gebhart/patrepeval huggingface dataset:
Translation arrest by oligodeoxynucleotides complementary to mRNA coding sequences yields polypeptides of predetermined length (1986)

We investigated the arrest of mRNA translation at predetermined sites by oligodeoxynucleotides complementary to defined coding sequences within a mRNA. An in vitro transcription and a wheat germ cell-free translation system were used for the synthesis of mRNA and protein, respectively. Oligodeoxynucleotides (10-, 15- and 20-mer) arrested polypeptide synthesis in a concentration-dependent manner at the site of their hybridization to the mRNA, as judged by the size of the translation products. A 5-mer oligodeoxynucleotide did not prevent synthesis of the full length protein. Ribosomes arrested by an oligodeoxynucleotide transiently stacked up and eventually disassembled. Upon dissociation of the ribosomes from the blocked site, nascent chains were released as peptidyl-tRNAs which in turn became rapidly converted to free polypeptide chains. None of these results was affected by the position within the reading frame to which the 3' end of the oligodeoxynucleotide hybridized. The general applicability of translation arrest by oligodeoxynucleotides was demonstrated for different mRNAs. Only partial arrest of translation was obtained when oligodeoxynucleotides were used to arrest translation in the reticulocyte cell-free system.
The Interleukin 1β Pathway in the Pathogenesis of Osteoarthritis (2008)

Osteoarthritis (OA) is a major disabling disease and is ranked as a major cause of chronic pain in adults. The pathology of the illness is characterized by a loss of articular cartilage leading to narrowing of joint space, increased joint friction, potential structural remodeling, persistent pain, and functional impairment. The proinflammatory cytokine interleukin 1beta (IL-1beta) has several chemical and bioactive characteristics allowing this catabolic protein to be involved in initiation and progression of OA. We review the current understanding of the pathogenesis of OA, and how upregulation of IL-1beta initiates a cascade of intracellular events that can culminate in activation of proteinases, creation of a pro-destructive articular milieu, suppression of anabolic pathways, and a decrease in the synthesis of cartilage extracellular matrix. Therapeutic approaches to block the action of IL-1beta and overcome its signal transduction to curtail disease progression are discussed.
Prevalence of Antibodies to Adenovirus Serotypes 4 and 7 among Unimmunized US Army Trainees: Results of a Retrospective Nationwide Seroprevalence Survey (1998)

The 1996 production halt of adenovirus types 4 and 7 vaccines prompted concerns about the resurgence of large respiratory disease outbreaks among US military basic trainees. This serosurvey was conducted to assess the current susceptibility of the trainee population to these viruses. A stratified, random sample (n=303) of trainees' sera was tested using a quantitative colorimetric microneutralization assay to demonstrate antibody titers considered to provide immunologic protection against each adenovirus type. Results were analyzed for relationships between susceptibility and 4 demographic factors-gender, race, prior military service, and age. Results showed that 66% and 73% of trainees were susceptible to serotypes 4 and 7, respectively. Nearly 90% were susceptible to at least one serotype. Susceptibility was significantly (P<.05) related to lack of prior military service and younger age. Consistent with a serosurvey conducted 20 years ago, these results demonstrated significant susceptibility to two vaccine-preventable causes of disease. These findings may have civilian implications.
Mechanisms of Ligand Binding to the Parathyroid Hormone (PTH)/PTH-Related Protein Receptor: Selectivity of a Modified PTH(1–15) Radioligand for GαS-Coupled Receptor Conformations (2005)

