gebhart/patrepeval huggingface dataset:
Evidence for Autotrophy via the Reverse Tricarboxylic Acid Cycle in the Marine Magnetotactic Coccus Strain MC-1 (2006)

Strain MC-1 is a marine, microaerophilic, magnetite-producing, magnetotactic coccus phylogenetically affiliated with the alpha-Proteobacteria. Strain MC-1 grew chemolithotrophically with sulfide and thiosulfate as electron donors with HCO3-/CO2 as the sole carbon source. Experiments with cells grown microaerobically in liquid with thiosulfate and H14CO3-/14CO2 showed that all cell carbon was derived from H14CO3-/14CO2 and therefore that MC-1 is capable of chemolithoautotrophy. Cell extracts did not exhibit ribulose-1,5-bisphosphate carboxylase-oxygenase (RubisCO) activity, nor were RubisCO genes found in the draft genome of MC-1. Thus, unlike other chemolithoautotrophic, magnetotactic bacteria, strain MC-1 does not appear to utilize the Calvin-Benson-Bassham cycle for autotrophy. Cell extracts did not exhibit carbon monoxide dehydrogenase activity, indicating that the acetyl-coenzyme A pathway also does not function in strain MC-1. The 13C content of whole cells of MC-1 relative to the 13C content of the inorganic carbon source (Deltadelta13C) was -11.4 per thousand. Cellular fatty acids showed enrichment of 13C relative to whole cells. Strain MC-1 cell extracts showed activities for several key enzymes of the reverse (reductive) tricarboxylic acid (rTCA) cycle including fumarate reductase, pyruvate:acceptor oxidoreductase and 2-oxoglutarate:acceptor oxidoreductase. Although ATP citrate lyase (another key enzyme of the rTCA cycle) activity was not detected in strain MC-1 using commonly used assays, cell extracts did cleave citrate, and the reaction was dependent upon the presence of ATP and coenzyme A. Thus, we infer the presence of an ATP-dependent citrate-cleaving mechanism. These results are consistent with the operation of the rTCA cycle in MC-1. Strain MC-1 appears to be the first known representative of the alpha-Proteobacteria to use the rTCA cycle for autotrophy.
Femoral bone plug recession in endoscopic anterior cruciate ligament reconstruction (1996)

Graft tunnel mismatch is a constant challenge in endoscopic ACL reconstruction with bone-patella tendon-bone allograft. Strategies for addressing this situation on the tibial side which include staple or suture fixation may compromise the postoperative pullout strength of the graft. We describe our technique for recession of the femoral bone plug as a solution to this problem and present our preliminary experience in a series of 100 consecutive patients followed-up to 1 year. Interference screw fixation was consistently achieved in both tunnels and recession did not influence anterior-posterior displacement by KT arthrometry.
Molecular cloning of a fourth member of a human alpha (1,3)fucosyltransferase gene family. Multiple homologous sequences that determine expression of the Lewis x, sialyl Lewis x, and difucosyl sialyl Lewis x epitopes. (1992)

We and others have previously described the isolation of three human alpha (1,3)fucosyltransferase genes which form the basis of a nascent glycosyltransferase gene family. We now report the molecular cloning and expression of a fourth homologous human alpha (1,3)fucosyltransferase gene. When transfected into mammalian cells, this fucosyltransferase gene is capable of directing expression of the Lewis x (Gal beta 1-->4[Fuc alpha 1-->3]GlcNAc), sialyl Lewis x (NeuNAc alpha 2-->3Gal beta 1-->4 [Fuc alpha 1-->3]GlcNAc), and difucosyl sialyl Lewis x (NeuNAc alpha 2-->3Gal beta 1-->4[Fuc alpha 1-->3]GlcNAc beta 1-->3 Gal beta 1-->4[Fuc alpha 1-->3]GlcNAc) epitopes. The enzyme shares 85% amino acid sequence identity with Fuc-TIII and 89% identity with Fuc-TV but differs substantially in its acceptor substrate requirements. Polymerase chain reaction analyses demonstrate that the gene is syntenic to Fuc-TIII and Fuc-TV on chromosome 19. Southern blot analyses of human genomic DNA demonstrate that these four alpha (1,3)fucosyltransferase genes account for all DNA sequences that cross-hybridize at low stringency with the Fuc-TIII catalytic domain. Using similar methods, a catalytic domain probe from Fuc-TIV identifies a new class of DNA fragments which do not cross-hybridize with the chromosome 19 fucosyltransferase probes. These results extend the molecular definition of a family of human alpha (1,3)fucosyltransferase genes and provide tools for examining fucosyltransferase gene expression.
Three-Dimensional Dynamic Simulation of Total Knee Replacement Motion During a Step-Up Task (2001)

