gebhart/patrepeval huggingface dataset:
Characterization of the Type 8 Capsular Gene Cluster of Streptococcus pneumoniae (1999)

The complete nucleotide sequence of the capsular gene cluster (cap8) responsible for the biosynthesis of the capsular polysaccharide of Streptococcus pneumoniae type 8 has been determined. The cap8 gene cluster, located between the genes dexB and aliA, is composed of 12 open reading frames. A 14.7-kb DNA fragment embracing the cap8 genes was sufficient to transform an unencapsulated type 3 S. pneumoniae strain to a strain with the type 8 capsule. A possible scenario for the evolution of pneumococcal types 2 and 8 is outlined.
Streptococcus mutans ffh, a gene encoding a homologue of the 54 kDa subunit of the signal recognition particle, is involved in resistance to acid stress (1999)

The ability of Streptococcus mutans, a bacterial pathogen associated with dental caries, to tolerate rapid drops in plaque pH (acidurance), is considered an important virulence factor. To study this trait, Tn917 mutants of S. mutans strain JH1005 which display acid sensitivity have been isolated and partially characterized. In this paper, the characterization of one of these mutants, AS17, is reported. Preliminary sequence analysis revealed that the transposon insertion in AS17 occurred in the intergenic region of a two-gene locus which has been named sat for secretion and acid tolerance. This locus displays a high degree of homology to the ylxM-ffh operon of Bacillus subtilis. The sat+ locus was cloned by complementation of a conditional Escherichia coli ffh mutant with an S. mutans genomic library. Sequencing of the complementing clone identified the intact ylxM and ffh genes as well as a partial ORF with homology to the proUlopuAC gene of B. subtilis which encodes the binding protein of the ProU/OpuA osmoregulated glycine betaine transport system. RNA dot blot experiments indicated steady-state levels of ffh mRNA in the mutant that were approximately eightfold lower compared to parental levels. This suggests a partial polar effect of the sat-1::Tn917 mutation on ffh expression. Upon acid shock (pH 5), wild-type ffh mRNA levels were found to increase approximately four- to eightfold compared to unstressed (pH 7.5) levels. Mutant levels remained unaltered under the same conditions. Experiments designed to investigate the origins of the acid-sensitivity of the mutant revealed a lack of an acid-adaptive/tolerance response. Assays of proton-extruding ATPase (H+/ATPase) specific activity measured with purified membranes derived from acid-shocked AS17 showed twofold lower levels compared to the parent strain. Also, AS17 was found to be unable to ferment sorbitol although it was able to grow in glucose and a variety of other sugar substrates. These findings suggest that Ffh may be involved in the maintenance of a functional membrane protein composition during adaptation of S. mutans to changing environmental conditions.
Local control of multiple module dc-dc converters (2010)

This paper introduces local control as applied to multiple module dc-dc converters. Local control is a form of distributed control that emphasizes each module's local information when making basic control decisions. There is no central controller or master controller. The design of simple, modular, and cooperative power converters is a primary motivating factor of this work. The challenges and opportunities of this control paradigm are placed in the context of other approaches. Simulation and experimental results for an input-series, output-parallel converter are included as an example of local control.
Immediate Early Gene Responses of NIH 3T3 Fibroblasts and NMuMG Epithelial Cells to TGFβ-1 (1991)

Transforming growth factor beta has a wide range of physiological effects on cell growth and metabolism. We have previously reported on the rapid induction of jun transcription factors in TGF beta-treated cells. Here we show that the early genomic response to TGF beta-1 includes activation of a broad spectrum of serum-inducible genes both in NIH 3T3 fibroblasts and in NMuMG epithelial cells, which are growth-stimulated and growth-inhibited by TGF beta, respectively. Of particular interest is the presence of a putative nuclear DNA-binding receptor (N10) and zinc finger transcription factors (Krox 20 and Krox 24) among the TGF beta-induced genes. In addition to the stimulatory effects of TGF beta, expression of a few genes including c-myc is decreased in both types of cells. In cells transformed by neu or ras oncogenes the immediate early mRNA responses to TGF beta are deregulated. Our results suggest that certain transcription factors are required for both positive and negative regulation of cell proliferation by TGF beta, and that their relative concentrations may determine the subsequent cellular responses.
Structure of SurE protein fromAquifex aeolicusVF5 at 1.5 Å resolution (2009)

