gebhart/patrepeval huggingface dataset:
Parasitic Mites of Honey Bees: Life History, Implications, and Impact (2000)

The hive of the honey bee is a suitable habitat for diverse mites (Acari), including nonparasitic, omnivorous, and pollen-feeding species, and parasites. The biology and damage of the three main pest species Acarapis woodi, Varroa jacobsoni, and Tropilaelaps clareae is reviewed, along with detection and control methods. The hypothesis that Acarapis woodi is a recently evolved species is rejected. Mite-associated bee pathologies (mostly viral) also cause increasing losses to apiaries. Future studies on bee mites are beset by three main problems: (a) The recent discovery of several new honey bee species and new bee-parasitizing mite species (along with the probability that several species are masquerading under the name Varroa jacobsoni) may bring about new bee-mite associations and increase damage to beekeeping; (b) methods for studying bee pathologies caused by viruses are still largely lacking; (c) few bee- and consumer-friendly methods for controlling bee mites in large apiaries are available.
The premyofibril: Evidence for its role in myofibrillogenesis (1994)

When cardiac muscle cells are isolated from embryonic chicks and grown in culture they attach to the substrate as spherical cells with disrupted myofibrils, and over several days in culture, they spread and extend lamellae. Based on antibody localizations of various cytoskeletal proteins within the spreading cardiomyocyte, three types of myofibrils have been identified: 1) fully formed mature myofibrils that are centrally positioned in the cell, 2) premyofibrils that are closest to the cell periphery, and 3) nascent myofibrils located between the premyofibrils and the mature myofibrils. Muscle-specific myosin is localized in the A-bands in the mature, contractile myofibrils, and along the nascent myofibrils in a continuous pattern, but it is absent from the premyofibrils. Antibodies to non-muscle isoforms of myosin IIB react with the premyofibrils at the cell periphery and with the nascent myofibrils, revealing short bands of myosin between closely spaced bands of alpha-actinin. In the areas where the nascent myofibrils border on the mature myofibrils, the bands of non-muscle myosin II reach lengths matching the lengths of the mature A-bands. With the exception of a small transition zone consisting of one myofibril, or sometimes several sarcomeres, bordering the nascent myofibrils, there is no reaction of these non-muscle myosin IIB antibodies with the mature myofibrils in spreading myocytes. C-protein is found only in the mature myofibrils, and its presence there may prevent co-polymerization of non-muscle and muscle myosins. Antibodies directed against the non-muscle myosin isoforms, IIA, do not stain the cardiomyocytes. In contrast to the cardiomyocytes, the fibroblasts in these cultures stain with antibodies to both non-muscle myosin IIA and IIB. The premyofibrils near the leading edge of the lamellae show no reaction with antibodies to either titin or zeugmatin, whereas the nascent myofibrils and mature myofibrils do. The spacings of the banded alpha-actinin staining range from 0.3 to 1.4 microns in the pre- and nascent myofibrils and reach full spacings (1.8-2.5 microns) in the mature myofibrils. Based on these observations, we propose a premyofibril model in which non-muscle myosin IIB, titin, and zeugmatin play key roles in myofibrillogenesis. This model proposes that pre- and nascent myofibrils are composed of minisarcomeres that increase in length, presumably by the concurrent elongation of actin filaments, the loss of the non-muscle myosin II filaments, the fusion of dense bodies or Z-bodies to form wide Z-bands, and the capture and alignment of muscle myosin II filaments to form the full spacings of mature myofibrils.
Use and uncertainties of mutual information for computed tomography/magnetic resonance (CT/MR) registration post permanent implant of the prostate (2005)

