gebhart/patrepeval huggingface dataset:
Supplementary Materials and Methods, Figure Legends from Molecular Profiling of Premalignant Lesions in Lung Squamous Cell Carcinomas Identifies Mechanisms Involved in Stepwise Carcinogenesis (2023)

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Phase I Safety and Immunogenicity of A Three‐Component H. Pylori Vaccine (2003)

Clinical Pharmacology &amp; Therapeutics (2003) 73 , P34–P34; doi:
A study of preferences for sharing and privacy (2005)

We describe studies of preferences about information sharing aimed at identifying fundamental concerns with privacy and at understanding how people might abstract the details of sharing into higher-level classes of recipients and information that are treated similarly. Thirty people specified what information they are willing to share with whom.. Although people vary in their overall level of comfort in sharing, we identified key classes of recipients and information. Such abstractions highlight the promise of developing expressive controls for sharing and privacy.
ChemInform Abstract: Chromophore‐Assisted Peroxy Bond Breakage: Laser Flash Spectroscopic Studies of a Benzophenone Perester. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Dual-side and three-dimensional microelectrode arrays fabricated from ultra-thin silicon substrates (2009)

A method for fabricating planar implantable microelectrode arrays was demonstrated using a process that relied on ultra-thin silicon substrates, which ranged in thickness from 25 to 50 µm. The challenge of handling these fragile materials was met via a temporary substrate support mechanism. In order to compensate for putative electrical shielding of extracellular neuronal fields, separately addressable electrode arrays were defined on each side of the silicon device. Deep reactive ion etching was employed to create sharp implantable shafts with lengths of up to 5 mm. The devices were flip-chip bonded onto printed circuit boards (PCBs) by means of an anisotropic conductive adhesive film. This scalable assembly technique enabled three-dimensional (3D) integration through formation of stacks of multiple silicon and PCB layers. Simulations and measurements of microelectrode noise appear to suggest that low impedance surfaces, which could be formed by electrodeposition of gold or other materials, are required to ensure an optimal signal-to-noise ratio as well a low level of interchannel crosstalk.
The Genetic Association of Variants in CD6, TNFRSF1A and IRF8 to Multiple Sclerosis: A Multicenter Case-Control Study (2011)

Variants in TNFRSF1A and in the vicinity of IRF8 were confirmed to be associated in these independent cohorts, which supports the role of these loci in etiology of multiple sclerosis. The variant in CD6 reached genome-wide significance after combining the data with the original meta-analysis. Fine mapping is required to identify the predisposing variants in the loci and future functional studies will refine their molecular role in MS pathogenesis.
Comparison of Silicon Ring Modulators With Interdigitated and Lateral p-n Junctions (2012)

We present a rigorous comparison between Si ring modulators based on interdigitated and lateral p-n junctions. A detailed Si ring modulator model is derived, which is used to fit and benchmark the measured modulation performance of both ring modulators. At 10 Gb/s and 1 <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">V</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">pp</sub> drive swing, the interdigitated ring modulator is found to exhibit a superior extinction ratio at low insertion loss as compared to the lateral ring modulator, at the expense of a higher capacitive load. Design improvements are proposed to obtain 25-Gb/s operation with similar extinction ratio and low insertion loss in future devices. Such devices are attractive to enable power-efficient scaling of optical interconnects to 400 Gb/s and beyond.
Initial steps of the pathogenesis of the infection caused byStreptococcus suis: fighting against nonspecific defenses (2016)

Interactions between a bacterial pathogen and its potentially susceptible host are initiated with the colonization step. During respiratory/oral infection, the pathogens must compete with the normal microflora, resist defense mechanisms of the local mucosal immunity, and finally reach, adhere, and breach the mucosal epithelial cell barrier in order to induce invasive disease. This is the case during infection by the swine and zoonotic pathogen Streptococcus suis, which is able to counteract mucosal barriers to induce severe meningitis and sepsis in swine and in humans. The initial steps of the pathogenesis of S. suis infection has been a neglected area of research, overshadowed by studies on the systemic and central nervous phases of the disease. In this Review article, we provide for the first time, an exclusive focus on S. suis colonization and the potential mechanisms involved in S. suis establishment at the mucosa, as well as the mechanisms regulating mucosal barrier breakdown. The role of mucosal immunity is also addressed. Finally, we demystify the extensive list of putative adhesins and virulence factors reported to be involved in the initial steps of pathogenesis by S. suis.
Optical Convolutional Neural Network With WDM-Based Optical Patching and Microring Weighting Banks (2020)

