gebhart/patrepeval huggingface dataset:
<title>Visual search in angiograms: does geometry play a role in saliency?</title> (1996)

Quantifying and modeling how the human eye searches medical images is important. Equally detectable lesions may not be equally salient in a visual search. This research investigates the effect of geometry on the saliency of stenoses in angiograms. A previous experiment suggested that stenoses located in areas of high curvature along vessels would be less salient. In this paper, we measure the saliency of stenoses in two steps: first, we measure stenoses amplitude detection thresholds for stenoses at three values of curvature along vessels; second, after adjusting the degree of stenosis at these curvatures to multiples of the measured thresholds to achieve equal detectability, we measure the saliency of the stenoses in a visual search experiment. Median reaction time is used as a measure of saliency. We found that thresholds increase as curvature increases. This finding explains the decrease in saliency found in a previous investigation. Results also show that median reaction time is constant across different curvatures for 70% and higher degrees of stenosis, indicating that saliency is independent of geometry for clinically significant angiographic lesions.
IDDF2021-ABS-0166 Transplantation of stool from obese patients promotes intestinal tumorigenesis in mice (2021)

<h3>Background</h3> Epidemiological evidence supports a relationship between adiposity and elevated risk of colorectal cancer (CRC). Nevertheless, the role of gut microbiota in mediating the carcinogenic effect of adiposity is unknown. In this study, we transplanted stool from obese patients to mice to evaluate its effects and mechanisms on intestinal carcinogenesis. <h3>Methods</h3> Azoxymethane (AOM)-treated mice,<i> Apc<sup>Min/+</sup></i> and germ-free mice were gavaged with feces from obese patients and control subjects respectively. The colonic tumor load and number were recorded at endpoint. The gut microbiota composition was assessed by metagenomic sequencing and colonic transcriptome was assessed by total RNA sequencing. <h3>Results</h3> The colonic tumor load and number were significantly higher in mice receiving feces from obese patients (OB), compared with those from control subjects (NB, normal BMI), in both AOM-induced and <i>Apc<sup>Min/+</sup></i> mice (IDDF2021-ABS-0166 Figure 1A-C). Histological assessments showed increased dysplasia proportions and Ki-67 positive cells (IDDF2021-ABS-0166 Figure 1D) in mice receiving feces from obese patients in both murine cancer models. Metagenomic analysis showed an altered microbiota composition (IDDF2021-ABS-0166 Figure 2A), with a lower alpha diversity (IDDF2021-ABS-0166 Figure 2B), decreased abundance of Faecalibaculum, Bifidobacterium and Lactobacillus, as well as increased abundance of Akkermansia in recipients of feces from obese patients (IDDF2021-ABS-0166 Figure 2C). Transcriptomic analysis on colon tissue showed upregulation of oncogenic (Wnt signaling pathway, MAPK signaling pathway and Rap1 signaling pathway) and pro-inflammatory pathways (TNF signaling pathway and chemokine signaling pathway). Mice received feces from obese patients showed impaired murine barrier function evidenced by decreased mucus layer thickness, loosened tight junction and over-expression of epithelial leaky protein Claudin-2 in the colonic crypt. <h3>Conclusions</h3> Feces from obese patients promoted colorectal carcinogenesis in mice. Such action was associated with the modulation of the gut microbiota composition, induction of oncogenic and pro-inflammatory factors and impairment of epithelial barrier. This study provides new insight into obesity-promoting colorectal carcinogenesis, at least in part by causing gut microbiome dysbiosis.
Universal scaling for diffusion-controlled reactions among traps (1997)

The determination of the mean survival time τ (i.e., inverse reaction rate) associated with diffusion-controlled reactions among static traps is a problem of long-standing interest, dating back to the classical work of Smoluchkowski. For the broad class of model particulate- and digitized-based models considered here, we find a universal curve for the mean survival time τ for a wide range of porosities. The functional form of this universal scaling relation is motivated by rigorous bounds on τ and is expressible as a simple function of porosity, specific surface, and mean pore size.
Enhanced siRNA Delivery and Selective Apoptosis Induction in H1299 Cancer Cells by Layer-by-Layer-Assembled Se Nanocomplexes: Toward More Efficient Cancer Therapy (2021)

