gebhart/patrepeval huggingface dataset:
The Stability of L3 Sponge Phase in Acidic Solutions (2006)

In the synthesis of the disordered lyotropic liquid crystalline L3 sponge phase prepared with the cosurfactants cetylpyridinium chloride and hexanol, aqueous NaCl solution is used as the solvent. When this sponge phase is used as the template for L3 silica-phase processing, we replace NaCl with HCl to facilitate the acid catalysis of tetramethoxysilane in forming a templated silica gel, assuming that changing the solvent from NaCl(aq) to HCl(aq) of equivalent ionic strength does not affect the stability range of the L3 phase. In this work, we confirm that changing the pH of the solvent from neutral to acidic (with HCl) has negligible effect on the L3 phase region. Equivalent ionic strength is provided by either NaCl(aq) or HCl(aq) solvent; therefore, a similar phase behavior is observed regardless of which aqueous solvent is used.
Quantitation and Identification of Antibodies to Outer-Membrane Proteins of Pseudomonas aeruginosa in Sera of Patients with Cystic Fibrosis (1984)

Chronic, overwhelming pulmonary infection with Pseudomonas aeruginosa is a frequent problem in patients with cystic fibrosis. Titers of antibody to the outer-membrane proteins of P aeruginosa were 10(1)-10(8) (as measured by an enzyme-linked immunosorbent assay) in the sera of 32 patients with cystic fibrosis. Fifteen patients who had been colonized with P aeruginosa for 18 months to nine years had a geometric mean antibody titer of 1.3 X 10(5)--a value approximately 500-fold higher than that for 13 patients with cystic fibrosis who had never been colonized or for 16 healthy adults without cystic fibrosis (P less than 0.001). A significant correlation was observed between the presence of antibody to outer-membrane proteins and the presence of antibody to mucoid exopolysaccharide (P less than 0.002). Nineteen serum specimens from the patients with cystic fibrosis were allowed to react with Western electophoretic blots of separated outer-membrane proteins. All of these sera contained antibodies to porin protein F. In addition, antibodies to outer-membrane proteins E, H2, and I and to a variety of minor protein components were observed in many sera.
Reduction-Responsive Polymeric Micelles and Vesicles for Triggered Intracellular Drug Release (2013)

Biophysical studies should be carried out to gain insight into the degradation and drug release behaviors of reduction-responsive nanocarriers inside the tumor cells. Furthermore, novel ligand-decorated reduction-sensitive nanoparticulate drug formulations should be designed and explored for targeted cancer therapy in vivo.
Increased phosphorylation of ACTN4 leads to podocyte vulnerability and proteinuric kidney disease and is stimulated by high glucose and TGF‐b (2020)

Defects in the podocyte cytoskeleton contribute to podocyte vulnerability within the glomerulus and proteinuric kidney disease. Genetic mutations in ACTN4—an essential crosslinker of the actin cytoskeleton—have been linked to proteinuric kidney disease in humans. However, how post‐translational modifications of ACTN4 affect podocyte integrity and kidney function remain unknown. We detected phosphorylation of ACTN4 at serine 159 (S159) by mass spectrometry. Our ACTN4 X‐ray crystal structure showed that phosphomimetic S159D ACTN4 changes the charge at S159 without changing the protein’s conformation. Phosphomimetic Actn4 mouse models were generated using CRISPR/Cas9 technology, and these mice developed proteinuria and glomerulosclerosis after subtotal nephrectomy. The link between ACTN4 phosphorylation at S159 and renal pathology prompted us to use targeted mass spectrometry to identify upstream signaling pathways that might increase ACTN4 phosphorylation at S159. Since high extracellular glucose and TGF‐b can both lead to kidney disease and podocyte dysfunction, we examined whether these stimuli lead to increased ACTN4 phosphorylation at S159. We found that mean S159 phosphorylation was nearly 2‐fold higher in podocytes treated with high glucose vs mannitol control (p&lt;0.05). Similarly, mean S159 phosphorylation was nearly 2‐fold higher in the podocytes treated with TGF‐b vs in untreated podocytes (p&lt;0.05). Moreover, we quantified the F‐actin alignment in phalloidin‐stained podocytes. WT podocytes treated with high glucose demonstrated more spatially correlated F‐actin alignment, similar to the alignment seen in phosphomimetic Actn4 podocytes but different from nonphosphorylatable Actn4 podocytes. Our findings suggest that ACTN4 may mediate podocyte injury as a consequence of both genetic mutations and signaling events that modulate phosphorylation. Future studies using whole animal models and human samples should determine the extent to which the detrimental effects of high glucose on the kidney are mediated by phosphorylation of ACTN4. Support or Funding Information K01DK114329, R37DK059588 and Wyss Institute for Biologically Inspired Engineering at Harvard University
<title>New method of aberration correction for ultrasonic brain imaging</title> (2001)

