gebhart/patrepeval huggingface dataset:
Applying in vitro elasticity imaging results to optimize in vivo breast lesion characterization using a combined 3D USs/digital X-ray system (2006)

Ultrasound-based reconstructive elasticity imaging has great potential for diagnosis and characterization of breast lesions. Applying external strain with a mammographic paddle as part of a combined 3D US/Digital X-ray system provides more uniform deformation and breast stability, offering opportunities to improve image fidelity. In this study, we examined phantom and in vivo strain image quality with three GE transducers (M12L, 10L, 7L) each operating at several frequencies between 5- 10 MHz and 3 TPX paddle thicknesses to predict optimal in vivo results with the combined system. Out-of-plane motion was measured by translating an ultrasonic transducer across a breast phantom (ATS, model BB-1) in 50um steps over 400um. Each image was correlated to the first in the sequence to determine rate of elevational decorrelation. Next, in-plane, strain-limited decorrelation was evaluated by correlating images at 0.25-1.0% steps up to 5% strain using two-pass 2D speckle tracking algorithms and accumulation. Adaptive strain estimation (ASE) was applied to maximize CNR throughout the final strain image. Overall the 10L transducer caused the least decorrelation due to out-of-plane motion (R = 0.97 at 7.5MHz and 400um elevational translation). In-plane decorrelation was also primarily strain- limited with the 10L transducer at 7.5MHz, with R = 0.9 for a 1.6% strain step. Accumulated strain images after ASE demonstrated a CNR = 13.6 with the 10L transducer at 7.5 MHz. Of the 3 paddles (0.25, 1.0, 2.5 mm) used in the phantom study, the 2.5mm paddle created strain images with less artifacts than the thinner paddles by providing more uniform deformation during compression. Next, we evaluated sources of in vivo chest wall motion in 7 subjects to minimize patient motion during the scan. Based on these experiments, patients were asked to breathe shallowly during exams as it caused less decorrelation due to chest wall motion (Ravg = 0.96 over 91 frames). In vivo results were acquired with the 10L at 7.5 MHz using continuous compression over 2.1 seconds. Strain images clearly distinguished between tissue types when accumulated up to 5% strain. In vivo results are limited by out-of-plane motion but are expected to improve with 3D tracking. These early successes indicate that using elasticity imaging with the combined system can potentially characterize breast lesions and monitor therapies.
Chronic liver disease not a significant comorbid condition for COVID-19 (2021)

To explore the role of chronic liver disease (CLD) in COVID-19. A total of 1439 consecutively hospitalized patients with COVID-19 from one large medical center in the United States from March 16, 2020 to April 23, 2020 were retrospectively identified. Clinical characteristics and outcomes were compared between patients with and without CLD. Postmortem examination of liver in 8 critically ill COVID-19 patients was performed. There was no significant difference in the incidence of CLD between critical and non-critical groups (4.1% vs 2.9%, p = 0.259), or COVID-19 related liver injury between patients with and without CLD (65.7% vs 49.7%, p = 0.065). Postmortem examination of liver demonstrated mild liver injury associated central vein outflow obstruction and minimal to moderate portal lymphocytic infiltrate without evidence of CLD. Patients with CLD were not associated with a higher risk of liver injury or critical/fatal outcomes. CLD was not a significant comorbid condition for COVID-19.
Both the Sequence and Length of the C Terminus of PEN-2 Are Critical for Intermolecular Interactions and Function of Presenilin Complexes (2004)

Presenilin 1 or presenilin 2, nicastrin, APH-1, and PEN-2 form high molecular weight complexes that play a pivotal role in the cleavage of various Type I transmembrane proteins, including the beta-amyloid precursor protein. The specific function of PEN-2 is unclear. To explore its function and intermolecular interactions, we conducted deletion and mutagenesis studies on a series of conserved residues at the C terminus of PEN-2. These studies suggest that: 1) both the presence and amino acid sequence of the conserved DYLSF domain at the C terminus of PEN-2 (residues 90-94) is critical for binding PEN-2 to other components in the presenilin complex and 2) the overall length of the exposed C terminus is critical for functional gamma-secretase activity.
Supplementary Figure 2 from VTX-2337 Is a Novel TLR8 Agonist That Activates NK Cells and Augments ADCC (2023)

