gebhart/patrepeval huggingface dataset:
Use of Lyophilised Microbiota Capsules for Fecal Microbiota Transplantation in Patients With Clostridium difficile Infection (2018)

Introduction: Fecal Microbiota Transplantation (FMT) using liquefied stool is an effective treatment of Clostridium difficile Infection (CDI). We aimed to examine the efficacy and feasibility of use of lyophilised microbiota capsules for patients with CDI in Australia where epidemic strains are rare. The primary outcome was the proportion of patients without recurrent CDI (rCDI) at 26 weeks. Secondary outcomes included optimal dose, adverse events and change in symptoms. Methods: Patients with CDI were prospectively entered into the FMT capsule trial between November 2015 and June 2017. Capsules comprised lyophilised full spectrum microbiota homogenised with phosphate buffer-saline. Given dosage was unknown, six capsules were chosen based on published data of bacterial viability counts of 1011 per capsule. However, severe CDI were treated with more. Patients completed a symptom questionnaire and stool tests pre- and at 1, 2, 3, 4, 6, 12 and 26 weeks post-treatment. Patients with concomitant inflammatory bowel disease [N=20] or treated for rCDI were excluded. Descriptive statistics were performed. Results: Nineteen patients (10M, 41±19yrs) were treated. At 26 weeks, 13 (68%) patients had no recurrence, five (26%) patients had recurrence of CDI and one patient was lost to follow up. Two patients with recurrence underwent treatment with 12 more capsules without recurrence after 12 weeks (Final efficacy: 79%). All patients indicated they would undergo the treatment again if needed. Six patients reported ’side effects’ (often pre-existent) within the first week including fatigue (n=3), abdominal pain (n=2) and nausea (n=2). At week six, four patients reported ‘ongoing side effects’ of flatulence and one reported nausea, bloating and abdominal pain. In patients with no recurrence of CDI the median number of bowel motions per day decreased from three (IQR:9) to one (IQR:2) at week 26. Median abdominal pain frequency decreased from three times/day (IQR:9) to once/day (IQR:9) and median bloating frequency decreased from frequently (3, IQR:3) to rarely (1, IQR:4) at week 26. Conclusion: FMT capsule therapy can effectively eradicate CDI provided dosage is adequate. It can also alleviate symptoms and is well accepted by patients. Further research is required to establish optimal dosing and duration for CDI treatment.
Methane emission estimates using chamber and tracer release experiments for a municipal waste water treatment plant (2015)

Abstract. This study presents two methods for estimating methane emissions from a waste water treatment plant (WWTP) along with results from a measurement campaign at a WWTP in Valence, France. These methods, chamber measurements and tracer release, rely on Fourier transform infrared spectroscopy and cavity ring-down spectroscopy instruments. We show that the tracer release method is suitable for quantifying facility- and some process-scale emissions, while the chamber measurements provide insight into individual process emissions. Uncertainties for the two methods are described and discussed. Applying the methods to CH4 emissions of the WWTP, we confirm that the open basins are not a major source of CH4 on the WWTP (about 10 % of the total emissions), but that the pretreatment and sludge treatment are the main emitters. Overall, the waste water treatment plant is representative of an average French WWTP.
Intrapilosins I−VII, Pentasaccharides from the Seeds of Ipomoea intrapilosa (2007)

Purification of a CHCl3-soluble extract from seeds of the Mexican medicinal arborescent morning glory, Ipomoea intrapilosa, by means of preparative-scale recycling HPLC, yielded seven new resin glycosides, intrapilosins I-VII (1-7). Their structures were established through the interpretation of their NMR spectroscopic and FABMS data. All pentasaccharides were found to be macrolactones of the known operculinic acid A with different fatty acids esterifying the same positions: C-2 on the second rhamnose unit and C-3 and C-4 on the third rhamnose moiety. The lactonization site of the aglycon could be placed at C-2 of the second saccharide. The fatty acid components of 1-7 were identified as (+)-(2S)-methylbutanoic, octanoic (caprylic), dodecanoic (lauric), and trans-cinnamic. The less common (-)-(2R)-methylbutanoic acid was also isolated as one of the saponification-liberated residues from intrapilosin IV (4). The presence of the (2R)- and (2S)-methylbutanoyl enantiomers bonded to the same oligosaccharide core in intrapilosins IV (4) and V (5) represents an example of diastereoisomerism due to a chiral esterifying moiety in the resin glycoside mixtures of a morning glory species.
ExclusiveJ/ψ and ψ(2S) production inppcollisions at $\protect \sqrt{s} = 7$ TeV (2013)

