gebhart/patrepeval huggingface dataset:
Guidelines for the use and interpretation of assays for monitoring autophagy (2012)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
Diglyphus isaea (Hymenoptera: Eulophidae): a probable complex of cryptic species that forms an important biological control agent of agromyzid leaf miners (2006)

Diglyphus isaea (Walker 1838) (Hymenoptera: Eulophidae) is a primary parasitoid of agromyzid leaf miners (Diptera: Agromyzidae) and has been commercialized as a biological control agent. Diglyphus isaea occurs throughout much of the world and different populations are morphologically identical. Using nuclear ribosomal internal transcribed spacer 1 (ITS1) sequences, we examined variation among Chinese populations of D. isaea. Phylogenetic analyses combined with an analysis of sympatry indicated that D. isaea consists of at least four species in mainland China. The results imply that ITS1 is an efficient marker for identifying congeneric species of parasitic waSPS, and that cryptic species could be common in temperate and subtropical regions.

Zusammenfassung

Diglyphus isaea (Walker, 1838) ist ein primarer Parasitoid von blattminierenden Agromyziden (Diptera) und wird zu ihrer biologischen Kontrolle vermarktet. Die in weiten Teilen der Welt vorkommenden verschiedenen Populationen sind morphologisch identisch. Untersucht wurden Unterschiede in den nuklearen ribosomalen ITS1-Sequenzen zwischen chinesischen Populationen. Ergebnisse der phylogenetischen Analysen, kombiniert mit einer Sympatrie-Analyse, zeigen, dass D. isaea auf dem chinesischen Kontinent aus mindestens vier Arten besteht. Aus den Ergebnissen geht hervor, dass ITS1 ein effizienter Marker zur Identifizierung congenerischer Arten parasitischer Wespen ist und dass kryptische Arten in gemasigten und subtropischen Regionen verbreitet sein konnen.
Nanofacet Lithography: A New Bottom‐Up Approach to Nanopatterning and Nanofabrication by Soft Replication of Spontaneously Faceted Crystal Surfaces (2007)

The faceting of unstable crystal surfaces provides self-assembling templates for soft lithography, enabling the facile generation of a variety of periodic nanopatterned monolayers, nanowires, nanogrooves, nanogrids, and nanowaffles of Au and Si (the figure shows the replication of faceted sapphire to an elastomeric stamp, and then to a patterned self-assembled monolayer). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2089/2007/c1625_s.pdf or from the author. 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.
Experience with the Use of an Investigational F(ab')2 Heptavalent Botulism Immune Globulin of Equine Origin During an Outbreak of Type E Botulism in Egypt (1996)

During an outbreak of type E foodborne botulism in Cairo in 1991, an investigational equine F(ab')2 "despeciated" heptavalent botulism immune globulin (dBIG) was provided to the Egyptian Ministry of Health by the U.S. Army. Of 54 patients known to have been treated with antitoxins, 4 received commercially available trivalent antitoxins, 45 received dBIG, and 5 received both commercial antitoxin and dBIG. Physicians recorded side effects in 10 (22%) of 45 patients who received dBIG; in nine cases, reactions were considered "mild," and in one case they were believed to be serum sickness. In contrast, possible serum sickness during hospitalization was recorded for two of four patients who were receiving commercial antitoxins. No complications of therapy were noted for any patient who was receiving both antitoxin types. In a separate study, 31 patients were contacted about their reactions to the antitoxin by telephone after discharge from the hospital. Seven (54%) of 13 patients attributed symptoms that they experienced while they were hospitalized to receipt of dBIG, while four (44%) of nine patients who indicated that they had received commercial antitoxins and one (20%) of five who received both commercial antitoxin and dBIG reported side effects before discharge. Data on the efficacy of the antitoxins were not obtained. In our experience, equine dBIG was at least as safe as commercially available antitoxins in treating type E foodborne botulism.
On the necessity of edible oil refining and possible sources of 3‐MCPD and glycidyl esters (2011)

Abstract A framework of collaborating research facilities in Germany investigates the reasons and conditions for the formation of 3‐monochloro‐1,2‐propanediol esters (3‐MCPD‐E) and of glycidyl esters (GE) during edible oil refining. The aim is the derivation of technological parameters to prevent or to reduce, respectively, the formation of these contaminants during the refining process, particularly for palm oil, because the highest contents of 3‐MCPD‐E and related compounds were found in refined palm oils. A strong influence of the deodorization conditions was proven on the potential to form 3‐MCPD‐E and related compounds. Above 240°C an increased formation especially of GE was observed. Deodorization temperatures up to 240°C lead to moderate concentrations ≤5 ppm. Degumming with water, neutralization with potassium hydroxide and bleaching before deodorization is advantageous with regard to reduce the capability of vegetable oils to form the contaminants 3‐MCPD and glycidyl esters. Practical application: There is a strong demand to guarantee a stable and reliable quality of refined edible oils. The problem of 3‐MCPD and glycidyl ester formation during refining has shown the sensitivity of the system to small variations in the refining conditions. In a first step it is necessary to explain the contribution of the different refining steps to the formation of contaminants.
On the uncertainty of interwell connectivity estimations from the capacitance-resistance model (2014)

