gebhart/patrepeval huggingface dataset:
Faculty Opinions recommendation of Conversion of Helicobacter pylori CagA from senescence inducer to oncogenic driver through polarity-dependent regulation of p21. (2010)

The Helicobacter pylori CagA bacterial oncoprotein plays a critical role in gastric carcinogenesis. Upon delivery into epithelial cells, CagA causes loss of polarity and activates aberrant Erk signaling. We show that CagA-induced Erk activation results in senescence and mitogenesis in nonpolarized and polarized epithelial cells, respectively. In nonpolarized epithelial cells, Erk activation results in oncogenic stress, up-regulation of the p21(Waf1/Cip1) cyclin-dependent kinase inhibitor, and induction of senescence. In polarized epithelial cells, CagA-driven Erk signals prevent p21(Waf1/Cip1) expression by activating a guanine nucleotide exchange factor-H1-RhoA-RhoA-associated kinase-c-Myc pathway. The microRNAs miR-17 and miR-20a, induced by c-Myc, are needed to suppress p21(Waf1/Cip1) expression. CagA also drives an epithelial-mesenchymal transition in polarized epithelial cells. These findings suggest that CagA exploits a polarity-signaling pathway to induce oncogenesis. PMID: 20855497
Pilus-mediated adherence of Escherichia coli K1 to human oral epithelial cells (1984)

We examined the effect of host age and health status on the adherence of mannose-sensitive piliated Escherichia coli K1 to human oral epithelial cells. Mannose-sensitive piliated bacteria adhered in comparable numbers to newborn, older infant, and adult cells (125 +/- 61, 198 +/- 54, and 139 +/- 69 bacteria per cell, respectively). Prematurity and serious illness did not alter adherence in newborns. The increased susceptibility of premature newborns to E. coli K1 cannot be explained by enhanced epithelial cell adherence.
First-in-Human Trial of Epichaperome-Targeted PET in Patients with Cancer (2020)

Our first-in-human results demonstrate the safety and feasibility of noninvasive <i>in vivo</i> detection of tumor epichaperomes using <sup>124</sup>I-PU-H71 PET, supporting clinical development of PU-H71 and other epichaperome-targeted therapeutics.
A pleurocidin analogue with greater conformational flexibility, enhanced antimicrobial potency and in vivo therapeutic efficacy (2020)

Antimicrobial peptides (AMPs) are a potential alternative to classical antibiotics that are yet to achieve a therapeutic breakthrough for treatment of systemic infections. The antibacterial potency of pleurocidin, an AMP from Winter Flounder, is linked to its ability to cross bacterial plasma membranes and seek intracellular targets while also causing membrane damage. Here we describe modification strategies that generate pleurocidin analogues with substantially improved, broad spectrum, antibacterial properties, which are effective in murine models of bacterial lung infection. Increasing peptide-lipid intermolecular hydrogen bonding capabilities enhances conformational flexibility, associated with membrane translocation, but also membrane damage and potency, most notably against Gram-positive bacteria. This negates their ability to metabolically adapt to the AMP threat. An analogue comprising D-amino acids was well tolerated at an intravenous dose of 15 mg/kg and similarly effective as vancomycin in reducing EMRSA-15 lung CFU. This highlights the therapeutic potential of systemically delivered, bactericidal AMPs.
Interactions between residues 2228–2240 within factor VIIIa C2 domain and factor IXa Gla domain contribute to propagation of clot formation (2011)