Exclusive J/ and (2S) vector meson production has been observed in the dimuon channel using the LHCb detector. The cross-section times branching fractions to two muons with pseudorapidities between 2.0 and 4.5 are measured to be
Adaptive Locally Low Rank and Sparsity Constrained Reconstruction for Accelerated Dynamic MRI (2020)

Globally low rank and sparsity (GLRS) constrained techniques perform well under high acceleration factors, but may blur spatial details. Locally low rank and sparsity (LLRS) constrained techniques preserve the spatial details better, but are sensitive to the size of the local patches. We propose a novel adaptive locally low rank and sparsity (ALLRS) constrained reconstruction for accelerated dynamic MRI that preserves the spatial details in heterogeneous regions, and smooths preferentially in homogeneous regions by adapting the local patch size to the level of spatial details. Results from in vivo dynamic cardiac and liver MRI demonstrate that ALLRS achieves improved sharpness as well as peak signal-to-noise ratio and visual information fidelity index with suppressed under-sampling artifacts for up to 16-fold undersampling.
The Dimpled Manifold Model of Adversarial Examples in Machine Learning (2021)

The extreme fragility of deep neural networks, when presented with tiny perturbations in their inputs, was independently discovered by several research groups in 2013. However, despite enormous effort, these adversarial examples remained a counterintuitive phenomenon with no simple testable explanation. In this paper, we introduce a new conceptual framework for how the decision boundary between classes evolves during training, which we call the {\em Dimpled Manifold Model}. In particular, we demonstrate that training is divided into two distinct phases. The first phase is a (typically fast) clinging process in which the initially randomly oriented decision boundary gets very close to the low dimensional image manifold, which contains all the training examples. Next, there is a (typically slow) dimpling phase which creates shallow bulges in the decision boundary that move it to the correct side of the training examples. This framework provides a simple explanation for why adversarial examples exist, why their perturbations have such tiny norms, and why they look like random noise rather than like the target class. This explanation is also used to show that a network that was adversarially trained with incorrectly labeled images might still correctly classify most test images, and to show that the main effect of adversarial training is just to deepen the generated dimples in the decision boundary. Finally, we discuss and demonstrate the very different properties of on-manifold and off-manifold adversarial perturbations. We describe the results of numerous experiments which strongly support this new model, using both low dimensional synthetic datasets and high dimensional natural datasets.
Tumor-cell heterogeneity in soft tissue sarcomas as defined by chemoradiotherapy (1984)

This report documents heterogeneous cell populations within high-grade soft tissue sarcomas in seven patients. The authors observed that, following chemoradiotherapy (five patients) or chemotherapy alone (two patients), surgically resected residual or recurrent sarcoma was found to be of low-grade histology. All chemotherapy was of Adriamycin (doxorubicin)-containing combinations. Seven other patients with regional recurrence after resection of high-grade sarcomas had high-grade recurrent tumors. Five of these patients had received no adjuvant therapy; two with extensive retroperitoneal liposarcomas and gross tumor-involved margins had received chemoradiotherapy. Follow-up ranged from 3 to 60 months (median, 12 months). These findings suggest that high-grade populations of sarcoma cells are more susceptible to chemoradiotherapy, as long as there is minimal residual disease. Low-grade clones of tumor cells may survive such therapy and present as clinical recurrence after initial treatment of low-grade or high-grade soft tissue sarcomas. Surgical resection is warranted for these recurrent lesions.
Glass-Ceramic Sol Gel Coating of Ceramic Fibers (2008)

