gebhart/patrepeval huggingface dataset:
Interplay in the Selection of Fluoroquinolone Resistance and Bacterial Fitness (2009)

Fluoroquinolones are antibacterial drugs that inhibit DNA Gyrase and Topoisomerase IV. These essential enzymes facilitate chromosome replication and RNA transcription by regulating chromosome supercoiling. High-level resistance to fluoroquinolones in E. coli requires the accumulation of multiple mutations, including those that alter target genes and genes regulating drug efflux. Previous studies have shown some drug-resistance mutations reduce bacterial fitness, leading to the selection of fitness-compensatory mutations. The impact of fluoroquinolone-resistance on bacterial fitness was analyzed in constructed isogenic strains carrying up to 5 resistance mutations. Some mutations significantly decreased bacterial fitness both in vitro and in vivo. We identified low-fitness triple-mutants where the acquisition of a fourth resistance mutation significantly increased fitness in vitro and in vivo while at the same time dramatically decreasing drug susceptibility. The largest effect occurred with the addition of a parC mutation (Topoisomerase IV) to a low-fitness strain carrying resistance mutations in gyrA (DNA Gyrase) and marR (drug efflux regulation). Increased fitness was accompanied by a significant change in the level of gyrA promoter activity as measured in an assay of DNA supercoiling. In selection and competition experiments made in the absence of drug, parC mutants that improved fitness and reduced susceptibility were selected. These data suggest that natural selection for improved growth in bacteria with low-level resistance to fluoroquinolones could in some cases select for further reductions in drug susceptibility. Thus, increased resistance to fluoroquinolones could be selected even in the absence of further exposure to the drug.
Comparison between planar arrays of perforated DRAs and microstrip patches (2005)

An array of dielectric resonator antenna (DRA) elements is formed by perforating a dielectric substrate with a lattice of holes. The performance of a 64-element prototype array designed at 25 GHz was compared to a corresponding array of microstrip patches. The perforated DRA array demonstrates a gain improvement of 1 dB and a broader gain bandwidth than the microstrip patch array. This technique of fabricating DRA using perforations eliminates the need to position and bond individual DRA elements in an array.
Benefits of the lateral resistor in a FED (2002)

A protective resistor in series with a microtip is known to homogenize field emission. It is not widely recognized, however, that this protective resistor must be fail-safe as well, since the microtips are exposed to rare but potentially destructive events during life. This paper addresses two proposed protective resistor concepts: (a) a vertical resistor located locally underneath each microtip, and (b) a lateral resistor radially distributed from the center of each microtip. It is shown by electrical and thermal analysis that the lateral resistor is significantly more fail-safe than the vertical resistor by factors of about 10/spl times/ and 100/spl times/, respectively.
Distance Metric Learning with Application to Clustering with Side-Information (2002)

Many algorithms rely critically on being given a good metric over their inputs. For instance, data can often be clustered in many &quot;plausible&quot; ways, and if a clustering algorithm such as K-means initially fails to find one that is meaningful to a user, the only recourse may be for the user to manually tweak the metric until sufficiently good clusters are found. For these and other applications requiring good metrics, it is desirable that we provide a more systematic way for users to indicate what they consider &quot;similar.&quot; For instance, we may ask them to provide examples. In this paper, we present an algorithm that, given examples of similar (and, if desired, dissimilar) pairs of points in , learns a distance metric over that respects these relationships. Our method is based on posing metric learning as a convex optimization problem, which allows us to give efficient, local-optima-free algorithms. We also demonstrate empirically that the learned metrics can be used to significantly improve clustering performance.
Biological Assembly of Nanocircuit Prototypes from Protein-Modified CdTe Nanowires (2004)

CdTe nanowires made by self-organization of CdTe nanoparticles in aqueous media were separately conjugated with complementary biological connectors, such as antigen-antibody and biotin-streptavidin. Transmission electron microscopy images and Forster resonance energy transfer measurements in nanowire superstructures with different diameters indicate that biological affinity of the attached proteins results in the formation of crossbar and end-to-side connections between the nanowires. A prototype of a logical circuit made from a triangular arrangement of the nanowires spontaneously assembled on a Si substrate was examined by conducting atomic force microscopy. While diode-like behavior was observed in the sides of the triangle, the nanowire junction points were found to be nonconductive. It was attributed to high tunneling barrier created by protein molecules wedged between the nanowires. Suggestions are made how to reduce it or use the insulating gap between the nanowires as a framework for single-electron devices.
Chromatin-associated HMG-17 is a major regulator of homeodomain transcription factor activity modulated by Wnt/ -catenin signaling (2007)

