gebhart/patrepeval huggingface dataset:
A Comparison of Membrane Bioreactor and Conventional-Activated-Sludge Mixed Liquor and Biosolids Characteristics (2005)

Characteristics and behavior of raw and digested mixed liquor derived from a membrane bioreactor (MBR) and a full-scale activated-sludge (FSAS) facility were compared. The accumulation of nondegradable chemical oxygen demand in the MBR appears to play an important role in increasing the observed biological yield coefficient (Y(obs)), reducing average floc size, decreasing total suspended solids/total solids and volatile suspended solids/volatile solids (VS) ratios, and reducing specific-oxygen-uptake rates of the mixed liquor relative to FSAS-derived biological solids. Membrane bioreactor sludges exhibited lower VS destruction following 30 days mesophilic-anaerobic and aerobic digestion when compared to FSAS sludges. Significant deterioration in dewatering behavior was observed for the FSAS biosolids after anaerobic digestion and, to a lesser extent, following aerobic digestion. In comparison, digestion had a small affect on dewatering efficiency and conditioner requirements for MBR biosolids. Full-scale facilities using membrane separation may need to tailor digestion and dewatering processes to the specific characteristics of MBR sludges.
CCDC 290456: Experimental Crystal Structure Determination (2006)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
ChemInform Abstract: Photoinduced Reduction of Group 16 Heteroatom Compounds with the Aid of Samarium Diiodide. (1998)

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.
Characterization of two-photon point-spread function in turbid medium by direct measurements, multicolor imaging, and blind deconvolution (2001)

Over the past decade, scanning fluorescence microscopy based on two-photon excitation has become an important branch of microscopic bio-imaging. Compared to traditional scanning techniques, two-photon microscopy offers a number of distinct advantages. First, scanning of the point-like excitation spot used for imaging results in images with excellent axial depth discrimination. In addition, the limited extent of the excitation volume also limits specimen photo-damage to the focal volume. Finally, the long, near-infixed wavelengths used for sample excitation allow in-depth, non-invasive imaging of optically turbid biological samples. For in-depth imaging, the microscopic objective and often optically heterogeneous biological specimen forms a complex system. To optimize imaging quality in two-photon microscopy, an understanding of the point-spread-function (PSF) is essential. In this work, we attempted to characterize the two-photon PSF by two methods: direct imaging of 0.1 ym fluorescent microspheres and multicolor imaging of 2 ym green fluorescent microspheres in a uniform blue fluorescent background. In both measurements, the turbidity of the surrounding medium was varied by changing the concentration of Liposyn III, a scattering component in the specimen. We found that at discrete Liposyn III concentrations between 0 and 2%, the PSF widths were not affected by the amount of scatterers present. However, the imaged contrast continued to degrade as a function of the amount of scatter. This suggests that the broadening of the tail region of the PSF can be the cause of image contrast loss. We will also discuss the possibility of using blind- deconvolution as a method to obtain PSF information in complex biological specimen.
A Bayesian Adaptive Design in Cancer Phase I Trials Using Dose Combinations in the Presence of a Baseline Covariate (2018)

A Bayesian adaptive design for dose finding of a combination of two drugs in cancer phase I clinical trials that takes into account patients heterogeneity thought to be related to treatment susceptibility is described. The estimation of the maximum tolerated dose (MTD) curves is a function of a baseline covariate using two cytotoxic agents. A logistic model is used to describe the relationship between the doses, baseline covariate, and the probability of dose limiting toxicity (DLT). Trial design proceeds by treating cohorts of two patients simultaneously using escalation with overdose control (EWOC), where at each stage of the trial, the next dose combination corresponds to the <i>α</i> quantile of the current posterior distribution of the MTD of one of two agents at the current dose of the other agent and the next patient's baseline covariate value. The MTD curves are estimated as function of Bayes estimates of the model parameters at the end of trial. Average DLT, pointwise average bias, and percent of dose recommendation at dose combination neighborhoods around the true MTD are compared to the design that uses the covariate to the one that ignores the baseline characteristic. We also examine the performance of the approach under model misspecifications for the true dose-toxicity relationship. The methodology is further illustrated by the case of a pre-specified discrete set of dose combinations.
Desorption-induced evolution of cubic and hexagonal ices in an ultrahigh vacuum and cryogenic temperatures (2021)