We propose an optical convolutional neural network (OCNN) architecture for high-speed and energy-efficient deep learning accelerators. The WDM-based optical patching scheme (WDM-OPS) is adopted as the data-feeding structure for its superior energy efficiency and the microring banks are used for the large-scale weighting and summing (the computing core). We thoroughly investigate the performance (including prediction accuracy, speed, and energy efficiency) of this architecture in different system defects. The results indicate that, the prediction accuracy of OCNN can reach 97% in the MNIST dataset with a computing speed of over 100 TMAC/s on condition of achievable low insertion loss. It is also observed that the WDM-OPS notably reduces the energy consumption of the electro-optic modulation and thus the OCNN becomes an exceptionally energy-efficient architecture among several well-known optical architectures. In the evaluations, instead of merely considering the computing core, we take the holistic optical system including lasers, electro-optic modulators, data preprocessing, photodetection and transimpedance amplification into consideration. Therefore, this work provides a potential guide for the systematic implementation of the OCNN architecture.
Thermal Management and Control in Testing Packaged Integrated Circuit (IC) Devices (1999)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;This paper describes the thermal management and design challenges of testing packaged integrated circuit (IC) devices, specifically device thermal conditioning and device-under-test (DUT) temperature control. The approach taken is to discuss the individual thermal design issues as defined by the device type (e.g. memory, microcontroller) and tester capabilities. The influence of performance-parameter specifications, such as the DUT parallelism, test time, index time, test-temperature range and test-temperature tolerance are examined. An understanding of these performance requirements and design constraints enables consideration of existing test handler thermal processing systems (e.g., gravity feed, pick and place), future test handler thermal concepts, and future high-parallelism testing needs for high-wattage memory and microprocessor devices. New thermal designs in several of these areas are described.&lt;/div&gt;&lt;/div&gt;
The Effects of Quadriceps Weakness on the Knee Adductor Moment During Gait (2004)

0356 A high knee adductor moment has been shown to exacerbate the progression of knee osteoarthritis (OA). Mechanical alignment of the lower limb is correlated with a high adductor moment. Alternatively, conservative treatment consisting of quadriceps strengthening minimizes progression of the disease, reduces pain and improves gait function. Thus, mechanical alignment and quadriceps weakness often co-exist in knee OA populations and the effect of quadriceps strengthening on gait function in this patient population is often confounded by the OA disease process itself. PURPOSE: To isolate the effect of quadriceps weakness on the adductor moment during the stance phase of gait, independent of alignment or OA severity. METHODS: Using an intra-articular knee insufflation technique, quadriceps strength was inhibited (≥ 20% of MVC as measured via Cybex isometry at 30°) and its effects on gait function were assessed in an otherwise healthy population (N = 10, who exhibit normal ranges of mechanical alignment) using traditional 3D gait analysis. RESULTS: Under speed controlled conditions, quadriceps weakness caused a significant increase in the peak knee adductor moment, a decrease in the knee midstance ROM, and medial change in the position of the Fy GRF (all P < 0.04). There were no changes in step width, stride length, foot progression angle, hip or ankle ROM, peak F1 vertical ground reaction force (VGRF) or loading rate of F1 VGRF (all P > 0.05). The peak adductor moment was best predicted by the mechanical alignment of the lower extremity (r = .88, p < 0.01) in pre-insufflation trials. However, the change in quadriceps strength was highly correlated with the change in adductor moment (semi-partial r = .84, p < 0.01) over and above alignment (semi-partial r = .25, p = 0.48) in post-insufflation trials. CONCLUSION: Mechanical alignment may better predict the adductor moment, but quadriceps weakness may exacerbate it's magnitude in unhealthy populations such as those with knee OA.
Carbonic anhydrase I, II, IV and IX inhibition with a series of 7-amino-3,4-dihydroquinolin-2(1H)-one derivatives (2017)

