gebhart/patrepeval huggingface dataset:
Journal of Liposome Research (1991-1997) (1997)

This issue of the Journal of Liposome Research (JLR) marks the end of an era, i.e. the period in which I am the Editor-in-Chief of the Journal.JLR was started in 1988 by Marc Ostro, who experienced some difficulties in getting the young journal off the ground.This is not unusual for a new scientific journal in a specialized discipline.When I took over the Journal in 199 1, coincidental to my move from Tennessee to Pittsburgh, my goal was simple and realistic.I simply wished to maintain a high level of quality in every issue we published and to ensure that every publication was on time.Looking back at the last six years, I believe that we have achieved those goals.
Independent components analysis for fetal electrocardiogram extraction: a case for the data efficient Mermaid algorithm (2004)

Fetal heart rate (FHR) monitoring is currently the primary methodology for antenatal determination of fetal well-being. Currently, the FHR can be detected with ultrasonography, but the additional information from fetal electrocardiogram (FECG) is only available via an invasive scalp electrode. A cost effective noninvasive monitoring through standard ECG electrodes could be used on nearly every patient in lieu of the ultrasound monitors. In this method, a number of electrodes are positioned on the abdomen of the mother to collect, simultaneously, various combinations of the signals including the heartbeats of the mother and the fetus. For accurate fetal heart-rate estimation, a clean FECG must be extracted from the collected mixtures. It is well known that this can be achieved using blind source separation (BSS) techniques. In this paper, the performance of the Mermaid algorithm, which is based on minimizing Renyi's mutual information, is evaluated on this problem of great practical importance. The effectiveness and data efficiency of Mermaid and its superiority over alternative information theoretic BSS algorithms are illustrated using artificially mixed ECG signals as well as fetal heart rate estimates in real ECG mixtures.
Expert Performance on a Virtual Reality Simulation System (2007)

The objective of this research was to determine if the essence of expert performance could be captured on a virtual reality simulation system. Six experts in operative dentistry, six experts in periodontology, and six novice dental students performed a Class II tooth preparation task on the lower left second premolar. All subjects performed a pre-test to assess the basic skill level of each group. During the (limited) training component of the study, the three groups practiced three tooth preparations and received augmented feedback. At both a one-minute and one-day interval, subjects performed a final test in the absence of augmented feedback. All preparations were graded by the simulation system. The results showed at pre-test a significantly better performance of the experts in operative dentistry as compared to the novices. During the practice (acquisition) phase, the experts in operative dentistry outperformed both the periodontologists and novices, whereas the experts in periodontology performed more accurately than the novices. After one minute and one day following practice, similar results were obtained. Retention performance was most accurate after a one-day delay. Based on these results, the simulator appears to be a valid and reliable tool to capture expert performance. It is an effective screening device for assessing the level of expert performance.
Leishmania-induced tyrosine phosphorylation in the host macrophage and its implication to infection. (1996)

Tyrosine phosphorylation is an important mechanism of cell regulation and has been recently implicated in defense strategies against a variety of pathogens. We have investigated the involvement of protein tyrosine kinase activity in the Leishmania attachment, invasion and survival within macrophages, as well as promastigote ability to trigger tyrosine phosphorylation, which could contribute to leishmanicidal activity. Treatment of murine macrophage monolayers with genistein, herbimycin A, tyrphostin 25 or staurosporine prior to infection decreased parasite invasion in a dose-dependent manner. Contrary, addition of sodium orthovanadate, a protein tyrosine phosphatase inhibitor, phosphotyrosine and p-nitrophenyl phosphate to the interaction medium, significantly increased parasite binding and internalization, whereas phosphoserine and phosphothreonine had no effect. The phosphatase activity of intact promastigotes was greater than that of macrophages. Western blot analysis revealed tyrosine-phosphorylated bands from 198 to 28 kDa following macrophage challenge with promastigotes. Uninfected macrophages displayed no detectable tyrosine phosphorylated proteins, possibly indicating an inducible process, while in parasites it was constitutive, as seen by the presence of 42, 40 and 35 kDa phosphoproteins on the Leishmania lysates. Immunofluorescence and immunogold detection of phosphotyrosine residues in some promastigote-macrophage attachment areas, but not in the vicinity of ingested parasites, suggest that Leishmania-induced tyrosine phosphorylation is an early, local and short-lived event. Genistein treatment of Leishmania-infected cells significantly enhanced the parasite burden. This antagonist also diminished nitric oxide production in resting and interferon gamma/lipopolysaccharide-activated infected macrophages, which may account for the increased parasite survival. We propose that protein tyrosine kinase-linked pathways regulate the Leishmania promastigote invasion and the macrophage microbicidal activity.
Lipid Raft Distribution of CD4 Depends on its Palmitoylation and Association with Lck, and Evidence for CD4-Induced Lipid Raft Aggregation as an Additional Mechanism to Enhance CD3 Signaling (2003)

