gebhart/patrepeval huggingface dataset:
Genes concerned with synthesis of poly(glycerol phosphate), the essential teichoic acid in Bacillus subtilis strain 168, are organized in two divergent transcription units (1991)

Insertional mutagenesis has revealed that a 22 kbp segment from the hisA region of the Bacillus subtilis 168 chromosome (310 degrees on the genetic map) contains at least six independent transcription units, all apparently devoted to production of cell envelope components. Genes concerned with synthesis of poly(glycerol phosphate), poly(groP), an essential cell wall polymer in B. subtilis 168, are organized in two divergently transcribed operons denoted tagABC and tagDEF. Nucleotide sequence analysis indicates that three of these six genes encode extremely basic polypeptides. The deduced products of the tagABC operon may be involved in poly(groP) assembly and export, whereas those of the tagDEF operon, which are very hydrophilic, are more likely to be implicated in poly(groP) precursor biosynthesis. The first gene of the tagDEF operon encodes glycerol-3-phosphate cytidylyltransferase (Pooley et al., 1991, Journal of General Microbiology 137, 921-928) and its deduced product has significant homology with cholinephosphate cytidylyltransferase from yeast. There is also substantial homology between the deduced products of tagB in the tagABC operon and tagF in the tagDEF operon.
User authentication and authorization in the Java/sup TM/ platform (2003)

Java/sup TM/ security technology originally focused on creating a safe environment in which to run potentially untrusted code downloaded from the public network. With the latest release of the Java/sup TM/ platform (the Java/sup TM/ 2 Software Development Kit, v 1.2), fine-grained access controls can be placed upon critical resources with regard to the identity of the running applets and applications, which are distinguished by where the code came from and who signed it. However, the Java platform still lacks the means to enforce access controls based on the identity of the user who runs the code. In this paper we describe the design and implementation of the Java/sup TM/ Authentication and Authorization Service (JAAS), a framework and programming interface that augments the Java/sup TM/ platform with both user-based authentication and access control capabilities.
Measuring bubble, drop and particle sizes in multiphase systems with ultrasound (2004)

Abstract A technique is developed for measurement of bubble, droplet and particle‐size distributions in multiphase systems, based on the propagation speed and attenuation of ultrasound. The measurement of the size distribution of the dispersed phase in multiphase systems was desired to analyze the mass‐transfer mechanism in gas‐liquid‐liquid and gas‐liquid‐solid systems. To obtain this information, both the ultrasonic velocity and the attenuation coefficient of tone‐burst signals are determined for a large frequency range (typically 100 kHz – 100 MHz). From these parameters, the size distributions and the volume fraction of the different dispersed phases can be determined using a scattering model. It was shown that the interfacial area can be determined very accurately, however, for the exact size distribution of the gas bubbles in the used size range (1–3 mm) an independent gas holdup determination is required. Experiments were performed in gas‐liquid, solid‐liquid, and gas‐liquid‐solid systems. The results showed good agreement of the particle‐size distribution compared to a commercial laser‐scattering analyzer, both with and without gas bubbles present. Furthermore, a good agreement between the scattering model and the experiments was found in the systems that contained gas bubbles, but these results should be validated using for instance, a digital camera technique. © 2004 American Institute of Chemical Engineers AIChE J, 50: 2750–2762, 2004
Aligned Porous Structures by Directional Freezing (2007)

Abstract Materials with aligned porous structures have broad potential in applications such as organic electronics, microfluidics, and tissue engineering. Materials of this type can be fabricated using techniques such as microfabrication, soft lithography, and photolithography. Directional freezing is a cheap, simple, and novel route to prepare aligned porous materials in the form of 2D surface patterns or 3D monolithic structures. A solvent—typically water but also organic solvents or carbon dioxide—is frozen unidirectionally and the pore structure is templated from the aligned solvent crystals that are formed. These methods can produce complex composite materials with a range of aligned pore architectures.
Generalized Optoelectronic Model of Series-Connected Multijunction Solar Cells (2015)

