gebhart/patrepeval huggingface dataset:
More Cercospora Species Infect Soybeans across the Americas than Meets the Eye (2015)

Diseases of soybean caused by Cercospora spp. are endemic throughout the world's soybean production regions. Species diversity in the genus Cercospora has been underestimated due to overdependence on morphological characteristics, symptoms, and host associations. Currently, only two species (Cercospora kikuchii and C. sojina) are recognized to infect soybean; C. kikuchii causes Cercospora leaf blight (CLB) and purple seed stain (PSS), whereas C. sojina causes frogeye leaf spot. To assess cryptic speciation among pathogens causing CLB and PSS, phylogenetic and phylogeographic analyses were performed with isolates from the top three soybean producing countries (USA, Brazil, and Argentina; collectively accounting for ~80% of global production). Eight nuclear genes and one mitochondrial gene were partially sequenced and analyzed. Additionally, amino acid substitutions conferring fungicide resistance were surveyed, and the production of cercosporin (a polyketide toxin produced by many Cercospora spp.) was assessed. From these analyses, the long-held assumption of C. kikuchii as the single causal agent of CLB and PSS was rejected experimentally. Four cercosporin-producing lineages were uncovered with origins (about 1 Mya) predicted to predate agriculture. Some of the Cercospora spp. newly associated with CLB and PSS appear to represent undescribed species; others were not previously reported to infect soybeans. Lineage 1, which contained the ex-type strain of C. kikuchii, was monophyletic and occurred in Argentina and Brazil. In contrast, lineages 2 and 3 were polyphyletic and contained wide-host range species complexes. Lineage 4 was monophyletic, thrived in Argentina and the USA, and included the generalist Cercospora cf. flagellaris. Interlineage recombination was detected, along with a high frequency of mutations linked to fungicide resistance in lineages 2 and 3. These findings point to cryptic Cercospora species as underappreciated global considerations for soybean production and phytosanitary vigilance, and urge a reassessment of host-specificity as a diagnostic tool for Cercospora.
Abstract 4060: Enriching for rrare subpopulations of circulating microvesicles by the depletion of endothelial- and leukocyte-derived microvesicles (2011)

Abstract Endothelial- and leukocyte-derived circulating microvesicles (cMV) represent a majority of the cMV present in the blood. The purpose of this study was to determine if depletion of these more common cMV populations is possible, allowing for the enrichment and analysis of the remaining subpopulations of cMV. Circulating microvesicles were isolated from the blood plasma of breast cancer patients. Magnetic beads conjugated to antibodies specific for either CD31 or CD45 were used to deplete the isolated endothelial- and leukocyte-derived cMV. The remaining cMV population was characterized with a multiplexed immunoassay against a panel of 20 different antigens. In addition to the expected depletion of the biomarker used to remove the targeted cMV in the remaining cMV population, a concomitant depletion of associated biomarkers was observed. In the case of the cMV population in which CD31 had been used to remove endothelial-derived cMV, for instance, there was a significant concomitant depletion of DLL4, a highly associated endothelial marker. This was not the case with general epithelial microvesicle markers, such as CD9, which were still very much present in the cMV population remaining after depletion. These findings suggest a potential method for a more complete characterization of biomarker profiles associated with cMV derived from disease-associated cells and provide the foundation for a novel cMV-based strategy for disease detection through a noninvasive blood test. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4060. doi:10.1158/1538-7445.AM2011-4060
Advances and challenges in adeno-associated viral inner-ear gene therapy for sensorineural hearing loss (2021)

There is growing attention and effort focused on treating the root cause of sensorineural hearing loss rather than managing associated secondary characteristic features. With recent substantial advances in understanding sensorineural hearing-loss mechanisms, gene delivery has emerged as a promising strategy for the biological treatment of hearing loss associated with genetic dysfunction. There are several successful and promising proof-of-principle examples of transgene deliveries in animal models; however, there remains substantial further progress to be made in these avenues before realizing their clinical application in humans. Herein, we review different aspects of development, ongoing preclinical studies, and challenges to the clinical transition of transgene delivery of the inner ear toward the restoration of lost auditory and vestibular function.
Use of Carbon Mesh Anodes and the Effect of Different Pretreatment Methods on Power Production in Microbial Fuel Cells (2009)

