gebhart/patrepeval huggingface dataset:
AML Risk Stratification Models Utilizing ELN-2017 Guidelines and Additional Prognostic Factors: A SWOG Report (2020)

Abstract Background The recently updated European LeukemiaNet risk stratification guidelines combine cytogenetic abnormalities and genetic mutations to provide the means to triage patients with acute myeloid leukemia for optimal therapies. Despite the identification of many prognostic factors, relatively few have made their way into clinical practice.Methods In order to assess and improve the performance of the European LeukemiaNet guidelines, we developed novel prognostic models using the biomarkers from the guidelines, age, performance status and select transcript biomarkers. The models were developed separately for mononuclear cells and viable leukemic blasts from previously untreated acute myeloid leukemia patients (discovery cohort, N = 185) who received intensive chemotherapy. Models were validated in an independent set of similarly treated patients (validation cohort, N = 166).Results Models using European LeukemiaNet guidelines were significantly associated with clinical outcomes and, therefore, utilized as a baseline for comparisons. Models incorporating age and expression of select transcripts with biomarkers from European LeukemiaNet guidelines demonstrated higher area under the curve and C-statistics but did not show a substantial improvement in performance in the validation cohort. Subset analyses demonstrated that models using only the European LeukemiaNet guidelines were a better fit for younger patients (age &lt; 55). Models integrating age and European LeukemiaNet guidelines visually showed more separation between risk groups in older patients. Models, which excluded results for ASXL1 , CEBPA , RUNX1 and TP53 , demonstrated a limited overall contribution to risk stratification across the entire population, given the low frequency of mutations and confounding risk factors.Conclusions While European LeukemiaNet guidelines remain a critical tool for triaging patients with acute myeloid leukemia, the findings illustrate the need for additional prognostic factors, including age, to improve risk stratification.
Metal Decorated Multi-Walled Carbon Nanotube/Polyimide Composites with High Dielectric Constants and Low Loss Factors (2009)

The measurement of observable electromagnetic phenomena in materials and their derived intrinsic electric material properties are of prime importance in the discovery and development of material systems for electronic and aerospace applications. Nanocomposite materials comprised of metal decorated multi-walled carbon nanotubes (MWCNTs) were prepared by a facile method and characterized. Metal particles such as silver, platinum and palladium with diameters ranging from less than 5 to over 50 nanometers were distributed randomly on the MWCNTs. The metal-containing MWCNTs were then melt mixed into a polymer matrix and the mixture extruded as ribbons. These extruded ribbons exhibited a moderate to high degree of MWCNT alignment as determined by HRSEM. These ribbons were then fabricated into test specimens while maintaining MWCNT alignment and subsequently characterized for electromagnetic properties at 8-12 GHz. The present study is focused on silver decorated MWCNTs dispersed in an Ultem polyimide matrix. The results of the electromagnetic characterization showed that certain sample configurations exhibited a decoupling of the permittivity and loss factor (?? and ??) indicating that these properties could be tailored within certain limits. The decoupling and independent control of these fundamental electrical material parameters offer a new class of materials with potential applications in electronics, microwave engineering and optics.
Hydrothermal Activity at the Ultraslow‐Spreading Mohns Ridge: New Insights From Near‐Seafloor Magnetics (2019)

Abstract Hydrothermal circulation is a process fundamental to all types of mid‐ocean ridges that largely impacts the chemical and physical balance of the World Ocean. However, diversity of geological settings hosting hydrothermal fields complicates the exploration and requires thorough investigation of each individual case study before effective criteria can be established. Analysis of high‐resolution bathymetric and magnetic data, coupled with video and rock samples material, furthers our knowledge about mid‐ocean‐ridge‐hosted venting sites and aid in the interpretation of the interplay between magmatic and tectonic processes along the axial volcanic ridges. The rock‐magnetic data provide constraints on the interpretation of the observed contrasts in crustal magnetization. We map the areal extent of the previously discovered active basalt‐hosted Loki's Castle and inactive sediment‐hosted Mohn's Treasure massive sulfide deposits and infer their subsurface extent. Remarkably, extinct hydrothermal sites have enhanced magnetizations and display clear magnetic signatures allowing their confident identification and delineation. Identified magnetic signatures exert two new fossil hydrothermal deposits, MT‐2 and MT‐3. The Loki's Castle site coincides with negative magnetic anomaly observed in the 2‐D magnetic profile data crossing the deposit. First geophysical investigations in this area reveal the complexity of the geological setting and the variation of the physical properties in the subsurface.
HARNESSING BTKI THERAPY BY CDK4/6I CONTROL OF T CELL SURVEILLANCE (2023)

