gebhart/patrepeval huggingface dataset:
Use of Bioorthogonal N‐ Acetylcysteamine (SNAc) Analogues and Peptidoglycan O‐ Acetyltransferase B (PatB) to Label Peptidoglycan (2018)

In Gram (−) bacteria, peptidoglycan O ‐acetyltransferase B (PatB) is responsible for the O‐ acetylation of peptidoglycan to prevent degradation by lysozyme and other lytic transglycosylases generated by its host. In this work, PatB was exploited as a tool to incorporate bioorthogonal functionality on the carbohydrate backbone of the peptidoglycan by using a variety of donors, either p ‐nitrophenol ( p NP) or N ‐acetylcysteamine (SNAc). Using tri‐ N‐ acetylglucosamine (GlcNAc) 3 as a peptidoglycan mimic, a variety of functionalities were installed, including an alkyne and azide handle, on this mimic. Further studies in vitro showed that these modifications have a protective effect on isolated peptidoglycan from B. subtilis, E. coli, P. putida, and V. parahaemolyticus against lysozyme degradation. Intrigued by these results, an alkyne handle was subsequently installed on whole bacterial cells of B. subtilis using the SNAc alkyne derivative and the carbohydrate backbone was fluorescently labeled via click chemistry. Altering the peptidoglycan post‐synthetically with these derivatives will aid in the isolation and identification of immune stimulatory fragments from bacteria, as well as in the development of antibiotics and immune modulators. Support or Funding Information The Delaware COBRE and INBRE programs supported this project with a grant from the NIGMS (5 P30GM110758‐02, P20GM104316‐01A1 and P20GM103446) from the NIH. This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .
10-Gb/s Burst-mode Receiver for Fast Settling Time (2009)

We developed a 10-Gb/s burst-mode receiver for a fast receiver settling time. The receiver has an ATC boost function and a differential output stabilization circuit to realized a fast settling time. We achieved 50-ns receiver settling time.
O6-Methylguanine-DNA Methyltransferase, O6-Benzylguanine, and Resistance to Clinical Alkylators in Pediatric Primary Brain Tumor Cell Lines (2005)

Our results support the use of O6-benzylguanine to achieve full benefit of alkylating agents, particularly temozolomide, in the chemotherapy of pediatric brain tumors.
Avalanche Pumping of Thulium Doped S-Band Fiber Amplifiers (2006)

In the last years a lot of different pump configurations were investigated for thulium doped fiber amplifiers (TDFA) in the S-band. Since the TDFA is using a four-level transition with long lifetime of the lower amplifier level, it turned out, that pumping with two wavelengths was most effective. Comparing the results of fluoride fibers doped with 2000 ppm and 5000 ppm thulium, we show that an avalanche effect significantly improves the efficiency of TDFAs with the highly thulium doped fiber when pumped at 1050 nm only and at the same time makes the dual-pump configuration 790/1050 nm inefficient. For the measurements we used self-made fluoride fibers
Tracing voice through the career of a musical pioneer: A conversation with Pauline Oliveros (2017)

Abstract In this conversation from 2014, composer Pauline Oliveros, one of the most important figures in American experimental music, provides insight into her relationship with the voice and when in her career it was most pivotal for her compositional development. Oliveros touches on her 1961 choral piece Sound Patterns, her Sonic Meditations, the works she performed for voice and accordion in the 1970s and 1980s, Deep Listening, and the late operas that she made with her partner, vocalist and poet Ione.
Analysis Of The Impact of Channel Estimation Errors on the Decomposition of Multiuser Mimo Channels (2006)

In the work at hand a general procedure to analyze the impact of channel estimation errors on the performance of decomposition techniques for multiuser MIMO channels is presented. In particular, this procedure is applied to a decomposition technique called cooperative zero-forcing with successive encoding and successive allocation method (CZF-SESAM). Based on the resulting analytical expressions the transmitter is able to adjust bit and power loading so that in spite of estimation errors transmission quality requirements can still be met
Measurement of optical reflection and temperature changes after blood occlusion using a wearable device (2020)

