gebhart/patrepeval huggingface dataset:
Effusive molecular beam-sampled Knudsen flow reactor coupled to vacuum ultraviolet single photon ionization mass spectrometry using an external free radical source (2013)

A new apparatus using vacuum ultraviolet single photon ionization mass spectrometry (VUV SPIMS) of an effusive molecular beam emanating from a Knudsen flow reactor is described. It was designed to study free radical-molecule kinetics over a significant temperature range (300-630 K). Its salient features are: (1) external free radical source, (2) counterpropagating molecular beam and diffuse VUV photon beam meeting in a crossed-beam ion source of a quadrupole mass spectrometer with perpendicular ion extraction, (3) analog detection of the photocurrent of the free radical molecular cation, and (4) possibility of detecting both free radicals and closed shell species in the same apparatus and under identical reaction conditions owing to the presence of photoelectrons generated by the photoelectric effect of the used VUV-photons. The measured thermal molecular beam-to-background ratio was 6.35 ± 0.39 for Ar and 10.86 ± 1.59 for i-C4H10 at 300 K, a factor of 2.52 and 1.50 smaller, respectively, than predicted from basic gas-dynamic considerations. Operating parameters as well as the performance of key elements of the instrument are presented and discussed. Coupled to an external free radical source a steady-state specific exit flow of 1.6 × 10(11) and 5.0 × 10(11) molecule s(-1) cm(-3) of C2H5(●) (ethyl) and t-C4H9(●) (t-butyl) free radicals have been detected using VUV SPIMS at their molecular ion m/z 29 and 57, respectively, at 300 K.
On the Importance of Mathematical Methods for Analysis of MALDI-Imaging Mass Spectrometry Data (2012)

Summary In the last decade, matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS), also called as MALDI-imaging, has proven its potential in proteomics and was successfully applied to various types of biomedical problems, in particular to histopathological label-free analysis of tissue sections. In histopathology, MALDI-imaging is used as a general analytic tool revealing the functional proteomic structure of tissue sections, and as a discovery tool for detecting new biomarkers discriminating a region annotated by an experienced histologist, in particular, for cancer studies. A typical MALDI-imaging data set contains 10 8 to 10 9 intensity values occupying more than 1 GB. Analysis and interpretation of such huge amount of data is a mathematically, statistically and computationally challenging problem. In this paper we overview some computational methods for analysis of MALDI-imaging data sets. We discuss the importance of data preprocessing, which typically includes normalization, baseline removal and peak picking, and hightlight the importance of image denoising when visualizing IMS data.
Renal impairment impact on CPX-351 pharmacokinetics and safety. (2015)

e13533 Background: A 300 patient randomized Phase 3 study comparing CPX-351 vs. 7+3 control is underway for newly diagnosed older patients (age 60-75) with secondary AML. Encapsulation of cytarabine (Ara-c) and daunorubicin (dauno) at a 5:1 molar ratio within stable low cholesterol liposomes (CPX-351) markedly alters the pharmacological characteristics of both drugs resulting in substantial increases in plasma half-life, AUC, and Cmax. Pharmacokinetic data (Phase 1, 100 and 134 units/m2) and safety data from a pair of randomized studies (Phase 2, 100 units/m2) were analyzed for the impact of renal function impairment on pharmacokinetics and safety to determine whether dose modifications would be necessary for patients with reduced renal function. Methods: See Feldman EJ, et al. J Clin Oncol 2011;29(8):979-85 (Phase 1); Lancet JE, et al., Blood 2014;123(21):3239-46 and Cortes JE, et al. Cancer 2015;121(2):234-42 (Phase 2) for details. Results: See Table. There was a proportional increase in the Cmax and AUC with increasing CPX-351 dose. Within each dose level there was little change in Cmax or AUC across the three renal function groups (≥90 vs. 60-89 vs. <60 mL/min GFR). Additional data for the safety of patients treated at 100 units/m2was reviewed without evidence of increased toxicity occurring in the presence of impaired renal function. Conclusions: Impaired renal function does not appear to significantly impact patient exposure to Ara-c or dauno or treatment safety following CPX-351 administration suggesting that dose modifications for renal impairment will not be necessary. This hypothesis is being tested in a Phase 3 study where CPX-351 dose is kept constant for all patients with baseline serum creatinine ≤2.0 mg/dL. Clinical trial information: NCT00389428.Impact of GFR on median drug exposure. CPX-351 Dose units/m2 GFR Group mL/min n Median CrCl mL/min Ara-c Dauno Cmax ng/mL AUC ng*hr/mL Cmax ng/mL AUC ng*hr/mL 101 ≥90 7 129.9 41,700 1,422,200 26,600 590,970 60-89 5 75.5 38,900 1,007,113 24,500 502,673 <60 1 53.3 41,500 1,166,425 25,000 556,153 134 ≥90 2 119.3 58,750 1,874,307 37,750 988,420 60-89 3 75.4 57,200 1,856,063 36,100 926,610 <60 1 27.5 67,900 2,114,600 44,400 1,114,750
A simple reversed-complexity Wyner-Ziv video coding mode based on a spatial reduction framework (2007)