SurE is a stationary-phase survival protein found in bacteria, eukaryotes and archaea that exhibits a divalent-metal-ion-dependent phosphatase activity and acts as a nucleotidase and polyphosphate phosphohydrolase. The structure of the SurE protein from the hyperthermophile Aquifex aeolicus has been solved at 1.5 A resolution using molecular replacement with one dimer in the asymmetric unit and refined to an R factor of 15.6%. The crystal packing reveals that two dimers assemble to form a tetramer, although gel-filtration chromatography showed the presence of only a dimer in solution. The phosphatase active-site pocket was occupied by sulfate ions from the crystallization medium.
Supplementary Figure 1 from STAT3 Inhibition Is a Therapeutic Strategy for ABC-like Diffuse Large B-Cell Lymphoma (2023)

Supplementary Figure 1 from STAT3 Inhibition Is a Therapeutic Strategy for ABC-like Diffuse Large B-Cell Lymphoma
2‘-O-[2-[2-(N,N-Dimethylamino)ethoxy]ethyl] Modified Oligonucleotides:  Symbiosis of Charge Interaction Factors and Stereoelectronic Effects (2003)

[structure: see text] Oligonucleotides with a novel, 2'-O-[2-[2-(N,N-dimethylamino)ethoxy]ethyl] (2'-O-DMAEOE) modification have been synthesized. This modification, a cationic analogue of the 2'-O-(2-methoxyethyl) (2'-O-MOE) modification, exhibits high binding affinity to target RNA (but not to DNA) and exceptional resistance to nuclease degradation. Analysis of the crystal structure of a self-complementary oligonucleotide containing a single 2'-O-DMAEOE modification explains the importance of charge factors and gauche effects on the observed antisense properties. 2'-O-DMAEOE modified oligonucleotides are ideal candidates for antisense drugs.
MPC based motion control of car-like vehicle swarms (2007)

In this paper we study low level motion control of car-like vehicles for applications of UAV swarms. First, a Suboptimal Continuous-Curvature trajectory generation approach is studied to generate suboptimal reference trajectories (‘tracks’) to connect desired way-point sequences. Two Model Predictive Control (MPC) based ‘track following’ control approaches are then proposed to deal with the multiple constraints present in practice; for example, actuator saturation, local collision avoidance. Simulations further confirm the motion control design.
ChemInform Abstract: Crystalline Microporous Phosphates: A Family of Versatile Catalysts and Adsorbents (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Catalytical removal of nitrate and nitrite from drinking water: 1. Screening for hydrogenation catalysts and influence of reaction conditions on activity and selectivity (1993)

Abstract The rising concentrations of nitrate in ground water make it necessary to use processes to remove nitrate from drinking water. Nitrate is removed at present either by physicochemical or biological processes. We describe here an efficient and rapid method to reduce nitrate and nitrite with hydrogen to nitrogen using supported precious metal catalysts. First, we screened for appropriate hydrogenation catalysts. Palladium on alumina was found to be favourable to reduce nitrite mainly to nitrogen. Ammonia as a by‐product is formed only in small amounts (98% nitrogen, 2% ammonia). Reduction of nitrate is possible by using bimetallic catalysts. We found the best results with a copper‐palladium bimetallic catalyst (nitrate removal activity of 3.13 mgNC3‐/(min∗gcat), ammonia formation of 18%. Compared to the biological denitrification, the catalysts show a 30 times higher nitrate removal activity.
Unroofed Midline Prostate Cyst Misled Into a Stricture With Obliterative Bladder Neck Contracture Following a Laser Prostatectomy (2013)

