gebhart/patrepeval huggingface dataset:
Characterization of a quadruple glycoprotein-deleted pseudorabies virus mutant for use as a biologically safe live virus vaccine (1994)

Herpesvirus envelope glycoproteins play important roles in mediating infection initiation and also represent major immunogens. We recently showed that a pseudorabies virus (PrV) mutant lacking the essential glycoprotein gD (gp50), after phenotypic complementation by propagation on genetically engineered PrV gD-expressing cell lines was able to infect primary target cells and spread exclusively by means of direct cell-to-cell transmission. Virions released from non-complementing cells that lacked gD were not infectious because of a defect in penetration and so free infectious virions did not arise after infection of animals by phenotypically complemented gD-negative PrV. This formed the basis for the development of novel non-spreading live herpes-virus vaccines. However, the gD-negative PrV mutant still retained a residual level of virulence, which prevented its use as vaccine, and the need to propagate the gD-negative PrV mutant on trans-complementing cell lines resulted in the appearance of wild-type revertants, rescued by the resident gene in the cell line. To overcome these problems we isolated a PrV mutant designated PrV(376) that, in addition to gD, also lacked the non-essential glycoproteins gG, gI and gE. PrV(376), because of the lack of gD, was also dependent on gD-expressing cells for productive replication. Non-complementing cells infected by phenotypically gD-complemented PrV(376) produced non-infectious particles lacking glycoproteins gD and gE as shown by immunoelectron microscopy. Owing to the absence of any homologous sequences between the viral genome and the viral genes resident in the complementing cell line, rescue by homologous recombination was impossible. In cell culture, plaques of PrV(376) were significantly smaller than those of either wild-type, or gD- or gE-deleted mutants, indicating an additive or synergistic effect of the combined deletion on viral cell-to-cell spread capability. Intranasal or intramuscular infection of pigs with phenotypically gD-complemented PrV(376) showed a complete attenuation of viral virulence, with an expected lack of shedding of infectious virus. The PrV(376)-vaccinated pigs exhibited a significant level of protection against challenge infection, measured by survival and weight loss. In summary, PrV(376) represents a novel type of herpesvirus vaccine that combines innocuity, efficacy and biological safety.
Redirecting Photosynthetic Reducing Power toward Bioactive Natural Product Synthesis (2013)

In addition to the products of photosynthesis, the chloroplast provides the energy and carbon building blocks required for synthesis of a wealth of bioactive natural products of which many have potential uses as pharmaceuticals. In the course of plant evolution, energy generation and biosynthetic capacities have been compartmentalized. Chloroplast photosynthesis provides ATP and NADPH as well as carbon sources for primary metabolism. Cytochrome P450 monooxygenases (P450s) in the endoplasmic reticulum (ER) synthesize a wide spectrum of bioactive natural products, powered by single electron transfers from NADPH. P450s are present in low amounts, and the reactions proceed relatively slowly due to limiting concentrations of NADPH. Here we demonstrate that it is possible to break the evolutionary compartmentalization of energy generation and P450-catalyzed biosynthesis, by relocating an entire P450-dependent pathway to the chloroplast and driving the pathway by direct use of the reducing power generated by photosystem I in a light-dependent manner. The study demonstrates the potential of transferring pathways for structurally complex high-value natural products to the chloroplast and directly tapping into the reducing power generated by photosynthesis to drive the P450s using water as the primary electron donor.
Effect of progestagen intravaginal sponges and PMSG on synchronisation of oestrus in maiden heifers and on interval from calving to oestrus in beef cows (1980)