Nanotechnology has made an important contribution to oncology in recent years, especially for drug delivery. While many different nano-delivery systems have been suggested for cancer therapy, selenium nanoparticles (SeNPs) are particularly promising anticancer drug carriers as their core material offers interesting synergistic effects to cancer cells. Se compounds can exert cytotoxic effects by acting as pro-oxidants that alter cellular redox homeostasis, eventually leading to apoptosis induction in many kinds of cancer cells. Herein, we report on the design and synthesis of novel layer-by-layer Se-based nanocomplexes (LBL-Se-NCs) as carriers of small interfering RNA (siRNA) for combined gene silencing and apoptosis induction in cancer cells. The LBL-Se-NCs were prepared using a straightforward electrostatic assembly of siRNA and chitosan (CS) on the solid core of the SeNP. In this study, we started by investigating the colloidal stability and protection of the complexed siRNA. The results show that CS not only functioned as an anchoring layer for siRNA, but also provided colloidal stability for at least 20 days in different media when CS was applied as a third layer. The release study revealed that siRNA remained better associated with LBL-Se-NCs, with only a release of 35% after 7 days, as compared to CS-NCs with a siRNA release of 100% after 48 h, making the LBL nanocarrier an excellent candidate as an off-the-shelf formulation. When applied to H1299 cells, it was found that they can selectively induce around 32% apoptosis, while significantly less apoptosis (5.6%) was induced in NIH/3T3 normal cells. At the same time, they were capable of efficiently inducing siRNA downregulation (35%) without loss of activity 7 days post-synthesis. We conclude that LBL-Se-NCs are promising siRNA carriers with enhanced stability and with a dual mode of action against cancer cells.
Alkylated derivatives of poly(ethylacrylic acid) can be inserted into preformed liposomes and trigger pH-dependent intracellular delivery of liposomal contents (2004)

Poly(ethylacrylic acid) (PEAA) is a pH-sensitive polymer that undergoes a transition from a hydrophilic to a hydrophobic form as the pH is lowered from neutral to acidic values. In this work we show that pH sensitive liposomes capable of intracellular delivery can be constructed by inserting a lipid derivative of PEAA into preformed large unilamellar vesicles (LUV) using a simple one step incubation procedure. The lipid derivatives of PEAA were synthesized by reacting a small proportion (3%) of the carboxylic groups of PEAA with C10 alkylamines to produce C10-PEAA. Incubation of C10-PEAA with preformed LUV resulted in the association of up to 8% by weight of derivatized polymer with the LUV without inducing aggregation. The resulting C10-PEAA-LUV exhibited pH-dependent fusion and leakage of LUV contents on reduction of the external pH below pH 6.0 as demonstrated by lipid mixing and release of calcein encapsulated in the LUV. In addition, C10-PEAA-LUV exhibited pH dependent intracellular delivery properties following uptake into COS-7 cells with appreciable delivery to the cell cytoplasm as evidenced by the appearance of diffuse intracellular calcein fluorescence. It is demonstrated that the cytoplasmic delivery of calcein by C10-PEAA-LUV could be inhibited by agents (bafilomycin or chloroquine) that inhibit acidification of endosomal compartments, indicating that this intracellular delivery resulted from the pH-dependent destabilization of LUV and endosomal membranes by the PEAA component of the C10-PEAA-LUV. It is concluded that C10-PEAA-LUV represents a promising intracellular delivery system for in vitro and in vivo applications.
Protocol for measurement of enamel loss from brushing with an anti-erosive toothpaste after an acidic episode. (2018)