We report on a case of a 67-year-old man who presented with persistent lower urinary tract symptoms following a potassium titanyl phosphate laser photoselective vaporization of prostate. Upon further diagnostic examinations were performed, he was noted to have an obliterative bladder neck contracture with an incidental, misleading, and rare presence of an unroofed midline anterior prostatic cyst presenting as a stricture. As we were presented with this case, it was imperative to address these complications of bladder neck contracture and incompletely ablated prostatic cyst. This report brings to light underestimated complicating factors in the urinary tract, and the diagnostic and therapeutic interventions we had undertaken to rectify the identified complications and improve patien's quality of life. The patient underwent internal urethrotomy, resection of prostatic cyst wall and transurethral resection of the prostate directed to improve his quality of life and prevent urinary retention.
Thermoelectrics by Computational Design: Progress and Opportunities (2021)

The performance of thermoelectric materials is determined by their electrical and thermal transport properties that are very sensitive to small modifications of composition and microstructure. Discovery and design of next-generation materials are starting to be accelerated by computational guidance. We review progress and challenges in the development of accurate and efficient first-principles methods for computing transport coefficients and illustrate approaches for both rapid materials screening and focused optimization. Particularly important and challenging are computations of electron and phonon scattering rates that enter the Boltzmann transport equations, and this is where there are many opportunities for improving computational methods. We highlight the first successful examples of computation-driven discoveries of high-performance materials and discuss avenues for tightening the interaction between theoretical and experimental materials discovery and optimization.
Heart Rate and Blood Pressure Estimation from Compressively Sensed Photoplethysmograph (2009)

In this paper we consider the problem of low power SpO2 sensors for acquiring Photoplethysmograph (PPG) signals. Most of the power in SpO2 sensors goes to lighting red and infra-red LEDs. We use compressive sensing to lower the amount of time LEDs are lit, thereby reducing the signal acquisition pow
Focusing of high power ultrasound beams and limiting values of shock wave parameters (2009)

In this work, the influence of nonlinear and diffraction effects on amplification factors of focused ultrasound systems is investigated. The limiting values of acoustic field parameters obtained by focusing of high power ultrasound are studied. The Khokhlov-Zabolotskaya-Kuznetsov (KZK) equation was used for the numerical modeling. Solutions for the nonlinear acoustic field were obtained at output levels corresponding to both pre- and post- shock formation conditions in the focal area of the beam in a weakly dissipative medium. Numerical solutions were compared with experimental data as well as with known analytic predictions.
Jitter-Camera: High Resolution Video from a Low Resolution Detector (2005)

Video cameras must produce images at a reasonable frame-rate and with a reasonable depth of field.These requirements impose fundamental physical limits on the spatial resolution of the image detector.As a result, current cameras produce videos with a very low resolution.The resolution of videos can be computationally enhanced by moving the camera and applying super-resolution reconstruction algorithms.However, a moving camera introduces motion blur, which limits super-resolution quality.We analyze this effect and derive a theoretical result showing that motion blur has a substantial degrading effect on the performance of super resolution.The conclusion is, that in order to achieve the highest resolution, motion blur should be avoided.Motion blur can be minimized by sampling the space-time volume of the video in a specific manner.We have developed a novel camera, called the "jitter camera," that achieves this sampling.By applying an adaptive super-resolution algorithm to the video produced by the jitter camera, we show that resolution can be notably enhanced for stationary or slowly moving objects, while it is improved slightly or left unchanged for objects with fast and complex motions.The end result is a video that has a significantly higher resolution than the captured one.
Chromosomal abnormalities and psychosis (2006)

The search for susceptibility genes for schizophrenia and severe affective disorder has been enhanced by the study of cytogenetic abnormalities that disrupt genes directly. One such gene is DISCI and there is increasing evidence that it may be an important modulator of risk of psychosis.
Blue Journal Conference. Aging and Susceptibility to Lung Disease (2015)

