gebhart/patrepeval huggingface dataset:
Combined Benefit of Quantitative Three-Compartment Breast Image Analysis and Mammography Radiomics in the Classification of Breast Masses in a Clinical Data Set (2018)

Purpose To investigate the combination of mammography radiomics and quantitative three-compartment breast (3CB) image analysis of dual-energy mammography to limit unnecessary benign breast biopsies. Materials and Methods For this prospective study, dual-energy craniocaudal and mediolateral oblique mammograms were obtained immediately before biopsy in 109 women (mean age, 51 years; range, 31-85 years) with Breast Imaging Reporting and Data System category 4 or 5 breast masses (35 invasive cancers, 74 benign) from 2013 through 2017. The three quantitative compartments of water, lipid, and protein thickness at each pixel were calculated from the attenuation at high and low energy by using a within-image phantom. Masses were automatically segmented and features were extracted from the low-energy mammograms and the quantitative compartment images. Tenfold cross-validations using a linear discriminant classifier with predefined feature signatures helped differentiate between malignant and benign masses by means of (a) water-lipid-protein composition images alone, (b) mammography radiomics alone, and (c) a combined image analysis of both. Positive predictive value of biopsy performed (PPV<sub>3</sub>) at maximum sensitivity was the primary performance metric, and results were compared with those for conventional diagnostic digital mammography. Results The PPV<sub>3</sub> for conventional diagnostic digital mammography in our data set was 32.1% (35 of 109; 95% confidence interval [CI]: 23.9%, 41.3%), with a sensitivity of 100%. In comparison, combined mammography radiomics plus quantitative 3CB image analysis had PPV<sub>3</sub> of 49% (34 of 70; 95% CI: 36.5%, 58.9%; P < .001), with a sensitivity of 97% (34 of 35; 95% CI: 90.3%, 100%; P < .001) and 35.8% (39 of 109) fewer total biopsies (P < .001). Conclusion Quantitative three-compartment breast image analysis of breast masses combined with mammography radiomics has the potential to reduce unnecessary breast biopsies. © RSNA, 2018 Online supplemental material is available for this article.
A gene from pea (Pisum sativum L.) with homology to metallothionein genes (1990)

While searching for 'organ-specific' genes in pea (Pisum sativum L.) we have isolated a gene (designated PsMTA) which has an ORF encoding a predicted protein with some similarity to metallothioneins (MTs). The PsMTA transcript is abundant in roots which have not been exposed to elevated concentrations of trace metals.
Auxiliary antenna-assisted interference mitigation for radio astronomy arrays (2005)

Interferometric image synthesis in radio astronomy is plagued by signal corruption from man-made sources. The very weak signals of interest can be overwhelmed by such interference. Recent work has proposed using array signal processing techniques of adaptive beamforming, adaptive filtering, and subspace projection to remove interference prior to image synthesis. In some practical scenarios, we have found poor cancellation performance when using such methods. Because signal-of-interest levels in radio astronomy (RA) are usually well below the noise, even interference to noise ratios (INR) less than unity can affect signal estimation. At these low INRs, it is difficult to estimate interference parameters or statistics with sufficient accuracy for high-performance adaptive cancellation or subspace projection. By adding a few (one to three) low-gain (relative to the primary telescope dishes) "auxiliary" antennas to an array, it is possible to overcome this problem. This paper will show that using such antennas (e.g. commercial-grade 3-m dishes) with an existing array can significantly improve interference rejection. New extensions to subspace projection spatial filtering methods are presented, along with analytical and simulated results for performance comparison.
Online Bayesian Passive-Aggressive Learning (2013)

Online Passive-Aggressive (PA) learning is an effective framework for performing max-margin online learning. But the deterministic formu-lation and estimated single large-margin model could limit its capability in discovering descrip-tive structures underlying complex data. This pa-per presents online Bayesian Passive-Aggressive (BayesPA) learning, which subsumes the online PA and extends naturally to incorporate latent variables and perform nonparametric Bayesian inference, thus providing great flexibility for ex-plorative analysis. We apply BayesPA to topic modeling and derive efficient online learning al-gorithms for max-margin topic models. We fur-ther develop nonparametric methods to resolve the number of topics. Experimental results show that our approaches significantly improve time efficiency while maintaining comparable results with the batch counterparts. 1.
TU-C-224-01: Womenˈs Professional SC Panel: Successful Career Strategies in Medical Physics (2011)

