gebhart/patrepeval huggingface dataset:
High-Throughput Real-Time RT-PCR Assay to Detect the Exotic Newcastle Disease Virus during the California 2002–2003 Outbreak (2005)

During the 2002--2003 Exotic Newcastle Disease (END) outbreak in Southern California, a high-throughput real-time reverse transcriptase-polymerase chain reaction (RRT-PCR) system was developed to respond to the large diagnostic and surveillance sample workload. A 96-well RNA extraction method, using magnetic bead technology, combined with a 96-well RRT-PCR assay, allowed 1 technician to process and test more than 400 samples per day. A 3-technician team could complete testing on approximately 1,900 samples per day. The diagnostic sensitivity of the high-throughput RRT-PCR assay was 0.9967 (95% CI 0.9937-0.9997) based on 926 virus isolation confirmed positive samples. Diagnostic specificity using an initial 434 virus isolation confirmed negative samples was 100%. A diagnostic specificity of 0.9999 (95% CI 0.9999, >0.9999) was subsequently calculated on the basis of 2 false-positive results among 65,343 surveillance samples collected after the final END-positive case was confirmed in May 2003. Assay performance over 500 replicates, including reproducibility of the combined extraction and RRT-PCR amplification steps yielded a standard deviation of 0.70 RRT-PCR cycle thresholds (Ct) and a standard deviation of 0.59 Ct for the RRT-PCR steps alone. The high-throughput RRT-PCR developed for END contributed significantly to the 2002--2003 END control effort, reducing the predicted timeline for eradication from 3 years to just 11 months, primarily because of the large number of samples that could be rapidly tested. The 96-well approach described for high-throughput END RRT-PCR could be adapted to other rapid, high-volume testing needs, as required for potential foreign animal disease responses or intensive surveillance efforts.
Swelling and Ketoprofen Release Characteristics of Thermo- and pH-Responsive Copolymer Gels (1999)

Swelling-controlled drug delivery copolymer gels were newly synthesized by introducing thermo- and pH-responsive methacryloyl-glycine (MA-Gly) or pH-responsive methacrylic acid (MA-Ac) for comparison with thermoresponsive acryloyl-L-proline ethyl ester (A-ProOEt). A homopolymer gel of A-ProOEt was kept at degrees of swelling that were less than 0.5 at a pH from 2.5 to 7.5 at 37 degrees C. The thresholds of swelling for copolymer gels consisting of A-ProOEt/MA-Gly and A-ProOEt/MA-Ac with a composition of 40/60 mol% were found to be pH 3.0 and pH 5.5, respectively, in buffer solutions at 37 degrees C. The diffusion characteristics of 2-(3-benzoylphenyl)propionic acid (ketoprofen) from such copolymer gels was evaluated in buffer solutions at pH's more than 5.5, and it was found that A-ProOEt/MA-Gly gel possesses a case II transport mechanism that is completely linear time dependent in both the amount diffused and the penetrating swelling front position. On the other hand, A-ProOEt/MA-Ac gel exhibited a non-Fickian (or anomalous) diffusion behavior under the same conditions.
Eppin: a molecular strategy for male contraception. (2007)

New male contraceptives, both hormonal and non-hormonal, have many obstacles to overcome before they reach the market as a product. For hormonal contraceptives the long-term efficacy of oligospermia in a large population of unselected men remains to be determined. For nonhormonal contraception target selection remains a primary goal. Immunocontraception, which showed great promise for many years, has recently lost its appeal. Nevertheless, immunocontraception can be utilised as a strategy, particularly in primates, to discern the function of target molecules in the male. As an example, we discuss Eppin, an epididymal protease inhibitor that coats the surface of human spermatozoa. Because Eppin is predicted to be a serine protease inhibitor with chymotrypsin-like specificity and binds semenogelin, the natural substrate of PSA (prostate specific antigen, a serine protease), we investigated whether Eppin would modulate PSA activity and the hydrolysis of semenogelin. Additionally, because antibodies to Eppin provide contraception in male monkeys, we investigated whether antibodies to Eppin would inhibit the PSA hydrolysis of semenogelin. Eppin is a specific inhibitor of PSA activity that requires leucine 87, Eppin's P1 reactive site. Although Eppin modulates the hydrolysis of semenogelin by PSA, antibodies to Eppin do not inhibit PSA activity.
[Orthologs of arabidopsis CLAVATA 1 gene in cultivated Brassicaceae plants]. (2004)