Introduction: Drug resistance remains a formidable challenge in mantle cell lymphoma (MCL). Cell cycle dysregulation driven by aberrant Cyclin D1 and CDK4 expression is a hallmark for MCL. By inhibition of CDK4/6, we have developed a novel strategy that both inhibits proliferation of MCL cells and reprograms them for cytotoxic killing. In a phase I clinical trial we investigated if inhibition of cyclin D1/CDK4 with palbociclib could reprogram recurrent MCL to deepen and prolong the ibrutinib response, and the mechanism for resistance by longitudinal genomic analysis of sequential samples from individual patients in the context of the clinical response. Methods: Palbociclib was administered to recurrent MCL patients on days 1–21 of a 28-day cycle; ibrutinib was given continuously. For longitudinal genomic analysis, sequential tissue and blood specimens from 27 evaluable MCL patients before, during therapy and on progression were collected. Single cell RNA-seq (scRNA-seq) of PBMC or the monocytic fractions from bone marrow and lymph node was performed using a unique in house MCL-specific library. The data were then subject to multiplex analysis with whole transcriptome sequencing and whole exome sequencing of purified MCL cells and flowcytometry of the same samples in conjunction with IHC. Results: Palbociclib appears to deepen and prolong the ibrutinib response; the CR rate was 42% CR, and 5 patients (2 CR and 3 PR) remained on therapy for >8 years. Longitudinal scRNA-seq further revealed that MCL cells comprise 4 major transcriptomically distinct clusters (C)s. Primary resistance and progression on therapy were associated with a marked expansion of either long-live non-proliferating C3 cells or C2 cells that fuel the proliferating C4 cells. Resistance was associated with a profound reduction in MHC I and MHC II expression and disease progression was further accompanied by a rapid loss of both CD8+ and CD+ T cells. This suggests T cell surveillance plays a critical role in maintaining a durable ibrutinib response. Guided by our discoveries, we have restored ibrutinib sensitivity by target patient-specific expansion of C2 or C3 MCL cells ex vivo. In one patient, this led to restoration of CD4+ and CD8+T cells and a CR over 2.5 years. Conclusion: T cell surveillance plays a critical role in prolonging the ibrutinib response by CDK4/6 inhibition, implicating genome-guided combination therapy to overcome ibrutinib resistance in MCL. The research was funded by: PO1 grant from the National Cancer Institute MCL-RI grant from Leukemia and Lymphoma Society Keywords: combination therapies, genomics, epigenomics, and other-omics, tumor biology and heterogeneity No conflicts of interests pertinent to the abstract.
<title>Effect of process-induced stress in InP/InGaAsP weakly confined waveguides</title> (2000)

InP/InGaAsP weakly confined wave guides, are of interest for the fabrication of a variety of optoelectronic devices, including optical cross point switches. Previous studies have shown that stress from metallization alters the behavior of these waveguides and the strain-induced changes in refractive index have been investigated by studying the degree of polarization (DOP) from the facets of ridge waveguide (RWG) lasers. However, in devices intended for waveguide routing or switching, e-beam deposited TiPtAu contacts, caused broadening and splitting of the optical near field mode profile after thermal annealing and increased waveguide loss. In this paper, we report the results of a study of process-induced changes on the optical near field mode profile, for different dielectric depositions, metallizations and anneal cycles. It was found that the addition of a layer of the TiPtAu. This not only eliminated the mode splitting, but for sufficiently high values of compressive stress, was found to actually sharpen the mode and enhance the guiding. On the basis of these results stable waveguides, suitable for routing or switching were achieved for a range of device parameters, operating conditions and process parameter variations.
Solid‐phase synthesis of chiral stationary phases based on 2,4,5,6‐tetrachloro‐1,3‐dicyanobenzene derivatives spaced from N‐3,5‐dinitrobenzoyl α‐amino acids: Comparative study of their resolution efficacy (2001)

