gebhart/patrepeval huggingface dataset:
Bioconversion of Thermochemical Intermediates (2022)

Thermochemical (TC) biofuels production via both pyrolysis and hydrothermal liquefaction produces aqueous waste streams, typically with organic compounds at concentrations of -50-100 g/L. These streams represent a wastewater treatment cost and carbon loss for the TC biorefinery, but the concentration range for these compounds is ideal for bioconversion. To that end, the Bioconversion of Thermochemical Intermediates (BTI) project is developing advanced analytics and engineered microbes to convert these waste streams to co-products, with the overall aim of improving the economics and carbon conversion efficiency of TC biorefining. To date, we have primarily focused on development of advanced analytical chemistry approaches to fully characterize TC aqueous streams and engineering of Pseudomonas putida for conversion of non-conventional substrates, including methylated phenolics, cyclic ketones, furans, and C1-C3 light oxygenates, into atom-efficient products. Two primary challenges are the rapid deployment of aqueous-compatible analytics to changing upstream conditions and dealing with the toxicity of the feed streams to engineered microbes. The project efforts have resulted in engineered strains of P. putida able to consume 90% of the organic compounds in aqueous waste streams from catalytic fast pyrolysis, more than 300-fold toxicity tolerance improvements in P. putida, and carbon closures exceeding 90% for TC wastewater streams across multiple processing technologies.
Stochastic natural gradient descent draws posterior samples in function\n space (2018)

Recent work has argued that stochastic gradient descent can approximate the\nBayesian uncertainty in model parameters near local minima. In this work we\ndevelop a similar correspondence for minibatch natural gradient descent (NGD).\nWe prove that for sufficiently small learning rates, if the model predictions\non the training set approach the true conditional distribution of labels given\ninputs, the stationary distribution of minibatch NGD approaches a Bayesian\nposterior near local minima. The temperature $T = \\epsilon N / (2B)$ is\ncontrolled by the learning rate $\\epsilon$, training set size $N$ and batch\nsize $B$. However minibatch NGD is not parameterisation invariant and it does\nnot sample a valid posterior away from local minima. We therefore propose a\nnovel optimiser, "stochastic NGD", which introduces the additional correction\nterms required to preserve both properties.\n
A Novel Urine Method for the Diagnosis of Active Tuberculosis by Immunoassay for the Detection of ESAT-6 Using Hydrogel Nanoparticles in HIV Patients (2021)

Background: In patients with HIV, conventional tests are of low sensitivity; therefore, a new diagnostic test with hydrogel nanoparticles with reactive blue dye is proposed, which allows the capture, conservation and concentration of ESAT-6 in urine. NIPAs are copolymers that capture low molecular weight proteins and protect against enzymatic degradation. Using an immunoassay, it is possible to detect and quantify ESAT-6 present in urine as a possible marker of active TB. Design/Methods: Study in Lima, Peru, HIV+ participants, ≥18 years with and without tuberculosis (TB). Smear microscopy, culture in solid medium and urine immunoassay were performed. The reference was the diagnosis of TB by radiological or clinical microbiological criteria (indication for TB treatment). There were 2 preanalytical processes: untreated and treated urine (centrifuged, heated), then incubation with NIPAm. After washing, elution, sonication, heat and centrifugation, the final eluate was obtained. This was placed on nitrocellulose membranes, which by means of fixation and incubation processes with anti-ESAT-6 and anti-IgG antibodies, revelation with C-DiGit&reg Blot Scanner and FluorChem R FR0001. Calibration curves were included in the membranes, density was measured using Image J software. ROC curves, sensitivity and specificity were obtained. Results: The result by groups was HIV+ patient: ROC: 0.75, cut-off point ≥24.06 ng/ml, sensitivity 76.32%, specificity 68.89%, patients ≤200 cells CD4 mm3/ml, ROC: 0.78, cutoff point ≥26.20 ng/ml, sensitivity 75.86%, specificity 71.88%, patients >200 CD4 mm3 cells/ml, ROC: 0.73, cutoff point ≥24.6 CD4 mm3/ml, sensitivity 73.68%, specificity 73.68%. Conclusions: The ESAT-6 detection assay using NIPAm was effective, with higher rates in patients with ≤200 CD4 cells/mm3, the test being more sensitive than smear and culture, but less specific.
Effects of human interleukin 1 and human tumor necrosis factor on human T lymphocyte colony formation. (1987)