Tooth erosion from an acidic insult may be exacerbated by toothbrushing. The purposes of this study were to develop an in vitro methodology to measure enamel loss after brushing immediately following an acidic episode and to investigate the effect of brushing with an anti-erosive toothpaste. The null hypotheses tested were that tooth erosion after brushing with the toothpaste would not be different from brushing with water and that a 1-hour delay before brushing would not reduce tooth erosion. Forty bovine enamel slabs were embedded, polished, and subjected to baseline profilometry. Specimens were bathed in hydrochloric acid for 10 minutes to simulate stomach acid exposure before post-acid profilometry. Toothbrushing was then simulated with a cross-brushing machine and followed by postbrushing profilometry. Group 1 was brushed with water; group 2 was brushed with a 50:50 toothpaste-water slurry; and groups 3 and 4 were immersed in artificial saliva for 1 hour before brushing with water or the toothpaste slurry, respectively. The depth of enamel loss was analyzed and compared using 1-way analysis of variance and post hoc testing (α = 0.05). Greater enamel loss was measured in groups brushed with toothpaste than in groups brushed with water. One-hour immersion in artificial saliva significantly reduced enamel loss when teeth were brushed with water (group 3; P < 0.05) but not with toothpaste (group 4). This study established a protocol for measuring enamel loss resulting from erosion followed by toothbrush abrasion. The results confirmed the abrasive action of toothpaste on acid-softened enamel.
Frontispiece: Lights and Shadows of DMSO as Solvent for Tin Halide Perovskites (2022)

Current protocols for solution-processed tin halide perovskite thin films rely on the use of DMSO. However, this solvent was recently found to oxidise tin species. This source of defects in the films may be the reason for the bottlenecks in device performance and reproducibility. DMSO-free processes may avoid this problem, but lack a controlled crystallization so far. Understanding the chemistry of tin perovskites in new solvent systems would allow fabricating thin films of the highest quality.
Development of an Automated, High-Throughput Bactericidal Assay That Measures Cellular Respiration as a Survival Readout for Neisseria meningitidis (2011)

Complement-mediated bactericidal activity has long been regarded as the serological correlate of protective immunity against Neisseria meningitidis. This was affirmed in 2005 at a WHO-sponsored meningococcal serology standardization workshop. The assay currently employed by most laboratories involves determining surviving bacterial colony counts on agar as a readout which is labor-intensive, time-consuming, and not amendable to rapid data analysis for clinical trials. Consequently, there is an acute need to develop a sensitive, high-throughput bactericidal assay to enable a rapid and robust assessment of the effectiveness of vaccine candidates. To this end, we have developed an automated, kinetic assay based on the fluorescent respiration product of resazurin which reduces assay volume, shortens assay time, and facilitates automation of data analysis. We demonstrate proof of concept for applicability of this high-throughput system with multiple meningococcal strains and utilizing different lots of human complement. The assay is robust and highly reproducible. Titers obtained by the fluorescence readout method are strongly correlated with the data obtained using the conventional, agar plate-based assay. These results demonstrate that the detection of bacteria that have survived the bactericidal reaction by measuring metabolic activity using a fluorescent dye as an alternative readout is a promising approach for the development of a high-throughput bactericidal assay.
Practical Phase Retrieval Using Double Deep Image Priors (2022)

Phase retrieval (PR) concerns the recovery of complex phases from complex magnitudes. We identify the connection between the difficulty level and the number and variety of symmetries in PR problems. We focus on the most difficult far-field PR (FFPR), and propose a novel method using double deep image priors. In realistic evaluation, our method outperforms all competing methods by large margins. As a single-instance method, our method requires no training data and minimal hyperparameter tuning, and hence enjoys good practicality.
Unsupervised Paraphrase Generation via Dynamic Blocking. (2020)

We propose Dynamic Blocking, a decoding algorithm which enables large-scale pretrained autoregressive models (such as BART, T5, GPT-2 and XLNet) to generate high-quality paraphrases in an unsupervised setting. In order to obtain an alternative surface form, whenever the language model emits a token that is present in the source sequence, we prevent the model from generating the subsequent source token for the next time step. We show that our approach achieves state-of-the-art results on benchmark datasets when compared to previous unsupervised approaches, and is even comparable with strong supervised, in-domain models. We also propose a new automatic metric based on self-BLEU and BERTscore which not only discourages the model from copying the input through, but also evaluates text similarity based on distributed representations, hence avoiding reliance on exact keyword matching. In addition, we demonstrate that our model generalizes across languages without any additional training.
Statins decrease leptin expression in human white adipocytes (2018)

