gebhart/patrepeval huggingface dataset:
A Phase I Clinical Trial of Single-Dose Intrapleural IFN-β Gene Transfer for Malignant Pleural Mesothelioma and Metastatic Pleural Effusions: High Rate of Antitumor Immune Responses (2007)

Intrapleural instillation of Ad.IFN-beta is a potentially useful approach for the generation of antitumor immune responses in MPM and MPE patients and should be investigated further for overall clinical efficacy.
Animal Models and Their Role in Imaging-Assisted Co-Clinical Trials (2023)

The availability of high-fidelity animal models for oncology research has grown enormously in recent years, enabling preclinical studies relevant to prevention, diagnosis, and treatment of cancer to be undertaken. This has led to increased opportunities to conduct co-clinical trials, which are studies on patients that are carried out parallel to or sequentially with animal models of cancer that mirror the biology of the patients' tumors. Patient-derived xenografts (PDX) and genetically engineered mouse models (GEMM) are considered to be the models that best represent human disease and have high translational value. Notably, one element of co-clinical trials that still needs significant optimization is quantitative imaging. The National Cancer Institute has organized a Co-Clinical Imaging Resource Program (CIRP) network to establish best practices for co-clinical imaging and to optimize translational quantitative imaging methodologies. This overview describes the ten co-clinical trials of investigators from eleven institutions who are currently supported by the CIRP initiative and are members of the Animal Models and Co-clinical Trials (AMCT) Working Group. Each team describes their corresponding clinical trial, type of cancer targeted, rationale for choice of animal models, therapy, and imaging modalities. The strengths and weaknesses of the co-clinical trial design and the challenges encountered are considered. The rich research resources generated by the members of the AMCT Working Group will benefit the broad research community and improve the quality and translational impact of imaging in co-clinical trials.
Diagnosis of Acute Kidney Injury Using Functional and Injury Biomarkers: Workgroup Statements from the Tenth Acute Dialysis Quality Initiative Consensus Conference (2013)

Acute kidney injury (AKI) commonly occurs in hospitalized patients and is independently and strongly associates with morbidity and mortality. The clinical benefits of a timely and definitive diagnosis of AKI have not been fully realized due to limitations imposed by the use of serum creatinine and urine output to fulfill diagnostic criteria. These restrictions often lead to diagnostic delays, potential misclassification of actual injury status, and provide little information regarding underlying cause. Novel biomarkers of damage have shown ability to reflect ongoing kidney injury and help further refine existing Risk, Injury, Failure, Loss, End-stage kidney disease (RIFLE) and Acute Kidney Injury Network (AKIN) diagnostic criteria. A comprehensive review of the published literature to date was performed using previously published methodology of the Acute Dialysis Quality Initiative (ADQI) working group to establish consensus statements regarding (i) the overall implementation of injury biomarkers in the concept of AKI diagnosis, (ii) their clinical use, and (iii) future research. On the basis of published data on the ability of novel damage biomarkers to provide diagnostic and prognostic information on AKI, we recommend that novel damage biomarkers may, in the appropriate clinical setting and context (situation consistent with AKI), be used to diagnose AKI even in the absence of changes in serum creatinine or the presence of oliguria as described in the existing RIFLE/AKIN criteria for diagnosis of AKI. Adding injury biomarkers as a criterion for AKI will complement the ability of RIFLE/AKIN to define AKI. Promising diagnostic injury markers include neutrophil gelatinase-associated lipocalin (NGAL), kidney injury molecule 1 (KIM-1), interleukin 18 (IL-18) and liver-type fatty acid binding protein (L-FABP). However, there are currently insufficient data on damage biomarkers to support their use for AKI staging. Rigorous validation studies measuring the association between the novel damage biomarker(s) and clinically relevant outcomes are needed.
Reducing electronic multiplexing costs in unidirectional SONET/WDM ring networks via efficient traffic grooming (2002)

We develop traffic grooming algorithms for unidirectional SONET/WDM ring networks. The objective is to assign low rate circuits to wavelengths in a way that minimizes the total cost of electronic equipment (e.g., the number of SONET add/drop multiplexers (ADMs)). When the traffic from all nodes is destined to a single node, and all traffic rates are the same, we obtain a solution that minimizes the number of ADMs. In the more general case of all-to-all uniform traffic we obtain a lower bound on the number of ADMs required, and provide a heuristic algorithm that performs close to that bound. Finally, we consider the use of a hub node, where traffic can be switched between different wavelengths, and obtain an optimal algorithm which minimizes the number of ADMs by efficiently multiplexing and switching the traffic at the hub. Moreover, we show that any solution not using a hub can be transformed into a solution with a hub using fewer or the same number of ADMs.
Improved Performance of Graphite/ LiNi0.5Mn1.5O4 Cells Cycled to High Voltage (4.8 V) with Electrolyte Additives (2014)