This session is directed at supporting the professional development of medical physicists, with special consideration for challenges that face women as they build their professional careers. The panelists are mid-career and senior women medical physicists in different practice settings. All panelists will share how their own career developed as well as strategies for success at different career stages. There will be a moderated panel discussion with ample time for questions from the audience. The panel discussion can include advice on getting your first position as a medical physicist, getting involved in national organizations such as the AAPM, defining success career, and balancing work and family. All members are welcome to attend. The Womenˈs Professional Subcommitee (WPSC) of the AAPM organized this panel. Learning objectives for this session: 1. The role of mentorship in career development 2. The benefits of volunteer opportunities to serve and build on your success 3. Considerations for advancing your career through different positions 4. Strategies for balancing a career and family
A Combined Experimental and Theoretical Study of Conformational Preferences of Molecular Semiconductors (2014)

Structural modules used for assembling molecular semiconductors have typically been chosen to give desirable optical and electronic properties. Growing evidence shows that chemical functionalities should be considered for controlling molecular shape, which is important for function because of its influence on polymer secondary structure, lattice arrangements in crystals, and crystallization tendencies. Using density functional theory (DFT) calculations, followed by a natural bond orbital (NBO) analysis, we examine eight molecular semiconductors with resolved single crystal X-ray structures to understand the features that dominate molecular conformations and ultimately develop practical rules that govern these preferences. All molecules can be described by a D′–A–D–A–D′ architecture and have a 4,4-dimethyl-4H-silolo[3,2-b:4,5-b′]dithiophene (DTS) donor (D) core unit, with [1,2,5]thiadiazolo[3,4-c]pyridine (PT), 5-fluorobenzo[c][1,2,5]thiadiazole (FBT), or benzo[1,2,5]thiadiazole (BT) electron acceptor (A) units, and either thiophene, 5-hexyl-2,2′-bithiophene, or benzofuran electron-donating end-caps (D′). The NBO analysis shows that the energy difference between the two alternative conformations, or rotamers, (ΔErot) is a delicate balance of multiple competing nonbonding interactions that are distributed among many atoms. These interactions include attractive “donor–acceptor” electron sharing, steric repulsion, and electrostatic stabilization or destabilization. A proper grouping of these interactions reveals two primary factors determining ΔErot. The first concerns heteroatoms adjacent to the bonds connecting the structural units, wherein the asymmetric distribution of π-electron density across the link joining the units results in stabilization of one of two rotamers. The second factor arises from electrostatic interactions between close-contact atoms, which may also shift the ΔErot of the two rotamers. When all these constituent interactions cooperate, the dihedral angle is “locked” in a planar conformation with a negligible population of alternative rotamers.
Residual Stresses and Damage in Unidirectional Model Composites (2008)

Unidirectional model composites were fabricated with silicon carbide fibers and different borosilicate glasses to study the effect of residual stress states on the damage progression in these composites. A specially designed straining stage was employed to study the failure modes in these materials under stepwise loading. Although both fiber and matrix cracks were observed in all specimens, the mechanisms of failure were found to be different and strongly dependent on the residual stress state in these materials.
A Two-Gene Methylation Signature for the Diagnosis of Bladder Cancer in Urine (2019)

We identified a novel two-gene panel with a high diagnostic accuracy for BC that can be applied in a noninvasive, urine-based test.
Authentication from Matrix Conjugation (2009)

We propose an authentication scheme where forgery (a.k.a. impersonation) seems infeasible without finding the prover's long-term private key. The latter would follow from solving the conjugacy search problem in the platform (noncommutative) semigroup, i.e., to recovering X from X –1 AX and A . The platform semigroup that we suggest here is the semigroup of n × n matrices over truncated multivariable polynomials over a ring.
Lung Bacterial Clearance in Murine Pneumococcal Pneumonia (1977)

