gebhart/patrepeval huggingface dataset:
Characterization of IS <i>1547</i> , a New Member of the IS <i>900</i> Family in the <i>Mycobacterium tuberculosis</i> Complex, and Its Association with IS <i>6110</i> (1999)

Unlike classically defined insertion sequence (IS) elements, which are delimited by their inverted terminal repeats, some IS elements do not have inverted terminal repeats. Among this group of atypical IS elements, IS116, IS900, IS901, and IS1110 have been proposed as members of the IS900 family of elements, not only because they do not have inverted terminal repeats but also because they share other features such as homologous transposases and particular insertion sites. In this study, we report a newly identified IS sequence, IS1547, which was first identified in a clinical isolate of Mycobacterium tuberculosis. Its structure, insertion site, and putative transposase all conform with the conventions of the IS900 family, suggesting that it is a new member of this family. IS1547 was detected only in isolates of the M. tuberculosis complex, where it had highly polymorphic restriction fragment length polymorphism patterns, suggesting that it may be a useful genetic marker for identifying isolates of the M. tuberculosis complex and for distinguishing different strains of M. tuberculosis. ipl is a preferential locus for IS6110 insertion where there are eight known different insertion sites for IS6110. Surprisingly, the DNA sequence of ipl is now known to be a part of IS1547, meaning that IS1547 is a preferential site for IS6110 insertion.
A New Predictive Lateral Load Transfer Ratio for Rollover Prevention Systems (2013)

In rollover prevention systems, a real-time lateral load transfer ratio (LTR) is typically computed to predict the likelihood of a vehicle to rollover and, hence, initiate rollover prevention measures. A traditional LTR largely relies on a lateral accelerometer signal to calculate rollover propensity. A new predictive LTR (PLTR) is developed in this paper, which utilizes a driver's steering input and several other sensor signals available from the vehicle's electronic stability control system. The new PLTR index can provide a time-advanced measure of rollover propensity and, therefore, offers significant benefits for closed-loop rollover prevention. Simulation results are presented using the industry-standard software CarSim to demonstrate the benefits of the new PLTR index. Experimental results of open-loop comparisons between LTR and PLTR indexes are presented, followed by experimental results on the closed-loop implementation of a PLTR-based rollover prevention system. The results in this paper document how a predictive rollover index can be developed and the advantages of such a system in rollover prevention.
The Death of Osteocytes via Apoptosis Accompanies Estrogen Withdrawal in Human Bone* (1997)

Estrogen withdrawal in women leads initially to rapid bone loss caused by increased numbers or activity of osteoclasts. We previously have noted apoptosis of lacunar osteocytes associated with conditions of high bone turnover. Therefore, in this study, we investigated whether the increased bone loss associated with GnRH analogue (GnRH-a)-induced estrogen withdrawal affects osteocyte viability in situ in a way that would be directly contrary to the effect of estrogens on osteoclast viability. Transiliac biopsies were obtained from six premenopausal women, between 30-45 yr old, diagnosed as having endometriosis. Biopsies were taken before and after 24 weeks of GnRH-a therapy. Biopsies were snap-frozen and cryostat sectioned. Osteocyte viability, determined by the presence of lactate dehydrogenase (LDH) activity, was reduced in all but one subject after treatment. Furthermore, in every subject, the proportion of osteocytes showing evidence of DNA fragmentation typical of apoptosis increased, as demonstrated using in situ DNA nick translation (P = 0.008). Gel electrophoresis of extracted DNA and morphological studies of chromatin condensation and nuclear fragmentation confirmed that changes typical of apoptosis were affecting the osteocytes. It was concluded that GnRH-a therapy caused a higher prevalence of dead osteocytes in iliac bone, probably caused by the increase in the observed proportion of osteocytes showing apoptotic changes. The capacity of bone to repair microdamage and to modulate the effects of mechanical strain is currently believed to be dependent on osteocyte viability. Our findings have therefore revealed a possible mechanism whereby estrogen deficiency could lead to increased bone fragility with or without an accompanying net bone loss.
Digitally controlled sonars (1983)