There is significant interest in the development of higher energy lithium ion batteries (LIB) for electric vehicles. One method of improving the energy density of lithium ion batteries is to increase the operating voltage of the cells by increasing the working potentials of positive electrode employing for example lithium nickel manganese spinel LiNi 0.5 Mn 1.5 O 4 as the active material. However, cycling of lithium-ion cells to high voltages (~5.0 V vs lithium reference electrode, LRE) proceeds with relatively low (99% and less) coulombic efficiency. Among the primary contributors to the poor cycling efficiency are the electrochemical oxidation reactions of the electrolytes at the high positive potentials of positive electrode. The failure mechanism of graphite /LiNi 0.5 Mn 1.5 O 4 cells cycled at 25 o C and 55 o C (1.2 M LiPF 6 in 3:7 EC/EMC) have been analyzed by electrochemical methods and ex-situ surface analysis of the electrodes. Graphite /LiNi 0.5 Mn 1.5 O 4 cells cycle well at 25 o C , but have rapid capacity fade upon cycling at 55 o C. Independent electrochemical analysis of anodes and cathodes extracted from cells cycled at 55 o C suggest that both electrodes have significant capacity loss, although the cathode capacity can be recovered with longer charging times. Ex-situ surface analysis of the cathode with SEM reveals that the bulk cathode particles and the cathode laminate are retained while XPS confirms the presence of a cathode electrolyte interface composed of the decomposition products of the electrolyte. Ex-situ analysis of the anode reveals a thick anode solid electrolyte interphase (SEI), anode delamination, and the presence of Mn. The results suggest that both the anode and the cathode contribute to performance loss in graphite/LiNi 0.5 Mn 1.5 O 4 cells. We are using this mechanistic information about capacity fade in graphite/LiNi 0.5 Mn 1.5 O 4 cells to develop novel additives to improve the performance of LiNi 0.5 Mn 1.5 O 4 cycled to high voltage (4.8 V vs Li). The additives include Lewis basic species which inhibit the thermal decomposition of LiPF 6 and cathode film forming additives. Preliminary investigations suggest that incorporation of the novel additives into graphite/ LiNi 0.5 Mn 1.5 O 4 cells significantly improves the capacity retention upon cycling at high voltage (4.8 V vs Li) and moderately elevated temperature (55 o C). Ex-situ surface analysis of the electrodes after cycling suggest that the additives modify the surface of the LiNi 0.5 Mn 1.5 O 4 cathode via the formation of a stable cathode electrolyte interface (CEI). The presence of the CEI inhibits the oxidation of the electrolyte and dissolution of Mn and Ni from the surface of the cathode particles. The additives, also stabilize the SEI on the anode by preventing Mn deposition on the anode surface and damage of the anode SEI. The details of our experimental results and our mechanistic interpretation will be presented.
Immunotherapy with Listeria reduces metastatic breast cancer in young and old mice through different mechanisms (2017)

Cancer immunotherapy is one of the most promising and benign therapies against metastatic cancer. However, most cancer patients are old and elderly react less efficient to cancer vaccines than young adults, due to T cell unresponsiveness. Here we present data of cancer vaccination in young and old mice with metastatic breast cancer (4T1 model). We tested adaptive and innate immune responses to foreign antigens (Listeria-derived) and self-antigens (tumor-associated antigens (TAA)) and their contribution to elimination of metastases at young and old age. Three different protocols were tested with Listeria: a semi- and exclusive-therapeutic protocol both one-week apart, and an exclusive therapeutic protocol frequently administered. Adaptive and innate immune responses were measured by ELISPOT in correlation with efficacy in the 4T1 model. We found that Listeria induced immunogenic tumor cell death, resulting in CD8 T cell responses to multiple TAA expressed by the 4T1 tumors. Only exclusive therapeutic frequent immunizations were able to overcome immune suppression and to activate TAA- and Listeria-specific CD8 T cells, in correlation with a strong reduction in metastases at both ages. However, MHC class Ia antibodies showed inhibition of CD8 T cell responses to TAA at young but not at old age, and CD8 T cell depletions <i>in vivo</i> demonstrated that the T cells contributed to reduction in metastases at young age only. These results indicate that CD8 T cells activated by Listeria has an antitumor effect at young but not at old age, and that metastases at old age have been eliminated through different mechanism(s).
IS INHALED TACROLIMUS A SAFE TREATMENT OPTION TO PREVENT ACUTE AND CHRONIC REJECTION IN AN AIRWAY TRANSPLANT MODEL? (2008)