Early detection of compromised circulation is essential for postoperative monitoring of free flap. Hourly clinical check-ups such as inspection and palpation still result in a delay in detection. Conversely, optical reflection and temperature measurement are useful alternatives for detecting blood circulation. However, conventional methods that verify ischemia and congestion within a short period have not been reported. In this study, we measured short-term changes in optical reflection and temperature in a rat flap using a wearable flexible sensor probe previously developed in our laboratory. Five ischemia and five congestion groin flap models were measured using a sensor probe and reference devices. Curve fitting was performed on transition signals to evaluate changes in signals and their time constants. The optical reflection signal decreased after venous ligation and increased after arterial ligation. The parameters of the fitted curves indicate a significant difference between congestion and ischemia at p < 0.01 (probability value), which was detected within a few minutes after ligation. However, insufficient significance was observed in the temperature signal. Our method gives supporting information to verify ischemia and congestion, and has the potential to rapidly detect compromised circulation.
Effect of naloxone on the pulmonary vascular responses to graded levels of intracranial hypertension in anesthetized sheep. (1983)

7.0 +/- 0.5 ml/s; ICP: 60 mmHg = 11.0 +/- 3.7 ml/s; ICP: 100 mmHg = 12.4 +/- 1.3 ml/s, p less than 0.05), and VH2O (CONTROL: 93 +/- 8% baseline; ICP: 60 mmHg = 112 +/- 6% of baseline; ICP: 100 mmHg = 129 +/- 13% of baseline, p less than 0.05) proportional to the level of ICP. Sheep with ICP raised to 100 mmHg had modestly increased lung water (pulmonary edema).(ABSTRACT TRUNCATED AT 250 WORDS)
Short- and long-term outcomes following atrial fibrillation in patients with acute coronary syndromes with or without ST-segment elevation (2008)

AF is more common in patients with STEMI. An association of AF with short- and long-term mortality among patients with STEMI and NSTE-ACS was found. Understanding these findings may lead to better care of patients with this common arrhythmia.
In the Golden Age of Organocatalysis (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Effect of Translational Energy on Ion-Molecule Reaction Rates (1967)

The kinetic energy dependence of ion-molecule reaction rates is reviewed from both experimental and theoretical viewpoints for typical systems. At low energy the theory of Gioumousis and Stevenson is an adequate framework when suitably modified to reflect characteristic properties of a given system. At higher energies it is necessary to invoke orientation effects appropriate to stripping mechanisms to rationalize experimental data. New information on energy dependent isotope effects and multiple dissociation paths for intermediate complexes provide suitable criteria for distinguishing the two fundamental mechanisms and also demonstrate the efficient conversion of translational energy into internal energy. On the basis of these results, certain particularly important areas for future research are suggested.
Efficacy of crizotinib in ROS1-rearranged lung cancer: The European experience. (2014)

11035 Background: ROS1 chromosomal rearrangement (ROS1+) was described as an oncogenic driver in approximately 1% of non-small cell lung cancers (NSCLC). Due to the structural analogy of ROS1 and ALK, crizotinib is a potent inhibitor of both targets. An expansion cohort of a phase I trial reported promising activity [Ou et al., ASCO 2013]. Here, we describe the characteristics and outcomes of ROS1+ NSCLC patients treated with crizotinib in a large European case series. Methods: We conducted a retrospective study among European clinicians screening ROS1+ NSCLC. Eligible patients had advanced NSCLC, known ROS1+ NSCLC diagnosed by FISH and received crizotinib for at least 1 week at the dose of 250 mg BID through national access program or an individual off-label use basis. Treatment response was performed according to RECIST criteria version 1.1. Informed consent and IRB approval were obtained according to local regulations. Data were analyzed centrally. Results: We identified 28 ROS1+ NSCLC patients treated with crizotinib. Our population was characterized by a median age of 58 yr (34 to 78 yr), a gender-ratio of 17 women and 11 men and a high proportion of never smokers (n = 19, 67.9%). All the patients had stage IV disease and were pretreated with none (n=2), one (n = 8), two (n = 5), three (n = 3) or more (n = 10) lines of chemotherapy before the administration of crizotinib. All tumors were adenocarcinomas including 4 with lepidic pattern. ROS1 rearrangement was the exclusive driver except for 2 tumors with concomitant KRAS mutation. Twenty-six patients were evaluable for response (the waterfall plot will be presented at the meeting). We observed 3 progressive diseases, 3 stable diseases and 20 objective responses including 4 complete responses (overall response rate 77%, disease control rate 88%). Crizotinib primary resistance was associated with concomitant KRAS mutation or progression in the brain. Crizotinib was generally well tolerated and no unexpected adverse effects were observed. Conclusions: These results confirm the high crizotinib activity in ROS1+ NSCLC. Further patients should be treated in ongoing clinical trials to test the long-term activity of ROS1 inhibitors.
A Molecular Basis for How a Single TCR Interfaces Multiple Ligands (1998)