The effectiveness of progestagen sponges plus PMSG in inducing and synchronising oestrus and pregnancy in nulliparous heifers was assessed. Eighty‐one percent of the treated heifers were synchronised, but none of the controls. The hormone treatment advanced the mean calving date by 19 days, but there was no difference between treated and control in the percentage of heifers that finally calved. The interval between calving and first oestrus for hill‐country beef cows 2–10 years old in an untreated control group was 94 days, in a group treated with progestagen‐impregnated sponges for 21 days was 98 days, and in a group treated with these sponges plus 1000 i.u. of PMSG at the time of withdrawal was 85 days. The last treatment reduced post‐partum anoestrus by 11 days in comparison with the mean of the other two treatments ( P < 0.01). There was no difference between age groups in the percentage of cows showing oestrus, conceiving to first service, and calving for the control treatment. However, in the two hormone treatments none of the 2‐year‐old cows conceived to first oestrus and 13% calved, but 46% of cows in the older age groups conceived to first oestrus and 79% calved.
Palatoglossus coupling in selective upper airway stimulation (2017)

4 Laryngoscope, 127:E378-E383, 2017.
Proton nuclear magnetic resonance evidence for the absence of a stable hydrogen bond between the active site aspartate and histidine residues of native subtilisins and for its presence in thiolsubtilisins (1981)

The very low field proton nuclear magnetic resonance (1H NMR) found in aqueous solutions of serine proteases and their zymogens is characteristic of the hydrogen bond between the imidazolium and aspartate groups of the catalytic triad: Ser-His-Asp [Robillard, G., & Shulman, R. G. (1972) J. Mol. Biol. 71, 507--511]. According to 1H correlation NMR spectroscopic studies performed in 80/20 (v/v) H2O/2H2O, no such resonance is found in native subtilisins (even at -2 degrees C and pH 6.0), but it is present in thiolsubtilisins and in the phenylboronic acid derivatives of the serine enzymes. The resonance was not visible in the mercuric or carboxamidomethyl derivatives of the thiol enzymes or in the phenylboronic acid--serine enzyme complex if the serine enzyme was first acylated with phenylmethanesulfonyl fluoride. The histidine at the catalytic site of thiolsubtilisin carries a positive charge between pH 5.6 and 8.4, in accord with previous data in favor of a mercaptide--imidazolium ion pair at the catalytic site. The charge distribution (- + -) at the active site of thiolsubtilisin and in the phenylboronic acid derivatives of the serine enzymes resembles that in the tetrahedral transition state formed between a serine enzyme and its substrate. Therefore, the stable hydrogen bond (found in the thiol enzyme and in the phenylboronic acid derivative of the serine enzyme) should be more important during catalysis than in the substrate-free enzyme.
Segmentation of Rectangular Objects Lying on an Unknown Background in a Small Preview Scan Image (2008)

We describe a method to segment rectangular objects that lie on a slightly textured background of an a-priori unknown colour. Our contribution consists of a fast and accurate background colour approximation method, a set of heuristics for accurate detection of rectangle sides, and procedures to generate imprecise hypotheses of rectangles, adjust hypotheses to fit the rectangles in the image, and verify or reject the hypotheses. Our algorithm is capable of detecting overlapping and touching objects such as photos, receipts, and business cards on a very small-sized preview scan image (79 by 109 pixels) on a coloured/textured background.
Scattering of GPS signals from the ocean with wind remote sensing application (2000)

A theoretical model that describes the power of a scattered Global Positioning System (GPS) signal as a function of geometrical and environmental parameters has been developed. This model is based on a bistatic radar equation derived using the geometric optics limit of the Kirchhoff approximation. The waveform (i.e., the time-delayed power obtained in the delay-mapping technique) depends on a wave-slope probability density function, which in turn depends on wind. Waveforms obtained for aircraft altitudes and velocities indicate that altitudes within the interval 5-15 km are the best for inferring wind speed. In some regimes, an analytical solution for the bistatic radar equation is possible. This solution allows converting trailing edges of waveforms into a set of straight lines, which could be convenient for wind retrieval. A transition to satellite altitudes, together with satellite velocities, makes the peak power reduction and the Doppler spreading effect a significant problem for wind retrieval based on the delay-mapping technique. At the same time, different time delays and different Doppler shifts of the scattered GPS signal could form relatively small spatial cells on sea surface, suggesting mapping of the wave-slope probability distribution in a synthetic-aperture-radar (SAR) fashion. This may allow more accurate measurements of wind velocity and wind direction.
Vaccination with recombinant modified vaccinia virus Ankara prevents the onset of intestinal allergy in mice (2013)