Deuse, T1; Weill, D1; Fink, J2; Blankenberg, F1; Peter, C1; Robbins, R1; Schrepfer, S1 Author Information
Double Trouble: How to not Explain a Text Classifier’s Decisions Using Counterfactuals Synthesized by Masked Language Models? (2022)

Thang Pham, Trung Bui, Long Mai, Anh Nguyen. Proceedings of the 2nd Conference of the Asia-Pacific Chapter of the Association for Computational Linguistics and the 12th International Joint Conference on Natural Language Processing (Volume 1: Long Papers). 2022.
Abstract B205: Therapeutically targeting redundant, growth factor-induced prosurvival signaling with MM-141, a novel bispecific antibody targeting IGF-1R and ErbB3. (2011)

Abstract Monoclonal antibodies have significantly advanced our ability to treat cancer, but most patients do not have durable responses to therapy. We find that the majority of tumor cell lines are responsive to activation by two or more growth factors. In particular cell lines grown in culture and in mice appear to frequently rely on Insulin-like growth factor 1 (IGF-1) and Heregulin (HRG) signaling to redundantly support their proliferation. Using a Network Biology approach, we have designed, constructed and optimized a novel bispecific antibody, MM-141, for simultaneous targeting and inhibition of ErbB3 and IGF-1R. MM-141 blocks IGF-1, IGF-2, and heregulin-induced AKT signaling, inhibits growth of multiple cancer cell lines, and is active in xenograft models of human pancreatic cancer (BxPC-3) and human prostate cancer (DU145). MM-141 does not bind the insulin receptor, thus strongly reducing the risk of metabolic side effects. MM-141 has favorable CMC and pharmacokinetic profiles and is being advanced into preclinical development. Taken together, these results suggest that MM-141 has the potential to be an effective therapeutic for treatment of patients with solid tumors. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2011 Nov 12-16; San Francisco, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2011;10(11 Suppl):Abstract nr B205.
Principles of Chemical Reactor Analysis and Design: New Tools for Industrial Chemical Reactor Operations (2009)

Preface. Notation. Chapter 1: Overview of Reaction Engineering. 1.1 Classification of 1.2 Classification of Reactors. 1.3 Phenomena and Concepts. 1.4 Common Practices. 1.5 Industrial Reactors. 1.6 Summary. Bibliography. Chapter 2: Stoichiometry . 2.1 The Four Contexts of Chemical Reactions. 2.2 Formula and Stoichiometic Relations. 2.3 Reaction Extent. 2.4 Independent and Dependent 2.5 Characterization of Reactor Feed. 2.6 Characterization of Reactor Performance. 2.7 Dimensionless Extents. 2.8 Independent Species Specifications. 2.9 Summary. Bibliography. Problems. Chapter 3: Kinetics. 3.1 Species Formation Rates. 3.2 Rates of 3.3 Rate Expressions of Reaction Rates. 3.4 Effects of Transport Limitations. 3.5 Characteristic Reaction Time. 3.6 Summary. Bibliography. Problems. Chapter 4: Species Balances and Design Equations. 4.1 Macroscopic Species Balances - General Species-based Design Equations. 4.2 Species-based Design Equations of Ideal Reactors. 4.3 Reaction-based Design Equations. 4.4 Dimensionless Design Equations. 4.5 Summary. Bibliography. Problems. Chapter 5: Energy Balances. 5.1 Review of Thermodynamic Relations. 5.2 Energy Balances. 5.3 Summary. Bibliography. Problems. Chapter 6: Ideal Batch Reactor. 6.1 Design Equations and Auxiliary Relations. 6.2 Isothermal Operations with Single 6.3 Isothermal Operations with Multiple 6.4 Non-Isothermal Operations. 6.5 Summary. Problems. Chapter 7: Plug Flow Reactor. 7.1 Design Equations and Auxiliary Relations. 7.2 Isothermal Operations with Single 7.3 Isothermal Operations with Multiple 7.4 Non-Isothermal Operations. 7.5 Effects of Pressure Drop. 7.6 Summary. Problems. Chapter 8: Continuous Stirred Tank Reactor (CSTR). 8.1 Design Equations and Auxiliary Relations. 8.2 Isothermal Operations with Single 8.3 Isothermal Operations with Multiple 8.4 Non-Isothermal Operations. 8.5 Summary. Problems. Chapter 9: Other Reactor Configurations. 9.1 Semi-Batch Reactors. 9.2 Plug-Flow Reactor with Distributed Feed. 9.3 Distillation Reactor. 9.4 Recycle Reactor. 9.5 Summary. Problems. Chapter 10: Economic-Based Optimization of Reactor Operations. 10.1 Economic Objective Functions. 10.2 Batch and Semi-Batch Reactors. 10.3 Flow Reactors. 10.4 Summary. Problems. Appendices. Appendix A: Summary of Key Relationships. Appendix B: Microscopic Species Balances - Continuity Equations. Appendix C: Summary of Numerical Methods. Index.
ChemInform Abstract: A Metal‐Catalyzed Intermolecular [5 + 2] Cycloaddition/Nazarov Cyclization Sequence and Cascade. (2010)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Faecal Short-chain Fatty Acid and Early Introduction of Foods in the First 200 Days of Infant’s Life in the District of Abidjan (Ivory Coast) (2023)