Flat electrodes are useful in microbial fuel cells (MFCs) as close electrode spacing improves power generation. Carbon cloth and carbon paper materials typically used in hydrogen fuel cells, however, are prohibitively expensive for use in MFCs. An inexpensive carbon mesh material was examined here as a substantially less expensive alternative to these materials for the anode in an MFC. Pretreatment of the carbon mesh was needed to ensure adequate MFC performance. Heating the carbon mesh in a muffle furnace (450 degrees C for 30 min) resulted in a maximum power density of 922 mW/m2 (46 W/m3) with this heat-treated anode, which was 3% more power than that produced using a mesh anode cleaned with acetone (893 mW/ m2; 45 W/m3). This power density with heating was only 7% less than that achieved with carbon cloth treated by a high temperature ammonia gas process (988 mW/m2; 49 W/m3). When the carbon mesh was treated by the ammonia gas process, power increased to 1015 mW/m2(51 W/m3). Analysis of the cleaned or heated surfaces showed these processes decreased atomic O/C ratio, indicating removal of contaminants that interfered with charge transfer. Ammonia gas treatment also increased the atomic N/C ratio, suggesting that this process produced nitrogen related functional groups that facilitated electron transfer. These results show that low cost heat-treated carbon mesh materials can be used as the anode in an MFC, providing good performance and even exceeding performance of carbon cloth anodes.
Schlußbetrachtung (1998)

In dieser Arbeit wurde die Unternehmensbewertung auf der Grundlage von Unternehmensnetzwerken als neue Methode zur Unternehmensbewertung — speziell im Hinblick auf die Bewertungsproblematik in den neuen Bundesländern — dargestellt. Diese Methode unterscheidet sich im wesentlichen von den bisher bekannten dadurch, daß sie in erster Linie auf der Analyse und Bewertung bestehender Unternehmensnetzwerke sowie auf den Synergiepotentialen, die sich aus der Zusammenlegung/Integration dieser Netzwerke mit denen potentieller Unternehmenskäufer ergeben, basiert.1 Bei der Bewertung in den neuen Bundesländern fanden im verstärkten Maße Substanzwertverfahren, insbesondere die Ermittlung von Teilrekonstruktionswerten auf der Basis materieller Werte, Anwendung. Es wurde aufgezeigt, daß diese Verfahren nicht zu korrekten Ergebnissen führen, d.h. auf diese begründete Kaufentscheidungen können zu Fehlinvestitionen führen. Hingegen können auf Basis der direkten Bewertung von Unternehmensnetzwerken geeignete Entscheidungs- und Argumentationswerte ermittelt werden.
HPLC METHOD FOR QUANTIFICATION OF ARGININE CONTAINING VASOPRESSIN (1999)

An isocratic technique was developed for the analysis of [Arg8]- vasopressin (AVP) by reverse-phase high performance liquid chromatography (RP-HPLC) using a 220 nm UV detection, Brownlee Spheri-5 ODS column (250 × 4.6 mm, 5 μm, 100 Å), mobile phase (methanol: 0.1% aqueous trifluoroacetic acid: : 3:7), and 1.5 mL/min flow rate. The coefficients of variation (C.V.) for precision and proportionality assays were lower than 2% for all concentrations studied. The detection limit, recovery rate, and tailing factor for AVP were 50 ng/mL (signal-to-noise ratio of 3:1), 0.97 ± 0.03, and 0.99–1.1, respectively.
Induction of myasthenia by immunization against muscle-specific kinase (2006)

Muscle-specific kinase (MuSK) is critical for the synaptic clustering of nicotinic acetylcholine receptors (AChRs) and plays multiple roles in the organization and maintenance of neuromuscular junctions (NMJs). MuSK is activated by agrin, which is released from motoneurons, and induces AChR clustering at the postsynaptic membrane. Although autoantibodies against the ectodomain of MuSK have been found in a proportion of patients with generalized myasthenia gravis (MG), it is unclear whether MuSK autoantibodies are the causative agent of generalized MG. In the present study, rabbits immunized with MuSK ectodomain protein manifested MG-like muscle weakness with a reduction of AChR clustering at the NMJs. The autoantibodies activated MuSK and blocked AChR clustering induced by agrin or by mediators that do not activate MuSK. Thus MuSK autoantibodies rigorously inhibit AChR clustering mediated by multiple pathways, an outcome that broadens our general comprehension of the pathogenesis of MG.
Distributed self-capacitance of magnetic resonance surface coils (1988)