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Groupthink (2010)

A fairly common modern setting entails users, each in possession of a personal wireless device, wanting to communicate securely, via their devices. If these users (and their devices) have no prior association, a new security context must be established. In order to prevent potential attacks, the initial context (association) establishment process must involve only the intended devices and their users.
Detection of Protein Aggregation in Neurodegenerative Diseases (2011)

Protein aggregates/inclusions are pathological hallmarks of a wide spectrum of neurodegenerative -diseases. These aggregates have different shapes, sizes, distribution, and protein composition, which are unique features used for pathological diagnosis. The aggregates per se are also used as molecular targets for designing therapeutic approaches. Detection of these aggregates is generally achieved by using immunostaining methods, most often by immunohistochemistry. In clinical and pathologic practice, the neurologic tissues to be examined are generally fixed with formalin and processed to paraffin-embedded tissue blocks. These treatments result in covalent cross-linking of the protein molecules and preserve the tissue morphology, but dramatically mask the antigens, making it often difficult to detect the aggregates. Therefore, removal of the cross-linking of antigens is a critical step for effective detection of these aggregates. In this chapter, we discuss and present immunostaining methods with a focus on the effectiveness of antigen-retrieval methods. In our experience, a treatment of tissues at 125°C for 20 min represents a relatively ideal antigen-retrieval method not only preserving the tissue morphology, but also providing efficient antigen retrieval. Using this method, we successfully detected some protein aggregates that escaped detection when other antigen-retrieval methods were employed.
FDG-PET for Assessment of Residual Tissue after Completion of Chemotherapy in Hodgkin Lymphoma - Report on the 2nd Interim Analysis of the PET Investigation in the Trial HD15 of the GHSG. (2007)

Abstract Introduction The prospectively randomized HD15 multicenter trial of the German Hodgkin Study Group (GHSG) included advanced-stage Hodgkin lymphoma patients comparing 8 cycles of BEACOPPescalated with 6 cycles or 8 cycles time-condensed BEACOPPbaseline. One other main study endpoint was the prognostic value of 18F-fluorodesoxyglucose (FDG) positron emission tomography (PET) following chemotherapy. The aim was to specify the negative predictive value of PET (NPV) in patients with residual tumour mass after chemotherapy. Methods Entry criteria for the PET question were partial remission (PR) after the end of chemotherapy with at least one involved nodal site measuring more than 2.5 cm in diameter by computed tomography (CT). Exclusion criteria included diabetes, elevated blood sugar levels and skeletal involvement with risk of instability. Calculations were restricted to those cases with either progressive disease (PD) or relapse within 12 months after PET or at least 12 months of follow-up. A total of 275 patients were eligible for this analysis. The assessment was based on those patients confirmed by an expert panel as being PET-negative. CT verification was performed to identify false positive PET findings. The NPV was defined as the proportion of patients without progression or relapse within 12 months. Results 9/216 patients with PET-negative residues and 9/59 patients with PET-positive residues had PD or relapse within one year of follow-up. The NPV was 0.958% (95% CI 0.931 – 0.985%). In 244/245 cases with PET-negative residual masses, no irradiation was given. In the 62/66 cases with PET-positive residues, additional radiotherapy was performed. Progression/relapse rates were significantly different between those patients with residual mass being PET-negative or PET-positive (p=0.0053). PET-negative patients, who were assessed as partial response by CT, had a prognosis similar to those in complete remission. There was no significant difference in the progression free survival in this trial and the prior GHSG trials HD12 (arms pooled) and HD9 (arm C) for advanced-stage HL (p=0.266). Importantly, the proportion of patients receiving radiotherapy decreased from 70% (HD9-C) to 39% (HD12) and 12% (HD15). Discussion The high NPV of PET suggests that radiotherapy following 6 or 8 cycles of BEACOPP might be restricted to those patients who are PET-positive after chemotherapy.
Representing and Determining Argumentative Relevance in Online Discussions: A General Approach (2023)

