gebhart/patrepeval huggingface dataset:
A soft expert system for the creative exploration of first principles of crystal-laser design (2004)

A soft expert system is defined to be one that is qualitatively fuzzy. We present such a system known as KASER which stands for Knowledge Amplification by Structural Expert Randomization. KASER facilitates reasoning using domain specific expert and commonsense knowledge. It accomplishes this through object-classed predicates and an associated novel inference engine. It addresses the high cost associated with the knowledge acquisition bottleneck. It also enables the entry of a basis of rules and provides for the automatic extension of that basis through domain symmetries. We demonstrate an application for KASER in the design of an intelligent tutoring system that teaches the basic science of crystal-laser design. It enables the student to experiment with various design concepts and receive feedback on the functionality of the proposed design. This is possible without a need to preprogram all possible scenarios.
Renal Epithelioid Angiomyolipoma: Genomic Characterization and Malignant Potential (2019)

Introduction: Renal angiomyolipoma (AML) is one of the most common benign kidney tumors diagnosed. Epithelioid angiomyolipoma (eAML) is a rare variant of these kind of masses that have been classified by the World Health Organization as a potentially malignant mesenchymal neoplasm that metastasizes in one-third of cases. However, conflicting reports have brought in to question the true malignant potential of eAML. Due to eAMLs overall rarity, few studies have characterized this entity. In this study, we further define eAML by describing its genomic alterations and malignant potential by comparing it to a cohort of AML patients at a large-volume cancer center. Methods: After IRB approval, a prospectively maintained kidney cancer database was queried for all patients with eAML and AML who underwent nephrectomy between 1994 and 2008 at the Memorial Sloan Kettering Cancer Center. Patients were separated into two histologic groups, those with eAML and those with AML. Clinicopathologic features and genomic alterations were analyzed and then compared between the two cohorts. Descriptive statistics were performed using Mann-Whitney U test, and Chi-squared test, where appropriate, and reported as either median with interquartile range (IQR) or number with percentage. Genomic data was available in 6 eAML and 10 AML patients with mutational burden described as a proportion. Overall survival (OS) and recurrence-free survival (RFS) data were analyzed using Kaplan-Meier method with significance determined by log-rank tests. All statistical analyses were performed using R 3.5.2 with significance set at <0.05. Results: Out of 103 patients, 44 had eAML and 59 had AML. Females in their fifth and sixth decade were more commonly diagnosed than males, Table 1. Patients with eAML had larger tumors (p<0.001) and underwent radical nephrectomy more often (p=0.014). Twelve (27.3%) eAML patients metastasized, while no metastases were observed in AML patients. Median RFS for eAML patients was 131 months, and median RFS was not reached in AML patients (p<0.0001), Figure 1. The most frequently mutated gene across both groups expectedly was TSC2, a mutation commonly found in AMLs. The mutational burden in eAMLs was heterogeneous compared to AMLs, with more mutations observed within TP53(43%), RB1 (14%), APC (14%), TERT (14%), ATRX (14%), TSC1 (14%), PIK3CA (14%), GNA11 (14%), and FGFR3 (14%), Figure 2. Conclusion: Patients with eAML were observed to have larger tumors and metastasized at a higher rate than patients with AML. A greater frequency of eAML patients underwent radical nephrectomy. The mutational burden across eAML was notable for a more heterogeneity, with largest mutations in TSC2 and TP53 genes. Further investigation into the impact of mutational burden on metastatic potential is warranted.
Cancer-Associated Neutropenic Fever: Clinical Outcome and Economic Costs of Emergency Department Care (2007)

Purpose. Febrile neutropenia (FN) is a common, costly, and potentially fatal complication in oncology. While FN in the inpatient setting has been extensively studied, only one study has evaluated emergency department (ED) care for FN cancer patients. That study found that 96% of patients survived the complication. We evaluated clinical and economic outcomes for cancer patients with chemotherapy-associated FN treated in an ED. Methods. ED records for consecutive oncology patients with FN were reviewed for information on death, intensive care unit (ICU) use, blood cultures, and costs. Results. Forty-eight patients (n = 57 visits) were evaluated. Six patients died from FN (12%) and four received ICU care within 2 weeks and survived (8%). Blood cultures were positive for 37% of the ED visits. The median ED time was 3.3 hours. In 91% of visits, i.v. antibiotics were administered in the ED, ordered at a median of 1.7 hours from triage (interquartile range [IQR], 1.2-2.8 hours). All patients with death or ICU in 2 weeks and all but one patient with positive blood cultures received antibiotics. The median per patient ED costs were $1,455 (IQR, $1,300-$1,579)-42.4% for hospital/nursing, 23.5% for radiology, 20.8% for physician services, 10.9% for diagnostic tests, and 2.4% for antibiotics. Conclusions. Cancer patients with FN in this sample presenting to the ED frequently had no identified source of infection. One third of the patients had positive ED blood cultures and one fifth died or required ICU care within 2 weeks. Costs of ED care were similar to the cost of a single day of inpatient care. Disclosure of potential conflicts of interest is found at the end of this article.
Synthesis of methyl 2-methoxy-5-hydroxycinnamate, a metabolite of Murraya paniculata (2002)

