gebhart/patrepeval huggingface dataset:
Microfluidics for genetic cancer diagnostics (2006)

Les microsystemes d'analyse integres, ou μTAS (Micro Total Analysis Systemes), permettent d'ameliorer considerablement la detection de cancers des les premiers stades d'apparition. En effet, ils interviennent au niveau moleculaire au lieu d'attendre que la maladie ne se manifeste sous forme de tumeurs detectables. Ils offrent egalement un bien meilleur rendement que les techniques courantes de laboratoire. Ce papier presente le developpement d'un microsysteme fluidique d'analyse integre pour la detection et la surveillance genetique de cancer. Des micro-reacteurs fluidiques, places dans des ecoulements liquides d'un macro-dispositif, representent l'aspect novateur du systeme developpe. Le haut rendement est obtenu par la combinaison de micro-reacteurs evoluant periodiquement en parallele. Cette approche permet de relever le challenge technologique qu'induit la rencontre des mondes macroscopiques et microscopiques. Parce que les reacteurs sont immerges dans un milieu liquide, la contamination du dispositif et le risque associe a de faux resultats sont minimises. Ce papier presente une vue d'ensemble sur la generation de micro-gouttes presentees comme les micro-reacteurs, le melange a micro-echelle de ceux-ci, l'amplification d'ADN par un systeme fluidique base sur la PCR et la detection utilisant des techniques optiques.
The Severe Acute Respiratory Syndrome (2003)

El propósito de esta investigación es determinar el impacto de la implementación de las medidas de salud contra Covid-19 emitidos por el ministerio de salud colombiano y la Organización Mundial de la Salud, durante la pandemia entre la semana epidemiológica 10 hasta la semana 27 de 2020, comparado con las medidas preventivas tomadas durante el mismo periodo del pico respiratorio en el 2019 en cuanto al uso de recursos sanitarios en niños mayores de 1 mes y menores de 5 años con infección respiratoria aguda que ingresan al servicio de urgencias del hospital Militar Central a través de la captura electrónica de datos de&#13;\nhistorias clínicas en los períodos analizados, la muestra fue de 583 sujetos de los cuales 542 consultaron por causa respiratoria en 2019 y 41 sujetos en 2020, encontrando una disminución significativa en las variables analizadas como ingreso a urgencias, ingreso a sala ERA, hospitalización e ingreso a unidad de cuidados intensivos pediátricos, lo que confirma una disminución en la demanda del uso de recursos sanitarios en la población estudiada, estos resultados podrán transformarse a costos sanitarios y de esta manera determinar si la estrategia de lineamientos de contención contra la pandemia Covid-19 resultarían costo-&#13;\nefectivas para futuras pandemias o para la contención de otros picos epidemiológicos virales.
Both the 5′ Untranslated Region and the Sequences Surrounding the Start Site Contribute to Efficient Initiation of Translation In Vitro (1991)

The role of RNA sequences in the 5' leader region between the cap site and initiating AUG in mediating translation was examined in vitro. Hybrid mRNAs were synthesized in which the cognate leader sequence was replaced with either optimized or compromised leader sequences, and translational efficiency was measured for six different coding regions. Translation was most efficient with a leader containing the 5' untranslated region from Xenopus beta-globin and an optimized initiation sequence. Compared with the cognate leaders, this hybrid was observed to increase translation of the various coding regions as much as 300-fold. The translational efficiencies of the different coding regions also varied substantially. In contrast to earlier suggestions that increased leader efficiency results from higher affinity of the leader for a limiting factor, our experiments suggest that increased translation from the beta-globin hybrid leader sequence results from more rapid initiation of translation.
Molecular Epidemiology and Brief History of Emerging Adenovirus 14–Associated Respiratory Disease in the United States (2010)

The current geographic distribution of HAdV-14p1 involves at least 15 states in the Unites States. The role of the fiber mutations in the recent emergence of HAdV-14p1 ARD in North America warrants further study.
Practical aerobic membrane filtration blood culture technique: development of procedure (1975)