电容抵抗模型(CRM ) 是常规水库模拟的一种选择。CRM，复杂数字模型的简化，使用生产和注射评价推断水库描述。没有优先的地质的模型。适合的 CRM 的主要产量是注射液体的部分(通常流水) 那在一个制片人被生产在不变。这些部分是 interwell 连接。Interwell 连接是需要在油水库管理 waterfloods 的基本信息。数据驱动的 CRM 是一个快工具在成熟的域里估计这些参数并且允许一个充分利用可得到的动态数据。这份报纸考虑为线性抑制模型将上面的界限放在 interwell 连接的无常上的问题。用分析界限和数字模拟，我们在能被用来确定的 interwell 连接的无常上导出一致上面的限制给定的数据集的信息内容。
A controlled field trial of plain and aluminium hydroxide-adsorbed cholera vaccines in Surabaya, Indonesia, during 1973--75. (1978)

A controlled field trial comparing the effectiveness of a plain cholera vaccine with that of a vaccine adsorbed to aluminium hydroxide was carried out in a cholera-endemic area of Indonesia during 1973-75. Tetanus toxoid adsorbed to aluminium phosphate was used as the control. In vaccinees aged 1-4 years, the adsorbed cholera vaccine provided about 88% protection for 6 months following vaccination and still provided about 50% protection between 11 and 14 months after vaccination. In the same age group, the plain vaccine provided only 53% protection during the first 6 months and no appreciable protection beyond that period. In those aged 5 years and over, both vaccines provided 50-60% protection throughout the period of observation (14 months). Neither vaccine caused any serious side effects.
Temperature-Controlled Flow Switching in Nanocapillary Array Membranes Mediated by Poly(N-isopropylacrylamide) Polymer Brushes Grafted by Atom Transfer Radical Polymerization (2006)

We report actively controlled transport that is thermally switchable and size-selective in a nanocapillary array membrane (NCAM) prepared by grafting poly(N-isopropylacrylamide) (PNIPAAm) brushes onto the exterior surface of a Au-coated polycarbonate track-etched membrane. A smooth Au layer on the membrane surface, which is key to obtaining a uniform polymer film, was prepared by thermal evaporation of approximately 50 nm Au on both exterior surfaces. After evaporation, the inner diameter of the pore is reduced slightly, but the NCAM retains a narrow pore size distribution. PNIPPAm brushes with 10-30 nm (dry film) thickness were grafted onto the Au surface through surface-initiated atom transfer radical polymerization (ATRP) using a disulfide initiator, (BrC(CH3)2COO(CH2)11S)2. Molecular transport through the PNIPAAm polymer brush-modified NCAMs was investigated by real-time fluorescence measurements using fluorescein isothiocyanate (FITC)-labeled dextrans ranging from 4.4 to 282 kDa in membranes with variable initial pore diameters (80, 100, and 200 nm) and different PNIPAAm thicknesses. Manipulating the temperature of the NCAM through the PNIPAAm lower critical solution temperature (LCST) causes large, size-dependent changes in the transport rates. Over specific ranges of probe size, transport is completely blocked below the LCST but strongly allowed above the LCST. The combination of the highly uniform PNIPAAm brush and the monodisperse pore size distribution is critical in producing highly reproducible switching behavior. Furthermore, the reversible nature of the switching raises the possibility of using them as actively controlled filtration devices.
Short, direct repeats at the breakpoints of deletions of the retinoblastoma gene. (1989)

We found deletions involving the retinoblastoma gene in 12 of 49 tumors from patients with retinoblastoma or osteosarcoma. After mapping the deletion breakpoints, we found that no two breakpoints coincided. Thus, our data do not support the conclusions of others regarding the existence of a "hotspot" for deletion breakpoints in this gene. In 4 of the tumors, we sequenced 200 base pairs surrounding each deletion breakpoint. Three deletions had termini within pairs of short, direct repeats ranging in size from 4 to 7 base pairs. These results indicate that the "slipped mispairing" mechanism may predominate in the generation of deletions at this locus. Our review of deletion breakpoints at other genetic loci reveals that the nature of the sequences present at deletion breakpoints (short, direct repeats versus middle repetitive elements) varies according to the genetic locus under study.
Genome-wide analysis of DNA methylation patterns (2007)

