gebhart/patrepeval huggingface dataset:
Structure–activity relationships in linear oligoester ion-channels (2008)

The ion transport activity of eighteen linear oligoesters was assessed using a quantitative fluorescence assay to monitor the collapse of a pH gradient across a vesicle bilayer membrane. Significant activity was associated with compounds that have extended lengths comparable to the thickness of the bilayer membrane, and with the most hydrophilic members of the compounds surveyed. Substantial differences in activity between constitutional isomers were also observed. The aggregation of active compounds in aqueous solution was detected by a pyrene fluorescence probe, and subsequently detected as a rate-limiting step in a sequential vesicle experiment.
ChemInform Abstract: SYNTHESIS OF FUNCTIONALIZED HYDROXYPHTHALIDES AND THEIR CONVERSION TO 3‐CYANO‐1(3H)‐ISOBENZOFURANONES. THE DIELS‐ALDER REACTION OF METHYL 4,4‐DIETHOXYBUTYNOATE AND CYCLOHEXADIENES (1985)

Abstract Die Synthese der substituierten Hydroxyphthalide (I) gelingt nach zwei Methoden: 1. Durch Metallierung von (II) bzw. (III) werden die Verbindungen (Ib) und (Ic) erhalten.
Correcting atmospheric CO 2 and CH 4 mole fractions obtained with Picarro analyzers for sensitivity of cavity pressure to water vapor (2019)

Abstract. Measurements of dry air mole fractions of atmospheric greenhouse gases are used in inverse models of atmospheric tracer transport to quantify their sources and sinks. The measurements have to be calibrated to a common scale to avoid bias in the inferred fluxes. For this purpose, the World Meteorological Organization (WMO) has set requirements for the interlaboratory compatibility of atmospheric greenhouse gas (GHG) measurements. A widely used series of devices for these measurements are the GHG analyzers manufactured by Picarro, Inc. These are often operated in humid air, and the effects of water vapor are corrected for in post-processing. Here, we report on rarely detected and previously unexplained biases of the water correction method for CO2 and CH4 in the literature. They are largest at water vapor mole fractions below 0.5 % H2O, which were undersampled in previous studies, and can therefore affect measurements obtained in humid air. Setups that dry sample air using Nafion membranes may be affected as well if there are differences in residual water vapor levels between sample and calibration air. The biases are caused by a sensitivity of the pressure in the measurement cavity to water vapor. We correct these biases by modifying the water correction method from the literature. Our method relies on experiments that maintain stable water vapor levels to allow equilibration of cavity pressure. In our experiments with the commonly used droplet method, this requirement was not fulfilled. Correcting CO2 measurements proved challenging, presumably because of our humidification method. Open questions pertain to differences among analyzers and variability over time. In our experiments, the biases amounted to considerable fractions of the WMO interlaboratory compatibility goals. Since measurements of dry air mole fractions of CO2 and CH4 are also subject to other uncertainties, correcting the cavity pressure-related biases helps keep the overall accuracy of measurements obtained with Picarro GHG analyzers in humid and potentially in Nafion-dried air within the WMO goals.
Reply to ‘Comment on ‘Efficacy and toxicity of treatment with the anti-CTLA-4 antibody ipilimumab in patients with metastatic melanoma after prior anti-PD-1 therapy’’ (2017)

Reply to ‘Comment on ‘Efficacy and toxicity of treatment with the anti-CTLA-4 antibody ipilimumab in patients with metastatic melanoma after prior anti-PD-1 therapy’’
Physicochemical Characterization of Solute Retention in Solvent Resistant Nanofiltration: the Effect of Solute Size, Polarity, Dipole Moment, and Solubility Parameter (2011)