By mutagenesis, we demonstrated that the palmitoylation of the membrane-proximal Cys(396) and Cys(399)of CD4, and the association of CD4 with Lck contribute to the enrichment of CD4 in lipid rafts. Ab cross-linking of CD4 induces an extensive membrane patching on the T cell surface, which is related to lipid raft aggregation. The lipid raft localization of CD4 is critical for CD4 to induce the aggregation of lipid rafts. The localization of CD4 in lipid rafts also correlates to the ability of CD4 to enhance receptor tyrosine phosphorylation. Thus, our data suggest that CD4-induced aggregation of lipid rafts may play an additional role in CD4 signaling besides its adhesion to MHC molecules and association with Lck.
An Alternative Procedure for the Aluminum-Mediated Conversion of Esters to Amides (1982)

Abstract A convenient method has been developed for directly converting esters to amides using reagents derived from the reaction of trimethylaluminum with ammonium chloride, methylamine hydrochloride or dimethylamine hydrochloride.
Stabilization of tetanus and diphtheria toxoids against moisture-induced aggregation. (1995)

The progress toward single-dose vaccines has been limited by the poor solid-state stability of vaccine antigens within controlled-release polymers, such as poly(lactide-co-glycolide). For example, herein we report that lyophilized tetanus toxoid aggregates during incubation at 37 degrees C and elevated humidity--i.e., conditions relevant to its release from such systems. The mechanism and extent of this aggregation are dependent on the moisture level in the solid protein, with maximum aggregation observed at intermediate moisture contents. The main aggregation pathway is consistent with formaldehyde-mediated cross-linking, where reactive electrophiles created and stored in the vaccine upon formalinization (exposure to formaldehyde during vaccine preparation) react with nucleophiles of a second vaccine molecule to form intermolecular cross-links. This process is inhibited by the following: (i) succinylating the vaccine to block reactive amino groups; (ii) treating the vaccine with sodium cyanoborohydride, which presumably reduces Schiff bases and some other electrophiles created upon formalinization; and (iii) addition of low-molecular-weight excipients, particularly sorbitol. The moisture-induced aggregation of another formalinized vaccine, diphtheria toxoid, is also retarded by succinylation, suggesting the generality of this mechanism for formalinized vaccines. Hence, mechanistic stability studies of the type described herein may be important for the development of effective single-dose vaccines.
Bis-Pyrene-Labeled Oligonucleotides:  Sequence Specificity of Excimer and Monomer Fluorescence Changes upon Hybridization with DNA (2002)

The design, synthesis, and properties of a new pyrene excimer-forming probe of DNA have been described. 2,2-(Aminomethyl)propanediol was converted by the reaction with 1-pyrenebutylic acid to bis-pyrene-modified propanediol as a fluorescent non-nucleosidic linker. The bis-pyrene-modified linker can be incorporated via phosphoramidite chemistry into the 5'-terminal or internal positions of oligonucleotides (ODNs). The terminally modified ODNs showed almost similar affinity for complementary DNA when compared with the corresponding unmodified ODNs. The duplexes containing the bis-pyrene in the main chain exhibited higher melting temperatures relative to the corresponding duplexes containing propanediol linker at the same position. The UV and CD spectral studies indicate that the stacking interactions between the pyrene and DNA bases occur in the internally modified duplex and do not in the terminally modified duplex. The bis-pyrene modified linker itself displays excimer (E at 480 nm) and monomer (M at 380 nm) emission in a quantum yield (QY) of 0.17 and the E/M intensity ratio of 15. Incorporation of this linker into the terminal or internal positions of ODNs reduced the QY (0.003-0.009) and the E/M ratio (0.3-0.8). While small changes in the QY and E/M ratio was obtained in binding of the internally labeled ODNs to DNA, up to 27-fold increase in the QY and 17-fold increase in the E/M ratio was observed upon hybridization of the terminally labeled ODNs with DNA. The excimer and monomer fluorescence changes were found to be sensitive to a mismatch base present in the target DNA. The bis-pyrene-modified ODNs thus provide a sequence-sepcific fluorescent probe of DNA.
Parkin prevents mitochondrial swelling and cytochrome c release in mitochondria-dependent cell death (2003)