A theoretical investigation of the capacitive coupling between a round, flat NMR surface coil and a dielectric medium is presented. The change in coil self-capacitance produced by the presence of the medium is calculated. These calculated results are compared with those observed experimentally in a series of NMR surface coils.
Factors associated with outcome after cord blood transplantation in children with acute leukemia. Eurocord-Cord Blood Transplant Group. (1999)

We have analyzed factors influencing the outcome of 102 children with acute leukemia given a cord blood transplantation (CBT) and reported to the Eurocord Registry. Seventy patients with acute lymphoblastic and 32 with acute myeloid leukemia were given either a related (n = 42) or an unrelated (n = 60) CBT. Children given CBT during first or second complete remission were considered as belonging to the good-risk group (n = 66), whereas those who received a transplant in a more advanced stage of disease were assigned to the poor-risk group (n = 36). In the related group (RCBT), 12 of 42 patients received transplantation from an HLA-disparate donor, whereas in the unrelated group (UCBT) 54 of 60 received an HLA mismatched CBT. Kaplan-Meier estimates for neutrophil recovery at day 60 were 84% +/- 7% in RCBT and 79 +/- 6% in UCBT (P =.16). In multivariate analysis, the most important factor influencing neutrophil engraftment in UCBT was a nucleated cell dose infused greater than 3.7 x 10(7)/kg (P =.05, relative risk [RR] of 1.85, 95% confidence interval [CI]: 0.98-3.4). The incidence of grade II through IV acute graft-versus-host disease was 41% +/- 8% in the RCBT group and 37% +/- 6% in the UCBT group (P =.59). Kaplan-Meier estimates of 2-year event-free survival (EFS) after RCBT or UCBT were 39% +/- 8% and 30% +/- 7%, respectively (P =.19). In multivariate analysis, the most important factor influencing EFS was disease status at time of transplantation: good-risk patients had a 2-year EFS of 49% +/- 7% as compared to 8% +/- 5% in patients with more advanced disease (P =.0003, RR: 0.40, 95% CI: 0.24 to 0. 65). This was a consequence of both an increased 1-year transplant related mortality and a higher 2-year relapse rate in the poor-risk group (65% +/- 9% and 77% +/- 14%, respectively), as compared with good risk patients (34% +/- 6% and 31% +/- 9%, respectively). These data confirm that allogeneic CBT from either a related or an unrelated donor is a feasible procedure able to cure a significant proportion of children with acute leukemia, especially if transplanted in a favorable phase of disease.
Auto-DeepLab: Hierarchical Neural Architecture Search for Semantic Image Segmentation (2019)

Recently, Neural Architecture Search (NAS) has successfully identified neural network architectures that exceed human designed ones on large-scale image classification. In this paper, we study NAS for semantic image segmentation. Existing works often focus on searching the repeatable cell structure, while hand-designing the outer network structure that controls the spatial resolution changes. This choice simplifies the search space, but becomes increasingly problematic for dense image prediction which exhibits a lot more network level architectural variations. Therefore, we propose to search the network level structure in addition to the cell level structure, which forms a hierarchical architecture search space. We present a network level search space that includes many popular designs, and develop a formulation that allows efficient gradient-based architecture search (3 P100 GPU days on Cityscapes images). We demonstrate the effectiveness of the proposed method on the challenging Cityscapes, PASCAL VOC 2012, and ADE20K datasets. Auto-DeepLab, our architecture searched specifically for semantic image segmentation, attains state-of-the-art performance without any ImageNet pretraining.
Microphone array post-filter for diffuse noise field (2002)

This paper proposes a novel technique for estimating the signal power spectral density to be used in the transfer function of a microphone array post-filter. The technique is a modification of the existing Zelinski post-filter, which uses the auto- and cross-spectral densities of the array inputs to estimate the signal and noise spectral densities. The Zelinski technique, however, assumes zero cross-correlation between noise on different sensors. This assumption is inaccurate in real conditions, particularly at low frequencies and for arrays with closely spaced sensors. In this paper we replace this with an assumption of a theoretically diffuse noise field, which is more appropriate in a variety of realistic noise environments. In experiments using noise recordings from an office of computer workstations, the modified post-filter results in significant improvement in terms of objective speech quality measures and speech recognition performance.
Mapping of DNA markers linked to the cystic fibrosis locus on the long arm of chromosome 7. (1987)