A three-dimensional dynamic model of the tibiofemoral and patellofemoral articulations was developed to predict the motions of knee implants during a step-up activity. Patterns of muscle activity, initial joint angles and velocities, and kinematics of the hip and tinkle were measured experimentally and used as inputs to the simulation. Prosthetic knee kinematics were determined by integration of dynamic equations of motion subject to forces generated by muscles, ligaments, and contact at both the tibiofemoral and patellofemoral articulations. The modeling of contacts between implants did not rely upon explicit constraint equations; thus, changes in the number of contact points were allowed without modification to the model formulation. The simulation reproduced experimentally measured flexion-extension angle of the knee (within one standard deviation), but translations at the tibiofemoral articulations were larger during the simulated step-up task than those reported for patients with total knee replacements.
Involvement of the Thalamocortical System in Epileptic Loss of Consciousness (2001)

Experiments on putative neuronal mechanisms underlying absence seizures as well as clinical observations are critically reviewed for their ability to explain apparent "loss of consciousness." It is argued that the initial defect in absences lies with corticothalamic (CT) neuronal mechanisms responsible for selective attention and/or planning for action, rather than with those establishing either the states or the contents of consciousness. Normally, rich thalamocortical (TC)-CT feedback loops regulate the flow of information to the cortex and help its neurons to organize themselves in discrete assemblies, which through high-frequency (>30 Hz) oscillations bind those distributed processes of the brain that are considered important, so that we are able to focus on what is needed from moment to moment and be aware of this fact. This ability is transiently lost in absence seizures, because large numbers of CT loops are recruited for seconds in much stronger, low-frequency ( approximately 3 Hz) oscillations of EPSP/IPSP sequences, which underlie electroencephalographic (EEG) spike-and-wave discharges (SWDs). These oscillations probably result from a transformation of the normal EEG rhythm of sleep spindles on an abnormal increase of cortical excitability that results in strong activation of inhibitory neurons in the cortex and in nucleus reticularis thalami. The strong general enhancement of CT feedback during SWDs may disallow the discrete feedback, which normally selects specific TC circuits for conscious perception and/or motor reaction. Such a mechanism of SWD generation allows variability in the extent to which different TC sectors are engaged in the SWD activity and thus explains the variable ability of some patients to respond during an absence, depending on the sensory modality examined.
Pathologic analysis of ex vivo plasma energy tumor destruction in patients with ovarian or peritoneal cancer. (2010)

Plasma energy can effectively vaporize ovarian and peritoneal cancer cells. Greater power and tissue interaction time results in more tumor vaporization while maintaining minimal LTD. This is an attractive characteristic of plasma energy that may be useful for eradicating tumor from visceral surfaces.
TRF1 is degraded by ubiquitin-mediated proteolysis after release from telomeres (2003)

Mammalian telomeres are coated by the sequence-specific, DNA-binding protein, TRF1, a negative regulator of telomere length. Previous results showed that ADP-ribosylation of TRF1 by tankyrase 1 released TRF1 from telomeres and promoted telomere elongation. We now show that loss of TRF1 from telomeres results in ubiquitination and degradation of TRF1 by the proteasome and that degradation is required to keep TRF1 off telomeres. Ubiquitination of TRF1 is regulated by its telomere-binding status; only the telomere-unbound form of TRF1 is ubiquitinated. Our findings suggest a novel mechanism of sequential post translational modification of TRF1 (ADP-ribosylation and ubiquitination) for regulating access of telomerase to telomeres.
Robotically Driven Interventions: A Method of Using CT Fluoroscopy without Radiation Exposure to the Physician (2002)