Post-implant dosimetric analysis for permanent implant of the prostate benefits from the use of a computed tomography (CT) dataset for optimal identification of the radioactive source (seed) positions and a magnetic resonance (MR) dataset for optimal description of the target and normal tissue volumes. The CT/MR registration process should be fast and sufficiently accurate to yield a reliable dosimetric analysis. Since critical normal tissues typically reside in dose gradient regions, small shifts in the dose distribution could impact the prediction of complication or complication severity. Standard procedures include the use of the seed distribution as fiducial markers (seed match), a time consuming process that relies on the proper identification of signals due to the same seed on both datasets. Mutual information (MI) is more efficient because it uses image data requiring minimal preparation effort. A comparison of MI registration and seed-match registration was performed for twelve patients. MI was applied to a volume limited to the prostate and surrounding structures, excluding most of the pelvic bone structures (margins around the prostate gland were approximately 2 cm right-left, approximately 1 cm anterior-posterior, and approximately 2 cm superior-inferior). Seeds were identified on a 2 mm slice CT dataset using an automatic seed identification procedure on reconstructed three-dimensional data. Seed positions on the 3 mm slice thickness T2 MR data set were identified using a point-and-click method on each image. Seed images were identified on more than one MR slice, and the results used to determine average seed coordinates for MR images and matched seed pairs between CT and MR images. On average, 42% (19%-64%) of the seeds (19-54 seeds) were identified and matched to their CT counterparts. A least-squares method applied to the CT and MR seed coordinates was used to produce the optimum seed-match registration. MI registration and seed match registration angle differences averaged 0.5 degrees, which was not significantly different from zero. Translation differences averaged 0.6 (1.2 standard deviation) mm right-left, -0.5(1.5) mm posterior-anterior, and -1.2(2.0) mm inferior-superior. Registration error estimates were approximately 2 mm for both the MI and seed-match methods. The observed standard deviations in the offset values were consistent with propagation of error. Registration methods as applied here using mutual information and seed matching are consistent, except for a small systematic difference in the inferior-superior axis for a minority of cases (approximately 15%). Cases registered with mutual information and with bony anatomy misregistration of greater than approximately 5 mm should be evaluated for rescan or seed-match registration. The improvement in efficiency of use for the MI registration method is substantial, approximately 30 min compared to several hours using seed match registration.
Antibody response to keyhole limpet hemocyanin (KLH) treatment in patients with superficial bladder carcinoma. (1996)

The dynamics of specific KLH-antibody production after intracutaneous and intravesical instillation was analysed. Nine patients (male, n = 7; female, n = 2, mean age 68.6 years, range 47-75) with primary superficial carcinomas of the bladder were intracutaneously immunized with 1 mg Keyhole limpet hemocyanin (KLH) after the complete resection of the tumors. Treatment was continued for 6 consecutive weeks, monthly for one year and thereafter bimonthly for 2 subsequent years, consisting of 20 mg KLH in 20 ml saline introduced intravesically. The antibodies against KLH in patient sera were determined by means of a specially developed direct enzyme-linked immunosorbent assay (ELISA; according to H. von der Kammer, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany). Blood was taken for antibody-titer examination before treatment and 8 weeks after treatment. The KLH-antibody titer increased significantly (Mann-Whitney-Test P = 0.02) after KLH therapy in bladder cancer patients, however the level varied considerably from patient to patient. 6 of 9 patients (67%) presented increased serum antibody titers to KLH after immunotherapy. 4 patients (44.4%) remained free of tumor during the established follow-up period of 10-45 months (median 30.7 months). One patient without increased antibody titer to KLH was free of tumor, 2 patients however, suffered from tumor recurrence after the KLH course. 2 patients presented with tumor recurrence in spite of increased antibody titers. No evidence of tumor progression occurred in patients with recurrence after KLH therapy. 4 of 5 patients (80%) without tumor recurrence presented with a positive skin test. Of patients with tumor recurrence, 50% had a negative skin test. 44.4% KLH-treated patients had tumor recurrence The recurrence rate was 1.6. The time to recurrence was 8.75 months. KLH instillation did not induce major side effects. Positive skin test reactivity and KLH antibody response were more commonly seen in responding patients (i.e. those who remained tumor free after therapy) than in non-responders. The production of KLH antibodies, apparently is the biological response to the antigen stimulus of KLH.
Shared HLA class II-associated genetic susceptibility and resistance, related to the HLA-DQB1 gene, in IgA deficiency and common variable immunodeficiency. (1992)

