gebhart/patrepeval huggingface dataset:
Integrated Genomic Map from Uropathogenic <i>Escherichia coli</i> J96 (2000)

Escherichia coli J96 is a uropathogen having both broad similarities to and striking differences from nonpathogenic, laboratory E. coli K-12. Strain J96 contains three large (>100-kb) unique genomic segments integrated on the chromosome; two are recognized as pathogenicity islands containing urovirulence genes. Additionally, the strain possesses a fourth smaller accessory segment of 28 kb and two deletions relative to strain K-12. We report an integrated physical and genetic map of the 5,120-kb J96 genome. The chromosome contains 26 NotI, 13 BlnI, and 7 I-CeuI macrorestriction sites. Macrorestriction mapping was rapidly accomplished by a novel transposon-based procedure: analysis of modified minitransposon insertions served to align the overlapping macrorestriction fragments generated by three different enzymes (each sharing a common cleavage site within the insert), thus integrating the three different digestion patterns and ordering the fragments. The resulting map, generated from a total of 54 mini-Tn10 insertions, was supplemented with auxanography and Southern analysis to indicate the positions of insertionally disrupted aminosynthetic genes and cloned virulence genes, respectively. Thus, it contains not only physical, macrorestriction landmarks but also the loci for eight housekeeping genes shared with strain K-12 and eight acknowledged urovirulence genes; the latter confirmed clustering of virulence genes at the large unique accessory chromosomal segments. The 115-kb J96 plasmid was resolved by pulsed-field gel electrophoresis in NotI digests. However, because the plasmid lacks restriction sites for the enzymes BlnI and I-CeuI, it was visualized in BlnI and I-CeuI digests only of derivatives carrying plasmid inserts artificially introducing these sites. Owing to an I-SceI site on the transposon, the plasmid could also be visualized and sized from plasmid insertion mutants after digestion with this enzyme. The insertional strains generated in construction of the integrated genomic map provide useful physical and genetic markers for further characterization of the J96 genome.
Effects of Salt Rich Diet in the Obese Zucker Rats: Studies on Renal Function During Isotonic Volume Expansion (2004)

Obese Zucker rats (OZR) are hyperinsulenemic, hyperglycemic and dyslipidemic and develop salt dependent hypertension. Since salt sensitivity is considered to be due to impaired handling of renal sodium excretion, these studies were conducted in the obese and lean Zucker rats (LZR) anesthetized with Inactin to evaluate renal function under basal conditions and during acute isotonic fluid volume expansion (VE). Mean Arterial blood pressure (MBP), heart rate (HR), renal blood flow(RBF) and glomerular filtration rate (GFR) were not significantly different between the lean Zucker rats fed normal diet or that fed salt rich diet(8% NaCI). However, basal UV and UNaV were significantly greater in the LZR fed high salt. During VE essentially identical increases occurred in GFR, UV and UNaV in both the lean groups. In the OZR fed salt rich diet also, there were no significant changes in the heart rate, RBF and GFR. However, arterial blood pressure of the OZR fed salt rich diet was significantly greater than that of the OZR on the normal diet as well as that of both the lean groups. Also, as in the LZR, basal UV and UNaV were significantly greater in the salt fed obese rats. During volume expansion there were no impairments in the ability of the obese groups fed normal or salt rich diet to eliminate sodium and water during volume load. In fact, the net sodium and water excretions during and 60 min after VE in both the obese groups were significantly greater than that of corresponding lean groups. Furthermore, these values in the OZR fed salt rich diet were significantly greater than that of the obese rats on normal salt diet perhaps due to the contribution of pressure natriuretic mechanisms'. These data demonstrate that although OZR are salt sensitive, the renal mechanisms that would collectively respond to acute isotonic VE were fully functional. An unexpected and a novel finding in these studies is that the salt rich diet, in addition to increasing arterial blood pressure also significantly lowered plasma of insulin levels and enhanced glucose and cholesterol levels in the obese Zucker rats.
A systems view of epithelial–mesenchymal transition signaling states (2010)