Ultrasonic imaging systems capabilities are strongly dependent on the focusing quality of the ultrasonic beam. In the case of brain imaging, the skull strongly degrades the ultrasonic focusing pattern by introducing strong phase and amplitude aberrations of the wavefront. In previous work, this degradation of the beam focus has been partially corrected by coupling the time reversal focusing process to an amplitude compensation of the emitted signals. In that case, the optimal focus was reproduced down to -20 dB, but the sidelobe level remained at about -25 dB. We propose here a new focusing technique, called spatio- temporal inverse filter, based on the inversion of the propagation operator at each frequency within the bandwidth of our transducers. Simulations and experiments will be presented that show the effectiveness of the technique. Experimental focusing through the skull is now comparable to the optimal focusing in homogeneous medium. It will be explained how the set of emission signals can be used in order to achieve both transmit and receive focusing. In the transmit-receive mode, focusing through the skull reaches the optimal level obtained in water down to -70 dB (i.e. constrained only by experimental noise levels). This could lead to high quality real time brain imaging and Doppler flow mapping.
CLINICAL CONTRAST RESEARCH OF OPTIMAL TIME WINDOW IN DIRECT PCI TREATMENT OF ELDERLY PATIENTS WITH ACUTE MYOCARDIAL INFARCTION (2012)

Objectives To investigate the optimal time window in treatment of elderly patients with acute myocardial infarction and primary percutaneous coronary intervention (PCI). Methods 196 patients were divided into three groups according to their symptom-to-balloon time: group A (&lt;3 h, n=48), group B (≥3 h, &lt;6 h, n=67) and group C (≥6 h, &lt;12 h, n=81). Achievement of TIMI grade 3 blood flow, degree of ST-segment resolution, left ventricular ejection fraction (LVEF) and the incidence of major adverse cardiac events (MACE) in hospital were compared among the three groups. Results The rate of postoperative TIMI grade 3 and LVEF in group A was significantly higher than those in group B and group C. The incidence of no ST-segment resolution and MACE in hospital in group A were significantly lower than those in group B and group C. There were no differences between group B and group C in terms of TIMI grade 3 achievement, ST-segment resolution, LVEF and incidence of MACE in hospital. Conclusions Compared with PCI 3 h after the onset of symptom, early PCI (&lt;3 h) can improve the rate of TIMI grade 3 achievement, myocardial reperfusion and LVEF, and reduce MACE in hospital.
Self-Referenced 32-kHz Rotating Capacitor Relaxation Oscillator with Chopped Comparator Offset-Voltage Cancellation (2021)

This work presents a novel relaxation oscillator architecture using a rotating capacitor integrator and a chopped comparator. The oscillator is self-referenced, using the resistor instead of the current source, together with the reference voltage realized with the resistor divider connected to the supply voltage. The oscillator prototype is designed and manufactured in 180 nm technology, typically consumes 1.5 µA at 32 kHz, has a frequency variation of ±0.44% in the temperature range from −40 to 105°C and ±0.3% in the power supply range from 1.62 to 1.98 V. The oscillator has a start-up time of 15.4 µs and is operational in the low supply voltage range.
Some conjectures on the behavior of acknowledgement-based transmission control of random access communication channels (1987)

A class of acknowledgment-based transmission control algorithms is considered. In the finite population case, we claim that algorithms based on backoff functions which increase faster than linearly but slower than exponentially are stable up to full channel capacity, whereas sublinear, exponential, and superexponential algorithms are not. In addition, comments are made about the nature of the quasistationary behavior in the infinite population case, and about how systems interpolate between the finite and infinite number of station cases. The treatment presented here is nonrigorous, consisting of approximate analytic arguments confirmed by detailed numerical simulations.
Teaching networking hardware (2005)