Homeodomain (HD) transcriptional activities are tightly regulated during embryogenesis and require protein interactions for their spatial and temporal activation. The chromatin-associated high mobility group protein (HMG-17) is associated with transcriptionally active chromatin, however its role in regulating gene expression is unclear. This report reveals a unique strategy in which, HMG-17 acts as a molecular switch regulating HD transcriptional activity. The switch utilizes the Wnt/beta-catenin signaling pathway and adds to the diverse functions of beta-catenin. A high-affinity HMG-17 interaction with the PITX2 HD protein inhibits PITX2 DNA-binding activity. The HMG-17/PITX2 inactive complex is concentrated to specific nuclear regions primed for active transcription. beta-Catenin forms a ternary complex with PITX2/HMG-17 to switch it from a repressor to an activator complex. Without beta-catenin, HMG-17 can physically remove PITX2 from DNA to inhibit its transcriptional activity. The PITX2/HMG-17 regulatory complex acts independently of promoter targets and is a general mechanism for the control of HD transcriptional activity. HMG-17 is developmentally regulated and its unique role during embryogenesis is revealed by the early embryonic lethality of HMG-17 homozygous mice. This mechanism provides a new role for canonical Wnt/beta-catenin signaling in regulating HD transcriptional activity during development using HMG-17 as a molecular switch.
Metadata Management for Distributed Multimedia Storage System (2008)

As a result of the multimedia rapid growth, there has been a huge increase in the amount of information generated and shared by people all over the world. Demand for large-scale multimedia storage system is growing rapidly. This paper describes the design and implementation of the Two-level metadata server for distributed multimedia storage system (DMSS). The DMSS divides the logical view of the stored data from the physical view. The logical view is managed by the metadata server which is called GMS (global metadata server), and the physical view is managed by a component of storage servers which is called LMS (local metadata server). Adopting LMS, each storage server can maintain its own storage resources and metadata and data independently, and can offer storage service independently. The DMSS allows the application servers to access the storage servers directly and in parallel providing very high performance.
Gln40 deamidation blocks structural reconfiguration and activation of SCF ubiquitin ligase complex by Nedd8 (2015)

The full enzymatic activity of the cullin-RING ubiquitin ligases (CRLs) requires a ubiquitin-like protein (that is, Nedd8) modification. By deamidating Gln40 of Nedd8 to glutamate (Q40E), the bacterial cycle-inhibiting factor (Cif) family is able to inhibit CRL E3 activities, thereby interfering with cellular functions. Despite extensive structural studies on CRLs, the molecular mechanism by which Nedd8 Gln40 deamidation affects CRL functions remains unclear. We apply a new quantitative cross-linking mass spectrometry approach to characterize three different types of full-length human Cul1-Rbx1 complexes and uncover major Nedd8-induced structural rearrangements of the CRL1 catalytic core. More importantly, we find that those changes are not induced by Nedd8(Q40E) conjugation, indicating that the subtle change of a single Nedd8 amino acid is sufficient to revert the structure of the CRL catalytic core back to its unmodified form. Our results provide new insights into how neddylation regulates the conformation and activity of CRLs.
Enhancement of Nd:YAG LIBS emission of a remote target using a simultaneous CO_2 laser pulse (2007)

For the first time to the best of our knowledge, a simultaneous 10.6 mum CO(2) laser pulse has been used to enhance the Laser Induced Breakdown Spectroscopy (LIBS) emission from a 1.064 mum Nd:YAG laser induced plasma on a hard target. The enhancement factor was on the order of 25 to 300 times, depending upon the emission lines observed. For an alumina ceramic substrate the Al emission lines at 308 nm and Fe impurity line at 278 nm showed an increase of 60x and 119x, respectively. The output energy of the Nd:YAG laser was 50 mJ/pulse focused to a 1 mm diameter spot to produce breakdown. The CO(2) laser pulse had a similar energy density of 40 mJ/mm(2). Timing overlap of the two laser pulses within 1 microsecond was important for enhancement to be observed. An observed feature was the differential enhancement between different elemental species and also between different ionization states, which may be helpful in the application of LIBS for multi-element analysis.
Oral analgesics for acute nonspecific pain. (2005)

