gebhart/patrepeval huggingface dataset:
Optical properties of normal and malignant tissues in the nasopharynx and larynx (1995)

Differences in tissue autofluorescence between normal bronchial tissue and cancerous or pre cancerous bronchial tissue have been documented and exploited for the early detection of lung cancer (1,2) The larynx and nasopharynx have not been so well studied. Even with the most advanced fiber-optic equipment in experienced hands, the nasopharynx is an accessible but challenging area to examine. Small nasopharyngeal carcinoma are difficult to detect. For the larynx the challenge is the precise tumour localization which will allow more accurate staging of the malignant disease. The thought is that the tissue autofluorescence and tissue optical properties (absorption and scattering) which allow one to detect and localize early lesions in the bronchial tree may be similar in the larynx and nasopharynx and likewise exploitable for detection and delineation of lesions. The major characteristics of the autofluorescence properties of bronchial tissue, which may be found to be similar in other sites, are summarized below.
Distributed Computation of A Posteriori Bit Likelihood Ratios in Cell-Free Massive MIMO (2021)

This paper presents a novel strategy to decentralize the soft detection procedure in an uplink cell-free massive multiple-input-multiple-output network. We propose efficient approaches to compute the a posteriori probability-per-bit, exactly or approximately when having a sequential fronthaul. More precisely, each access point (AP) in the network computes partial sufficient statistics locally, fuses it with received partial statistics from another AP, and then forwards the result to the next AP. Once the sufficient statistics reach the central processing unit, it performs the soft demodulation by computing the log-likelihood ratio (LLR) per bit, and then a channel decoding algorithm (e.g., a Turbo decoder) is utilized to decode the bits. We derive the distributed computation of LLR analytically.
Log files: an extended file service exploiting write-once storage (1987)

A log service provides efficient storage and retrieval of data that is written sequentially (append-only) and not subsequently modified. Application programs and subsystems use log services for recovery, to record security audit trails, and for performance monitoring. Ideally, a log service should accommodate very large, long-lived logs, and provide efficient retrieval and low space overhead.
Synthesis of Aryl‐Substituted Naphthalene‐Linked Pyrrolobenzodiazepine Conjugates as Potential Anticancer Agents with Apoptosis‐Inducing Ability (2011)

A library of new aryl-substituted naphthalene C8-linked pyrrolo[2,1-c][1,4]benzodiazepine (PBD) conjugates with various linker architectures were designed, synthesized, and evaluated for their anticancer activity against a panel of 11 human cancer cell lines. All 32 conjugates show anticancer potential, with some of them exhibiting particularly high activity (0.01-0.19 μM). Thermal denaturation studies showed effective DNA binding capacity relative to DC-81. In assays for biological activity relating to cell-cycle distribution, these PBD conjugates induce G₀/G₁-phase arrest and also cause an increase in the levels of p53 and caspase-9 proteins, followed by apoptotic cell death. One conjugate in particular is the most promising candidate of the series, with the potential to be selected for further studies, either alone or in combination with existing anticancer therapies.
In Situ Electrochemical Raman Spectroscopy of Air-Oxidized Semiconducting Single-Walled Carbon Nanotube Bundles in Aqueous Sulfuric Acid Solution (2016)

In this study, we oxidized approximately 90% semiconducting, highly crystalline single-walled carbon nanotube (hc-SWCNT) bundles in the atmosphere at 450 °C for 30 min to obtain SWCNTs modified with oxygen-containing functional groups and investigated not only the influence of air oxidation on the electrochemical doping of the air-oxidized SWCNT (AO-SWCNT) bundles in aqueous sulfuric acid solution using in situ Raman spectroscopy, but also the relationship between the in situ electrochemical Raman data and the properties of electric double-layered supercapacitors (EDLSCs). By oxidizing the hc-SWCNTs in air, AO-SWCNTs with a small diameter distribution could be prepared. When a negative charge was applied to the AO-SWCNTs used as a working electrode in a three-electrode electrochemical cell for in situ Raman spectroscopy, a large downshift of the G+ line of the AO-SWCNTs was observed compared to that before air oxidation. On increasing the ratio of small-diameter nanotubes/total nanotubes, the Raman data obtained in situ revealed that the effect of the weakening of the C–C bond was stronger than that of the renormalization of the phonon energy. In contrast, in the case of applying a positive charge to the AO-SWCNTs, the magnitude of the upshift of the G+ line for the AO-SWCNTs was slightly larger than that for the hc-SWCNTs. The influent electric charges per unit mass and the specific capacitances of the AO-SWCNT electrodes for the maximum magnitude of the shift of the G+ line (10.7 cm–1) were 60.1 C/g and 50.1 F/g, respectively, which are larger than those of hc-SWCNT electrodes. In situ Raman spectroscopy is a useful method to simultaneously assess the increase or decrease in the diameter distribution of small nanotubes and the specific capacitances of electric double-layered supercapacitors of chemically functionalized SWCNTs by the magnitude of the shift of the G+ line compared to unfunctionalized SWCNTs.
Use of Guanidine Compounds in the Treatment of Neglected Tropical Diseases (2014)