Growing interest in nanofiltration for solvent purification requires a fundamental understanding of the physicochemical mechanisms of solute retention in organic solvent nanofiltration. In this study, the retention of a similar series of azo dyes with approximately similar molar mass (around 350 Da) by four nanofiltration membranes was studied. The membranes used are commercially available polymeric nanofiltration membranes with molecular weight cutoff between 150 and 300 Da (DuraMem150, StarMem122, NF270 and Desal-Dk). In order to correlate the retention with the size of the molecules, which is assumed to be one of the main factors that determines the retention, use was made of different parameters for the molecular size: molar mass, the Stokes diameter, the equivalent molar diameter, and the cavity surface in methanol and ethanol. All parameters were calculated by using molecular dynamics simulations. For each size parameter, the correlation with retention in nanofiltration experiments was calculated. For the StarMem122 membrane, zero retentions were observed due to the swelling of the membrane and pore size enlargement in methanol and ethanol. For the three other membranes, a fairly good correlation of the retention with the size could only be observed if the size difference between compounds is sufficiently large. Two other factors were studied by using molecular dynamics, i.e., the polarity of the molecule and the electron density of the molecule. The importance of these factors depends on the structure of the molecule as well as the functional groups of the polymer. A very good correlation has been observed for retention of dyes versus their dipole moment. Finally, the effect of solubility parameters of dyes on their retention did not show any significant effect.
Protective effect of an elastase inhibitor in a neuromyelitis optica-like disease driven by a peptide of myelin oligodendroglial glycoprotein (2012)

The similarities between Th17 EAE and NMO indicate that this model represents several aspects of NMO. Neutrophils are critical in the pathologies of both Th17-EAE and NMO, and therefore blockade of neutrophil elastase is a promising target in treating NMO.
Processing techniques for novel BARC chemistries (2002)

Previous generations of Bottom Anti-Reflective Coatings (BARCs) have had excellent optical properties but the etch performance for these BARC's were only 30% faster than the photoresist at best. A novel BARC chemistry has increased the capability of the photolithography process; this new chemistry has the capability to change etch and optical properties by the BARC bake process. This paper will present the bake process changes required to modify both etch characteristics and optical properties. Etch characteristics that were measured were bulk etch rate and etch selectivity to photoresist. Index of refraction and the absorption coefficients were measured for optical properties. Photolithography results focusing on Acetal and Hybrid photoresist types will be presented with specific attention to critical dimension control and focus latitude shifts, if any, associated with these BARC bake process changes.
Room temperature processed high mobility W-doped In2O3 electrodes coated via in-line arc plasma ion plating for flexible OLEDs and quantum dots LEDs (2018)

We fabricated W-doped In<sub>2</sub>O<sub>3</sub> (IWO) films at room temperature on a flexible PET substrate using an in-line arc plasma ion plating system for application as flexible transparent conducting electrodes (FTCEs) in flexible organic light emitting diodes (OLEDs) and quantum dots light emitting diodes (QDLEDs). Due to the high-energy flux of the sublimated ions generated from the plasma region, the IWO films showed a well-developed crystalline structure with a low sheet resistance of 36.39 Ohm/square and an optical transmittance of 94.6% even though they were prepared at room temperature. The low sheet resistance of the IWO film processed at room temperature is attributed to the high mobility (59 cm<sup>2</sup>/V-s) in the well-developed crystalline structure of the ion-plated IWO film and screening effect of W dopants. In addition, the better adhesion of the ion-plated IWO film on the PET substrate led to small critical outer and inner bending radii of 6 and 3 mm, respectively, against substrate bending. Due to the low sheet resistance, high optical transmittance, better crystallinity, better adhesion, and outstanding flexibility of the ion-plated IWO films, the flexible OLEDs and QDLEDs with the IWO electrodes showed better performances than flexible OLEDs and QDLEDs with sputtered flexible ITO anodes. This indicates that in-line arc plasma ion plating is a promising large area coating technique to realize room temperature processed high-quality FTCEs for flexible OLEDs and QDLEDs.
Slow-Channel Transgenic Mice: A Model of Postsynaptic Organellar Degeneration at the Neuromuscular Junction (1997)