The emission of light from each junction in a series-connected multijunction solar cell both complicates and elucidates the understanding of its performance under arbitrary conditions. Bringing together many recent advances in this understanding, we present a general 1-D model to describe luminescent coupling that arises from both voltage-driven electroluminescence and voltage-independent photoluminescence in nonideal junctions that include effects such as Sah-Noyce-Shockley (SNS) recombination with n ≠ 2, Auger recombination, shunt resistance, reverse-bias breakdown, series resistance, and significant dark area losses. The individual junction voltages and currents are experimentally determined from measured optical and electrical inputs and outputs of the device within the context of the model to fit parameters that describe the devices performance under arbitrary input conditions. Techniques to experimentally fit the model are demonstrated for a four-junction inverted metamorphic solar cell, and the predictions of the model are compared with concentrator flash measurements.
Pertussis Toxin Gene: Nucleotide Sequence and Genetic Organization (1986)

The current pertussis vaccines, although efficacious, in some instances produce undesirable side effects. Molecular engineering of pertussis toxin, the major protective antigen, could provide a safer, new generation of vaccines against whooping cough. As a first critical step in the development of such a vaccine, the complete nucleotide sequence of the pertussis toxin gene was determined and the amino acid sequences of the individual subunits were deduced. All five subunits are coded by closely linked cistrons. A promoter-like structure was found in the 5'-flanking region, suggesting that the toxin is expressed through a polycistronic messenger RNA. The order of the cistrons is S1, S2, S4, S5, and S3. All subunits contain signal peptides of variable length. The calculated molecular weights of the mature subunits are 26,024 for S1, 21,924 for S2, 21,873 for S3, 12,058 for S4, and 11,013 for S5. Subunits S2 and S3 share 70% amino acid homology and 75% nucleotide homology. Subunit S1 contains two regions of eight amino acids homologous to analogous regions in the A subunit of both cholera and Escherichia coli heat labile toxins.
Comparison of addition of theophylline to inhaled steroid with doubling of the dose of inhaled steroid in asthma (1997)

The anti-asthmatic effects of theophylline may supplement those of inhaled steroids in asthma. The aim of the present trial was to study how the addition of theophylline compares to doubling the dose of inhaled steroid in asthmatics who remain symptomatic on beclomethasone dipropionate (BDP) 400 microg x day(-1). The trial was designed as a randomized, double-blind, parallel-group study in several European countries. Sixty nine patients were treated for 6 weeks with theophylline plus BDP 400 microg x day(-1), compared to 64 patients treated with BDP 800 micro x day(-1). The mean+/-SD serum theophylline concentration was 10.1+/-4.2 mg x L(-1). Lung function measurements were made throughout the study and patients kept daily records of peak expiratory flow (PEF), symptoms and salbutamol usage. Forced expiratory volume in one second and PEF at week 6 were significantly increased by both treatments (p<0.01). PEF variability was reduced by about 30% in both groups. There were significant improvements in asthma symptoms and rescue medication use (p<0.001). There were no significant differences between the treatment groups. The study demonstrated clinical equivalence of theophylline plus beclomethasone dipropionate 400 microg x day(-1) and beclomethasone dipropionate 800 microg x day(-1) in patients whose asthma is not controlled on beclomethasone dipropionate 400 microg x day(-1). The results support the use of theophylline as a steroid-sparing agent. The combination of low-dose inhaled steroid plus theophylline is a suitable treatment for moderate asthma.
Pim serine/threonine kinases regulate the stability of Socs-1 protein (2002)

Studies of SOCS-1-deficient mice have implicated Socs-1 in the suppression of JAK-STAT (Janus tyrosine kinase-signal transducers and activators of transcription) signaling and T cell development. It has been suggested that the levels of Socs-1 protein may be regulated through the proteasome pathway. Here we show that Socs-1 interacts with members of the Pim family of serine/threonine kinases in thymocytes. Coexpression of the Pim kinases with Socs-1 results in phosphorylation and stabilization of the Socs-1 protein. The protein levels of Socs-1 are significantly reduced in the Pim-1(-/-), Pim-2(-/-) mice as compared with wild-type mice. Similar to Socs-1(-/-) mice, thymocytes from Pim-1(-/-), Pim-2(-/-) mice showed prolonged Stat6 phosphorylation upon IL-4 stimulation. These data suggest that the Pim kinases may regulate cytokine-induced JAK-STAT signaling through modulation of Socs-1 protein levels.
Structure and properties of hydrogen-impurity pairs in elemental semiconductors (1989)

