gebhart/patrepeval huggingface dataset:
Specific and sensitive detection of <b> <i>Trichomonas tenax</i> </b> by the polymerase chain reaction (1997)

A polymerase chain reaction (PCR) protocol was developed for specific detection of Trichomonas tenax by using a pair of primers designed for its 18S rRNA gene. The detection was specific for T. tenax, since no amplification was detected with DNAs from Trichomonas vaginalis, which belongs to the same genus as T. tenax, in addition to various species of oral protists, fungi and bacteria, and human leukocytes. This method had a detection limit of 100 fg for T. tenax genomic DNA and could detect T. tenax cells in dental plaque at a concentration of as low as 5 cells per PCR mixture. Direct detection from clinical dental plaque samples was also possible; therefore, the present PCR procedure could provide a simple and rapid detection method of T. tenax in dental plaque.
Design and prototyping of location management and handoff protocols for wireless ATM networks (2002)

This paper deals with design and prototyping of mobility support protocols for mobile/wireless ATM networks. Specific ATM UNI/NNI protocol extensions for location management and handoff control are proposed and described in context of existing ATM networks. The viability of these protocols is established via the implementation of a proof-of-concept prototype mobile ATM network. The prototype system is used to validate the proposed location management and handoff protocols and/or to demonstrate support of both ATM and non-ATM mobile devices.
Glucose kinetics in interstitial fluid can be predicted by compartmental modeling (1997)

The purposes of this study were to define in sheep a compartmental model for glucose kinetics in the basal condition and to test the hypothesis that interstitial fluid obtained by sampling thoracic duct lymph (TDL) represents one or more peripheral compartments of the glucose model. A bolus of [6,6-(2)H]glucose was injected in nine animals, followed by frequent sampling of blood and TDL. Linear kinetic modeling has been applied to plasma data, indicating that a three-compartment model adequately describes glucose kinetics. Both catenary and mammillary models were identified, and their predictions for the tracer behavior in nonaccessible pools were evaluated. In all experiments, regardless of the model structure, predictions in the compartment most rapidly exchanging with blood (pool 2) well matched the measured tracer-to-tracee ratio in TDL. Furthermore, modeling analysis showed that 90-95% of the tracer in TDL comes from this pool. This supported the physiological identification of a peripheral pool of glucose kinetics as extracellular fluid represented by TDL measurements.
The three SoxC proteins—Sox4, Sox11 and Sox12—exhibit overlapping expression patterns and molecular properties (2008)

The group C of Sry-related high-mobility group (HMG) box (Sox) transcription factors has three members in most vertebrates: Sox4, Sox11 and Sox12. Sox4 and Sox11 have key roles in cardiac, neuronal and other major developmental processes, but their molecular roles in many lineages and the roles of Sox12 remain largely unknown. We show here that the three genes are co-expressed at high levels in neuronal and mesenchymal tissues in the developing mouse, and at variable relative levels in many other tissues. The three proteins have conserved remarkable identity through evolution in the HMG box DNA-binding domain and in the C-terminal 33 residues, and we demonstrate that the latter residues constitute their transactivation domain (TAD). Sox11 activates transcription several times more efficiently than Sox4 and up to one order of magnitude more efficiently than Sox12, owing to a more stable alpha-helical structure of its TAD. This domain and acidic domains interfere with DNA binding, Sox11 being most affected and Sox4 least affected. The proteins are nevertheless capable of competing with one another in reporter gene transactivation. We conclude that the three SoxC proteins have conserved overlapping expression patterns and molecular properties, and might therefore act in concert to fulfill essential roles in vivo.
The effect of copper design rules on inductor performance (2004)

In this paper, the effect of process-related design rules on inductor performance are shown. In advanced processes the copper line width is limited, and the metal pattern density must be as uniform as possible. The results obtained on inductors fabricated in-one metal layer with a different number of parallel tracks, with and without copper tiles are presented. The geometry and the orientation of the tiles are also varied. The comparison allows us to quantify the influence of copper tiles on the inductor quality factor.
Relationships between voltage and tension in sheep cardiac Purkinje fibers. (1975)