A series of new derivatives was prepared by derivatisation of the 7-amino moiety present in 7-amino-3,4dihydroquinolin-2(1H)-one, a compound investigated earlier as CAI. The derivatisation was achieved by: i) reaction with arylsulfonyl isocyanates/aryl isocyanates; (ii) reaction with fluorescein isothiocyanate; (iii) condensation with substituted benzoic acids in the presence of carbodiimides; (iv) reaction with 2,4,6-trimethyl-pyrylium tetrafluoroborate; (v) reaction with methylsulfonyl chloride and (vi) reaction with maleic anhydride. The new compounds were assayed as inhibitors of four carbonic anhydrases (CA, EC 4.2.1.1) human (h) isoforms of pharmacologic relevance, the cytosolic hCA I and II, the membrane-anchored hCA IV and the transmembrane, tumour-associated hCA IX. hCA IX was the most inhibited isoform (K(I)s ranging between 243.6 and 2785.6 nm) whereas hCA IV was not inhibited by these compounds. Most derivatives were weak hCA I and II inhibitors, with few of them showing K(I)s&lt; 10 mu m. Considering that the inhibition mechanism with these lactams is not yet elucidated, exploring a range of such derivatives with various substitution patterns may be useful to identify leads showing isoform selectivity or the desired pharmacologic action.
How to Provide the Needed Protection from COVID-19 to Patients with Hematologic Malignancies (2021)

Patients with hematologic malignancies are particularly vulnerable to COVID-19 infections, and upon a pooled data analysis of 24 publications, there is evidence that they have suboptimal antibody responses to COVID-19 vaccination and boosters. To provide them the needed additional protection from COVID-19, it is imperative to achieve a 100% full immunization rate in health care workers and adult caretakers, and to foster research to test higher doses and repeated rounds of COVID-19 vaccines and the use of passive immune prophylaxis and therapy.
Supplementary Figures 1-4, Tables 1-6 from Mutational and Functional Analysis Reveals <i>ADAMTS18</i> Metalloproteinase as a Novel Driver in Melanoma (2023)

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Bacteriophage biocontrol: the technology matures (2008)

Use of bacteriophages (phages) as bacterial biocontrol agents was first envisioned by the phage pioneer Felix d’Herelle, and an increasing number of peer-reviewed studies point to the potential of phages to control spoilage and pathogenic bacteria in food. Several such phage-based biocontrol products have recently received regulatory approval and some have been commercialised. Obstacles nevertheless remain before widespread implementation can be achieved. These include consumer acceptance of the addition of ‘viruses’ to food as well as various commercial-production issues. Reviews of basic principles of phage-based biocontrol can be found elsewhere. Here we document recent phage-biocontrol regulatory successes as well as production considerations relevant to phage utilisation as a food additive.
Calcium waves in mammalian heart: quantification of origin, magnitude, waveform, and velocity (1990)

A dual, digital, indo-1 fluorescence imaging system was used to obtain high-speed ratiometric images of [Ca2+]i waves in single voltage-clamped mammalian cardiac cells. The spatiotemporal origin of [Ca2+]i waves in depolarized cells was detected as the spontaneous appearance, over 100-300 ms, of domelike regions of elevated [Ca2+]i, approximately 20 microns in diameter and 300 nM at the center. Images of [Ca2+]i taken at 67-ms intervals during propagation of [Ca2+]i waves revealed that the [Ca2+]i wave front was 1) constant in shape, 2) spatially steep, typically rising from 500 to 1200 nM in about 10 microns, and 3) propagating at constant velocity, typically 100 microns/s at 22 degrees C. The observed spatial and temporal patterns of origin and propagation of [Ca2+]i waves are consistent with the hypothesis that [Ca2+]i waves arise from propagating Ca2(+)-induced release of Ca2+ mediated by diffusion of cytosolic Ca2+. The [Ca2+]i waves are smaller in peak magnitude and can occupy a larger fraction of the cell than thought previously on the basis of indirect observations.
TRTH-21. GLIOMA SURVIVAL BENEFITS FROM NEUROSURGICAL DELIVERY OF PLGA/PEG INTERSTITIAL THERAPY (2017)