The slow-channel congenital myasthenic syndrome (SCCMS) is a dominantly inherited disorder of neuromuscular transmission characterized by delayed closure of the skeletal muscle acetylcholine receptor (AChR) ion channel and degeneration of the neuromuscular junction. The identification of a series of AChR subunit mutations in the SCCMS supports the hypothesis that the altered kinetics of the endplate currents in this disease are attributable to inherited abnormalities of the AChR. To investigate the role of these mutant AChR subunits in the development of the synaptic degeneration seen in the SCCMS, we have studied the properties of the AChR mutation, epsilonL269F, found in a family with SCCMS, using both in vitro and in vivo expression systems. The mutation causes a sixfold increase in the open time of AChRs expressed in vitro, similar to the phenotype of other reported mutants. Transgenic mice expressing this mutant develop a syndrome that is highly reminiscent of the SCCMS. Mice have fatigability of limb muscles, electrophysiological evidence of slow AChR ion channels, and defective neuromuscular transmission. Pathologically, the motor endplates show focal accumulation of calcium and striking ultrastructural changes, including enlargement and degeneration of the subsynaptic mitochondria and nuclei. These findings clearly demonstrate the role of this mutation in the spectrum of abnormalities associated with the SCCMS and point to the subsynaptic organelles as principal targets in this disease. These transgenic mice provide a useful model for the study of excitotoxic synaptic degeneration.
Shoulder Scoring Scales for the Evaluation of Rotator Cuff Repair (2004)

Various assessment tools have been proposed for evaluation of shoulder function. Analyses of comparability, validity, and reliability among shoulder assessment tools are lacking. The purpose of our investigation was to compare the results of three commonly used shoulder assessment tools in the evaluation of a specific shoulder condition. Seventy-two full-thickness rotator cuff tears were treated with an open rotator cuff repair from 1986-1993. The average age of the patients at surgery was 58 years (range, 24-92 years). The median duration of followup at the time of evaluation for this study was 55 months (range, 24-102 months; standard deviation, 22 months). Correlation among the results of the UCLA, Constant-Murley, and the Simple Shoulder Test scales was fair (range, 0.66-0.76). More importantly, the three systems were evaluated for their ability to accurately predict improved motion, strength, and patient satisfaction. The Simple Shoulder Test and the Constant-Murley scales showed the highest positive predictive values. The Simple Shoulder Test is a patient-based self-assessment device that easily can be incorporated into a busy clinical practice, providing outcome data comparable with complex evaluation systems when evaluating the results of rotator cuff repair.
Three-dimensional capillary force assembly: Fabrication of white light emitters (2012)

This work uses convective assisted capillary force assembly from a collection of 100 nm fluorescent polystyrene nanoparticles to fabricate 4 μm wide and 1 μm high localized light-emitting superstructures. Large scale superstructures of about 10 000 particles are transferred on free silicon surfaces by microcontact printing. Optical characterization reveals that these sources emit polychromatic visible light from 400 to 800 nm equivalent to a white spectrum. Finally, single objects are studied to characterize the spatial distribution of the emitted color.
ChemInform Abstract: Catalytic Tandem Oxy‐Palladation and Vinylation. (1994)

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.
A putative oncogenic role for MPP11 in head and neck squamous cell cancer. (2000)

Genetic alterations of chromosome 7 are common in human cancer. Furthermore, previous studies have supported the presence of a gene important in a broad range of cancers at 7q22-31.1. There is evidence that supports an oncogenic function for this putative gene, as well as evidence that supports a tumor suppressive role. In this study, we used a cross-species candidate gene approach in combination with physical mapping to identify MPP11 as a candidate for the putative cancer-related activity at 7q22-31.1. We then analyzed primary head and neck squamous cell tumors (HNSCCs) for loss of heterozygosity/allelic imbalance (LOH/AI) at the MPP11 genomic locus. Thirty-eight percent of tumors examined displayed LOH/AI involving the MPP11 genomic locus. Mutation analysis of MPP11 in the latter samples did not identify any inactivating mutations. However, immunohistochemical staining of primary tumor sections and Western blot analysis of HNSCC cell lines revealed a tumor-specific high level of expression of MPP11p. Fluorescence in situ hybridization analysis done on the cell lines identified increased chromosome 7 copy number with a concomitant increase in MPP11 copy number. These results suggest an oncogenic role for MPP11 in HNSCC.
Environmental Enrichment Alters Splenic Immune Cell Composition and Enhances Secondary Influenza Vaccine Responses in Mice (2014)