The two-microelectrode technique of voltage clamping sheep cardiac Purkinje fibers was used to examine the changes in contraction which occur during trains of voltage clamps. (A "train" is defined as a series of voltage clamps delivered at a particular rate, beginning after a rest long enough that the effects of previous stimulation have died away.) Contractions showed striking staircases, or progressive changes in peak isometric tension, during trains. Short clamps, clamps to voltages more negative than --20 or --30 mV, or holding potentials less negative than the resting potential favored negative staircases, while long clamps, clamps to positive voltages, and holding potentials near the resting potential each favored positive staircases. The staircase behavior appeared to be due to changes in the initial rate of recovery of the ability to contract. The changes in staircase behavior as a function of clamp voltage suggested that the relationship between peak tension and clamp voltage should depend on the experimental design. When the steady-state contraction was plotted as a function of clamp voltage, voltage-tension relations like those recently reported for working ventricle were obtained, with a threshold between --30 and --40 mV and a steep relation between tension and voltage. When the first contraction after a rest was plotted, the threshold voltage was more negative, the curve was flatter, and the peak tensions at inside positive voltages were reduced.
Proppant Placement Using Alternate-Slug Fracturing (2013)

Abstract New fracturing techniques such as hybrid fracturing (Sharma et. al., 2004), reverse hybrid fracturing (Liu et. al., 2007) and channel (HiWAY) fracturing (Gillard et al. 2010) have been deployed over the past few years to effectively place proppants in fractures. The goal of these methods is to generate a network of open channels within the proppant pack, providing highly conductive paths for hydrocarbons to flow from the reservoir to the wellbore. This paper presents an experimental study on proppant placement using a new method of fracturing, referred to as Alternate-Slug fracturing, which involves alternate injection of low viscosity and high viscosity fluids into the fracture. Alternate-slug fracturing ensures deeper placement of proppants through two primary mechanisms: (a) proppant transport in viscous fingers formed by the low viscosity fluid and (b) an increase in drag force in the polymer slug leading to better entrainment and displacement of any proppant banks that may have formed. Both these effects lead to longer propped fracture length and better vertical placement of proppants in the fracture. In addition the method offers lower polymer costs, lower pumping horsepower, smaller fracture widths, better control of fluid leakoff and less gel damage compared to conventional gel fracs. Experiments are conducted in simulated fractures (slot cells) to study the mixing of fluids over a wide range of viscosity ratios. Data is presented to show that the finger velocities and mixing zone velocities increase with viscosity ratio up to viscosity ratios of about 350 and the trend is consistent with Koval’s theory. However, at higher viscosity ratios the mixing zone velocity values plateau signifying no further effect of viscosity contrast on the growth of fingers and mixing zone. Fluid elasticity is observed to slow down the growth of fingers and leads to growth of multiple thin fingers as compared to a single thick dominant finger in less elastic fluids. Experiments are conducted with fluids of different viscosity and elasticity, with proppants being carried by the low viscosity fluid. It is shown that the injection rate, slug size and viscosity ratio can be used to control the geometry of the fingers created and, therefore, the proppant distribution in the fracture. The non-uniform placement of proppant in the viscous fingers leads to the creation of high permeability paths in the proppant pack.
Aberrant Crypt Foci in the Colonic Mucosa of Rats Treated with a Genotoxic and Nongenotoxic Colon Carcinogen (1996)