The aging of the population in the United States and throughout the developed world has increased morbidity and mortality attributable to lung disease, while the morbidity and mortality from other prevalent diseases has declined or remained stable. Recognizing the importance of aging in the development of lung disease, the American Thoracic Society (ATS) highlighted this topic as a core theme for the 2014 annual meeting. The relationship between aging and lung disease was discussed in several oral symposiums and poster sessions at the annual ATS meeting. In this article, we used the input gathered at the conference to develop a broad framework and perspective to stimulate basic, clinical, and translational research to understand how the aging process contributes to the onset and/or progression of lung diseases. A consistent theme that emerged from the conference was the need to apply novel, systems-based approaches to integrate a growing body of genomic, epigenomic, transcriptomic, and proteomic data and elucidate the relationship between biologic hallmarks of aging, altered lung function, and increased susceptibility to lung diseases in the older population. The challenge remains to causally link the molecular and cellular changes of aging with age-related changes in lung physiology and disease susceptibility. The purpose of this review is to stimulate further research to identify new strategies to prevent or treat age-related lung disease.
Experience Using the First Commercial Pad and Probe Style Formation Tester While Drilling Service Has Led To Value Creation at the Valhall Flank Development (2005)

Abstract GeoTap®, a new formation testing while drilling (FTWD) service, was introduced to the Valhall Flank Drilling campaign in May 2003. Introduction of this service was anticipated to be the most cost effective solution for gathering pressure data on these long horizontal wells. After the first well, the equipment was modified; and the rate of success increased from 20% to 90 %. As of November 2004, the service has been run in seven wells. In this paper, we review the value the service has added to the drilling campaign and also review the experience gained with the service during its first year. The drilling environment is dynamic with hydrostatic pressure constantly changing. The new tool offers the capability to perform pressure tests in this environment with the mud pumps on or off. As an essential part of FTWD job planning, estimates are made concerning the impact of hydrostatic pressure changes and supercharging prior to logging a well. In most cases, these estimates show that pressure data gathered with this service compare favorably to other pressure measurements, such as those gathered during perforating and stimulating. The field examples presented demonstrate the field procedures used to gather pressure measurements and the added value from acquiring this data during the drill phase. Knowledge of the reservoir pressure distribution in these wells was crucial to understanding flow dynamics across the field and optimizing well decisions. These data have also impacted perforation and stimulation procedures that would not have been foreseen using conventional wireline tests. The data have been used to optimize the drilling process by providing key information for the TD decision. Finally, conclusions are drawn regarding FTWD technology today and regarding its future direction for the Valhall Flank drilling campaign in particular.
Cascadability of optically latching vertical-cavity surface-emitting laser (1992)

The cascadability of an optically latching vertical-cavity surface-emitting laser is investigated through the use of a wavelength-tunable optical probe. The bistable vertical cavity laser emits at a wavelength of 0.98 μm, and shows a sensitivity peak to probe light generated from a gratingtunable edge-emitting laser in the 0.98μm wavelength range. The sensitivity peak occurs in a window of ∼50Å around the vertical-cavity lasing wavelength, and corresponds to the Fabry-Perot transmission window of the surface-emitter.
Noninvasive control of stochastic resonance (2001)

External feedback can enhance (or depress) the response of a noisy bistable system to monochromatic signals, significantly magnifying its natural stochastic resonance. We compare and contrast a variety of such feedback strategies, using both numerical simulations and analog electronic experiments. These noninvasive control techniques are especially valuable for noisy bistable systems that are difficult or impossible to modify internally.
Hyperthermia as an adjuvant to radiation therapy of recurrent or metastatic malignant melanoma. A multicentre randomized trial by the European Society for Hyperthermic Oncology (2009)