Radiation exposure to physicians' hands during interventional procedures with computed tomography (CT) fluoroscopic guidance may be high. A robot was developed that could hold, orient, and advance a needle, with CT fluoroscopic guidance. This robot could be either computer or joystick controlled. Twenty-three robotically guided percutaneous interventions were performed without complication. Physician radiation exposure was negligible during the CT fluoroscopy-guided procedures.
Anti‐tumor effects of toxins targeted to the prostate specific membrane antigen (2002)

Anti-PSMA ITs appear to be promising for use in the eradication of small prostate tumor cell aggregates present in tissues and in the bone marrow.
Evidence of Price Change Volatility Induced by the Number and Proportion of Orders of a Given Size (1998)

We examine the contribution of order flow parameters (order size, number of orders and proportions of orders conditioned on order size) to the volatility of price change. To a lesser extent, we also examine the impact of these parameters on the mean of price change. Innovations in this study include the use of orders rather than trades and the testing of robustness of results across calendar and transaction time sampling. We find that: (a) there is a positive correlation between the number of orders, of any size, and volatility; (b) the price change in each order size category increases as order size increases; (c) number and proportion of orders are uncorrelated with price change per se; and (d) volatility appears negatively correlated with the proportion of small orders, uncorrelated with the proportion of medium‐sized orders, and positively correlated with the proportion of large orders.
Efficient Schemes for Broadcasting Popular Videos TITLE2 (1998)

We provide a formal framework for studying broadcasting schemes and design a family of schemes for broadcasting popular videos, called {\it Greedy Disk-conserving Broadcasting} (GDB) scheme. We analyze the resource requirements for GDB, i.e., the number of server broadcast channels, the client storage space, and the client I/O bandwidth required by GDB. The analysis shows that GDB exhibits a tradeoff between any two of the three resources. We compare our scheme with a recently proposed broadcasting scheme, {\it Skyscraper Broadcasting} (SB). With GDB, we can reduce the client storage space by as much as 50\% or the number of server channels by as much as 30\% at the cost of small additional client I/O bandwidth. If we require the client I/O bandwidth of GDB to be identical to that of SB, GDB needs only 70\% of the client storage space required by SB or one less server channel than SB does. In addition, we show that with small client I/O bandwidth, the resource requirement of GDB is close to the minimum achievable by {\it any} disk-conserving broadcasting scheme.
Effects of Sitagliptin Treatment on Dysmetabolism, Inflammation, and Oxidative Stress in an Animal Model of Type 2 Diabetes (ZDF Rat) (2010)

The purpose of this paper is to evaluate the chronic effect of sitagliptin on metabolic profile, inflammation, and redox status in the Zucker Diabetic Fatty (ZDF) rat, an animal model of obese type 2 diabetes. Diabetic and obese ZDF (fa/fa) rats and their controls (ZDF +/+) were treated during 6 weeks with vehicle (control) and sitagliptin (10 mg/kg/bw). Glucose, HbA1c, insulin, Total-c, TGs, IL-1beta, TNF-alpha, CRPhs, and adiponectin were assessed in serum and MDA and TAS in serum, pancreas, and heart. Pancreatic histology was also evaluated. Sitagliptin in diabetic rats promoted a decrease in glucose, HbA1c, Total-c, and TGs accompanied by a partial prevention of insulinopenia, together, with a decrease in CRPhs and IL-1beta. Sitagliptin also showed a positive impact on lipid peroxidation and hypertension prevention. In conclusion, chronic sitagliptin treatment corrected the glycaemic dysmetabolism, hypertriglyceridaemia, inflammation, and hypertension, reduced the severity of the histopathological lesions of pancreatic endocrine and exocrine tissues, together with a favourable redox status, which might be a further advantage in the management of diabetes and its proatherogenic comorbidities.
A Distributed Object Model for the Java System. (1996)

We show a distributed object model for the Java^TM System [1,6] (hereafter referred to simply as &amp;quot;Java&amp;quot;) that retains as much of the semantics of the Java object model as possible, and only includes differences where they make sense for distributed objects. The distributed object system is simple, in that a) distributed objects are easy to use and to implement, and b) the system itself is easily extensible and maintainable. We have designed such a model and implemented a system that supports remote method invocation (RMI) for distributed objects in Java. This system combines aspects of both the Modula-3 Network Objects system [3] and Spring&amp;apos;s subcontract [8] and includes some novel features. To achieve its goal of seamless integration in the language, the system exploits the use of pickling [14] to transmit arguments and return values and also exploits unique features of Java in order to dynamically load stub code to clients. The final system will include distributed reference-counting garbage collection for distributed objects as well as lazy activation [11,16].
Taxation : The Tax Treatment of Funded Pensions (2005)