INTRODUCTION: The blood brain barrier is a critical limiting step to achieving therapeutic CNS drug concentrations. We have developed a poly(lactic-co-glycolic acid)/poly(ethylene glycol) (PLGA/PEG)-based Platform Technology to interstitially deliver multiple chemotherapy agents from a single thermo-setting paste, potentially filling the 3-week therapy gap that currently exists between surgery and commencement of radiotherapy in the treatment of high grade gliomas. Here we evaluate mouldable PLGA/PEG paste for combined temozolomide (TMZ) and etoposide (ETOP) delivery in an orthotopic high grade glioma model. METHODS: Drug release and preserved stability of the active TMZ molecule (AIC) was evaluated by fluoroscopic and LC-mass spectrometer based methods. In vitro cytotoxicity of released TMZ/ETOP was evaluated against high grade glioma cell lines and patient-derived primary cultures using metabolic assays. In vivo efficacy and overall survival were evaluated in the syngenic orthotopic 9L glioma rat model of intra cavity chemotherapy. RESULTS: TMZ and ETOP were released from PLGA/PEG alone or in combination over 2 weeks in vitro. Cytotoxicity of released drugs in vitro is comparable to directly applied agents, demonstrating the retained molecular integrity of TMZ/ETOP upon loading and releasing from PLGA/PEG. Both high (20% w/w TMZ / 50% w/w ETOP) and low (10% w/w TMZ / 25% w/w ETOP) doses were well tolerated in vivo, with no observable weight loss nor neurological deficits. Significant survival benefits from PLGA/PEG/TMZ/ETOP therapy were observed compared to surgery alone (49 vs. 14 days; p < 0.001), surgery with blank paste (49 vs. 14 days; p < 0.001) or surgery with daily oral TMZ (49 vs. 33 days; p < 0.004). CONCLUSIONS: This study demonstrates that interstitial delivery of TMZ/ETOP achieves significant glioma survival benefits. As such, PLGA/PEG paste applied to the post-surgical resection cavity offers a realistic opportunity for localised control of residual disease in pediatric and adult high grade gliomas.
Glial cell line-derived neurotrophic factor-secreting human neural progenitors show long-term survival, maturation into astrocytes, and no tumor formation following transplantation into the spinal cord of immunocompromised rats (2013)

Human neural progenitor cells (hNPCs) derived from the fetal cortex can be expanded in vitro and genetically modified through lentiviral transduction to secrete growth factors shown to have a neurotrophic effect in animal models of neurological disease. hNPCs survive and mature following transplantation into the central nervous system of large and small animals including the rat model of amyotrophic lateral sclerosis. Here we report that hNPCs engineered to express glial cell line-derived neurotrophic factor (GDNF) survive long-term (7.5 months) following transplantation into the spinal cord of athymic nude rats and continue to secrete GDNF. Cell proliferation declined while the number of astrocytes increased, suggesting final maturation of the cells over time in vivo. Together these data show that GDNF-producing hNPCs may be useful as a source of cells for long-term delivery of both astrocytes and GDNF to the damaged central nervous system.
Superconductivity in an Orbital‐Reoriented SnAs Square Lattice: A Case Study of Li0.6Sn2As2 and NaSnAs (2022)

Searching for functional square lattices in layered superconductor systems offers an explicit clue to modify the electron behavior and find exotic properties. The trigonal SnAs<sub>3</sub> structural units in SnAs-based systems are relatively conformable to distortion, which provides the possibility to achieve structurally topological transformation and higher superconducting transition temperatures. In the present work, the functional As square lattice was realized and activated in Li<sub>0.6</sub> Sn<sub>2</sub> As<sub>2</sub> and NaSnAs through a topotactic structural transformation of trigonal SnAs<sub>3</sub> to square SnAs<sub>4</sub> under pressure, resulting in a record-high T<sub>c</sub> among all synthesized SnAs-based compounds. Meanwhile, the conductive channel transfers from the out-of-plane p<sub>z</sub> orbital to the in-plane p<sub>x</sub> +p<sub>y</sub> orbitals, facilitating electron hopping within the square 2D lattice and boosting the superconductivity. The reorientation of p-orbital following a directed local structure transformation provides an effective strategy to modify layered superconducting systems.
When IC yield missed the target, who is at fault? (2004)

Silicon yield once was dominated by contaminants and particulates, making yield a process issue. But with today's electronics supply chain, multiple suspects may be indicted on manufacturability issues. Who is responsible for preventative actions in manufacturability and yield? The AUTHORs, representing a foundry, a fabless company, an IP provider, two EDA vendors, and an IC design team, will discuss the problems and the solutions for achieving manufacturability and yield goals.
Cross‐linking of aqueous base‐developable, photosensitive polynorbornene (2010)