Sonars are usually designed and constructed as stand alone instruments. That is, all elements or subsystems of the sonar are provided: power conditioning, displays, intercommunications, control, receiver, transmitter, and transducer. The sonars which are a part of the Advanced Ocean Test Development Platform (AOTDP) represent a departure from this manner of implementation and are configured more like an instrumentation system. Only the transducer, transmitter, and receiver which are unique to a particular sonar function; Up, Down, Side Scan, exist as separable subsystems. The remaining functions are reserved to the AOTDP and serve all sonars and other instrumentation in a shared manner. The organization and functions of the common AOTDP elements were described and then the interface with the sonars discussed. The techniques for software control of the sonar parameters were explained followed by the details of the realization of the sonar functions and some discussion of the performance of the side scan sonars.
Facile Production of <scp>d</scp>-Histidine by Asymmetric Transformation of <scp>l</scp>-Histidine (1991)

Abstract An asymmetric transformation from l-histidine [l-His] to d-His was achieved by using salicylaldehyde as a catalyst for epimerization, and (2R, 3R)-tartaric acid as a resolving agent, in acetic acid. Treatment of the obtained salt with triethylamine in methanol gave d-His with 100% optical purity in 95% yield based on the starting l-His.
Autophagy and senescence: A new insight in selected human diseases (2019)

Senescence and autophagy play important roles in homeostasis. Cellular senescence and autophagy commonly cause several degenerative processes, including oxidative stress, DNA damage, telomere shortening, and oncogenic stress; hence, both events are known to be interrelated. Autophagy is well known for its disruptive effect on human diseases, and it is currently proposed to have a direct effect on triggering senescence and quiescence. However, it is yet to be proven whether autophagy has a positive or negative impact on senescence. It is known that elevated levels of autophagy induce cell death, whereas inadequate autophagy can trigger cellular senescence. Both have important roles in human diseases such as aging, renal degeneration, neurodegenerative disorders, and cancer. Therefore, this review aims to highlight the relevance of senescence and autophagy in selected human ailments through a summary of recent findings on the connection and effects of autophagy and senescence in these diseases.
New semiconductor glucose sensor using sputtered LaF/sub 3/ film (2002)

A sputtered LaF/sub 3/ (solid electrolyte) film was used to construct a novel MOS=type glucose sensor. The sensor, having a structure of GOD (glucose oxidase) immobilized film/Pt/LaF/sub 3//SiO/sub 2//Si/Al multiple layers, needs no external reference electrode. A stable response was obtained in the glucose concentration range from 2*10/sup -4/ to 2*10/sup -2/ M in a phosphate buffer solution of pH 6.9, with a 90% response time of ca. 1 min. Preliminary discussions on the response mechanism are also presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Efficient <i>in Vivo</i> Gene Transfer by Intraperitoneal Injection of Plasmid DNA and Calcium Carbonate Microflowers in Mice (2012)

Gene transfer to intraperitoneal organs is thought to be a promising approach to treat such conditions as peritoneal fibrosis and peritoneal dissemination of cancers. We previously discovered that simple instillation of naked plasmid DNA (pDNA) onto intraperitoneal organs such as the liver and stomach could effectively transfer foreign genes in mice. In this study, we developed a novel nonviral method to enhance transfection efficiency of naked pDNA to intraperitoneal organs using a calcium carbonate suspension containing pDNA. Using commercially available calcium carbonate, we successfully transfected pDNA to the stomach. Handling of commercially available calcium carbonate, however, was troublesome owing to rapid precipitation and caking. To obtain slowly settling particles of calcium carbonate, we tried to synthesize novel versions of such particles and succeeded in creating flower-shaped particles, named calcium carbonate microflowers. Sedimentation of calcium carbonate microflowers was sufficiently slow for in vivo experiments. Moreover, the transfection efficiency of the suspension of calcium carbonate microflowers to the stomach was more effective than that of commercially available calcium carbonate, especially at low concentrations. Intraperitoneal injection of the suspension of calcium carbonate microflowers containing pDNA greatly enhanced naked pDNA transfer to whole intraperitoneal organs in mice. Furthermore, lactate dehydrogenase activities in intraperitoneal fluid and plasma were not raised by the suspension of calcium carbonate microflowers.
Increasing system availability through on-line software version change (2002)

