gebhart/patrepeval huggingface dataset:
An ileX tRNA gene is located close to the Shiga toxin II operon in enterohemorrhagic Escherichia coli O157 and non-O157 strains (2006)

A cosmid library of enterohemorrhagic Escherichia coli (EHEC) O157:H7 strain EDL 933 was constructed and clones carrying the stx2 gene were identified by colony blot hybridization with a stx2B specific probe. Nucleotide sequencing upstream of the stx2A gene revealed high sequence identities of 89.5% to the ileX tRNA gene found in E. coli. The ileX gene was located 260 bp from the translational start codon of stx2A. PCR analysis with primers specific for this analyzed region showed that in 11 Stx2-producing EHEC strains from patients with hemolytic uremic syndrome, all PCR-positive strains carried the ileX tRNA gene. However, PCR analysis of the respective region in 11 Stxl-producing EHEC strains detected no ileX genes. Although the role of ileX in Stx2-producing EHEC strains is not clear, its function in regard to the use of rare codons and as an integration site is discussed.
Portable mechanical ventilation with closed-loop control of inspired fraction of oxygen maintains oxygenation in the setting of hemorrhage and lung injury (2015)

Adequate oxygenation can be maintained in the setting of hemorrhage and lung injury using a portable ventilator embedded with a CLC of FIO2 based on pulse oximetry. These devices may be valuable for providing advanced medical care in resource-limited environments.
Air-dropped sensor network for real-time high-fidelity volcano monitoring (2009)

This paper presents the design and deployment experience of an air-dropped wireless sensor network for volcano hazard monitoring. The deployment of five stations into the rugged crater of Mount St. Helens only took one hour with a helicopter. The stations communicate with each other through an amplified 802.15.4 radio and establish a self-forming and self-healing multi-hop wireless network. The distance between stations is up to 2 km. Each sensor station collects and delivers real-time continuous seismic, infrasonic, lightning, GPS raw data to a gateway. The main contribution of this paper is the design and evaluation of a robust sensor network to replace data loggers and provide real-time long-term volcano monitoring. The system supports UTC-time synchronized data acquisition with 1ms accuracy, and is online configurable. It has been tested in the lab environment, the outdoor campus and the volcano crater. Despite the heavy rain, snow, and ice as well as gusts exceeding 120 miles per hour, the sensor network has achieved a remarkable packet delivery ratio above 99% with an overall system uptime of about 93.8% over the 1.5 months evaluation period after deployment. Our initial deployment experiences with the system have alleviated the doubts of domain scientists and prove to them that a low-cost sensor network system can support real-time monitoring in extremely harsh environments.
Isolation of <i>Drosophila</i> CREB-B: A Novel CRE-Binding Protein (1993)

CREB is a DNA-binding protein that stimulates gene transcription upon activation of the cAMP signaling pathway. The mammalian CREB protein consists of an amino-terminal transcriptional activation domain and a carboxy-terminal DNA-binding domain comprised of a basic region and a leucine zipper. Recent studies have shown that the mammalian CREB is one of many transcription factors that can bind to the cAMP regulated enhancer (CRE) sequence. Consequently, a complete understanding of regulation through the CRE sequence requires the elucidation of how the various CRE-binding proteins interact with each other. To accomplish this goal, we have begun to characterize the family of CRE-binding proteins in a system that is amenable to genetic manipulations, Drosophila melanogaster. We have previously cloned a protein designated dCREB-A from a Drosophila embryonic cDNA library. Here, we describe an additional member of the Drosophila CREB gene family, isolated by screening a lambda gt11 library of adult Drosophila head cDNAs with a multimerized CRE sequence. This protein, dCREB-B, contains 285 amino acids and is remarkably similar within the basic/zipper region to the corresponding portion of mammalian CREB. In contrast, the dCREB-B and mammalian CREB zipper domains differ considerably from the dCREB-A zipper in both length and composition. However, the putative DNA binding domains for all three proteins are highly conserved. The activator region of dCREB-B is completely different from that of both mammalian CREB and dCREB-A. Northern blot analysis shows that multiple transcripts of the dCREB-B gene are expressed in embryonic and adult tissues and that these transcripts arise from both strands of the DNA.(ABSTRACT TRUNCATED AT 250 WORDS)
[Follow-up study of the effect of acute lower respiratory tract infection during childhood on chronic bronchitis in adults]. (1992)