Two new chiral stationary phases, 3-[5-chloro-1,3-dicyano-2,4-[2'-(N'-1,3-dinitrobenzoyl-D-phenylglycinyl) aminoethyl]aminophen-1-yl] aminopropyl silica (CSP-1) and 3-[5-chloro-1,3-dicyano-2,4-[2'-(N'-1,3-dinitrobenzoyl-L-leucinyl) aminoethyl] aminophen-1-yl] aminopropyl silica (CSP-2), were prepared by solid-phase synthesis. They comprise chiral unit, 3,5-dinitrobenzoyl derivative of the amino acid, D-PhGly or L-Leu, bound via spacer 1,2-diaminoethane to 2,4-positions of the persubstituted benzene ring, derived from compound 1, and possess pseudo-C2 symmetry. Preparation of model compounds 6 and 7 confirmed the structure of chiral selectors, which comprise pi-donor persubsituted aromatic ring and two strong pi-acceptor 3,5-dinitrobenzoyl amido units. CD spectra of model selectors 6 and 7, run in DMSO above 250 nm, exhibit negative exciton coupling (EC) between pi-acceptor and pi-donor chromophores, C(1) symmetric model compound 8 exhibited much weaker EC and 9, devoid of pi-donor unit, does not exhibit any significant CD. Combined pi-donor and pi-acceptor properties enable the new CSPs to separate a broad range of racemates. The columns with CSP-1 and CSP-2 were tested for the separation of 22 racemates by HPLC with two different mobile phase systems and the results are compared with those obtained by using a structurally related commercial column.
Host plant resistance for fall armyworm management in maize: relevance, status and prospects in Africa and Asia (2022)

Sustainable control of fall armyworm (FAW) requires implementation of effective integrated pest management (IPM) strategies, with host plant resistance as a key component. Significant opportunities exist for developing and deploying elite maize cultivars with native genetic resistance and/or transgenic resistance for FAW control in both Africa and Asia. The fall armyworm [Spodoptera frugiperda (J.E. Smith); FAW] has emerged as a serious pest since 2016 in Africa, and since 2018 in Asia, affecting the food security and livelihoods of millions of smallholder farmers, especially those growing maize. Sustainable control of FAW requires implementation of integrated pest management strategies, in which host plant resistance is one of the key components. Significant strides have been made in breeding elite maize lines and hybrids with native genetic resistance to FAW in Africa, based on the strong foundation of insect-resistant tropical germplasm developed at the International Maize and Wheat Improvement Center, Mexico. These efforts are further intensified to develop and deploy elite maize cultivars with native FAW tolerance/resistance and farmer-preferred traits suitable for diverse agro-ecologies in Africa and Asia. Independently, genetically modified Bt maize with resistance to FAW is already commercialized in South Africa, and in a few countries in Asia (Philippines and Vietnam), while efforts are being made to commercialize Bt maize events in additional countries in both Africa and Asia. In countries where Bt maize is commercialized, it is important to implement a robust insect resistance management strategy. Combinations of native genetic resistance and Bt maize also need to be explored as a path to more effective and sustainable host plant resistance options. We also highlight the critical gaps and priorities for host plant resistance research and development in maize, particularly in the context of sustainable FAW management in Africa and Asia.
Scalable E-mode N-polar GaN MISFET devices and process with self-aligned source/drain regrowth (2010)

E-mode GaN FETs fabricated on N-polar GaN have several unique scaling advantages such as vertical scaling of channel with back barrier for better electron confinement and regrowth of the n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> source/drain regions for reduced access resistance. They can also be integrated with recently demonstrated high performance N-polar D-mode devices enabling novel circuit functionalities. Ga-polar E-mode devices with good performance have been demonstrated; however in these devices source/drain contacts are invariably made to wideband gap Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> Ga <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1-x</sub> N barriers leading to higher contact resistances which considerably limit the aggressive scaling of the device. Here we report E-mode N-polar GaN FETs fabricated with a scalable gate first process with self-aligned regrown source/drain regions and non-alloyed ohmic contacts for low access resistances. These devices show a peak drive current (I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">d</sub> ) of 0.74 A/mm and peak transconductance (g <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</sub> ) of 250 mS/mm at L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</sub> = 0.55 μm with a threshold voltage (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> ) of 0.8 V.
Full Scale Test on Chemical P Removal during a Step Feed BNR Study at John E. Egan Water Reclamation Plant (2006)