The usual way of installing a new version of a software is to shut down the running program and then installing the new version. This necessitates a delay during which service is denied to the users of the software, and has the effect of reducing the overall availability of the system. An online software replacement system replaces parts of the software while it is in execution, thereby eliminating shutdown of the software and increasing the availability of the system. The authors describe an approach for performing online version change and a system for online software version change that implements that approach. In the proposed method, for performing an online change, the system creates a new process with the new version of the software, and monitors the execution of the old version. When certain conditions are met, it transfers the state of the old process and the control to the new process, thereby affecting the change. The user sees a minimal delay in this switchover. The system has been implemented for C programs on a Sun workstation.
Terlipressin Versus Norepinephrine to Correct Refractory Arterial Hypotension After General Anesthesia in Patients Chronically Treated with Renin-Angiotensin System Inhibitors (2004)

Survey of Anesthesiology: February 2004 - Volume 48 - Issue 1 - p 11-12 doi: 10.1097/01.sa.0000108434.59995.38
The Cleavage of Semaphorin 3C Induced by ADAMTS1 Promotes Cell Migration (2009)

Metastasis is a sequential process that allows cells to move from the primary tumor and grow elsewhere. Because of their ability to cleave a variety of extracellular signaling and adhesion molecules, metalloproteases have been long considered key components of the metastatic program. However, the function of certain metalloproteases, such as ADAMTS1, is not clear and seems to depend on the cellular environment and/or the stage of tumor progression. To characterize the function of ADAMTS1, we performed two alternative proteomic approaches, difference gel electrophoresis and stable isotope labeling by amino acids in cell culture, to identify novel substrates of the metalloprotease. Both techniques showed that overexpression of ADAMTS1 leads to the release of semaphorin 3C from the extracellular matrix. Although semaphorins are well known regulators of axon guidance, accumulating evidence shows that they may also participate in tumor progression. Here, we show that the cleavage of semaphorin 3C induced by ADAMTS1 promotes the migration of breast cancer cells, indicating that the co-expression of these molecules in tumors may contribute to the metastatic program.
LDL- is a lipid hydroperoxide-enriched circulating lipoprotein (1997)

A subclass of LDL described on the basis of its greater electronegativity and oxidative status is further characterized using a new, highly sensitive single photon counting technique to measure lipid hydroperoxides. We describe in this report that these particles, which we refer to as LDL-, are enriched in lipid peroxides and other peroxidation products as compared to the bulk of the unmodified, normal LDL (nLDL) recovered from human plasma. This chemiluminescence-based, single photon counting technique has unique advantages in that analyses are performed on whole LDL, thus avoiding artifactual lipid peroxidation during lipid extraction. Evidence for increased amounts of lipid hydroperoxides in LDL- versus nLDL are in agreement with other analytical methods such as measurement of conjugated dienes as well as cholesterol oxidation products. LDL- also has lower proportions of polyunsaturated fatty acids than nLDL. Analysis of the amino acid composition of apoB-100 and fatty acid composition of total LDL lipids also revealed major differences between nLDL and LDL- consistent with an oxidative modification of the latter. Thus, LDL- has significantly lower proportions of the oxidizable amino acids histidine and lysine, and marked differences in other neutral and acidic amino acids. The deficit in specific amino acids is in agreement with a reduced TNBS reactivity and increased relative electrophoretic mobility of LDL-. We postulate that LDL- is a major carrier of lipid hydroperoxides associated with plasma LDL and may arise from oxidative events in the vasculature and/ or by ingestion of peroxide-enriched meals.
Cyclizations of 1′,8′-dimethyl-a,c-biladiene salts to give porphyrins: a study with various oxidizing agents (1986)