We studied the bactericidal capacity of the rat lung during the development of pneumococcal pneumonia. Pneumonia was produced in a lower lobe by the intrabronchial instillation of 10(4)Streptococcus pneumoniae cells in buffer. Lung bacterial counts progressively increased, reaching 10(7) per lung within 48 h, and the increase was associated with localized atelectasis and consolidation. Bacterial multiplication was inhibited with tetracycline at various intervals after infection, and the subsequent clearance of pneumococci was determined. Viable pneumococci were rapidly killed by lung defenses if bacterial multiplication was inhibited within 12 h of the onset of infection. No change occurred in the bacterial populationif tetracycline was delayed until 24 h after infection, indicating that pneumococcal killing by lung defenses had ceased. This effect could be reproduced with the addition of pneumococcal capsular polysaccharide to the inoculum, which produced a dose-related inhibition of pneumococcal clearance. The clearance of S. epidermidis was not impaired in the presence of pneumococcal pneumonia or by administration of exogenous capsular polysaccharide. These data indicate that pneumococcal pneumonia causes a marked impairment in lung antipneumococcal defenses within 24 h of the onset of infection. This acquired defect in antibacterial defenses may be due to the accumulation of pneumococcal capsular material in the lungs of infected animals.
miR-212 Increases Tumor Necrosis Factor–Related Apoptosis-Inducing Ligand Sensitivity in Non–Small Cell Lung Cancer by Targeting the Antiapoptotic Protein PED (2010)

PED/PEA-15 (PED) is a death effector domain family member of 15 kDa with a broad antiapoptotic function found overexpressed in a number of different human tumors, including lung cancer. To date, the mechanisms that regulate PED expression are unknown. Therefore, we address this point by the identification of microRNAs that in non-small cell lung cancer (NSCLC) modulate PED levels. In this work, we identify miR-212 as a negative regulator of PED expression. We also show that ectopic expression of this miR increases tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-induced cell death in NSCLC cells. In contrast, inhibition of endogenous miR-212 by use of antago-miR results in increase of PED protein expression and resistance to TRAIL treatment. Besides, in NSCLC, we show both in vitro and in vivo that PED and miR-212 expressions are inversely correlated, that is, PED is upregulated and miR-212 is rarely expressed. In conclusion, these findings suggest that miR-212 should be considered as a tumor suppressor because it negatively regulates the antiapoptotic protein PED and regulates TRAIL sensitivity.
Plasma‐assisted molecular beam epitaxy of Sn‐doped In2O3: Sn incorporation, structural changes, doping limits, and compensation (2013)