We have used a panel of eight human/mouse somatic-cell hybrids, each containing various portions of human chromosome 7, and three patient cell lines with interstitial deletions on chromosome 7 for localization of six DNA markers linked to the cystic fibrosis locus. Our data suggest that D7S15 is located in the region 7 cen----q22, that MET is located in 7q22----31, and that D7S8 and 7C22 are located in q22----q32. The hybridization results for COL1A2 and TCRB are consistent with their previous assignment to 7q21----q22 and 7q32, respectively. Given the location of these six markers and their linkage relationships, it is probable that the cystic fibrosis locus is in either the distal region of band q22 or the proximal region of q31. Using the same set of cell lines, we have also examined the location of another chromosome 7 marker PGY1. The data show that PGY1 is located in the region 7cen----q22, a position very different from its previous assignment.
CONCENTRIC RISER WILL REDUCE MUD WEIGHT MARGINS, IMPROVE GAS-HANDLING SAFETY (1998)

A high-pressure concentric riser, consisting of a surface casing string run within the riser, will have the potential to use a dual-density mud system to reduce mud weight margins, allowing operators to set fewer casing strings in deepwater environments. An additional benefit includes improved gas-handling safety above the seafloor. In comparison with the concentric riser system, conventional marine risers are not designed to contain pressure; instead, they serve primarily as a conduit between the seafloor blowout preventer (BOP) and the rig floor. The paper describes the development, configuration, and safety of the riser. To illustrate the potential benefits, an example application is described. The paper also discusses additional advantages and operational limitations.
Iterative Optimization of High-Affinity Protease Inhibitors Using Phage Display. 2. Plasma Kallikrein and Thrombin (1996)

As discussed in the accompanying paper [Markland, W., Ley, A. C., & Ladner, R. C. (1996) Biochemistry 35, 8045-8057], we generated libraries from the first Kunitz domain of human lipoprotein-associated coagulation inhibitor (LACI-D1) using multivalent M13 III display and derived potent inhibitors of human plasmin (PLA) by iterative variegation and selection. Here, we show that high-affinity, high-specificity binders to human plasma kallikrein (pKAL) and human thrombin (THBN) can be obtained starting from the identical library and employing the same iterative variegation procedures used to obtain PLA inhibitors. Lib#1 (allowing 31 200 variants involving five positions near the P1 residue of LACI-D1) and its pKAL-biased derivative, Lib#4 (allowing an additional 1600 variants at residues 31, 32, 34, and 39), were screened against pKAL, yielding potent inhibitors. One of these, EPI-K401, has Ki = 284 pM, very high specificity, and excellent stability. We used information from Lib#4 selectants to design Lib#5 (allowing 1.5 x 10(6) amino-acid sequences involving nine varied positions) from which we obtained an inhibitor (EPI-K503) having high affinity for pKAL (Ki = 40 pM) and retaining the high specificity of EPI-K401. When we screened Lib#1 and its THBN-tailored derivative, Lib#6, against THBN, we obtained a different and very homogeneous population of selected molecules. The purified proteins derived from Lib#6 selectants bound to THBN-agarose beads but did not inhibit proteolytic activity of THBN, suggesting that these selectants bind to a site on THBN other than the catalytic site. Thus, a single large combinatorial library can serve as a source to obtain highly specific, high-affinity binding molecules for each of several targets. Furthermore, the results with THBN show that the binding of Kunitz domains to other proteins is not limited to the catalytic sites of trypsin-homologous proteases.
Lumbar Intervertebral Disc Transfer A Canine Study (1994)

The structure and function of autograft intervertebral discs were maintained after disc transfer surgery; the transplant discs, however, were not completely normal in either their morphology or their metabolic functioning.
Inactivation ofBacillusSpores by the Supercritical Carbon Dioxide Micro-bubble Method (1997)

Bacillus spores were effectively inactivated by the supercritical (SC) CO2 micro-bubble method. The micro-bubble SC CO2 treatment of B. cereus, B. subtilis, B. megaterium, B. polymyxa, and B. coagulans at 40 degrees C and 30 MPa for 30 min produced greater reduction (about 3 log cycles of reduction) than a similar treatment without a filter. The SC CO2 treatment of B. polymyxa, B. cereus, and B. subtilis spores at 45 degrees C, 50 degrees C, respectively, and 30 MPa for 60 min resulted in a 6-log cycle reduction of survival. The SC CO2 treatment under the foregoing conditions should offer higher efficiency than that of heat treatment at 100 degrees C for 60 min. In addition, the SC CO2 treatment (30 MPa, 60 degrees C, 30 min) of B. polymyxa and B. cereus spores also produced a 6-log cycle reduction.
Conserved markers of fetal pancreatic epithelium permit prospective isolation of islet progenitor cells by FACS (2006)