Reflection absorption infrared spectroscopic investigations of multilayer films of acetonitrile (ACN) and water in an ultrahigh vacuum under isothermal conditions showed the emergence of cubic (ice I<sub>c</sub>) and hexagonal (ice I<sub>h</sub>) ices depending on the composition of the film. The experiments were conducted with a mixed film of 300 monolayers in thickness and the ACN : H<sub>2</sub>O monolayer ratios were varied from 1 : 5 to 5 : 1. Mixed films were deposited at 10 K and warmed to 130-135 K, where ACN desorbed subsequently and IR spectral evolution was monitored continuously. While the emergence of ice I<sub>c</sub> at 130 K has been reported, the occurrence of ice I<sub>h</sub> at this temperature was seen for the first time. Detailed investigations showed that ice I<sub>h</sub> can form at 125 K as well. Crystallization kinetics and activation energy (<i>E</i><sub>a</sub>) for the emergence of ice I<sub>h</sub> were evaluated using the Avrami equation.
Techniques for measurement of the optical properties of materials (1990)

This effort is aimed at the general area of measurement of the optical properties of materials. The type of measurement techniques addressed here are applicable to any studies where optical means are used to study the characteristics of a material. However, the devices developed were designed to accommodate materials as they might be found exposed outdoors, as well as prepared laboratory samples. 35 refs., 42 figs., 16 tabs.
Zinc-Induced Metallothionein in Centenarian Offspring From a Large European Population: The MARK-AGE Project (2017)

Metallothionein (MT) family are cysteine-rich proteins that regulate zinc (Zn) homeostasis and protect against oxidative damage. Studies in transgenic mice have shown that MT favorably influence longevity, although their role in human aging is not completely understood. Within the European multicenter study MARK-AGE, we analyzed MT induction after Zn treatment in peripheral blood mononuclear cells (PBMCs) and its relation with redox biomarkers in 2,936 age-stratified subjects (35-75 years) including the general population (RASIG), centenarian offspring (GO), and their spouses (SGO). We found that the lymphocyte capability to induce MT in response to Zn is not affected by aging. However, GO participants showed lower Zn-induced MT and increased basal expression of MT1A, MT1X, and ZnT-1 genes than RASIG subjects. Moreover, Zn-induced MT levels were found to be inversely related with oxidative stress markers (plasma protein carbonyls, 3-nitrotyrosine, and malondialdehyde) in the whole population, but not in GO subjects. In conclusion, our results support the hypothesis that the response to Zn is attenuated in PBMCs of centenarian offspring compared to the general population as a consequence of a tighter control of Zn homeostasis which is likely to provide them constant protection against stress stimuli over the whole lifespan.
Synchronized TV Whitespace Spectrum Access (2014)

Restrictions on adjacent channel interference leave large swath of spectrum unused. According to FCC, the adjacent channels of an active TV channel are excluded from unlicensed usage. This protection is crucial when estimating the amount of available TV whitespace. By its nature this limitation is t
Prion-like domains drive CIZ1 assembly formation at the inactive X chromosome (2021)

CIZ1 forms large assemblies at the inactive X chromosome (Xi) in female fibroblasts in an Xist lncRNA-dependent manner and is required for accurate maintenance of polycomb targets genome-wide. Here we address requirements for assembly formation and show that CIZ1 undergoes two direct interactions with Xist, via independent N- and C-terminal domains. Interaction with Xist, assembly at Xi, and complexity of self-assemblies formed in vitro are modulated by two alternatively spliced glutamine-rich prion-like domains (PLD1 and 2). PLD2 is dispensable for accumulation at existing CIZ1-Xi assemblies in wild-type cells but is required in CIZ1-null cells where targeting, assembly, and enrichment for H3K27me3 and H2AK119ub occur de novo. In contrast, PLD1 is required for both de novo assembly and accumulation at preexisting assemblies and, in vitro, drives formation of a stable fibrillar network. Together they impart affinity for RNA and a complex relationship with repeat E of Xist. These data show that alternative splicing of two PLDs modulates CIZ1's ability to build large RNA-protein assemblies.
Video-rate stereo matching using markov random field TRW-S inference on a hybrid CPU+FPGA computing platform (2013)

