gebhart/patrepeval huggingface dataset:
Computational adaptive optics for broadband interferometric tomography of tissues and cells (2016)

Adaptive optics (AO) can shape aberrated optical wavefronts to physically restore the constructive interference needed for high-resolution imaging. With access to the complex optical field, however, many functions of optical hardware can be achieved computationally, including focusing and the compensation of optical aberrations to restore the constructive interference required for diffraction-limited imaging performance. Holography, which employs interferometric detection of the complex optical field, was developed based on this connection between hardware and computational image formation, although this link has only recently been exploited for 3D tomographic imaging in scattering biological tissues. This talk will present the underlying imaging science behind computational image formation with optical coherence tomography (OCT) &mdash; a beam-scanned version of broadband digital holography. Analogous to hardware AO (HAO), we demonstrate computational adaptive optics (CAO) and optimization of the computed pupil correction in 'sensorless mode' (Zernike polynomial corrections with feedback from image metrics) or with the use of 'guide-stars' in the sample. We discuss the concept of an 'isotomic volume' as the volumetric extension of the 'isoplanatic patch' introduced in astronomical AO. Recent CAO results and ongoing work is highlighted to point to the potential biomedical impact of computed broadband interferometric tomography. We also discuss the advantages and disadvantages of HAO vs. CAO for the effective shaping of optical wavefronts, and highlight opportunities for hybrid approaches that synergistically combine the unique advantages of hardware and computational methods for rapid volumetric tomography with cellular resolution.
Characterization and Reactivity of Iron Nanoparticles prepared with added Cu, Pd, and Ni (2010)

The association of a secondary metal with iron particles affects redox reactivity in engineered remediation systems. However, the structural characteristics of the metal additives and mechanism responsible for changes in reactivity have not been fully elucidated. Here, we synthesized iron nanoparticles with Cu, Pd, and Ni content ranging from 0-2 mol % via a solution deposition process (SDP), hydrogen reduction process (HRP), or hydrogen reduction of ferrihydrite coprecipitated with the metal cations (HRCO). Results from solid-state characterization show that the synthesis methods produced similar iron core/magnetite shell particles but produced substantial differences in terms of the distribution of the metal additives. In SDP, the metal additives were heterogeneously distributed on the surface of the particles. The metal additives were clearly discernible in TEM images as spherical nanoparticles (5-20 nm) on the HRP and HRCO particles. Because the metals were integral to the synthesis process, we hypothesize that the metal additive is present as solute within the iron core of the HRCO particles. Kinetic batch experiments of carbon tetrachloride (CT) degradation were performed to quantitatively compare the redox reactivity of the particles. Overall, metal additives resulted in enhanced pseudo-first-order rate constants of CT degradation (k(O,CT)) compared to that of the iron nanoparticles. For the bimetallic iron nanoparticles prepared by SDP and HRP, k(O,CT) increased with the concentration of metal additives. The values of chloroform yield (Y(CF)) were independent of the identity and amount of metal additives. However, both k(O,CT) and Y(CF) of the HRCO iron particles were significantly increased. Results suggest that it is the distribution of the metal additives that most strongly impacts reactivity and product distribution. For example, for materials with ca. 0.9 mol % Ni, reactivity and Y(CF) varied substantially (HRCO > SDP > HRP), and HRCO-NiFe resulted in the lowest final chloroform concentration because chloroform was rapidly dechlorinated. In addition, sequential spike experiments for long-term reactivity demonstrated that the presence of the metal additives facilitated reduction by enabling greater utilization of Fe(0).
High Tolerance, Micron Scale, Inline Embedded Resistors using Thin Film Additive Manufacturing (2015)