CD8+ T cells respond to Ags when their clonotypic receptor, the TCR, recognizes nonself peptides displayed by MHC class I molecules. The TCR/ligand interactions are degenerate because, in its life time, the TCR interacts with self MHC class I-self peptide complexes during ontogeny and with self class I complexed with nonself peptides to initiate Ag-specific responses. Additionally, the same TCR has the potential to interact with nonself class I complexed with nonself peptides. How a single TCR interfaces multiple ligands remains unclear. Combinatorial synthetic peptide libraries provide a powerful tool to elucidate the rules that dictate how a single TCR engages multiple ligands. Such libraries were used to probe the requirements for TCR recognition by cloned CD8+ T cells directed against Ags presented by H-2Kb class I molecules. When H-2Kb contact residues were examined, position 3 of the peptides proved more critical than the dominant carboxyl-terminal anchor residue. Thus, secondary anchor residues can play a dominant role in determining the antigenicity of the epitope presented by class I molecules. When the four solvent-exposed potential TCR contact residues were examined, only one or two of these positions required structurally similar residues. Considerable structural variability was tolerated at the remaining two or three solvent-exposed residues of the Kb-binding peptides. The TCR, therefore, requires close physico-chemical complementarity with only a few amino acid residues, thus explaining why TCR/MHC interactions are of low affinity and degenerate.
Alkalinization of Intracuff Lidocaine: Efficacy and Safety (2005)

When alkalinized lidocaine instead of air is used to fill the endotracheal tube (ETT) cuff, coughing, and bucking are decreased during extubation when ventilation is controlled with N2O. However, sodium bicarbonate (NaHCO3) used to transform lidocaine hydrochloride (L-HCl) to lidocaine base induces a pH increase that could be irritating for mucosa in the case of cuff rupture. Therefore, we determined, in a randomized controlled study with controlled patient ventilation without N2O, whether the smallest concentrations of NaHCO3 (1.4% versus 8.4%) reduced diffusion (in vitro evaluation) and other secondary clinical benefits. After pH determination of different solutions (2 mL of 2% L-HCl and 2 to 6 mL of 8.4%, or 1.4% NaHCO3), an in vitro lidocaine diffusion through the ETT cuffs was evaluated (2 mL of 2% L-HCl and 3 mL of 8.4% or 1.4% NaHCO3). Then, adult patients scheduled for total thyroidectomy surgery were consecutively enrolled (n = 20 for each group). The ETT cuff was filled with air (group air) or with alkalinized lidocaine (2 mL of 2% L-HCl) using 8.4% (group large dose) or 1.4% (group small dose) of NaHCO3. After tracheal extubation, sore throat was evaluated by visual analog scale as the main end-point of the study. Hoarseness, bucking, dysphonia, dysphagia, cough, restlessness, and postoperative nausea and vomiting were also evaluated. There was a slight tendency toward a slower release when a small concentration of NaHCO3 was used (i.e., 1.4%). Compared with group air, the alkalinized-lidocaine groups had a significant reduction in sore throat during the 24-h postoperative period (P < 0.0001). The difference was not significant between the two alkalinized lidocaine groups. This increase in ETT tolerance was confirmed by the analysis of secondary end-points. No laryngospasm, rupture of ETT cuff, or depression of the swallowing reflex were recorded. A decrease in sore throat during the postoperative period was recorded when the cuff was inflated with a small dose of alkalinized lidocaine (i.e., 40 mg of L-HCl and 1.4% of NaHCO3) rather than with air when ventilation was controlled without N2O.
Therapeutic Apheresis in Myasthenia Gravis (2000)