Chronic stress has deleterious effects on immune function, which can lead to adverse health outcomes. However, studies investigating the impact of stress reduction interventions on immunity in clinical research have yielded divergent results, potentially stemming from differences in study design and genetic heterogeneity, among other clinical research challenges. To test the hypothesis that reducing glucocorticoid levels enhances certain immune functions, we administered influenza vaccine once (prime) or twice (boost) to mice housed in either standard control caging or environmental enrichment (EE) caging. We have shown that this approach reduces mouse corticosterone production. Compared with controls, EE mice had significantly lower levels of fecal corticosterone metabolites (FCMs) and increased splenic B and T lymphocyte numbers. Corticosterone levels were negatively associated with the numbers of CD19(+) (r(2) = 0.43, p = 0.0017), CD4(+) (r(2) = 0.28, p = 0.0154) and CD8(+) cells (r(2) = 0.20, p = 0.0503). Vaccinated mice showed nonsignificant differences in immunoglobulin G (IgG) titer between caging groups, although EE mice tended to exhibit larger increases in titer from prime to boost than controls; the interaction between the caging group (control versus EE) and vaccine group (prime versus boost) showed a strong statistical trend (cage-group*vaccine-group, F = 4.27, p = 0.0555), suggesting that there may be distinct effects of EE caging on primary versus secondary IgG vaccine responses. Vaccine-stimulated splenocytes from boosted EE mice had a significantly greater frequency of interleukin 5 (IL-5)-secreting cells than boosted controls (mean difference 7.7, IL-5 spot-forming units/10(6) splenocytes, 95% confidence interval 0.24-135.1, p = 0.0493) and showed a greater increase in the frequency of IL-5-secreting cells from prime to boost. Our results suggest that corticosterone reduction via EE caging was associated with enhanced secondary vaccine responses, but had little effect on primary responses in mice. These findings help identify differences in primary and secondary vaccine responses in relationship to stress mediators that may be relevant in clinical studies.
SecureDAV: a secure data aggregation and verification protocol for sensor networks (2005)

Sensor networks include nodes with limited computation and communication capabilities. One of the basic functions of sensor networks is to sense and transmit data to the end users. The resource constraints and security issues pose a challenge to information aggregation in large sensor networks. Bootstrapping keys is another challenge because public key cryptosystems are unsuitable for use in resource-constrained sensor networks. In this paper, we propose a solution by dividing the problem in two domains. First, we present a protocol for establishing cluster keys in sensor networks using verifiable secret sharing. We chose elliptic curve cryptosystems for security because of their smaller key size, faster computations and reductions in processing power. Second, we develop a secure data aggregation and verification (SecureDAV) protocol that ensures that the base station never accepts faulty aggregate readings. An integrity check of the readings is done using Merkle hash trees, avoiding over-reliance on the cluster-heads.
Classical and quantum tensor product expanders (2009)

We introduce the concept of quantum tensor product expanders. These generalize the concept of quantum expanders, which are quantum maps that are efficient randomizers and use only a small number of Kraus operators. Quantum tensor product expanders act on several copies of a given system, where the Kraus operators are tensor products of the Kraus operator on a single system. We begin with the classical case, and show that a classical two-copy expander can be used to produce a quantum expander. We then discuss the quantum case and give applications to the Solovay-Kitaev problem. We give probabilistic constructions in both classical and quantum cases, giving tight bounds on the expectation value of the largest nontrivial eigenvalue in the quantum case.
Functional recovery following peripheral nerve injury in the transgenic Thy1‐GFP rat (2013)

