gebhart/patrepeval huggingface dataset:
Abstraction, Validation, and Generalization for Explainable Artificial Intelligence (2021)

Neural network architectures are achieving superhuman performance on an expanding range of tasks. To effectively and safely deploy these systems, their decision-making must to be understandable to a wide range of stakeholders. Methods to explain AI have been proposed to answer this challenge, but a lack of theory impedes the development of systematic abstractions which are necessary for cumulative knowledge gains. We propose Bayesian Teaching as a framework for unifying explainable AI (XAI) by integrating machine learning and human learning. Bayesian Teaching formalizes explanation as a communication act of an explainer to shift the beliefs of an explainee. This formalization decomposes any XAI method into four components: (1) the inference to be explained, (2) the explanatory medium, (3) the explainee model, and (4) the explainer model. The abstraction afforded by Bayesian Teaching to decompose any XAI method elucidates the invariances among them. The decomposition of XAI systems enables modular validation, as each of the first three components listed can be tested semi-independently. This decomposition also promotes generalization through recombination of components from different XAI systems, which facilitates the generation of novel variants. These new variants need not be evaluated one by one provided that each component has been validated, leading to an exponential decrease in development time. Finally, by making the goal of explanation explicit, Bayesian Teaching helps developers to assess how suitable an XAI system is for its intended real-world use case. Thus, Bayesian Teaching provides a theoretical framework that encourages systematic, scientific investigation of XAI.
Identification of Wee1 as Target in Combination with Avapritinib for the Treatment of Gastrointestinal Stromal Tumor (2020)

Abstract Management of gastrointestinal stromal tumor (GIST) has been revolutionized by the identification of activating mutations in KIT and PDGFRA, and the clinical application of receptor tyrosine kinase (RTK) inhibitors in the advanced disease setting. Stratification of GIST into molecularly defined subsets provides insight into clinical behavior and response to approved targeted therapies. Although these RTK inhibitors are effective in the majority of GIST, resistance to these agents remains a significant clinical problem. Development of effective treatment strategies for refractory GIST subtypes requires identification of novel targets to provide additional therapeutic options. Global kinome profiling has the potential to identify critical signaling networks and reveal protein kinases that are essential in GIST. Using Multiplexed Inhibitor Beads and Mass Spectrometry, we explored the majority of the kinome in GIST specimens from the three most common molecular subtypes to identify novel kinase targets. Kinome profiling revealed distinct signatures in GIST subtypes and identified kinases that are universally activated in all GIST, as well as kinases that are unique to each subtype. Kinome profiling in combination with loss-of-function assays identified a significant role for the G2-M tyrosine kinase, Wee1, in GIST cell survival. In vitro and in vivo studies revealed significant efficacy of MK-1775 (Wee1 inhibitor) in combination with avapritinib in KIT and PDGFRA -mutant GIST cell lines, and notable efficacy of MK-1775 as a single agent in the PDGFRA -mutant line. These studies provide strong preclinical justification for the use of MK-1775 in GIST.
Program learning for beginners: Survey and taxonomy of programming learning tools (2017)

Occasionally a game or visual programming language tool designed for programming education is used to teach programming. In general, these tools have various attributes, which inhibit a great learning effect if the tool and learning objectives are not aligned. However, which tool is most appropriate for a given objective remains unknown. In this research, we propose a taxonomy table to evaluate program learning tools and demonstrate its usefulness by researching and comparing 43 kinds of program learning tools in the taxonomy table. This research should contribute to the selection of suitable tools for program learning.
Advances in surgery of lung cancer (2012)