Embedded passive components have certain advantages over surface mount components. These advantages include: Increased circuit density through real-estate savings, decreased end product weight, improved electrical properties through additional termination and filter layout options, shortening of electrical connections, increased product quality through elimination of incorrectly attached devices and improved reliability through the reduction of solder joints [1]. The disadvantages to their current implementation include a limited range of resistance values and broader resistance tolerances [2]. In this paper, we discuss an additive print technology for custom embedded resistors with tolerances better than 10% and feature size geometries below 1 mil (25 μm). This technology produces a wide range of custom resistance values on typical PCB substrate materials thus combatting the noted disadvantages. The resistors are printed in-line on the signal layer eliminating the need of additional PCB resistor layers. Manufacturing challenges and design rules of this process are discussed and the DC and RF performance extrapolated to 15 GHz are presented.
Asymmetric polar localization dynamics of the serine chemoreceptor protein Tsr in Escherichia coli (2018)

The spatial location of proteins in living cells can be critical for their function. For example, the E. coli chemotaxis machinery is localized to the cell poles. Here we describe the polar localization of the serine chemoreceptor Tsr using a strain synthesizing a fluorescent Tsr-Venus fusion at a low level from a single-copy chromosomal construct. Using photobleaching and imaging during recovery by new synthesis, we observed distinct asymmetry between a bright (old) pole and a dim (new) pole. The old pole was shown to be a more stable cluster and to recover after photobleaching faster, which is consistent with the hypothesis that newly synthesized Tsr proteins are inserted directly at or near the old pole. The new pole was shown to be a less stable cluster and to exchange proteins freely with highly mobile Tsr-Venus proteins diffusing in the membrane. We propose that the new pole arises from molecules escaping from the old pole and diffusing to the new pole where a more stable cluster forms over time. Our localization imaging data support a model in which a nascent new pole forms prior to stable cluster formation.
Flexible modem interface — Enabling DoD wideband SATCOM enterprise (2017)

Today, rapid business and technology innovations are producing an array of advanced commercial satellite communications (COMSATCOM) systems that can deliver massive amounts of SATCOM capacity at a fraction of current cost and offer communications diversity that is critical for achieving resilience in a military contested environment. Recognizing the alignment of commercial capabilities with the Department of Defense (DoD) requirements for high capacity, global coverage, lower cost, and resilience, the department is proactively engaging the industry to formulate strategies leading towards a DoD Wideband SATCOM Enterprise that efficiently acquires and effectively manages advanced commercial capabilities in its architecture. To fully leverage the expanded space resources, the DoD must also address the integration of commercial waveforms into the DoD tactical terminals. The terminal flexibility for operating across multiple operator networks, in multiple frequency bands, and support different waveforms/modems is not only a pre-requisite for accessing advanced services but also key in providing resilience against threats. The purpose of this paper is to provide an architectural overview of the flexible terminal and Flexible Modem Interface (FMI) concepts. The FMI enables managed terminal flexibility and should be considered as an important step in converging DoD tactical terminal segment capabilities for various types of satellite networks and managed services.
Mannan-binding lectin serine protease-2 (MASP-2) in human kidney and its relevance for proteolytic activation of the epithelial sodium channel (2022)

Proteolytic activation of the renal epithelial sodium channel (ENaC) is increased by aldosterone. The aldosterone-sensitive protease remains unidentified. In humans, elevated circulating aldosterone is associated with increased urinary extracellular vesicle (uEVs) excretion of mannan-binding lectin associated serine protease-2 (MASP-2). We hypothesized that MASP-2 is a physiologically relevant ENaC-activating protease. It was confirmed that MASP2 mRNA is abundantly present in liver but not in human and mouse kidneys. Aldosterone-stimulation of murine cortical colleting duct (mCCD) cells did not induce MASP-2 mRNA. In human kidney collecting duct, MASP-2 protein was detected in AQP2-negative/ATP6VB1-positive intercalated cells suggestive of MASP2 protein uptake. Plasma concentration of full-length MASP-2 and the short splice variant MAp19 were not changed in a cross-over intervention study in healthy humans with low (70 mmol/day) versus high (250 mmol/day) Na<sup>+</sup> intake despite changes in aldosterone. The ratio of MAp19/MASP-2 in plasma was significantly increased with a high Na<sup>+</sup> diet and the ratio correlated with changes in aldosterone and fractional Na<sup>+</sup> excretion. MASP-2 was not detected in crude urine or in uEVs. MASP2 activated an amiloride-sensitive current when co-expressed with ENaC in Xenopus oocytes, but not when added to the bath solution. In monolayers of collecting duct M1 cells, MASP2 expression did not increase amiloride-sensitive current and in HEK293 cells, MASP-2 did not affect γENaC cleavage. MASP-2 is neither expressed nor co-localized and co-regulated with ENaC in the human kidney or in urine after low Na<sup>+</sup> intake. MASP-2 does not mediate physiological ENaC cleavage in low salt/high aldosterone settings.
Synthetic routes toward MOF nanomorphologies (2012)

