gebhart/patrepeval huggingface dataset:
Donor-dependent Fecal Microbiota Transplantation Efficacy Against Necrotizing Enterocolitis in Preterm Pigs (2020)

Abstract Background Fecal microbiota transplantation (FMT) has shown high cure rates against recurrent Clostridioides difficile infection regardless of donor microbiota characteristics, whereas the clinical response of FMT in inflammatory bowel disease appears to be donor-dependent. We recently showed that FMT from healthy suckling piglet donors to newborn preterm piglets decreased the risk of necrotizing enterocolitis (NEC), a serious gastrointestinal disease of preterm infants, but could not replicate this finding in a follow-up study using phenotypically similar donors. This gave us the opportunity to directly investigate the microbiota dynamics of clinically efficient FMT. In this experiment, preterm piglets (n=38) were randomly allocated to receive control saline or FMT from inferior (FMT1) or superior donors (FMT2) by rectal administration. All animals were fed infant formula for four days to induce NEC-like lesions before necropsy and gut pathological evaluation. Donor and recipient colonic microbiotas were analyzed by 16S rRNA gene amplicon sequencing and shotgun metagenomics. Results Although the two donor microbiotas closely resembled one another, only FMT2 recipients had improved body growth and lower intestinal permeability relative to control, and were protected against NEC. Both FMT groups had shifted colon microbiota composition relative to CON, with increased lactobacilli relative abundance, but FMT2 recipients had a higher lactobacilli abundance relative to FMT1. Limosilactobacillus reuteri and Lactobacillus crispatus strains of FMT recipients showed high phylogenetic similarity with their respective donors, indicating successful engraftment. Further, NEC severity was positively associated with Clostridoides difficile , Clostridium perfringens and Enterococcus faecium abundance, while Lmb. reuteri and Lb. crispatus negatively correlated with diarrhea severity. Genome-resolved analysis indicated a higher gut replication rate of lactobacilli in FMT2 recipients, and identified specific glycosaminoglycan-degrading Bacteroides in the superior donor. Conclusions FMT efficacy against NEC is donor-dependent, and introduced lactobacilli manifest strain-level differences with respect to colonizing recipients. Using shotgun metagenomics, we traced the engrafted strains back from donors and identified donor-specific microbes of potential importance. This may accelerate our understanding of optimal donor selection for clinical FMT.
Factorization of Discrete Probability Distributions (2012)

We formulate necessary and sufficient conditions for an arbitrary discrete probability distribution to factor according to an undirected graphical model, or a log-linear model, or other more general exponential models. This result generalizes the well known Hammersley-Clifford Theorem.
Weighted median filters: a tutorial (1996)

Weighted Median (WM) filters have the robustness and edge preserving capability of the classical median filter and resemble linear FIR filters in certain properties. Furthermore, WM filters belong to the broad class of nonlinear filters called stack filters. This enables the use of the tools developed for the latter class in characterizing and analyzing the behavior and properties of WM filters, e.g. noise attenuation capability. The fact that WM filters are threshold functions allows the use of neural network training methods to obtain adaptive WM filters. In this tutorial paper we trace the development of the theory of WM filtering from its beginnings in the median filter to the recently developed theory of optimal weighted median filtering. Applications discussed include: idempotent weighted median filters for speech processing, adaptive weighted median and optimal weighted median filters for image and image sequence restoration, weighted medians as robust predictors in DPCM coding and Quincunx coding, and weighted median filters in scan rate conversion in normal TV and HDTV systems.
ChemInform Abstract: Early Transition Metal Induced Intramolecular Cocyclization/Elaboration Reactions Using a Cleavable Silicon Linker. (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.
Numerical Study of Human Pulmonary Cilia in the Periciliary Liquid Layer (2012)