Abstract The effect of epoxy‐based cross‐linking additives with different functionalities on the photolithographic properties, adhesion to substrates, and cross‐link density of a tetramethyl ammonium hydroxide‐developable polynorbornene‐based dielectric was investigated. Three different multifunctional epoxy additives were investigated: difunctional, trifunctional, and tetrafunctional compounds. It was found that incorporation of a small quantity (1 wt % of solution) of an ultraviolet‐absorbing tetrafunctional cross‐linker, tetraphenylol ethane tetraglycidyl ether, activated the photo‐catalyst and improved the sensitivity of a previously photosensitive polynorbornene‐based formulation by a factor of 3.7. The impact of the epoxy cross‐linkers on the physical and optical properties of the polymer formulations was evaluated. The contrast was improved from 7.37, for the control formulation, to 24.2. The polymer‐to‐substrate adhesion was also improved by addition of the tetrafunctional epoxy cross‐linker, which facilitates the development of high‐aspect‐ratio structures. Hollow‐core pillar structures in 40‐μm‐thick films with a depth‐to‐width aspect ratio of 13 : 1 were produced. The cross‐link density was studied by using swelling measurements of cured films to evaluate the average molecular weight between cross‐links. © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
Implications of Nitrosative Stress-Induced Protein Misfolding in Neurodegeneration (2011)

Several chronic neurodegenerative disorders manifest deposits of misfolded or aggregated proteins. Genetic mutations are the root cause for protein misfolding in rare families, but the majority of patients have sporadic forms possibly related to environmental factors. In some cases, the ubiquitin-proteasome system or molecular chaperones can prevent accumulation of aberrantly folded proteins. Recent studies suggest that generation of excessive nitric oxide (NO) and reactive oxygen species, in part due to overactivity of the N-methyl-D-aspartate (NMDA) subtype of glutamate receptor, can mediate protein misfolding in the absence of genetic mutation. S-Nitrosylation, or covalent reaction of NO with specific protein thiol groups, represents one mechanism contributing to NO-induced protein misfolding and neurotoxicity. Here, we present evidence suggesting that NO contributes to protein misfolding via S-nitrosylating protein-disulfide isomerase or the E3 ubiquitin ligase parkin. We discuss how the drugs memantine or NitroMemantine can inhibit excessive NMDA receptor activity to ameliorate NO production, protein misfolding, and neurodegeneration.
Criterion for finding the optimal electrocatalyst at any overpotential (2021)

The generic volcano plot is a widely employed practical tool to display and compare the activity of different electrocatalysts in dependence of a small number of descriptors. It is known that the apex of the volcano curve shifts with applied potential. However, the trend of the potential-dependent shift of the volcano apex has remained unclear. Herein, we address this question for a two-step electrocatalytic reaction. With the transfer coefficient assumed as 1/2, our analysis reveals that the adsorbate coverage at the volcano apex equals 1/2 regardless of potential. We present a criterion to predict the direction and magnitude of the apex shift as a function of the activation energies of the two steps. Thereafter, the criterion is extended to the oxygen reduction reaction. The influence of the transfer coefficient and the potential of zero charge on the volcano plot is revealed. Implications of the presented criterion for targeted design of electrocatalysts are discussed.
Pores Formed by Bis-macrocyclic Bola-amphiphiles in Vesicle and Planar Bilayer Membranes (1996)

A new series of bis-macrocyclic bola-amphiphiles were prepared, and their transport activities in vesicle and planar bilayer membranes were evaluated. From vesicle experiments, the apparent kinetic order in transporter indicates that aggregates are the kinetically active species. Step-conductance changes observed in planar bilayer membranes indicate that the compounds act as channels. Multiple copies of the same channel form in which the conductance is controlled by the macrocyclic portions of the structures. The pores are ion-selective in the sequence Cs(+) > K(+) > Na(+) > Cl(-), controlled by the polar head-groups of the structures. The data are consistent with a model involving the formation of active dimers.
Eliminating Structural Loss In Optomechanical Resonators Using Elastic Wave Interference (2013)

Ekinci, K.L., Roukes, M.L., Nanoelectromechanical systems (2005) Review of Scientific Instruments, 76 (6), pp. 061101-061112