A comprehensive study of Sn doping in In 2 O 3 during plasma‐assisted molecular beam epitaxy (PA‐MBE) is given, covering growth aspects and application‐relevant aspects such as structural and transport properties. Single crystalline, (001) oriented indium oxide (In 2 O 3 ) thin films were grown on Y‐stabilized ZrO 2 (001) and systematically doped with 10 18 cm −3 to 6 × 10 21 cm −3 tin (Sn) by PA‐MBE. The Sn incorporation was proportional to the Sn flux up to a Sn concentration of ≈10 20 cm −3 indicating well‐controllable doping in this regime. Toward higher Sn concentrations the Sn incorporation was increasingly impeded, which could be somewhat mitigated by increasing the oxygen‐to‐indium flux ratio. The surface faceting of undoped In 2 O 3 (001) during growth under oxygen rich conditions was prevented by doping to Sn concentrations 4×10 20 cm −3 . Up to Sn concentrations of 1.4 × 10 21 cm −3 no detrimental effects on the film crystal quality were observed by X‐ray diffraction, but concentrations cm −3 resulted in structural deterioration with the formation of secondary crystalline phases. The electron concentration increased and resistivity decreased with increasing Sn concentration. The electron concentration was limited to ≈2 × 10 21 cm −3 despite higher Sn concentrations and a minimum resistivity of 9 × 10 −5 Ω cm was reached at a Sn concentration of ≈10 21 cm −3 . The highest electron concentrations and lowest resistivities were realized by a post‐growth vacuum annealing to remove compensating acceptors. Guidelines to obtain low resistivity, high‐quality indium tin oxide (ITO) films are given. Textured reference films grown on r‐plane sapphire, Al 2 O 3 (10–12), showed very similar behavior in terms of incorporation, doping limit, and compensation, which indicates that our results are qualitatively not limited to single crystalline films.
Data from Modulation of Target Antigen Density Improves CAR T-cell Functionality and Persistence (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Chimeric antigen receptor T-cell (CART) therapy targeting CD22 induces remission in 70% of patients with relapsed/refractory acute lymphoblastic leukemia (ALL). However, the majority of post-CD22 CART remissions are short and associated with reduction in CD22 expression. We evaluate the implications of low antigen density on the activity of CD22 CART and propose mechanisms to overcome antigen escape.&lt;/p&gt;Experimental Design:&lt;p&gt;Using ALL cell lines with variable CD22 expression, we evaluate the cytokine profile, cytotoxicity, and &lt;i&gt;in vivo&lt;/i&gt; CART functionality in the setting of low CD22 expression. We develop a high-affinity CD22 chimeric antigen receptor (CAR) as an approach to improve CAR sensitivity. We also assess Bryostatin1, a therapeutically relevant agent, to upregulate CD22 and improve CAR functionality.&lt;/p&gt;Results:&lt;p&gt;We demonstrate that low CD22 expression negatively impacts &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt; CD22 CART functionality and impairs &lt;i&gt;in vivo&lt;/i&gt; CART persistence. Moreover, low antigen expression on leukemic cells increases naïve phenotype of persisting CART. Increasing CAR affinity does not improve response to low-antigen leukemia. Bryostatin1 upregulates CD22 on leukemia and lymphoma cell lines for 1 week following single-dose exposure, and improves CART functionality and &lt;i&gt;in vivo&lt;/i&gt; persistence. While Bryostatin1 attenuates IFNγ production by CART, overall &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt; CART cytotoxicity is not adversely affected. Finally, administration of Bryostain1 with CD22 CAR results in longer duration of &lt;i&gt;in vivo&lt;/i&gt; response.&lt;/p&gt;Conclusions:&lt;p&gt;We demonstrate that target antigen modulation is a promising strategy to improve CD22 CAR efficacy and remission durability in patients with leukemia and lymphoma.&lt;/p&gt;&lt;p&gt;&lt;i&gt;See related commentary by Guedan and Delgado, p. 5188&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
Serendipitous Language Learning in Mixed Reality (2017)

Mixed Reality promises a new way to learn in the world: blending holograms with our surroundings to create contextually rich experiences that find their place in our daily routine. Existing situated learning platforms limit the learner and implicitly enforce the designer's intent by hard-coding content and predetermining what elements in the environment are actionable. In this paper, we define the framework of Serendipitous Learning in Mixed Reality as situated, incidental learning that occurs naturally in the user's environment and stems from the learner's curiosity. This framework is explored within the context of second language acquisition. We present WordSense, a Mixed Reality platform that recognizes objects in the learner's vicinity and embeds holographic content that identifies the corresponding word, provides sentence and definition cues for practice, and displays dynamic audiovisual content that shows example usage. By employing markerless tracking and dynamically linked content, WordSense enables serendipitous language learning in the wild.
Replication of ϕX174 DNA by Escherichia coli polA - In Vitro (1972)

Lysates of an Escherichia coli polA(-) strain convert single-stranded DNA from varphiX174 virus to the double-stranded replicative form with high efficiency on cellophane discs. The initiation of synthesis of the complementary strand appears to be rate limiting; once initiation occurs, the chain is propagated rapidly. Under these conditions, the unsealed replicative form accumulates and is slowly converted to the sealed form; this conversion requires the activity of the DPN-dependent DNA ligase.
Low-grade waste heat driven desalination technology (2014)