A three-dimensional numerical mdoel is developed to study the human pulmonary cilia motion in the periciliary liquid (PCL) layer. The governing equations are solved using the immersed boundary method coupled with the pressure increment projection method. The cilia beating pattern is prescribed for the simulations. The fluid-cilia interaction forces are computed by the direct forcing method. The effect of the phase difference between cilia on the PCL motion is investigated by employing different phasing. The present numerical results exhibit that the maximul PCL velocity in the stream-wise direction occurs if cilia have phase differences in both the flow and orthogonal directions.
Hand Gesture Recognition With Acoustic Myography and Wavelet Scattering Transform (2022)

In the past decade, improving upper limb prostheses control methods with pattern recognition (PR) has been the focus of an extended amount of research. However, several challenges associated with the processing of the Electromyogram (EMG) signals still need to be tackled to enable widespread and clinical implementation of upper limb prostheses with PR. As a result, alternative modalities functioning as promising control signals have been proposed as source of control input rather than the surface EMG, such as Acoustic myography (AMG) and Force myography. In this paper, eight high sensitivity array microphones were utilized to acquire the AMG signals, with 8 custom-built 3D printed microphone housing developed for the purpose of this research. Twenty subjects were recruited for data collection in this paper with the hardware design developed specifically by our research team, making our database the largest open-access dataset in the AMG literature. We proposed a novel feature extraction (FE) method based on the Wavelet Scattering Transform (WST) to tackle the challenge of extracting the relevant information from AMG to classify 14 hand and finger movement classes. The WST is a translation-invariant non-linear signal representation that has a strong theoretical support as it maintains stability to time-warping deformations, while preserving a high degree of discriminability. The performance results showed that WST outperformed all state-of-the-art FE methods with an accuracy of 88% on average across 20 subjects when classified with Quadratic Discriminant Analysis (QDA) classifier for a large dataset of AMG signals. These results suggest that the AMG signals can be utilized as a reliable source of control, especially when the windows sizes and number of channels are carefully selected. The AMG dataset is available from the link <uri xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">https://drive.google.com/drive/folders/1r0rBnrNG5c8qegffKUhAYYHQUT8cGVHD?usp=sharing</uri> .
High energy electron fluxes in dc-augmented capacitively coupled plasmas. II. Effects on twisting in high aspect ratio etching of dielectrics (2010)

In high aspect ratio (HAR) plasma etching of holes and trenches in dielectrics, sporadic twisting is often observed. Twisting is the randomly occurring divergence of a hole or trench from the vertical. Many causes have been proposed for twisting, one of which is stochastic charging. As feature sizes shrink, the fluxes of plasma particles, and ions in particular, into the feature become statistical. Randomly deposited charge by ions on the inside of a feature may be sufficient to produce lateral electric fields which divert incoming ions and initiate nonvertical etching or twisting. This is particularly problematic when etching with fluorocarbon gas mixtures where deposition of polymer in the feature may trap charge. dc-augmented capacitively coupled plasmas (dc-CCPs) have been investigated as a remedy for twisting. In these devices, high energy electron (HEE) beams having narrow angular spreads can be generated. HEEs incident onto the wafer which penetrate into HAR features can neutralize the positive charge and so reduce the incidence of twisting. In this paper, we report on results from a computational investigation of plasma etching of SiO2 in a dc-CCP using Ar/C4F8/O2 gas mixtures. We found that HEE beams incident onto the wafer are capable of penetrating into features and partially neutralizing positive charge buildup due to sporadic ion charging, thereby reducing the incidence of twisting. Increasing the rf bias power increases the HEE beam energy and flux with some indication of improvement of twisting, but there are also changes in the ion energy and fluxes, so this is not an unambiguous improvement. Increasing the dc bias voltage while keeping the rf bias voltage constant increases the maximum energy of the HEE and its flux while the ion characteristics remain nearly constant. For these conditions, the occurrence of twisting decreases with increasing HEE energy and flux.
Development and Evaluation of a Head-Controlled Human-Computer Interface with Mouse-Like Functions for Physically Disabled Users (2009)

The developed pointing device adequately emulates the movement functions of the computer cursor. It is easy to use and can be learned quickly when operated by quadriplegic individuals.
Developing new treatments for Alzheimer's disease: the who, what, when, and how of biomarker-guided therapies (2008)

