gebhart/patrepeval huggingface dataset:
Sternum lifting technique for thoracoscopic internal thoracic artery harvest (2005)

We employed the Laparolift and Laparofan (Origin Medsystems Inc., CA, USA) and developed a sternum lifting technique to create a sufficient intra-pleural space between the heart and the sternum in which the left internal thoracic artery (ITA) in situ graft could be thoracoscopically mobilized. Between June and December 2004, this technique was applied to 12 consecutive patients (eight men, four women, aged 68.5+/-9.6 years) undergoing minimally invasive coronary artery bypass grafting via a left mini-thoracotomy. The Laparofan, connected to the arm of the lift machine (Laparolift), was introduced through a subxyphoidal entry and opened beneath the sternum. The sternum was elevated by about 5 cm until a sufficient working space was created under the sternum. With left hemipulmonary collapse, the left ITA was thoracoscopically taken down through the axillary ports. There was no procedural conversion to direct harvesting. The mean thoracoscopic harvesting time was 34.5+/-7.7 min. There was no mortality and no instrument-related morbidities. Patency of each ITA graft was angiographically confirmed. In conclusion, despite the limited experience, the present sternum elevation technique using the Laparolift system is a viable method for increasing the intra-pleural working space beneath the sternum during thoracoscopic ITA harvesting.
Hemolytic, but Not Cell-invasive Activity, of Adenylate Cyclase Toxin Is Selectively Affected by Differential Fatty-acylation in Escherichia coli (1995)

Adenylate cyclase toxin from Bordetella pertussis requires posttranslational acylation of lysine 983 for the ability to deliver its catalytic domain to the target cell interior and produce cyclic adenosine monophosphate (cell-invasive activity) and to form transmembrane channels (hemolytic activity). When the toxin is expressed in Escherichia coli, it has reduced hemolytic activity, but comparable cell-invasive activity to that of adenylate cyclase toxin from B. pertussis. In contrast to the native protein from B. pertussis, which is exclusively palmitoylated, recombinant toxin from E. coli is acylated at lysine 983 with about 87% palmitoylated and the remainder myristoylated. Furthermore, the recombinant toxin contains an additional palmitoylation on approximately two-thirds of the lysines at position 860. These observations suggest that the site and nature of posttranslational fatty-acylation can be dictated by the bacterial host used for expression and can have a significant, but selective, effect on protein function.
Validity of Diagnostic and Treatment Decisions of Fissure Caries (1991)

The purpose of this in vitro study was to test the accuracy and the reproducibility of diagnostic and treatment decisions of fissure caries with and without explorer. 34 dentists were asked to diagnose 61 teeth and decide upon possible treatment. The teeth were then histologically prepared and diagnosed. The agreement between histological and clinical diagnoses was assessed. The results showed no difference in diagnostic accuracy between explorer and visual technique only. Sensitivity (62%) and specificity (84%) showed that the dentists were more likely not to treat decayed teeth than to restore sound teeth. The percentage 'correctly diagnosed teeth' was approximately 42%. As there was an inherent possibility of a correct diagnosis by chance, this value had to be corrected to 23% (kappa statistics). The percentage of 'clinically' correct treatment decisions, however, was 73%. The reproducibility test gave kappa values of 0.47 for diagnostic and 0.44 for treatment decisions. It was concluded that the use of an explorer does not improve the validity of the diagnosis of fissure caries when compared to that of a visual inspection alone.
A Kinetic Model for the Metabolic Interaction of Two Substrates at the Active Site of Cytochrome P450 3A4 (2001)