INTRODUCTION In this review, recent advances in the surgical treatment of lung cancer are presented and discussed. Many controversial issues remain regarding the role of surgery in the diagnosis, staging, and treatment of nonsmall cell lung cancer (NSCLC). The role of invasive staging and restaging techniques are currently debated and their present-day applications are discussed in this chapter. The different types of operative procedures that are available to the thoracic surgeon are also described. In the consideration of the surgical treatment for NSCLC, a distinction has to be made between early stage disease (stages IA/B and IIA/B), locoregionally advanced disease (stages IIIA/B), and metastatic disease (stage IV). The different indications for surgical treatment of NSCLC are discussed according to the recently introduced seventh TNM classifi cation taking into account that surgery for locoregionally advanced disease remains a highly controversial topic. Intraoperative staging of lung cancer is extremely important to determine the extent of resection according to the intraoperative tumor (T) and nodal (N) status. Systematic nodal dissection is generally advocated to determine the precise nodal involvement which not only determines prognosis but also the application of adjuvant therapy. In 2011, a new adenocarcinoma classifi cation was published introducing the concepts of adenocarcinoma in situ and minimally invasive adenocarcinoma. Its surgical implications including the role of limited resection are discussed. Except for very early stages of NSCLC, combined modality therapy including surgery is more frequently utilized. The impact and infl uence of surgery on prognosis, morbidity, and mortality are discussed in this chapter.
Complementary Graph Entropy, AND Product, and Disjoint Union of Graphs (2023)

In the zero-error Slepian-Wolf source coding problem, the optimal rate is given by the complementary graph entropy $\overline{H}$ of the characteristic graph. It has no single-letter formula, except for perfect graphs, for the pentagon graph with uniform distribution $G_5$, and for their disjoint union. We consider two particular instances, where the characteristic graphs respectively write as an AND product $\wedge$, and as a disjoint union $\sqcup$. We derive a structural result that equates $\overline{H}(\wedge \: \cdot)$ and $\overline{H}(\sqcup \: \cdot)$ up to a multiplicative constant, which has two consequences. First, we prove that the cases where $\overline{H}(\wedge \:\cdot)$ and $\overline{H}(\sqcup \: \cdot)$ can be linearized coincide. Second, we determine $\overline{H}$ in cases where it was unknown: products of perfect graphs; and $G_5 \wedge G$ when $G$ is a perfect graph, using Tuncel et al.'s result for $\overline{H}(G_5 \sqcup G)$. The graphs in these cases are not perfect in general.
Thermal Effects in a Hartmann-Sprenger Tube (1979)

In applied investigations of the thermal effects in the Hartmann-Sprenger (HS) tube, it is interesting to find out the heating rate and finally attainable temperature of the oscillating gas in the tube. In this paper, the experimental results of heating rates and finally attainable temperature of the tube wall are presented for some kinds of tube materials and exciting conditions, and the analysis of rising processes of gas and wall temperatures are done. In the analysis, assuming a simplified flow model, the basic equations for gas and wall temperatures are numerically solved by a finite difference method. On the basis of the comparison between the experimental results and the analytical results of wall temperature, the rising processes of gas temperature in the HS tube are discussed. The analytical results of the wall temperature are in good agreement with the experimental results. Thus the initial rising rate and the attainable limit of the gas temperature in the HS tube are theoretically estimated.
CLONIDINE DOES NOT DEPRESS THE VENTILATORY RESPONSE TO CO2 IN MAN (1990)

Sperry, R. J. M.D.; Bailey, P. L. M.D.; Pace, N. L. M.D.; Eldredge, S. M.D.; Johnson, K. M.D.; Stanley, T. H. M.D. Author Information
Activity of a heptad of transcription factors is associated with stem cell programs and clinical outcome in acute myeloid leukemia (2013)

Aberrant transcriptional programs in combination with abnormal proliferative signaling drive leukemic transformation. These programs operate in normal hematopoiesis where they are involved in hematopoietic stem cell (HSC) proliferation and maintenance. Ets Related Gene (ERG) is a component of normal and leukemic stem cell signatures and high ERG expression is a risk factor for poor prognosis in acute myeloid leukemia (AML). However, mechanisms that underlie ERG expression in AML and how its expression relates to leukemic stemness are unknown. We report that ERG expression in AML is associated with activity of the ERG promoters and +85 stem cell enhancer and a heptad of transcription factors that combinatorially regulate genes in HSCs. Gene expression signatures derived from ERG promoter-stem cell enhancer and heptad activity are associated with clinical outcome when ERG expression alone fails. We also show that the heptad signature is associated with AMLs that lack somatic mutations in NPM1 and confers an adverse prognosis when associated with FLT3 mutations. Taken together, these results suggest that transcriptional regulators cooperate to establish or maintain primitive stem cell-like signatures in leukemic cells and that the underlying pattern of somatic mutations contributes to the development of these signatures and modulate their influence on clinical outcome.
Approximated Structured Prediction for Learning Large Scale Graphical Models (2010)