We present our experience with the design and teaching of a graduate-level networking hardware course in which students design and build an Internet router. Each team of two students (one proficient in hardware and one proficient in software) design and develop a fully functional router that routes live Internet traffic and inter-operates with other students' routers via a simple routing protocol. Hardware is designed in Verilog using an industry-standard design flow on a specially designed platform, called NetFPGA. Software is written in user-space using a high-level language. Software and hardware are combined and tested using real network traffic over arbitrary private topologies using a custom tool, called VNS. Our approach is distinguished in that both hardware and software can be designed, tested and deployed remotely over the Internet. Our goal is to give students experience in the design of complex networking systems. In our initial course offering in Spring 2004, all teams successfully implemented fully functional routers in less than ten weeks. We will pilot courses outside of Stanford using the remote teaching infrastructure presented in this paper.
Fluorous methods for synthesis and separation of organic molecules (2000)

Abstract Fluorous molecules partition out of an organic phase and into a fluorous (highly fluorinated) phase in a liquid-liquid extraction. New fluorous techniques allow simple yet substantive separations of organic reaction mixtures based on the presence or absence of a fluorous tag. Fluorous-tagged molecules can also be separated from nontagged molecules by solid phase extraction over fluorous reverse-phase silica gel. This technique is ideal for solution-phase parallel synthesis because it allows simple yet substantive separations of organic reaction mixtures.
Coalescence in blends of thermoplastic polyurethane with polyolefins (1999)

Abstract The coalescence behavior of immiscible blends was determined by annealing the melt without shear. The kinetics and the mechanism of coalescence were observed for blends of thermoplastic polyurethane (TPU) and polyolefins. Two different types of measurements were used to observe coalescence in quiescent melt at the processing temperature. On the one hand, the blend granules were annealed in bulk. The resulting particle sizes were determined by light microscopy and by SEM on particles separated from the blend. On the other hand, thin samples were annealed on a hot stage. Coalescence was observed in situ by light microscopy or static laser light scattering. It was found that the higher viscosity and elasticity ratios between polyethylene and TPU lead to a more pronounced coarsening of the morphology of 80/20 blends than in TPU/polypropylene. It has been shown that the process of reshaping coalescence is one mechanism of coalescence that occurs in quiescent melt. Another mechanism that was directly observed is a “domino effect” where one coalescence process causes the next one.
The oxidation of Fe(II) with Cu(II) in acidic sulfate solutions with air at elevated pressures (2018)

The oxidation of ferrous ions in acidic sulfate solutions in the presence of cupric ions at elevated air pressures was investigated in a high-intensity gas–liquid contactor. The study was required for the design of the regeneration steps of the novel Vitrisol® desulphurization process. The effects of the Fe2+ concentration, Cu2+ concentration, Fe3+ concentration, initial H2SO4 concentration, and partial oxygen pressure on the reaction rate were determined at three different temperatures, i.e., T = 50 °C, 70 °C, and 90 °C. Most of the experiments were determined to be affected by the mass transfer of oxygen, and therefore true intrinsic kinetics could not be fully determined. An increase in Fe2+ and Cu2+ concentrations, as well as the partial pressure of oxygen and temperature, increased the Fe2+ oxidation rate. H2SO4 did not influence the Fe2+ oxidation rate. An increase in Fe3+ concentration decreased the Fe2+ oxidation rate. Although determined from experiments partially affected by mass transfer, a first order of reaction in Fe2+ was observed, fractional orders in both Cu2+ and O2 were measured, a zero order in H2SO4 was determined, and a negative, fractional order in Fe3+ was obtained. The activation energy was estimated to be 31.3 kJ/mol.
Casing eccentering sensitivity of pulsed eddy current sensors in multiple-casing corrosion analysis (2019)

The performance and potential ambiguity in casing thickness evaluation using pulsed eddy current (PEC) measurement interpretation based on response time to depth mapping is assessed for realistic downhole settings. Casing eccentering sensitivity analysis based on 3D finite-element method is performed for PEC sensors of variable lengths. The effect of defect size, approaching defects and casing collars for three casing configurations is also studied to highlight the increased interpretation uncertainty in realistic noncentered environments.
Register file port requirements of transport triggered architectures (2005)