Cyclizations of the a,c-biladiene salts (3) and (4) to give the porphyrins (5) and (6), respectively, have been studied in the presence of a variety of chelating agents and oxidants. As a standard, the established procedure [copper(II) chloride–boiling dimethylformamide–6 min] gave compounds (5) and (6), in 37 and 20% yields respectively. Using zinc(II) acetate as a chelating agent for the a,c-biladienes, a large number of oxidants have been studied (in place of the copper chloride); best yields of porphyrin were obtained with potassium chromate [31% of (5); 22% of (6)] and silver iodate [35% of (5); 31% of (6)]. Other oxidants [PbO2, K2Cr2O7, Kl, Hg(OAc)2, Ag2O, and AgOAc] gave moderate yields of porphyrin, and others (Table 1 ) gave either a trace of porphyrin, or none at all. In a useful modification of the copper(II) chloride cyclization, a,c-biladienes have been cyclized during 2 h at room temperature to give porphyrins in yields of 34–65% after removal of chelated copper.
Development of assisted conception (1990)

Advances in assisted human conception in the last twenty years were founded on the detailed knowledge of the mammalian reproductive cycle gained in the earlier years of this century. Several lines of study coincided in the 1960's, including the use of ovarian stimulants to regulate follicle growth, oocyte maturation and ovulation, fertilization and embryonic growth in vitro, and the introduction of safer and better methods of laparoscopy. A combination of these techniques with embryo replacements in the uterus permitted the introduction of IVF for the alleviation of infertility. In turn, these methods were extended to other forms of assisted conception, including GIFT, which gave a wider choice of methods for the treatment of specific causes of infertility. Advances during the last decade include rapid progress in the use of ultrasound, the introduction of the LHRH agonists in new forms of stimulation, embryo cryopreservation, and micromanipulative techniques on oocytes and embryos for the alleviation of male infertility and the diagnosis of genetic disease in preimplantation embryos.
Antibacterial Activity of Restorative Dental Biomaterials in vitro (2002)

This study investigated the antibacterial effects against Streptococcus mutans of a fine-hybrid resin composite (FH-RC; Tetric ceram), an ion-releasing resin composite (Ariston pHc), a self-curing glass ionomer cement (SC-GIC; Ketac-Molar), a resin-modified GIC (RM-GIC; Photac-Fil), and a zinc oxide eugenol cement (ZOE; IRM). In a novel assay, bacterial suspensions were placed into narrow 20-microl conical cavities within the materials. After 0, 4, 8, 24, 48 h and 1 week of incubation, the suspensions were removed from the restoratives and the numbers of viable bacteria were determined. After incubation periods of 8 h or more, all restorative materials except the FH-RC showed significant growth inhibition when compared with controls. The strongest antibacterial activity was observed with ZOE. The inhibitory effect of Ariston pHc was similar to that of the SC-GIC and the RM-GIC. In the second assay, growth inhibition was evaluated in liquid cultures by incubating eluates of the materials with suspensions of S. mutans. Bacterial growth was determined up to 6 h by measuring absorption at 600 nm. The most marked inhibitory effect was again observed with ZOE. The SC-GIC caused a significant inhibition at all time intervals but the FH-RC, the RM-GIC and Ariston pHc exhibited no significant antibacterial effects. It is recommended to employ more than one method for assessing the antibacterial potential of restorative materials. Long-term clinical trials are necessary to determine whether the antimicrobial effects of dental materials are able to reduce the risk of secondary caries formation.
Generation and Analysis of 25 Mb of Genomic DNA from the Pufferfish <i>Fugu rubripes</i> by Sequence Scanning (1999)

We have generated and analyzed >50,000 shotgun clones from 1059 Fugu cosmid clones. All sequences have been minimally edited and searched against protein and DNA databases. These data are all displayed on a searchable, publicly available web site at. With an average of 50 reads per cosmid, this is virtually nonredundant sequence skimming, covering 30%-50% of each clone. This essentially random data set covers nearly 25 Mb (>6%) of the Fugu genome and forms the basis of a series of whole genome analyses which address questions regarding gene density and distribution in the Fugu genome and the similarity between Fugu and mammalian genes. The Fugu genome, with eight times less DNA but a similar gene repertoire, is ideally suited to this type of study because most cosmids contain more than one identifiable gene. General features of the genome are also discussed. We have made some estimation of the syntenic relationship between mammals and Fugu and looked at the efficacy of ORF prediction from short, unedited Fugu genomic sequences. Comparative DNA sequence analyses are an essential tool in the functional interpretation of complex vertebrate genomes. This project highlights the utility of using the Fugu genome in this kind of study.
Datacenters as Controllable Load Resources in the Electricity Market (2013)