Epithelial-mesenchymal transition (EMT) is an important contributor to the invasion and metastasis of epithelial-derived cancers. While considerable effort has focused in the regulators involved in the transition process, we have focused on consequences of EMT to prosurvival signaling. Changes in distinct metastable and 'epigentically-fixed' EMT states were measured by correlation of protein, phosphoprotein, phosphopeptide and RNA transcript abundance. The assembly of 1167 modulated components into functional systems or machines simplified biological understanding and increased prediction confidence highlighting four functional groups: cell adhesion and migration, metabolism, transcription nodes and proliferation/survival networks. A coordinate metabolic reduction in a cluster of 17 free-radical stress pathway components was observed and correlated with reduced glycolytic and increased oxidative phosphorylation enzyme capacity, consistent with reduced cell cycling and reduced need for macromolecular biosynthesis in the mesenchymal state. An attenuation of EGFR autophosphorylation and a switch from autocrine to paracrine-competent EGFR signaling was implicated in the enablement of tumor cell chemotaxis. A similar attenuation of IGF1R, MET and RON signaling with EMT was observed. In contrast, EMT increased prosurvival autocrine IL11/IL6-JAK2-STAT signaling, autocrine fibronectin-integrin α5β1 activation, autocrine Axl/Tyro3/PDGFR/FGFR RTK signaling and autocrine TGFβR signaling. A relatively uniform loss of polarity and cell-cell junction linkages to actin cytoskeleton and intermediate filaments was measured at a systems level. A more heterogeneous gain of ECM remodeling and associated with invasion and migration was observed. Correlation to stem cell, EMT, invasion and metastasis datasets revealed the greatest similarity with normal and cancerous breast stem cell populations, CD49f(hi)/EpCAM(-/lo) and CD44(hi)/CD24(lo), respectively.
Plasma ω-3 fatty acid levels negatively and ω-6 fatty acid levels positively associated with other cardiovascular risk factors including homocysteine in severe obese subjects. (2012)

Obesity and homocysteine (tHcy) are important risk factors for cardiovascular diseases (CVD). Plasma omega-3 fatty acids (ω-3 FAs) and omega-6 fatty acids (ω-6 FAs) are essential fatty acids with diverse biological effects in human health and disease. We have investigated the relation of plasma ω-3 FAs and ω-6 FAs levels with other cardiovascular risk factors including tHcy in severe obese subjects. This study was performed on 96 severe obese and 65 normal weight subjects. Plasma fatty acid composition was measured by GC/MS and serum tHcy level was measured by HPLC methods. There were no differences between groups in terms of concentrations of serum tHcy, plasma ω-3 FAs, ω-6 FAs and ω-3/ω-6 ratio, whereas serum vitamin B-12 (p<0.01) and folic acid (p<0.05) levels were lower than those of the normal weight subjects. Homocysteine positively correlated with ω-6 FAs and negatively correlated with ω-3 FAs in severe obese and normal weight subjects. Serum vitamin B-12 positively correlated with ω-3 FAs (p<0.01) and ω-3/ω-6 ratio (p<0.01) and negatively correlated with ω-6 FAs (p<0.05) in severe obese subjects. Serum folic acid positively correlated with ω-3 FAs (p<0.01) in severe obese subjects. Our results suggest an association between the plasma ω-3 FAs and ω-6 FAs and serum tHcy concentrations in severe obese and normal weight subjects. Low levels vitamin B-12 and folic acid may have been responsible for the elevated tHcy levels in severe obese subjects, increasing the risk for future development of cardiovascular diseases.
Using atom interferometry to search for new forces (2010)

Atom interferometry is a rapidly advancing field and this Letter proposes an experiment based on existing technology that can search for new short distance forces. With current technology it is possible to improve the sensitivity by up to a factor of 102 and near-future advances may be able to rewrite the limits for forces with ranges from 1 mm to 100 m.
Application of teaching and learning principles to computer-aided instruction. (1991)

Many authors of software providing computer-aided instruction (CAI) have no background in educational theories. This paper reviews teaching theories and ways in which instructional principles can be applied to CAI. While the lecture form of teaching has often been maligned, there are techniques for enhancing lectures that can also apply to CAI. Effective communication methods, both verbal and audiovisual, are as important in computer modules as they are in face-to-face teaching. The quality of interactive questioning and the nature and timing of feedback are critical to the success of instruction by computer. Appropriate feedback can improve retention, as can the use of proper distractors in multiple-choice questions. We present steps for developing a CAI learning module based on established principles of teaching and learning, as well as proper identification of educational goals.
Treatment of humoral rejection after heart transplantation. (1998)