Cytosine methylation is the most common covalent modification of DNA in eukaryotes. DNA methylation has an important role in many aspects of biology, including development and disease. Methylation can be detected using bisulfite conversion, methylation-sensitive restriction enzymes, methyl-binding proteins and anti-methylcytosine antibodies. Combining these techniques with DNA microarrays and high-throughput sequencing has made the mapping of DNA methylation feasible on a genome-wide scale. Here we discuss recent developments and future directions for identifying and mapping methylation, in an effort to help colleagues to identify the approaches that best serve their research interests.
Applications of the signal space separation method (2005)

The reliability of biomagnetic measurements is traditionally challenged by external interference signals, movement artifacts, and comparison problems caused by different positions of the subjects or different sensor configurations. The Signal Space Separation method (SSS) idealizes magnetic multichannel signals by transforming them into device-independent idealized channels representing the measured data in uncorrelated form. The transformation has separate components for the biomagnetic and external interference signals, and thus, the biomagnetic signals can be reconstructed simply by leaving out the contribution of the external interference. The foundation of SSS is a basis spanning all multichannel signals of magnetic origin. It is based on Maxwell's equations and the geometry of the sensor array only, with the assumption that the sensors are located in a current free volume. SSS is demonstrated to provide suppression of external interference signals, standardization of different positions of the subject, standardization of different sensor configurations, compensation for distortions caused by movement of the subject (even a subject containing magnetic impurities), suppression of sporadic sensor artifacts, a tool for fine calibration of the device, extraction of biomagnetic DC fields, and an aid for realizing an active compensation system. Thus, SSS removes many limitations of traditional biomagnetic measurements.
Intravenous Cidofovir for Peripheral Cytomegalovirus Retinitis in Patients with AIDS (1997)

Cidofovir was efficacious in delaying progression of previously untreated CMV retinitis. Treatment was associated with manageable side effects; strict adherence to monitoring of renal function before cidofovir was administered and concomitant administration of probenecid and saline hydration appeared to minimize drug-related nephrotoxicity.
The Effect of Severe Plastic Deformation on the Brittle-Ductile Transition in Low Carbon Steel (2009)

Brittle-ductile transition (BDT) behaviour was investigated in low carbon steel deformed by an accumulative roll-bonding (ARB) process. The temperature dependence of its fracture toughness was measured by conducting four-point bending tests at various temperatures and strain rates. The fracture toughness increased while the BDT temperature decreased in the specimens deformed by the ARB process. Arrhenius plots between the BDT temperatures and the strain rates indicated that the activation energy for the controlling process of the BDT was not changed by the deformation with the ARB process. It was deduced that the decrease in the BDT temperature by grain refining was not due to the increase in the dislocation mobility controlled by short-range barriers. Quasi-three-dimensional simulations of dislocation dynamics, taking into account of crack tip shielding due to dislocations, were performed to investigate the effect of a dislocation source spacing along a crack front on the BDT. The simulation indicated that the BDT temperature is decreased with decreasing in the dislocation source spacing. Molecular dynamics simulations revealed that moving dislocations were impinged against grain boundaries and were reemitted from there with increasing strain. It indicates that grain boundaries can be new sources in ultra-fine grained materials, which increases toughness at low temperatures.
Towards software defined ICN based edge-cloud services (2013)

ICN deployment will be based on the grounds of saving CAPEX/OPEX and/or enabling new services. This paper makes a case for the latter leveraging, emerging technologies such as network function virtualization (NFV) and software defined networking (SDN). We propose a framework to enable ICN based service platform as virtualized network functions to enable several edge-cloud services such as enterprise applications, big data analytic, or M2M/IoT services. This platform is generic to support several ICN protocols and corresponding real-time and non-real time services leveraging ICN features such as name based routing, caching, multicasting, and flexible security techniques. As an implementation of this architecture, we discuss how a scalable network based conferencing solution can be realized over the proposed ICN platform and compare it with a peer-to-peer design through a performance analysis.
Organ Messenger Ribonucleic Acid and Plasma Proteome Changes in the Adjuvant-Induced Arthritis Model: Responses to Disease Induction and Therapy with the Estrogen Receptor-β Selective Agonist ERB-041 (2005)