Factor (F)VIII functions as a cofactor in the tenase complex responsible for phospholipid (PL)-dependent FXa generation by FIXa. We have recently reported that the FVIIIa C2 domain (residues 2228-2240) interacts with the FIXa Gla domain in this complex. We examined the role of this interaction in the generation of tenase activity during the process of clot formation, using a synthetic peptide corresponding to residues 2228-2240. The peptide 2228-2240 inhibited FVIIIa/FIXa-mediated FX activation dose-dependently in the presence of PL by >95% (IC50; ~10 μM). This effect was significantly greater than that obtained by peptide 1804-1818 (IC50; ~180 μM) which corresponds to another FIXa-interactive site in the light chain that provides the majority of binding energy for FIXa interaction. Peptide 2228-2240 had little effect on the prothrombin time and did not inhibit FIX activation in the coagulation process mediated by FVIIa/tissue factor or FXIa, suggesting specific inhibition of the intrinsic tenase complex. Clot waveform analysis, a plasma based-assay used to evaluate the process of intrinsic coagulation, demonstrated that peptide 2228-2240 significantly depressed both maximum coagulation velocity (|min1|) and acceleration (|min2|), reflecting the propagation of clot formation, although the clotting time was only marginally prolonged. Thromboelastography, an alternative whole blood based-assay, demonstrated that the peptide inhibited clot formation time, α-angle and maximal clot firmness, but had little effect on the clotting time. Interactions of the FVIIIa C2 domain (residues 2228-2240) with the FIXa Gla domain in the tenase complex appeared to contribute essentially to the propagation of clot formation.
One-Pot Synthesis of Keto Thioethers by Palladium/Gold-Catalyzed Click and Pinacol Reactions (2014)

An atom-efficient synthesis of keto thioethers was devised via tandem gold/palladium catalysis. The reaction proceeds through a regioselective thiol attack at the β-position of the alcohol, followed by an alkyl, aryl, or benzyl 1,2-shift. Both acyclic and cyclic systems were studied, in the latter case leading to the ring expansion of cyclic substrates.
Sensitizing Cancer Cells to TRAIL-Induced Death by Micellar Delivery of Mitoxantrone (2013)

TNFα-related apoptosis-inducing ligand (TRAIL) induces death selectively in cancer cells. However, subpopulations of cancer cells are either resistant to or can develop resistance to TRAIL-induced death. As a result, strategies that overcome this resistance are currently under investigation. We have recently identified several US FDA-approved drugs with TRAIL-sensitization activity against prostate, breast and pancreatic cancer cells. Mitoxantrone, a previously unknown TRAIL sensitizer identified in the screen, was successfully encapsulated in methoxy-, amine- and carboxyl-terminated PEG-DSPE micelles in order to facilitate delivery of the drug to cancer cells. All three micelle types were extensively characterized for their physicochemical properties and evaluated for their ability to sensitize cancer cells to TRAIL-induced death. Our results indicate that micelle-encapsulated mitoxantrone can be advantageously employed in synergistic treatments with TRAIL, leading to a biocompatible delivery system and amplified cell killing activity for combination chemotherapeutic cancer treatments.
Secondary structure of the circular form of the Tetrahymena rRNA intervening sequence: a technique for RNA structure analysis using chemical probes and reverse transcriptase. (1985)

The structure of the intervening sequence (IVS) of the Tetrahymena rRNA precursor mediates cleavage-ligation reactions that result in pre-rRNA splicing and IVS cyclization. We have developed a method for RNA structure analysis and applied it to the circular form of the IVS RNA. The native RNA was treated with dimethyl sulfate or diethyl pyrocarbonate to modify bases not involved in secondary or tertiary interactions. The RNA was then used as a template for reverse transcription. Elongation of synthetic oligodeoxynucleotide primers was found to stop (or pause) one nucleotide prior to 1-methyladenosine, 3-methylcytidine, and 7-ethoxycarbonyladenosine residues. The detection of 1-methyladenosine is particularly useful for locating single-stranded regions. After chemical cleavage of the RNA, 7-methylguanosine also could be detected. In general, the sites of modification were consistent with a previous model of the secondary structure of the linear form of the IVS RNA, a model based on enzymatic cleavage data, free energy calculations, and phylogenetic comparison. Thus, IVS RNA autocyclization does not involve major rearrangements of the secondary structure, although there is evidence for a conformational change in one region of the molecule. The methods described here should be of general use for obtaining information about structure far from the ends of RNA molecules.
Utilization of Electropolymerized Films of Cobalt Porphyrin for the Reduction of Carbon Dioxide in Aqueous Media (2016)