Over one billion people worldwide are afflicted by a group of 17 infectious diseases, known as the neglected tropical diseases (NTDs), reaching mainly undeveloped countries that suffer with a lack of economic incentive, research and policy for new drug discovery. Compounds with guanidine moiety are privileged structures and are attractive as scaffold for the discovery of new drug candidates. This functional group is an important pharmacophore moiety in several therapeutically active compounds. Guanidine-containing heterocycles have been reported to exhibit different biological properties including antiprotozoal and antiparasitic activity such as mebendazole and pyrimethamine used in current therapeutics. The present review covers the progress of guanidine derivatives for NTDs (Human African Trypanosomiasis, Chagas Disease, Leishmaniasis, Buruli Ulcer, Echinococcosis, Taeniasis/Cysticercosis, Lymphatic Filariasis and Onchocerciasis). Also, review the development of new guanidine derivatives in Malaria and Tuberculosis. Keywords: Antiparasitic, antiprotozoal, guanidine derivatives, guanidine, neglected tropical diseases.
Adversarial Robustness Verification and Attack Synthesis in Stochastic Systems (2021)

Probabilistic model checking is a useful technique for specifying and verifying properties of stochastic systems including randomized protocols and reinforcement learning models. Existing methods rely on the assumed structure and probabilities of certain system transitions. These assumptions may be incorrect, and may even be violated by an adversary who gains control of system components. In this paper, we develop a formal framework for adversarial robustness in systems modeled as discrete time Markov chains (DTMCs). We base our framework on existing methods for verifying probabilistic temporal logic properties and extend it to include deterministic, memoryless policies acting in Markov decision processes (MDPs). Our framework includes a flexible approach for specifying structure-preserving and non structure-preserving adversarial models. We outline a class of threat models under which adversaries can perturb system transitions, constrained by an $\varepsilon$ ball around the original transition probabilities. We define three main DTMC adversarial robustness problems: adversarial robustness verification, maximal $δ$ synthesis, and worst case attack synthesis. We present two optimization-based solutions to these three problems, leveraging traditional and parametric probabilistic model checking techniques. We then evaluate our solutions on two stochastic protocols and a collection of Grid World case studies, which model an agent acting in an environment described as an MDP. We find that the parametric solution results in fast computation for small parameter spaces. In the case of less restrictive (stronger) adversaries, the number of parameters increases, and directly computing property satisfaction probabilities is more scalable. We demonstrate the usefulness of our definitions and solutions by comparing system outcomes over various properties, threat models, and case studies.
The Methods for Fractionation, Analytical Separation and Identification of Polynuclear Aromatic Hydrocarbons in Complex Mixtures (1974)

The fractionation and analysis scheme for the enrichment and subsequent determination of trace polynuclear aromatics is described. The method is generally applicable to a detailed analysis of any complex mixture containing polynuclears, but the example was chosen from the application to airborne particulate matter. After the extraction of polynuclear hydrocarbons and several partitioning steps, the sample was subjected to fractionation on a lipophilic gel. The collected fractions were further chromatographed by high-resolution LC on polar chemically bonded stationary phases. Fraction trapping was followed by capillary column GC, and non-destructive spectral methods such as UV, fluorescence emission, and NMR spectroscopy were also used to yield additional information.
Successive-Cancellation Decoding of Reed-Muller Codes with Fast Hadamard Transform (2021)