A lithium aluminosilicate sol gel designed to have a composition corresponding to 1Li2O-1Al2O3-4SiO2 was formulated using tetraethyl orthosilicate, lithium nitrate, and aluminum nitrate. This solution was used to coat Nicalon SiC fiber tows (∼500 fibers) using a dipping process. An oxide concentration of 70–90 g oxide per liter water/methanol showed the most uniform fiber coating, with a minimum of bridging between fibers. Higher methanol/water ratios fostered improved coatings. Heat treatment of the coated fibers to 900°C caused them to devitrify to predominantly β-spodumene (LiAlSi2O6) solid solution.
4040 Investigation of a Series of 1,4-diaryl-pyrazolo-pyridinones as Anti-Leishmanial Agents (2020)

OBJECTIVES/GOALS: This study was conducted in order to identify novel chemical compounds that exhibit anti-leishmanial activity and to further characterize their efficacy and toxicity in in vitro and in vivo systems in the hopes of future chemotherapeutic developments. METHODS/STUDY POPULATION: We developed a novel, target-free fluorometric high-throughput screen (HTS) to identify small molecules with anti-leishmanial activity. Screening of 10,000 small molecules from the ChemBridge DIVERset-EXP library cassette #5 yielded 210 compounds that killed 80% of parasites. One hundred nine (109) molecular scaffolds were represented within the hit compounds, including the 1,4-diaryl-pyrazolo-pyridinone (1,4-DAPP). A total of 27 novel 1,4-DAPP compounds were synthesized and anti-leishmanial efficacy and host cell toxicity was determined using L. donovani mCherry expressing amastigotes and THP-1 macrophages. Additional pharmacokinetic analyses of a potent 1,4-DAPP compound were conducted. RESULTS/ANTICIPATED RESULTS: Four experimental compounds had IC50 values less than 5μM, providing similar anti-leishmanial activity to miltefosine. Compound 9279817 had a clearance almost twice the rate of normal hepatic blood flow and had a relatively high volume of distribution, indicating this compound is rapidly cleared and distributes into tissues. in vitro rat liver microsome assays suggest a rapid metabolism of 9279817, and MS/MS results suggest this metabolite is most likely formed via oxidation of the sulfur on the lower aromatic ring. DISCUSSION/SIGNIFICANCE OF IMPACT: This study revealed a novel structural class of compounds that have anti-leishmanial activity. in vitro experiments show compounds with similar efficacy as miltefosine while having significantly less toxicity, suggesting that this class could be further developed as a potential chemotherapeutic.
Suppression of short-channel effects in organic thin-film transistors (2006)

To improve the speed of organic thin-film transistor (TFT) circuits device architectures with submicrometer channel length are of interest. However, in conventional, submicrometer TFT structures the performance is degraded as a result of short-channel effects. Here we present an architecture for short-channel organic TFTs which is based on incorporating an insulating mesa structure in between source and drain electrodes. For submicrometer organic TFTs the mesa structure results in a significant enhancement of the on-off ratio and saturation characteristics. Device modeling shows that the mesa improves the ability of the gate electrode to modulate the carrier concentration in a submicrometer channel.
Polymeric Nanopillars Reinforced with Metallic Shells in the Lower Stem Region (2011)

The lower part of polymeric nanopillars is made mechanically stiff by surrounding it with metal, while the top part of the pillars is soft. The metal-shell-free tops of the pillars could be used for fabricating hollow structures or decorated with functional materials. This mechanical reinforcement shows stability against capillary-force-induced clustering and enables applications in a water environment.
Effects of Annealing and Atomic Hydrogen Treatment on Aluminum Oxide Passivation Layers for Crystalline Silicon Solar Cells (2011)

The effects of annealing and atomic hydrogen treatment (AHT) on the interface between hydrogenated aluminum oxide (a-Al1-xOx:H) and crystalline silicon (c-Si) were investigated. The annealing increased the negative interface fixed charge density (Qf) from -4.0×1011 to -3.0×1012 cm-2, whereas AHT reduced Qf from -3.0×1012 to 8.3×1011 cm-2. Chemical composition analyses revealed the existence of a hydrogenated silicon oxide (a-Si1-xOx:H) interfacial layer. It was also found that annealing and AHT strongly affected the chemical compositions near the interfacial layer. The change in Qf is probably caused by the reaction at the interface between the a-Al1-xOx:H and a-Si1-xOx:H.
Next Generation, Si-Compatible Materials and Devices in the Si-Ge-Sn System (2015)