Methyl 2-methoxy-5-hydroxycinnamate 1 has been obtained from 2-hydroxy-5-benzyloxybenzaldehyde 2 in four steps with an overall yield of 26%.
Processing Ultrafast Optical Signals in Broadband Telecom Systems by means of Cascaded Quadratic Nonlinearities (2006)

Quadratic optical nonlinearities offer several attractive features for the implementation of ultra-fast, low-noise and transparent telecom devices. Technological progress has dramatically increased their efficiency, driving a steady move towards practical applications. In this talk we shall discuss the use of cascaded quadratic interactions in LiNbO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> integrated devices for pulse diagnostics, format conversion and signal regeneration in ultra-fast multi-wavelength telecom systems
Evolution of Messaging Standards (1994)

There are two dominant sets of standards for messaging systems and services: the International Telecommunications Union (ITU) X.400 Recommendations and the Internet messaging standards. This paper describes and compares their architectures, message formats, naming and addressing schemes, protocols, security features, multimedia support, and management services.
Application of the Mayo Periprosthetic Joint Infection Risk Score for Total Ankle Arthroplasty (2023)

Level II, developing diagnositic criteria with consecutive cases.
Agénésies d’incisives : changer de paradigme. Étude d’une population orthodontique. Cas cliniques (2014)

Notre étude d’une population orthodontique de 1 095 patients indique que 9 % environ des sujets sont porteurs d’au moins 1 agénésie (dont 3 % d’une incisive (latérale maxillaire ou centrale/latérale mandibulaire). Considérant les traitements possibles, nous avons évalué les différentes solutions, de la moins invasive à la plus invasive : fermeture simple de l’espace, fermeture de l’espace avec adjonction de facettes céramiques, ouverture d’espace avec bridge cantilever de remplacement, ouverture d’espace avec implant de remplacement. Les évolutions récentes de la dentisterie biomimétique nous invitent à changer de paradigme.
Data from High &lt;i&gt;FGFR1–4&lt;/i&gt; mRNA Expression Levels Correlate with Response to Selective FGFR Inhibitors in Breast Cancer (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;&lt;i&gt;FGFR1&lt;/i&gt; amplification (&lt;i&gt;FGFR1&lt;/i&gt;amp) is recurrent in metastatic breast cancer (MBC) and is associated with resistance to endocrine therapy and CDK4/6 inhibitors (CDK4/6is). Multi-tyrosine kinase inhibitors (MTKIs) and selective pan-FGFR inhibitors (FGFRis) are being developed for &lt;i&gt;FGFR1&lt;/i&gt;amp breast cancer. High-level &lt;i&gt;FGFR&lt;/i&gt; amplification and protein expression by IHC have identified breast cancer responders to FGFRis or MTKIs, respectively.&lt;/p&gt;Experimental Design:&lt;p&gt;Here, we used preclinical models and patient samples to identify predictive biomarkers to these drugs. We evaluated the antitumor activity of an FGFRi and an MTKI in a collection of 17 breast cancer patient–derived xenografts (PDXs) harboring amplification in &lt;i&gt;FGFR1/2/3/4&lt;/i&gt; and in 10 patients receiving either an FGFRi/MTKI. mRNA levels were measured on FFPE tumor samples using two commercial strategies. Proliferation and angiogenesis were evaluated by detecting Ki-67 and CD31 in viable areas by immunofluorescence.&lt;/p&gt;Results:&lt;p&gt;High &lt;i&gt;FGFR1–4&lt;/i&gt; mRNA levels but not copy-number alteration (CNA) is associated with FGFRi response. Treatment with MTKIs showed higher response rates than with FGFRis (86% vs. 53%), regardless of the &lt;i&gt;FGFR1–4&lt;/i&gt; mRNA levels. FGFR-addicted PDXs exhibited an antiproliferative response to either FGFRis or MTKIs, and PDXs exclusively sensitive to MTKI exhibited an additional antiangiogenic response. Consistently, the clinical benefit of MTKIs was not associated with high &lt;i&gt;FGFR1–4&lt;/i&gt; mRNA levels and was observed in patients previously treated with antiangiogenic drugs.&lt;/p&gt;Conclusions:&lt;p&gt;Tailored therapy with FGFRis in molecularly selected MBC based on high &lt;i&gt;FGFR1–4&lt;/i&gt; mRNA levels warrants prospective validation in patients with CDK4/6i-resistant luminal breast cancer and in patients with TNBC without targeted therapeutic options.&lt;/p&gt;&lt;/div&gt;
Mechanism and function of root circumnutation (2021)