This manuscripts contains the proofs for "A Primal-Dual Message-Passing Algorithm for Approximated Large Scale Structured Prediction".
Sarcomeric Auto-Oscillations in Single Myofibrils From the Heart of Patients With Dilated Cardiomyopathy (2018)

Sarcomere dynamics was found to be depressed under loaded conditions in DCM myofibrils because of impairment of thick-thin filament sliding. Thus, microscopic analysis of Ca-SPOC in human cardiac myofibrils is beneficial to systematically unveil the kinetic properties of single sarcomeres in various types of heart disease.
Primary Malignant Cardiac Tumors: A Rare Disease With an Adventurous Journey (2020)

It is very rare or almost impossible that an event can be negative from all points of view -Dalai Lama XIV C ardiac masses and tumors have always fascinated pathologists and cardiovascular physicians/surgeons alike. Before the mid-1950s, primary cardiac tumors were usually reported at autopsies. With the development of echocardiography, the imaging and diagnosis of tumors like myxoma became a possibility. With advancements in cardiopulmonary bypass, their resection and thus a cure became an exciting reality. Further developments in imaging, particularly echocardiography, 3-dimensional echocardiography, multidetector cardiac computed tomography (MDCT), and cardiac magnetic resonance imaging (CMR), have facilitated antemortem diagnosis of cardiac tumors.
Efficient Macrocyclization of Preorganized Palindromic Oligosquaramides (2006)

Wasserstoffbrücken bewirken, dass sich Oligo(quadratsäureamide) unterschiedlicher Länge in protischen wie aprotischen Lösungsmitteln zu Haarnadelstrukturen falten. Diese Verbindungen sind nützliche präorganisierte Makrocyclisierungsvorstufen. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2006/z602790_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Data from Dual Roles for CXCL4 Chemokines and CXCR3 in Angiogenesis and Invasion of Pancreatic Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;The CXCL4 paralog CXCL4L1 is a less studied chemokine that has been suggested to exert an antiangiogenic function. However, CXCL4L1 is also expressed in patient tumors, tumor cell lines, and murine xenografts, prompting a more detailed analysis of its role in cancer pathogenesis. We used genetic and antibody-based approaches to attenuate CXCL4L1 in models of pancreatic ductal adenocarcinoma (PDAC). Mechanisms of expression were assessed in cell coculture experiments, murine, and avian xenotransplants, including through an evaluation of CpG methylation and mutation of critical CpG residues. &lt;i&gt;CXCL4L1&lt;/i&gt; gene expression was increased greatly in primary and metastatic PDAC. We found that myofibroblasts triggered cues in the tumor microenvironment, which led to induction of CXCL4L1 in tumor cells. CXCL4L1 expression was also controlled by epigenetic modifications at critical CpG islands, which were mapped. CXCL4L1 inhibited angiogenesis but also affected tumor development more directly, depending on the tumor cell type. &lt;i&gt;In vivo&lt;/i&gt; administration of an mAb against CXCL4L1 demonstrated a blockade in the growth of tumors positive for CXCR3, a critical receptor for CXCL4 ligands. Our findings define a protumorigenic role in PDAC development for endogenous CXCL4L1, which is independent of its antiangiogenic function. &lt;i&gt;Cancer Res; 76(22); 6507–19. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
An overview of the James Webb Space Telescope (JWST) project (2005)