The tax treatment of funded pensions is a critical policy choice in pension reform. In countries with mature funded systems, like the Netherlands, Switzerland, the United Kingdom and the United States, pension funds are worth 85 per cent of GDP on average. Pension funds in mature systems are large and could prove an attractive revenue target. They are a major force in private savings flows, supplying capital to industry and providing retirement incomes. The note continues with an in depth analysis of taxing pensions, and further, highlights the question, how generous a tax treatment? There are three arguments for taxing pensions more generously that other kinds of savings. a) to ensure people have a standard of living in retirement close to when they were working, b) to cut the cost of social security benefits for pensioners, and to increase long-term savings. The note concludes that : the 'expenditure tax' taxes pension savings once, either when contributions are made or benefits withdrawn it is the best way of taxing pensions, because it is neutral between consuming now and consuming in the future; most countries treat pensions close to the expenditure tax, the pre-paid tax, which exempts benefits, collects more revenue now, but may not be credible.
Matrix molecule interactions with hematopoietic stem cells. (1995)

We have reviewed some aspects of the production, distribution, and organization of fibronectin in the bone marrow ECM and discussed HSC-fibronectin interactions. Many questions remain. Which isoforms of fibronectin are produced in the bone marrow during ontogeny, normal hematopoiesis, and pathophysiologic challenges to the marrow microenvironment? Do HSCs interact with ED-A- and ED-B-containing fibronectin isoforms the same way they interact with plasma fibronectin? Are different fibronectin isoforms selectively expressed in different regions of the bone marrow, in keeping with the spatial organization of HSC and hematopoietic progenitor cell compartments? Addressing these questions may give us a better understanding of the role of fibronectin in HSC localization, proliferation, and differentiation. Considerable information regarding the synthesis and secretion of other ECM molecules by adherent stromal cells has been derived from in vitro analysis of LTBMCs [3]. As with fibronectin, much remains to be learned of the precise distribution and composition of bone marrow ECM molecules during in vivo development; how in vivo bone marrow ECM secretion, turnover, and remodeling are regulated during normal and pathologic hematopoietic states; and the nature and importance of in vivo cellular interactions that occur between PHSC and individual constituents of the bone marrow ECM.
Contact dermatitis (1987)

In recent years, there has been a dramatic rise in our understanding of contact dermatitis. This paper is a review of our knowledge of the mechanisms involved in contact dermatitis and related phenomena, the investigation of these events and the emergence of significant new allergens during the last 5 years.
Cavity resonance shift and bandwidth enhancement in semiconductor lasers with strong light injection (2003)

We theoretically investigated the physical mechanism of significant bandwidth enhancement in injection-locked semiconductor lasers with strong light injection. Strong light injection can increase the semiconductor laser bandwidth to several times the free-running relaxation oscillation bandwidth. We focused on the fact that an injection-locked semiconductor laser can operate at an optical frequency different from its cavity resonance condition. Resonance is shifted from solitary resonance through the carrier-induced refractive-index change due to strong optical injection. We then framed a theory in which the enhanced resonance can be generated by transient interference between the injection-locked field and the field corresponding to the shifted cavity resonance. To examine the theory, we numerically investigated the rate equations and found that the numerical and theoretical results agree well over a wide range for strong injection. A stability analysis for the rate equations revealed that there is a mode transition from relaxation oscillation to interference-induced oscillation with increased injection, and the relaxation oscillation can become suppressed for higher injection levels. We believed that negligibly small fluctuations of the carrier suppressed the relaxation oscillation and examined it numerically. We also predict that, at strong injection levels, semiconductor lasers can be lower-dimensional systems because of the possibility of adiabatic elimination of the carrier. We further conclude that such low-dimensional systems can generate a high-frequency interference beat in the laser cavity and the resultant enhanced resonance.
Metabolic & Therapeutic Aspects of Amino Acids in Clinical Nutrition (2003)