A spatial-resolution reduction based framework for incorporation of a Wyner-Ziv frame coding mode in existing video codecs is presented, to enable a mode of operation with low encoding complexity. The core Wyner-Ziv frame coder works on the Laplacian residual of a lower-resolution frame encoded by a regular codec at reduced resolution. The quantized transform coefficients of the residual frame are mapped to cosets to reduce the bit-rate. A detailed rate-distortion analysis and procedure for obtaining the optimal parameters based on a realistic statistical model for the transform coefficients and the side information is also presented. The decoder iteratively conducts motion-based side-information generation and coset decoding, to gradually refine the estimate of the frame. Preliminary results are presented for application to the H.263+ video codec.
Laser frequency control using an optical resonator locked to an electronic oscillator (1997)

A new method for controlling a laser's center frequency is reported. This method extends the Pound-Drever-Hall technique, which delivers exceptional laser linewidth. The new technique, applicable over a broad range of wavelengths, produces a laser beam with both narrow linewidth and stable center frequency. A diode-pumped ring laser is locked to an ultrahigh-finesse, tunable optical resonator which, in turn, is locked to an electronic (5 MHz) oscillator using a difference frequency developed by locking a second laser to the resonator. A 1064-nm beam is reported with linewidth less than 0.004 Hz and center-frequency stability given by the electronic reference. For the case of an oven-controlled quartz crystal, the laser center-frequency stability is less than 1 part in 10/sup 11/ per day with root Allan variance of 10/sup -12/ for a 1000-s time delay. The entire system is compact, and all elements are solid-state, making it useful both in the laboratory and in a number of space-based applications.
Space-time transmit strategies and channel feedback generation for wireless fading channels (2002)

The performance of future cellular and personal communications is expected to be limited by the "down-link" from the base station to the mobile. In this context, using sophisticated processing at the base station transmitter represents a promising method for enhancing the downlink capacity. Specifically, we consider space-time transmit processing, which exploits antenna arrays at the base station. Two extreme strategies for achieving this are space-time codes, which provide transmit diversity for combating Rayleigh fading without requiring knowledge of the space-time channel to the receiver, and transmit beamforming, which uses feedback regarding the space-time channel to increase the effective channel gain to the user of interest. We review some results regarding both space-time codes and transmit beamforming, including information-theoretic insights that show that transmit beamforming offers significant performance gains even with imperfect channel feedback. We then present the main result of the paper, which is a novel method for generating space-time channel feedback.
Suture Growth Modulated by the Oscillatory Component of Micromechanical Strain (2003)