Exploitation of large amounts of instruction level parallelism requires a large amount of connectivity between the shared register file and the function units; this connectivity is expensive and increases the cycle time. This paper shows that the new class of transport triggered architectures requires fewer ports on the shared register file than traditional operation triggered architectures. This is achieved by programming data-transports instead of operations. Experiments with our extended basic block scheduler have shown that the reduction of the required number of register file ports is substantial. The average requirement for scalar applications is 0.50 read and 0.35 write ports per operation instead of 2 read and 1 write ports. Due to this reduction it is possible to execute 2 operations per cycle with a two-ported register file and 3.6 operations per cycle with a six-ported register file.
Carbamylated LL-37 as a modulator of the immune response (2016)

Carbamylation of lysine residues and protein N-termini is an ubiquitous, non-enzymatic post-translational modification. Carbamylation at sites of inflammation is due to cyanate formation during the neutrophil oxidative burst and may target lysine residues within the antimicrobial peptide LL-37. The bactericidal and immunomodulatory properties of LL-37 depend on its secondary structure and cationic nature, which are conferred by arginine and lysine residues. Therefore, carbamylation may affect the biological functions of LL-37. The present study examined the kinetics and pattern of LL-37 carbamylation to investigate how this modification affects the bactericidal, cytotoxic and immunomodulatory function of the peptide. The results indicated that LL-37 undergoes rapid modification in the presence of physiological concentrations of cyanate, yielding a spectrum of diverse carbamylated peptides. Mass spectrometry analyses revealed that theN-terminal amino group of Leu-1 was highly reactive and was modified almost instantly by cyanate to generate the predominant form of the modified peptide, named LL-37(C1) This was followed by the sequential carbamylation of Lys-8, Lys-12, and Lys-15 to yield LL-37(C8), and Lys-15 to yield LL-37(C12,15) Carbamylation had profound and diverse effects on the structure and biological properties of LL-37. In some cases, anti-inflammatory LL-37 was rapidly converted to pro-inflammatory LL-37.
A 2.6 mV/b Resolution, 1.2 GHz Throughput, All-Digital Voltage Droop Monitor Using Coupled Ring Oscillators in Intel 4 CMOS (2023)

We present an all-digital voltage droop monitor (VDM) with coupled ring-oscillators (CoRO) for accurate in-situ droop monitoring every clock cycle. Measurements from a 3.2mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> testchip in Intel 4 CMOS containing 9 3-way CoRO and baseline RO VDMs demonstrate 3X improvement in CoRO resolution $(\sim 2.6$ mV/b) over the baseline. In addition, measurements show $3 \sigma$ uncertainty (repeatability) error of CoRO VDM (+/-9mV) is $\sim25$ % lower than the baseline. The overall droop detection error improvements achieved by CoRO VDM are 12mV, 15mV and 17mV, respectively, depending on the type of calibration used - per instance/temperature/die, per temperature/die, or per die. This corresponds to associated IP power savings of 2.9%, 3.2% and 3.7% during functional use.
Fe3O4 Nanoparticles Confined in Mesocellular Carbon Foam for High Performance Anode Materials for Lithium‐Ion Batteries (2011)