Abstract A facile electropolymerization process was utilized to prepare electrodes modified with thin films of cobalt protoporphyrin IX. These thin films exhibited a high Faradaic efficiency (84±2 %) for the reduction of CO 2 to CO in aqueous solutions near neutral pH with 450 mV of overpotential and a turnover frequency at zero overpotential (log(TOF 0 )) of −5.9. The production of CO was stable over several hours at these modest potentials. The use of a 13 CO 2 reactant led exclusively to 13 CO as the product. Polymeric films of the unmetalated porphyrin did not demonstrate catalysis for CO 2 reduction. UV/Vis spectroelectrochemical experiments indicate that the parent Co II complex is reduced to Co I at the electrode surface before interaction with CO 2 . It is proposed that the rate‐determining step in the reduction of CO 2 is the initial reduction of the Co II moiety to Co I , which binds CO 2 and then undergoes a proton‐coupled electron transfer and a loss of water to form CO. Additionally, a new metric for the evaluation of electrocatalysts, the catalytic efficiency, is proposed. The catalytic efficiency is the ratio of the power stored to power consumed for a given electrochemical reaction and can be used to describe both the kinetics and overpotential considerations of a given system.
Effect of Pneumococcal Vaccination on Nasopharyngeal Carriage of Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Staphylococcus aureus in Fijian Children (2011)

The 7-valent pneumococcal conjugate vaccine (PCV7) reduces carriage of vaccine type Streptococcus pneumoniae but leads to replacement by nonvaccine serotypes and may affect carriage of other respiratory pathogens. We investigated nasopharyngeal carriage of S. pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Staphylococcus aureus in Fijian infants participating in a pneumococcal vaccine trial using quantitative PCR. Vaccination did not affect pathogen carriage rates or densities, whereas significant differences between the two major ethnic groups were observed.
A Novel Content-Aware Stitching Algorithm for Real-Time Video Sequences (2011)

The panorama image obtained by image stitching can have visible artifacts due to the limitation of alignment accuracy and defects of the optical systems. Moreover, conventional image stitching algorithms cannot be directly applied to a real-time video stitching due to its complexity and waving artifacts. In this paper, we propose a real-time content-aware stitching algorithm which not only finds a seam by using path searching based on the greedy method, but also adaptively updates the seam by detecting objects moving toward the seam. Experimental results show that the proposed algorithm can successfully produce stitched video sequences without the waving and ghost artifacts commonly found in conventional stitching algorithms.
On the Evolution of Amplitude Modulated Excitation in Still Air (2011)

Active flow control that is coupled with flow instability has the potential to be energy efficient. However, many applications especially those characterized by large dimensions and low speeds dictate Strouhal numbers which require low frequencies, typically below 100Hz. These frequencies can be orders of magnitude smaller than the efficient operating frequency of common zero-mass-flux actuators. Therefore, the effects of different excitation modes, capable of generating low frequencies from actuators resonating at much higher frequencies, were studied experimentally. The excitation signals included a pure sine wave (as a reference) and amplitude modulated sine wave, in order to generate low frequency excitation through nonlinearity. Detailed particle image velocimetry (PIV) and hot wire measurement are presented and discussed.The findings of the current study show that when the actuator operates in still air and is excited by a pure sine wave, the nominally 2D excitation creates a train of quasi-2D vorte...
Suppression of diode emission in the triode CNT field emitter arrays by forming the electroplated Ni wall structure (2002)

In this paper, the electroplated Ni wall structure (NWS) is applied to screen-printed carbon nanotube (SPCNT) field emitter arrays (FEAs) to suppress the diode emission during triode operation of the FEAs.
Mutational analysis of cytocentrifugation supernatant fluid from pancreatic solid mass lesions (2013)