Sutures are fibrous connective tissue articulations between intramembranous craniofacial bones. Sutures are composed of fibroblastic cells with their matrices in the center and osteogenic cells in the periphery producing a matrix that is mineralized during skeletal growth. Whether oscillatory forces stimulate sutural growth is unknown. In the present work, we applied static and cyclic forces with the same peak magnitude of 5N to the maxilla in growing rabbits and quantified (1) acute in vivo sutural bone strain responses and (2) chronic growth responses in the premaxillomaxillary suture (PMS) and nasofrontal suture (NFS). Bone strain recordings showed that the waveforms of static force and 1-Hz cyclic force were expressed as corresponding static and cyclic sutural strain patterns in both the PMS and NFS, with the mean peak PMS strain (-1451 +/- 137 microepsilon for the cyclic and -1572 +/- 138 microepsilon for the static) approximately 10-fold higher than the mean peak NFS strain (124 +/- 9 microepsilon for the cyclic and 134 +/- 9 microepsilon for the static). Strain polarity was the opposite: compressive for the PMS but tensile for the NFS. However, on application of repetitive 5N cyclic and static forces in vivo for 10 minutes/day over 12 days, cyclic loading induced significantly greater sutural widths for the compressed PMS (95.1 +/- 8.3 microm) than sham control (69.8 +/- 8.2 microm) and static loading (58.9 +/- 2.8 microm; p < 0.01). Interestingly, the same trend was true for the NFS under tensile strain: significantly greater sutural width for cyclic loading (267.4 +/- 64.2 microm) than sham control (196.0 +/- 10.1 microm) and static loading (169.9 +/- 11.4 microm). Cell counting in 110 x 110 microm grids laid over sutures disclosed significantly more sutural cells on repetitive cyclic loading than sham control and static loading (p < 0.05) for both the PMS and NFS. Fluorescent labeling of newly formed sutural bone demonstrated more osteogenesis on cyclic loading in comparison with sham control and static loading. Thus, the oscillatory component of cyclic force or more precisely the resulting cyclic strain experienced in sutures is a potent stimulus for sutural growth. The increased sutural growth by cyclic mechanical strain in the tensed NFS and compressed PMS suggests that both microscale tension and compression induce anabolic sutural growth response.
Predictors and outcomes of histological remission in ulcerative colitis treated to endoscopic healing (2020)

In patients with active ulcerative colitis treated-to-target of endoscopic healing, 55% simultaneously achieved histologic remission. Histologic remission, particularly in patients achieving modified Mayo endoscopy score 1, was associated with favourable outcomes. Treating to a target of histologic remission over endoscopic healing requires prospective evaluation.
C-type natriuretic peptide in the cardiac ventricle in mice (2001)

C-type natriuretic peptide (CNP) is a third member of the natriuretic peptide family, which was originally isolated from the porcine brain. Subsequent investigations have revealed that CNP is localized in human, bovine and canine vascular endothelial cells and inner medullary collecting duct cells of the human kidney. Although both atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) are present in the heart, reports have been negative for CNP in either mammalian atria or ventricles. With the increasing use of the mouse in integrative physiology, the goal of the current study was to determine for the first time, the relative quantity of the natriuretic peptide family, including ANP, BNP, CNP and Dendroaspis natriuretic peptide (DNP) in the ventricle of normal adult male mice by immunohistochemistry. The antibody employed for ANP and DNP was cross-reactive in all species, BNP was directed toward porcine, and CNP to human, porcine and rat. The relative quantity of different peptides was estimated from the staining score of microscopic observations by independent observers. In contrast to the previous findings in other mammalian ventricular myocardium, the staining score of murine ventricular CNP was significantly higher than ANP (3.0±0.5 vs. 0.4±0.2, n=7, P<0.05). There was no significant difference between CNP and DNP, which tended to be higher than BNP (3.0±0.5 and 2.4±0.4 vs.1.6±0.3, respectively, n=7) where 0=no staining and 4=marked intensity. In addition, the presence of CNP immunostaining was markedly positive in both cardiac myocytes and cardiac fibroblast-like cells. These studies importantly report that unlike other mammalian species, the normal murine ventricular myocardium may produce CNP. Based upon the known growth-inhibiting properties of CNP, this natriuretic peptide may play an important local role in the control of myocardial hypertrophy and fibrosis.
A highly decoupled transmit–receive array design with triangular elements at 7T (2018)

An array design with triangular coils provides effective decoupling mechanisms for nearest and next-nearest neighboring elements, as well as diversity in B<sub>1</sub> profiles along the z-direction, although this also means that individual slices must be shimmed separately. This design is well suited for parallel transmit applications while also having high receive sensitivity.
Festphasensynthese von Thiooligosacchariden (1999)

Keine Schutzgruppen enthalten die hochreaktiven, polymergebundenen Zucker-1-thiolate 1, die mit Zuckertriflaten 2 in hohen Ausbeuten zu Thiooligosacchariden 3 umgesetzt wurden. Tr = Trityl = Triphenylmethyl, Tf = Trifluormethansulfonyl, Bz = Benzoyl.
Final Report: Development of Renewable Microbial Polyesters for Cost Effective and Energy- Efficient Wood-Plastic Composites (2010)