Understanding an online argumentative discussion is essential for understanding users' opinions on a topic and their underlying reasoning. A key challenge in determining completeness and persuasiveness of argumentative discussions is to assess how arguments under a topic are connected in a logical and coherent manner. Online argumentative discussions, in contrast to essays or face-to-face communication, challenge techniques for judging argument relevance because online discussions involve multiple participants and often exhibit incoherence in reasoning and inconsistencies in writing style. We define relevance as the logical and topical connections between small texts representing argument fragments in online discussions. We provide a corpus comprising pairs of sentences, labeled with argumentative relevance between the sentences in each pair. We propose a computational approach relying on content reduction and a Siamese neural network architecture for modeling argumentative connections and determining argumentative relevance between texts. Experimental results indicate that our approach is effective in measuring relevance between arguments, and outperforms strong and well-adopted baselines. Further analysis demonstrates the benefit of using our argumentative relevance encoding on a downstream task, predicting how impactful an online comment is to certain topic, comparing to encoding that does not consider logical connection.
Alleviation of glucose repression of maltose metabolism by MIG1 disruption in Saccharomyces cerevisiae (1996)

The MIG1 gene was disrupted in a haploid laboratory strain (B224) and in an industrial polyploid strain (DGI 342) of Saccharomyces cerevisiae. The alleviation of glucose repression of the expression of MAL genes and alleviation of glucose control of maltose metabolism were investigated in batch cultivations on glucose-maltose mixtures. In the MIG1-disrupted haploid strain, glucose repression was partly alleviated; i.e., maltose metabolism was initiated at higher glucose concentrations than in the corresponding wild-type strain. In contrast, the polyploid delta mig1 strain exhibited an even more stringent glucose control of maltose metabolism than the corresponding wild-type strain, which could be explained by a more rigid catabolite inactivation of maltose permease, affecting the uptake of maltose. Growth on the glucose-sucrose mixture showed that the polypoid delta mig1 strain was relieved of glucose repression of the SUC genes. The disruption of MIG1 was shown to bring about pleiotropic effects, manifested in changes in the pattern of secreted metabolites and in the specific growth rate.
Liquid Crystals Based on Hypervalent Sulfur Fluorides: Exploring the Steric Effects of ortho‐Fluorine Substituents (2005)

Abstract Liquid crystals that have ortho‐ fluorinated pentafluoro‐λ 6 ‐sulfanyl terminal groups are the most polar materials that are still compatible with current active matrix LCD technology. The synthesis of the first examples of this class of substance has been achieved by direct fluorination. The physico‐chemical characterization, supported by DFT calculations, revealed some surprising features of these new compounds: the bulky SF 5 group is easily deformed and responds in a quite unusual way to the steric strain exerted by its ortho substituents. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2005)
Titan cells formation in Cryptococcus neoformans is finely tuned by environmental conditions and modulated by positive and negative genetic regulators (2018)