A novel permuted fast successive-cancellation list decoding algorithm with fast Hadamard transform (FHT-FSCL) is presented. The proposed decoder initializes $L$ $(L\ge1)$ active decoding paths with $L$ random codeword permutations sampled from the full symmetry group of the codes. The path extension in the permutation domain is carried out until the first constituent RM code of order $1$ is visited. Conventional path extension of the successive-cancellation list decoder is then utilized in the information bit domain. The simulation results show that for a RM code of length $512$ with $46$ information bits, by running $20$ parallel permuted FHT-FSCL decoders with $L=4$, we reduce $72\%$ of the computational complexity, $22\%$ of the decoding latency, and $84\%$ of the memory consumption of the state-of-the-art simplified successive-cancellation decoder that uses $512$ permutations sampled from the full symmetry group of the code, with similar error-correction performance at the target frame error rate of $10^{-4}$.
Nanostructured resistive memory cells based on 8-nm-thin TiO2 films deposited by atomic layer deposition (2011)

S.01AD011-01AD015
Stereotactic robotic radiosurgery for localized prostate cancer: Initial evaluation of acute toxicities (2009)

e16006 Background: We evaluated the initial acute toxicities experienced by patients treated with cyberknife fractionated radiosurgery for low and low-intermediate risk prostate cancer. Methods: Twenty-two patients with low or low-intermediate risk prostate cancer (T2a, GG 3+3=6 or 3+4=7, PSA &lt;10) were enrolled prospectively on an IRB approved protocol and treated the planning target volume (PTV)(prostate+5mm margin) with cyberknife fractionated radiosurgery to a dose of 36.25 Gy in 5 fractions (7.25Gy/fraction). The target volume included the prostate and seminal vesicles. PSA values, AUA symptom scores (AUA SS), and NCI CTC acute toxicities were analyzed prior to radiosurgery and at 1 month (N=16), 3 months (N=12) and 6 months (N=5)post-treatment. Results: Patients treated on study included 12 with GG 3+3=6 cancer and 10 with GG 3+4=7 cancer. Mean patient age was 66 years old (range 49–79). Mean pre-treatment PSA was 5.29 (range 0.64–9.36) declining to 3.44 (range 0.00–10.43) at 1 month post treatment, 1.99 (range 0.31–3.99) at 3 months post-treatment and 2.08 (1.05–3.13) at 6 months post-treatment. Mean pre-treatment AUA SS was 7 (range 0.–18) increasing to 12 (range 2–29) at 1 month post treatment, decreasing to 8 (range 2–17) at 3 months post-treatment and 11 (3–17). There were 5 grade 1 acute toxicities including (diarrhea, fatigue, mild urinary frequency, hemorrhoid and a rash) and 7 grade 2 toxicities including (bladder spasms, painful urinary, bowel irregularity, rectal pain, urethritis and numbness in the upper thigh), all grade 1 and 2 toxicities resolved within three months of treatment. The one patient with grade 2 thigh numbness was not thought to be study related toxicity. Two patients developed grade 3 toxicity. One developed bacteremia after the transrectal ultrasound guided placement of the fiducials, the infection completely resolved after treatment with antibiotics. One patient on Coumadin developed hematuria which resolved with conservative management. Conclusions: Cyberknife fractionated radiosurgery for patients with early stage prostate cancer appears to be safe on our early initial assessment.Continued evaluation and longer follow-up ongoing. [Table: see text]
Palladium-Catalyzed Hydroxylation of Aryl and Heteroaryl Halides Enabled by the Use of a Palladacycle Precatalyst (2014)

[Image: see text] A method for the hydroxylation of aryl and heteroaryl halides, promoted by a catalyst based on a biarylphosphine ligand tBuBrettPhos (L5) and its corresponding palladium precatalyst (1), is described. The reactions allow the cross-coupling of both potassium and cesium hydroxides with (hetero)aryl halides to afford a variety of phenols and hydroxylated heteroarenes in high to excellent yield.
Quantifying Intrinsic Ion-Driven Conformational Changes in Diphenylacetylene Supramolecular Switches with Cryogenic Ion Vibrational Spectroscopy (2013)