Modified vaccinia virus Ankara-ovalbumin (MVA-OVA) vaccination induces a strong OVA-specific TH 1- immune response, likely mediated by the induction of IFN-γ and IgG2a. Finally, MVA-based vaccines need to be evaluated for their therapeutic potential in established allergy models.
Effect of methylprednisolone on complications after removal of impacted mandibular third molars. (1985)

Bilateral impacted mandibular third molars were surgically removed in 20 healthy patients. The effects of methylprednisolone on postoperative healing was investigated in a double-blind, cross-over study. Some decrease in postoperative discomfort (swelling and trismus) was noted in the methylprednisolone group. No statistically significant difference was noted, however in comparison with a placebo group.
MPTP Mouse Models of Parkinson's Disease: An Update (2011)

Among the most widely used models of Parkinson's disease (PD) are those that employ toxins, especially 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). Depending on the protocol used, MPTP yields large variations in nigral cell loss, striatal dopamine loss and behavioral deficits. Motor deficits do not fully replicate those seen in PD. Nonetheless, MPTP mouse models mimic many aspects of the disease and are therefore important tools for understanding PD. In this review, we will discuss the ability of MPTP mouse models to replicate the pathophysiology of PD, the mechanisms of MPTP-induced neurotoxicity, strain differences in susceptibility to MPTP, and the models' roles in testing therapeutic approaches.
Auto-checking speech transcriptions by multiple template constrained posterior (2009)

Checking transcription errors in speech database is an important but tedious task that traditionally requires intensive manual labor. In [9], Template Constrained Posterior (TCP) was proposed to automate the checking process by screening potential erroneous sentences with a single context template. However, single template-based method is not robust and requires parameter optimization that still involves some manual work. In this work, we propose to use multiple templates which is more robust and requires no development data for parameter optimization. By using its multiple hypothesis sifting capabilities -from well-defined, full context to loosely defined context like wild card, the confidence for a focus unit can be measured at different expected accuracy. The joint verification by multiple TCP improves measured confidence of each unit in the transcription and is robust across different speech databases. Experimental results show that the checking process automatically separates erroneous sentences from correct ones: the sentence error hit rate decrease rapidly in the sorted TCP values, from 59% to 7% for the Mexican Spanish database and from 63% to 11% for the American English database, among the top 10% sentences in the rank lists.
The effect of wortmannin on the localisation of lysosomal type I integral membrane glycoproteins suggests a role for phosphoinositide 3-kinase activity in regulating membrane traffic late in the endocytic pathway (1996)

Addition of wortmannin to normal rat kidney cells caused a redistribution of the lysosomal type I integral membrane proteins Igp110 and Igp120 to a swollen vacuolar compartment. This compartment did not contain the cation independent mannose 6-phosphate receptor and was depleted in acid hydrolases. It was distinct from another swollen vacuolar compartment containing the cation independent mannose 6-phosphate receptor. The swollen Igp110-positive compartment was accessible to a monoclonal antibody against Igp120 added extracellularly, showing that it had the characteristics of an endosomal compartment. Wortmannin had no gross morphological effect on the trans-Golgi network or lysosomes nor any effect on the delivery to the trans-Golgi network of endocytosed antibodies against the type I membrane protein TGN38. We propose that the observed effects of wortmannin were due to inhibition of membrane traffic between cation independent mannose 6-phosphate receptor-positive late endosomes and the trans-Golgi network and to inhibition of membrane traffic between a novel Igp120-positive, cation independent mannose 6-phosphate receptor-negative late endosomal compartment and lysosomes. The effects of wortmannin suggest a function for a phosphatidylinositol 3-kinase(s) in regulating membrane traffic in the late endocytic pathway.
The Effect of Urodynamic Testing on Clinical Diagnosis, Treatment Plan and Outcomes in Women Undergoing Stress Urinary Incontinence Surgery (2012)