Physicians most often recommend or prescribe oral medication for relief of acute pain. This review of the available evidence supports the use of acetaminophen in doses up to 1,000 mg as the initial choice for mild to moderate acute pain. In some cases, modest improvements in analgesic efficacy can be achieved by adding or changing to a nonsteroidal anti-inflammatory drug (NSAID). The safest NSAID is ibuprofen in doses of 400 mg. Higher doses may offer somewhat greater analgesia but with more adverse effects. Other NSAIDs have failed to demonstrate consistently greater efficacy or safety than ibuprofen. Although they may be more expensive, these alternatives may be chosen for their more convenient dosing. Cyclooxygenase-2 inhibitors provide equivalent efficacy to traditional NSAIDs but lack a demonstrable safety advantage for the treatment of acute pain. For more severe acute pain, the evidence supports the addition of oral narcotic medications such as hydrocodone, morphine, or oxycodone. Specific oral analgesics that have shown poor efficacy and side effects include codeine, propoxyphene, and tramadol.
Prevalence and risk factors for overweight horses at premises in Sweden assessed using official animal welfare control data (2016)

Official animal welfare control data may be used to monitor the premises prevalence of overweight horses in Sweden. Strategies to reduce the prevalence of overweight horses should focus on education about equine care and nutrition, especially summer grazing.
Potentiation of cytotoxicity and antitumor activity of adenosine analogs by the adenosine deaminase inhibitor adecypenol. (1989)

The enzyme adenosine deaminase (ADA) (adenosine aminohydrolase, EC 3.5.4.4), which is widespread in mammalian tissue, is involved in the regulation of the intracellular levels of adenosine and deoxyadenosine, which control a number of important physiological functions and serve as precursors of nucleic acid biosynthesis. ADA inhibitors such as deoxycoformycin are considered to be responsible for alterations in adenosine and deoxyadenosine levels, lymphocytic growth and functions, and also to enhance the chemotherapeutic effects of adenosine analogs which serve as a substrate of ADA1\ Recently, we found two new ADAinhibitors, adechlorin
Expression von Stammzellmarkern in peritonealen Endometrioseläsionen (2005)

Fragestellung: Die Pathogenese der Endometriose ist bislang nicht bekannt. Neuere Theorien vermuten, dass durch eine Hyper- und Dysperistaltik des Uterus eine unphysiologische Expulsation von Basalisfragmenten stattfindet. Dadurch gelangen die stammzellartige Zellen mittels retrograder Menstruation in den Bauchraum gelangen und sich dort adhärieren. Bestärkt wird diese Annahme dadurch, dass das Expressionsmuster des Östrogen- und Progesteron-Rezeptors der peritonealen Läsionen das der Basalis widerspiegelt. Es wird angenommen, dass die Basalis als ‘Stammzellreservoir' des Endometriums fungiert, diese Hypothese ist aber bislang nicht bewiesen. Ob in peritonealen Endometrioseläsionen solche stammzellartigen Zellen identifiziert werden können, sollte die mittels der beiden etablierten Stammzellmarker CD 34 und c-kit analysiert werden. Methode: Es wurden 15 peritoneale Endometrioseläsionen, sowie 20 Endometriumsproben immunhistochemisch auf die Anwesenheit und das Expressionsmuster der Stammzellmarkern CD 34 und c-kit untersucht. Ergänzend wurde CD 31 zur Identifizierung von Gefäßen und Mastzellen-Tryptase zur Identifizierung von Mastzellen mitgefärbt. Ergebnisse: Es zeigte sich eine starke CD 34 Expression der Stromazellen sowie erwartungsgemäß der Gefäße in den peritonealen Endometrioseläsionen. Dabei waren die direkt an den Drüsen anliegenden oder die peripherer liegenden Stromazellen immunreaktiv. Im Endometrium wurde eine zyklusabhängige Expression von CD 34 beobachtet. Es waren in der frühen Proliferationsphase wenige positive Zellen vorhanden, periovulatorisch waren nur die Stromazellen der Basalis stark angefärbt und in der sekretorischen Phase war das komplette endometrielle Stroma gefärbt. C-kit zeigte eine positive Färbung vereinzelter Zellen im Stroma der peritonealen Endometrioseläsionen sowie des Endometriums, welche mithilfe der Mastzell-Tryptase als Mastzellen charakterisiert wurden. Die Drüsenzellen der peritonealen Läsionen und des Endometriums zeigten mit keinem der beiden Marker eine Färbung. Schlussfolgerung: CD 34 ist ein hämatopoetischer Stammzellmarker, zudem steht er im Zusammenhang mit dem Adhäsionsvermögen und dem Differenzierungsgrad verschiedener Zellen. Aufgrund der zum Teil starken Expression von CD 34 im Stroma der Läsionen kann man annehmen, dass unreife Stromazellen in den Endometrioseläsionen mit CD 34 identifiziert werden. Interessant ist auch die zyklusabhängige Expression von CD 34 im endometriellen Stroma. Diese CD 34-positiven Zellen könnten eine weitere Charaktereigenschaft in Hinblick auf ihre Zell-Zell-Kontakte aufweisen, da ein Stammzellenvorkommen in dem Ausmaß unwahrscheinlich erscheint. C-kit scheint in der Endometriose wie auch im Endometrium eher in der Rolle als Mastzellmarker zu fungieren.
Correction of a phase dependent error in a time-of-flight range sensor (2013)