Parkin gene mutations have been implicated in autosomal-recessive early-onset parkinsonism and lead to specific degeneration of dopaminergic neurons in midbrain. To investigate the role of Parkin in neuronal cell death, we overproduced this protein in PC12 cells in an inducible manner. In this cell line, neuronally differentiated by nerve growth factor, Parkin overproduction protected against cell death mediated by ceramide, but not by a variety of other cell death inducers (H(2)O(2), 4-hydroxynonenal, rotenone, 6-OHDA, tunicamycin, 2-mercaptoethanol and staurosporine). Protection was abrogated by the proteasome inhibitor epoxomicin and disease-causing variants, indicating that it was mediated by the E3 ubiquitin ligase activity of Parkin. Interestingly, Parkin acted by delaying mitochondrial swelling and subsequent cytochrome c release and caspase-3 activation observed in ceramide-mediated cell death. Subcellular fractionation demonstrated enrichment of Parkin in the mitochondrial fraction and its association with the outer mitochondrial membrane. Together, these results suggest that Parkin may promote the degradation of substrates localized in mitochondria and involved in the late mitochondrial phase of ceramide-mediated cell death. Loss of this function may underlie the degeneration of nigral dopaminergic neurons in patients with Parkin mutations.
The IGF system in thyroid cancer: new concepts (2001)

In recent years, the activation of the insulin-like growth factor (IGF) system in cancer has emerged as a key factor for tumour progression and resistance to apoptosis. Therefore, a variety of strategies have been developed to block the type I IGF receptor (IGF-I-R), which is thought to mediate the biological effects of both IGF-I and IGF-II. However, recent data suggest that the IGF signalling system is complex and that other receptors are involved. To unravel the complexity of the IGF system in thyroid cancer, IGF-I and IGF-II production, and the expression and function of their cognate receptors were studied. Both IGFs were found to be locally produced in thyroid cancer: IGF-I by stromal cells and IGF-II by malignant thyrocytes. Values were significantly higher in malignant tissue than in normal tissue. IGF-I-Rs were overexpressed in differentiated papillary carcinomas but not in poorly differentiated or undifferentiated tumours, whereas insulin receptors (IRs) were greatly overexpressed in all tumour hystotypes, with a trend for higher values in dedifferentiated tumours. As a consequence of IR overexpression, high amounts of IR/IGF-I-R hybrids (which bind IGF-I with high affinity) were present in all thyroid cancer histotypes. Because of recent evidence that isoform A of IR (IR-A) is a physiological receptor for IGF-II in fetal life, the relative abundance of IR-A in thyroid cancer was measured. Preliminary data indicate that overexpressed IRs mainly occur as IR-A in thyroid cancer. These data indicate that both IR/IGF-I-R hybrids and IR-A play an important role in the overactivation of the IGF system in thyroid cancer and in IGF-I mitogenic signalling in these tumours. J Clin Pathol: Mol Pathol
Sum Rate Analysis of ZF Receivers in Distributed MIMO Systems (2013)

The performance of single-cell distributed multiple-input multiple-output (D-MIMO) systems is not only affected by small-scale Rayleigh fading but also from large-scale fading and path-loss. In this paper, we elaborate on the sum rate of D-MIMO systems employing linear zero-forcing receivers, accounting for both large and small-scale fading effects, as well as spatial correlation at the transmit side. In particular, we consider the classical lognormal model and propose closed-form upper and lower bounds on the achievable sum rate. Using these bounds as a starting point, we pursue a "large-system" analysis and provide asymptotic expressions when the number of antennas at the base station (BS) grow large, and when the number of antennas at both ends grow large with a fixed and finite ratio. A detailed characterization in the asymptotically high and low signal to noise ratio regimes is also provided. An interesting observation from our results is that in order to maximize the sum rate, the RPs should be placed at unequal distances to the BS when they experience the same level of shadowing. The resulting closed-form expressions are compared with the corresponding results on MIMO optimal receivers.
Thermodynamic stability of high-K dielectric metal oxides ZrO2 and HfO2 in contact with Si and SiO2 (2002)