The advantages of a membrane filter system for blood culturing have been realized for many years. Lysing of the blood prior to filtration is a convenient way to proceed, but previously described lysing procedures result in loss of certain organisms, particularly gram-negative bacilli. Four concentrations of Triton X-100 and sodium carbonate were studied in vitro, and their lysing and antibacterial properties were observed. A solution of 0.08% Na2CO3 and 0.005% Triton X-100 was found to have the least antibacterial effect and gave consistently good lysis and filtration times (under 3 min). An 8.3-ml amount of blood added to 190 ml of this concentration of lysing solution, filtered through three 47-mm membrane filters (0.45-mum pore size), led to recovery of 85% or more of various aerobic and facultative organisms in studies of artificially seeded blood.
Flexible Methods for Microfluidics (2001)

Devices for handling nanoliter quantities of fluids are creating new fabrication challenges and finding new applications in biology, chemistry, and materials science.
r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock (2003)

The linux executable, C source code, sample data sets and user manual are available free at http://ginger.ucdavis.edu/r8s.
Adenovirus origin of DNA replication: sequence requirements for replication in vitro. (1987)

The initiation of adenovirus DNA takes place at the termini of the viral genome and requires the presence of specific nucleotide sequence elements. To define the sequence organization of the viral origin, we tested a large number of deletion, insertion, and base substitution mutants for their ability to support initiation and replication in vitro. The data demonstrate that the origin consists of at least three functionally distinct domains, A, B, and C. Domain A (nucleotides 1 to 18) contains the minimal sequence sufficient for origin function. Domains B (nucleotides 19 to 40) and C (nucleotides 41 to 51) contain accessory sequences that significantly increase the activity of the minimal origin. The presence of domain B increases the efficiency of initiation by more than 10-fold in vitro, and the presence of domains B and C increases the efficiency of initiation by more than 30-fold. Mutations that alter the distance between the minimal origin and the accessory domains by one or two base pairs dramatically decrease initiation efficiency. This critical spacing requirement suggests that there are specific interactions between the factors that recognize the two regions.
Query Sentences as Semantic (Sub) Networks (2009)

This paper presents an approach for representing queries in natural language as semantic networks. The semantic representation is intended to facilitate the translation between natural language and database queries. A domain agnostic algorithm, based on shallow features, is used to map a sentence to a sub-network of concepts within a larger ontology. This work focuses on transportation information systems and gives promising preliminary results.
A New Five-Year Plan for the U.S. Human Genome Project (1993)

The U.S. Human Genome Project is part of an international effort to\ndevelop genetic and physical maps and determine the DNA sequence of the human\ngenome and the genomes of several model organisms. Thanks to advances in\ntechnology and a tightly focused effort, the project is on track with respect\nto its initial 5-year goals. Because 3 years have elapsed since these goals\nwere set, and because a much more sophisticated and detailed understanding of\nwhat needs to be done and how to do it is now available, the goals have been\nrefined and extended to cover the first 8 years (through September 1998) of\nthe 15-year genome initiative....Four areas were identified by advisers to the\nELSI program for initial emphasis: privacy of genetic information, safe and\neffective introduction of genetic information in the clinical setting,\nfairness in the use of genetic information, and professional and public\neducation....
Global profiling of co- and post-translationally N-myristoylated proteomes in human cells (2014)

Protein N-myristoylation is a ubiquitous co- and post-translational modification that has been implicated in the development and progression of a range of human diseases. Here, we report the global N-myristoylated proteome in human cells determined using quantitative chemical proteomics combined with potent and specific human N-myristoyltransferase (NMT) inhibition. Global quantification of N-myristoylation during normal growth or apoptosis allowed the identification of >100 N-myristoylated proteins, >95% of which are identified for the first time at endogenous levels. Furthermore, quantitative dose response for inhibition of N-myristoylation is determined for >70 substrates simultaneously across the proteome. Small-molecule inhibition through a conserved substrate-binding pocket is also demonstrated by solving the crystal structures of inhibitor-bound NMT1 and NMT2. The presented data substantially expand the known repertoire of co- and post-translational N-myristoylation in addition to validating tools for the pharmacological inhibition of NMT in living cells.
comparison of bio-oil produced in a fractionated bio-oil collection system (2009)