The JWST project at the GSFC is responsible for the development, launch, operations and science data processing for the James Webb Space Telescope. The JWST project is currently in phase B with its launch scheduled for August 2011. The project is a partnership between NASA, ESA and CSA. The U.S. JWST team is now fully in place with the selection of Northrop Grumman Space Technology (NGST) as the prime contractor for the telescope and the Space Telescope Science Institute (STScI) as the mission operations and science data processing lead. This paper will provide an overview of the current JWST architecture and mission status including technology developments and risks.
A BW Reporter System for Studying Receptor-Ligand Interactions (2019)

Interactions between receptors and ligands constitute a fundamental biological process. However, direct experiments with cells that express the native receptor and the ligand are challenging since the ligand of a specific receptor may be unknown and experimental procedures with the native ligand can be technically complicated. To address these obstacles, we describe a reporter system to detect the binding and activation of a specific receptor by a ligand of interest. In this reporter system, the extracellular domain of a specific receptor is conjugated to mouse CD3ζ and this chimeric protein is then expressed in mouse BW cells. These transfected BW cells can then be incubated with different targets (e.g., cells or antibodies). Activation of a transfected receptor leads to the secretion of mouse interleukin-2 (mIL-2) which can be detected by enzyme-linked immunosorbent assay (ELISA). This reporter system has the advantages of being sensitive and specific to a single receptor. In addition, the activation level of a specific receptor can easily be quantified and can be used even in cases where the ligand of the receptor is unknown. This system has been implemented successfully in many of our studies to characterize receptor-ligand interactions. We have recently employed this system to study the activation of human Fcγ receptors (FcγRs) by different monoclonal anti-CD20 antibodies in clinical use.
Supplemental Figure 2 from MHC Class I Loss Is a Frequent Mechanism of Immune Escape in Papillary Thyroid Cancer That Is Reversed by Interferon and Selumetinib Treatment <i>In Vitro</i> (2023)

&lt;p&gt;Supplemental Figure 2. &lt;b&gt;Peripheral blood leukocyte controls for tumor cell line co-cultures showing baseline and increased IL-2 production and T cell activation after CD3/CD28 stimulation.&lt;/b&gt; Healthy donor peripheral blood leukocytes (PBL) were cultured alone in the presence or absence of anti-CD3/CD28 stimulation beads, as experimental controls for tumor cell line-PBL co-cultures. Mean (n=4) IL-2 production and T cell activation (percent CD25&lt;sup&gt;+&lt;/sup&gt; of CD3&lt;sup&gt;+&lt;/sup&gt; T-cells) is shown.&lt;/p&gt;
Predicted Extragalactic T[CLC]e[/CLC]V Gamma-Ray Sources (1996)

We suggest that low-redshift XBLs (X-ray selected BL Lacertae objects) may be the only extragalactic gamma-ray sources observable at TeV energies. We use simple physical considerations involving synchrotron and Compton component spectra for blazars to suggest why the observed TeV sources are XBLs, whereas mostly RBLs and FSRQs are seen at GeV energies. These considerations indicate that the differences between XBLs and RBLs cannot be explained purely as relativistic jet orientation effects. We note that the only extragalactic TeV sources which have been observed are XBLs and that a nearby RBL with a very hard spectrum in the GeV range has not been seen at TeV energies. We also note that of the 14 BL Lacs observed by EGRET, 12 are RBLs, whereas only 2 are XBLs. We give a list of nearby XBLs which we consider to be good candidate TeV sources and predict estimated TeV fluxes for these objects.
Relevance feedback for best match term weighting algorithms in information retrieval (2001)

Personalisation in full text retrieval or full text filtering implies reweighting of the query terms based on some explicit or implicit feedback from the user. Relevance feedback inputs the user&amp;apos;s judgements on previously retrieved documents to construct a personalised query or user profile. This paper studies relevance feedback within two probabilistic models of information retrieval: the first based on statistical language models and the second based on the binary independence probabilistic model. The paper shows the resemblance of the approaches to relevance feedback of these models, introduces new approaches to relevance feedback for both models, and evaluates the new relevance feedback algorithms on the TREC collection. The paper shows that there are no significant differences between simple and sophisticated approaches to relevance feedback. 1
Meta-taxonomic analysis of prokaryotic and eukaryotic gut flora in stool samples from visceral leishmaniasis cases and endemic controls in Bihar State India (2019)