We present theoretical and experimental results regarding the thermodynamic stability of the high-k dielectrics ZrO2 and HfO2 in contact with Si and SiO2. The HfO2/Si interface is found to be stable with respect to formation of silicides whereas the ZrO2/Si interface is not. The metal–oxide/SiO2 interface is marginally unstable with respect to formation of silicates. Cross-sectional transmission electron micrographs expose formation of nodules, identified as silicides, across the polycrystalline silicon/ZrO2/Si interfaces but not for the interfaces with HfO2. For both ZrO2 and HfO2, the x-ray photoemission spectra illustrate formation of silicate-like compounds in the MO2/SiO2 interface.
A graph cut based adaptive structured light approach for real-time range acquisition (2004)

This work describes a new algorithm that yields dense range maps in real-time. Reconstructions are based on a single frame structured light illumination. On-the-fly adaptation of the projection pattern renders the system more robust against scene variability. A continuous trade off between speed and quality is made. The correspondence problem is solved by using geometric pattern coding in combination with sparse color coding. Only local spatial and temporal continuity are assumed. This allows to construct a neighbor relationship within every frame and to track correspondences over time. All cues are integrated in one consistent labeling. This is achieved by reformulating the problem as a graph cut. Every cue is weighted based on its average consistency with the result within a small time window. Integration and weighting of additional cues is straightforward. The correctness of the range maps is not guaranteed, but an estimation of the uncertainty is provided for each part of the reconstruction. Our prototype is implemented using unmodified consumer hardware only. Frame rates vary between 10 and 25 fps dependent on scene complexity.
B‐COMPLEX GENETIC CONTROL OF IMMUNE RESPONSE TO HSA, (T,G)‐A–L, GT AND OTHER SUBSTANCES IN CHICKENS (1979)

Immune response to poly-(L-tyrosine-L-glutamic acid)-poly-D,L-alanine-poly-L-lysine (T,G)-A--L), human serum albumin (HSA), and (L-glutamic acid50, L-tyrosine50)n (GT) was found to be linked to the B complex in an outbred line of Leghorns segregating for the B1, B2, and B19 alleles. Birds of the blood group genotypes B1B1, B2B2, and B19B19 were low, intermediate, and high responders, respectively to either (T,G)-A--L or HSA. Response to GT, however, differed, with the B2B2 genotype being the only responder. No real genotype differences in immune response to DNP-congugates and sheep red blood cells (SRBC) could be detected.
ATP Hydrolysis by Mammalian RAD51 Has a Key Role during Homology-directed DNA Repair (2002)

Disruption of the gene encoding RAD51, the protein that catalyzes strand exchange during homologous recombination, leads to the accumulation of chromosome breaks and lethality in vertebrate cells. As RAD51 is implicated in BRCA1- and BRCA2-mediated tumor suppression as well as cellular viability, we have begun a functional analysis of a defined RAD51 mutation in mammalian cells. By using a dominant negative approach, we generated a mouse embryonic stem cell line that expresses an ATP hydrolysis-defective RAD51 protein, hRAD51-K133R, at comparable levels to the endogenous wild-type RAD51 protein, whose expression is retained in these cells. We found that these cells have increased sensitivity to the DNA-damaging agents mitomycin C and ionizing radiation and also exhibit a decreased rate of spontaneous sister-chromatid exchange. By using a reporter for the repair of a single chromosomal double-strand break, we also found that expression of the hRAD51-K133R protein specifically inhibits homology-directed double-strand break repair. Furthermore, expression of a BRC repeat from BRCA2, a peptide inhibitor of an early step necessary for strand exchange, exacerbates the inhibition of homology-directed repair in the hRAD51-K133R expressing cell line. Thus, ATP hydrolysis by RAD51 has a key role in various types of DNA repair in mammalian cells.
Evidence for a mu-oxo-bridged binuclear iron cluster in the hydroxylase component of methane monooxygenase. Mössbauer and EPR studies. (1988)