Most cases of selective IgA deficiency (IgA-D) and common variable immunodeficiency (CVID) occur sporadically. However, familial clustering is not uncommon, and the two disorders can occur within the same family. We have previously described positive associations with three DR-DQ haplotypes as well as a strong negative association with DRw15,DQw6,Dw2 in IgA-D. Different amino acids at position 57 of the HLA-DQ beta chain were found to be related to susceptibility and resistance to IgA-D. Now we have found identical, although somewhat weaker, positive and negative DR-DQ associations in a large group of CVID patients (n = 86), as well as the same associations with codon 57 of the DQB1 gene. In addition, we have confirmed our earlier observations in an independent group of IgA-D individuals (n = 69), and in sib-pair analysis we have found linkage of the genetic susceptibility to IgA-D to the HLA class II region. In IgA-D individuals not carrying the three overrepresented DR-DQ haplotypes, the same positive association with a non-aspartic acid residue at position 57 of the HLA-DQ beta chain was seen. The previously reported associations with deletions of the HLA class III genes C4A (fourth component of complement) and CYP21P (steroid 21-hydroxylase pseudogene) were, in our groups of immunodeficient individuals, statistically secondary to the association with the DQB1 allele 0201. The shared HLA class II associations in the two humoral immunodeficiencies support the hypothesis that IgA-D and CVID are related disorders. Disease susceptibility and resistance are most closely associated with a gene(s) within the DR-DQ region, alleles of the DQB1 locus being candidate genes.
A NEW METHOD FOR THE GENERATION AND USE OF FOCUSED ULTRASOUND IN EXPERIMENTAL BIOLOGY (1942)

1. An efficient generator of focused ultrasound has been designed, built, and successfully operated. 2. The generator has been used to produce focal heating in the centers of paraffin blocks, and in a similar manner, focal areas of destruction were obtained deep in fresh liver tissue with minimal effects at the surface and no effects on the intervening tissue. 3. In animals, focused ultrasound of high intensity produced local cerebral changes as inferred from behavior disabilities and as demonstrated at autopsy. This local brain effect was achieved through intervening scalp, skull, and meninges. The resulting behavior disabilities disappeared in from 2 to 16 hours. 4. To date, it has not been possible to produce such brain changes without incidental injury to the skin and subcutaneous tissue lying at the base of the cone of radiation. 5. Improvements in generation and application of the focused supersonic beam are suggested whereby it should be possible to increase still further the focal effects in the brain, with a corresponding decrease or elimination of complicating surface injury.
Increased efficiency of targeted mutagenesis by CRISPR/Cas9 in plants using heat stress (2017)

The CRISPR/Cas9 system has greatly improved our ability to engineer targeted mutations in eukaryotic genomes. While CRISPR/Cas9 appears to work universally, the efficiency of targeted mutagenesis and the adverse generation of off-target mutations vary greatly between different organisms. In this study, we report that Arabidopsis plants subjected to heat stress at 37°C show much higher frequencies of CRISPR-induced mutations compared to plants grown continuously at the standard temperature (22°C). Using quantitative assays relying on green fluorescent protein (GFP) reporter genes, we found that targeted mutagenesis by CRISPR/Cas9 in Arabidopsis is increased by approximately 5-fold in somatic tissues and up to 100-fold in the germline upon heat treatment. This effect of temperature on the mutation rate is not limited to Arabidopsis, as we observed a similar increase in targeted mutations by CRISPR/Cas9 in Citrus plants exposed to heat stress at 37°C. In vitro assays demonstrate that Cas9 from Streptococcus pyogenes (SpCas9) is more active in creating double-stranded DNA breaks at 37°C than at 22°C, thus indicating a potential contributing mechanism for the in vivo effect of temperature on CRISPR/Cas9. This study reveals the importance of temperature in modulating SpCas9 activity in eukaryotes, and provides a simple method to increase on-target mutagenesis in plants using CRISPR/Cas9.
Studies of the lamin proteinase reveal multiple parallel biochemical pathways during apoptotic execution. (1995)