Fast pyrolysis bio-oil, char and non-condensable gases were produced from a 8 kg/hr fluidized bed reactor. The bio-oil was collected in a fractionating bio-oil collection system that produced multiple fractions of bio-oil. This bio-oil was fractionated through two separate, but equally important, mechanisms within the collection system. The aerosols and vapors were selectively collected by utilizing laminar flow conditions to prevent aerosol collection and electrostatic precipitators to collect the aerosols. The vapors were successfully collected through a selective condensation process. The combination of these two mechanisms has created the ability to effectively fractionate the bio-oil into distinct fractions with improved characteristics. The fractions of bio-oil each contained different properties. Bio-oil properties that were improved included the energy content, water content, acid content and distribution of certain carbohydrates (levoglucosan and acetic acid). The improved properties that are associated with the fractionated bio-oil could allow bio-oil to be used in new markets, preferably without further upgrading. The decreased water and acid contents in the first four (of five) fractions could allow for easier upgrading of the bio-oil into transportation fuels or other valuable products.
Sequential expression of antigens on sexual stages of Plasmodium falciparum accessible to transmission-blocking antibodies in the mosquito. (1985)

Plasmodium falciparum gametocytes contain specific antigens, some of which (Mr 230,000, 48,000, 45,000) are expressed on the surface of the newly emerged macrogamete. A different antigen (Mr 25,000) surrounds the surface of the ookinete and, although present to some extent in the developing gametocyte, is synthesized in high quantities by the macrogamete/zygote and expressed progressively on the transforming zygote surface. These antigens are targets of transmission blocking antibodies that are effective at two distinct points after gametogenesis: fertilization of the macrogamete and ookinete to oocyst development. The antigens involved in the fertilization blockade are the Mr 48 and 45 proteins, which are expressed on the macrogamete surface. The Mr 230 K coprecipitating protein probably plays no part in transmission block. mAb directed against the Mr 25 K ookinete surface protein blocked transmission without inhibiting ookinete formation, indicating that this protein has an important role in the transformation of ookinete into oocyst. A combination of mAb recognizing different epitopes on the same protein molecule acted synergistically in inhibiting oocyst formation. Using a mixture of two blocking mAb reacting against the Mr 48/45 and 25 K proteins, respectively, an additive blocking effect could be demonstrated.
Optimizing blood collection, transport and storage conditions for cell free DNA increases access to prenatal testing (2013)

Maternal plasma DNA stabilized for 0 to 7 days in Streck BCTs can be used for non-invasive prenatal molecular applications, when temperatures are maintained within the broad parameters assessed in this study.
Radio wave propagation in potato fields (2005)

Abstract — Reliable communication is crucial for successful deployment of wireless sensor networks. Therefore, it is important to understand the impact of environmental conditions on the performance of the radios (Chipcon CC1000 transceivers) used in typical sensor nodes. This paper reports on an extensive set of measurements taken in a potato field, where the foliage has an important effect on the propagation of radio waves. The influence of the growth stage of the potato crop is significant. We observed a reduction of 15 dB in signal strength at 15 m between nodes, when a flowering crop is compared to a crop on its return. This effectively reduces the radio range from 23 m to 10 m. Another important result is that radio waves propagate better in conditions with a high humidity (i.e., at night and during rain). We attribute this to changes in the reflection coefficient of the top of the potato canopy. I.
Signal Transduction between the Chloroplast and the Nucleus (2002)

Chloroplasts are essential for the unique photoautotrophic and sessile existence of higher plants. Chloroplasts account for >50% of the total soluble protein in leaves, and these proteins are encoded by both nuclear and chloroplast genomes. This separation of genetic information necessitates
Semantic Web Service Composition Planning with OWLS-Xplan ∗ (2005)

We present an OWL-S service composition planner, called OWLS-Xplan, that allows for fast and flexible composition of OWL-S services in the semantic Web. OWLS-Xplan con-verts OWL-S 1.1 services to equivalent problem and domain descriptions that are specified in the planning domain descrip-tion language PDDL 2.1, and invokes an efficient AI plan-ner Xplan to generate a service composition plan sequence that satisfies a given goal. Xplan extends an action based FastForward-planner with a HTN planning and re-planning component.
End-to-end optimization of nonlinear transform codes for perceptual quality (2016)