In this project, we proposed to produce wood fiber reinforced thermoplastic composites (WFRTCs) using microbial thermoplastic polyesters in place of petroleum-derived plastic. WFRTCs are a rapidly growing product area, averaging a 38% growth rate since 1997. Their production is dependent on substantial quantities of petroleum based thermoplastics, increasing their overall energy costs by over 230% when compared to traditional Engineered Wood Products (EWP). Utilizing bio-based thermoplastics for these materials can reduce our dependence on foreign petroleum. We have demonstrated that biopolymers (polyhydroxyalkanoates, PHA) can be successfully produced from wood pulping waste streams and that viable wood fiber reinforced thermoplastic composite products can be produced from these materials. The results show that microbial polyester (PHB in this study) can be extruded together with wastewater-derived cell mass and wood flour into deck products having performance properties comparable to existing commercial HDPE/WF composite products. This study has thus proven the underlying concept that the microbial polyesters produced from waste effluents can be used to make cost-effective and energy-efficient wood-plastic composites. The cost of purified microbial polyesters is about 5-20 times that of HDPE depending on the cost of crude oil, due to high purification (40%), carbon substrate (40%) and sterilized fermentation (20%) costs for the PHB. Hence, the ability to produce competitive and functional composites with unpurified PHA-biomass mixtures from waste carbon sources in unsterile systems—without cell debris removal—is a significant step forward in producing competitive value-added structural composites from forest products residuals using a biorefinery approach. As demonstrated in the energy and waste analysis for the project, significant energy savings and waste reductions can also be realized using this approach. We recommend that the next step for development of useful products using this technology is to scale the technology from the 700-L pilot reactor to a small-scale production facility, with dedicated operation staff and engineering controls. In addition, we recommend that a market study be conducted as well as further product development for construction products that will utilize the unique properties of this bio-based material.
Multiplex-PCR method for the simultaneous detection of lactic acid bacteria producing in foods the biogenic amines histamine, tyramine, and putrescine (2005)

n a screening of primers, we have selected three pairs of primers for a multiplex PCR assay for the simultaneous detection of lactic acid bacteria (LAB) strains, which potentially produce histamine, tyramine, and putrescine on fermented foods. These primers were based on sequences from histidine, tyrosine, and ornithine decarboxylases from LAB. Under the optimized conditions, the assay yielded a 367-bp DNA fragment from histidine decarboxylases, a 924-bp fragment from tyrosine decarboxylases, and a 1,446-bp fragment from ornithine decarboxylases. When the DNAs of several target organisms were included in the same reaction, two or three corresponding amplicons of different sizes were observed. This assay was useful for the detection of amine-producing bacteria in control collection strains and in a LAB collection. No amplification was observed with DNA from nonproducing LAB strains. This article is the first describing a multiplex PCR approach for the simultaneous detection of potentially amine-producing LAB in foods. It can be easily incorporated into the routine screening for the accurate selection of starter LAB and in food control laboratories.
Control of the Swelling Rate of Superporous Hydrogels (2001)

Superporous hydrogels (SPHs) have a fast swelling property because of the presence of interconnected pores. While the fast swelling property is an advantage, sometimes it is necessary to control the swelling rate. A method of coating the SPH surface with a polymer layer was studied to control the swelling kinetics of SPHs in aqueous solutions. Poly(ethylene glycol-b-tetramethylene oxide) (PEGTMO), an amphiphilic block copolymer, dissolved in ethanol was used. The coating was done by dipping and equilibrium soaking in PEGTMO solutions. The delay in swelling of PEGTMO-coated SPHs was dependent on the PEGTMO concentration used. Poly(acrylamide-co-acrylic acid)-SPHs coated with a PEGTMO film showed lower hydrophilicity as measured by contact angle. SEM analysis revealed that the number of surface pores of SPHs was decreased by coating with PEGTMO. It appears that the PEGTMO coating reduced the surface hydrophilicity as well as the porosity, leading to slower swelling in aqueous solution.
974 MODULATION OF AKT/MTOR SIGNALING OVERCOMES SUNITINIB RESISTANCE IN RENAL AND PROSTATE CANCER CELLS (2012)