Time-of-Flight (TOF) 3D cameras determine the distance information by means of a propagation delay measurement. The delay value is acquired by correlating the sent and received continuous wave signals in discrete phase delay steps. To reduce the measurement time as well as the resources required for signal processing, the number of phase steps can be decreased. However, such a change results in the arising of a crucial systematic distance dependent distance error. In the present publication we investigate this phase dependent error systematically by means of a fiber based measurement setup. Furthermore, the phase shift is varied with an electrical delay line device rather than by moving an object in front of the camera. This procedure allows investigating the above mentioned phase dependent error isolated from other error sources, as, e.g., the amplitude dependent error. In other publications this error is corrected by means of a look-up table stored in a memory device. In our paper we demonstrate an analytical correction method that dramatically minimizes the demanded memory size. For four phase steps, this approach reduces the error dramatically by 89.4 % to 13.5 mm at a modulation frequency of 12.5 MHz. For 20.0 MHz, a reduction of 86.8 % to 11.5 mm could be achieved.
Gene Expression from Both Intronless and Intron-Containing Rous Sarcoma Virus Clones Is Specifically Inhibited by Anti-Sense RNA (1985)

To distinguish the inhibitory effect of anti-sense RNA on translation from the effect on splicing, a plasmid (pLC32) was constructed from a cDNA clone of the Rous sarcoma virus (RSV) envelope gene (env) mRNA. Transcription of this plasmid results in the synthesis of RNA identical to the RSV env gene mRNA which does not require splicing to be expressed. Plasmids derived from pLC32 were also constructed in which the env gene coding sequence and 5' noncoding leader sequences were inserted in the opposite orientation relative to the RSV long terminal repeats (LTRs). pLC32 DNA transfected by the calcium phosphate coprecipitation technique efficiently rescued infectious virus from quail cells infected with an RSV mutant deleted in the env gene [R(-)Q cells], indicating that the intron sequences are dispensable in env gene expression. When the inverted constructs were cotransfected with pLC32, significantly less infectious virus was produced. The extent of the inhibition depended upon the concentration ratio of the two plasmids. The maximum inhibition (80%) occurred when the ratio of inverted constructs to pLC32 was 12:1. The inhibition is specific for the inverted orientation since cotransfection of pLC32 with several other plasmids containing viral LTRs and defective src and env genes at similar concentrations did not inhibit the production of infectious virus. In addition, the inverted constructs did not interfere with the expression of an LTR-driven chloramphenicol acetyltransferase gene. When cotransfected with a wild-type Prague A RSV DNA plasmid (pJD100), the inverted constructs also greatly inhibited expression and replication of virus in R(-)Q quail cells. These data suggest that the specific inhibition is caused by hybridization of complementary RNA transcribed from the inverted constructs to the env mRNA, thereby blocking its expression. The fact that expression of both intron-containing and intronless clones are inhibited to the same extent suggest that inhibition by anti-sense RNA from the env exon regions does not act at the level of RNA splicing.
Regulation of the Cinnamate 4-Hydroxylase (CYP73A1) in Jerusalem Artichoke Tubers in Response to Wounding and Chemical Treatments (1997)

