with medical benefits, especially with anti-malarial and anti-microbial activities. Certain quinoline-based compounds also show effective anticancer activity. This broad spectrum of biological and biochemical activities has been further facilitated by the synthetic versatility of quinoline, which allows the generation of a large number of structurally diverse derivatives. This includes numerous analogues derived from substitution of the quinoline ring system, and derivatization of quinoline ring structure. Quinoline and its analogs have recently been examined for their modes of function in the inhibition of tyrosine kinases, proteasome, tubulin polymerization and DNA repair. In this review, we have summarized our knowledge on quinoline compounds with respect to their anticancer activities, mechanisms of action, structure-activity relationship (SAR), and selective and specific activity against various cancer drug targets. In particular, we focus our review on in vitro and in vivo anticancer activities of quinoline and its analogs in the context of cancer drug development and refinement.
SIRT1/PGC1α-Dependent Increase in Oxidative Phosphorylation Supports Chemotherapy Resistance of Colon Cancer (2015)

Chemotherapy of colorectal tumors induces a SIRT1/PGC1α-dependent increase in OXPHOS that promotes tumor survival during treatment. This phenomenon is also observed in chemotherapy-exposed resected liver metastases, strongly suggesting that chemotherapy induces long-lasting changes in tumor metabolism that potentially interfere with drug efficacy. In conclusion, we propose a novel mechanism of chemotherapy resistance that may be clinically relevant and therapeutically exploitable.
Group A Streptococcal Infections of the Skin and Pharynx (1977)

Group A streptococci produce many infections, but the two most common are pharyngitis and impetigo. In a pediatric practice in Rochester, New York, approximately 10 per cent of office visits were related to streptococcal disease, and half these cases were pharyngitis.1 In spite of this high prevalence a study group found that recent medical-school graduates are not well versed in the microbiology or therapy of Group A streptococcal disease.2 These considerations prompt this review of the pathogenesis and management of two common streptococcal infections.The OrganismStreptococci are gram-positive, facultatively an-aerobic cocci that grow in chains . . .
Antisense Inhibition of Flavonoid Biosynthesis in Petunia Anthers Results in Male Sterility (1992)

Ingrid M. van der Meer, Maike E. Stam, Arjen J. van Tunen, Joseph N. M. Mol, Antoine R. Stuitje, Antisense Inhibition of Flavonoid Biosynthesis in Petunia Anthers Results in Male Sterility, The Plant Cell, Vol. 4, No. 3 (Mar., 1992), pp. 253-262