This synthetic review presents an approach to the use of biomarkers for the development of new treatments for Alzheimer's disease (AD). After reviewing the process of translation as applied to AD, the paper provides a general update on what is known about the biology of the disease, and highlights currently available treatments. This is followed by a discussion of future drug development for AD emphasizing the roles that biomarkers are likely to play in this process: (1) define patients who are going to progress rapidly for the purpose of trial enrichment; (2) differentiate disease and therapeutically relevant AD subtypes; (3) assess the potential activity of specific therapies in vivo or ex vivo; and (4) measure the underlying disease state, so as to (a) detect disease and assess drug response in asymptomatic patients, (b) serve as a secondary outcome measure in clinical trials of symptomatic patients, and (c) decide if further development of a treatment should be stopped if not likely to be effective. Several examples are used to illustrate each biomarker utility in the AD context.
Rotamedusa roztocensis gen. et sp. nov., meduza z eoceńskiego fliszu karpackiego (1969)

Rotamedusa roztocensis gen. et sp. nov., a medusa from the Eocene flysch of the Carpathians

Markings, circular in outline and made up exclusively of radial and concentric, morphological elements, were found on the upper surface of a cross-laminated sandstone layer in the Middle Eocene Hieroglyphic Beds of the Magura Series. The structures are interpreted as the counterparts of medusae, deposited from suspension with the silt size-fraction. All specimens are assigned to a common species, Rotamedusa roztocensis gen. et sp. nov., here described.
Automatic detection of motion artifacts in MR images using CNNS (2017)

Considerable practical interest exists in being able to automatically determine whether a recorded magnetic resonance image is affected by motion artifacts caused by patient movements during scanning. Existing approaches usually rely on the use of navigators or external sensors to detect and track patient motion during image acquisition. In this work, we present an algorithm based on convolutional neural networks that enables fully automated detection of motion artifacts in MR scans without special hardware requirements. The approach is data driven and uses the magnitude of MR images in the spatial domain as input. We evaluate the performance of our algorithm on both synthetic and real data and observe adequate performance in terms of accuracy and generalization to different types of data. Our proposed approach could potentially be used in clinical practice to tag an MR image as motion-free or motion-corrupted immediately after a scan is finished. This process would facilitate the acquisition of high-quality MR images that are often indispensable for accurate medical diagnosis.
Prevalence of Cam and Pincer Deformities in the X-Rays of Asymptomatic Individuals (2017)

According to our data, radiological signs of cam and pincer deformities are common in asymptomatic people. In clinical practice, patients presenting with hip pain and radiological signs of FAI should undergo further diagnostic evaluation. However, in asymptomatic patients, no further evaluation is recommended.
Coordinated Replenishments in a Multi-Item Inventory System with Compound Poisson Demands (1984)

In many practical applications or multi-item inventory systems significant economies of scale can be exploited when coordinating replenishment orders for groups of items. This paper considers a continuous review multi-item inventory system with compound Poisson demand processes; excess demands are backlogged and each replenishment requires a lead time. There is a major setup cost associated with any replenishment of the family of items, and a minor (item dependent) setup cost when including a particular item in this replenishment. Moreover there are holding and penalty costs. We present an algorithm which searches for a simple coordinated control rule minimizing the long-run average cost per unit time subject to a service level constraint per item on the fraction of demand satisfied directly from on-hand inventory. This algorithm is based on a heuristic decomposition procedure and a specialized policy-iteration method to solve the single-item subproblems generated by the decomposition procedure. The model applies to multi-location inventory systems with similar cost structures for coordinated deliveries.
Loss of basement membrane, receptor and cytoskeletal lattices in a laminin-deficient muscular dystrophy (2004)