In arabidopsis (Arabidopsis thaliana), the CLAVATA1 (CLV1) gene is involved in maintaining the balance between the stem cells in the central zone of the stem apical meristem and the determined cells at its periphery. However, CLV1 has not been previously characterized in other Brassicaceae. Using the direct amplification of genomic DNA, we obtained a full-length CLV1 ortholog from canola plants (Brassica napus), and also three CLV1 fragments from rape (B. rapa), canola (B. napus), and false flax (Camelina sativa), which corresponded to the transmembrane domain and a part of the kinase domain of the CLAVATA1 protein. The nucleotide and deduced amino acid sequences of the full-size CLV1 ortholog from B. napus were similar by 81 and 87% to the prototype gene from arabidopsis; in the case of shorter gene fragments, the similarity was as high as 91-93 and 98%, respectively. By their primary structure, the CLV1 genes in the Brassicaceae considerably differ from its putative structural homologs beyond this family.
Room‐Temperature Deoxygenation of Epoxides with CO Catalyzed by Hydrotalcite‐Supported Gold Nanoparticles in Water (2010)

Epoxide deoxygenation: Hydrotalcite-supported gold nanoparticles (Au/HT) efficiently catalyze the deoxygenation of epoxides to alkenes in water at room temperature under CO at atmospheric pressure and in the absence of organic solvents (see graphic). Moreover, Au/HT retains its activity and selectivity and can be reused. 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.
[The role of positron emission tomography (PET) in tumor diagnostics and therapy monitoring]. (2018)

Positron emission tomography (PET) is a medical imaging method belonging to the realm of nuclear medicine. It has been a clinical research tool since the sixties but during the late nineties it became widely utilized in clinical practice too. PET technique requires special radioactive isotopes, which may be generated only in particle accelerators (cyclotrons) and their transport is limited owing to the short physical half-life. PET/CT was born from the combination of PET and CT (computer tomography). The first combined PET/CT scanner began to operate in 1998 and the method has been used in clinical practice since 2001. It is a hybrid (multi-modality) medical imaging equipment which can provide anatomical, morphologic (CT) and functional, metabolic information (PET) simultaneously. PET/CT imaging has gained clinical acceptance mainly in oncology - owing to the attributes of the most frequently used PET tracer, fluoro-deoxy glucose (FDG) - and in a lesser extent in neuropsychiatry and cardiology. The authors in this paper review the basics and key indications of the method, the wider used radiofarmacons, including potential neurological and psychiatric applications, and the possible causes of false positivity and false negativity.
Effects of serum on (-)-gossypol-suppressed growth in human prostate cancer cells. (2006)

The data suggested that (-)-gossypol-suppressed prostate cancer cell growth may be influenced through cell cycle regulators, which may lead to better prognosis. We further speculate that (-)-gossypol might serve as a chemotherapeutic agent for human prostate cancer patients.
Insertion study of antimicrobial peptide mimicking polymer, meta-phenylene ethynylenes, with model cell membranes (2005)

421A-421A
1839-P: GLP-1 Receptor Antagonism Using Exendin-9,39 in the Fasting State Modulates a-Cell Function in Humans with Type 2 Diabetes (2019)