The growth of T lymphocyte colonies in agar is dependent on the cooperation of a number of different cell types and their products. Among these interacting cells are monocytes and/or macrophages. Monocytes are capable of producing both interleukin 1 (IL-1) and tumor necrosis factor (TNF). These two factors display a positive influence on T cell colony formation. Recombinant IL-1 and recombinant TNF were both shown to stimulate T cell colony growth in a dose-dependent manner, and this stimulation could be blocked by prior incubation with anti-IL-1 or anti-TNF, respectively. In addition, conditioned medium obtained from monocytes cultured in the presence of endotoxin also stimulated T cell colony formation. This stimulation by monocyte-conditioned medium was partially suppressed by incubation with anti-TNF or anti-IL-1, while incubation with both antibodies together displayed greater suppression. In conclusion, monocytes produce at least two factors, IL-1 and TNF, which can stimulate T cell colony formation by peripheral blood lymphocytes.
ChemInform Abstract: Convenient Preparation of Mononuclear and Dinuclear Ruthenium Hydride Complexes for Catalytic Application. (2000)

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.
ChemInform Abstract: The Michael Addition of Sulfur Anions to β,β‐Substituted Nα‐Formyl‐α,β‐dehydroamino Acid Esters. (1988)

Abstract Ethyl cyanoacetate (I) is coupled with the ketones (II) to produce the N‐formyl α,β‐unsaturated amino acid esters (III).
Direct Band Gap Tensile-Strained Germanium (2009)

We report up to 2.3% biaxial tensile-strained Ge layers grown on InGaAs/GaAs buffer layers. Low-temperature photoluminescence shows a dramatic intensity increase for &gt;2% tensile strained Ge, confirming the existence of a direct band gap Ge.
Controlled Functionalization of Polystyrene:  Introduction of Reactive Groups by Multisite Metalation with Superbase and Reaction with Electrophiles (1996)

The controlled functionalization of polystyrene using a process of metalation with a potassium superbase followed by reaction with electrophiles is described. The method is advantageous because metalation is extremely efficient, occurring rapidly even at room temperature, and the degree of functionalization can be controlled over a very broad range. Functionalization with trimethylsilyl groups allows effective monitoring and quantification of the metalation process. Other examples of modification include the introduction of small dendritic fragments by reaction with a dendron having an aldehydic focal point or the introduction of carboxylic acid pendant groups. This method, which has little effect on the polydispersity of the polymer, has broad applicability for the functionalization of a wide spectrum of polymers containing active hydrogens and may also be used to prepare randomly branched or star structures.
Discovery of Latent 3D Keypoints via End-to-end Geometric Reasoning (2018)

This paper presents KeypointNet, an end-to-end geometric reasoning framework to learn an optimal set of category-specific 3D keypoints, along with their detectors. Given a single image, KeypointNet extracts 3D keypoints that are optimized for a downstream task. We demonstrate this framework on 3D pose estimation by proposing a differentiable objective that seeks the optimal set of keypoints for recovering the relative pose between two views of an object. Our model discovers geometrically and semantically consistent keypoints across viewing angles and instances of an object category. Importantly, we find that our end-to-end framework using no ground-truth keypoint annotations outperforms a fully supervised baseline using the same neural network architecture on the task of pose estimation. The discovered 3D keypoints on the car, chair, and plane categories of ShapeNet are visualized at http://keypointnet.github.io/.
Measuring and correcting wobble in large-scale transmission radiography (2016)

The method improves the precision of wobble affected images, which should help improve detection of threats and the identification of different materials in the image.
MEC: Network Optimized Multi-stage Erasure Coding for Scalable Storage Systems (2017)