Datacenters, being major consumers of power, can play an important role in the efficient operation of electrical grids. This paper develops an optimization framework to allow datacenters to operate as controllable load resources within the demand dispatch regime, a demand response (DR) program in which incentives are designed to induce lower electricity use not just during times of high prices but also when the reliability of the local grid is jeopardized or when the electricity supply and demand are unbalanced. Assuming the availability of geographically distributed and virtualized datacenters situated in multiple regional electrical markets, the basic idea is to migrate the workload in the form of virtual machines (VMs) between these centers to maximize the expected payoff. The proposed framework addresses issues specific to the demand dispatch of datacenters such as timeliness of VM migrations and the impact of geographic distance on migration times. It also explicitly incorporates risks that may cause the load curtailment operation to be ultimately unsuccessful and result in monetary losses to datacenter operators; specifically, variability in network bandwidth that can cause uncertainty in VM migration times as well as the uncertain payoff when participating in DR markets. A set of case studies involving datacenters participating in an economic DR program is used to validate the framework.
Identification of reentry circuit sites during catheter mapping and radiofrequency ablation of ventricular tachycardia late after myocardial infarction. (1993)

BACKGROUNDVentricular tachycardia reentry circuits in chronic infarct scars can contain slow conduction zones, which are difficult to distinguish from bystander areas adjacent to the circuit during catheter mapping. This study developed criteria for identifying reentry circuit sites using computer simulations. These criteria then were tested during catheter mapping in humans to predict sites at which radiofrequency current application terminated ventricular tachycardia.METHODS AND RESULTSIn computer simulations, effects of single stimuli and stimulus trains at sites in and adjacent to reentry circuits were analyzed. Entrainment with concealed fusion, defined as ventricular tachycardia entrainment with no change in QRS morphology, could occur during stimulation in reentry circuit common pathways and adjacent bystander sites. Pacing at reentry circuit common pathway sites, the stimulus to QRS (S-QRS) interval equals the electrogram to QRS interval (EG-QRS) during tachycardia. The postpacing interval from th...
Space-Vector PWM With Common-Mode Voltage Elimination for Multiphase Drives (2016)

Switching common-mode voltage (CMV) generated by the pulse width modulation (PWM) of the inverter causes common-mode currents, which lead to motor bearing failures and electromagnetic interference problems in multiphase drives. Such switching CMV can be reduced by taking advantage of the switching states of multilevel multiphase inverters that produce zero CMV. Specific space-vector PWM (SVPWM) techniques with CMV elimination, which only use zero CMV states, have been proposed for three-level five-phase drives, and for open-end winding five-, six-, and seven-phase drives, but such methods cannot be extended to a higher number of levels or phases. This paper presents a general (for any number of levels and phases) SVPMW with CMV elimination. The proposed technique can be applied to most multilevel topologies, has low computational complexity and is suitable for low-cost hardware implementations. The new algorithm is implemented in a low-cost field-programmable gate array and it is successfully tested in the laboratory using a five-level five-phase motor drive.
ApoE knockout mice expressing human matrix metalloproteinase-1 in macrophages have less advanced atherosclerosis (2001)

Matrix metalloproteinase-1 (MMP-1), or interstitial collagenase, has been hypothesized to contribute to the progression of the human atherosclerotic lesions by digesting the fibrillar collagens of the neointimal ECM. The apolipoprotein E knockout (apoE0) mouse model develops complex atherosclerotic lesions, but mice do not possess a homologue for MMP-1. To provide an in vivo evaluation of the role of MMP-1 in atherogenesis, we created a transgenic mouse model that expresses this enzyme specifically in the macrophage, under the control of the scavenger receptor A (SCAV) enhancer/promoter. The MMP-1 transgenic mice were crossed into the apoE0 background and fed an atherogenic diet for 16-25 weeks. Surprisingly, the transgenic mice demonstrated decreased lesion size compared with control littermates. The lesions of the transgenic animals were less extensive and immature, with fewer cellular layers and a diminished content of fibrillar collagen. There was no evidence of plaque rupture. Our data suggest that remodeling of the neointimal extracellular matrix by MMP-1 is beneficial in the progression of lesions.