The first edition of this innovative book brought a new perspective to the metabolic and therapeutic aspects of amino acids in clinical nutrition. Since its publication, a number of very important advances have been made in the field and interesting new findings have emerged. Until now, no reference has fully explored the promising new developments
Adaptive antennas for OFDM (2002)

This paper explores the combination of adaptive antennas and orthogonal frequency division multiplexing (OFDM) for operation in a faded delay-spread channel. We consider the performance of the well-known sample matrix inversion (SMI) algorithm for controlling an adaptive antenna in a pilot-symbol-assisted OFDM system. Several strategies are considered for deploying SMI with different levels of tracking capability over an OFDM time-frequency slot. We propose a modification to the SMI method which incorporates the concept of pilot-interpolation into the computation of the sample covariance matrix. This modified SMI algorithm is shown to provide performance superior to the other variations of SMI under consideration.
Janus Kinase (JAK) Inhibitors in Rheumatoid Arthritis (2011)

Treatment of rheumatoid arthritis (RA) with biologic agents targeting inflammatory cytokines and cell surface molecules such as Tumor necrosis factor (TNF), Interleukin-6 (IL-6) and CTLA-4 has become a major focus in the field. Biologic agents are generally more effective than traditional disease-modifying antirheumatic drugs (DMARDs) when combined with MTX. However, not only about 30% of patients respond poorly to treatment but also the parenteral mode of administration and expenses are issues to be solved. Recently, a kinase inhibitor targeting Janus kinases (JAKs), has shown high efficacy on active RA in clinical trials. Among several JAK inhibitors under clinical trials for RA, tofacitinib (former CP690,550) which is highly specific for JAK3 is a step ahead for use in clinic. Kinase inhibitors are orally available, which is a major advantage over biologic agents, in addition to being less expensive than biologics. This review describes recent advances in JAK inhibitors for the treatment of RA and their possible mechanism of action. Keywords: Rheumatoid arthritis, Janus kinase, Kinase inhibitor, tacositinib, tofacitinib
RNA Interference–Mediated Silencing of the Acetyl-CoA-Carboxylase-α Gene Induces Growth Inhibition and Apoptosis of Prostate Cancer Cells (2005)

Overexpression of lipogenic enzymes is a common characteristic of many cancers. Thus far, studies aimed at the exploration of lipogenic enzymes as targets for cancer intervention have focused on fatty acid synthase (FAS), the enzyme catalyzing the terminal steps in fatty acid synthesis. Chemical inhibition or RNA interference (RNAi)-mediated knockdown of FAS consistently inhibits the growth and induces death of cancer cells. Accumulation of the FAS substrate malonyl-CoA has been implicated in the mechanism of cytotoxicity of FAS inhibition. Here, using RNAi technology, we have knocked down the expression of acetyl-CoA carboxylase-alpha (ACC-alpha), the enzyme providing the malonyl-CoA substrate. Silencing of the ACC-alpha gene resulted in a similar inhibition of cell proliferation and induction of caspase-mediated apoptosis of highly lipogenic LNCaP prostate cancer cells as observed after FAS RNAi. In nonmalignant cells with low lipogenic activity, no cytotoxic effects of knockdown of ACC-alpha or FAS were observed. These findings indicate that accumulation of malonyl-CoA is not a prerequisite for cytotoxicity induced by inhibition of tumor-associated lipogenesis and suggest that in addition to FAS, ACC-alpha is a potential target for cancer intervention.
Quantum dot-based resonance energy transfer and its growing application in biology (2008)

We provide an overview of the progress made in the past few years in investigating fluorescence resonance energy transfer (FRET) using semiconductor quantum dots (QDs) and the application of QD-based FRET to probe specific biological processes. We start by providing some of the pertinent conceptual elements involved in resonance energy transfer, and then discuss why the Förster dipole-dipole mechanism applies to QD fluorophores. We then describe the unique QD photophysical properties of direct relevance to FRET and summarize the main advantages offered, along with some of the limitations encountered by QDs as exciton donors and/or acceptors. Next we describe the overall progress made and discuss a few representative examples where QD-based FRET sensing of specific biological processes has been demonstrated. We also detail some of the advances of single molecule FRET using QD-conjugates and highlight the unique information that can be extracted. We conclude by providing an assessment of where QD-based FRET investigations may be evolving in the near future.