Aberrant crypt foci (ACFs) are putative preneoplastic lesions in the colonic mucosa identified by examining methylene blue-stained whole mounts of colon. ACFs have been previously described in rats treated with genotoxic colon carcinogens. This study determined whether or not a nongenotoxic colon carcinogen could induce ACFs and compared the morphology of these ACFs with those induced by a genotoxic colon carcinogen. Six-wk-old Fischer-344 rats were administered dextran sulfate (DSS, nongenotoxin) in the drinking water or azoxymethane (AOM, genotoxin) by single subcutaneous injection. Rats were sacrificed at 9 and 14 wk after study initiation. Colons were fixed and stained with methylene blue, and the mucosal surface of transilluminated whole mounts was examined with a microscope. The number of ACFs and number of crypts per focus (multiplicity) were recorded. Representative ACFs were processed into glycol methacrylate for hexosaminidase enzyme histochemistry and sections of the remaining colon containing ACFs were embedded in paraffin for morphologic evaluation. In whole mounts, ACFs from AOM- and DSS-treated rats had elongated slit-to-oval-shaped lumens surrounded by a thickened and intensely stained epithelium. DSS-induced aberrant crypts differed from those induced by AOM in that they were frequently larger, tended not to form discrete foci circumscribed by normal crypts, and were located adjacent to ulcers. Total ACFs and large foci (4 or more crypts/focus) were significantly more numerous in AOM-treated rats at both time points. Histologically, DSS-induced ACFs had segmental to diffuse loss of hexosaminidase activity, mucin depletion to increased prominence of goblet cells, and marked distortion of crypt architecture. AOM-induced ACFs had diffuse loss of hexosaminidase activity, variable depletion of mucin, and less distortion of crypt architecture. Variable degrees of epithelial dysplasia were seen in ACFs with both carcinogens, but dysplasia was more severe in DSS-induced ACFs. Colonic mucosal neoplasms were induced by both carcinogens. In subchronic studies, the ACF assay may be a useful method to improve the identification and characterization of xenobiotic-induced changes in colonic mucosal crypts.
Energy aware software (2002)

The concept of energy aware software is introduced. A simple energy model for software is presented that separates the switching and leakage components and predicts its total energy consumption with less than 5% error for a set of benchmark programs. The experiments have been performed on the StrongARM SA-1100 microprocessor. A mathematical model for the total leakage current has also been proposed and it has been shown that they can account for about 10% of the energy dissipation for low threshold voltage microprocessors and, assuming continuous operation, the leakage energy fraction gets significantly higher for lowest duty cycle.
Protease specificity and heparin binding and activation of recombinant protease nexin I. (1991)

Structural and functional properties of alpha-protease nexin I (alpha-PNI) expressed in Chinese hamster ovary cells were studied. All three cysteines were in the reduced form, showing that the potential disulfide bridge between residues Cys117 and Cys131 was not formed. Heparin association rate enhancements were from ka = 8.3 x 10(5) to 0.7-1.6 x 10(9) M-1 s-1 for the interaction of PNI with thrombin, from ka = 5.1 x 10(3) to 3.5 x 10(5) M-1 s-1 for interaction with Factor Xa, and from ka = 2.2 x 10(6) to 1.0 x 10(7) M-1 s-1 for interaction with trypsin; there was no rate enhancement of the plasmin interaction (ka = 1.0 x 10(5) M-1 s-1). The minimal heparin pentasaccharide had no effect on these interactions. Cleavage of the reactive center loop of PNI by three different proteases gave the typical stressed to relaxed change in thermal stability, but unlike with antithrombin III, there was no loss of heparin affinity. A similar difference from antithrombin was that PNI-thrombin complexes retained normal heparin affinity. These results are compatible with a role for protease nexin I as a cell-associated thrombin inhibitor that remains bound to the cell surface even after complexing with the protease, as compared with the role of antithrombin III as a circulating inhibitor of thrombin that becomes activated on binding to the microvasculature and is released on complex formation.
Durgun Su Yöntemi Kullanarak Çipura (Sparus aurata) Yumurtalarının Embriyolojik Gelişiminin İncelenmesi (2012)