As metal–organic frameworks (MOFs) are coming of age, their structural diversity, exceptional porosity and inherent functionality need to be transferred into useful applications. Fashioning MOFs into various shapes and at the same time controlling their size constitute an essential step toward MOF-based devices. Moreover, downsizing MOFs to the nanoscale triggers a whole new set of properties distinguishing nanoMOFs from their bulk counterparts. Therefore, dimensionality-controlled miniaturization of MOFs enables the customised use of nanoMOFs for specific applications where suitable size and shape are key prerequisites. In this feature article we survey the burgeoning field of nanoscale MOF synthesis, ranging from classical protocols such as microemulsion synthesis all the way to microfluidic-based techniques and template-directed epitaxial growth schemes. Along these lines, we will fathom the feasibility of rationally designing specific MOF nanomorphologies—zero-, one- and two-dimensional nanostructures—and we will explore more complex “second-generation” nanostructures typically evolving from a high level of interfacial control. As a recurring theme, we will review recent advances made toward the understanding of nucleation and growth processes at the nanoscale, as such insights are expected to further push the borders of nanoMOF science.
A Novel Countermeasure to Resist Side Channel Attacks on FPGA Implementations (2009)

Abstract—Side Channel Attacks (SCAs) have proven to be very effective in extracting information from algorithmically secure systems. Since the earliest reports of attacks exploiting side channels such as power consumption, timing behavior and electromagnetic radiation etc., the countermeasures to resist such attacks have also been proposed. A variety of countermeasures resisting SCAs have been presented that continue to fade away as resistant attack techniques are developed. Field Programmable Gate Arrays (FPGAs) were originally thought to be resistant to such attacks because of some inherent characteristics. Later, they were also found to leak information over the side channels. In this article a novel countermeasure is presented that hardens an FPGA based system with cipher embodiment, against SCAs. The proposed methodology of embedding single inverter ring oscillators within the synchronous cores helps improve immunity against electromagnetic, fault and glitch attacks, while the introduction of frequency hopping by randomly varying frequency driving the cipher hardens the system against power and timing attacks. The incorporated countermeasure enhances the immunity of FPGA based implementation against multiple types of SCAs without adversely affecting cost or performance. Keywords-Side Channel Attacks; countermeasures; FPGAs; frequency hopping
Adjuvant UK: Validation of a UK prognostic model for early breast cancer (2009)