Urodynamic studies significantly changed clinical diagnoses but infrequently changed the global treatment plan or influenced surgeon decision to cancel, change or modify surgical plans. Global treatment plan changes were associated with increased treatment for postoperative urgency urinary incontinence.
Instrumentation and clinical applications in frequency-domain optical mammography (1997)

We describe an instrument for frequency-domain light mammography (LIMA), and we present clinical results obtained on patients affected by breast cancer. This instrument uses two laser diodes emitting at 690 and 825 nm. Their intensities are modulated at a frequency of 110 MHz. The amplitude and the phase of the intensity wave are the measured quantities. The breast is slightly compressed between two glass plates and the optical signal is detected in transmission, i.e. on the opposite side of the illuminated spot of the breast. The acquisition time for a full breast image is about 3 minutes. Edge effects (that are mainly due to the breast thickness variability within the scanned area) are corrected by an algorithm of data analysis which enhances the contrast of the optical mammograms. In the clinical applications, we successfully detected 27 out of 37 malignant tumors (73%). This result shows the practical feasibility and the significant potential of frequency-domain optical mammography.
Source localization by inversion of the parabolic equation method (1989)

The inverse split-step parabolic equation method is derived. Spatial localization of single and multiple low-frequency harmonic point sources in a deep ocean is demonstrated by using simulated pressure field measurements from a vertical array. In addition, the method is applied to a source extended in range and depth. This method is solved in a single iteration, unlike some inverse techniques that vary parameters.
<i>Chlamydia pneumoniae</i> -Atherosclerosis Link (2002)

he potential role of Chlamydia pneumoniae (Cpn) in atherosclerosis has attracted considerable attention.On the basis of early encouraging results, it was anticipated that infection with Cpn might prove a novel treatable risk factor for atherosclerosis, with a relevance comparable to that of Helicobacter pylori in peptic ulcer disease.The effect of antibiotic treatment on clinical outcome became widely accepted as benchmark for the Cpn-atherosclerosis link.2][3][4] Due to limited sample sizes, however, most of these trials need to be interpreted cautiously.At the 51st Annual Scientific Sessions of American College of Cardiology, 2002, two adequately sized antibiotic trials, WIZARD (Weekly Intervention with Zithromax for Atherosclerosis and its Related Disorders) and AZACS (AZithromycin in Acute Coronary Syndromes), were reported.The negative results of these trials deadened the enthusiasm for the role of Cpn in atherosclerosis.WIZARD included 7747 patients with previous myocardial infarction (MI) and elevated Cpn titers who were randomly assigned to placebo or azithromycin for 11 weeks.During 2-year followup, the composite of all-cause mortality, recurrent MI, revascularization, and hospitalization for angina was not significantly affected by antibiotic treatment.Likewise, AZACS did not show a significant effect of short-term treatment with azithromycin on 6-month rate of all-cause mortality, nonfatal MI, or recurrent ischemia requiring revascularization in 1400 patients with unstable angina.
Placental but Not Heart Defects Are Associated with Elevated Hypoxia-Inducible Factor α Levels in Mice Lacking Prolyl Hydroxylase Domain Protein 2 (2006)