Prospective isolation and characterization of progenitor cells is a paradigmatic strategy for studies of organ development. However, extraction of viable cells, fractionation of lineages, and in vitro analysis of progenitors from the fetal pancreas in experimental organisms like mice has proved challenging and has not yet been reported for human fetal pancreas. Here, we report isolation of pancreatic islet progenitor cells from fetal mice by FACS. Monoclonal antibodies that recognize cell-surface proteins on candidate stem cells in brain, skin, and other organs enabled separation of major pancreatic cell lineages and isolation of native pancreatic cells expressing neurogenin 3, an established marker of islet progenitors. New in vitro cell culture methods permitted isolated mouse islet progenitors to develop into hormone-expressing endocrine cells. Insulin-producing cells derived in vitro required or expressed factors that regulate fetal beta cell differentiation; thus, the genetic programs normally controlling in vivo mouse islet development are similarly required in our system. Moreover, antibodies that recognize conserved orthologous cell-surface epitopes in human fetal pancreas allowed FACS-based enrichment of candidate islet progenitor cells expressing neurogenin 3. Our studies reveal previously undescribed strategies for prospective purification and analysis of pancreatic endocrine progenitor cells that should accelerate studies of islet development and replacement.
The properties and applications of single-molecule DNA sequencing (2011)

Single-molecule sequencing enables DNA or RNA to be sequenced directly from biological samples, making it well-suited for diagnostic and clinical applications. Here we review the properties and applications of this rapidly evolving and promising technology.
Development of an IMS-PCR assay for the detection of Mycobacterium avium ssp. paratuberculosis in water (2005)

A sensitive method for the detection of Map in water involving addition of 0.4% Tween 80, centrifugation and IMS-PCR was developed.
The Prevalence of Diet-Induced Migraine (1984)

Nineteen percent of about 490 patients with classical or common migraine reported that headaches can be precipitated by chocolate, 18% by cheese and 11% by citrus fruit, and a highly significant majority of these patients were sensitive to all three foods. Twenty-nine percent of the patients reported sensitivity to alcohol; again this was significantly associated with sensitivity to the three food stuffs, though a substantial number of patients were sensitive to alcohol but not foods. Thirty-one percent of 331 female patients believed that oral contraceptives precipitated headaches, but this could not be related to any dietary response. Patients with affected relatives were significantly more likely to report sensitivity to alcohol and chocolate; sensitivity to cheese and citrus fruit was less strongly related, and there was no relationship at all for oral contraceptives. These correlations suggest that food induced headaches are mediated by chemical constituents common to these foods.
A General Fixed Rate Arithmetic Coding Method for Constrained Channels (1983)

This paper extends the result of earlier work on the application of arithmetic codes to the constrained channel problem. We specifically present a general length-based fixed rate implementation technique which performs the arithmetic coding recursions during each channel time unit. This technique is superior to an earlier unpublished code for general constrained channels. The approach permits the design of codes for sophisticated channel constraints.
Activity of ABT-773 against Mycobacterium avium Complex in the Beige Mouse Model (2000)

ABT-773, a new ketolide antimicrobial agent, was evaluated in comparison to clarithromycin (CLA) in vitro against Mycobacterium avium complex (MAC) and in a beige mouse model of disseminated MAC infection. The MICs at which 50 and 90% of the isolates tested were inhibited were 2 and 4 microg/ml, respectively, for CLA and 8 and 16 microg/ml, respectively, for ABT-773. Eight CLA-resistant isolates were found to be resistant to ABT-773 (MICs > 64 microg/ml). In the in vivo study mice were treated with ABT-773 (50, 100, and 200 mg/kg of body weight) or CLA (200 mg/kg). Both ABT-773 (100 and 200 mg/kg) and CLA significantly decreased the viable cell counts in spleens and lungs. ABT-773 (200 mg/kg) and CLA had similar activities in lungs, but the former was more active in spleens.