Early root growth is critical for plant establishment and survival. We have identified a molecular pathway required for helical root tip movement known as circumnutation. Here, we report a multiscale investigation of the regulation and function of this phenomenon. We identify key cell signaling events comprising interaction of the ethylene, cytokinin, and auxin hormone signaling pathways. We identify the gene <i>Oryza sativa</i> histidine kinase-1 (<i>HK1</i>) as well as the auxin influx carrier gene <i>OsAUX1</i> as essential regulators of this process in rice. Robophysical modeling and growth challenge experiments indicate circumnutation is critical for seedling establishment in rocky soil, consistent with the long-standing hypothesis that root circumnutation facilitates growth past obstacles. Thus, the integration of robotics, physics, and biology has elucidated the functional importance of root circumnutation and uncovered the molecular mechanisms underlying its regulation.
ChemInform Abstract: BENZO(C)THIOPHENE DERIVATIVES. IV. SYNTHESIS AND DISPROPORTIONATION OF 1,1′,3,3′‐TETRAHYDRO‐1,1′‐BIS(METHOXYCARBONYL)‐1,1′‐BIBENZO(C)THIOPHENE (1984)

Abstract Durch Zersetzung des Benzothiophens (I) unter den gegebenen Bedingungen läßt sich die Titelverbindung (II) (Auftrennung in die Diastereomeren) in guter Ausb. darstellen.
URA/SISA Analysis for GPS-Galileo ARAIM Integrity Support Message (2015)

This paper presents a URA/SISA analysis to support ARAIM based on a time-dependent statistical characterization of orbit and clock errors observations. For each individual GPS and Galileo satellites, by comparing precise orbits to broadcast ephemeris data, this work computes the Signal in Space Range Error (SISRE) which needs to be overbounded by the URA/SISA value included in the ISM. Over seven years of service history data for GPS and four months for Galielo are computed in this analysis, showing that range error is manly driven by satellite's clock performance. Satellites that historically have presented well behaved $\sigma_{SISRE}$ are equipped with stable clocks which display small error dispersion. A particular example is provided through GPS SVN65/PRN24 whose Cesium clock worsens satellite's performance as compared to the rest of the GPS block IIF equipped with Rubidium clocks. Time-dependent results show that orbit and clock error distributions are not zero mean on a monthly basis, although they do not exhibit a significant bias in a long-term scale. This fact might open the possibility of a short-time adaptable $b_{nom}$ and $\sigma_{URA}$ overbounding parameters contained in the ISM.
Early Warning Indicators for HIV Drug Resistance in Cameroon during the Year 2010 (2012)

The poor performance of the national ART programme, due to patient non-adherence and drug stock outs, requires corrective measures to limit risks of HIVDR emergence in Cameroon.
Abstract 1738: DNA-launched nanoparticle vaccines induce cytolytic T cell responses for <i>in vivo</i> tumor control (2022)