We demonstrate a video-rate stereo matching system implemented on a hybrid CPU+FPGA platform (Convey HC-1). Emerging applications such as 3D gesture recognition and automotive navigation demand fast and high quality stereo vision. We describe a custom hardware-accelerated Markov Random Field inference system for this task. Starting from a core architecture for streaming tree-reweighted message passing (TRW-S) inference, we describe the end-to-end system engineering needed to move from this single frame message update to full stereo video. We partition the stereo matching procedure across the CPU and the FPGAs, and apply both function-level pipelining and frame-level parallelism to achieve the required speed. Experimental results show that our system achieves a speed of 12 frames per second for challenging video stereo matching tasks. We note that this appears to be the first implementation of TRW-S inference at video rates, and that our system is also significantly faster than several recent GPU implementations of similar stereo inference methods based on belief propagation (BP).
Oral desensitization therapy for peanut allergy induces dynamic changes in peanut‐specific immune responses (2022)

Oral desensitization therapy with AR101 leads to decreased basophil sensitivity to peanut and reshapes peanut-reactive T effector cell responses supporting its potential as an immunomodulatory therapy.
Supplementary Methods from Therapeutic Destruction of Insulin Receptor Substrates for Cancer Treatment (2023)

&lt;p&gt;PDF file - 102K, Additional data regarding experimental procedures, kinetic experiments and anti-tumor activity of NT 157.&lt;/p&gt;
Automated Segmented-Flow Analysis – NMR with a Novel Fluoropolymer Flow Cell for High-Throughput Screening (2022)

High-throughput analysis in fields such as industrial biotechnology, combinatorial chemistry, and life sciences is becoming increasingly important. Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique providing exhaustive molecular information on complex samples. Flow NMR in particular is a cost- and time-efficient method for large screenings. In this study, we have developed a novel 3.0 mm inner diameter polychlorotrifluoroethylene (PCTFE) flow cell for a segmented-flow analysis (SFA) - NMR automated platform. The platform uses FC-72 fluorinated oil and fluoropolymer components to achieve a fully fluorinated flow path. Samples were repeatably transferred from 96-deepwell plates to the flow cell by displacing a fixed volume of oil, with a transfer time of 42 s. <sup>1</sup>H spectra were acquired fully automated with 500 and 600 MHz NMR spectrometers. The spectral performance of the novel PCTFE cell was equal to that of commercial glass cells. Peak area repeatability was excellent with a relative standard deviation of 0.1-0.5% for standard samples, and carryover was below 0.2% without intermediate washing. The sample temperature was conditioned by using a thermostated transfer line in order to reduce the equilibration time in the probe and increase the throughput. Finally, analysis of urine samples demonstrated the applicability of this platform for screening complex matrices.
ChemInform Abstract: CYANOPHOSPHORUS COMPOUNDS. 6. THE :P‐CN GROUP AS A PSEUDO‐CHALCOGEN; CYANOPHOSPHINIDENE‐SUBSTITUTED HETEROCYCLENE (1980)

Abstract Das durch Methylierung des entsprechenden 2‐Chlor‐heterocyclus erhältliche Tetrafluoroborat (I) setzt sich mit [1 8]Krone‐ 6‐Na‐ oder ‐triethylammonium‐dicyandiphosphid zu dem 2‐(Dicyanphosphino)‐chlorid (II) um.
Sprayable and biodegradable, intrinsically adhesive wound dressing with antimicrobial properties (2019)