Basement membrane laminins bearing the alpha2-subunit interact with alpha-dystroglycan and beta1-integrins, cell-surface receptors that are found within the rectilinear costameric lattices of skeletal muscle sarcolemma. Mutations of the alpha2 subunit are a major cause of congenital muscular dystrophy. To determine whether the costameres are altered as a result of laminin alpha2-mutations, the skeletal muscle surface of a dystrophic mouse (dy(2J)/dy(2J)) lacking the alpha2-LN domain was examined by confocal and widefield deconvolution immunomicroscopy. Although the dy(2J) dystrophic fibers possessed a normal-appearing distribution of alpha2-laminins and alpha-dystroglycan within a rectilinear costameric lattice at 6.5 weeks of age, by 11 weeks the surface architecture of these components were found to be disorganized, with frequent effacement of the circumferential and longitudinal lattice striations. The defect in the lattice organization was also noted to be a characteristic of type IV collagen, nidogen, perlecan, beta1(D)-integrin, dystrophin and vinculin. The development of this pattern change occurring only after birth suggests that although alpha2-laminins are not essential for the initial assembly of the costameric framework, they play a role in maintaining the stability and organization of the framework.
γ‐Ray‐induced degradation of lignocellulosic materials (1981)

Abstract Lignocellulosic plant materials were treated with various swelling agents and exposed to γ radiation from 60 Co or 137 Cs. At dosages of 50 Mrad or above, lignocellulosic materials were extensively degraded and solubilized in water. Addition of water, NaOH, or H 2 SO 4 to the substrate increased the degree of solubilization. Complete solubilization was achieved for samples of sugarcane bagasse, newspaper, cotton linters, cotton cloth, sawdust, and α‐cellulose powder. About 35% total sugar and 5% reducing sugar per dry weight of sugarcane bagasse could be obtained by this method. Most of the soluble carbohydrates seemed to be disaccharides or larger molecules and glucose degradation products. Solubilization of cellulose was dosage dependent and although the rate of solubilization was increased by adding alkali, released sugar was further decomposed by the alkali and by high dosage of radiation.
Spray Plasma Processing of Barrier Films Deposited in Air for Improved stability of Flexible Electronic Devices (2018)

We report on submicron organosilicate barrier films produced rapidly in ambient by a scalable spray plasma process for improved solar cell stability. The plasma is at a sufficiently low temperature to be compatible with flexible electronic devices. The thickness of the barrier films is tunable and fully transparent over the visible spectrum. The morphology and density of the barrier are shown to improve with the addition of a fluorine-based precursor. Thin-film perovskite solar cells with submicron coatings exhibited significant improvements in stability when exposed to light, heat, and moisture. X-ray diffraction measurements performed while heating showed the barrier film dramatically slows the formation of PbI2. When deposited on a flexible substrate, the barrier films exhibit no signs of cracking or delamination after 10,000 bending cycles on a 127 μm substrate with a bending radius of 1 cm.
Data from B-Cell Lymphoma Patient-Derived Xenograft Models Enable Drug Discovery and Are a Platform for Personalized Therapy (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Patients with B-cell lymphomas often relapse after frontline therapy, and novel therapies are urgently needed to provide long-term remission. We established B-cell lymphoma patient-derived xenograft (PDX) models to assess their ability to mimic tumor biology and to identify B-cell lymphoma patient treatment options.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We established the PDX models from 16 patients with diffuse large B-cell lymphoma, mantle cell lymphoma, follicular lymphoma, marginal zone lymphoma, or Burkitt lymphoma by inoculating the patient tumor cells into a human bone chip implanted into mice. We subjected the PDX models to histopathologic and phenotypical examination, sequencing, and drug efficacy analysis. Primary and acquired resistance to ibrutinib, an oral covalent inhibitor of Bruton tyrosine kinase, were investigated to elucidate the mechanisms underlying ibrutinib resistance and to identify drug treatments to overcome resistance.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; The PDXs maintained the same biological, histopathologic, and immunophenotypical features, retained similar genetic mutations, and produced comparable drug responses with the original patient tumors. In the acquired ibrutinib-resistant PDXs, PLC-γ2, p65, and Src were downregulated; however, a PI3K signaling pathway member was upregulated. Inactivation of the PI3K pathway with the inhibitor idelalisib in combination with ibrutinib significantly inhibited the growth of the ibrutinib-resistant tumors. Furthermore, we used a PDX model derived from a clinically ibrutinib-relapsed patient to evaluate various therapeutic choices, ultimately eliminating the tumor cells in the patient's peripheral blood.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Our results demonstrate that the B-cell lymphoma PDX model is an effective system to predict and personalize therapies and address therapeutic resistance in B-cell lymphoma patients. &lt;i&gt;Clin Cancer Res; 23(15); 4212–23. ©2017 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Exploiting invariant NKT cells to promote T-cell responses to cancer vaccines (2013)