Abstract : The program demonstrated synthesis, optical and electrical characterizations, and device fabrication of GeSn and GeSiSn alloys integrated on Si platforms. These materials were produced via next generation deposition chemistries based on industrially viable hydride compounds. Emphasis was placed on the fabrication of direct-gap GeSn binaries grown on Ge buffered Si as well as light-emitting GeSiSn ternaries covering a broad band of tunable wavelengths from 1300 nm to 2500 nm for the first time. First generation GeSiSn LEDs and IR photodetectors were also demonstrated establishing the ternary as a thermally robust alternative to the binary for long wavelength applications. New breakthrough designs of direct-gap GeSn LEDs were introduced and shown to exhibit superior response relative to the state-of-the-art. The latter technology was further advanced via the creation of degenerate pn junctions representing the basic building block of quasi-direct diode lasers. The demonstration of electrically injected devices in this study was made possible by the ability to dope the materials p- and n-type at levels up to 10E20/cm3 using practical in situ methods developed under the grant.
Picosecond, wavelength tunable SOA-based laser sources at 10-40 GHz repetition rates (2003)

Summary from only given. A convenient method for generating short pulses at high repetition rates is based on active modelocking in erbium fiber ring lasers (FRL). The use of a semiconductor optical amplifier (SOA) as active medium in the ring is attractive, since it can provide both gain over a broad wavelength range and modulation due to its fast gain and refractive index dynamics. In this work we compare two mode-locked fiber ring lasers. The first is based on cross-gain modulation in a SOA. The second is a novel design based on cross-phase modulation in SOAs and is proposed here for the first time. Pulses of 1.8 ps width at 10 GHz repetition rate and 3.6 ps at 40 GHz with more than 30 nm tuning range have been achieved.
Complete set of homogeneous isotropic analytic solutions in scalar-tensor cosmology with radiation and curvature (2012)

We study a model of a scalar field minimally coupled to gravity, with a specific potential energy for the scalar field, and include curvature and radiation as two additional parameters. Our goal is to obtain analytically the complete set of configurations of a homogeneous and isotropic universe as a function of time. This leads to a geodesically complete description of the Universe, including the passage through the cosmological singularities, at the classical level. We give all the solutions analytically without any restrictions on the parameter space of the model or initial values of the fields. We find that for generic solutions the Universe goes through a singular (zero-size) bounce by entering a period of antigravity at each big crunch and exiting from it at the following big bang. This happens cyclically again and again without violating the null-energy condition. There is a special subset of geodesically complete nongeneric solutions which perform zero-size bounces without ever entering the antigravity regime in all cycles. For these, initial values of the fields are synchronized and quantized but the parameters of the model are not restricted. There is also a subset of spatial curvature-induced solutions that have finite-size bounces in the gravity regime and never enter the antigravity phase. These exist only within a small continuous domain of parameter space without fine-tuning the initial conditions. To obtain these results, we identified 25 regions of a 6-parameter space in which the complete set of analytic solutions are explicitly obtained.
From Polypharmacology to Target Specificity: The Case of PARP Inhibitors (2013)

Poly(ADP-ribose)polymerases (PARPs) catalyze a post-transcriptional modification of proteins, consisting in the attachment of mono, oligo or poly ADP-ribose units from NAD+ to specific polar residues of target proteins. The scientific interest in members of this superfamily of enzymes is continuously growing since they have been implicated in a range of diseases including stroke, cardiac ischemia, cancer, inflammation and diabetes. Despite some inhibitors of PARP-1, the founder member of the superfamily, have advanced in clinical trials for cancer therapy, and other members of PARPs have recently been proposed as interesting drug targets, challenges exist in understanding the polypharmacology of current PARP inhibitors as well as developing highly selective chemical tools to unravel specific functions of each member of the superfamily. Beginning with an overview on the molecular aspects that affect polypharmacology, in this article we discuss how these may have an impact on PARP research and drug discovery. Then, we review the most selective PARP inhibitors hitherto reported in literature, giving an update on the molecular aspects at the basis of selective PARP inhibitor design. Finally, some outlooks on current issues and future directions in this field of research are also provided.
Optical Properties and Two‐Dimensional Electronic Structure in Wide‐Gap Layered Oxychalcogenide: La2CdO2Se2. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Approximately Optimal Fixed-Structure Controllers Using Neural Networks (2021)