Two receptors [estrogen receptor (ER)alpha and ERbeta] mediate the manifold effects of estrogens throughout the body. Although a clear role has been established for ERalpha in the classical effects of estrogen activity, the physiological role of ERbeta is less well understood. A small-molecule ERbeta selective agonist, ERB-041, has potent antiinflammatory activity in the Lewis rat model of adjuvant-induced arthritis. To characterize the response of target organs and pathways responsible for this antiinflammatory effect, mRNA expression profiling of the spleen, lymph node, and liver was performed, in conjunction with a global analysis of the plasma proteome. We find that the expression of a large number of genes and proteins are altered in the disease model and the majority of these are partially or fully reversed by ERB-041 treatment. Regulated pathways include the acute-phase response, eicosanoid synthesis, fatty acid metabolism, and iron metabolism. In addition, many of the regulated genes and proteins are known to be dysregulated in human rheumatoid arthritis, providing further evidence that the manifestations of the Lewis rat adjuvant-induced arthritis model bear similarity to the human disease.
Proliferation, differentiation, and cytogenetics of chronic leukemic B lymphocytes cultured with mitomycin-treated normal cells (1981)

Lymphocytes from 6 patients with chronic lymphocytic leukemia of the B-cell variety (B-CLL) were cultured with equal numbers of mitomycin-treated mononuclear cells from normal blood. When stimulated with pokeweed mitogen (PWM), phytohemagglutinin (PHA), or the tumor-promoting agent, phorbol tetradecanoyl-acetate (TPA), the CLL cells proliferated actively by day 3 or 4 of culture, and in four cases, differentiated to significant numbers of immunoglobulin-containing cells. Chromosome studies on the proliferating lymphocytes demonstrated a cytogenetically abnormal clone in three patients, including two with a 14q+ marker chromosome and two with a translocation involving the short arm of chromosome 9. One patient had a translocation from 22q to 14q, producing a Philadelphia chromosome as well as the 14q+ marker. The results indicate that the neoplastic lymphocytes of B-CLL may proliferate and differentiate when appropriately stimulated in vitro, and that chromosomally abnormal clones are not uncommon. With several techniques now available for successful short-term culture of B-CLL lymphocytes, there is opportunity for better understanding of the cellular alterations in this disease.
Neurostimulation for Obstructive Sleep Apnea: Investigations (1993)

Neurostimulation of the upper airway muscles (accessory muscles of respiration) was accomplished in anesthetized dogs and sleeping humans by electrical stimulation of the hypoglossal nerves. Such stimulations relieved partial airway obstructions in dogs. They also aborted (shortened) obstructive sleep apnea events in humans who suffer with obstructive sleep apnea syndrome. In one subject, stimulations delivered in advance of apneic events (by automatic cycling) prevented apneas. Neurostimulation for obstructive sleep apnea may be an important concept for future research and development.
Cerebrospinal Fluid Vasopressin Levels (1998)

Central AVP may play a role in enhancing, while serotonin plays a role in inhibiting, aggressive behavior in personality-disordered individuals. In addition to the possibility of central AVP and serotonin interacting to influence human aggression, central AVP may also influence human aggressive behavior through a mechanism independent of central serotonin in personality-disordered subjects.
Pharmacodynamic Properties of Antibiotics: Application to Drug Monitoring and Dosage Regimen Design (1990)

The goal of antimicrobial chemotherapy is to effectively eradicate pathogenic organisms while minimizing the likelihood of drug-related adverse effects. In this era of cost containment, consideration should also be given to performing this task with the smallest total dose of drug and the shortest duration of therapy. Determination of the appropriate dose and dosing interval of an antimicrobial requires knowledge and integration of both its pharmacokinetic and pharmacodynamic properties.
Autonomous Index Optimization in XML Databases (2005)

Defining suitable indexes is a major task when optimizing a database. Usually, a human database administrator defines a set of indexes in the design phase of the database. This can be done manually or with the help of so called index wizard tools analyzing predefined database operations. Even having an optimal initial set of indexes when setting up a database, there is no guarantee that these indexes will suit future demands. Rather, it is realistic that the typical usage of the database will change after a while because new queries appear, for instance. In consequence, the existing indexes are suboptimal. The typical way to handle this problem is that a database administrator maintains the database permanently. In XML database management systems (XDBMS) this problem becomes even worse: Because XML queries cover both content and structure the number of possible queries and indexes is significantly higher. Additionally, for XML data without schema information, queries and indexes cannot be defined in advance, because the structure and the content of the data is not restricted. Both facts tend to result in higher maintenance costs for XML indexes compared to relational indexes. In this paper we show by performance measurements that an adaptive XDBMS that analyzes its workload periodically and creates/drops XML indexes automatically guarantees a high performance over the total life time of a database. Although we present our index system called KeyX the idea and the results are transferable to other XML indexing approaches.