We introduce a general framework for end-to-end optimization of the rate-distortion performance of nonlinear transform codes assuming scalar quantization. The framework can be used to optimize any differentiable pair of analysis and synthesis transforms in combination with any differentiable perceptual metric. As an example, we consider a code built from a linear transform followed by a form of multi-dimensional local gain control. Distortion is measured with a state-of-the-art perceptual metric. When optimized over a large database of images, this representation offers substantial improvements in bitrate and perceptual appearance over fixed (DCT) codes, and over linear transform codes optimized for mean squared error.
Antiphospholipid syndrome and the idiotypic network (1995)

To study whether monoclonal anticardiolipin antibodies (aCL), derived from patients with antiphospholipid syndrome (APS), have similar pathogenic potential, we have employed an experimental model of antiphospholipid syndrome. Monoclonal aCL were produced by the combined method of EBV transformation and somatic cell hybridization of lymphocytes, derived from patients with APS. The monoclonal aCL were used to immunize mice at the footpads and the mice were followed for serological and clinical manifestations of APS. The monoclonal antibody EY2C9, was found to bind weakly to cardiolipin and other phospholipids (i.e. phosphatidyl-serine, phosphatidyl-ethanolamine and phosphatidyl-inositol). The antibody TM1B9, although derived from a patient with SLE and with secondary APS, did not react with phospholipids. Immunization of naive BALB/c mice with EY2C9 was followed by production of sustained high titers of antiphospholipid antibodies associated with prolonged activated partial thromboplastin time (APTT) (46.8 +/- 5.0 s vs. 22.4 +/- 1.7 s, in the non-immunized mice). Mice immunized with TM1B9 had a more moderate titer of antiphospholipid antibodies and did not show prolonged APTT. The pregnant mice, that were immunized with EY2C9, had increased fetal resorption rate (the equivalent of fetal loss in the human) of 36.8 +/- 10% (vs. 2 +/- 4% in mice immunized with TM1B9). Our results confirm that monoclonal aCL, derived from a patient with APS, can have a pathogenic potential, dysregulating the idiotypic network and leading to the development of characteristic signs of APS.(ABSTRACT TRUNCATED AT 250 WORDS)
Estimation of auditory spatial cues for Binaural Cue Coding (2002)

Binaural Cue Coding (BCC) offers a compact parametric representation of auditory spatial information. This representation can be applied to stereophonic or multi-channel audio compression. It allows to reconstruct the spatial image given a mono audio signal and spatial cues that require only a low data volume. This paper focuses on the extraction of the spatial cues from a stereophonic signal with a BCC analyzer. Results of a first subjective quality evaluation confirm that this technique is able to approximate the spatial image of critical reference signals. Thus BCC has the potential to offer highly efficient stereophonic or multi-channel coding, even at very low bit rates that currently permit coding of only one mono channel.
Combinatorial libraries: A tool to design antimicrobial and antifungal peptide analogues having lytic specificities for structure-activity relationship studies (2000)

In the race for supremacy, microbes are sprinting ahead. This warning by the World Health Organization clearly demonstrates that the spread of antibiotic-resistant bacteria leads to a global health problem and that antibiotics never seen before by bacteria are urgently needed. Antimicrobial peptides represent such a source for novel antibiotics due to their rapid lytic activity (within minutes) through disruption of cell membranes. However, due to the similarities between bacterial, fungal, and mammalian plasma cell membranes, a large number of antimicrobial peptides have low lytic specificities and exhibit a broad activity spectrum and/or significant toxic effect toward mammalian cells. Mutation strategies have allowed the development of analogues of existing antimicrobial peptides having greater lytic specificities, although such methods are lengthy and would be more efficient if the molecular mechanisms of action of antimicrobial peptides were clearly elucidated. Synthetic combinatorial library approaches have brought a new dimension to the design of novel biologically active compounds. Thus, a set of peptide analogues were generated based on the screening of a library built around an existing lytic peptide, and on a deconvolution strategy directed toward activity specificity. These peptide analogues also served as model systems to further study the effect of biomembrane mimetic systems on the peptides structural behavior relevant to their biological activities.
Interactive information extraction with constrained conditional random fields (2004)