Visceral leishmaniasis (VL) caused by Leishmania donovani remains of public health concern in rural India. Those at risk of VL are also at risk of other neglected tropical diseases (NTDs) including soil transmitted helminths. Intestinal helminths are potent regulators of host immune responses sometimes mediated through cross-talk with gut microbiota. We evaluate a meta-taxonomic approach to determine the composition of prokaryotic and eukaryotic gut microflora using amplicon-based sequencing of 16S ribosomal RNA (16S rRNA) and 18S rRNA gene regions. The most abundant bacterial taxa identified in faecal samples from Bihar State India were Prevotella (37.1%), Faecalibacterium (11.3%), Escherichia-Shigella (9.1%), Alloprevotella (4.5%), Bacteroides (4.1%), Ruminococcaceae UCG-002 (1.6%), and Bifidobacterium (1.5%). Eukaryotic taxa identified (excluding plant genera) included Blastocystis (57.9%; Order: Stramenopiles), Dientamoeba (12.1%; Family: Tritrichomonadea), Pentatrichomonas (10.1%; Family: Trichomonodea), Entamoeba (3.5%; Family: Entamoebida), Ascaridida (0.8%; Family: Chromodorea; concordant with Ascaris by microscopy), Rhabditida (0.8%; Family: Chromodorea; concordant with Strongyloides), and Cyclophyllidea (0.2%; Order: Eucestoda; concordant with Hymenolepis). Overall alpha (Shannon's, Faith's and Pielou's indices) and beta (Bray-Curtis dissimilarity statistic; weighted UniFrac distances) diversity of taxa did not differ significantly by age, sex, geographic subdistrict, or VL case (N = 23) versus endemic control (EC; N = 23) status. However, taxon-specific associations occurred: (i) Ruminococcaceae UCG- 014 and Gastranaerophilales_uncultured bacterium were enriched in EC compared to VL cases; (ii) Pentatrichomonas was more abundant in VL cases than in EC, whereas the reverse occurred for Entamoeba. Across the cohort, high Escherichia-Shigella was associated with reduced bacterial diversity, while high Blastocystis was associated with high bacterial diversity and low Escherichia-Shigella. Individuals with high Blastocystis had low Bacteroidaceae and high Clostridiales vadin BB60 whereas the reverse held true for low Blastocystis. This scoping study provides useful baseline data upon which to develop a broader analysis of pathogenic enteric microflora and their influence on gut microbial health and NTDs generally.
A Review of Various Neural Network Algorithms for Operation of AC Microgrids (2022)

Over the last few years, Neural Network (NN) along with their unique characteristics have paved the way to develop control/operational schemes for microgrids. The microgrid contains many Distributed Energy Resources (DERs) connected with various components, which makes it a complex system with diversified equipment. Thus, the big challenge is to get the optimum performance of all these DERs within the microgrid. The main aim of developing such control/operational schemes is to make the microgrid more reliable, efficient and meet the power requirements. This paper reviews the employment of NN algorithms within the control/operational scheme and sheds light on prospective applications of NN to the various aspects of microgrid control/operation. Future trends and research directions are also presented.
Metrics to assess fracture quality for variable shaped beam lithography (2006)

CD control requirements for advanced node masks are in the low single digit nanometer range. CD control for Variable Shaped Beam (VSB) lithography that is used to manufacture these masks is dependent on the post-fracture figure layout. Shot linearity, shot size repeatability, and shot placement repeatability can affect CD control differently based on the figure layout. The potential CD error contribution from poorly optimized fracture strategies thus can be a significant contributor to the total CD error. In this paper we present a set of fracture quality metrics based on the impact on mask CD control and methods using EDA software to grade fracture strategies based on these fracture quality metrics. We also discuss applications of this metric for fracture tool design and the implementation of different fracture strategies into mask manufacturing including examinations of the predictability of fracturing results. Finally, we will discuss the usage of existing information about the design (such as design intent) in conjunction with the proposed quality metrics to judge different fracture strategies.