In order to study the relationship between the acute lower respiratory tract infection (ALRTI) during childhood and the occurrence of chronic bronchitis in adults, 90 cases (infection group) admitted to hospital for ALRTI before 7 yr old were followed up 24-31 years later. Their siblings without ALRTI during childhood were selected as the control group. The prevalence of chronic bronchitis in the infection group (12.2%) is significantly higher than that of the control group (2.2%). It is concluded that ALRTI during childhood may play an important role in the occurrence of chronic bronchitis in adults. Further analysis showed that infection and smoking have synergic effects on the occurrence of chronic bronchitis.
The Community College Professoriate: Expanding the Dialogue about Faculty Roles. (1994)

We propose a surface modification procedure to construct DNA arrays for use in surface plasmon resonance (SPR) imaging studies for the highly sensitive detection of a K-ras point mutation, enhanced with hydrogel nanospheres. A homobifunctional alkane dithiol was adsorbed on Au film to obtain the thiol surface, and ethyleneglycol diglycidylether (EGDE) was reacted to insert the ethyleneglycol moiety, which can suppress nonspecific adsorption during SPR analysis. Then streptavidin (SA) was immobilized on EGDE using tosyl chloride activation. Biotinylated DNA ligands were bound to the SA surface via biotin-SA interaction to fabricate DNA arrays. In SPR analysis, the DNA analyte was exposed on the DNA array and hybridized with the immobilized DNA probes. Subsequently, the hydrogel nanospheres conjugated with DNA probes were bound to the DNA analytes in a sandwich configuration. The DNA-carrying nanospheres led to SPR signal enhancement and enabled us to discriminate a K-ras point mutation in the SPR difference image. The application of DNA-carrying hydrogel nanospheres for SPR imaging assays was a promising technique for high throughput and precise detection of point mutations.
Expression patterns of bone-related proteins during osteoblastic differentiation in MC3T3-E1 cells. (1996)

Bone formation involves several tightly regulated gene expression patterns of bone-related proteins. To determine the expression patterns of bone-related proteins during the MC3T3-E1 osteoblast-like cell differentiation, we used Northern blotting, enzymatic assay, and histochemistry. We found that the expression patterns of bone-related proteins were regulated in a temporal manner during the successive developmental stages including proliferation (days 4-10), bone matrix formation/maturation (days 10-16), and mineralization stages (days 16-30). During the proliferation period (days 4-10), the expression of cell-cycle related genes such as histone H3 and H4, and ribosomal protein S6 was high. During the bone matrix formation/maturation period (days 10-16), type I collagen expression and biosynthesis, fibronectin, TGF-beta 1 and osteonectin expressions were high and maximal around day 16. During this maturation period, we found that the expression patterns of bone matrix proteins were two types: one is the expression pattern of type I collagen and TGF-beta 1, which was higher in the maturation period than that in both the proliferation and mineralization periods. The other is the expression pattern of fibronectin and osteonectin, which was higher in the maturation and mineralization periods than in the proliferation period. Alkaline phosphatase activity was high during the early matrix formation/maturation period (day 10) and was followed by a decrease to a level still significantly above the baseline level seen at day 4. During the mineralization period (days 16-30), the number of nodules and the expression of osteocalcin were high. Osteocalcin gene expression was increased up to 28 days. Our results show that the expression patterns of bone-related proteins are temporally regulated during the MC3T3-E1 cell differentiation and their regulations are unique compared with other systems. Thus, this cell line provides a useful in vitro system to study the developmental regulation of bone-related proteins in relation to the different stages during the osteoblast differentiation.
Characterization of volume-sensitive, calcium-permeating pathways in the osteosarcoma cell line UMR-106-01 (1989)