We report how two flexible diphenylacetylene (DPA) derivatives distort to accommodate both cationic and anionic partners in the binary X(±)·DPA series with X = TMA(+) (tetramethylammonium), Na(+), Cl(-), Br(-), and I(-). This is accomplished through theoretical analysis of X(±)·DPA·2D2 vibrational spectra, acquired by predissociation of the weakly bound D2 adducts formed in a 10 K ion trap. DPA binds the weakly coordinating TMA(+) ion with an arrangement similar to that of the neutral compound, whereas the smaller Na(+) ion breaks all intramolecular H-bonds yielding a structure akin to the transition state for interconversion of the two conformations in neutral DPA. Halides coordinate to the urea NH donors in a bidentate H-bonded configuration analogous to the single intramolecular H-bonded motif identified at high chloride concentrations in solution. Three positions of the "switch" are thus identified in the intrinsic ion accommodation profile that differ by the number of intramolecular H-bonds (0, 1, or 2) at play.
Supplemental File 1 from AACR Project GENIE: Powering Precision Medicine through an International Consortium (2023)

&lt;p&gt;AACR GENIE Data Guide&lt;/p&gt;
Sodium Ion Conductor Based Sensor Attached with NaNO2 for Amperometric Detection of  NO 2 (1996)

An amperometric limiting current sensor was fabricated by combining a conductor (Na superionic conductor, NASICON) with (or ) layers. The device using gave a much higher sensitivity at 200°C compared to that using . The current response of the ‐attached device was almost linear with the concentration in the range of 0 to 80 ppm. In addition, the selectivity of the device to was fairly high with respect to other gases which are usually coexistent in combustion exhausts. A sensing mechanism of the device is discussed briefly.
Surgeon Willingness to Participate in Randomized Controlled Trials for the Treatment of Femoroacetabular Impingement (2015)

The feasibility of completing RCTs for the management of FAI is limited even among high-volume hip preservation surgeons; however, surgeons are willing to participate.
Zliding (2005)

High precision parameter manipulation tasks typically require adjustment of the scale of manipulation in addition to the parameter itself. This paper introduces the notion of Zoom Sliding, or Zliding, for fluid integrated manipulation of scale (zooming) via pressure input while parameter manipulation within that scale is achieved via x-y cursor movement (sliding). We also present the Zlider (Figure 1), a widget that instantiates the Zliding concept. We experimentally evaluate three different input techniques for use with the Zlider in conjunction with a stylus for x-y cursor positioning, in a high accuracy zoom and select task. Our results marginally favor the stylus with integrated isometric pressure sensing tip over bimanual techniques which separate zooming and sliding controls over the two hands. We discuss the implications of our results and present further designs that make use of Zliding.
Development of a Novel In Vitro Co-Culture System for Discrete Subaortic Stenosis (2023)

The aim of this study was to investigate the survival, distribution and reaction of different cell types on a monolayer disk, as well as their behavior under bioreactor treatment. Specifically, porcine EEC and porcine fibroblasts (PCF) were labeled with GFT and Texas Red, respectively, to track their viability and distribution. The experiments involved monitoring the cells using various microscopy techniques and comparing the results with controls. These findings have important implications for understanding cell behavior and potential applications for Discrete Subaortic Stenosis. This paper aims to discuss the implications of the findings in the context of existing literature and future research directions.
Pathophysiology and Advanced Hemodynamic Assessment of Cardiogenic Shock (2020)

Cardiogenic shock (CGS) is common and highly morbid. According to the National Inpatient Sample, there are more than 100,000 cases per year, and 30-day mortality approaches 50% despite improvements in critical care practices and novel mechanical therapies targeted at restoring normal hemodynamics. This issue aims to enhance clinicians' understanding of CGS, and this review specifically focuses on the underlying pathophysiology. We examine the definition and etiologies of CGS, approaches to risk assessment, and the pressure-volume loop framework that is the foundation for conceptualizing ventricular mechanics, ventricular-vascular interactions, and the derangements observed in CGS. This overview will also contextualize subsequent chapters that discuss nuances of CGS encountered in particular scenarios (ie, post-myocardial infraction, acutely decompensated chronic heart failure, post-cardiac surgery), address pharmacological and mechanical treatments for CGS, and review CGS in a case-based format.
Mucosal exfoliation as a selective reaction to etoricoxib (2016)