Abstract Nanotechnology-based approaches have achieved promising results for the development of novel immunotherapeutic cancer vaccines through the decoration of antigens on nanoparticle scaffolds for multivalent display. However, their translation have been limited due to challenges with purification, scalability, and robust induction of cytolytic T cell responses critical to anti-tumor activity. We designed a nanovaccine construct by fusing the HPV E7 immunodominant epitope onto lumazine synthase scaffold. We demonstrate that through electroporation-facilitated DNA delivery encoding the antigen-scaffold construct, this nanovaccine is expressed and self-assembles in vivo into 60-mer nanoparticles. Compared to CpG-adjuvanted peptide and monomeric DNA vaccination, this DNA-launched nanovaccine induced greater CD8+ cellular responses against the E7 epitope and target tumor cells. In both flank and lung models of TC-1 HPV-associated cancers, the nanovaccine achieved significant tumor regression and prolonged survival compared to CpG-adjuvanted peptide. Anti-tumor immunity was retained upon rechallenge &amp;gt;150 days after initial challenge, supporting the induction of long-term immune memory. In addition, we demonstrate that this DNA-launched nanovaccine platform can be used to form hybrid nanoparticles displaying multiple antigens simultaneously. These hybrid nanoparticles exhibit synergistic efficacy, with improved tumor control over administration of separate single-antigen nanovaccines. These promising results, along with facile characterization, scalability, and stability, support that DNA-launched nanovaccines can induce potent anti-tumor cellular immunity and are ideally positioned for further translational development for clinical evaluation. Citation Format: Kevin Liaw, Ziyang Xu, Neethu Chokkalingam, Daniel Kulp, David Weiner. DNA-launched nanoparticle vaccines induce cytolytic T cell responses for in vivo tumor control [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1738.
Nitrogen and sulphur co-doped crumbled graphene for the oxygen reduction reaction with improved activity and stability in acidic medium (2016)

A crumbled graphene structure with heteroatom doped active sites derived through the pyrolysis of polyethylenedioxythiophene served as an efficient platinum-free electrocatalyst for oxygen reduction under acidic conditions.
Simplifying living donor liver transplantation. (2010)

The most practical way to achieve high graft and recipient survival rates with an acceptably low donor risk is through design of a protocol that simplifies the surgery and postoperative management.
Cover Picture: Increased Enantioselectivity by Engineering Bottleneck Mutants in an Esterase from <i>Pseudomonas fluorescens</i> (ChemBioChem 18/2009) (2009)

The cover picture shows (R)-1-phenyl-2-propyl acetate docked in the active site of a quadruple mutant (mutant Q) of the Pseudomonas fluorescens esterase I. The four point mutations involved the replacement of four Phe with Leu residues in the area lining the entrance to the active site, which was termed the bottleneck (in blue). Substitutions in this area cause changes in enantioselectivity, both due to direct interaction with the substrate and to restriction of substrate access to the active site. The detail shows the catalytic residues in green, and the bottleneck residues of the wild-type (in dark red) and of mutant Q (in dark blue) interacting in a clearly different way with (R)-1-phenyl-2-propyl acetate (light red and light blue for the interaction with the wild-type enzyme and mutant Q, respectively). More information can be found on p. 2920 ff, U. Bornscheuer et al. Cover art by J. Belio.
A Systematic Review of Reproducibility Research in Natural Language Processing (2021)

Against the background of what has been termed a reproducibility crisis in science, the NLP field is becoming increasingly interested in, and conscientious about, the reproducibility of its results. The past few years have seen an impressive range of new initiatives, events and active research in the area. However, the field is far from reaching a consensus about how reproducibility should be defined, measured and addressed, with diversity of views currently increasing rather than converging. With this focused contribution, we aim to provide a wideangle, and as near as possible complete, snapshot of current work on reproducibility in NLP, delineating differences and similarities, and providing pointers to common denominators.
Motion of Long Levitating Drops in Tubes in an Anti-Bretherton Configuration (2020)

In his seminal paper, Bretherton studied the motion of long bubbles in capillary tubes. Here, we unveil the negative configuration wherein a long liquid drop is stably transported in a capillary tube and surrounded by a flow-induced air cushion. These drops are formed when a liquid plug is pushed above a critical velocity sufficient to induce an inversion of the front meniscus with a radius of curvature smaller than the tube radius. The drop shape and lubricating air film thickness is reminiscent of Bretherton's calculation and can be inferred from an adapted analytical theory.
Supplemental Methods from Systematic Analysis of AU-Rich Element Expression in Cancer Reveals Common Functional Clusters Regulated by Key RNA-Binding Proteins (2023)

&lt;p&gt;Supplemental methods on statistical correlation modeling, RNA-IP, and Taqman assays.&lt;/p&gt;
[Proceedings: Experimentally induced effects on the plasma renin activity]. (1975)

In dogs, plasma renin activity (PRA) was increased by anesthesia, by hypercapnia and by extreme hypoxia (paO2 47.6 mm Hg). Relatively moderate hypoxia (paO2 47.6 mm Hg) and artificial respiration had no appreciable influence on PRA. It appears that the sympathomimetic stimulus of CO2 has an important bearing on PRA.
ChemInform Abstract: Enantioselective Fluoroamination: 1,4‐Addition to Conjugated Dienes Using Anionic Phase‐Transfer Catalysis. (2013)