Measurements of cell volume changes, free cytosolic Ca2+ concentration [( Ca2+]i) with Fura 2 and cell membrane potential with 3,3'-dipropylthiodicarbocyanine iodide were used to study the effect of cell volume change on Ca2+ influx and the membrane potential of the osteoblastic osteosarcoma cell line, UMR-106-01. Swelling the cells by hypo-osmotic stress was followed by reduction in cell volume which was markedly impaired by removal of medium Ca2+. Accordingly, cell swelling resulted in [Ca2+]i increase only in the presence of medium Ca2+. The cell swelling-activated Ca2+ entry pathway was active at resting membrane potentials, and Ca2+ influx through this pathway markedly increased upon cell hyperpolarization. A linear relationship between Ca2+ entry and the potential across the plasma membrane was observed. Thus, the volume-activated Ca2+ permeating pathway in UMR-106-01 cells has conductive properties. These pathways do not spontaneously inactivate with time when the cells are not allowed to volume regulate. The pathway can be blocked by micromolar concentrations of nicardipine and La3+ but display very low sensitivity to diltiazem and verapamil. Activation of the volume-sensitive, Ca2+ permeating pathway was not dependent on an increase in [Ca2+]i. Likewise, activation of the pathway was independent of a change in membrane potential between -85 and -3 mV. The increase in [Ca2+]i resulted in hyperpolarization of the cells, probably due to activation of Ca2+-activated K+ channels. The volume-sensitive pathways were partially active under isotonic conditions. Their activity was inhibited by cell shrinkage and increased by cell swelling. The pathways were sensitive to small changes in cell volume, particularly around a medium osmolarity of 310 mosM.
Deodorization 1975 (1976)

Abstract Current deodorization equipment available worldwide is reviewed with a general discussion of process innovations, operating conditions, and process‐quality control problems. Flavor, color, odor, and stability of finished products are considered as affected by deodorization.
Solid-Phase Synthesis of Anandamide Analogues (2004)

The endocannabinoids are amides and esters of arachidonic acid that can mimic the pharmacological properties of Delta(9)-tetrahydrocannabinol (Delta(9)-THC). Anandamide, the most prominent of the endocannabinoids, has been implicated in both metabolic/physiological roles of the central nervous system, making it an attractive medicinal target. As such, we report the first solid-phase methodology that expedites access to various anandamide analogues. Our synthesis features a repetitive Cu-mediated coupling reaction between terminal alkynes and propargyl halides or allylic halides.
Thermochemical Hydrogen Generation (1974)

The basic concepts for thermochemical hydrogen generation processes have been summarized in this article. A useful set of criteria has been described for the screening and selection of potentially viable, multistep, closedcycle thermochemical processes for hydrogen generation. Three illustrative, new closed-cycle processes have been discussed, indicating potential, overall thermal efficiencies ranging from approximately 40 to 60 percent. Combined thermochemical-electrolytic schemes also warrant further consideration. Principal technical problems in the development of such thermochemical closed-cycle and mixed-cycle processes are expected to include primarily materials compatibility, reaction kinetics, separation techniques, and heat-exchanger systems. As natural gas supplies decline and prices rise, new open-cycle thermochemical processes based on water and other fossil fuel feedstocks will be the first important new technology in supplying the growing hydrogen needs of industry for at least the next two decades. Conventional electrolysis technology does not appear to be a competitor for large-scale supplies in this century unless very low off-peak electrical power rates become available, although electrolysis will be the best technique for some small-scale uses. Further analysis will be required to determine if closed-cycle thermochemical or mixed-cycle methods will displace electrolysis or other methods as the principal technology for the production of hydrogen on a large scale for the longer term.
Synthetic oligopeptides bearing a common or subtypic determinant of hepatitis B surface antigen. (1990)

