gebhart/patrepeval huggingface dataset:
Gene Acquisition at the Insertion Site for SCC mec , the Genomic Island Conferring Methicillin Resistance in Staphylococcus aureus (2007)

Staphylococcus aureus becomes resistant to methicillin by acquiring a genomic island, known as staphylococcal chromosome cassette mec (SCCmec), which contains the methicillin resistance determinant, mecA. SCCmec is site-specifically integrated into the staphylococcal chromosome at a locus known as the SCCmec attachment site (attB). In an effort to gain a better understanding of the potential that methicillin-sensitive S. aureus (MSSA) isolates have for acquiring SCCmec, the nucleotide sequences of attB and surrounding DNA regions were examined in a diverse collection of 42 MSSA isolates. The chromosomal region surrounding attB varied among the isolates studied and appears to be a common insertion point for acquired foreign DNA. Insertions of up to 15.1 kb were found containing open reading frames with homology to enterotoxin genes, restriction-modification systems, transposases, and several sequences that have not been previously described in staphylococci. Two groups, containing eight and four isolates, had sequences found in known SCCmec elements, suggesting SCCmec elements may have evolved through repeated DNA insertions at this locus. In addition, the attB sequences of the majority of MSSA isolates in this collection differ from the attB sequences of strains for which integrase-mediated SCCmec insertion or excision has been demonstrated, suggesting that some S. aureus isolates may lack the ability to site-specifically integrate SCCmec into their chromosomes.
Crystal structure of a complex between β-glucopyranose and a macrocyclic receptor with dendritic multicharged water solubilizing chains (2016)

Using commercial screens for crystallization of biomolecules and taking advantage of the use of racemic crystallography allowed the production of X-ray quality single crystals and the elucidation at 1.08 Å resolution of the solid state structure of a difficult target: the complex between glucopyranose and a water soluble macrocyclic receptor equipped with dendritic multianionic solubilizing chains.
Diagnosing Pulmonary Embolism in Pregnancy: Are Biomarkers and Clinical Predictive Models Useful? (2016)

Objective The objective of this study was to evaluate whether trimester-specific D-dimer levels or the modified Wells score (MWS) is a useful risk stratification tool to exclude pregnant women at low risk of pulmonary embolism (PE) from diagnostic imaging. Study Design This is a prospective and retrospective cohort study. Pregnant women who underwent diagnostic imaging for suspected PE were prospectively enrolled. D-dimer serum levels were drawn, and a MWS was assigned. Pregnant women diagnosed with a PE before study launch who underwent diagnostic imaging and had a D-dimer level drawn were also evaluated. Results In this study, 17 patients were diagnosed with a PE and 42 patients had no PE on diagnostic imaging. Sixteen out of 17 patients with a PE versus 11 out of 42 without PE had an abnormal D-dimer level (p = 0.001). Four patients with a PE versus zero without a PE had an abnormal MWS (p = 0.005). The combination of a trimester-specific D-dimer level along with the MWS was abnormal in all 17 patients with a documented PE versus 11/42 (26.2%) patients without a documented PE (p = 0.001). Conclusion A combination of trimester-specific D-dimer levels along with a MWS can be used in pregnancy to triage women into a low-risk category for PE and thereby avoid radiation exposure in a majority of pregnant patients.
Project-based teaching unit using energetic macroscopic representation to design drive controllers (2010)

This paper describes an example of a student's simulation project based on a steer-by-wire system. The approach followed during this project relies on the Energetic Macroscopic Representation to help students to organize their simulation worksheet, and to deduce by inversion the control laws.
Biochemical bone markers and bone density in hip fracture patients: Weak correlation in 106 women (2000)

Biochemical markers of bone formation and bone resorption were measured preoperatively, within 18 hours after a hip fracture (n 106) and bone mineral density (BMD) was measured with quantitative computer tomography (QCT), dual-energy x-ray absorptiometry (DXA) and heel ultrasound in 63 hip fracture patients. Patients with pertrochanteric fractures had more osteoporosis in all measurements than patients with femoral neck fractures. We found no differences in biochemical markers of bone formation or bone resorption in patients with femoral neck fractures and in those with pertrochanteric fractures. Correlations between biochemical bone markers and bone density, bone mass and stiffness on admission were weak.
Design of Interstellar Digital Communication Links: Some Insights from Communication Engineering - eScholarship (2011)