By diluting inflammatory mediators, apheresis leads to a rapid improvement in cardiac function during severe humoral rejection after head transplantation. Neither apheresis nor cyclophosphamide therapy are able to have an immediate positive influence on the activation of the immune cascade and to prevent an ongoing rejection.
Wound Complications in Total Knee Arthroplasty (1997)

Knee Arthroplasty: Technique & Management Issues
9, 11, 12, 13, 13a, 14‐Hexahydro‐dibenzo[f,h]pyrrolo[1,2‐b]‐isochinoline durch Diels‐Alder‐Reaktion (1977)

Abstract Bei der Diels‐Alder ‐Reaktion von Phenanthrochinodimethan mit methylsubstituierten Pyrrolinen bilden sich 9, 11, 12, 13, 13a, 14‐Hexahydro‐dibenzo[f, h]pyrrolo[1,2‐b] isochinolin‐Derivate, deren NMR‐Spektren im Bereich der aliphatischen Protonen beschrieben werden. 2‐Cyano‐5,5‐dimethyl‐Δ1‐pyrrolin wurde synthetisiert; jes reagiert nicht im o. a. Sinne.
Measurement of Radiation-Induced DNA Double-Strand Breaks by Pulsed-Field Gel Electrophoresis (1990)

We have examined the use of pulsed-field gel electrophoresis (PFGE) to measure DNA double-strand breaks induced in CHO cells by ionizing radiation. The PFGE assay provides a simple method for the measurement of DNA double-strand breaks for doses as low as 3-4 Gy ionizing radiation, and appears applicable for the measurement of damage produced by any agent producing double-strand breaks. The conditions of transverse alternating field electrophoresis determined both the sensitivity of the assay and the ability to resolve DNA fragments with different sizes. For example, with 0.8% agarose and a 1-min pulse time at 250 V for 18 h of electrophoresis, 0.39% of the DNA per gray migrated into the gel, and only molecules less than 1500 kb could be resolved. With 0.56% agarose and a 60-min pulse time at 40 V for 6 days of electrophoresis, 0.55-0.90% of the DNA per gray migrated into the gel, and molecules between 1500 and 7000 kb could be resolved.
Use of Polyglycolic Acid Unwoven and Woven Fibers for Tendon Engineering In Vitro (2005)

Objective: To compare biocompatibility, degradation, and mechanical properties of polyglycolic acid (PGA) unwoven and woven fibers as scaffolding materials for tendon engineering in vitro. Methods: Three kinds of PGA fibers were included in this study. PGA raw material (Purac Co, Holland) was spun into single PGA filaments that were further twisted into woven fibers (PGA- 1). PGA filaments (Nantong Holycon, China) were twisted into woven fibers (PGA-2) as well. PGA-1 and PGA-2 served as experimental groups 1 and 2, while unwoven PGA fibers (Albany Co, USA) served as control group. Three types of PGA fibers were made into cord-like scaffolds that mimic tendon shape and compared with each other for biocompatibility, degradation and biomechanical properties. Avian tenocytes were isolated from digital flexor tendon and expanded in vitro. Cells of the second passage were seeded onto the PGA scaffolds. In the first 2 weeks, the cell- PGA constructs were in vitro cultured without tension and observed for cell adhesion and matrix production. The constructs were then cultured under dynamic loading in a bioreactor for another 2 weeks followed by gross and histological examinations. Results: PGA unwoven fibers have the median diameter of 10µm, while PGA-1 and PGA-2 fibers have the median diameters of 200µm and 60µm, respectively. Microscopy showed that tenocytes adhered well to all three types of PGA fibers in the first 10 days and produced abundant matrices. However, cells showed poor viability on PGA-2 fibers after 10 days, yet good viability on the other two PGA fibers over 2 weeks of observation period. H&E staining showed that there were viable cells and abundant matrices in the control and PGA-1 groups, but not in PGA-2 group after 4 weeks of in vitro culture. Additionally, PGA unwoven fibers degraded faster than woven fibers (PGA-1 and -2). Interestingly, the PGAtenocyte constructs formed tendon-like tissue after 4 weeks of in vitro culture grossly and histologically. Furthermore, mechanical test demonstrated that both PGA woven fibers had much higher tensile strength than unwoven fibers. Conclusion: Different PGA fibers have different biocompatibility with seeded tenocytes. PGA woven fibers could bear more intense mechanical loading and degrade slower than unwoven fibers, which is essential for in vitro generation of tendon tissue. Thus PGA woven fibers might serve as a proper form of scaffolding material for in vitro tendon engineering in a bioreactor.
Wnt-mediated self-renewal of neural stem/progenitor cells (2008)