Conventional wound dressings are difficult to apply to large total body surface area (TBSA) wounds, as they typically are prefabricated, require a layer of adhesive coating for fixation, and need frequent replacement for entrapped exudate. Large TBSA wounds as well as orthopedic trauma and low-resource surgery also have a high risk of infection. In this report, a sprayable and intrinsically adhesive wound dressing loaded with antimicrobial silver is investigated that provides personalized fabrication with minimal patient contact. The dressing is composed of adhesive and biodegradable poly(lactic-<i>co</i>-glycolic acid) and poly(ethylene glycol) (PLGA/PEG) blend fibers with or without silver salt (AgNO<sub>3</sub>). in vitro studies demonstrate that the PLGA/PEG/Ag dressing has antimicrobial properties and low cytotoxicity, with antimicrobial silver controllably released over 7-14 days. In a porcine partial-thickness wound model, the wounds treated with both antimicrobial and nonantimicrobial PLGA/PEG dressings heal at rates similar to those of the clinical, thin film polyurethane wound dressing, with similar scarring. However, PLGA/PEG adds a number of features beneficial for wound healing: greater exudate absorption, integration into the wound, a 25% reduction in dressing changes, and tissue regeneration with greater vascularization. There is also modest improvement in epidermis thickness compared to the control wound dressing.
Closure Schemes for Nonlinear Bistable Systems Subjected to Correlated Noise: Applications to Energy Harvesting from Water Waves (2015)

Moment Equation Closure Minimization (MECM) method has been developed for the inexpensive approximation of the steady state statistical structure of bistable systems which have bimodal potential shapes and which are subjected to correlated excitation.Our approach relies on the derivation of moment equations that describe the dynamics governing the two-time statistics.These are then combined with a closure scheme which arises from a non-Gaussian pdf representation for the joint response-excitation statistics.We demonstrate its effectiveness through the application on a bistable nonlinear singledegree-of-freedom ocean wave energy harvester with linear damping and the results compare favorably with direct Monte Carlo Simulations.
Supplementary Figure 4 from HO-3867, a Safe STAT3 Inhibitor, Is Selectively Cytotoxic to Ovarian Cancer (2023)

&lt;p&gt;PDF file - 220K, Representative Annexin V flow cytomety plots of CHO, H9c2 and A2780 cells.&lt;/p&gt;
Assessment of the clinical utility of four NGS panels in myeloid malignancies. Suggestions for NGS panel choice or design (2020)

The diagnosis of myeloid neoplasms (MN) has significantly evolved through the last few decades. Next Generation Sequencing (NGS) is gradually becoming an essential tool to help clinicians with disease management. To this end, most specialized genetic laboratories have implemented NGS panels targeting a number of different genes relevant to MN. The aim of the present study is to evaluate the performance of four different targeted NGS gene panels based on their technical features and clinical utility. A total of 32 patient bone marrow samples were accrued and sequenced with 3 commercially available panels and 1 custom panel. Variants were classified by two geneticists based on their clinical relevance in MN. There was a difference in panel's depth of coverage. We found 11 discordant clinically relevant variants between panels, with a trend to miss long insertions. Our data show that there is a high risk of finding different mutations depending on the panel of choice, due both to the panel design and the data analysis method. Of note, CEBPA, CALR and FLT3 genes, remains challenging the use of NGS for diagnosis of MN in compliance with current guidelines. Therefore, conventional molecular testing might need to be kept in place for the correct diagnosis of MN for now.
TSC1 Promotes B Cell Maturation but Is Dispensable for Germinal Center Formation (2015)

Accumulating evidence indicates that the tuberous sclerosis complex 1 (TSC1), a tumor suppressor that acts by inhibiting mTOR signaling, plays an important role in the immune system. We report here that TSC1 differentially regulates mTOR complex 1 (mTORC1) and mTORC2/Akt signaling in B cells. TSC1 deficiency results in the accumulation of transitional-1 (T1) B cells and progressive losses of B cells as they mature beyond the T1 stage. Moreover, TSC1KO mice exhibit a mild defect in the serum antibody responses or rate of Ig class-switch recombination after immunization with a T-cell-dependent antigen. In contrast to a previous report, we demonstrate that both constitutive Peyer's patch germinal centers (GCs) and immunization-induced splenic GCs are unimpaired in TSC1-deficient (TSC1KO) mice and that the ratio of GC B cells to total B cells is comparable in WT and TSC1KO mice. Together, our data demonstrate that TSC1 plays important roles for B cell development, but it is dispensable for GC formation and serum antibody responses.
Analytical solution for phonon transport across thin films (2013)