The design of an end-to-end digital interstellar communication system at radio frequencies is discussed, drawing on the disciplines of digital communication engineering and computer network engineering in terrestrial and near-space applications. One goal is a roadmap to the design of such systems, aimed at future designers of either receivers (SETI) or transmitters (METI). In particular we emphasize the implications arising from the impossibility of coordination between transmitter and receiver prior to a receiver's search for a signal. A system architecture based on layering, as commonly used in network and software design assists in organizing and categorizing the various design issues and identifying dependencies. Implications of impairments introduced in the interstellar medium, such as dispersion, scattering, Doppler, noise, and signal attenuation are discussed. Less fundamental (but nevertheless influential) design issues are the motivations of the transmitter designers and associated resource requirements at both transmitter and receiver. Unreliability is inevitably imposed by non-idealities in the physical communication channel, and this unreliability will have substantial implications for those seeking to convey interstellar messages.
Bioflavonoid effects on the mitochondrial respiratory electron transport chain and cytochromecredox state (1999)

The polyphenolic structure common to flavonoids enables them to donate electrons and exert antioxidant activity. Since the mitochondrial electron transport chain consists of a series of redox intermediates, the effect of flavonoids in a complex mixture of polyphenols, as well as related pure flavonoids, was evaluated on the rat liver mitochondrial electron transport chain. A French maritime pine bark extract (PBE), a complex mixture of polyphenols and related pure flavonoids, was able to reduce cytochrome c reversibly, possibly by donation of electrons to the iron of the heme group; the donated electrons can be utilized by cytochrome c oxidase. Among single flavonoids tested, (-)-epicatechin gallate had the greatest ability to reduce cytochrome c. In addition, PBE competitively inhibited electron chain activity in both whole mitochondria and submitochondrial particles. A 3.5-fold increase in the apparent Km value for succinate was calculated from reciprocal plots. Among the flavonoids tested, taxifolin and (-)-epicatechin gallate showed minor inhibitory effects, while (+/-)-catechin and (+)-epicatechin were ineffective. Activities of NADH-ubiquinone, succinate-ubiquinone, and ubiquinol-cytochrome c reductases were inhibited by low concentrations of PBE to a similar extent. However, inhibition of cytochrome c oxidase activity required 4-fold higher PBE concentrations. These results suggest that flavonoids reduce cytochrome c and that PBE inhibits electron transport chain activity mainly through NADH-ubiquinone, succinate-ubiquinone, and ubiquinol-cytochrome c reductases.
Supplementary Figure 2 from Migratory and Antigen Presentation Functions of IFN-Producing Killer Dendritic Cells (2023)

Supplementary Figure 2 from Migratory and Antigen Presentation Functions of IFN-Producing Killer Dendritic Cells
<p>Photocatalytic antibacterial application of zinc oxide nanoparticles and self-assembled networks under dual UV irradiation for enhanced disinfection</p> (2019)

The results suggested that ZnO nanoparticles and their networks can be promising photocatalytic antibiotics for use in next-generation disinfection systems. Their application could also be extended to industrial and clinical use as effective and safe photocatalytic antibiotics.
Toll‐like receptor ligand activation of murine bone marrow‐derived dendritic cells (2008)