Although specific proteinases play a critical role in the active phase of apoptosis, their substrates are largely unknown. We previously identified poly(ADP-ribose) polymerase (PARP) as an apoptosis-associated substrate for proteinase(s) related to interleukin 1 beta-converting enzyme (ICE). Now we have used a cell-free system to characterize proteinase(s) that cleave the nuclear lamins during apoptosis. Lamin cleavage during apoptosis requires the action of a second ICE-like enyzme, which exhibits kinetics of cleavage and a profile of sensitivity to specific inhibitors that is distinct from the PARP proteinase. Thus, multiple ICE-like enzymes are required for apoptotic events in these cell-free extracts. Inhibition of the lamin proteinase with tosyllysine "chloromethyl ketone" blocks nuclear apoptosis prior to the packaging of condensed chromatin into apoptotic bodies. Under these conditions, the nuclear DNA is fully cleaved to a nucleosomal ladder. Our studies reveal that the lamin proteinase and the fragmentation nuclease function in independent parallel pathways during the final stages of apoptotic execution. Neither pathway alone is sufficient for completion of nuclear apoptosis. Instead, the various activities cooperate to drive the disassembly of the nucleus.
Fas-induced B Cell Apoptosis Requires an Increase in Free Cytosolic Magnesium as an Early Event (1999)

Ligation of the Fas molecule expressed on the surface of a cell initiates multiple signaling pathways that result in the apoptotic death of that cell. We have examined Mg2+ mobilization as well as Ca2+ mobilization in B cells undergoing Fas-initiated apoptosis. Our results indicate that cytosolic levels of free (non-complexed) Mg2+ ([Mg2+]i) and Ca2+ ([Ca2+]i) increase in cells undergoing apoptosis. Furthermore, the percentages of cells mobilizing Mg2+, fragmenting DNA, or externalizing phosphatidylserine (PS) increase in parallel as the concentration of anti-Fas monoclonal antibody is raised. Kinetic analysis suggests that Mg2+ mobilization is an early event in apoptosis, clearly preceding DNA fragmentation and probably occurring prior to externalization of PS as well. The source of Mg2+ that produces the increases in [Mg2+]i is intracellular and most likely is the mitochondria. Extended pretreatment of B cells with carbonyl cyanide m-chlorophenylhydrazone, an inhibitor of mitochondrial oxidative phosphorylation, produces proportional decreases in the percentage of cells mobilizing Mg2+, fragmenting DNA, and externalizing PS in response to anti-Fas monoclonal antibody treatment. These observations are consistent with the hypothesis that elevated [Mg2+]i is required for apoptosis. Furthermore, we propose that the increases in [Mg2+]i function not only as cofactors for Mg2+-dependent endonucleases, but also to facilitate the release of cytochrome c from the mitochondria, which drives many of the post-mitochondrial, caspase-mediated events in apoptotic cells.
Identifying sensors from fingerprint images (2009)

In this paper we study the application of hardware fingerprinting based on PRNU noise analysis of biometric fingerprint devices for sensor identification. For each fingerprint sensor, a noise reference pattern is generated and subsequently correlated with noise residuals extracted from test images. We experiment on three different databases including a total of 20 fingerprint sensors. Our results indicate that fingerprint sensor identification at unit level is attainable with promising prospects. Our analysis indicates that in many cases identification can be performed even when one only has access to a limited number of samples. For two of the three databases one can train on less than 8 images per device and establish sensor identification with little or no misclassification error. On the third database, high levels of identification performance can be achieved when training on similar amounts of images required for other types of sensor identification such as cameras or scanners.
Recent advances in the management of nausea and vomiting caused by antineoplastic agents. (1989)

The pathophysiology of nausea and vomiting caused by antineoplastic therapy is described, and the literature on selected recent pharmacologic approaches to antiemetic therapy is reviewed. Nausea and vomiting associated with antineoplastic therapy remain serious deterrents to continued, potentially curative therapy for many patients. Although much research has been conducted in the area of antiemetic therapy over the past decade, the mechanisms by which antineoplastic agents cause nausea and vomiting are still not well defined. The most effective antiemetic agents to date are those that antagonize dopamine receptors. Metoclopramide is a dopamine antagonist that has been widely studied for the prevention of antineoplastic-agent-induced nausea and vomiting. Recent studies with this agent focus on routes of administration other than the traditional high-dose intermittent bolus intravenous injections. Continuous intravenous infusions of the drug and high-dose oral administration have been studied in an attempt to decrease the adverse effects associated with the traditional regimen and to allow administration on an outpatient basis. Prochlorperazine, a phenothiazine derivative, has been a mainstay of antiemetic therapy for many years. Although it is generally reserved for use with regimens that cause mild to moderate emesis, recent data suggest that higher-than-traditional doses given intravenously impart greater antiemetic protection. Perhaps the most promising antiemetic research has been conducted with a new group of agents, the serotonin antagonists. Preliminary trials suggest that these agents are comparable in efficacy to high doses of metoclopramide but devoid of many of the adverse effects commonly associated with metoclopramide. Further research in the area of neuropharmacology is necessary to direct the development of the most effective antiemetic agents.
Advances in the therapy of chronic lymphocytic leukemia (2003)