Statin use is associated with increased calorie intake and consequent weight gain. It is speculated that statin-dependent improvements in lipid profile may undermine the perceived need to follow lipid-lowering and other dietary recommendations leading consequently to increased calorie intake. However, increases in calorie intake in statin users may also be related to statin-dependent decreases in satiety factors such as leptin, an adipocyte-derived adipokine. The objective of our study was to examine the direct effects of statins on leptin expression. Adipocytes are the main source of circulating leptin. Therefore, we examined the effects of atorvastatin and simvastatin on leptin expression in cultured human white adipocytes. We show that treatment of white adipocytes with simvastatin and atorvastatin decreases leptin mRNA expression (simvastatin: P = 0.008, atorvastatin: P = 0.03) and leptin secretion (simvastatin: P = 0.0001, atorvastatin: P = 0.0001). Both simvastatin and atorvastatin mediate decreases in leptin expression via extracellular-signal-regulated kinases 1/2 and peroxisome proliferator-activated receptor gamma pathways (simvastatin: P = 0.01, atorvastatin: P = 0.026). Additionally, statin treatment also induced expected increases in adiponectin, while decreasing monocyte chemoattractant protein 1 (MCP1) mRNA. Furthermore, statins increased secretion of both total as well as high molecular weight adiponectin while decreasing MCP1 secretion. To conclude, statins act directly on human white adipocytes to regulate adipokine secretion and decrease leptin expression. Leptin is an important satiety factor. Hence, statin-dependent decreases in leptin may contribute, at least in part, to increases in food intake in statin users.
Notes (2021)

The figure of $650 billion is an unofficial estimate provided by FCA research based upon a survey of revenues and costs for UK industry.Potential ranges are from $500 billion to $750 billion.Significantly, the FCA's own report in 2017 highlighted that the estimated margins of asset managers averaged more than 38 per cent, which is far greater than the industries in which their customers' money is invested.As the FCA report concedes, precise figures are hard to obtain as the industry claims not to maintain records of individual fund costs and profitability.Our intention here is to point to the likely size of the revenues, not to provide that precise figure.
Supplementary Tables1-2 from Selective Inhibition of Matrix Metalloproteinase-14 Blocks Tumor Growth, Invasion, and Angiogenesis (2023)

Supplementary Tables1-2 from Selective Inhibition of Matrix Metalloproteinase-14 Blocks Tumor Growth, Invasion, and Angiogenesis
End-to-End Learning of Geometry and Context for Deep Stereo Regression (2017)

We propose a novel deep learning architecture for regressing disparity from a rectified pair of stereo images. We leverage knowledge of the problem's geometry to form a cost volume using deep feature representations. We learn to incorporate contextual information using 3-D convolutions over this volume. Disparity values are regressed from the cost volume using a proposed differentiable soft argmin operation, which allows us to train our method end-to-end to sub-pixel accuracy without any additional post-processing or regularization. We evaluate our method on the Scene Flow and KITTI datasets and on KITTI we set a new state-of-the-art benchmark, while being significantly faster than competing approaches.
Regulation of bone mass by the gut microbiota is dependent on NOD1 and NOD2 signaling (2017)

Germ-free (GF) mice have increased bone mass that is normalized by colonization with gut microbiota (GM) from conventionally raised (CONV-R) mice. To determine if innate immune signaling pathways mediated the effect of the GM, we studied the skeleton of GF and CONV-R mice with targeted inactivation of MYD88, NOD1 or NOD2. In contrast to WT and Myd88<sup>-/-</sup> mice, cortical bone thickness in mice lacking Nod1 or Nod2 was not increased under GF conditions. The expression of Tnfα and the osteoclastogenic factor Rankl in bone was reduced in GF compared to CONV-R WT mice but not in Nod1<sup>-/-</sup> or Nod2<sup>-/-</sup> mice indicating that the effect of the GM to increase Tnfα and Rankl in bone and to reduce bone mass is dependent on both NOD1 and NOD2 signaling.
ChemInform Abstract: Organocatalytic Highly Enantioselective α‐Selenenylation of Aldehydes. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Phenotypic, Functional, and Kinetic Parameters Associated with Apparent T-Cell Control of Human Immunodeficiency Virus Replication in Individuals with and without Antiretroviral Treatment (2005)