Dendritic cells (DCs) are required for the initiation of primary immune responses. The pattern of Toll-like receptor (TLR) expression on various subsets of these cells has been shown to differ, suggestive of distinct roles in influencing immune responses. We have examined here the responses of immature DCs derived from murine bone marrow (BMDCs) to a range of TLR ligands. BMDCs cultured for 6 days in the presence of granulocyte-macrophage colony-stimulating factor were stimulated for 24 hr with ligands to TLR1-2 [Pam(3)Cys-Ser-(Lys)(4) (PAM)], TLR2-6 (macrophage-activating lipopeptide-2 (MALP-2); zymosan or peptidoglycan (PG)], TLR3 (polyinosinic-polycytidylic acid), TLR4 [lipopolysaccharide R515 (LPS)], TLR5 (flagellin), TLR7 (polyuridylic acid) and TLR9 [CpG ODN2395 (CpG)]. DC activation was monitored using membrane marker expression and analysis of culture supernatants for cytokine/chemokine release. Ligands to TLR3 and TLR7 failed to activate BMDCs. All other TLR ligands caused elevated expression of membrane markers. PAM, MALP-2 and LPS induced high-level expression of proinflammatory cytokines and chemokines. Treatment with CpG was associated with a preferential type 1 cytokine and chemokine profile. Zymosan and PG were proinflammatory but also skewed towards a type 2 pattern of cytokines and chemokines. In contrast, flagellin did not cause marked secretion by BMDCs of cytokines or chemokines. These data for BMDCs are largely consistent with the reported TLR repertoire of freshly isolated murine Langerhans cells. In addition, murine BMDCs show selective responses to TLR ligands with respect to general activation, with differentiated cytokine patterns suggestive of potential priming for divergent immune responses.
BTG gene expression in the p53-dependent and -independent cellular response to DNA damage (2000)

Exposure of mammalian cells to genotoxic agents evokes a complex cellular response. An ordered series of molecular events is necessary to sense DNA damage, transduce the signal, and ultimately delay the cell cycle or trigger apoptosis. Recently, we have shown that BTG2/TIS21 gene expression was induced in response to DNA damage through a p53-dependent pathway. This gene belongs to a newly identified family of structurally related genes whose other known human members are BTG1, BTG3, and Tob. To define the respective involvement of these four related genes in the cellular response to DNA damage, we studied their expression in human cell lines after a variety of genotoxic treatments. Our results demonstrated that were BTG1, BTG2/TIS21, and Tob genes the DNA damage--inducible genes. However, BTG2/TIS21 appeared to be the only p53-transcriptional target gene. We speculate that BTG proteins may play a coordinate role in a general transduction pathway that is induced in response to DNA damage. It has been previously described that recombinant BTG1 and BTG2/TIS21 can physically interact with PRMT1, an arginine methyl transferase, suggesting that BTG1 and BTG2/TIS21 induction may lead to posttranslational modifications of cellular proteins. In support of this hypothesis, we showed that the endogenous induction of BTG1 and BTG2 after genotoxic treatment was correlated with a modulation of protein methylation.
Dynamically Reconfigurable QoS-aware Embedded Systems (2007)

This book, equally applicable for a CSE or ECE course, gives an extensive account of Embedded Systems, keeping a balanced coverage of hardware and software concepts. Adhering to syllabus needs, this title is ‘microprocessor’ and ‘software design methodology’ specific, giving due weightage to architecture, programming and design aspects.
Prospective Studies of Dairy Product and Calcium Intakes and Prostate Cancer Risk: A Meta-Analysis (2005)

High intake of dairy products and calcium may be associated with an increased risk of prostate cancer, although the increase appears to be small.
Evidence for the formation of clathrate structures of protonated water–methanol clusters at thermal energy (1994)

Gas phase ion–molecule reactions of large protonated water clusters with methanol are studied in a flow reactor under thermal conditions. A distinct feature at H+(H2O)21 corresponding to a stable clathrate structure is observed. Upon the addition of methanol from a reactant gas inlet, products of the general form H+(H2O)n(CH3OH)m (m=1–5) are detected. Distinct features at n+m=21 are observed under different experimental conditions, which are indicative of the formation of clathrate-like structures for mixed water–methanol cluster ions. A switching reaction mechanism rather than an association is found to be operative. Considering the results of the present study and those from previous molecular beam experiments suggests that clathrate structures arise from their inherent stabilities rather than due to kinetic effects.
Figure S3 from MAPK7 Regulates EMT Features and Modulates the Generation of CTCs (2023)