INTRODUCTION AND OBJECTIVES: The androgen receptor (AR) plays a critical role progression of castration-resistant prostate cancer (CRPC) following first line androgen deprivation therapy. Several 2nd generation anti-androgens (AA) have demonstrated anticancer activity in CRPC models. In this study, we evaluated the effects of a novel AA, PF-05234848, on cell growth and AR transcriptional activity in prostate cancer compared to the second generation antiandrigen MDV-3100.
Molecular coevolution of kisspeptins and their receptors from fish to mammals (2010)

Kisspeptin and its receptor, GPR54, play a pivotal role in vertebrate reproduction. Recent advances in bioinformatic tools combined with comparative genomics have led to the identification of a large number of kisspeptin and GPR54 genes in a variety of vertebrate species. Genome duplications may have produced at least two isoforms of both ligand (KiSS1 and KiSS2) and receptor (GPR54-1 and GPR54-2). Additional isoforms of kisspeptin (KiSS1b) and GPR54 (GPR54-1b) have been found in an amphibian species, Xenopus (Silurana) tropicalis. Here, we describe the evolutionary lineages of these kisspeptin and GPR54 isoforms using genome synteny and phylogenetic analyses, and possible molecular interactions between kisspeptin and GPR54 subtypes based on ligand-receptor selectivity. Together, kisspeptin and GPR54 provide an excellent model for understanding molecular coevolution of the peptide ligand and GPCR pairs.
Mass Transfer Studies in a Pilot Scale RPB with Different Packing Diameters (2018)

Rotating packed beds (RPBs) aim to intensify mass transfer processes by exploiting centrifugal forces. The limited use of RPBs in the chemical industry can be explained among others by missing comparative studies between state of the art equipment (e.g., packed columns) and RPBs to quantify the benefits that come along by the use of RPBs. The effective interfacial area, mainly dependent on the rotational speed, was found to be equal for both rotors (outer packing radii of 0.18 and 0.28 m, respectively) for rotational speeds larger than 20 s–1. The specific energy dissipation per provided interfacial area is newly introduced in order to link the pressure drop with the mass transfer. Compared to packed columns, the moles of CO2 absorbed per packing volume were found to increase by a factor of up to 3 in RPBs.
Comparative analysis of IL6 and IL6 receptor gene polymorphisms in mastocytosis (2012)

Mastocytosis is a rare disease with reported high interleukin-6 (IL6) levels influencing disease severity. The present study investigated polymorphisms within the genes that encode IL6 and its receptor (IL6R) in relation to mastocytosis development in a case-control design. Analysis of the IL6R Asp358Ala polymorphism showed that carriers of the AA genotype had a 2·5-fold lower risk for mastocytosis than those with the AC or CC genotypes. No association with mastocytosis was found for the IL6-174G/C polymorphism, however, it may influence the effect of IL6R polymorphism. To the best of our knowledge this is the first study analysing IL6/IL6R polymorphisms in mastocytosis.
Effect of Interference Screw Depth on Fixation Strength in Biceps Tenodesis (2013)

This study shows the importance of determining the optimal depth of interference screw placement during biceps tenodesis to obtain optimal biomechanical performance and reduce the risk of fixation failure.
Instabilities of Offline RL with Pre-Trained Neural Representation (2021)

In offline reinforcement learning (RL), we seek to utilize offline data to evaluate (or learn) policies in scenarios where the data are collected from a distribution that substantially differs from that of the target policy to be evaluated. Recent theoretical advances have shown that such sample-efficient offline RL is indeed possible provided certain strong representational conditions hold, else there are lower bounds exhibiting exponential error amplification (in the problem horizon) unless the data collection distribution has only a mild distribution shift relative to the target policy. This work studies these issues from an empirical perspective to gauge how stable offline RL methods are. In particular, our methodology explores these ideas when using features from pre-trained neural networks, in the hope that these representations are powerful enough to permit sample efficient offline RL. Through extensive experiments on a range of tasks, we see that substantial error amplification does occur even when using such pre-trained representations (trained on the same task itself); we find offline RL is stable only under extremely mild distribution shift. The implications of these results, both from a theoretical and an empirical perspective, are that successful offline RL (where we seek to go beyond the low distribution shift regime) requires substantially stronger conditions beyond those which suffice for successful supervised learning.