Bu çalışmada durgun su yöntemiyle, karanlık ortamda, farklı stok miktarları üzerine çalışılmıştır. Çalışmada 10\nL'lik su sirkülasyonu olmayan inkibatörler kullanılmıştır. 4 değişik stok miktarı mevcuttur. Bu stoklar 250, 500,\n750 ve 1000 yum/L'dir. Kuluçkalama işlemi yapıldıktan sonra oksijen ve sıcaklık değerleri alınmıştır. Yumurtalar\n39 saatte açılım göstermiş ve yumurtadan çıkan larvalar hacimsel metotla sayılmış ve yaşama yüzdeleri\nhesaplanmıştır. Buna göre en iyi açılım oranı 250 adet/L'ye % 92 açılım gösteren A gurubunda tespit edilmiş,\nbunu 500 adet/L'ye % 86 açılım gösteren B gurubu takip etmiştir. Açılım oranı C ve D guruplarında ise % 62 ile %\n59 arasında değişim göstermiştir. Durgun su yöntemi ile yapılan çalışmada bu açılım yüzdeleri bize stok miktarı\nartıkça açılımın düştüğünü belirtmektedir.
Association of Presence of <i>Aspergillus</i> Antibodies with Hemoptysis in Patients with Old Tuberculosis or Bronchiectasis but No Radiologically Visible Mycetoma (2004)

Old tuberculosis and bronchiectasis are the two most important causes of chronic structural changes of lungs in our locality. In the absence of radiologically visible mycetoma, the cause of hemoptysis in these two groups of patients is largely unknown. A 17-month prospective study was carried out to compare the prevalence of Aspergillus fumigatus and Aspergillus flavus antibodies in hemoptysis patients with old tuberculosis or bronchiectasis but no radiologically visible mycetoma (cases, n = 38), hemoptysis patients with other diagnosis (control group 1, n = 29), and patients with old tuberculosis or bronchiectasis but no hemoptysis (control group 2, n = 47) by a recently developed sensitive and specific A. fumigatus and A. flavus antibody assay. There were a significantly larger number of patients with antibody against A. fumigatus or A. flavus among the cases than among the patients in control groups 1 and 2 (P < 0.05 in both comparisons). Molds were not recovered from any of the patients. Among the 10 cases with Aspergillus antibody, eight and two had antibody against A. flavus and A. fumigatus, respectively. We conclude that there was an association between the presence of Aspergillus antibodies and hemoptysis in patients with old tuberculosis or bronchiectasis, suggesting that these patients probably had occult infections caused by the corresponding fungi. Development of serological tests against other Aspergillus species as well as other causes of mycetoma will probably increase the detection of occult mold infections in patients with existing parenchymal lung diseases, and treatment of fungal microinvasion may help to alleviate hemoptysis in these patients with bronchiectasis or old tuberculosis who have Aspergillus antibodies.
A packet loss recovery method using packet arrived behind the playout time for CELP decoding (2002)

This paper proposes a packet loss recovery method using a packet arrived behind the playout time for CELP decoding. The proposed method recovers synchronization of the filter states between encoding and decoding in the period following packet loss. The recovery is performed by replacing the degraded filter states with ones adaptively calculated from the late arrival packet in decoding. When the proposed method is applied to the AMR speech decoder, it improves the segmental SNR by 0.2 to 1.8 dB at packet loss rates of 1 to 10 %, where all the packet losses occur due to their late arrival. The subjective test results show that five-grade mean opinion scores are improved by 0.3 and 0.2 at a packet loss rate of 5 % at speech coding bitrates of 7.95 and 12.2 kbps, respectively.
Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome (2009)

Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e.g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an improved pseudomolecule for annotation. The sequence segment was comprehensively ordered, oriented, and confirmed using the maize optical map. Nearly 84% of the sequence is composed of transposable elements (TEs) that are mostly nested within each other, of which most families are low-copy. We identified 544 gene models using multiple levels of evidence, as well as five miRNA genes. Gene fragments, many captured by TEs, are prevalent within this region. Elimination of gene redundancy from a tetraploid maize ancestor that originated a few million years ago is responsible in this region for most disruptions of synteny with sorghum and rice. Consistent with other sub-genomic analyses in maize, small RNA mapping showed that many small RNAs match TEs and that most TEs match small RNAs. These results, performed on approximately 1% of the maize genome, demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets. Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses.
GMM-Based Hidden Markov Random Field for Color Image and 3D Volume Segmentation (2012)