In many cases, CYP3A4 exhibits unusual kinetic characteristics that result from the metabolism of multiple substrates that coexist at the active site. In the present study, we observed that alpha-naphthoflavone (alpha-NF) exhibited a differential effect on CYP3A4-mediated product formation as shown by an increase and decrease, respectively, of the carboxylic acid (P(2)) and omega-3-hydroxylated (P(1)) metabolites of losartan, while losartan was found to be an inhibitor of the formation of the 5,6-epoxide of alpha-NF. Thus, to address this problem, a kinetic model was developed on the assumption that CYP3A4 can accommodate two distinct and independent binding domains for the substrates within the active site, and the resulting velocity equations were employed to predict the kinetic parameters for all possible enzyme-substrate species. Our results indicate that the predicted values had a good fit with the experimental observations. Therefore, the kinetic constants can be used to adequately describe the nature of the metabolic interaction between the two substrates. Applications of the model provide some new insights into the mechanism of drug-drug interactions at the level of CYP3A4.
Peptide ligands for a sugar-binding protein isolated from a random peptide library. (1992)

Peptide ligands for the carbohydrate-binding protein concanavalin A (Con A) have been identified by screening a large, diverse peptide library expressed on the surface of filamentous phage. A dodecapeptide containing the consensus sequence Tyr-Pro-Tyr was found to bind Con A with an affinity (dissociation constant, Kd) of 46 microM, comparable to that of a known carbohydrate ligand, methyl alpha-D-mannopyranoside (Kd of 89 microM). In addition the peptide inhibited precipitation of the alpha-glucan dextran 1355 by Con A. Given the complexity of oligosaccharide synthesis, the prospect of finding peptides that competitively inhibit carbohydrate-specific receptors may simplify the development of new therapeutic agents.
Agent-Based Computational Modeling of Wounded Epithelial Cell Monolayers (2004)

Computational modeling of biological systems, or in silico biology, is an emerging tool for understanding structure and order in biological tissues. Computational models of the behavior of epithelial cells in monolayer cell culture have been developed and used to predict the healing characteristics of scratch wounds made to urothelial cell cultures maintained in low- and physiological [Ca2+] environments. Both computational models and in vitro experiments demonstrated that in low exogenous [Ca2+], the closure of 500-microm scratch wounds was achieved primarily by cell migration into the denuded area. The wound healing rate in low (0.09 mM) [Ca2+] was approximately twice as rapid as in physiological (2 mM) [Ca2+]. Computational modeling predicted that in cell cultures that are actively proliferating, no increase in the fraction of cells in the S-phase would be expected, and this conclusion was supported experimentally in vitro by bromodeoxyuridine incorporation assay. We have demonstrated that a simple rule-based model of cell behavior, incorporating rules relating to contact inhibition of proliferation and migration, is sufficient to qualitatively predict the calcium-dependent pattern of wound closure observed in vitro. Differences between the in vitro and in silico models suggest a role for wound-induced signaling events in urothelial cell cultures.
A simulation tool for dynamically reconfigurable field programmable gate arrays (1996)

The emergence of static memory-based field programmable gate arrays (FPGAs) that are capable of being dynamically reconfigured, i.e., partially reconfigured while active, has initiated research into new methods of digital systems synthesis. At present, however, there are virtually no specific CAD tools to support the design and investigation of digital systems using dynamic reconfiguration. This paper reports on an investigation of new CAD tools and the development of a new simulation technique, called dynamic circuit switching (DCS), for dynamically reconfigurable systems. The principles of DCS are presented and examples of its application are described.
<i>p53</i> Gene Mutation, Microsatellite Instability and Adjuvant Chemotherapy: Impact on Survival of 388 Patients with Dukes’ C Colon Carcinoma (2000)

Two common genetic alterations in colon carcinoma, p53 mutation and microsatellite instability (MSI), were investigated to determine their prognostic importance for cancer-specific survival and response to adjuvant chemotherapy in patients with Dukes' C colon cancer. The p53 tumour suppressor gene encodes for a nuclear phosphoprotein involved in cellular response to DNA damage, while MSI is a characteristic feature of tumours with defective DNA mismatch repair. The cellular response mechanisms to DNA-damaging agents in tumours with mutant p53 or MSI may as a consequence differ, and this might translate into different outcomes following adjuvant chemotherapy. A consecutive series of 388 Dukes' C colon carcinomas with 5-year median follow-up was analysed for p53 mutation and for MSI (in proximal/transverse carcinomas only) using polymerase chain reaction single-strand conformation polymorphism. The incidence of p53 mutation was 28% in all carcinomas while that of MSI in proximal/transverse carcinomas was 19%. One hundred and thirty-three patients (34%) received adjuvant chemotherapy (5-fluorouracil/levamisole) with curative intent. The presence of p53 mutation did not predict for survival in either the treated or untreated groups. The presence of MSI in the proximal/transverse colon carcinoma group was associated with significantly better 5-year survival: 58 versus 32% (p = 0.015, log rank test). This was largely due to better survival observed in the MSI subgroup that received adjuvant chemotherapy (p = 0.017, log rank test). Further work in prospective, randomised clinical trials investigating the effects of adjuvant therapy should consider incorporating MSI status in order to determine whether this is an independent predictive factor for survival and/or response to adjuvant chemotherapy.
Multiple differences between the nucleic acid sequences of the IgG2aa and IgG2ab alleles of the mouse. (1981)