The peculiarities of our case are the rare clinical manifestation and the selective hypersensitivity to COX-2 inhibitor with tolerance to a non-selective NSAID.
1.2.1 Engineering Information Assurance for Critical Infrastructures: The DITSCAP Automation Study (2005)

Abstract Recent advances in information technology have transformed the way in which mission‐critical services get delivered and are evaluated today. These services are heavily and increasingly relying on an interdependent crossed network of critical information infrastructures, spanning from private to government sectors. In order to enable such infrastructures to efficiently mitigate risks, optimize their security posture and evaluate their information assurance (IA) practices, we identify the need for a structured and comprehensive methodology for IA‐aware critical infrastructure protection. In this paper, we focus on the automation study of the Department of Defense Information Technology Security Certification and Accreditation Process (DITSCAP) that is a standard for certifying and accrediting the information networks that comprise of the Defense Information Infrastructure (DII). We attempt to generalize a course of actions in DITSCAP that motivate our design principles and modeling techniques, supported by their theoretical backgrounds and demonstrable prototype interfaces to establish their appropriateness.
Prostate cancer treatment with Irreversible Electroporation (IRE): Safety, efficacy and clinical experience in 471 treatments (2019)

The results indicate comparable efficacy of IRE to standard radical prostatectomy in terms of 5-year recurrence rates and better preservation of urogenital function, proving the safety and suitability of IRE for PCa treatment. The data also shows that IRE, besides focal therapy of early PCa, can also be used for whole-gland ablations, in patients with recurrent PCa, and as a problem-solver for local tumor control in T4-cancers not amenable to surgery and radiation therapy anymore.
Escherichia coli Protein Expression System for Acetylcholine Binding Proteins (AChBPs) (2016)

Nicotinic acetylcholine receptors (nAChR) are ligand gated ion channels, identified as therapeutic targets for a range of human diseases. Drug design for nAChR related disorders is increasingly using structure-based approaches. Many of these structural insights for therapeutic lead development have been obtained from co-crystal structures of nAChR agonists and antagonists with the acetylcholine binding protein (AChBP). AChBP is a water soluble, structural and functional homolog of the extracellular, ligand-binding domain of nAChRs. Currently, AChBPs are recombinantly expressed in eukaryotic expression systems for structural and biophysical studies. Here, we report the establishment of an Escherichia coli (E. coli) expression system that significantly reduces the cost and time of production compared to the existing expression systems. E. coli can efficiently express unglycosylated AChBP for crystallography and makes the expression of isotopically labelled forms feasible for NMR. We used a pHUE vector containing an N-terminal His-tagged ubiquitin fusion protein to facilitate AChBP expression in the soluble fractions, and thus avoid the need to recover protein from inclusion bodies. The purified protein yield obtained from the E. coli expression system is comparable to that obtained from existing AChBP expression systems. E. coli expressed AChBP bound nAChR agonists and antagonists with affinities matching those previously reported. Thus, the E. coli expression system significantly simplifies the expression and purification of functional AChBP for structural and biophysical studies.
Supplementary Legends for Figures 1-4, Table 1 from Human Renal Cancer Cells Express a Novel Membrane-Bound Interleukin-15 that Induces, in Response to the Soluble Interleukin-15 Receptor α Chain, Epithelial-to-Mesenchymal Transition (2023)

Supplementary Legends for Figures 1-4, Table 1 from Human Renal Cancer Cells Express a Novel Membrane-Bound Interleukin-15 that Induces, in Response to the Soluble Interleukin-15 Receptor α Chain, Epithelial-to-Mesenchymal Transition
Kerr-Lens Modelocked Ti:Sapphire Laser Oscillator Directly Pumped with Blue Diodes (2012)

We describe a Ti:sapphire laser pumped directly with 445nm laser diodes. With 70 mW average power at 800 nm and bandwidth for &lt;13 fs pulses, Kerr-lens-modelocked pulses are available with dramatically decreased pump cost.