Two determinants of hepatitis B surface Ag (HBsAg), identified by mAb raised against polypeptide components, were characterized immunochemically. One was expressed on HBsAg irrespective of the four major subtypes, i.e., adw, adr, ayw, and ayr, whereas the other was subtypic but not identical to any of d, y, w, and r determinants. The common determinant was generated by a synthetic pentadecapeptide with a sequence of Thr-Thr-Ser-Thr-Gly-Pro-Cys-Lys-Thr-Cys-Thr-Ile-Pro-Ala-Gln representing amino acids 115-129 of the S gene product, and detected invariably in 366 HBsAg samples in sera from asymptomatic carriers in Japan. The activity of the S gene product, as well as the peptide (115-129), to bind with the mAb was not affected by alkylation alone, but was completely lost after reductive alkylation. The antigenic activity was lost when the S gene product was severed between Lys122 and Thr123 by trypsin. A microconformation maintained by the -Cys121-Cys124 bond, therefore, would be required for the common determinant. The other mAb identified an epitope of HBsAg that was mimicked by a synthetic tetradecapeptide with a sequence of Thr-Cys-Thr-Ile-Pro-Ala-Gln-Gly-Thr-Ser-Met-Phe-Pro-Ser, representing amino acids 123-136 of the S gene product. Among 16 HBsAg samples with known S gene sequences, 5 with Ile126 possessed this subtypic determinant, but the remaining 11 with Thr126 did not. The 5 hepatitis B virus genomes encoding the subtypic determinant differed less than 5.6% from each other in the entire nucleotide sequence, but by 8.0% or more from any of the other 11 genomes without the capacity to encode it.
THE ALCOHOLYSIS OF CHLOROSILANES AND THE SYNTHESIS OF SILANE COUPLING AGENTS (1980)

The alcoholysis of a series of chlorosilanes in the presence of petroleum ether gave the corresponding alkoxy silanes in good yields and some of them were converted to the corresponding coupling agents.Reaction between thiourea and γ-chloropropyltrimethoxysilane followed by basic hydrolysis gave γ-mercaptopropyltrimethoxysilane which was useful as a protective coating for metal surfaces.In the presence of the conventional catalysts, allylamine could be added directly to trialkoxysilanes.p-Chlorophenyltrichlorosilane and a series of its alcoholytic products were synthesized in good yield.
Pediatric acne: clinical presentations, evaluation, and management. (2007)

Acne vulgaris can be easy to diagnose yet difficult to evaluate and manage, especially when it presents in infancy and childhood. The differential diagnosis of acne varies by age and, in some cases, may warrant a work-up in order to rule out underlying systemic abnormalities. Likewise, treatment strategies can be influenced by the patient's age. In this article, we present an overview of the clinical presentations of acne by age, an approach to patient evaluation, and a general strategy for management of this common and important disease.
Attitude monitoring and surveillance system for Lapan payload test rocket (2013)

This paper describes the design and implementation of a rocket payload system that functions as an attitude monitoring and surveillance systems. The system is designed to monitor rocket's dynamics and take aerial photographs. The measured data is sent via radio frequency (RF) modem to a ground control system (GCS) in real-time. The rocket dynamics comprises of rocket's linear acceleration and orientation data. The rocket's orientation is represented in the roll, pitch, and yaw angles. The Attitude and Heading Reference System (AHRS) integrate accelerometer, gyroscope, and magnetometer data to obtain accurate attitude angles. Unlike Inertial Navigation System (INS) which also provide position estimation, AHRS only provide attitude estimation. INS suffer accumulated error on position estimation so that the system need correction which is solved by global measurement such as GPS. AHRS also suffer accumulated error on orientation estimation due to gyroscope drift. This problem on this case is solved by drift correction block. Additionally, the payload system is capable for aerial surveillance in the form of a still image. In June 2012, the system is fitted to the Indonesian National Aeronautics and Space Agency (LAPAN) RUM-70 payload test rocket and is successfully launched. The monitored data clearly shows the five stages of the launch. Moreover, the imagery system managed to take a clear picture of the Congot coastline in 52,63 second with 2.075 % data losses.
Using Smart Phones to Access Site-Specific Services (2005)