Mechanisms of ligand binding to the PTH/PTHrP receptor (PTHR) were explored using PTH fragment analogs as radioligands in binding assays. In particular, the modified amino-terminal fragment analog, (125)I-[Aib(1,3),Nle8,Gln10,homoarginine11,Ala12,Trp14,Tyr15]rPTH(1-15)NH2, (125)I-[Aib(1,3),M]PTH(1-15), was used as a radioligand that we hypothesized to bind solely to the juxtamembrane (J) portion of the PTHR containing the extracellular loops and transmembrane helices. We also employed (125)I-PTH(1-34) as a radioligand that binds to both the amino-terminal extracellular (N) and J domains of the PTHR. Binding was examined in membranes derived from cells expressing either wild-type or mutant PTHRs. We found that the binding of (125)I-[Aib(1,3),M]PTH(1-15) to the wild-type PTHR was strongly (approximately 90%) inhibited by guanosine 5'-O-(3-thio)triphosphate (GTPgammaS), whereas the binding of (125)I-PTH(1-34) was only mildly (approximately 25%) inhibited by GTPgammaS. Of these two radioligands, only (125)I-[Aib(1,3),M]PTH(1-15) bound to PTHR-delNt, which lacks most of the receptor's N domain, and again this binding was strongly inhibited by GTPgammaS. Binding of (125)I-[Aib(1,3),M]PTH(1-15) to the constitutively active receptor, PTHR-H223R, was only mildly (approximately 20%) inhibited by GTPgammaS, as was the binding of (125)I-PTH(1-34). In membranes prepared from cells lacking Galpha(S) via knockout mutation of Gnas, no binding of (125)I-[Aib(1,3),M]PTH(1-15) was observed, but binding of (125)I-[Aib(1,3),M]PTH(1-15) was recovered by virally transducing the cells to heterologously express Galpha(S). (125)I-PTH(1-34) bound to the membranes with or without Galpha(S). The overall findings confirm the hypothesis that (125)I-[Aib(1,3),M]PTH(1-15) binds solely to the J domain of the PTHR. They further show that this binding is strongly dependent on coupling of the receptor to Galpha(S)-containing heterotrimeric G proteins, whereas the binding of (125)I-PTH(1-34) can occur in the absence of such coupling. Thus, (125)I-[Aib(1,3),M]PTH(1-15) appears to function as a selective probe of Galpha(S)-coupled, active-state PTHR conformations.
Bacteria Identification From Microscopic Morphology Using Naïve Bayes (2014)

Great knowledge and experience on microbiology are required for accurate bacteria identification. Automation of bacteria identification is required because there might be a shortage of skilled microbiologists and clinicians at a time of great need. We propose an automatic bacteria identification framework that can classify three famous classes of bacteria namely Cocci, Bacilli and Vibrio from microscopic morphology using the Nave Bayes classifier. The proposed bacteria identification framework comprises two steps. In the first step, the system is trained using a set of microscopic images containing Cocci, Bacilli, and Vibrio. The input images are normalized to emphasize the diameter and shape features. Edge-based descriptors are then extracted from the input images. In the second step, we use theNave Bayes classifier to performprobabilistic inference based on the input descriptors. 64 images for each class of bacteria were used as the training setand 222 images consisting of the three classes of bacteria and other random images such as humans and airplanes were used as the test set. There are no images overlapped between the training set and the test set. The system was found to be able to accurately discriminate the three classes of bacteria. Moreover, the system was also found to be able to reject images that did not belong to any of the three classes of bacteria. The preliminary results demonstrate how a simple machine learning classifier with a set of simple image-based features can result in high classification accuracy. The preliminary results also demonstrate the efficacy and efficiency of our two-step automatic bacteria identification approach and motivate us to extend this framework to identify a variety of other types of bacteria.
c-myb effects on kinetic events during MEL cell differentiation. (1992)

During dimethylsulfoxide (DMSO)-induced differentiation of Friend mouse erythroleukemia (MEL) cells there is a biphasic fall in c-myb mRNA levels. We have previously shown that constitutive expression of c-myb blocks differentiation. To delineate more accurately the point at which Myb blocks differentiation, MEL cells were transfected with a human c-myb construct under the control of the beta-globin promoter and enhancers. In concert with endogenous DMSO-induced globin transcription during MEL cell differentiation, the beta-globin c-myb transcription unit of the transfected plasmid is activated after 3-5 days of culture in media containing DMSO. Here we describe c-myb-transformed MEL clones which undergo delayed expression of the exogenous c-myb following 3-5 days of culture in DMSO. In contrast to wild-type MEL cells, both clones failed to display phenotypic markers of differentiation and continued to proliferate for up to 10 days of culture. These data suggest that the late fall in c-myb levels may be required in order for differentiation to occur. Additionally, we suggest that constitutive expression of c-myb does not block early commitment events such as activation of histone Hl', subsequent chromatin condensation, and alteration of proliferation-related gene expression. Taken together, these results show that c-myb acts very late in the process of differentiation.
Technical design and concept of a 0.35 T MR-Linac (2019)