The pathogenic fungus Cryptococcus neoformans exhibits morphological changes in cell size during lung infection, producing both typical size 5 to 7 μm cells and large titan cells (> 10 μm and up to 100 μm). We found and optimized in vitro conditions that produce titan cells in order to identify the ancestry of titan cells, the environmental determinants, and the key gene regulators of titan cell formation. Titan cells generated in vitro harbor the main characteristics of titan cells produced in vivo including their large cell size (>10 μm), polyploidy with a single nucleus, large vacuole, dense capsule, and thick cell wall. Here we show titan cells derived from the enlargement of progenitor cells in the population independent of yeast growth rate. Change in the incubation medium, hypoxia, nutrient starvation and low pH were the main factors that trigger titan cell formation, while quorum sensing factors like the initial inoculum concentration, pantothenic acid, and the quorum sensing peptide Qsp1p also impacted titan cell formation. Inhibition of ergosterol, protein and nucleic acid biosynthesis altered titan cell formation, as did serum, phospholipids and anti-capsular antibodies in our settings. We explored genetic factors important for titan cell formation using three approaches. Using H99-derivative strains with natural genetic differences, we showed that titan cell formation was dependent on LMP1 and SGF29 genes. By screening a gene deletion collection, we also confirmed that GPR4/5-RIM101, and CAC1 genes were required to generate titan cells and that the PKR1, TSP2, USV101 genes negatively regulated titan cell formation. Furthermore, analysis of spontaneous Pkr1 loss-of-function clinical isolates confirmed the important role of the Pkr1 protein as a negative regulator of titan cell formation. Through development of a standardized and robust in vitro assay, our results provide new insights into titan cell biogenesis with the identification of multiple important factors/pathways.
Phase tuning by length contraction (2018)

Typical integrated optical phase tuners alter the effective index. In this paper, we explore tuning by geometric deformation. We show that tuning efficiency, Vπ L, improves as the device size shrinks down to the optimal bend radius, contrary to conventional index-shift based approaches where Vπ L remains constant. We demonstrate that this approach is capable of ultra-low power tuning across a full FSR in a low-confinement silicon nitride based ring resonator of 580 μm radius. We demonstrate record performance with V<sub>FSR</sub> = 16 V, Vπ L = 3.6 V dB, Vπ Lα = 1.1 V dB, tuning current below 10 nA, and unattenuated tuning response up to 1 MHz. We also present optimized designs for high confinement silicon nitride and silicon based platforms with radius down to 80 μm and 45 μm, respectively, with performance well beyond current state-of-the-art. Applications include narrow-linewidth tunable diode lasers for spectroscopy and non-linear optics, optical phased array beamforming networks for RF antennas and LIDAR, and optical filters for WDM telecommunication links.
Electronic structure and protonation of alkyl chlorides (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectronic structure and protonation of alkyl chloridesWilliam L. JorgensenCite this: J. Am. Chem. Soc. 1978, 100, 4, 1049–1056Publication Date (Print):February 1, 1978Publication History Published online1 May 2002Published inissue 1 February 1978https://pubs.acs.org/doi/10.1021/ja00472a005https://doi.org/10.1021/ja00472a005research-articleACS PublicationsRequest reuse permissionsArticle Views109Altmetric-Citations19LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
A System for Classification of Propositions of the Indian Supreme Court Judgements (2013)

In this work, we describe a system for classification of propositions from legal judgements of the Supreme Court of India. The system was submitted for participation to the Information Access in the Legal Domain track at the Forum for Information Retrieval Evaluation (FIRE) 2013. The system uses a multi-class Maximum Entropy classifier and various specially designed features to capture the underlying characteristics of the legal propositions. The best performing feature set was chosen by 10-fold cross-validation over the training set. The system achieved an accuracy of 65.03% on the training set and an accuracy of 51.02% on the test set.
Laryngeal Epithelial Defenses against Laryngopharyngeal Reflux: Investigations of E-Cadherin, Carbonic Anhydrase Isoenzyme III, and Pepsin (2005)

The findings of depleted E-cadherin and CAIII and the presence of pepsin appear to correlate with LPR. The reduced protective response indicated by the reduced expression of CAIII may play an important role in the disruption of the intercellular barrier associated with the down-regulation of E-cadherin.
Small Marker Tracking with Low-Cost, Unsynchronized, Movable Consumer Cameras For Augmented Reality Surgical Training (2020)