&lt;p&gt;Figure S3. Illustration of modeling and correcting for dependence of each marker through the expression level of housekeeping genes.&lt;/p&gt;
Supplemental Figure 2 from Phase I Study of GDC-0425, a Checkpoint Kinase 1 Inhibitor, in Combination with Gemcitabine in Patients with Refractory Solid Tumors (2023)

&lt;p&gt;Supplemental Figure 2. Preclinical xenograft immunohistochemistry. HT-29 xenografts were analyzed for pCDK1/2 and Ki-67 expression. Representative images from 2 unique animals in each treatment group (n=5 animals per group) are shown. Ki-67 expression in surviving tumor cells is relatively consistent among treatment groups. pCDK1/2 expression increases from baseline (A, B) after gemcitabine treatment (I, J), whereas GDC-0425 alone (E, F) had little effect. In contrast, GDC-0425 given 16 hours after gemcitabine caused marked inhibition of the gemcitabine-induced expression of pCDK1/2. Scale bar=90 Âµm.&lt;/p&gt;
Data from Global microRNA Analysis of the NCI-60 Cancer Cell Panel (2023)

&lt;div&gt;Abstract&lt;p&gt;MicroRNAs (miRNA) are a group of short noncoding RNAs that regulate gene expression at the posttranscriptional level. They are involved in many biological processes, including development, differentiation, apoptosis, and carcinogenesis. Because miRNAs may play a role in the initiation and progression of cancer, they comprise a novel class of promising diagnostic and prognostic molecular markers and potential drug targets. By applying an LNA-enhanced microarray platform, we studied the expression profiles of 955 miRNAs in the NCI-60 cancer cell lines and identified tissue- and cell-type–specific miRNA patterns by unsupervised hierarchical clustering and statistical analysis. A comparison of our data to three previously published miRNA expression studies on the NCI-60 panel showed a remarkably high correlation between the different technical platforms. In addition, the current work contributes expression data for 369 miRNAs that have not previously been profiled. Finally, by matching drug sensitivity data for the NCI-60 cells to their miRNA expression profiles, we found numerous drug–miRNAs pairs, for which the miRNA expression and drug sensitivity profiles were highly correlated and thus represent potential candidates for further investigation of drug resistance and sensitivity mechanisms. &lt;i&gt;Mol Cancer Ther; 10(3); 375–84. ©2011 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Changes to the Editorial Board (2019)

sketch of Dr. Gossner's research interests can be found below
Cumulant-based adaptive multichannel filtering for wireless communication systems with multipath RF propagation using antenna arrays (1998)

A method based on high-order statistics is proposed to mitigate the performance degradation caused by multipath RF propagation in a mobile radio communication system using a linear antenna array at the base-station receiver. It is shown that an overdetermined system of linear equations (involving only cumulants of the received baseband digitized signal) can be obtained to perform noniterative deconvolution. An efficient adaptive algorithm based on square-root decomposition is proposed to avoid numerical problems when real-time tracking of moving transmitters is needed.
Human lupus anti-spliceosome A protein autoantibodies bind contiguous surface structures and segregate into two sequential epitope binding patterns (1996)

High levels of anti-spliceosomal autoantibodies are commonly found in systemic lupus erythematosus (lupus) sera. We have evaluated the binding of lupus autoantibodies to octapeptides of nuclear ribonucleoprotein (nRNP) A, identified patterns of binding that vary between sera, quantified the proportion of anti-nRNP that binds individual peptides, and related these data to the partial tertiary structure of nRNP A. Anti-nRNP A-positive lupus sera share binding to eight antigenic groups of octapeptides from nRNP A. The four shared antigenic sites in the known nRNP A tertiary structure are contiguous on its surface and include surface loops between beta sheets and/or alpha helices. Anti-peptide Abs account for a significant portion of the human autoimmune response to nRNP A. Lupus sera are also obviously divisible into two subsets by their binding to nRNP A-derived peptides. Eight of the thirteen anti-nRNP A sera tested bind most of the eight common antigenic regions of nRNP A. All five sera in the other subset bind to two and only two groups of nRNP A octapeptides. Of this subset, absorption experiments show that as much as 75% of the anti-nRNP found in a patient serum is bound to these two octapeptides from nRNP A. The 70K spliceosome protein contains similar peptides that are also bound by these sera (OR=13.5, p<0.001). Lupus autoantibodies bind to peptides of nRNP A in discernibly consistent patterns that identify serologic subsets and in a manner that provides useful insights into the autoimmunity and antigenic structure of the nRNP A spliceosomal protein.
Analysis of Load-Balancing of Web Cluster Based on TLS Session Sharing (2009)