Glucagon-Like Peptide-1 (GLP-1) potentiates insulin secretion in response to an oral challenge. Exendin-(9,39) a competitive antagonist of GLP-1, has been used to quantify the contribution of endogenous GLP-1 to glucose tolerance. In nondiabetic subjects, Exendin-(9,39) infused for three hours altered the subsequent β-cell response to an i.v. glucose challenge. Similar results were observed using perifused human islets from nondiabetic donors. We hypothesized that the effects of fasting GLP-1 secretion on β-cell response would be similar in people with type 2 diabetes (T2D). We studied 9 subjects with T2D in random order. Glucose containing [3-3H]-glucose was infused to mimic the systemic appearance of glucose after a meal. On one occasion, saline, was infused for 3 hours prior (-180 to 0 minutes) to the I.V. challenge, while on the other Exendin-(9,39) was infused at 750pmol/kg/minutes. Exendin-(9,39) infusion prior to the i.v. challenge increased fasting (8.7 ± 0.6 vs. 7.8 ± 0.5 mmol/l, p &amp;lt; 0.01) and peak (13.3 ± 0.8 vs. 12.5 ± 0.6 mmol/l, p = 0.05) glucose concentrations. These differences were not explained by altered insulin secretion: insulin and C-peptide concentrations did not differ between study days. On the other hand, fasting glucagon concentrations were increased (70 ± 8 vs. 53 ± 1 ng/l, p = 0.01) by Exendin-(9,39) and this was accompanied by increased endogenous glucose production (23 ± 1 vs. 20 ± 1 μmol/kg/minutes, p = 0.02). In separate experiments using perifused isolated human islets from diabetic donors, pretreatment with Exendin-(9,39) did not alter integrated insulin secretion in response to hyperglycemia (0.6 ± 0.2 vs. 0.9 ± 0.4 nmol/Islet/30 minutes, p = 0.49). Taken together these results suggest that in T2D fasting GLP-1 receptor activation may augment glucagon suppression in response to subsequent challenges. This may represent an adaptive mechanism not seen in nondiabetic subjects that restrains α-cell function to decrease postprandial hyperglycemia. Disclosure M.D. Hurtado: None. A.M. Egan: None. M.C. Laurenti: Employee; Self; GlySens Incorporated. J. Adams: None. R.A. Rizza: Advisory Panel; Self; Lilly Diabetes, Metavention, Novo Nordisk A/S, vTv Therapeutics. C. Cobelli: None. A. Matveyenko: None. C. Dalla Man: None. A. Vella: Advisory Panel; Self; vTv Therapeutics. Research Support; Self; Novo Nordisk Inc. Funding Endocrine Fellows Foundation; National Institutes of Health
Modal approach to the morphology of spiral galaxies. 3: Application to the galaxy M81 (1994)

The modal approach to the morphology of spiral galaxies is applied to the galaxy NGC 3031 (M81) to demonstrate how the shape of the spiral pattern, specifically that obtained by Elmegreen et al. for the distribution of the stellar objects, may be used to help with the determination of the axisymmetric basic state of a galaxy with a reasonably regular spiral structure. The parameters of the basic state are narrowly constrained when all available observational data are taken into consideration, including both the mass distribution and the two components of velocity dispersion in the stellar disk. The ratio of the two components of velocity dispersion is found to be similar to that observed in the solar vicinity-a result that supports the reasonableness of the model. The mass distribution and the mass-to-light ratio obtained agree with that given by Kent from analysis of rotation curves. When compared with the work of Visser, it appears that he might have tended to use a heavier disk to support the gravitational field without including a sufficient amount of spherical components. The success of the present modeling process also supports the view that, to a first approximation, the spiral structure in many galaxies, essentially isolated at the present time, is a long-lasting, but in general slowly evolving, largely intrinsic characteristic of a galaxy. The possible influence of the companion NGC 3077 is discussed: the global spiral structure is approximately an intrinsic mode, but its exact nature is likely to be related to an earlier passage of this small companion.
Supplementary Figures S1-S4 from The CDK4/6 Inhibitor LY2835219 Overcomes Vemurafenib Resistance Resulting from MAPK Reactivation and Cyclin D1 Upregulation (2023)

&lt;p&gt;Supplementary figure S1 describes the molecular mechanisms of resistance across vemurafenib-resistant cell line models. Supplementary figure S2 serves as a repeat of figure 3a describing development of in vivo model of resistance, and demonstrates the effect of vemurafenib withdrawl on the resistant tumors. Supplementary figure S3 describes the effect of vemurafenib treatment on MAPK pathway inhibition in A375-RV2 cells. Supplementary figure S4 shows that selective cyclin D1 knockdown or CDK4/6 inhibition induces apoptosis in A375-R1 and M14-R vemurafenib-resistant melanoma cells.&lt;/p&gt;
The modern management of incisional hernias (2012)

#### Summary points

Before the introduction of general anaesthesia by Morton in 1846, incisional hernias were rare. As survival after abdominal surgery became more common so did the incidence of incisional hernias.1 Since then, more than 4000 peer reviewed articles have been published on the topic, many of which have introduced a new or modified surgical technique for prevention and repair. Despite considerable improvements in prosthetics used for hernia surgery, the incidence of incisional hernias and the recurrence rates after repair remain high. Arguably, no other benign disease has seen so little improvement in terms of surgical outcome.