Dosage of short chain fatty acids (SCFAs) according to food diet showed that the content of acetate was high in newborn feaces. Infants receiving food supplements have a complex and diverse gut microbiota. Moreover, the results show that infants from poor districts have an abundant concentration of SCFAs in their faeces compared to those living in places with a relatively high standard of living. Among infants receiving milk, the highest proportion of SCFA is acetate in breastfed infants (BF) at a rate of 15.025 ± 2.23 Î¼mol/g, followed by propionate in infants receiving mixed feeding (BF+FF), at a rate of 13.58 ± 1.03 Î¼mol/g and butyrate in infants taking mixed feeding at a rate of 0.32 ± 0.72 Î¼mol/g. However, among infants starting early diet diversification, acetate is higher in infants receiving milk formula and diet diversification (FF+FD) with a concentration of 25.4 ± 0 Î¼mol/g, followed by propionate (2.36 ± 0 Î¼mol/g) in infants receiving mixed feeding (BF+FF) and butyrate in those fed with (BF+FD). Partial breastfeeding is associated with a higher proportion of acetate, butyrate and propionate. The study of the correlation between the different SCFAs produced and the ASV (Variants of Microbial Amplicon Sequences) of the intestinal community of the child, shows that acetate is positively correlated with Bifidobacterium and negatively with Streptococcus and Escherichia-Shigella. Propionate is positively correlated with Bifido bacterium and negatively with Escherichia-Shigella. Similarly, butyrate is positively correlated with Bifidobacterium and negatively with Escherichia-Shigella.
Approaches to the synthesis of pancratistatin and the creation and development of the contiguous chiral carbon catalog (1998)

Approaches towards the total synthesis of Pancratistatin are described herein. In addition, this thesis describes the creation and development of a powerful new approach to the synthesis of asymmetric synthons. This method relies upon a single catalytic step to introduce asymmetry from readily available starting materials and introduces further stereocenters via scaleable, environmentally-friendly transformations. Subsequent, high-yielding chemistry allows for easy access to both highly-functionalized cyclic and acylic substrates, thereby greatly increasing the scope of this methodology.
Precursor-Directed Biosynthesis of 5-Hydroxytryptophan Using Metabolically Engineered E. coli (2014)

A novel biosynthetic pathway was designed and verified reversely leading to the production of 5-hydroxytryptophan (5-HTP) from glucose. This pathway takes advantage of the relaxed substrate selectivities of relevant enzymes without employing the unstable tryptophan 5-hydroxylase. First, high-titer of 5-HTP was produced from 5-hydroxyanthranilate (5-HI) by the catalysis of E. coli TrpDCBA. Then, a novel salicylate 5-hydroxylase was used to convert the non-natural substrate anthranilate to 5-HI. After that, the production of 5-HI from glucose was achieved and optimized with modular optimization. In the end, we combined the full pathway and adopted a two-stage strategy to realize the de novo production of 5-HTP. This work demonstrated the application of enzyme promiscuity in non-natural pathway design.
Spectroscopic Characterization of the Soluble Guanylate Cyclase-like Heme Domains from Vibrio cholerae and Thermoanaerobacter tengcongensis (2004)