11086 Background: To develop and validate a prognostication model to predict overall survival for women treated for early breast cancer in the UK based on cancer registry data. The main advantages are that unlike SEER, this dataset includes accurate information on mode of detection as well as systemic therapy. Methods: Using the Eastern Cancer Registration &amp; Information Centre (ECRIC) dataset, information was collated for 5,818 women diagnosed with invasive breast cancer in East Anglia from 1999–2003. All patients underwent surgery, had records of pathological staging (tumour size, grade, lymph node status, ER status) and systemic treatment (chemotherapy, hormone therapy, both), mode of detection (screen-detected, symptomatic) and were followed up to December 2007. A model was derived from these data using Cox proportional hazards and this was subsequently validated in an external dataset of 5,468 patients from the West Midlands Cancer Intelligence Unit (WMCIU). Validation was performed by comparing (a) observed and predicted mortality - overall and by risk group decile - and (b) receiver operating characteristic (ROC) curves in both ECRIC &amp; WMCIU datasets. Results: ECRIC dataset: Observed/predicted deaths were: 2 years (262/267), 5 years (868/867), 8 years (1108/1093). Area under ROC curve was 0.800WMCIU dataset: Observed/predicted deaths were: 2 years (317/298), 5 years (862/919), 8 years (955/999). Area under ROC curve was 0.783. The model and validation worked equally well at all time points (2, 5, 8 years) and in all risk group deciles. In the validation dataset the observed and predicted 8-year OS was within 1% (17.5% versus 18.3%). There was no significant statistical difference between the ROC curves (X 2 = 2.35, P=.12) for prediction at 8 years in ECRIC and WMCIU data. Conclusions: We have developed a prognostication model for early breast cancer based on data from a UK cancer registry and validated the model using data from another UK registry. The model was well calibrated and provides a high degree of discrimination. This model will underpin the first web-based prognostication and treatment benefit tool for early breast cancer in the UK (Adjuvant UK). No significant financial relationships to disclose.
Tuning the threshold voltage of carbon nanotube transistors by n-type molecular doping for robust and flexible complementary circuits (2014)

Tuning the threshold voltage of a transistor is crucial for realizing robust digital circuits. For silicon transistors, the threshold voltage can be accurately controlled by doping. However, it remains challenging to tune the threshold voltage of single-wall nanotube (SWNT) thin-film transistors. Here, we report a facile method to controllably n-dope SWNTs using 1H-benzoimidazole derivatives processed via either solution coating or vacuum deposition. The threshold voltages of our polythiophene-sorted SWNT thin-film transistors can be tuned accurately and continuously over a wide range. Photoelectron spectroscopy measurements confirmed that the SWNT Fermi level shifted to the conduction band edge with increasing doping concentration. Using this doping approach, we proceeded to fabricate SWNT complementary inverters by inkjet printing of the dopants. We observed an unprecedented noise margin of 28 V at V(DD) = 80 V (70% of 1/2V(DD)) and a gain of 85. Additionally, robust SWNT complementary metal-oxide-semiconductor inverter (noise margin 72% of 1/2VDD) and logic gates with rail-to-rail output voltage swing and subnanowatt power consumption were fabricated onto a highly flexible substrate.
Molecular dynamics simulation of formation and growth of CdS nanoparticles (2013)

AbstractMonodispersed semiconducting nanoparticles are usually synthesised in a liquid medium using injection of an appropriate solution. A key factor in attaining a narrow particle size distribution (PSD) is the temporal separation of the nucleation and growth stages, where the former takes place during the injection. Faster injection produces a larger number of nuclei and a narrower PSD. The injection speed is expected to affect the diffusion of the ions in the solution and to create uniformly high supersaturation for a short period of time. In this paper, we study the growth of CdS nanoparticles during the injection by molecular dynamics simulation. A solution of Cd ions is injected into the simulation cell that contains sulphure ions; the variation of the PSD and its mean and variance are studied as functions of the injection velocity. Higher injection velocities produce narrower PSDs and smaller particles, hence providing a precise method for controlling both.Keywords:: CdS nanoparticlemolecular simulationsemiconducting particles AcknowledgementWork at USC was supported in part by the National Science Foundation.
Certainly More Guidelines than Rules (2010)

The updated clinical practice guidelines for testosterone (T) therapy in androgen deficiency (AD) have been crafted by a panel of internationally recognized leaders in clinical practice and translational research (1). They have synthesized the current evidence and made recommendations and suggestions that align broadly with recent internationalguidelines(2).Theevidencebasis for informingclinical practice has developed only marginally; among the 45 new references cited from 2006, there are seven small to moderate-sized randomized controlled trials and several controlled studies of T responses in young vs. older men; the remainder are commentaries, meta-analyses, or epidemiological studies. With their intimate understanding of the knowledge gaps, and as required for writing summary guidelines, the authors have “filled in the blanks” with considered commentary. But consequent upon the lack of definitive data, rather vague terms (“unequivocally low”) and statements (measurement in “some” patients) necessarily appear that may obscure theoretical and pragmatic problems. These need to be recognized so that the reader is under no illusions about what is firm ground as opposed to potentially shifting sands. AD is a “syndromic” diagnosis (3), a synthesis of clinical features and confirmatory low T levels. But how reliable is our evaluation of these two planks of diagnosis? More fundamentally, are we always thinking in terms of a classic hormonal deficiency state that demands replacement or in the many gray zones, with androgens as therapeutic agents to improve health outcomes in eugonadal men, and then seeking to retrofit the diagnostic criteria to legitimize such replacement therapy?
Figure S1 from Polyamine Blocking Therapy Decreases Survival of Tumor-Infiltrating Immunosuppressive Myeloid Cells and Enhances the Antitumor Efficacy of PD-1 Blockade (2023)