The ESHO protocol 3-85 is a multicentre randomized trial investigating the value of hyperthermia as an adjuvant to radiotherapy in treatment of malignant melanoma. A total of 134 metastatic of recurrent malignant melanoma lesions in 70 patients were randomized to receive radiotherapy alone (3 fractions in 8 days) or each fraction followed by hyperthermia (aimed for 43°C for 60 min). Radiation was given with high voltage photons or electrons. Tumours were stratified according to institution and size (above or below 4 cm) and randomly assigned to a total radiation dose of either 24 or 27 Gy to be given with or without hyperthermia. The endpoint was persistent complete response in the treated area. A number of 128 tumours in 68 patients were evaluable, with an observation time between 3 and 72 months. Sixty-five tumours were randomized to radiation alone and 63 to radiation + heat. Sixty received 24 Gy and 68 tumours received 27 Gy, respectively. Size was ≤4 cm in 81 and >4 cm in 47 tumours. Overall the 2-year actuarial local tumour control was 37%. Univariate analysis showed prognostic influence of hyperthermia (rad alone 28% vs. rad + heat 46%, p = 0.008) and radiation dose (24 Gy 25% vs. 27 Gy 56%, p = 0.02), but not of tumour size (small 42% vs. large 29%, p = 0.21). A Cox multivariate regression analysis showed the most important prognostic parameters to be: hyperthermia (odds ratio: 1.73 (1.07-2.78), p = 0.02), tumour size (odds ratio: 0.91 (0.85-0.99), p = 0.05) and radiation dose (odds ratio: 1.17 (1.01—1.36), p = 0.05). Analysis of the heating quality showed a significant relationship between the extent of heating and local tumour response. Addition of heat did not significantly increase the acute or late radiation reactions. The overall 5-year survival rate of the patients was 19%, but 38% in patients if all known disease was controlled, compared to 8% in the patients with persistent active disease.
Giant Permittivity in Epitaxial Ferroelectric Heterostructures (1996)

A giant permittivity associated with the motion of domain walls is reported in epitaxial hetero- structures having alternating layers of ferroelectric and nonferroelectric oxides. At low frequencies, permittivities as high as 420 000 are found. Real and imaginary parts of the dielectric constant show large dispersion at high frequencies. In dc measurements, a nonlinear resistance is observed with a well-defined threshold field correlated with the dc bias-field dependence of ac permittivities. We interpret the observations as a result of the motion of a pinned domain wall lattice at low electric fields and sliding-mode motion at high electric fields.
Fine-Tuning Electronic Properties of Luminescent Pt(II) Complexes via Vertex-Differentiated Coordination of Sterically Invariant Carborane-Based Ligands (2018)

We report the synthesis of two isomeric Pt(II) complexes ligated by doubly deprotonated 1,1′-bis(&lt;i&gt;o&lt;/i&gt;-carborane) (&lt;b&gt;bc&lt;/b&gt;). This work provides a potential route to fine-tune the electronic properties of luminescent metal complexes by virtue of vertex-differentiated coordination chemistry of carborane-based ligands.
Primary testicular diffuse large B‐cell lymphomas have activated B‐cell‐like subtype characteristics (2006)

Diffuse large B-cell lymphomas (DLBCLs) constitute a heterogeneous group of lymphomas in which germinal centre B-cell-like and activated B-cell-like subtypes can be discerned based on pathology, clinical presentation, and gene expression patterns. Testicular DLBCLs form an immune-privileged site-related subgroup of DLBCLs with an unfavourable prognosis. In the present study, cDNA microarray analysis, immunohistochemistry for CD10, Bcl6 and MUM1, and somatic hypermutation analysis of the immunoglobulin heavy chain gene rearrangements were used to determine the subtype of primary testicular DLBCL. Immunohistochemistry revealed 14/22 testicular DLBCLs with an activated B-cell-like immunophenotype and 8/22 with an ambiguous immunophenotype co-expressing CD10 and high levels of MUM1. cDNA microarray analysis of these 22 and four additional cases showed a uniform activated B-cell-like gene expression pattern for both immunophenotypes. Somatic hypermutation analysis of immunoglobulin heavy chain genes showed a very high mutation load in seven cases tested, but intraclonal heterogeneity was found at low level in only one of these cases. It is concluded that primary testicular DLBCLs have uniform activated B-cell-like subtype characteristics despite a number of cases showing an ambiguous immunophenotype.