In scalable storage systems, there are two kinds of methods for data redundancy: mirroring and parity. Each has its pros and cons. Mirroring creates a large amount of redundancy data, resulting in less usable space. Write performance degrades proportionally to the redundancy level due to an increase in communication. Parity-based methods partition data into multiple pieces, add parity information, and distribute the pieces of data and parity information. Parity-based methods are not often used with memory class media that are faster than the network, because distributing the data across servers results in low read performance. This research aims to establish an efficient data protection method that can be applied to fast, memory class media. We propose a new parity-based method called Multi-stage Erasure Coding (MEC), which creates two different erasure codes: one at the data transmission source server, and the other at the destination server. We show that our method reduces the space required to achieve redundancy while achieving high performance by making the amount of write communication independent of the redundancy level. We built a prototype program using MEC on a commodity cluster server. We show that compared with conventional parity-based methods with redundancy level 2, read I/O throughput is over one order of magnitude higher thanks to local reads and that write I/O throughput is almost the same due to network bottleneck.
Small Molecule Mediated Proliferation of Primary Retinal Pigment Epithelial Cells (2013)

Retinal pigment epithelial (RPE) cells form a monolayer adjacent to the retina and play a critical role in the visual light cycle. Degeneration of RPE cells results in retinal disorders such as age-related macular degeneration. Cell transplant strategies have potential therapeutic value for such disorders; however, risks associated with an inadequate supply of donor cells limit their therapeutic success. The identification of factors that proliferate RPE cells ex vivo could provide a renewable source of cells for transplantation. Here, we report that a small molecule (WS3) can reversibly proliferate primary RPE cells isolated from fetal and adult human donors. Following withdrawal of WS3, RPE cells differentiate into a functional monolayer, as exhibited by their expression of mature RPE genes and phagocytosis of photoreceptor outer segments. Furthermore, chemically expanded RPE cells preserve vision when transplanted into dystrophic Royal College of Surgeons (RCS) rats, a well-established model of retinal degeneration.
Structure of Brewer’s Spent Grain Lignin and Its Interactions with Gut Microbiota in Vitro (2016)

Lignin is part of dietary fiber, but its conversion in the gastrointestinal tract is not well understood. The aim of this work was to obtain structural information on brewer's spent grain (BSG) lignin and to understand the behavior of the polymeric part of lignin exposed to fecal microbiota. The original BSG and different lignin fractions were characterized by pyrolysis-GC/MS with and without methylation. Methylation pyrolysis proved that the ratio between guaiacyl and syringyl units was similar in all lignin samples, but the ratio between p-coumaric and ferulic acids varied by the isolation method. Combined pyrolysis results indicated higher acylation of γ-OH groups in syringyl than in guaiacyl lignin units. The polymeric lignin structure in the alkali-soluble fraction after enzymatic hydrolysis was slightly altered in the in vitro colon fermentation, whereas lignin in the insoluble residue after enzymatic treatments remained intact.
Establishment of a biophysical model to optimize endoscopic targeting of magnetic nanoparticles for cancer treatment (2017)

Superparamagnetic iron oxide nanoparticles (SPION) may be used for local tumor treatment by coupling them to a drug and accumulating them locally with magnetic field traps, that is, a combination of permanent magnets and coils. Thereafter, an alternating magnetic field generates heat which may be used to release the thermosensitively bound drug and for hyperthermia. Until today, only superficial tumors can be treated with this method. Our aim was to transfer this method into an endoscopic setting to also reach the majority of tumors located inside the body. To find the ideal endoscopic magnetic field trap, which accumulates the most SPION, we first developed a biophysical model considering anatomical as well as physical conditions. Entities of choice were esophageal and prostate cancer. The magnetic susceptibilities of different porcine and rat tissues were measured with a superconducting quantum interference device. All tissues showed diamagnetic behavior. The evaluation of clinical data (computed tomography scan, endosonography, surgical reports, pathological evaluation) of patients gave insight into the topographical relationship between the tumor and its surroundings. Both were used to establish the biophysical model of the tumors and their surroundings, closely mirroring the clinical situation, in which we could virtually design, place and evaluate different electromagnetic coil configurations to find optimized magnetic field traps for each tumor entity. By simulation, we could show that the efficiency of the magnetic field traps can be enhanced by 38-fold for prostate and 8-fold for esophageal cancer. Therefore, our approach of endoscopic targeting is an improvement of the magnetic drug-targeting setups for SPION tumor therapy as it holds the possibility of reaching tumors inside the body in a minimal-invasive way. Future animal experiments must prove these findings in vivo.
PRINCIPLES OF ENERGY CONSERVATION IN EVOLUTIONARY GENETICS ANALYSIS (2005)