To compare the structure of IgG2a alleles we have determined the complete DNA sequence of the constant region, coding sequence, and 3' untranslated region of a cDNA clone, pAB gamma 2a-1, which was derived from the C57BL/6 mouse strain (b allotype). This sequence was compared with the corresponding IgG2a DNA sequence of BALB/c origin (a allotype). The DNA sequences showed 10% differences, and the deduced protein sequences differed by about 15%. These differences were not evenly distributed: most differences were in the hinge region, the CH3 domain and the 3' untranslated region. It is evident that many alterations in the IgG2a alleles have occurred since the a and b haplotypes were separated--some of these changes were point mutations but some appear to have resulted from gene conversion of the IgG2ab allele by the IgG2bb allele.
Conjugated linoleic acid suppresses the growth of human breast adenocarcinoma cells in SCID mice. (1997)

Conjugated linoleic acid (CLA), which is mainly derived from dairy products, has been shown both in vitro and in animal models to have strong anti-tumor activity. Particular effects were observed on the growth and metastatic spread of transplantable mammary tumors. In this study, we examined the effect of dietary CLA on the growth of human breast adenocarcinoma cells in severe combined immunodeficient (SCID) mice. Mice were fed 1% CLA for two weeks prior to subcutaneous inoculation of 10(7) MDA-MB468 cells and throughout the study. Dietary CLA inhibited local tumor growth by 73% and 30% at 9 and 14 weeks post-inoculation, respectively. Moreover, CLA completely abrogated the spread of breast cancer cells to lungs, peripheral blood, and bone marrow. These results indicate the ability of dietary CLA to block both the local growth and systemic spread of human breast cancer via mechanisms independent of the host immune system.
Seven-Year Trends in Employee Health Habits From a Comprehensive Workplace Health Promotion Program at Vanderbilt University (2011)

This 7-year evaluation, with high participation and large sample size, provides robust estimates of health improvements that can be achieved through a voluntary incentive-based wellness program.
Inhibition of activated pericentromeric SINE/Alu repeat transcription in senescent human adult stem cells reinstates self-renewal (2011)

Cellular aging is linked to deficiencies in efficient repair of DNA double strand breaks and authentic genome maintenance at the chromatin level. Aging poses a significant threat to adult stem cell function by triggering persistent DNA damage and ultimately cellular senescence. Senescence is often considered to be an irreversible process. Moreover, critical genomic regions engaged in persistent DNA damage accumulation are unknown. Here we report that 65% of naturally occurring repairable DNA damage in self-renewing adult stem cells occurs within transposable elements. Upregulation of Alu retrotransposon transcription upon ex vivo aging causes nuclear cytotoxicity associated with the formation of persistent DNA damage foci and loss of efficient DNA repair in pericentric chromatin. This occurs due to a failure to recruit of condensin I and cohesin complexes. Our results demonstrate that the cytotoxicity of induced Alu repeats is functionally relevant for the human adult stem cell aging. Stable suppression of Alu transcription can reverse the senescent phenotype, reinstating the cells' self-renewing properties and increasing their plasticity by altering so-called "master" pluripotency regulators.
Significance of E-cadherin/β-catenin complex and cyclin D1 in breast cancer (2002)