trans-Cinnamate 4-hydroxylase (C4H) is a plant-specific cytochrome (P450) that is encoded by the gene CYP73A and catalyzes the second step of the multibranched phenylpropanoid pathway. Increases in C4H activity in response to physical and chemical stresses have been well documented, but the mechanism of these increases has never been studied in detail. This paper reports on the regulatory mechanism controlling C4H activity in Jerusalem artichoke (Helianthus tuberosus) tubers in response to wounding and chemical treatments. We compared induction of C4H and other P450-catalyzed activities. C4H was moderately induced by chemicals relative to other P450s. Increases in enzyme activity, C4H protein, and transcripts were quantified and compared in tuber tissue 48 h after wounding and chemical treatments. Our data suggest that induction of the enzyme activity results primarily from gene activation. Time-course experiments were performed after wounding and aminopyrine treatment. Compared with wounded tissues, aminopyrine triggered an additional and delayed peak of transcript accumulation. The timing of the induced changes in activity, protein, and transcripts confirms that C4H induction results primarily from an increase in CYP73A1 mRNA, in both wounded and aminopyrine-treated tissues. However, posttranscriptional mechanisms might also contribute to the regulation of C4H activity.
7.5 kW/mm <sup>2</sup> current switch using AlGaN/GaNmetal-oxide-semiconductor heterostructure field effect transistors on SiC substrates (2000)

A fast high-power solid-state switch based on a novel large periphery multigate AlGaN/GaN metal-oxide-semiconductor heterostructure field effect transistor (MOSHFET) over 4H-SiC substrates is demonstrated. For a device with 1 mm periphery and 10 µm gate-drain spacing, 7.5 kW/mm2 of switched power with on-state resistance of 75 mΩ × mm2 is obtained. The pulse response of the MOSHFET switch exhibited a rise-time < 5 ns in pulsemode operation.
Shrinkage and peel strength of adhesive joints (1973)

A theory for the effect of shrinkage stresses on the peel strength of a joint between rubber and glass is developed. The theory suggests that shrinkage weakens the joint, the weakening becoming more noticeable with rise in shrinkage strain and rubber film thickness. Peeling experiments on a rubber-glass bond verify the theory and justify a discussion of shrinkage in butt joints.
Analysis of different endoscopic methods for resection of rectal neuroendocrine tumors: A 10‐year experience at a secondary care hospital (2018)

Rectal neuroendocrine tumors (NETs) account for one‐third of all digestive NETs and are often incidentally found during colonoscopy. They also carry the risk of metastasis. Given their subepithelial growth, complete removal, R0 resection, is a challenge for endoscopists. Inadequate endoscopic management would lead to incomplete removal and additional complications for surveillance. The aim of this study is to compare R0 resection rates among all endoscopic methods. The database of our pathology department was reviewed from January 2005 to July 2015. Diagnoses of carcinoid and NETs located at rectum were enrolled. NETs removed by endoscopy were further selected for analysis. R0 resection was defined as being free of tumor at lateral and vertical margins on pathological examination. Three methods of endoscopic management were performed for our patients; these were snare polypectomy, endoscopic submucosal resection‐ligation assisted (ESMR‐L), and endoscopic submucosal dissection (ESD). In all, 48 rectal NETs were diagnosed. Thirty‐six rectal NETs were removed by endoscopy. Pathology validated hepatic metastasis was found in a patient with18 mm tumor size and G2 mitosis. The R0 resection rates for snare polypectomy, ESMR‐L, and ESD were 33.3% (6/18), 90.9% (10/11), and 100% (7/7) respectively ( P = 0.001). Procedure time for the ESMR‐L group (5.36 min) was shorter than the ESD group (38.86 min) ( P < 0.001). Percentage of patients receiving endoscopic ultrasonography before endoscopic management also revealed significant differences among the three groups (3/18, 16.7%; 6/11, 54.5%; 7/7, 100%; P = 0.001). ESD offered the highest R0 resection rate, followed by ESMR‐L and snare polypectomy. However, ESMR‐L has shorter procedure time.
Decision feedback equalization for Volterra systems-a root method (2002)

The need to recover the original input from the output of a nonlinear system is a problem common to many applications. In this paper, we propose a Volterra decision feedback equalizer that is based on finding the roots of a polynomial function of the input. It is capable of equalizing severely nonlinear systems under the assumption that the input comes from a finite symbol set. A modification is also proposed which allows for the extension of the root method to baseband Volterra systems with complex inputs and the analysis of the effects of noise on the current symbol estimate. Simulations demonstrate the performance of the proposed algorithm.