Transgenic mice have been previously used to assess nerve regeneration following peripheral nerve injury. However, mouse models are limited by their small caliber nerves, short nerve lengths, and their inability to fully participate during behavioral assessments. The transgenic Thy1 GFP rat is a novel transgenic rat model designed to assess regeneration following peripheral nerve injury. However, return of functional and behavioral recovery following nerve injury has not yet been evaluated in these rats. In this study, we ask whether differences in anatomy, recovery of locomotion, myological, and histomorphological measures exist between transgenic Thy1 GFP rats when compared to wild type (WT) Sprague Dawley rats following unilateral sciatic nerve injury. We found that both motor and sensory neuronal architecture, overground and skilled locomotion, muscle force, motor unit number estimation (MUNE) and wet muscle weights, and histomorphometric assessments are similar between both genetic phenotypes. Overall, these data support the use of the transgenic Thy1-GFP rat in experiments assessing functional and behavioral recovery following nerve injury and repair.
Influence of Disc Degeneration on Mechanism of Thoracolumbar Burst Fractures (1992)

In order to clarify the pathomechanism of thoracolumbar burst fractures and to evaluate the influence of disc degeneration and bone mineral density, a biomechanical study was performed using cadaveric spines. Eleven motion segments of thoracolumbar spines from human cadavers were compressed vertically until a fracture occurred. In addition, bone mineral density and degree of disc degeneration were determined for each specimen. Compression of 7 of 11 specimens resulted in the typical burst fracture characterized by retropulsion of a bony fragment into the spinal canal and an increase of the interpedicular distance. All seven specimens showed disruptions of the middle end plate and disc materials in the vertebral body. The fracture line was located between the middle of the end plate and the middle of the posterior wall cortex. No burst fractures were seen in the specimens with severely degenerated discs and osteoporosis. In order to confirm the stress state in a vertebra that induces the burst fracture, finite element analysis of one motion segment was also carried out under the same mechanical conditions as the experiments in this study. As a result of calculation for the healthy disc, the highest stresses under axial compression were concentrated in the following areas: the middle of the end plate, the cancellous bone under the nucleus pulposus, and the middle of the posterior wall cortex. This implies that the above regions are more vulnerable to vertical compressive load. In the analysis of specimens with severely degenerated discs, stresses were very low at the end plate and cancellous bone under the nucleus.(ABSTRACT TRUNCATED AT 250 WORDS)
Guiding atypical facial growth back to normal. Part 2: Causative factors, patient assessment, and treatment planning. (2012)

It has been well-documented that the most common factors associated with atypical facial growth involve the airway, which when compromised, leads to mouth breathing and associated aberrant tongue function. The most common changes include downward and backward rotation of the mandible, deficient nasomaxillary complex, a vertical growth pattern, posterior displacement of the TMJ, narrow maxillary arch, dental malocclusions, and dental crowding. It is imperative that clinicians recognize, diagnose, and begin treatment as early as possible when facial growth deviates from normal. Several specific diagnostic tools, coupled with traditional diagnostic records, assist the clinician in determining the degree and direction of atypical growth. Such a clear-cut diagnostic process sets in motion the treatment plan requirements necessary to accomplish the goal of returning facial growth to normal. Diagnosis and treatment planning requires that each practitioner has a broad base of knowledge, a good power of observation, and insight into the complex subject of facial growth and development.
Development of Bevirimat (PA-457): first-in-class HIV maturation inhibitor (2006)

Bevirimat is the first in a new class of HIV drugs called maturation inhibitors that specifically inhibit the last step in processing of Gag, the conversion of capsid-SP1 (p25) to capsid (p24). Following bevirimat treatment, viral particles released from infected cells have abnormal core structures and are non-infectious. The compound is a potent inhibitor of HIV-1 replication and retains activity against drug resistant isolates. It is synergistic with most approved drugs in vitro. Bevirimat is metabolized by glucuronidation and has minimal potential for clinically significant drug interactions.

Bevirimat has good oral bioavailability and long half-life (2.5–3 days) in humans, making it suitable for once-daily oral dosing. It has been well tolerated in clinical studies, following administration to more than 300 people for up to 2 weeks. In a Phase 2a study, 10 days of bevirimat monotherapy at 200 mg/day resulted in >1 log median viral load reduction. A Phase 2b study was recently initiated where bevirimat is being studied in combination with approved drugs in a dose escalation format, in order to identify optimal dose(s) for Phase 3 clinical trials.