A variety of experiments have revealed several puzzling properties of hydrogen-impurity pairs. For example, H atoms passivate the electrical activity of some impurities, whereas they induce electrical activity in others; they appear to tunnel around some impurities but not around others. We report first-principles pseudopotential-density-functional calculations for several hydrogen-impurity complexes and unravel the origins and intricacies of the rich behavior of H bound to different substitutional impurities in Si and Ge.
Hemoglobin measured by Hemocue and a reference method in venous and capillary blood: a validation study (2002)

The difference in Hb between venous and capillary blood is likely related to biological variability. Hemoglobin concentration in capillary blood assessed by Hemocue provides an adequate estimation of population anemia prevalence but may result in excess false negative diagnoses among individuals. The results of this study stress the importance of sample collection technique, particularly for children. Method of analysis and sampling site need to be taken into consideration in field studies. The English version of this paper is available too at: http://www.insp.mx/salud/index.html.
Effect of Different Dietary Protein Composition on Skeletal Muscle Atrophy by Suspension Hypokinesia/Hypodynamia in Rats. (2002)

Under microgravity conditions similar to those in space, it is known that various nutritional and physiological changes in the body are induced. Especially in the aspect of nutrition, muscle atrophy is a characteristic phenomenon accompanying weightlessness. This study was conducted to investigate the ameliorated effect of muscle atrophy caused by suspension hypokinesia by using the soy protein isolate (SPI) as the protein source in comparison with casein. Male Wistar strain rats (8 wk old) were divided into two groups, each suspended with a suspension harness, and fed on a 20% SPI diet or a 20% casein diet for 10 d. The body weights of the suspended rats fed casein or SPI decreased similarly. The weight of the gastrocnemius and soleus muscle were decreased by suspension hypokinesia; however, the degree of the decrease of the muscle weights, especially soleus muscles, of rats fed the SPI diet was smaller than that of rats fed the casein diet. Serum Ntau-methylhistidine concentration was significantly lower in rats fed the SPI diet than in rats fed the casein diet. Similarly, the activities of muscle protein-degrading enzymes such as calpain and proteasome were significantly lower in rats fed the SPI diet than in rats fed the casein diet. Cathepsin B+L activities were not affected by the SPI or the casein diet. Therefore it is suggested that SPI caused a reduction of the proteolysis of myofibrillar protein in skeletal muscles through a reduction of calpain and proteasome activities, in consequence to ameliorate the muscle atrophy.
General purpose bidirectional optical backplane: high-performance bus for multiprocessor systems (2002)

We report the first bidirectional optical backplane bus for a high performance multiprocessor system operating at wavelengths of 632.8 nm and 1300 nm. The optical backplane employs an array of multiplexed holograms, in conjunction with a waveguiding plate within which cascaded fanouts are generated. Data transfer rate of 1.2 Gbit/sec at 1300 nm is demonstrated with a single bus line for a system composed of nine processor/memory boards. To provide a reliable system, packaging-related issues, such as the detector size and misalignment effects are addressed. Theoretical treatment to minimize fluctuations among the received power at each processor/memory board is further presented and an optimum design rule is provided. The backplane demonstrated here is for general-purpose. It can support standard multiprocessor buses such as Futurebus+, Multibus II, etc. It also can function as a backplane bus in existing computing systems and significantly reduce the bottlenecks that accompany electrical interconnects.
Lysozyme-enhanced killing ofCandida albicansandCoccidioides immitisby amphotericin B (1974)