In this work we have uncovered a role for Wnt signaling as an important regulator of stem cell self-renewal in the developing brain. We identified Wnt-responsive cells in the subventricular zone of the developing E14.5 mouse brain. Responding cell populations were enriched for self-renewing stem cells in primary culture, suggesting that Wnt signaling is a hallmark of self-renewing activity in vivo. We also tested whether Wnt signals directly influence neural stem cells. Using inhibitors of the Wnt pathway, we found that Wnt signaling is required for the efficient cloning and expansion of single-cell derived populations that are able to generate new stem cells as well as neurons, astrocytes, and oligodendrocytes. The addition of exogenous Wnt3a protein enhances clonal outgrowth, demonstrating not only a critical role for the Wnt pathway for the regulation of neurogenesis but also its use for the expansion of neural stem cells in cell culture and in tissue engineering.
Graph search based detection of periodic activations in complex periodic signals: Application in atrial fibrillation electrograms (2015)

A novel method for automatic detection of peaks corresponding to the periodic activations in complex periodic signals is proposed. The approach involves dominant frequency-based periodicity detection combined with a graph search algorithm to identify periodic activations or peaks of interest. The performance of the proposed method is demonstrated in human atrial fibrillation electrograms with simulated periodic activations corrupted by complex aperiodic signal features. The proposed method is compared to two state-of-the-art peak detection algorithms and is shown to be more accurate in detecting periodic peaks.
Orexin receptor antagonists as therapeutic agents for insomnia (2013)

Insomnia is a common clinical condition characterized by difficulty initiating or maintaining sleep, or non-restorative sleep with impairment of daytime functioning. Currently, treatment for insomnia involves a combination of cognitive behavioral therapy (CBTi) and pharmacological therapy. Among pharmacological interventions, the most evidence exists for benzodiazepine (BZD) receptor agonist drugs (GABAA receptor), although concerns persist regarding their safety and their limited efficacy. The use of these hypnotic medications must be carefully monitored for adverse effects. Orexin (hypocretin) neuropeptides have been shown to regulate transitions between wakefulness and sleep by promoting cholinergic/monoaminergic neural pathways. This has led to the development of a new class of pharmacological agents that antagonize the physiological effects of orexin. The development of these agents may lead to novel therapies for insomnia without the side effect profile of hypnotics (e.g., impaired cognition, disturbed arousal, and motor balance difficulties). However, antagonizing a system that regulates the sleep-wake cycle may create an entirely different side effect profile. In this review, we discuss the role of orexin and its receptors on the sleep-wake cycle and that of orexin antagonists in the treatment of insomnia.
Radioimmunoscintigraphy with<sup>111</sup>Indium Labeled Cyt-356 for the Detection of Occult Prostate Cancer Recurrence (1994)

We assessed the safety and ability of the 111indium labeled immunoconjugate 7E11-C5.3-glycyl-tyrosyl-(N,e-diethylenetriaminepentaacetic acid)-lysine (CYT-356) to detect sites of occult prostate cancer in 27 subjects who had undergone radical prostatectomy and whose only evidence of recurrent disease was an increasing (0.8 ng./ml. or greater) serum prostate specific antigen (PSA). All subjects underwent whole body scintigraphy between 2 and 4 days following the radiopharmaceutical injection. Routine blood work and human anti-mouse antibody titers were monitored. Scintigraphic findings were compared with clinical parameters, prostatic fossa biopsy results and conventional imaging techniques. Except for transient hypotension in 1 subject following the second infusion, no side effects or human anti-mouse antibody titers were detected. In 22 subjects 1 or more lesions were detected, of which 11 (50%) were confirmed by biopsy, computerized tomography or magnetic resonance imaging. Of 14 subjects with lesions in the prostatic fossa 13 had biopsies performed, 8 (62%) of which were positive. Magnetic resonance imaging confirmed tumor in the spine and chest computerized tomography findings were compatible with lesions seen in the mediastinum in 1 subject each. There was a statistically significant relationship between detecting a scan abnormality and the initial pathological stage of disease but not with the serum PSA. These data provide preliminary evidence that 111indium labeled CYT-356 can be safely administered and readministered, and it detects sites of occult prostate cancer recurrence in subjects whose PSA is increasing following radical prostatectomy.
Separation and characterization of microtubule proteins from calf brain (1977)