The integration of magnetic resonance (MR) imaging and linear accelerators into hybrid treatment systems has made MR-guided radiation therapy a clinical reality. This work summarizes the technical design of a 0.35 T MR-Linac and corresponding clinical concepts. The system facilitates 3D-conformal as well as IMRT treatments with 6MV photons. Daily MR imaging provides superior soft-tissue contrast for patient setup and also enables on-table adaption of treatment plans, which is fully integrated into the treatment workflow of the system. Automated beam gating during delivery is facilitated by cine MR imaging and structure tracking. Combining different novel features compared to conventional image-guided radiotherapy, this technology offers the potential for margin reduction as well as dose escalation.
Curative effect of DL-2-difluoromethylornithine on mice bearing mutant L1210 leukemia cells deficient in polyamine uptake. (1988)

The objective of the present investigation was to determine to what extent polyamine uptake from the host contributes to the ability of tumor cells in overcoming the antiproliferative effect of a polyamine synthesis inhibitor. A mutant L1210 leukemia cell line deficient in polyamine transport was isolated by selection for resistance to methylglyoxal bis(guanylhydrazone), an extremely cytotoxic agent which is taken up by the same transport system as the polyamines. C57BL/6 x DBA/2 F1 mice inoculated with mutant L1210 cells survived on the average 60 to 70% longer than mice inoculated with the parental cells. The therapeutic effect of a polyamine synthesis inhibitor, DL-2-difluoromethylornithine (3% in the drinking water), was much greater on mice bearing mutant L1210 cells (87% increase in median survival time; 13 of 40 mice cured) than on mice inoculated with parental cells (22% increase in median survival time). Similar results, although not as striking, were obtained using athymic nude mice, indicating that the therapeutic difference is not merely due to increased immunogenicity of the mutant cells.
Disabilities and quality of life in pure and comorbid generalized anxiety disorder and major depression in a national survey (2000)

Using a nationally representative sample, this study examines the disease-specific impairments of DSM-IV generalized anxiety disorder (GAD) by comparing them to the impairments associated with major depressive disorder (MDD). Results are based on 4181 respondents between the ages of 18-65 years who were interviewed with the 12-month version of the Munich-Composite International Diagnostic Interview as part of the German National Health Interview and Examination Survey-Mental Health Supplement (GHS). After controlling for age, gender, and other psychopathology, 'pure' current GAD without MDD (n = 33), pure MDD (n = 344) and comorbid GAD and MDD (n = 40) were each associated with high impairment as defined by poor self-perceived health, at least 3 days limited or impaired in the past month, and low quality of life scores [from the Short Form-36 Health Survey (SF-36)]. Quality of life scores on several of the SF-36 scales were significantly lower for respondents with pure GAD as compared to respondents with pure MDD. Overall, the results show that DSM-IV GAD is associated with high impairment even after controlling for other psychopathology. The impairment outcomes for GAD were comparable in size to those for MDD. These findings underline the significance of this disorder from a clinical and social perspective and provide support for the independent diagnostic status of GAD.
Pixel Circuits and Driving Schemes for Active-Matrix Organic Light-Emitting Diode Displays (2007)

Rapid progress over the last decade on thin film transistor (TFT) active matrix organic light emitting (AMOLED) displays led to the emergence of high-performance, low-power, low-cost flat panel displays. Despite the shortcomings of the active matrix that are associated with the instability and low mobility of TFTs, the amorphous silicon TFT technology still remains the primary solution for the AMOLED backplane. To take advantage of this technology, it is crucial to develop driving schemes and circuit techniques to compensate for the limitations of the TFTs. &#13;\nThe driving schemes proposed in this thesis address these challenges, in which, the sensitivity of the OLED current to the transistor variations is reduced significantly. This is achieved by comparing the data signal with a feedback signal associated with the pixel current by means of an external driving circuit through a column feedback line. Depending on the nature of the feedback signal, (i.e. current or voltage) several pixel circuits and external drivers are proposed. &#13;\nNew AMOLED pixel circuits with voltage and current feedback are designed, simulated, fabricated, and tested. The performance of these circuits is analyzed in terms of their stability, settling time, power efficiency, noise, and temperature-dependence. For the pixel circuits with current feedback, an operational transresistance amplifier is designed and implemented in a high-voltage CMOS process. Measurement results for both voltage and current feedback driving schemes indicate less than a 2%/V sensitivity to shifts in the threshold voltage of the TFTs. By using current feedback and an accelerating pulse, programming times less than 50 s are achieved.
Creating, transporting, cutting, and merging liquid droplets by electrowetting-based actuation for digital microfluidic circuits (2003)