#### Sources and selection criteria

We searched PubMed from 1970-2012 and Embase and the Cochrane Library from inception using the terms “hernia” and “incisional” (using the Boolean operator AND) and “ventral” (using the Boolean operator OR). The reference lists were also used to identify studies of interest. Both authors independently identified publications for inclusion and differences were resolved by discussion. We gave priority to research published in the past five years and highly regarded older publications.

Unlike other abdominal wall hernias, which occur through anatomical points of weakness, incisional hernias occur through a weakness at the site of abdominal wall closure. Why, unlike primary abdominal wall hernias, are the results after repair so poor? Perhaps it is because in the repair of incisional hernias several problems need to be overcome: a multilayered wall structure of different tissue properties in constant motion has to be sutured; positive abdominal …
Development of direct gene transfer technologies by electroporation of higher plant protoplasts (1987)

Development of direct gene transfer technologies by electroporation of higher plant protoplasts. Moët-Hennessy Conference Electronique et Pilotage des Plants
Evaluation of mineral composition and antioxidant capacity of three brown macroalgae species (Phaeophyceae) from the Portuguese Coast (2014)

Seaweeds are a great source of valuable compounds, including essential minerals and antioxidants [1]. Notably, the content of these components in a macroalgae species depend on distinct factors, such as the type of habitat, the quality and the intensity of light, exposure to UV-radiation, temperature, and salinity, among others [2]. Up to this moment, the knowledge of the chemical compositionof seaweeds from the Portuguese Coast is still very limited. Hence, this study aimed to characterize the mineral composition and antioxidant contents of Sargassum muticum, Fucus vesiculosos and Bifurcaria bifurcata.
Assisted Reproduction-In Vitro Fertilization Success Is Improved by Ovarian Stimulation with Exogenous Gonadotropins and Pituitary Suppression with Gonadotropin-Releasing Hormone Analogues* (1999)

I. Introduction II. Ovarian Stimulation with Exogenous Gonadotropin Improves In Vitro Fertilization and Embryo Transfer (IVF-ET) Success III. Pituitary Suppression Improves IVF-ET Success: GnRH Agonist Analogues IV. Pituitary Suppression Improves IVF-ET Success: GnRH Antagonist Analogues
Biliprotein in adult icteric serum--demonstrated by extension of the alkaline methanolysis procedure. (1982)

We confirmed that the alkaline methanolysis procedure of Blanckaert (Biochem. J. 185: 115-128, 1980) converts the sugar conjugates of bilirubin (Bc) into their corresponding methyl and dimethyl esters, which can be extracted into chloroform along with underivatized unconjugated bilirubin (Bu). By this procedure, we accounted for Bu nearly quantitatively, but only 76-83% of total Bc. By pretreating samples containing Bu and (or) Bc with a caffeine/benzoate reagent, we improved the analytical recovery of Bc to 85-93% without affecting the Bu. When the method (+ caffeine/benzoate) was applied to adult icteric serum, a variable fraction (20-75%) of the original total bilirubin (based on diazo reactivity) remained with the protein pellet, which is routinely discarded in the original methanolysis procedure. In this pellet we demonstrated the occurrence of a strongly protein-bonded bilirubin fraction (biliprotein) similar to the recently described "delta" fraction (Clin. Chem. 28: 629-637, 1982). The analytical and clinical implications of our findings are discussed.
Electric vehicles in volatile power system operations (2011)

In this paper, the optimal hourly integration of EV fleets with the stochastic operation of wind energy is presented. The stochastic security constrained unit commitment (SCUC) is proposed to procure an hourly commitment and dispatch schedule for security-constrained power generation facilities (including thermal, hydro, wind, and EV fleets) that would minimize the operation cost of power systems while satisfying the required EV charging and utilization requirements.
Direct C‐Allylation of Aryl‐Alkyl/Glycosyl Carbinols: Facile Synthesis of C‐Linked Carbo‐β2‐/γ2‐/δ2‐Amino Acids. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Regulation of relaxed static stability aircraft (1991)