PHD1, PHD2, and PHD3 are prolyl hydroxylase domain proteins that regulate the stability of hypoxia-inducible factor alpha subunits (HIF-alpha). To determine the roles of individual PHDs during mouse development, we disrupted all three Phd genes and found that Phd2(-/-) embryos died between embryonic days 12.5 and 14.5 whereas Phd1(-/-) or Phd3(-/-) mice were apparently normal. In Phd2(-/-) mice, severe placental and heart defects preceded embryonic death. Placental defects included significantly reduced labyrinthine branching morphogenesis, widespread penetration of the labyrinth by spongiotrophoblasts, and abnormal distribution of trophoblast giant cells. The expression of several trophoblast markers was also altered, including an increase in the spongiotrophoblast marker Mash2 and decreases in the labyrinthine markers Tfeb and Gcm1. In the heart, trabeculae were poorly developed, the myocardium was remarkably thinner, and interventricular septum was incompletely formed. Surprisingly, while there were significant global increases in HIF-alpha protein levels in the placenta and the embryo proper, there was no specific HIF-alpha increase in the heart. Taken together, these data indicate that among all three PHD proteins, PHD2 is uniquely essential during mouse embryogenesis.
The occurrence of <i>Actinobacillus actinomycetemcomitans, Bacteroides gingivalis, Bacteroides intermedius</i> and spirochaetes in the subgingival microflora of adolescents and their relationship with the amount of supragingival plaque and gingivitis (1988)

The subgingival microflora of 89 children aged 14–15 years was investigated by anaerobic culture and dark‐field microscopy. Actinobacillus actinomycetemcomitans was isolated from 13 subjects and black‐pigmented Bacteroides from 83 subjects. B. intermedius was the most commonly isolated Bacteroides species and was identified in 76 subjects, whereas B. gingivalis was observed in only two subjects. Spirochaetes were found in 79 of the subjects. No statistically significant differences in the clinical condition of the subjects were noted in relation to the presence or absence of A. actinomycetemcomitans. Statistically significant direct relationships were observed between the number of sites with clinical signs of gingivitis and the proportion of spirochaetes and the number and proportion of black‐pigmented Bacteroides in the subgingival sample. These relationships were independent of the effect of the amount of supragingival plaque on either gingivitis or the composition of the subgingival flora.
Ultrastructural epithelial zonation of the primate endometrium (rhesus monkey) (1989)

The uterine endometrium of menstruating primates (rhesus monkey, human) consists of a germinal basalis that regenerates a transient functionalis during each menstrual cycle. The endometrium is further subdivided into 4 zones that differ histologically and in epithelial mitotic rate along the longitudinal axes of the uterine glands and microvasculature (Bartelmez et al: Contrib. Embryol. Carnegie Inst., 34:99-146, 1951; Bartelmez: Am. J. Obstet. Gynecol., 74:931-955, 1957; Padykula et al.: Biol. Reprod., 32:1103-1118, 1118, 1984; Biol. Reprod., in press, 1988). The zones are defined as follows: functionalis I, luminal epithelium; functionalis II (upper straight gland segments); basalis III (middle gland segments), and basalis IV (bottoms of the glands). The surrounding stroma and microvasculature also differ zonally. Ultrastructural epithelial differences are evident among the 4 zones during 3 distinct functional states during natural menstrual cycles and after ovariectomy: 1) basal level after ovariectomy and 2) estrogen dominance and 3) progesterone dominance. Zonal structural differences persist at a minimal level of differentiation after ovariectomy and thus zonation is an inherent property. During estrogen dominance, distinctive ultrastructural differences are evident among the 4 zones, such as epithelial cell heterogeneity in functionalis I and homogeneity in functionalis II. Also a distinctive glandular cell type occurs in basalis III and IV that is recognized by a highly irregular cisternal rough endoplasmic reticulum that permeates the cytoplasm. During progesterone dominance, ultrastructural differences exist among the 4 zones except for similarity between the epithelial cells of functionalis II and basalis III. Postovulatory epithelial cells of functionalis I and II and basalis III become postmitotic via progesterone inhibition but intracellular differentiation continues progressively. Postovulatory epithelial mitotic activity in basalis IV escapes progesterone inhibition as the [3H]thymidine labeling index continues to increase from 1 to 12% during the menstrual cycle (Padykula et al.: Reprod., 30(Suppl.1):92 (Abstr. 123), 1984). This post-ovulatory proliferation coupled with progressive differentiation in basalis IV may represent a stem-progenitor set of cells for postmenstrual endometrial regeneration or alternatively for creation of the maternal placenta.