Chronic lymphocytic leukemia therapy has changed dramatically over the past decade, with recent studies supporting the use of fludarabine as the initial therapy for symptomatic disease. New findings relative to the use of fludarabine and complications arising from this therapy are reviewed. Exciting combination approaches using monoclonal antibodies such as rituximab or Campath-1H in combination with fludarabine offer the opportunity to improve the complete response rate further in chronic lymphocytic leukemia. Furthermore, the field of experimental therapeutics for chronic lymphocytic leukemia was advanced by the description of a new mouse model of human chronic lymphocytic leukemia and identification of several disrupted signal transduction pathways in this disease. The description of therapies that target AKT, protein kinase C, phosphodiesterase 4, mammalian target of rapamycin, histone deacetylase, and methyltransferase offer the opportunity to utilize molecularly targeted therapy for this disease. Such targeted approaches offer hope that we might be on the threshold to changing the natural history of chronic lymphocytic leukemia.
Health and Growth of Veal Calves Fed Milk Replacers With or Without Probiotics (2005)

Four experiments with 1-wk-old veal calves were conducted to assess the influence of probiotics on growth and health indicators. In experiments 1 and 2, the liquid probiotic supplements were administered daily from experimental d 1 to 15. The treatment period in experiments 3 and 4 was extended to 56 d. The probiotics used were a multispecies probiotic (MSPB) containing different probiotic species of human origin, or a calf-specific probiotic (CSPB) containing 6 Lactobacillus species isolated from calf feces and selected on the basis of a combination of characteristics. When the data for the 4 experiments were pooled, the probiotics enhanced growth rate during the first 2 wk. During the 8-wk experimental period, average daily gain and feed efficiency were significantly improved in the probiotic-treated groups. The MSPB-induced increase in weight gain was greater when the control calves were considered less healthy based on a health score (an index of diarrhea and therapeutic treatments). Probiotic treatment tended to diminish mortality. The CSPB treatment reduced the incidence of diarrhea and the fecal counts of coliforms. When therapeutic treatment was intensive in the control calves, the ingestion of probiotics reduced the percentage of calves that required therapy and the amount of treatments needed against digestive or respiratory diseases. There was no clear difference in the efficiency of the MSPB and CSPB preparations. Further research is necessary to identify underlying mechanisms and to evaluate the potential of probiotics to improve respiratory health in veal calf production.
Cloning and Expression of Fructosyl-amino Acid Oxidase Gene fromCorynebacteriumsp. 2-4-1 inEscherichia coli (2002)

The gene encoding the fructosyl-amino acid oxidase (fructosyl-alpha-L-amino acid: oxygen oxidoreductase (defructosylating); EC 1.5.3) of Corynebacterium sp. 2-4-1 was cloned and expressed in Escherichia coli. The gene consists of 1,116 nucleotides and encodes a protein of 372 amino acids with a predicted molecular mass of 39,042. The open reading frame was confirmed as the gene of the fructosyl-amino acid oxidase by comparison with the N-terminal amino acid sequence of the purified fructosyl-amino acid oxidase from Corynebacterium sp. 2-4-1. The sequence of the AMP-binding motif, GXGXXG, was found in the deduced N-terminal region. The amino acid sequence of the fructosyl-amino acid oxidase showed no similarity to that of fungal fructosyl-amino acid oxidases. In addition, substrate specificities of this fructosyl-amino acid oxidase were different from those of other fructosyl-amino acid oxidases. The fructosyl-amino acid oxidase of Corynebacterium sp. 2-4-1 is an enzyme that has unique substrate specificity and primary structure in comparison with fungal fructosyl-amino acid oxidases.