Fixed structure controllers (such as proportional-integral-derivative controllers) are used extensively in industry. Finding a practical and versatile method to tune these controllers, particularly with imprecise process models and limited online computational resources, is an industrially relevant problem which could improve the efficiency of many plants. In this paper, we present two flexible neural network-based approaches capable of tuning any fixed structure controller for any control objective and process model and compare their advantages and disadvantages. The first approach is derived from supervised learning and classical optimization techniques, while the second approach applies techniques used in deep reinforcement learning. Both approaches incorporate model uncertainties when selecting controller parameters, reducing the need for costly experiments to precisely estimate model parameters in a plant. Both methods are also computationally efficient online, enabling their widespread usage.
Focused ultrasound opens the blood–brain barrier in vivo (2000)

The blood–brain barrier (BBB) consists of specialized endothelial cells that line the capillaries within the brain whose overlapping regions are held firm by ‘‘tight junctions.’’ In the central nervous system (CNS) the BBB plays a protective role, restricting the movement of molecules into the brain. It is also the major impediment to the flux of therapeutic drugs into the CNS. High-intensity focused ultrasound (HIFU) has been shown to induce the displacement of ordinarily impermeable vital dyes from the blood stream into the brain without damage to the CNS in the proximity of the flux. However, there has been no elucidation of the biological response to ultrasound that allows this flux. We show using a rat model that, by opening the tight junctions or by causing the endothelial cells to retract, HIFU can selectively disrupt the BBB in a reversible, controlled manner without injury to the surrounding CNS. Moreover, this effect reverses within 96 h. We believe that this work will lay the foundation for the development of therapies designed to optimize and take advantage of this novel biological response to ultrasound.
New Pilot Designs and ICI Mitigation for OFDM Downlink Systems based on IEEE 802.16m Standards over High Speed Vehicular Channels (2009)

Two new pilot patterns and channel estimation methods robust to inter-channel-interference (ICI) caused by fast fading channels are proposed which are applicable to 802.16m standards. A number of clusters of pilot subcarriers are used for channel estimation. In addition, the number of needed parameters for channel estimation is reduced by some properties of ICI in the time and frequency domains. Simulation results show that the proposed channel estimation has good bit-error- rate (BER) performance compared to conventional method based on 802.16m standards at the velocity of 350 km/h and has the same performance at the velocity of 3 km/h. Moreover, if the target BER is lower than the supportable BER of conventional method with uncoded 16 QAM, then the proposed method can be better option compared to diminish the modulation scheme as 8 PSK considering both BER and throughput.
Use of monoclonal antiacetylcholine receptor antibodies to investigate the macrophage inflammation of acute experimental myasthenia gravis (1985)

The acute phase of experimental autoimmune myasthenia gravis (EAMG) is characterized by macrophage inflammation of muscle endplates and by muscle fiber necrosis. We induced acute EAMG by passive transfer of monoclonal antibodies (mAbs) directed against the acetylcholine receptor (AChR) to investigate this brief and self-limited disorder. After the initial acute phase, animals were refractory to induction of a second episode by subsequent injection of the same mAb, or another anti-AChR mAb of different idiotype and which binds to a separate epitope. Therefore, the refractory state was not caused by an anti-idiotypic response or epitopic modulation. Adoptive transfer of spleen cells from refractory animals had no effect, excluding a role of suppressor lymphocytes, and there was no evidence from experiments involving adoptive transfer of spleen cells from naive animals to refractory animals that refractory animals lacked effector cells.