Surgeons improve their skills through repetition of training tasks in order to operate on living patients, ideally receiving timely, useful, and objective performance feedback. However, objective performance measurement is currently difficult without 3D visualization, with effective surgical training apparatus being extremely expensive or limited in accessibility. This is problematic for medical students, especially in situations such as the COVID-19 pandemic in which they are needed by the community but have few ways of practicing without lab access. In this work, we propose and prototype a system for augmented reality (AR) visualization of laparoscopic training tasks using cheap and widely-compatible borescopes, which can track small objects typical of surgical training. We use forward kinematics for calibration and multi-threading to attempt synchronization in order to increase compatibility with consumer applications, resulting in an effective AR simulation with low-cost devices and consumer software, while also providing dynamic camera and marker tracking. We test the system with a typical peg transfer task on the HoloLens 1 and MagicLeap One.
STONE: Signal Temporal Logic Neural Network for Time Series Classification (2021)

In this paper, we propose a neuro-symbolic frame-work called signal temporal logic neural network (STONE) that combines the characteristics of neural networks and temporal logics. Weighted Signal Temporal Logic (wSTL) formulas are recursively composed of subformulas connected using logical and temporal operators. The quantitative semantics of wSTL is defined such that the quantitative satisfaction of subformulas with higher weights have a more significant influence on the quantitative satisfaction of a wSTL formula. In the STONE, each neuron represents a component of a wSTL formula, and the output of STONE corresponds to the quantitative satisfaction of a wSTL formula. We use STONE to represent wSTL formulas and classify time-series data. WSTL formulas are more interpretable and human-readable than classical time series classification models. The STONE is end-to-end differentiable, which allows learning of wSTL formulas to be done using back-propagation. Experiments on benchmark time-series datasets show that STONE is comparable to the state-of-the-art time series classification models and the wSTL learning algorithm is faster than the traditional STL learning algorithm.
Automated Gene Ontology annotation for anonymous sequence data (2003)

Gene Ontology (GO) is the most widely accepted attempt to construct a unified and structured vocabulary for the description of genes and their products in any organism. Annotation by GO terms is performed in most of the current genome projects, which besides generality has the advantage of being very convenient for computer based classification methods. However, direct use of GO in small sequencing projects is not easy, especially for species not commonly represented in public databases. We present a software package (GOblet), which performs annotation based on GO terms for anonymous cDNA or protein sequences. It uses the species independent GO structure and vocabulary together with a series of protein databases collected from various sites, to perform a detailed GO annotation by sequence similarity searches. The sensitivity and the reference protein sets can be selected by the user. GOblet runs automatically and is available as a public service on our web server. The paper also addresses the reliability of automated GO annotations by using a reference set of more than 6000 human proteins. The GOblet server is accessible at http://goblet.molgen.mpg.de.
Cross-species hybridization of woodchuck hepatitis virus-induced hepatocellular carcinoma using human oligonucleotide microarrays (2006)

Many of our microarray results were validated using RT-PCR or literature search. Hence, we believe that woodchuck HCC and non-cancerous liver samples can be used on human microarrays to yield meaningful results.
Learning Linear Programs from Optimal Decisions (2020)

We propose a flexible gradient-based framework for learning linear programs from optimal decisions. Linear programs are often specified by hand, using prior knowledge of relevant costs and constraints. In some applications, linear programs must instead be learned from observations of optimal decisions. Learning from optimal decisions is a particularly challenging bi-level problem, and much of the related inverse optimization literature is dedicated to special cases. We tackle the general problem, learning all parameters jointly while allowing flexible parametrizations of costs, constraints, and loss functions. We also address challenges specific to learning linear programs, such as empty feasible regions and non-unique optimal decisions. Experiments show that our method successfully learns synthetic linear programs and minimum-cost multi-commodity flow instances for which previous methods are not directly applicable. We also provide a fast batch-mode PyTorch implementation of the homogeneous interior point algorithm, which supports gradients by implicit differentiation or backpropagation.