&lt;p&gt;Supplementary Figure/Legend S1&lt;/p&gt;
Phase 1 study evaluating the safety, tolerability, pharmacokinetics (PK), and efficacy of AMG 510, a novel small molecule KRASG12C inhibitor, in advanced solid tumors. (2019)

3003 Background: The KRAS G12C mutation is found in approximately 13% of lung adenocarcinomas and 1–3% of other solid tumors, but there is no approved therapy that targets this mutation. AMG 510 is a novel small molecule that specifically and irreversibly inhibits KRAS G12C by locking it in an inactive GDP-bound state. Methods: This phase 1, first-in-human, open-label, multicenter study (NCT03600883) is evaluating the safety, tolerability, PK, and efficacy of AMG 510 in adult patients (pts) with locally-advanced or metastatic KRAS G12C mutant solid tumors. The primary endpoint is safety; key secondary endpoints include PK, ORR (assessed every 6 weeks [wks]), DOR, and PFS. Key inclusion criteria: KRAS G12C mutation identified through DNA sequencing, measurable or evaluable disease, ECOG PS ≤2, life expectancy &gt;3 months (mo). Key exclusion criteria: active brain metastases, myocardial infarction within 6 mo. A dose exploration will determine the maximum tolerated dose (MTD) or recommended phase 2 dose (RP2D). A dose expansion will enroll pts with NSCLC, CRC, and other advanced solid tumors carrying the KRAS G12C mutation. AMG 510 will be given PO until disease progression, intolerance, or withdrawal of consent. Results: 22 pts (8 men, 14 women; median age 55.5 y) were enrolled in the first 3 dose cohorts. Tumor types: 6 NSCLC, 15 CRC, 1 other. Most pts (n=17) had ≥3 prior lines of treatment (tx). Median tx duration was 28 d (range: 8–134). 5 pts reported 10 treatment-related AEs (grade 1, n=9; grade 2, n=1); there were no DLTs. Tumor response was evaluated in 9 pts (4 with ≥2 assessments); 13 pts have not reached their first assessment.1 pt had a PR (NSCLC at wks 6 and 12, tx ongoing), 6 pts had SD (4 CRC and 2 NSCLC; median tx duration 9.7 wks [range: 6.3–19.1], tx ongoing), 2 pts had PD. 20 pts are continuing to receive AMG 510. A second PR (NSCLC at wk 6, tx ongoing) was reported after data cutoff. Conclusions: AMG 510 has been well tolerated at the dose levels tested and has shown antitumor activity when administered as monotherapy to patients with advanced KRAS G12C mutant solid tumors. MTD has not been determined, and enrollment into the dose exploration is ongoing. Clinical trial information: NCT03600883.
Elements of practical coal mining (1981)

Twenty-seven chapters are included in the book. A separate abstract was prepared for each of 23 chapters for the data base.
Pointer-induced aliasing: a problem taxonomy (1991)

A?iasing occurs at some program point during execution when two or more names exist for the same location. We have isolated various programming language mechanisms which create aliases. We have classified the complexity of the fllas problem induced by each mechanism alone and in combination, as AfP-hard, complement tip-hard, or polynomial (’P). We present our problem classification, give an overview of our proof that finding interprocedural aliases in the presence of single level pointers is in 7, and present a represent tive proof for the NP-hard problems.