The concentration of amphotericin B required to inhibit the growth in chemically defined media of 3 strains of Candida albicans and the spherule and mycelial growth phases of Coccidioides immitis Silveira strain was decreased 4-to-16-fold by the incorporation of 5–10 μg lysozyme /ml. Despite this enhancement of sensitivity to amphotericin B by physiological (serum) concentrations of lysozyme, the 3 C. albicans strains and the mycelial phase of C. immitis in the absence of amphotericin B were not inhibited by 1000–2000 μg lysozyme/ml. In contrast, the spherule phase of C. immitis was inhibited by 5–20 μg lysozyme/ml. Ten μg lysozyme/ml markedly but reversibly altered the characteristic absorption spectra of amphotericin B and amphotericin B- cholesterol complexes thus suggesting that the lysozyme enhanced sensitivity to amphotericin B shown in lysozyme-insensitive strains may be a consequence of lysozyme binding to cell membrane sterol-amphotericin B complexes. La concentración de anfotericina B requerida para inhibir el crecimiento en medio definido quimicamente de tres (cepas) de Candida albicans y las fases de crecimento esferular y miceliar de Coccidioides immitis cepa Silveira fue disminuida de 4 a 16 veces incorporando 5 a 10 μg de lisozima por cada ml. A pesar de este aumento de sensibilidad a anfotericina B por medio de concentraciones fisiológicas de lisozima, las tres cepas de C. albicans y la fase miceliar de C. immitis en ausencia de anfotericina B no fueron inhibidas por 1000 or 2000 μg de lisozima por cada ml. En contraste, la fase esferular de C. immitis fue inhibida por medio de 5 a 20 μg por cada ml. Diez μg de lisozima por cada ml alteró considerablemente, aunque en forma reversible, el espectro de absorción characteristico de los complejos de anfotericina B y anfotericina B-colesterol sugiriendo que la sensibilidad a anfotericina B aumentada por la lisozima en cepas no sensibles a lisozima, puede ser consecuencia de la union de lisozima a la membrana celular de complejos esterol-anfotericin B.
Expression and Isolation of Recombinant Antibody Fragments in E. coli (2004)

Central to the rapid growth in the study and application of recombinant antibodies in recent years is the ability to reliably and cost-effectively produce large quantities of functional protein. In contrast to glycosylated whole monoclonal antibodies (MAbs), functional derivatives (antibody fragments) carrying antigen (Ag)-binding activities, and comprising at minimum the antibody variable heavy- and light-chain domains, can be readily produced in bacterial cells (1). The range of antibody (Ab) fragments that can be produced in this way includes F(ab)2 and Fab′, which can also be generated by proteolytic digestion of MAb, and smaller variants such as Fv, scFv, and scAb (single-chain antibody). Even single domains that comprise only the heavy-chain or the light-chain variable region can display Ag-binding activity, although these are not discussed specifically in this chapter. The smallest derivatives that retain the Ag-binding specificity of parental MAbs are Fv fragments. However, as the two domains are held together only by non-covalent hydrophobic interactions, they are prone to dissociate. This can be overcome by chemical crosslinking or the introduction of inter-chain disulfide bonds, or more often by the inclusion of a short peptide linker into expression constructs to produce scFv. Further variants include the addition of a range of suitable (C-terminal) tags for the purification or detection of expressed protein, such as a human Cκ domain (scAb) (2), c-myc, or hexahistidine.
The Clinical Importance of Proton Pump Inhibitor Pharmacokinetics (2002)

Achieving the optimal clinical response for patients with upper gastrointestinal peptic disease is important. This response depends on the pathology treated as well as on the choice of proton pump inhibitor. Here, we identify factors in specific disease therapy and proton pump inhibitor (PPI) pharmacokinetic and pharmacodynamic characteristics that help us achieve this goal. These include differences in PPI bioavailability and acid-suppressive effects. Available data indicate that PPIs appear to have similar potency on a milligram basis, and that omeprazole and lansoprazole are more frequently double dosed than pantoprazole. The lower propensity for double dosing with pantoprazole may also result in lower medication acquisition costs and a reduction in physician visits due to ineffective therapy with the standard dosing of these other agents.
Directional and ionized physical vapor deposition for microelectronics applications (1998)