Plasma exchange (PE) is an easily applicable technique for rapid and massive removal of antibodies, and its beneficial role is well established in the management of myasthenia gravis (MG), an antibody-mediated disorder of the neuromuscular junction. PE is useful in myasthenic crisis, in most severe forms of MG before thymectomy, in the early postoperative period, and in cases of symptom worsening during tapering or initiation of immunosuppressive therapy. Clinical efficacy varies from 55% to 100%, and improvement rarely persists for more than 4-10 weeks; thus immunosuppressive therapy has to be associated. New apheretic techniques (double filtration plasmapheresis, immunoadsorption systems with staphylococcal protein A columns or thryptophan-polyvinyl alcohol gel columns) that allow the selective removal of IgG and anti-AChR antibody were recently used in the management of MG with positive effects. Whether their therapeutic effect and cost effect prove more favorable than those obtained by PE still must be demonstrated.
Review of the Merits in Class Action Certification (2004)

In Eisen v. Carlisle &amp; Jacquelin, the Supreme Court declared that federal courts may not conduct a preliminary inquiry into the merits of a suit in order to determine whether it may be maintained as a class action. This proscription - sometimes known as the Eisen rule - has become a pillar of class action practice, both under Federal Rule of Civil Procedure 23 and under state-court class action procedures. The rule can have a crucial influence on whether a case is certified as a class action - and, given the importance of certification, on the success or failure of the litigation. This Article analyzes the proper scope of a court's inquiry into merits issues when ruling on motions to certify a class. Part I of the Article distinguishes three approaches to this question: strong-form rules that prohibit inquiries into the merits and require the court to accept as true the well-pleaded allegations in the complaint; weak-form rules that permit reasonable inquiries into the merits as relevant to certification and usually place burdens of production and persuasion on the plaintiff; and super-weak rules which permit or require the court to investigate the class's chances of success in the litigation and place burdens of production and persuasion on the plaintiff. Parts II-VI compare these rules with respect to the values of fidelity to law, accuracy in adjudication, fairness in judgments, fairness in settlements, and judicial economy. Part VII argues that weak-form rules are superior to the alternative approaches.
Doubled-layered polycrystalline cadmium sulfide on lithium niobate (1978)

We have developed a technique for fabricating polycrystalline thin films of CdS on z-cut LiNbO3. A single film will show a light-to-dark–conductivity ratio of approximately unity with very high sheet resistance after curing. To make a good photoconductor, a second film is then deposited. This film is protected during the subsequent curing from out-diffusion from the LiNbO3 by the first film and develops a light-to-dark–conductivity ratio of 10 000 in room light with a sheet conductivity of 10−10 s/⧠ mcd. Films produced by this layered process also possess a remarkably large conductivity-modulation dependence (20%) on the square of an impressed electric field provided by a traveling surface acoustic wave in the LiNbO3 substrate.
The Src Family Kinase c-Yes Is Required for Maturation of West Nile Virus Particles (2005)

ABSTRACT The role of cellular genes in West Nile virus (WNV) replication is not well understood. Examination of cellular transcripts upregulated during WNV infection revealed an increase in the expression of the src family kinase (SFK) c-Yes. WNV-infected cell lines treated with the SFK inhibitor PP2 demonstrated a 2- to 4-log decrease in viral titers, suggesting that SFK activity is required for completion of the viral replication cycle. RNA interference mediated knock-down of c-Yes, but not c-Src, and similarly reduced virus yield, specifically implicating c-Yes in WNV production. Interestingly, PP2 treatment did not reduce intracellular levels of either viral RNA or protein, suggesting that the drug does not act on the early stages of replication. However, endoglycosidase H (endoH) digestion of the viral envelope (E) glycoprotein revealed that the acquisition of endoH-resistant glycans by E, but not endogenous major histocompatibility complex class I, was reduced in PP2-treated cells, demonstrating that E specifically does not traffic beyond the endoplasmic reticulum in the absence of SFK activity. Electron microscopy further revealed that PP2-treated WNV-infected cells accumulated an increased number of virions in the ER compared to untreated cells. Therefore, we conclude that inhibition of SFK activity did not interfere with virus assembly but prevented transit of virions through the secretory pathway. These results identify c-Yes as a cellular protein that is involved in WNV assembly and egress.
Experimental Study on the Compressive Strength of Nano-Concrete (2014)