The authors formulate and solve a regulator problem for nonlinear parameter-dependent dynamics. It is shown that the problem is solvable except at parameter values associated with bifurcation of the equilibrium equations and that such bifurcations are inherently linked to the system zero dynamics. These results are applied to the study of the regulation of the longitudinal dynamics of aircraft. It is shown how bifurcation points arise in these problems and why they affect solvability of the regulator problem. The relationships between bifurcation, system zeros, and dynamic and static stability are illustrated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Preliminary investigation of Boltzmann machine classifiers for speaker recognition. (2012)

We propose a novel generative approach to speaker recognition using Boltzmann machines, a fledgeling non-Gaussian probabilistic framework that is increasingly gaining attention in several machine learning fields. We show how a modified i-vector representation of speech utterances enables the development of several Boltzmann machine architectures for speaker verification and we report some preliminary speaker recognition results obtained with one of them, which we refer to as Siamese twins. The Siamese twin architecture is designed to capture correlations between utterances spoken by a single speaker and it can be regarded as probabilistic analogue of the well known cosine distance metric. A relative improvement of 27% is reported on NIST-2010 telephone female data.
Integrating and Live-time Radiation Dosimetry by Optical Crystal Damage, Initial Results with Neutrons (2018)

Radiation damage can be assessed through many techniques, though the assessment is usually offline and shows only integrated dose. Transparent crystals can be optically monitored for radiation damage nondestructively, to serve as a detector for both immediate dose and integrated dose for signatures of radiation exposure history. There is also some difference in gamma-ray and neutron interactions which can be observed. Gamma ray interactions primarily produce electron displacements, which are preserved as color centers in ionic crystals and produce specific spectral absorption lines. Neutron interactions strongly produce lattice displacements that affect the index of refraction. The differences may allow us to use inexpensive crystals for long time neutron monitoring. Spectroscopic absorption lines can be quantified using prior technology, but due to prior limits in phase sensitivity there was no previous use of index of refraction measurements. Using novel techniques based on intracavity phase interferometry to assess lattice displacements, we are able to examine neutron irradiation in CaF2 crystals. Initial results with neutrons will be presented.
JAZ repressors of metabolic defense promote growth and reproductive fitness in Arabidopsis (2018)

Plant immune responses mediated by the hormone jasmonoyl-l-isoleucine (JA-Ile) are metabolically costly and often linked to reduced growth. Although it is known that JA-Ile activates defense responses by triggering the degradation of JASMONATE ZIM DOMAIN (JAZ) transcriptional repressor proteins, expansion of the <i>JAZ</i> gene family in vascular plants has hampered efforts to understand how this hormone impacts growth and other physiological tasks over the course of ontogeny. Here, we combined mutations within the 13-member <i>Arabidopsis JAZ</i> gene family to investigate the effects of chronic JAZ deficiency on growth, defense, and reproductive output. A higher-order mutant (<i>jaz</i> decuple, <i>jazD</i>) defective in 10 <i>JAZ</i> genes (<i>JAZ1</i>-<i>7</i>, <i>-9</i>, <i>-10</i>, and <i>-13</i>) exhibited robust resistance to insect herbivores and fungal pathogens, which was accompanied by slow vegetative growth and poor reproductive performance. Metabolic phenotypes of <i>jazD</i> discerned from global transcript and protein profiling were indicative of elevated carbon partitioning to amino acid-, protein-, and endoplasmic reticulum body-based defenses controlled by the JA-Ile and ethylene branches of immunity. Resource allocation to a strong defense sink in <i>jazD</i> leaves was associated with increased respiration and hallmarks of carbon starvation but no overt changes in photosynthetic rate. Depletion of the remaining JAZ repressors in <i>jazD</i> further exaggerated growth stunting, nearly abolished seed production and, under extreme conditions, caused spreading necrotic lesions and tissue death. Our results demonstrate that JAZ proteins promote growth and reproductive success at least in part by preventing catastrophic metabolic effects of an unrestrained immune response.