The manufacturing of interconnect features on semiconductor wafers has evolved from lift-off-based evaporation to reactive ion etching metallization and now to Damascene technology. Physical sputter deposition has been widely used for blanket metal film deposition, but is impractical for high aspect topographies. Filtered, or directional sputter techniques, such as long throw or collimation, have been used for some high aspect ratio applications, but suffer from poor efficiency, high cost, and/or poor scaling. Ionized sputter deposition, which uses in-flight ionization of sputtered metal atoms and subsequent film deposition by means of a substrate potential, has been developed as a technique to extend physical vapor deposition into higher aspect ratios.
A method for computation of velocity profiles by inversion of large-offset records (1984)

Abstract This paper describes a new method for recovering velocity profiles utilizing both phase and amplitude information including wide-angle arrivals, post- and pre-critical reflections.This method is based on a double spatial transformation with a minimization procedure. The first transformation is slant stacking of the observed wave field (seismogram). The second is projecting the slant stacked wave field into the domain of horizontal slowness p and depth z. In this domain the inverse problem is reduced to finding the critical path p = V (super -1) (z) where V(z) is the true velocity of the compressional waves. A numerical algorithm based on a minimization technique is used to find the critical path, which is equivalent to the set of turning points of the critically reflected rays. When this path is found, then the following criteria are satisfied:(1) most of the energy is concentrated away from the precritical region;(2) the computed reflection coefficients reach their maximum on this path; and(3) for horizontally stratified media or CMP data, the reflectors are aligned in the p-z domain.In tests, this method has been shown to recover the velocity profile from both synthetic and real data. It is shown that the method is able to recover accurately velocity profiles even if only part of the data are given. For example, only part of the data are available when low- and high-frequency components are missing or when the data are truncated in lateral extent due to the finite length of the recording system. Moreover, the method is able to handle virtually any vertical velocity gradients in a medium; therefore, it can be applied to complicated geologic structures. The method does not require elimination of multiples, but it is not applicable to the case of a medium with a large lateral velocity gradient. It can be used even for an elastic medium when the mode-converted energy is not small.
Clinical Implications of Fibroblast Activation Protein in Patients with Colon Cancer (2007)

Our data indicate that patients whose colon tumors have high levels of stromal FAP are more likely to have aggressive disease progression and potential development of metastases or recurrence. This study affirms the rationale for ongoing clinical investigations using FAP as a therapeutic target to disrupt FAP-driven tumor progression in patients with metastatic disease. It also suggests that the effects of FAP inhibition should be investigated in earlier-stage tumors, given its high levels and potential effect earlier in the course of the disease.
Comparison of urban propagation models with CW-measurements (2003)

The European research committee COST 231 has developed a propagation model for the estimation of urban transmission loss in cellular mobile radio. This model considers the diffraction loss due to equidistantly spaced buildings along the direct radio path and the diffraction and scatter losses from the rooftop down to the mobile. CW measurements in the 900- and 1800-MHz bands were performed in the cities of Mannheim and Darmstadt, Germany. Mannheim can be characterized as a homogeneously structured urban area with a rectangular street grid. The land cover in Darmstadt, on the other hand, is characterized by an inhomogeneous structure. The influences of base station antenna height, radio frequency, and street orientation are analyzed in detail. The quality of path-loss estimation and the shortcomings of the COST-231 model are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Primary Pulmonary Hypertension (1997)

Primary pulmonary hypertension is a condition characterized by sustained elevations of pulmonary-artery pressure without a demonstrable cause. The diagnostic criteria used in the National Institutes of Health (NIH) registry1 include a mean pulmonary-artery pressure of more than 25 mm Hg at rest, or more than 30 mm Hg with exercise, and the exclusion of left-sided cardiac valvular disease, myocardial disease, congenital heart disease, and any clinically important respiratory, connective-tissue, or chronic thromboembolic diseases. Pulmonary vascular disease with clinical and pathological features similar to those of primary pulmonary hypertension can occur in patients with portal hypertension,2 infection with the human immunodeficiency . . .
High resolution imaging of normal and osteoarthritic cartilage with optical coherence tomography. (1999)

OCT represents an attractive new technology for intraarticular imaging due to its high resolution (greater than any available clinical technology), ability to be integrated into small arthroscopes, compact portable design, and relatively low cost.