E-cadherin and beta-catenin are important epithelial adhesion molecules in normal epithelium. Loss of E-cadherin - beta-catenin adhesion is an important step in the progression of many epithelial malignancies. beta-catenin plays also a role in intracellular signaling and can function as an oncogene when binds to the T-cell factor 4 (Tcf4)-binding site in the promotor region of cyclin D1 and transactivates genes after translocation to the nucleus. We evaluated the immunohistochemical expression pattern of E-cadherin, beta-catenin in relationship with cyclin D1 overexpression, tumor stage, clinicopathologic parameters and patient survival in 128 mammary infiltrating duct carcinomas. The expression of E-cadherin/beta-catenin complex and beta-catenin/cyclin D1 double staining with confocal scanning laser microscope was evaluated. There were aberrant expressions in 78% of E-cadherin, 79% of beta-catenin, and 66% of cyclin D1 in breast cancer. There was correlation of aberrant expression of E-cadherin or beta-catenin with lymph node metastasis, survival rate, and survival length. However, there was no correlation of cyclin D1 overexpression with aberrant expression of E-cadherin or beta-catenin. No death was found in normal expression of beta-catenin, however lowest survival (50%) was found in nuclear beta-catenin expression. There was correlation of overexpression of cyclin D1 with survival rate and survival length. The highest survival rate and survival length were found in membranous normal beta-catenin expression group, however significant decrement of survival length was found in the groups of aberrant expression one or both of E-cadherin or/and beta-catenin. These results suggest that aberrant expression of E-cadherin, beta-catenin, and cyclin D1 may be involved in tumor metastasis, and analysis of the degree or the pattern of E-cadherin, beta-catenin, cyclin D1, and E-cadherin/beta-catenin complex may be good prognostic markers of mammary infiltrating duct carcinoma.
Adjuvant effect of dendritic cells transduced with recombinant vaccinia virus expressing HPV16-E7 is inhibited by co-expression of IL12. (2004)

Dendritic cells (DC) enhanced the immunogenicity of recombinant vaccinia viruses (rVV) expressing the E7 protein of HPV16, a tumor-associated antigen (TAA). Immunization with DC transduced by rVV generated from strain Praha or MVA induced better protection against the growth of transplanted TC-1 tumors in C57Bl/6 mice than did immunization with either of these rVVs administered alone by the same route. Interestingly, DC transduced with a double recombinant vaccinia virus expressing E7 protein together with the Th1-polarizing cytokine IL12, which has been shown to enhance the cellular response in several other systems, induced lower anti-tumor immunity than DC transduced with rVV expressing E7 protein alone. The inhibitory effect mediated by IL12 on immunization with rVV-infected DC was dose-dependent and was observed after immunization with DC transduced with IL12-expressing rVV even at low multiplicity.
Risk Factors Associated With Acute Respiratory Distress Syndrome and Death in Patients With Coronavirus Disease 2019 Pneumonia in Wuhan, China (2020)

Older age was associated with greater risk of development of ARDS and death likely owing to less rigorous immune response. Although high fever was associated with the development of ARDS, it was also associated with better outcomes among patients with ARDS. Moreover, treatment with methylprednisolone may be beneficial for patients who develop ARDS.
Low Power Ultrasound Delivered Through a PTCA‐Like Guidewire: Preclinical Feasibility and Safety of a Novel Technology for Intracoronary Thrombolysis (2006)

Use of a transverse cavitation therapeutic wire is feasible and well tolerated acutely in the normal porcine coronary. At 60 and 90 days, no angiographically apparent damage, no clinically significant pathologic changes, and no adverse events were seen. This technology may be safely used during percutaneous coronary intervention. Further studies are justified to evaluate its efficacy for intracoronary thrombus ablation.
Multi-layered image-based rendering (1999)