Soluble guanylate cyclase (sGC) is a nitric oxide- (NO-) sensing hemoprotein that has been found in eukaryotes from Drosophila to humans. Prokaryotic proteins with significant homology to the heme domain of sGC have recently been identified through genomic analysis. Characterization of two of these proteins is reported here. The first is a 181 amino acid protein cloned from Vibrio cholerae (VCA0720) that is encoded in a histidine kinase-containing operon. The ferrous unligated form of VCA0720 is 5-coordinate, high-spin. The CO complex is low-spin, 6-coordinate, and the NO complex is high-spin and 5-coordinate. These ligand-binding properties are very similar to those of sGC. The second protein is the N-terminal 188 amino acids of Tar4 (TtTar4H), a predicted methyl-accepting chemotaxis protein (MCP) from the strict anaerobe Thermoanaerobacter tengcongensis. TtTar4H forms a low-spin, 6-coordinate ferrous-oxy complex, the first of this sGC-related family that binds O2. TtTar4H has ligand-binding properties similar to those of the heme-containing O2 sensors such as AxPDEA1. sGC does not bind O2 despite having a porphyrin with a histidyl ligand like the globins. The results reported here, with sequence-related proteins from prokaryotes but in the same family as the sGC heme domain, show that these proteins have evolved to discriminate between ligands such as NO and O2; hence, we term this family H-NOX domains (heme-nitric oxide/oxygen).
Enhancement of Trans-Tympanic Drug Delivery by Pharmacological Induction of Inflammation (2023)

Drug delivery directly across the tympanic membrane (TM) could eliminate systemic exposure to antibiotics prescribed for otitis media, the most common reason for pediatricians to prescribe antibiotics. Here, we hypothesized that inducing inflammation of the TM could enhance drug flux across the TM. We demonstrated that the flux of ciprofloxacin across the TM was greatly increased by treatment with the proinflammatory agent histamine. That enhancement was blocked by concurrent treatment with blockers of histamine receptor 1. Treatment of the TM with histamine was able to enhance drug flux sufficiently to eradicate otitis media in vivo in chinchillas, but only if the histamine was applied prior to treatment with antibiotics.
Thermally Annealed Iron (Oxide) Thin Film on an Alumina Barrier Layer, by XPS (2013)

Herein we show characterization of an Fe thin film on Al2O3 after thermal annealing under H2 using AlKα x-rays. The XPS survey spectrum, Fe 2p and O 1s narrow scans, and valence band regions are presented. The survey spectrum shows aluminum signals due to exposure of the underlying Al2O3 film during Fe nanoparticle formation.
Distributed join algorithms on thousands of cores (2017)

Traditional database operators such as joins are relevant not only in the context of database engines but also as a building block in many computational and machine learning algorithms. With the advent of big data, there is an increasing demand for efficient join algorithms that can scale with the input data size and the available hardware resources. In this paper, we explore the implementation of distributed join algorithms in systems with several thousand cores connected by a low-latency network as used in high performance computing systems or data centers. We compare radix hash join to sort-merge join algorithms and discuss their implementation at this scale. In the paper, we explain how to use MPI to implement joins, show the impact and advantages of RDMA, discuss the importance of network scheduling, and study the relative performance of sorting vs. hashing. The experimental results show that the algorithms we present scale well with the number of cores, reaching a throughput of 48.7 billion input tuples per second on 4,096 cores.
NHC‐Cu‐Catalyzed Enantioselective Hydroboration of Acyclic and Exocyclic 1,1‐Disubstituted Aryl Alkenes (2011)

Tough nut to crack: Chiral bidentate N-heterocyclic carbene copper complexes were designed that promote enantioselective hydroborations of one of the most difficult substrate classes: acyclic and exocyclic 1,1-disubstituted alkenes undergo reaction with >98 % site selectivity, in up to >98 % yield and e.r=96.5:3.5 (see scheme, B2(pin)2 = bis(pinacolato)diboron).
Copper-catalyzed asymmetric addition of olefin-derived nucleophiles to ketones (2016)

Enantioenriched alcohols found in an array of bioactive natural products and pharmaceutical agents are often synthesized by asymmetric nucleophilic addition to carbonyls. However, this approach generally shows limited functional-group compatibility, requiring the use of preformed organometallic reagents in conjunction with a stoichiometric or substoichiometric amount of chiral controller to deliver optically active alcohols. Herein we report a copper-catalyzed strategy for the stereoselective nucleophilic addition of propargylic and other alkyl groups to ketones, using easily accessible (poly)unsaturated hydrocarbons as latent carbanion equivalents. Our method features the catalytic generation of highly enantioenriched organocopper intermediates and their subsequent diastereoselective addition to ketones, allowing for the effective construction of highly substituted stereochemical dyads with excellent stereocontrol. Moreover, this process is general, scalable, and occurs at ambient temperature.