The use of concepts from evolutionary genetics in the solution of optimization problems, widely known as evolutionary computing, is a well-known and nowadays mature field. Recently, evolutionary computing has also been successfully applied to the solution of boundary value problems in engineering, namely, heat conduction problems. Here, we present an extension of that work in which the reverse is attempted: Evolutionary computing methodology is used in conjunction with concepts of energy conservation in order to study Darwinian evolution itself. The motivation and methodology are presented in the first section of the paper, while a particularly interesting and controversial problem, namely, the introduction of transgenic organisms into the wild, is discussed in the second part.
ChemInform Abstract: Synthesis and Antiviral Activity of Oxaselenolane Nucleosides. (2001)

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.
Staphylococcal Exfoliative Toxins Cleave α- and β-Melanocyte-Stimulating Hormones (2000)

The staphylococcal exfoliative toxins (ETs) A and B (ETA and ETB) are 27-kDa exotoxins produced by certain strains of Staphylococcus aureus and are the causative agents of staphylococcal scalded-skin syndrome. The crystal structures of the ETs strongly indicate that the proteins are members of the serine protease family of enzymes, although protease activity until now has not yet been conclusively demonstrated. Here, we show that the peptide beta-melanocyte-stimulating hormone (beta-MSH) is cleaved by ETA and that both ETA and ETB are capable of cleaving alpha-MSH. Both toxins exhibit cleavage at specific glutamic acid residues in MSH peptides. Moreover, biologically inactive mutants of ETA were incapable of cleaving beta-MSH.
Abnormal corneal epithelial maintenance in mice heterozygous for the micropinna microphthalmia mutation Mp (2016)

We investigated the corneal morphology of adult Mp/+ mice, which are heterozygous for the micropinna microphthalmia mutation, and identified several abnormalities, which implied that corneal epithelial maintenance was abnormal. The Mp/+ corneal epithelium was thin, loosely packed and contained goblet cells in older mice. Evidence also suggested that the barrier function was compromised. However, there was no major effect on corneal epithelial cell turnover and mosaic patterns of radial stripes indicated that radial cell movement was normal. Limbal blood vessels formed an abnormally wide limbal vasculature ring, K19-positive cells were distributed more widely than normal and K12 was weakly expressed in the peripheral cornea. This raises the possibilities that the limbal-corneal boundary was poorly defined or the limbus was wider than normal. BrdU label-retaining cell numbers and quantitative clonal analysis suggested that limbal epithelial stem cell numbers were not depleted and might be higher than normal. However, as corneal epithelial homeostasis was abnormal, it is possible that Mp/+ stem cell function was impaired. It has been shown recently that the Mp mutation involves a chromosome 18 inversion that disrupts the Fbn2 and Isoc1 genes and produces an abnormal, truncated fibrillin-2(MP) protein. This abnormal protein accumulates in the endoplasmic reticulum (ER) of cells that normally express Fbn2 and causes ER stress. It was also shown that Fbn2 is expressed in the corneal stroma but not the corneal epithelium, suggesting that the presence of truncated fibrillin-2(MP) protein in the corneal stroma disrupts corneal epithelial homeostasis in Mp/+ mice.
Large-scale fiber interferometric sensor arrays with multiple optical amplifiers (2002)

Many applications require using common input and output fibers to support a large number of interferometric fiber sensors located far from the receiving electronics. Passive multiplexing of sensors is limited by splitting and dissipative losses to approximately 10 sensors per pair of fibers. A large scale array (200-1000 sensors) will thus require 40-200 telemetry fibers, which is unmanageable in practice. We report a novel method for multiplexing hundreds of sensors per pair of fibers, which incorporates fiber amplifiers into a time-domain multiplexed array with a ladder topology.
An Integrated Design Pipeline for Tactile Sensing Robotic Manipulators (2022)