Low-grade heat driven multi-effect distillation (MED) desalination is a very promising environmentally friendly, low emission technology. Many countries, such as Australia, are water short and conventional desalination technology is energy intensive. If a primary fossil fuel source is used, then desalination will significantly contribute to carbon dioxide emission. Low-grade waste heat from process plants and power plants generate minimal additional carbon dioxide. This source of energy is typically abundant at a temperature around 65–90 °C, which dovetails with MED technology. In this paper, we report on a new MED technology that couples perfectly with low grade waste heat to give at least a 25% freshwater yield improvement compared with conventional MED design. Typical applications and their expected improvement will also be reported.
Osteocytic Pericellular Matrix (PCM): Accelerated Degradation under In Vivo Loading and Unloading Conditions Using a Novel Imaging Approach (2021)

The proteoglycan-containing pericellular matrix (PCM) controls both the biophysical and biochemical microenvironment of osteocytes, which are the most abundant cells embedded and dispersed in bones. As a molecular sieve, osteocytic PCMs not only regulate mass transport to and from osteocytes but also act as sensors of external mechanical environments. The turnover of osteocytic PCM remains largely unknown due to technical challenges. Here, we report a novel imaging technique based on metabolic labeling and "click-chemistry," which labels de novo PCM as "halos" surrounding osteocytes in vitro and in vivo. We then tested the method and showed different labeling patterns in young vs. old bones. Further "pulse-chase" experiments revealed dramatic difference in the "half-life" of PCM of cultured osteocytes (~70 h) and that of osteocytes in vivo (~75 d). When mice were subjected to either 3-week hindlimb unloading or 7-week tibial loading (5.1 N, 4 Hz, 3 d/week), PCM half-life was shortened (~20 d) and degradation accelerated. Matrix metallopeptidase MMP-14 was elevated in mechanically loaded osteocytes, which may contribute to PCM degradation. This study provides a detailed procedure that enables semi-quantitative study of the osteocytic PCM remodeling in vivo and in vitro.
Pt based thin films deposited by magnetron sputtering for PEMFC and DMFC fuel cells (2011)

International audience
Dynamic Protein Pathway Activation Mapping of Adipose-Derived Stem Cell Differentiation Implicates Novel Regulators of Adipocyte Differentiation (2013)

Next to embryonic stem cell research, adult stem cell research is providing a promising alternative for enhanced tissue regeneration and transplantation. The key biochemical networks controlling the differentiation processes regulating stem cell biology remain largely disputed and or undefined, contributing to a lack of knowledge of the principle phosphoregulatory events propagating signal transduction. To effectively monitor these events relative to adipocyte differentiation, this study utilized a high throughput reverse phase protein microarray platform and characterized adult adipose-derived stem cell (ASC) differentiation through the monitoring of ∼100 phosphospecific endpoints with 33 distinct time points examined across 14 days. This kinetic-based analysis showed time ordered signal transduction ultimately implicating pathways correlated with adipogenic differentiation. To further validate the causal significance of these network activations, pharmacological targeting was implemented to include the chemical inhibitors MAPK inhibitor PD169316, rapamycin, and HNMPA-(AM)3 yielding partial or complete disruption of adipocytic differentiation, as noted by a decrease or lack of lipid formation within the mature adipocytes. Based on this analysis, v-crk sarcoma virus CT10 oncogene homolog (CRKII) and c-abl oncogene 1, non-receptor tyrosine kinase (c-ABL) were implicated as novel key regulators of adipocyte differentiation, with v-akt murine thymoma viral oncogene (AKT), mammalian target of rapamycin (mTOR), and SMAD family member (SMAD) pathways being implicated as secondary regulators. This dynamic molecular profiling provides a novel insight into the signaling architecture of mesenchymal stem cell differentiation and may be useful in the development of therapeutic modulators for clinical applications; in addition to advancing the collective understanding of key cellular processes, ultimately contributing to more confident stem cell manipulation.
Measurement of P-violating neutron spin rotation in the p-wave resonance of 139La (1995)

P‐violating neutron spin rotation angle is being measured in the p‐wave resonance of 139La with a new apparatus developed at KEK. Present status and preliminary results of the measurement is reported in this paper. The value of parity mixing matrix element in the compound state deduced from the result is consistent with the theoretical prediction within the experimental errors.