The human immunodeficiency virus (HIV)-mediated immune response may be beneficial or harmful, depending on the balance between expansion of HIV-specific T cells and the level of generalized immune activation. The current study utilizes multicolor cytokine flow cytometry to study HIV-specific T cells and T-cell activation in 179 chronically infected individuals at various stages of HIV disease, including those with low-level viremia in the absence of therapy ("controllers"), low-level drug-resistant viremia in the presence of therapy (partial controllers on antiretroviral therapy [PCAT]), and high-level viremia ("noncontrollers"). Compared to noncontrollers, controllers exhibited higher frequencies of HIV-specific interleukin-2-positive gamma interferon-positive (IL-2(+) IFN-gamma(+)) CD4(+) T cells. The presence of HIV-specific CD4(+) IL-2(+) T cells was associated with low levels of proliferating T cells within the less-differentiated T-cell subpopulations (defined by CD45RA, CCR7, CD27, and CD28). Despite prior history of progressive disease, PCAT patients exhibited many immunologic characteristics seen in controllers, including high frequencies of IL-2(+) IFN-gamma(+) CD4(+) T cells. Measures of immune activation were lower in all CD8(+) T-cell subsets in controllers and PCAT compared to noncontrollers. Thus, control of HIV replication is associated with high levels of HIV-specific IL-2(+) and IFN-gamma(+) CD4(+) T cells and low levels of T-cell activation. This immunologic state is one where the host responds to HIV by expanding but not exhausting HIV-specific T cells while maintaining a relatively quiescent immune system. Despite a history of advanced HIV disease, a subset of individuals with multidrug-resistant HIV exhibit an immunologic profile comparable to that of controllers, suggesting that functional immunity can be reconstituted with partially suppressive highly active antiretroviral therapy.
Basic structures for photonic integrated circuits in Silicon-on-insulator (2004)

For the compact integration of photonic circuits, wavelength-scale structures with a high index contrast are a key requirement. We developed a fabrication process for these nanophotonic structures in Silicon-on-insulator using CMOS processing techniques based on deep UV lithography. We have fabricated both photonic wires and photonic crystal waveguides and show that, with the same fabrication technique, photonic wires have much less propagation loss than photonic crystal waveguides. Measurements show losses of 0.24dB/mm for photonic wires, and 7.5dB/mm for photonic crystal waveguides. To tackle the coupling to fiber, we studied and fabricated vertical fiber couplers with coupling efficiencies of over 21%. In addition, we demonstrate integrated compact spot-size converters with a mode-to-mode coupling efficiency of over 70%.
Noncontact Stimulation of the Cavernous Nerves in the Rat Prostate Using a Tunable-Wavelength Thulium Fiber Laser (2008)

A significant increase in the intracavernosal pressure was detected on laser stimulation, with pressure returning to baseline values after stimulation ceased. This study demonstrates the feasibility of noncontact stimulation of the cavernous nerves using near-infrared laser radiation.
Clinical Characteristics of Migraine in A Population-Based Twin Sample: Similarities and Differences Between Migraine with and Without Aura (1999)

There are clinical differences between IHS defined migraine with and without aura; even the headache phase between the two entities differs. It is worthwhile distinguishing between them when looking for the elusive genes for these more common forms of migraine.
Measurement of the charged-particle multiplicity inside jets from $$\sqrt{s}=8$$ s = 8 $${\mathrm{TeV}}$$ TeV pp collisions with the ATLAS detector (2016)

The number of charged particles inside jets is a widely used discriminant for identifying the quark or gluon nature of the initiating parton and is sensitive to both the perturbative and non-perturbative components of fragmentation. This paper presents a measurement of the average number of charged particles with [Formula: see text] [Formula: see text] inside high-momentum jets in dijet events using 20.3 fb[Formula: see text] of data recorded with the ATLAS detector in <i>pp</i> collisions at [Formula: see text] [Formula: see text] collisions at the LHC. The jets considered have transverse momenta from 50 [Formula: see text] up to and beyond 1.5 [Formula: see text]. The reconstructed charged-particle track multiplicity distribution is unfolded to remove distortions from detector effects and the resulting charged-particle multiplicity is compared to several models. Furthermore, quark and gluon jet fractions are used to extract the average charged-particle multiplicity for quark and gluon jets separately.