We investigate how smart phones can augment site-specific services - that is, electronic services or applications that reside in a specific location. Site-specific services already exist in the form of ticket machines, electronic information kiosks, interactive product catalogues, and so on. However, integrating users' smart phones into these interactions can enhance service functionality while reducing deployment costs. Our approach offers several benefits. By using personal information stored on smart phones, site-specific services can automatically tailor their actions to suit a particular user. Our research led us to develop the Mobile Service Toolkit: a client-server software framework supporting the development of site-specific services that exploit interaction with smart phones. We discuss the Mobile Service Explorer (MST) and present case studies of two site-specific services implemented using it.
A deconvolution filter for improvement of time-delay estimation in elastography (1998)

In elastography, tissue under investigation is compressed, and the resulting strain is estimated from the gradient of displacement estimates. Therefore, it is important to accurately estimate the displacements (time-delay) for good quality elastograms. A principal source of error in time-delay estimation in elastography is the decorrelation of the echo signal due to tissue compression (decorrelation noise). Temporal stretching of the postcompression signals has been shown to reduce the decorrelation noise at small strains. In this article, we present a deconvolution filter that reduces the decorrelation even further when applied in conjunction with signal stretching. The performance of the proposed filter is evaluated using simulated data.
Biology of the scleroderma fibroblast (1998)

Abnormalities of matrix biosynthesis by systemic sclerosis fibroblasts underlie the cutaneous and visceral fibrosis seen in this disease. The fundamental basis of the abnormal fibroblast phenotype has not been determined but primary metabolic abnormalities, responses to abnormal environmental signals, and clonal selection have all been hypothesized to play a role. In the past year, evidence supporting each of these explanations was forthcoming. In a study of Choctaw Indians with a high incidence of scleroderma, it was shown that genetic linkage to fibrillin may play a role. This should be considered in light of demonstrated abnormalities of fibrillin structure in the tight skin mouse. Other studies have shown that abnormalities of transforming growth factor beta receptor levels, abnormalities of production and response to tissue inhibitor of matrix metal-loproteinase, and abnormalities of response to endothelial cell factors are all present in scleroderma fibroblasts. In addition to these studies in scleroderma fibroblasts, work elucidating the role of transcription factors Sp1, Sp3, and cKrox in regulating collagen metabolism provided important data upon which future studies may build.
Inca: a novel p21-activated kinase-associated protein required for cranial neural crest development (2007)

Inca (induced in neural crest by AP2) is a novel protein discovered in a microarray screen for genes that are upregulated in Xenopus embryos by the transcriptional activator protein Tfap2a. It has no significant similarity to any known protein, but is conserved among vertebrates. In Xenopus, zebrafish and mouse embryos, Inca is expressed predominantly in the premigratory and migrating neural crest (NC). Knockdown experiments in frog and fish using antisense morpholinos reveal essential functions for Inca in a subset of NC cells that form craniofacial cartilage. Cells lacking Inca migrate successfully but fail to condense into skeletal primordia. Overexpression of Inca disrupts cortical actin and prevents formation of actin "purse strings", which are required for wound healing in Xenopus embryos. We show that Inca physically interacts with p21-activated kinase 5 (PAK5), a known regulator of the actin cytoskeleton that is co-expressed with Inca in embryonic ectoderm, including in the NC. These results suggest that Inca and PAK5 cooperate in restructuring cytoskeletal organization and in the regulation of cell adhesion in the early embryo and in NC cells during craniofacial development.
Mutations in Pneumococcal <i>cpsE</i> Generated via <i>In Vitro</i> Serial Passaging Reveal a Potential Mechanism of Reduced Encapsulation Utilized by a Conjunctival Isolate (2015)

While the capsule of Streptococcus pneumoniae is required for colonization and invasive disease, most conjunctival isolates are acapsular by virtue of deletion of the entire capsular operon. We show that spontaneous acapsular mutants isolated in vitro harbor mostly nonrevertible single nucleotide polymorphism (SNP) null mutations in cpsE, encoding the initiating glycosyltransferase. From a small collection of acapsular conjunctival isolates, we identified one strain with a complete capsular operon but containing a SNP in cpsE that we show is responsible for the acapsular phenotype. We propose that acapsular conjunctival isolates may arise initially from such nonreverting SNP null mutations in cpsE, which can be followed later by deletion of portions or all of the cps operon.