Diagnosis of fine-needle aspirations of pancreatic solid masses is complicated by many factors that keep its false-negative rate high. Our novel approach analyzes cell-free cytocentrifugation supernatant, currently a discarded portion of the specimen. Supernatant and cytology slides were collected from 25 patients: 11 cases with confirmed outcome [five positive (adenocarcinoma) and six negative (inflammatory states)], plus 14 without confirmed outcomes. Slides were microdissected, DNA was extracted from microdissections and corresponding supernatants, and all were analyzed for KRAS point mutation and loss of heterozygosity. Notably, higher levels of free DNA were found in supernatants than in corresponding microdissected cells. Supernatants contained sufficient DNA for mutational profiling even when samples contained few to no cells. Mutations were present in 5/5 malignancies and no mutations were present in inflammatory states. In conclusion, these findings support using supernatant for mutational genotyping when diagnostic confirmation is required for pancreatic solid masses.
Electric-field-induced deformation dynamics of a single nematic disclination (2005)

Disclinations in nematic liquid crystals usually adopt a straight shape in order to minimize their elastic energy. Once created in the course of a nonequilibrium process such as a temperature quench from the isotropic to the nematic phase, the topologically stable disclinations of half-integer strength either annihilate each other in pairs of opposite strength or form topologically unstable disclinations of integer strength. In this article, we demonstrate that the annihilation process can be inhibited and the defects can be deformed by an applied electric field. We study the disclination lines in the deep uniaxial nematic phase, located at the boundary between two different types of walls, the so-called pi wall (a planar soliton stabilized by the surface anchoring) and the Brochard-Léger (BL) wall stabilized by the applied electric field. By changing the electric voltage, one can control the energy of director deformations associated with the two walls and thus control the deformation and dynamics of the disclination line. At small voltages, the disclinations are straight lines connecting the opposite plates of the cell, located at the two ends of the pi walls. The pi walls tend to shrink. When the voltage increases above E(F), the Fréedericksz threshold, the BL walls appear and connect pairs of disclinations along a path complementary to the pi wall. At E>2 E(F), the BL walls store sufficient energy to prevent shrinking of the pi walls. Reconstruction of the three-dimensional director configuration using a fluorescent confocal polarizing microscopy demonstrates that the disclinations are strongly bent in the region between the pi and the BL walls. The distortions and the related dynamics are associated with the transformation of the BL wall into two surface disclination lines; we characterize it experimentally as a function of the applied electric field, the cell thickness, and the sample temperature. A simple model captures the essential details of the experimental data.
Tristimulus Colorimetric Metasurface: Mimicking the Human Eye (2022)

Using local and nonlocal optimization, we design and fabricate a metasurface to mimic the color response and focusing functions of the human eye. Qualitative match between the theory and experiment have been measured.
Conductivity Measurements of Few Molecule Systems in Metal-Molecule-Metal device Structures (2006)

In this paper, we have developed a technique for realizing ultraflat Au using a procedure that should be compatible with microfabricating techniques. We have applied the resulting Au layers in both lateral (few molecule) and vertical (many molecules) molecular electronic device structures. The lateral and vertical device structures are both enabled by the process for realizing ultraflat Au layer. The availability of two molecular test beds provides the ability to compare molecular conduction properties in different local environments. Experiments are in progress to compare conduction properties of various molecular species in the two test beds
Deep cytometry (Conference Presentation) (2019)

Flow cytometry is the standard tool for blood analysis which generates information gathered from the interaction of lasers with cell flowing in a stream to classify them based on their size, granularity and fluorescent emission from biomarkers used as labels. However, for many emerging applications the use of labels is undesirable because they alter the cell behavior through activation or inhibition of cellular functions and hinder downstream genetic studies. We have previously described an ultrahigh-throughput label-free imaging ﬂow cytometer that analyzes cells using their biophysical features. Label-free ultrafast imaging in flow is implemented by photonic time stretch and the trade-off between sensitivity and speed is mitigated by using ampliﬁed time-stretch dispersive Fourier transform, a technique that was originally developed to enable realtime analog-to-digital data conversion with femtoseconds sampling resolution. In the application to time stretch to imaging, cells are illuminated by spatially dispersed broadband pulses, and the spatial features of the target are encoded into the short pulse spectrum. Both phase and intensity images are simultaneously captured, and this provides ample features such as the concentration of proteins, optical loss, and cell morphology, which are then used by a neural network to classify cells. However, image processing needed to extract these features from label-free images takes time and renders this technique unsuitable for cell sorting where decisions must be made in realtime before cells exist the fluidic stream. To eliminate this predicament we have a deep convolutional neural network that directly processes the raw time stretch waveforms from the imaging ﬂow cytometer. Eliminating the requirement of an image processing pipeline prior to the classiﬁer, the running time of cell analysis can be reduced signiﬁcantly, and cell sorting decisions can be made in less than a millisecond, orders of magnitude faster than the previous state of the art.
In Vivo Microscopy for Real-Time Structural and Functional Cellular Imaging. (2007)