Reports the completion of four fundamental fluidic operations considered essential to build digital microfluidic circuits, which can be used for lab-on-a-chip or micro total analysis system (μTAS): 1) creating, 2) transporting, 3) cutting, and 4) merging liquid droplets, all by electrowetting, i.e., controlling the wetting property of the surface through electric potential. The surface used in this report is, more specifically, an electrode covered with dielectrics, hence, called electrowetting-on-dielectric (EWOD). All the fluidic movement is confined between two plates, which we call parallel-plate channel, rather than through closed channels or on open surfaces. While transporting and merging droplets are easily verified, we discover that there exists a design criterion for a given set of materials beyond which the droplet simply cannot be cut by EWOD mechanism. The condition for successful cutting is theoretically analyzed by examining the channel gap, the droplet size and the degree of contact angle change by electrowetting on dielectric (EWOD). A series of experiments is run and verifies the criterion.
Computing TaqMan Probes for Multiplex PCR Detection of E. coli O157 Serotypes in Water (2005)

Diarrheagenic E. coli strains contribute to water related diseases in urban and rural environment in developing and developed world. E. coli pathotype and pathogenicity varies due to complex multifactorial mechanism involving a large number of virulence factors. Rapid assessment of the virulence pattern of E. coli isolates is possible by Real-Time PCR probes like TaqMan. For designing TaqMan probes and primers for multiplex PCR selected E. coli gene sequences: stx1, stx2, hlyA, chuA, eae, lacZ, lamB and fimA were retrieved from NCBI's GenBank database. The alignment of the multiple sequences and analysis of conserved sequences was carried out using ClustalW and BLAST programs. The primers and Taqmen probes were designed using Beacon Designer software version 2.1 for two multiplexed PCR assays. In silico PCR simulation of these assays showed PCR products for stx2 (248bp) stx1 (102 bp), lacZ (228bp) and lamB (86 bp) in multiplex #1 and eae (200bp), chuA (147 bp), hlyA (141bp) and fimA (79 bp) in multiplex #2, respectively. These multiplexed PCR amplification products and probes can be used to identify and confirm presence of O157:H7/ H7-, O157:H43/45 and O26:H-/H11 serotypes. In conclusion, multiplex Real-Time Polymerase Chain Reaction oligomers and TaqMan probes designed and validated in silico will be helpful in management of water quality and outbreaks, by improving specificity and minimizing time needed for in vitro verification work.
Method development in quantitative NMR towards metrologically traceable organic certified reference materials used as 31P qNMR standards (2014)

Quantitative nuclear magnetic resonance (qNMR) spectroscopy is employed by an increasing number of analytical and industrial laboratories for the assignment of content and quantitative determination of impurities. Within the last few years, it was demonstrated that (1)H qNMR can be performed with high accuracy leading to measurement uncertainties below 1 % relative. It was even demonstrated that the combination of (1)H qNMR with metrological weighing can lead to measurement uncertainties below 0.1 % when highly pure substances are used. Although qNMR reference standards are already available as certified reference materials (CRM) providing traceability on the basis of (1)H qNMR experiments, there is an increasing demand for purity assays on phosphorylated organic compounds and metabolites requiring CRM for quantification by (31)P qNMR. Unfortunately, the number of available primary phosphorus standards is limited to a few inorganic CRM which only can be used for the analysis of water-soluble analytes but fail when organic solvents must be employed. This paper presents the concept of value assignment by (31)P qNMR measurements for the development of CRM and describes different approaches to establish traceability to primary Standard Reference Material from the National Institute of Standards and Technology (NIST SRM). Phosphonoacetic acid is analyzed as a water-soluble CRM candidate, whereas triphenyl phosphate is a good candidate for the use as qNMR reference material in organic solvents. These substances contain both nuclei, (1)H and (31)P, and the concept is to show that it is possible to indirectly quantify a potential phosphorus standard via its protons using (1)H qNMR. The same standard with its assigned purity can then be used for the quantification of an analyte via its phosphorus using (31)P qNMR. For the validation of the concept, triphenyl phosphate and phosphonoacetic acid have been used as (31)P qNMR standards to determine the purity of the analyte tris(2-chloroethyl) phosphate, and the resulting purity values perfectly overlap within their expanded measurement uncertainties.
The Vacuolating Virus, S.V.40 (1960)