Abstract Fe 3 O 4 nanocrystals confined in mesocellular carbon foam (MSU‐F‐C) are synthesized by a “ host–guest ” approach and tested as an anode material for lithium‐ion batteries (LIBs). Briefly, an iron oxide precursor, Fe(NO 3 ) 3 ·9H 2 O, is impregnated in MSU‐F‐C having uniform cellular pores ∼30 nm in dia­meter, followed by heat‐treatment at 400 °C for 4 h under Ar. Magnetite Fe 3 O 4 nanocrystals with sizes between 13–27 nm are then successfully fabricated inside the pores of the MSU‐F‐C, as confirmed by transmission electron microscopy (TEM), dark‐field scanning transmission electron microscopy (STEM), energy dispersive X‐ray spectroscopy (EDS), X‐ray diffraction (XRD), and nitrogen sorption isotherms. The presence of the carbon most likely allows for reduction of some of the Fe 3+ ions to Fe 2+ ions via a carbothermoreduction process. A Fe 3 O 4 /MSU‐F‐C nanocomposite with 45 wt% Fe 3 O 4 exhibited a first charge capacity of 1007 mA h g −1 (Li + extraction) at 0.1 A g −1 (∼0.1 C rate) with 111% capacity retention at the 150 th cycle, and retained 37% capacity at 7 A g −1 (∼7 C rate). Because the three dimensionally interconnected open pores are larger than the average nanosized Fe 3 O 4 particles, the large volume expansion of Fe 3 O 4 upon Li‐insertion is easily accommodated inside the pores, resulting in excellent electrochemical performance as a LIB anode. Furthermore, when an ultrathin Al 2 O 3 layer (&lt;4 Å) was deposited on the composite anode using atomic layer deposition (ALD), the durability, rate capability and undesirable side reactions are significantly improved.
Supplementary Figure 2 from Upregulation of ER Signaling as an Adaptive Mechanism of Cell Survival in HER2-Positive Breast Tumors Treated with Anti-HER2 Therapy (2023)

&lt;p&gt;Supplementary Figure 2. ER expression changes upon neoadjuvant treatment with trastuzumab&lt;/p&gt;
Quantification of HFV-Integrated DNA in Human Cells by <I>Alu</I>-LTR Real-Time PCR (2005)

Integration is described as a key step in viral replication of all retroviruses. A sensitive and quantitative measure of an integrated molecule is a good way to examine the importance of the integration step and to evaluate efficiency of retroviral vectors for gene transfer or anti-integrase drugs. Here, we report a sensitive and quantitative real-time polymerase chain reaction (PCR) technique to measure integrated viral DNA in human cells during a foamy virus (HFV) infection. This technique is based on two steps of PCR. The first round amplifies Alu-LTR (long terminal repeat) sequences resulting from viral integration. The second round of PCR is performed to quantify these events of integration. Quantification is monitored by the comparison of the amplification curve of the sample against a standard scale constituted of viral DNA from chronically infected cells. Sensitivity of this technique allows us to detect as few as 25 copies of HFV-integrated DNA in 50,000 cells.
On the Number of Samples Needed to Learn the Correct Structure of a Bayesian Network (2012)

Bayesian Networks (BNs) are useful tools giving a natural and compact representation of joint probability distributions. In many applications one needs to learn a Bayesian Network (BN) from data. In this context, it is important to understand the number of samples needed in order to guarantee a successful learning. Previous work have studied BNs sample complexity, yet it mainly focused on the requirement that the learned distribution will be close to the original distribution which generated the data. In this work, we study a different aspect of the learning, namely the number of samples needed in order to learn the correct structure of the network. We give both asymptotic results, valid in the large sample limit, and experimental results, demonstrating the learning behavior for feasible sample sizes. We show that structure learning is a more difficult task, compared to approximating the correct distribution, in the sense that it requires a much larger number of samples, regardless of the computational power available for the learner.
Polymer Homo‐Tandem Solar Cells with Best Efficiency of 11.3% (2015)

Rational materials design and interface engineering are both essential to realize a high performance for tandem cells. Two identical bulk heterojunctions are connected in series using novel interconnection layers combining pH-neutral conjugated polyelectrolytes and a thin film of ZnO nanoparticles by a solution process. The best performing tandem cells achieve a power conversion efficiency of 11.3%, with 25% enhancement in efficiency compared with single cells, which arises primarily from the increased light absorption.
Power transformers for the 21st century (2003)

Transformer technology is a mature technology. A characteristic of such technologies is that most advances tend to be incremental. Improvements also are often related to the demands of the 20th century manufacturing techniques rather than to the fundamental physics governing the concept. Returning to basic physics and for example reconsidering Maxwell's equations opens new possibilities for efficient design. Additionally, safety and environmental issues, much more relevant now than in the early 1900s, can be addressed in a new way. The new technology that is presented in this work describes the resulting revolutionary changes for both manufacturer and user. High voltage dry power transformers replace conventional power transformer technology based on oil/cellulosic insulation. The marriage of the well-proven high voltage power cable technology with transformer technology sets a new standard in reaching the environmental goals of the 21st century.