In this project, we first study the Gaussian-based hidden Markov random field (HMRF) model and its expectation-maximization (EM) algorithm. Then we generalize it to Gaussian mixture model-based hidden Markov random field. The algorithm is implemented in MATLAB. We also apply this algorithm to color image segmentation problems and 3D volume segmentation problems.
Regiospecific attack of nitrogen and sulfur nucleophiles on quinones derived from poison oak/ivy catechols (urushiols) and analogs as models for urushiol-protein conjugate formation (1981)

Attempts to characterize potential biologically important covalent interactions between electrophilic quinones derived from catechols present in poison oak/ivy (urushiol) and biomacromolecules have led to the analysis of model reactions involving sulfur and amino nucleophiles with 3-heptadecylbenzoquinone. Characterization of the reaction products indicates that this quinone undergoes regiospecific attack by (S)-N-acetylcysteine at C-6 and by 1-aminopentane at C-5. The red solid obtained with 1-aminopentane proved to be 3-heptadecyl-5-(pentylamino)-1,2-benzoquinone. Analogous aminobenzoquinones were obtained with the quinones derived from the 4- and 6-methyl analogues of 3-pentadecylcatechol. All three adducts absorbed visible light at different wavelengths. When the starting catechols were incubated with human serum albumin almost identical chromophores were formed. These results establish that cathechols responsible for the production of the poison oak/ivy contact dermatitis in humans undergo a sequence of reactions in the presence of human serum albumin that lead to covalent attachment of the catechols to the protein via carbon-nitrogen bonds. Estimations of the extent of this binding indicate that, at least with human serum albumin, the reaction is quantitative.
Genetic Polymorphism of<i>CYP2D6</i>and Clomiphene Concentrations in Infertile Patients with Ovulatory Dysfunction Treated with Clomiphene Citrate (2016)

CYP2D6 is primarily responsible for the metabolism of clomiphene citrate (CC). The purpose of the present study was to investigate the relationship between CYP2D6 genotypes, concentrations of CC and its major metabolites and drug response in infertility patients. We studied 42 patients with ovulatory dysfunction treated with only CC. Patients received a dose of 100 mg/day CC on days 3-7 of the menstrual cycle. CYP2D6 genotyping and measurement of CC and the major metabolite concentrations were performed. Patients were categorized into CC responders or non-responders according to one cycle response for the ovulation. Thirty-two patients were CC responders and 10 patients were non-responders with 1 cycle treatment. The CC concentrations were highly variable within the same group, but non-responders revealed significantly lower (E)-clomiphene concentration and a trend of decreased concentrations of active metabolites compared to the responders. Nine patients with intermediate metabolizer phenotype were all responders. We confirmed that the CC and the metabolite concentrations were different according to the ovulation status. However, our results do not provide evidence for the contribution of CYP2D6 polymorphism to either drug response or CC concentrations.
Does "ICU psychosis" really exist? (2000)

In summary, ICU psychosis does not develop in all patients. Instead, many patients are at risk for hypoactive, hyperactive, or mixed hypoactive and hyperactive delirium. Prevention of delirium should always be foremost, including recognition of patients at high risk, minimal use of causative medications, and treatment of physiological conditions that are often unrelated to a patient's admitting diagnosis. When prevention fails, early diagnosis and treatment can make a marked difference in patients' outcomes. The potential adverse outcomes of delirium are well documented. These include increased mortality; increased length of stay; reduced level of functioning in the elderly, which often leads to placement in a nursing home; and stress response syndrome after hospitalization. The value of nursing in preventing delirium is evident when nurses apply their knowledge of potential causes and develop strategies to avoid these causes in their patients. Nurses provide early detection and coordinate with other members of the healthcare team to initiate a plan of care that includes prompt treatment of delirium to reduce the signs and symptoms, duration, and potential adverse sequelae of this disorder. Nursing interventions are designed to enhance patients' cognitive status, sense of security, safety, and comfort. Nurses are instrumental in providing appropriate choices, doses, and administration of medications and in recognizing side effects. Use of medications ordered to treat delirium is often left to nurses' discretion because the orders specify that the drugs should be given as needed. Finally, nurses are the ones who recognize the need for additional assistance via psychiatric consultations or for more intensive observation and management of patients to ensure quality care.