The numerical solution of the Boltzmann equation for the thin film applications requires extensive computational power. An analytical solution to the phonon transport equation is fruitful in order to reduce the computational effort and cost. In the present study, an analytical solution for the phonon radiative transport equation in thin film is carried out. The analytical treatment of the problem reduces the two identical radiative transport equations to Fredholm integral equation of the second kind. The resulting phonon intensity data are presented in terms of the dimensionless temperature across the gray thin films of silicon and diamond. The findings are compared with their counterparts predicted from the numerical simulations. The study is extended to include the effect of the film thickness on the dimensionless temperature distribution. It is found that the analytical solution for temperature agrees well with the numerical predictions. Reducing the film thickness increases the temperature jump at the film edges, which is more pronounced for the diamond film.
The complete genome and methylome of Helicobacter pylori hpNEAfrica strain HP14039 (2019)

We have described the complete genome of <i>H. pylori</i> strain HP14039. The information regarding phylo-geography, methylome and associated metadata would help scientific community to study more about hpNEAfrica population type.
An antidote approach to reduce risk and broaden utility of antibody-based therapeutics (2017)

Antibody therapeutics offer effective treatment options for a broad range of diseases. One of the greatest benefits of antibody therapeutics is their extraordinarily long serum half-life, allowing infrequent dosing with long-lasting effects. A characteristic of antibodies that drives long half-life is the ability to interact with the recycling receptor, FcRn, in a pH-dependent manner. The benefit of long half-life, however, carries with it liabilities. Although the positive effects of antibody therapeutics are long-lasting, any acute adverse events or chronic negative impacts, such as immunosuppression in the face of an infection, are also long-lasting. Therefore, we sought to develop antibodies with a chemical handle that alone would enjoy the long half-life of normal antibodies but, upon addition of a small-molecule antidote, would interact with the chemical handle and inhibit the antibody recycling mechanism, thus leading to rapid degradation and shortened half-life <i>in vivo</i> Here we present a proof of concept study where we identify sites to incorporate a non-natural amino acid that can be chemically modified to modulate FcRn interaction <i>in vitro</i> and antibody half-life <i>in vivo</i> This is an important first step in developing safer therapeutics, and the next step will be development of technology that can perform the modifying chemistry <i>in vivo</i>.
Facial cleft presenting as a congenital facial papule (2022)

Tessier number 3 craniofacial clefts are a rare congenital deformity of the oronasoocular region with variable severity, most often with serious impacts on appearance and function due to involvement of the bone and soft tissue. However, they can occasionally manifest mildly as a skin-colored congenital facial papule present with subtle anatomic anomalies and signs of deeper involvement, such as crusting and oozing. Recognizing that a congenital facial papule, including non-midline lesions, may be the presenting sign of an underlying developmental anomaly is important to avoid missing the diagnosis of a more extensive underlying congenital defect. We present a rare case of a forme fruste variant of a Tessier number 3 craniofacial cleft to raise awareness of its presentation and advise initial management in hopes of improving outcomes.
Enterogenous bacterial glycolipids are required for the generation of natural killer T cells mediated liver injury (2016)

Glycolipids are potent activator of natural killer T (NKT) cells. The relationship between NKT cells and intestinal bacterial glycolipids in liver disorders remained unclear. We found that, in sharp contrast to specific pathogen-free (SPF) mice, germ-free (GF) mice are resistant to Concanavalin A (ConA)-induced liver injury. ConA treatment failed to trigger the activation of hepatic NKT cells in GF mice. These defects correlated with the sharply reduced levels of CD1d-presented glycolipid antigens in ConA-treated GF mice compared with SPF counterparts. Nevertheless, CD1d expression was similar between these two kinds of mice. The absence of intestinal bacteria did not affect the incidence of αGalCer-induced liver injury in GF mice. Importantly, we found the intestinal bacteria contain glycolipids which can be presented by CD1d and recognized by NKT cells. Furthermore, supplement of killed intestinal bacteria was able to restore ConA-mediated NKT cell activation and liver injury in GF mice. Our results suggest that glycolipid antigens derived from intestinal commensal bacteria are important hepatic NKT cell agonist and these antigens are required for the activation of NKT cells during ConA-induced liver injury. These finding provide a mechanistic explanation for the capacity of intestinal microflora to control liver inflammation.