Current medical practice is moving towards more quantitative and personalized methods of diagnosis and decisionmaking. This has led to a need for more complex and detailed patient-specific digital models. The resolution at which the model is described is important and may vary from macroscopic to microscopic and even molecular scales, ideally through multiscale descriptions. As these individualized models start to integrate knowledge of cellular dynamics, it becomes crucial to acquire patientspecific information at the cellular level.
Axillary to Common Iliac Arteriovenous Graft for Hemodialysis Access: Case Report and Review of “Exotic” Axillary-Based Grafts (2005)

A 58-year-old Caucasian male with end-stage renal disease and peripheral arterial disease was referred to us for management of his complex vascular access. His vascular access history included a left wrist primary fistula, a left upper arm access graft, a left leg loop graft, and multiple PermCaths in his jugular veins with recurrent infections. Magnetic resonance venography (MRV) of his chest revealed extensive bilateral venous occlusions due to numerous past hemodialysis access catheters. The patient was scheduled for right lower extremity arteriovenous graft placement, but intraoperatively was found to have severe peripheral arterial disease and a thromboendarterectomy was performed instead. Lower body venous imaging demonstrated patent iliac veins. Based on these anatomic considerations a right axillary artery to right common iliac vein polytetrafluoroethylene (PTFE) graft was placed. The graft required revision twice--once for graft ultrafiltration at the arterial end of the graft and once for needle stick infection--but continues to serve as sufficient access after 15 months. Grafts based off the axillary artery have become increasingly popular in recent years and several venous outflow options have been considered, each with distinct advantages. The common iliac vein offers a central location with high flow rate and low probability of infection. Axillary artery to iliac vein arteriovenous grafting may have a place in the vascular surgeon's armamentarium for complex vascular access cases.
Pre-Colonial Zuruland - Studies in the History of the People of the Zuru Emirate. Edited by A. R. Augi and S. U. Lawal. Enugu, Nigeria: Fourth Dimension Publishing, 1990. Pp. xvi+192. £16.75; $30 (paperback £12; $21.50). (1993)

Pre-Colonial Zuruland - Studies in the History of the People of the Zuru Emirate. Edited by A. R. Augi and S. U. Lawal. Enugu, Nigeria: Fourth Dimension Publishing, 1990. Pp. xvi+192. £16.75; 21.50). - Volume 34 Issue 1
AI SoC Design Challenges in the Foundation Model Era (2023)

Despite its unprecedented prevalence, a foundation model’s exponentially growing training cost, dataset sizes, and model capacity hinder the democratization of modern AI technology and require novel system design solutions. In this paper, we review state-of-the-art (SOTA) challenges and methodologies in scaling AI system-on-chip (SoC) design to harness the power of the foundation model. We organize our discussions four-fold. First, we discuss AI SoC architecture design to enable high-performance training for foundation models. Second, we discuss challenges in managing foundation model training with dataflow accelerators. We show that data flow accelerators, a class of promising architectures removing execution bottlenecks through overlapping computation and data fetching, pose new challenges for hardware resource mapping and allocation. Third, we discuss challenges for exploiting parallelism encompassing multiple dimensions, e.g., tensor, model, and data-level parallelism. Mapping models over tensor and model dimensions enables large model training at the cost of introducing distributed and orchestrated gradient synchronization. Last, we discuss electrical and energy design trade-offs for implementing massive computation and memory units capturing computation and data locality on a dataflow accelerator. The solution to all four aspects lies at the intersection of system-aware machine learning algorithms, dataflow-driven software systems, and scalable hardware design.