Traditional robotic manipulator design methods require extensive, time-consuming, and manual trial and error to produce a viable design. During this process, engineers often spend their time redesigning or reshaping components as they discover better topologies for the robotic manipulator. Tactile sensors, while useful, often complicate the design due to their bulky form factor. We propose an integrated design pipeline to streamline the design and manufacturing of robotic manipulators with knitted, glove-like tactile sensors. The proposed pipeline allows a designer to assemble a collection of modular, open-source components by applying predefined graph grammar rules. The end result is an intuitive design paradigm that allows the creation of new virtual designs of manipulators in a matter of minutes. Our framework allows the designer to fine-tune the manipulator's shape through cage-based geometry deformation. Finally, the designer can select surfaces for adding tactile sensing. Once the manipulator design is finished, the program will automatically generate 3D printing and knitting files for manufacturing. We demonstrate the utility of this pipeline by creating four custom manipulators tested on real-world tasks: screwing in a wing screw, sorting water bottles, picking up an egg, and cutting paper with scissors.
Evaluation of laser-induced breakdown spectroscopy (LIBS) as a new in situ chemical sensing technique for the deep ocean (2006)

Present day expeditionary oceanography based on short term ship and submersible deployments is beginning to shift to an ocean observatory mode where long term temporally focused studies become feasible. As a result, a greater need for in situ chemical and biological sensors is evolving. Laser-induced breakdown spectroscopy (LIBS) possesses many of the characteristics required for such in situ chemical sensing, and is a promising technique for field measurements in extreme environments. LIBS has many possible applications in the ocean, including the analysis of rocks, sediments, and hydrothermal vent fluids. Although many LIBS researchers have focused their work on solids, very little attention has been paid to bulk liquid analysis, and especially on the effect of oceanic pressures on LIBS signals. In this work, preliminary laboratory experiments are presented to validate the technique in a simulated deep ocean environment; more specifically, the focus is on using LIBS to study hydrothermal vent fluids.
Polarization Aberration Diagrams (1989)

Polarization aberrations are variations of the polarization associated with different ray paths through an optical system. This paper presents particular polarization aberration expansion that is second order in the object and pupil coordinates and describes polarization effects that are functionally equivalent to the wavefront aberration terms: piston, tilt, and defocus. This polarization aberration expansion is applicable to weakly polarizing systems, such as radially symmetric systems of lenses and coatings, as well as to strongly polarizing systems incorporating polarizers and retarders. A computer simulation of this expansion has been performed, and graphical results are presented displaying the effect of 24 of these polarization aberrations acting on linearly and circularly polarized light.
Prostaglandin F2 alpha effects on intraocular pressure negatively correlate with FP-receptor stimulation. (1989)

According to the current working classification for prostanoid receptors, the prostaglandin F2 alpha-sensitive receptor (FP-receptor) may be identified by comparing the rank order of activity of prostaglandin F2 alpha (PGF2 alpha) and its analogues. In order to further understand the pharmacology of PGF2 alpha-induced ocular hypotension, the intraocular pressure response to PGF2 alpha and selected analogues was compared with their rank order of activity in typical FP-receptor preparations such as contraction of the cat iris sphincter and affinity for corporal luteal membrane binding sites. The rank order of potency for decreasing intraocular pressure was as follows: PGF2 alpha greater than PGF1 alpha greater than 16-phenoxytetranor PGF2 alpha greater than 17-phenyltrinor PGF2 alpha = fluprostenol (inactive). For cat iris sphincter contraction, the rank order of potency appears to be fluprostenol = 17-phenyltrinor PGF2 alpha greater than 16-phenoxytetranor PGF2 alpha = PGF2 alpha greater than PGF1 alpha. The rank order of potency for PGF2 alpha analogues in decreasing intraocular pressure appears to negatively correlate with the rank order for cat iris sphincter contraction and literature values for corporal luteal membrane binding. It is concluded that the ocular hypotensive effect of PGF2 alpha is not mediated by the FP-receptor.