The newly discovered vacuolating virus, S.V.40, appears to be a common and essentially ubiquitous contaminant of rhesus monkey kidney cell cultures and a likely common contaminant of cynomolgus kidney cultures in which it develops to high titer without evident cytopathic change. The virus grows readily in grivet, vervet and patas kidney and in rhesus testicle cultures causing a unique cytopathology characterized by ballooning and intense vacuolation. Some biological and biophysical properties of the virus are described. Principal interest in and importance of the vacuolating virus arise from its demonstrated presence in all 3 types of Sabin's live poliovirus vaccines and in numerous respiratory virus seed lines employed in human volunteer inoculation experiments. Demonstration of the virus has raised the question of safety following administration to human subjects, especially infants, and of possible lack of validity of conclusions reached from experiments to measure neurovirulence or “genetic” markers of attenuated poliovirus vaccine strains and to determine the pathogenicity of respiratory viruses for man. The vacuolating virus is effectively dealt with in killed virus vaccines by virtue of its susceptibility to formalin. The optimal solution to the live virus vaccine problem appears to lie in elimination of the virus from such preparations.
Implementing an accurate and rapid sparse sampling approach for low-dose atomic resolution STEM imaging (2016)

While aberration correction for scanning transmission electron microscopes (STEMs) dramatically increased the spatial resolution obtainable in the images of materials that are stable under the electron beam, the practical resolution of many STEM images is now limited by the sample stability rather than the microscope. To extract physical information from the images of beam sensitive materials, it is becoming clear that there is a critical dose/dose-rate below which the images can be interpreted as representative of the pristine material, while above it the observation is dominated by beam effects. Here, we describe an experimental approach for sparse sampling in the STEM and in-painting image reconstruction in order to reduce the electron dose/dose-rate to the sample during imaging. By characterizing the induction limited rise-time and hysteresis in the scan coils, we show that a sparse line-hopping approach to scan randomization can be implemented that optimizes both the speed of the scan and the amount of the sample that needs to be illuminated by the beam. The dose and acquisition time for the sparse sampling is shown to be effectively decreased by at least a factor of 5× relative to conventional acquisition, permitting imaging of beam sensitive materials to be obtained without changing the microscope operating parameters. The use of sparse line-hopping scan to acquire STEM images is demonstrated with atomic resolution aberration corrected the Z-contrast images of CaCO3, a material that is traditionally difficult to image by TEM/STEM because of dosage issues.
Emergency contraception (2000)

Knowledge and use of emergency contraception world-wide is extremely limited. Recent research has demonstrated that levonorgestrel alone is at least as effective as the Yuzpe regimen and is much better tolerated. Levonorgestrel is likely to become the method of choice in the early 21st century. Mifepristone is highly effective even at doses which are not abortifacient. Efficacy cannot be calculated precisely, but all presently available methods seem to prevent at least 74% of unwanted pregnancies. The Yuzpe regimen inhibits or delays ovulation, but there is no good evidence that it prevents implantation. There are no data on the mechanism of action of levonorgestrel alone and the mode of action of mifepristone depends on when in the reproductive cycle it is used. Accessibility to emergency contraception is limited by the requirement for it to be prescribed by a doctor. Advanced provision of emergency contraception may prevent a significant number of unwanted pregnancies.