Abstract This is the first report of a metal‐free catalytic asymmetric 1,4‐fluoroamination of conjugated dienes.
Development of antitumor biguanides targeting energy metabolism and stress responses in the tumor microenvironment (2021)

To develop antitumor drugs capable of targeting energy metabolism in the tumor microenvironment, we produced a series of potent new biguanide derivatives via structural modification of the arylbiguanide scaffold. We then conducted biological screening using hypoxia inducible factor (HIF)-1- and unfolded protein response (UPR)-dependent reporter assays and selective cytotoxicity assay under low glucose conditions. Homologation studies of aryl-(CH<sub>2</sub>)<sub>n</sub>-biguanides (n = 0-6) yielded highly potent derivatives with an appropriate alkylene linker length (n = 5, 6). The o-chlorophenyl derivative 7l (n = 5) indicated the most potent inhibitory effects on HIF-1- and UPR-mediated transcriptional activation (IC<sub>50</sub>; 1.0 ± 0.1 μM, 7.5 ± 0.1 μM, respectively) and exhibited selective cytotoxicity toward HT29 cells under low glucose condition (IC<sub>50</sub>; 1.9 ± 0.1 μM). Additionally, the protein expression of HIF-1α induced by hypoxia and of GRP78 and GRP94 induced by glucose starvation was markedly suppressed by the biguanides, thereby inhibiting angiogenesis. Metabolic flux and fluorescence-activated cell sorting analyses of tumor cells revealed that the biguanides strongly inhibited oxidative phosphorylation and activated compensative glycolysis in the presence of glucose, whereas both were strongly suppressed in the absence of glucose, resulting in cellular energy depletion and apoptosis. These findings suggest that the pleiotropic effects of these biguanides may contribute to more selective and effective killing of cancer cells due to the suppression of various stress adaptation systems in the tumor microenvironment.
Data from Modified RANO, Immunotherapy RANO, and Standard RANO Response to Convection-Enhanced Delivery of IL4R-Targeted Immunotoxin MDNA55 in Recurrent Glioblastoma (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;The current study compared the standard response assessment in neuro-oncology (RANO), immunotherapy RANO (iRANO), and modified RANO (mRANO) criteria as well as quantified the association between progression-free (PFS) and overall survival (OS) in an immunotherapy trial in recurrent glioblastoma (rGBM).&lt;/p&gt;Patients and Methods:&lt;p&gt;A total of 47 patients with rGBM were enrolled in a prospective phase II convection-enhanced delivery of an IL4R-targeted immunotoxin (MDNA55-05, NCT02858895). Bidirectional tumor measurements were created by local sites and centrally by an independent radiologic faculty, then standard RANO, iRANO, and mRANO criteria were applied.&lt;/p&gt;Results:&lt;p&gt;A total of 41 of 47 patients (mean age 56 ± 11.7) were evaluable for response. PFS was significantly shorter using standard RANO compared with iRANO (log-rank, &lt;i&gt;P&lt;/i&gt; &lt; 0.0001; &lt;i&gt;HR&lt;/i&gt; = 0.3) and mRANO (&lt;i&gt;P&lt;/i&gt; &lt; 0.0001; &lt;i&gt;HR&lt;/i&gt; = 0.3). In patients who died and had confirmed progression on standard RANO, no correlation was observed between PFS and OS (local, &lt;i&gt;P&lt;/i&gt; = 0.47; central, &lt;i&gt;P&lt;/i&gt; = 0.34). Using iRANO, a weak association was observed between confirmed PFS and OS via local site measurements (&lt;i&gt;P&lt;/i&gt; = 0.017), but not central measurements (&lt;i&gt;P&lt;/i&gt; = 0.18). A total of 24 of 41 patients (59%) were censored using iRANO and because they lacked confirmation of progression 3 months after initial progression. A strong correlation was observed between mRANO PFS and OS for both local (&lt;i&gt;R&lt;sup&gt;2&lt;/sup&gt;&lt;/i&gt; = 0.66, &lt;i&gt;P&lt;/i&gt; &lt; 0.0001) and centrally determined reads (&lt;i&gt;R&lt;sup&gt;2&lt;/sup&gt;&lt;/i&gt; = 0.57, &lt;i&gt;P&lt;/i&gt; = 0.0007).&lt;/p&gt;Conclusions:&lt;p&gt;No correlation between radiographic PFS and OS was observed for standard RANO or iRANO, but a correlation was observed between PFS and OS using the mRANO criteria. Also, the iRANO criteria was difficult to implement due to need to confirm progression 3 months after initial progression, censoring more than half the patients.&lt;/p&gt;&lt;/div&gt;