Information Extraction methods can be used to automatically "fill-in" database forms from unstructured data such as Web documents or email. State-of-the-art methods have achieved low error rates but invariably make a number of errors. The goal of an Interactive Information Extraction system is to assist the user in filling in database fields while giving the user confidence in the integrity of the data. The user is presented with an interactive interface that allows both the rapid verification of automatic field assignments and the correction of errors. In cases where there are multiple errors, our system takes into account user corrections, and immediately propagates these constraints such that other fields are often corrected automatically. Linear-chain conditional random fields (CRFs) have been shown to perform well for information extraction and other language modelling tasks due to their ability to capture arbitrary, overlapping features of the input in a Markov model. We apply this framework with two extensions: a constrained Viterbi decoding which finds the optimal field assignments consistent with the fields explicitly specified or corrected by the user; and a mechanism for estimating the confidence of each extracted field, so that low-confidence extractions can be highlighted. Both of these mechanisms are incorporated in a novel user interface for form filling that is intuitive and speeds the entry of data -- providing a 23% reduction in error due to automated corrections.
Highly Efficient Blue‐Emitting Iridium(III) Carbene Complexes and Phosphorescent OLEDs (2008)

Bright & blue: A strategy for reducing metal-chelate internal strain enables the preparation of blue emitting iridium(III) carbene complexes (see picture; Ir red, N light blue, F green). The phosphorescent OLED fabricated from one of these complexes shows remarkable CIE coordinates of (0.16, 0.13) and peak efficiencies of 6.0 % photons per electron, 6.3 cd A−1, and 4.0 lm W−1.
F(ab′)2 Reagents Are not Required If Goat, Rather Than Rabbit, Antibodies Are Used to Detect Human Surface Immunoglobulin (1977)

The present report provides evidence that whole goat anti-human immunoglobulin, unlike similar reagents produced in the rabbit, binds both to the same number of and the same individual cells as the F(ab')2 fragments of rabbit or goat anti-human immunoglobulin. These results suggest that goat IgG has a lower affinity for the Fc receptors of human lymphocytes and monocytes than rabbit IgG. Because of this property, whole goat antibodies against human immunoglobulin can be used as simple, convenient relatively inexpensive reagents for the routine detection of immunoglobulin on cell surfaces by immunofluorescence microscopy. The preparation of F(ab')2 fragments of anti-immunoglobulin, which are necessary when rabbit antibodies are used, does not appear to -e required if goat antibodies can be empolyed. This observation has multiple practival applications in cellular immunology.
Synthesis of Trans-cinnamic Acids from Aryl Aldehydes and Aryl Aldehyde Bisulfite Adducts with Malonic Acid Using Piperazine (2005)

Piperazine as a new reagent for the condensation of aryl aldehydes and their bisulfite adducts with malonic acid are described which afford the corresponding cinnamic acids in excellent yields and short reaction times in the absence of solvents under microwave irradiation.
Evaluation of Antihemagglutinin and Antineuraminidase Antibodies as Correlates of Protection in an Influenza A/H1N1 Virus Healthy Human Challenge Model (2016)

This study represents the first time the current gold standard for evaluating influenza vaccines as set by the U.S. Food and Drug Administration and the European Medicines Agency Committee for Medicinal Products for Human Use, a "protective" hemagglutination inhibition (HAI) titer of ≥1:40, has been evaluated in a well-controlled healthy volunteer challenge study since the cutoff was established. We used our established wild-type influenza A healthy volunteer human challenge model to evaluate how well this antibody titer predicts a reduction in influenza virus-induced disease. We demonstrate that although higher HAI titer is predictive of some protection, there is stronger evidence to suggest that neuraminidase inhibition (NAI) titer is more predictive of protection and reduced disease. This is the first time NAI titer has been clearly identified in a controlled trial of this type to be an independent predictor of a reduction in all aspects of influenza.