In this paper, we describe a multi-layered image-based rendering system that can use different types of input to produce and render new environments. Each separate input that can be manipulated independently is called a layer. In our implementation, the types of layers that can be manipulated are the image-based and 3-D-based layers. The computation required for rendering the newly-crafted environment is reduced by using cached composite snapshots of that environment at reference poses. These cached snapshots are used to directly generate novel views, and the original layers are used only when necessary. Another key concept is the identification of types of holes generated as a result of pixel transfer from the composite snapshots to the generated view. For optimal rendering quality, the algorithm used in filling these holes is specific to the hole type (either intralayer or interlayer). The ideas embodied in our multi-layered IBR system are useful in augmenting the capabilities of applications that require fast and geometrically consistent rendering of 3-D scenes such as video editing.
The evolutionary ecology of clonally propagated domesticated plants (2010)

While seed-propagated crops have contributed many evolutionary insights, evolutionary biologists have often neglected clonally propagated crops. We argue that widespread notions about their evolution under domestication are oversimplified, and that they offer rich material for evolutionary studies. The diversity of their wild ancestors, the diverse ecologies of the crop populations themselves, and the intricate mix of selection pressures, acting not only on the parts harvested but also on the parts used by humans to make clonal propagules, result in complex and diverse evolutionary trajectories under domestication. We examine why farmers propagate some plants clonally, and discuss the evolutionary dynamics of sexual reproduction in clonal crops. We explore how their mixed clonal/sexual reproductive systems function, based on the sole example studied in detail, cassava (Manihot esculenta). Biotechnology is now expanding the number of clonal crops, continuing the 10 000-yr-old trend to increase crop yields by propagating elite genotypes. In an era of rapid global change, it is more important than ever to understand how the adaptive potential of clonal crops can be maintained. A key component of strategies for preserving this adaptive potential is the maintenance of mixed clonal/sexual systems, which can be achieved by encouraging and valuing farmer knowledge about the sexual reproductive biology of their clonal crops.
Weighted importance sampling for off-policy learning with linear function approximation (2014)

Importance sampling is an essential component of off-policy model-free reinforcement learning algorithms. However, its most effective variant, weighted importance sampling, does not carry over easily to function approximation and, because of this, it is not utilized in existing off-policy learning algorithms. In this paper, we take two steps toward bridging this gap. First, we show that weighted importance sampling can be viewed as a special case of weighting the error of individual training samples, and that this weighting has theoretical and empirical benefits similar to those of weighted importance sampling. Second, we show that these benefits extend to a new weighted-importance-sampling version of off-policy LSTD(λ). We show empirically that our new WIS-LSTD(λ) algorithm can result in much more rapid and reliable convergence than conventional off-policy LSTD(λ) (Yu 2010, Bertsekas & Yu 2009).
Size based separation of microparticles using a dielectrophoretic activated system (2010)

This work describes the separation of polystyrene microparticles suspended in deionized (DI) water according to their dimensions using a dielectrophoretic (DEP) system. The DEP system utilizes curved microelectrodes integrated into a microfluidic system. Microparticles of 1, 6, and 15 μm are applied to the system and their response to the DEP field is studied at different frequencies of 100, 200, and 20 MHz. The microelectrodes act as a DEP barrier for 15 μm particles and retain them at all frequencies whereas the response of 1 and 6 μm particles depend strongly on the applied frequency. At 100 kHz, both particles are trapped by the microelectrodes. However, at 200 kHz, the 1 μm particles are trapped by the microelectrodes while the 6 μm particles are pushed toward the sidewalls. Finally, at 20 MHz, both particles are pushed toward the sidewalls. The experiments show the tunable performance of the system to sort the microparticles of various dimensions in microfluidic systems.
Cyclosporin A inhibits H2O2‐induced apoptosis of human fibroblasts (1999)

Several clinical studies have shown that cyclosporin A (CsA) is effective for treating a variety of chronic inflammatory and autoimmune diseases. Because reactive oxygen species are believed to play a key role in the development of these diseases, causing cell apoptosis, we investigated whether CsA inhibits H2O2-induced apoptosis. Preincubation of human fibroblasts with CsA dose-dependently decreased H2O2-induced apoptosis. Apoptosis suppression by CsA was correlated with the prevention of mitochondrial dysfunction and caspase activation. Thus, our results suggest that the inhibition of apoptosis by CsA may at least partly contribute to the anti-inflammatory effect of CsA.