In order to investigate the effect of Nano-SiO 2 on the compressive strength of concrete, the paper studies the effect of different mixing ratios (0%~3%) on the compressive strength, and the effect of age on the compressive strength of nano-concrete. Research shows that the incorporation of Nano-SiO 2 increased the compressive strength of concrete: it increases slowly with the mixing ratio 0%~1%; the growth rate is declining when the mixing ratio is 1.5%~3%; the optimal mixing ratio is 1.0~1.5%, which can replace 3.33~10% of cement.
A Novel Method to Balance and Reconfigure Series-Connected Battery Strings (2016)

Cell failure and imbalance are critical problems in battery storage systems, especially in series-connected battery strings. The reconfiguration function and the balancing function are both of great importance, but it is very challenging and problematic to own both functions simultaneously. This paper attempts to make contributions on realizing both functions through new circuits and new control strategies. Firstly, a reconfigurable balancing circuit is proposed, which is able to simultaneously balance and reconfigure the battery string. In the circuits, a new way to achieve passive balancing with no bleeding resistor is realized, and the failure cells in the battery string can be bypassed with the same circuits. By taking advantage of fewer switches in the circuits, the method owns the merits of low cost and low system complexity. Secondly, to efficiently balance and reconfigure the battery string, a control strategy is proposed according to the unique structure of the circuits. Thirdly, the reconfigurable balancing circuits are fabricated and an experimental test workbench is established. The reconfigurable balancing circuits and the control strategy are validated in the experimental test workbench. The experimental results indicate that the proposed method is able to realize both the balancing function and the reconfiguration function well, and the performance of the battery string can be maintained and improved significantly. The improvements are 13% and 34% for 4 cell- and 100 cell- series-connected battery strings, respectively.
Validating physics-based clutter from seafloor roughness and biologic scattering (2006)

Two physics-based clutter models were developed for comparison and to study the merits and limitations of both approaches. The stochastic approach [Newhall and Arvelo, J. Acoust. Soc. Am. 118, 2041 (2005)] makes use of perturbation theory, to relate the mean seafloor scattering strength to the mean surface wavenumber spectrum, and the extrapolation of this spectrum to the Bragg wavenumber to generate the clutter distribution from the seafloor roughness. The semi-deterministic approach [Monjo and Arvelo, J. Acoust. Soc. Am. 118, 2041 (2005)] is based on 2-D power-law fractal realizations of the ocean floor, coherent modal addition, and the microscale bathymetric slopes. Biologic scattering was later included where spatial distribution and nonstationarity of schools of fish and individual marine mammals are realistically represented [Frankel et al. J. Acoust. Soc. Am. 119, 3437 (2006)] through individual-based modeling of their movements, school size, and target strengths. Clutter distributions from both approaches are compared against each other, for selected test cases, and against clutter measurements. [This effort was funded by the Maritime Sensing Program of the Office of Naval Research (ONR Code MS 321).]
Numerical simulation of flow in fluidized beds (2015)

The article provides a brief overview of a one-dimensional model of two-phase flow in the geometry of a circulating fluidized bed combustor exhibiting vertical variability of cross-section.The model is based on numerical solution of conservation laws for mass, momentum and energyof gas and solid components of the fluidized-bed system by means of the finite-volume method in space and of a multistep higher-order solver in time.The presented computational results reproduce characteristic behavior of fluidized beds in the given geometry.
DNA-Encoded Chemistry: Drug Discovery from a Few Good Reactions (2020)

Click chemistry, proposed nearly 20 years ago, promised access to novel chemical space by empowering combinatorial library synthesis with a "few good reactions". These click reactions fulfilled key criteria (broad scope, quantitative yield, abundant starting material, mild reaction conditions, and high chemoselectivity), keeping the focus on molecules that would be easy to make, yet structurally diverse. This philosophy bears a striking resemblance to DNA-encoded library (DEL) technology, the now-dominant combinatorial chemistry paradigm. This review highlights the similarities between click and DEL reaction design and deployment in combinatorial library settings, providing a framework for the design of new DEL synthesis technologies to enable next-generation drug discovery.