TLS (Transport Layer Security) is one of the most popular protocols to provide a secure channel between the client and Web server; however, the high overhead of which degrades the server performance considerably. Existing load-balancing schemes for TLS Web system can improve the performance of the system, but the balance of loads is very difficult for the features of TLS, which results in degrading total systempsilas performance caused by existing load-balancing schemes for TLS Web system. In this paper, TLS handshake and session resumption will run at the whole cluster. TLS session was broadcasted to all of the servers in the cluster when it is generated in a server and which will be reused in all servers. Finally, a new load-balancing cluster is proposed to share TLS session in cluster, and which can effectively improve the performance of TLS web cluster.
Assessing Clinical Prospects of Silicon Quantum Dots: Studies in Mice and Monkeys (2013)

Silicon nanocrystals can provide the outstanding imaging capabilities of toxic heavy-metal-based quantum dots without employing heavy metals and have potential for rapid progression to the clinic. Understanding the toxicity of silicon quantum dots (SiQDs) is essential to realizing this potential. However, existing studies of SiQD biocompatibility are limited, with no systematic progression from small-animal to large-animal studies that are more clinically relevant. Here, we test the response of both mice and monkeys to high intravenous doses of a nanoconstruct created using only SiQDs and FDA-approved materials. We show that (1) neither mice nor monkeys show overt signs of toxicity reflected in their behavior, body mass, or blood chemistry, even at a dose of 200 mg/kg. (2) This formulation did not biodegrade as expected. Elevated levels of silicon were present in the liver and spleen of mice three months post-treatment. (3) Histopathology three months after treatment showed adverse effects of the nanoformulation in the livers of mice, but showed no such effects in monkeys. This investigation reveals that the systemic reactions of the two animal models may have some differences and there are no signs of toxicity clearly attributable to silicon quantum dots.
Quantum Mechanics/Molecular Mechanics Calculations of the Vanadium Dependent Chloroperoxidase (2005)

Large quantum mechanics/molecular mechanics (QM/MM) calculations are used to probe the resting and initial protonated states of the vanadium dependent chloroperoxidase from the pathogenic fungus Curvularia inaequalis. QSite was used to model 433 residues and 24 structural waters with molecular mechanics, while 8 active-site residues and the vanadate cofactor (161 atoms) were represented at the B3LYP/lacvp* level of theory. Our previous study of small model systems implied that the resting state of the enzyme contains a trigonal bipyramidal vanadate with one hydroxyl group in the equatorial plane and another in the axial position. This study uses a much larger model of the biological system at a higher level of theory to identify the location of the equatorial hydroxo group with respect to the enzyme active site. We also identify a second resting-state configuration with an axial water and three equatorial oxo moieties that is nearly isoenergetic with the previously identified state. We propose that the resting state is a hybrid of these two configurations, stabilized by the long-range electrostatic field of the protein environment. The first step in catalysis is believed to be protonation of the vanadate. Our previous small models indicated that there were two protonated configurations, but this study shows that the configuration containing an axial water and one hydroxo group in the equatorial plane is significantly lower in energy than any other configuration. Additionally, we can now assign an important role for lysine 353 in the catalytic cycle. Based on our calculations and other model studies, we provide an updated catalytic cycle for vanadium dependent haloperoxidase activity. Further, we demonstrate the importance of system set up. In particular, maintaining the proper electrostatic field at the active site is crucial for identifying the correct minima in a truncated protein model.