Invariant natural killer T (iNKT) cells have the capacity to amplify adaptive immune responses by licensing antigen-presenting cells. A simple vaccine consisting of whole tumor cells pulsed with an iNKT-cell agonist efficiently delivers antigens plus adjuvants to endogenous dendritic cells and has potential for clinical applications.
Effect of gene amplification on mercuric ion reduction activity of Escherichia coli (1991)

The mercury resistance (mer) operon of plasmid R100 was cloned onto various plasmid vectors to study the effect of mer gene amplification on the rate of Hg2+ reduction by Escherichia coli cells. The plasmids were maintained at copy numbers ranging from 3 to 140 copies per cell. The overall Hg2+ reduction rate of intact cells increased only 2.4-fold for the 47-fold gene amplification. In contrast, the rate of the cytoplasmic reduction reaction, measured in permeabilized cells, increased linearly with increasing gene copy number, resulting in a 6.8-fold overall amplification. RNA hybridizations indicated that mRNA of the cytoplasmic mercuric reductase (merA gene product) increased 11-fold with the 47-fold gene amplification, while mRNA of the transport protein (merT gene product) increased only 5.4-fold. Radiolabeled proteins produced in maxicells were used to correlate the expression levels of the mer polypeptides with the measured reduction rates. The results indicated that, with increasing gene copy number, there was an approximately 5-fold increase in the merA gene product compared with a 2.5-fold increase in the merT gene product. These data demonstrate a parallel increase of Hg2+ reduction activity and transport protein expression in intact cells with plasmids with different copy numbers. In contrast, the expression level of the mercuric reductase gene underwent higher amplification than that of the transport genes at both the RNA and protein levels as plasmid copy number increased.
Test generation for embedded circuits under the transparent-scan approach (2005)

A new test generation procedure is introduced for scan circuits under an approach called transparent-scan. The new test generation procedure targets a circuit-under-test that is embedded in a larger design (it is also applicable to an interconnection of embedded circuits). Transferring deterministic test data to the primary inputs of an embedded circuit from an external source can be expensive. This problem is alleviated as follows. The test generation procedure starts from a given input sequence Ψ that specifies the values of the original primary inputs of the circuit (the primary inputs before scan was added). In this implementation, Ψ is a random input sequence that can be generated by an on-chip test-pattern generator (e.g. a linear-feedback shift register) driving the original primary inputs of the circuit. The test generation procedure transforms Ψ into a test sequence T for the scan circuit under the transparent-scan approach by adding to Ψ the values of the scan select and scan chain inputs. These inputs are easily controllable from the primary inputs of the design.
A fully-integrated low-power BPSK based wireless inductive link for implantable medical devices (2004)

During the past decades, research has progressed on the biomedical implantable electronic devices that require power and data communication through a wireless inductive link. In this paper, we present a fully integrated binary phase-shift-keying (BPSK) demodulator based on a hard-limited COSTAS loop topology. The demodulator features with a data transmission rate of 1.12 Mbps and consumes less than 0.5 mW under a supply voltage of 1.8 V, which has been implemented in a CMOS 0.18 /spl mu/m technology. In addition, the employment of BPSK demodulation combined with a passive modulation method allows full-duplex data communication between an external controller and the implant device, which may improve the controllability and observability of the whole implanted system.