Mössbauer and EPR studies of a highly active hydroxylase component of methane monooxygenase isolated from Methylosinus trichosporium OB3b are reported. The Mössbauer spectra of the oxidized (as isolated) hydroxylase show iron in a diamagnetic cluster containing an even number of Fe3+ sites. The parameters are consistent with an antiferromagnetically coupled binuclear cluster similar to those of hemerythrin and purple acid phosphatases. Upon partial reduction of the hydroxylase, an S = 1/2 EPR spectrum with g values at 1.94, 1.86, and 1.75 (gav = 1.85) is observed. Such spectra are characteristic of oxo-bridged iron dimers in the mixed valent Fe(II).Fe(III) state. Further reduction leads to the appearance of a novel EPR resonance at g = 15. Comparison with an inorganic model compound for mu-oxo-bridged binuclear iron suggests that the g = 15 signal is characteristic of the doubly reduced state of the cluster in the protein. In this state, the Mössbauer spectra exhibit two quadrupole doublets typical of high spin Fe2+, consistent with the Fe(II).Fe(II) form of the cluster. The spectral features of the iron center of the hydroxylase in three oxidation states are all similar to those reported for mu-oxo (or mu-hydroxo)-bridged binuclear iron clusters. Since no known monooxygenase contains such a cluster, a new oxygenase mechanism is suggested. Three different preparative methods yielded hydroxylases spanning a 9-fold range in specific activity, yet the same cluster concentration and spectral characteristics were observed. Thus, other parameters than those measured here have a major influence on the activity.
First Tarsometatarsal Fusion Using Saw Preparation vs. Standard Preparation of the Joint: A Cadaver Study (2019)

Category: Basic Sciences/Biologics, Midfoot/Forefoot Introduction/Purpose: First tarsometatarsal (TMT) joint fusion is indicated for several underlying causes of first ray dysfunction and pain, including arthritis, traumatic injury, and recurrent hallux valgus. Preparation of the joint surface by denuding the articular cartilage is a key step for arthrodesis, as inadequate preparation may result in poor fixation and non-union. However, excessive removal of cartilage and bone may result in excessive shortening of the ray. Despite the importance of joint preparation on the outcomes of fusion, the effects of using a bone saw versus osteotome on ray length is poorly documented in the literature. The purpose of this study was to investigate whether utilization of an osteotome or saw would minimize shortening of the first ray in TMT arthrodesis. Methods: Ten fresh-frozen cadaver specimens without evidence of musculoskeletal abnormalities were used for this anatomic dissection study. A medial incision was made along the first ray from the medial aspect of the medial cuneiform to the base of the first metatarsal. The first TMT joint was exposed through transverse capsulotomy. The soft tissues surrounding the joint were not removed from the bone. The specimens were randomly assigned to undergo cartilage removal and joint preparation using either an osteotome (n=5) or saw (n=5). Care was taken to reach the plantar-most aspect of the joint. Fusion was then performed using a cross-screw construct through the dorsal aspect of the proximal phalanx and the medial cuneiform. Pre- and post-operative x- rays were taken with a radiopaque ruler in the field, and length changes were compared between osteotome and sawblade groups. Results: The average change in metatarsal length was significantly smaller in the osteotome group (1.6 mm) as compared to the saw group (4.4 mm) (p=0.031). The average percent change in metatarsal length was also significantly smaller in the osteotome group (3.0%) compared to the saw group (8.4%) (p=0.025). There was no significant difference between the two groups with respect to change in cuneiform length. The osteotome group demonstrated a significantly smaller average measured change (3.0 mm vs. 6.9 mm, p=0.001) and percent change (4.1% vs. 9.3%, p&lt;0.001) in total length (cuneiform plus metatarsal) in comparison to the saw group. Conclusion: The results of this study demonstrate that first TMT joint preparation with an osteotome may prevent over- shortening of the first ray, thereby theoretically decreasing the risk of metatarsalgia and the need for additional procedures when compared to utilization of a bone saw. Judicious use of the bone saw for joint preparation may still be beneficial in some cases. This information can be used clinically to implement evidence-based standardization of operative techniques to improve the outcomes of these cases.