Electrophoresis of microtubule preparations purified from calf brain by repeated cycles of assembly and disassembly shows that they contain many proteins in addition to alpha- and beta-tubulin. These additional proteins constitute about 17% of the total material present after five cycles of assembly and disassembly. Both one-dimensional and two-dimensional (P.H. O'Farrell (1975), J. Biol. Chem. 250, 4007) electrophoretic techniques have been used to characterize them. They can be divided into two groups: one that contains proteins which remain in constant quantitative ratio to tubulin during the purification cycles, and one composed of proteins which are removed during purification, although inefficiently. Gel-filtration chromatography of cold-depolymerized microtubule preparations yields a polydisperse fraction of high molecular weight containing most of the non-tubulin proteins. This fraction contains flexible filaments about 100 A in diameter similar to those reported by R.A.B. Keats and R.H. Hall ((1975), Nature (London) 247, 418). It is suggested that these fibers are neurofilaments, and that they may be the major source of the group of inefficiently removed proteins.
Transgenic strategies for improving rice disease resistance. (2009)

Rice diseases are among the most significant limiting factors threatening food productivity. Genetic engineering provides promising strategies to develop and improve disease resistance in rice. This minireview summarizes the recent progress on studies of genetic engineering for improvement of rice disease resistance against fungal, bacterial and viral pathogens. Improvement of virus resistance can be achieved by generating transgenic rice lines with expression of genes encoding viral coat protein or replication enzymes, expression of RNA interference constructs and suppression of insect vectors. Varieties with improved resistance against fungal and bacterial pathogens can be developed through transgenic expression of cloned disease resistance genes, antimicrobial protein genes, and defense signaling genes or through pyramiding different defense genes. Future direction and strategies on genetic engineering of rice disease resistance are also discussed.
Engineered human antibodies as immunologic quality control reagents. (1990)

This study demonstrates the utility of a panel of genetically-engineered human-mouse chimeric antibodies with variable region specificity for a hapten, NP, and constant regions analogous to the different human immunoglobulin isotypes as quality control reagents. They performed well as isotype-restricted human immunoglobulin proteins to test the specificity to total serum Ig immunoenzymetric assays and as antibodies to validate selected conjugated reagents used in human antibody immunoassays. The chimeric antibodies studied have several advantages over human paraproteins as quality control reagents for clinical assays. They possess single isotypes, are free of other human immunoglobulin isotypes, can be produced in large quantities in cell culture, and have a defined specificity for NP, an antigen that can be conjugated to BSA and isolubilized on most solid phase surfaces.
Pilot-plant study of a high recovery membrane filtration process for drinking water treatment (2000)

Successful application of energy efficient dead-end micro-filtration (MF), which does not require recirculation like cross-flow filtration, depends on achieving high recovery rates. In this study, two different types of pilot scale membrane systems (horizontally and vertically stretched membrane filters) were evaluated based on the effects of pre-chlorination, intermittent chlorination and circulation flow by air-scrubbing. Additionally, the effects of operating factors including physical cleaning and chemical cleaning on membrane fouling were examined. The vertically stretched membranes showed better performance than horizontally stretched membranes at filtration fluxes of either 0.55 m/day or 0.78 m/day even under 2.6 to 27.5°C and raw water turbidity higher than 300 units, as long as intermittent chlorination (10 mg/l once a week) along with the circulation flow by air-scrubbing (once in 30 minutes) in the housing were employed. It was demonstrated that the vertically stretched membranes have been operated for one year without chemical cleaning of the membranes, wherein the recovery of raw water as a filtrate was 97.0% or 98.9%.
High-speed double mesa Si/SiGe heterojunction bipolar transistor fabricated by selfalignment technology (1992)

A process technology is presented for a selfaligned double mesa Si/SiGe HBT. The technology is based on ion implanted device contacts and on the formation of an oxide spacer surmounting the emitter mesa edge, thus permitting a simple separation of base and emitter metal contacts. Transit frequency measurements resulted in 39GHz (VCB = 1 V). Semiconductor devices and material