A full scale nutrient removal study was conducted at the 30-MGD John E. Egan Water Reclamation Plant with a single-stage nitrification activated sludge process and sand filtration. One quarter of the plant’s secondary treatment capacity was used in the study. Simultaneous nitrogen removal through a step feed BNR process and phosphorus (P) removal by chemical precipitation with ferric chloride (FeCl3) were tested to investigate the potential impact of adding FeCl3 to mixed liquor for P removal on the step feed BNR process and on the operation of other unit processes in the plant. During the P removal tests, which were conducted once in early spring and again in early fall of 2005, solutions containing approximately 33% FeCl3 by weight were injected at two different target rates into mixed liquor at the effluent end of the aeration tank. The average daily FeCl3 concentrations applied with respect to 7.5 MGD inflow to the aeration tank were 32.5 to 44.6 mg/L. The average soluble phosphorus (Sol-P) concentrations in 24-hour composite samples of the secondary effluent during the P removal tests ranged from 0.05 to 0.82 mg/L with an arithmetic mean of 0.27 mg/L. The total nitrogen (TN) removal by the step feed BNR process tested averaged 52% and 54% before and during the chemical P removal test in the spring and 52% and 58% in the fall. This indicates that adding ferric chloride to mixed liquor up to 44.6 mg/L for removing particulate FePO4 in the secondary clarifiers has no adverse impact on the step feed BNR process for biological nitrogen removal. The higher percentage TN removal during the P removal test in the fall was probably attributed to the higher MLVSS in the aeration tank resulting from higher solids content in the returned sludge after ferric chloride addition. The accumulation of ferric particles in WAS during the P removal tests appears to have caused the clogging of cloth belt used in the gravity belt thickeners (GBT) for sludge thickening. The sludge thickening performance of the GBT deteriorated during the chemical P removal tests. The performance was improved after the addition of ferric chloride to mixed liquor stopped.
Photoinduced synthesis of Ag nanoparticles on ZnO nanowires for real-time SERS systems (2014)

Hierarchical nanostructure of Ag nanoparticles on ZnO nanowires is introduced by using a photoinduced synthesis. A real-time, <italic>in situ</italic> SERS detection system is achieved with a microfluidic channel. The hierarchical nanostructure shows 6.36 × 10<sup>11</sup> of SERS enhancement factor.
Video Instance Segmentation Tracking With a Modified VAE Architecture (2020)

We propose a modified variational autoencoder (VAE) architecture built on top of Mask R-CNN for instance-level video segmentation and tracking. The method builds a shared encoder and three parallel decoders, yielding three disjoint branches for predictions of future frames, object detection boxes, and instance segmentation masks. To effectively solve multiple learning tasks, we introduce a Gaussian Process model to enhance the statistical representation of VAE by relaxing the prior strong independent and identically distributed (iid) assumption of conventional VAEs and allowing potential correlations among extracted latent variables. The network learns embedded spatial interdependence and motion continuity in video data and creates a representation that is effective to produce high-quality segmentation masks and track multiple instances in diverse and unstructured videos. Evaluation on a variety of recently introduced datasets shows that our model outperforms previous methods and achieves the new best in class performance.
On {h,1,1}<1/h,1,2>, the Recrystallisation Texture of Heavily Cold Rolled BCC Steel (2004)

Heavily cold rolled BCC steel has been indicated to generate {411}&lt;148&gt; recrystallisation texture and its family orientations which might be represented as {h,1,1}&lt;1/h,1,2&gt;. As a-fibre structure, or RD//&lt;011&gt; texture is significantly developed during the cold rolling, it is naturally speculated to be the recrystallisation site of {h,1,1}&lt;1/h,1,2&gt; fibre. The present paper prompts to demonstrate the recrystallisation procedure by utilising EBSP-OIM analysis. The first demonstration was carried out with OIM analysis on partially recrystallised cold rolled steel. At the stage of 50% recrystallisation, only ND//&lt;111&gt; texture has appeared for the recrystallised area. {100}&lt;011&gt; - {211}&lt;011&gt; a-fibre remains as deformed structure, and several {h,1,1}&lt;1/h,1,2&gt; grains could be found at the grain boundaries. Therefore, a bi-crystal of {100}&lt;011&gt; was employed to simulate the irregular deformation at the grain boundary. After cold rolling, a warp toward the grain boundary was observed. Although the interior of the {100}&lt;011&gt; single crystal was hardly recrystallised, sharp {411}&lt;148&gt; texture was created along the grain boundary. In order to confirm the phenomenon, another experiment was carried out that a cold rolled {100}&lt;011&gt; single crystal was bent along the rolling direction and annealed. Very sharp {411}&lt;148&gt; recrystallisation texture was formed again at the bent perimeter. These experimental results lead us to conclude that the irregular strain was sufficiently piled at the grain boundary after the heavy deformation and generates {h,1,1}&lt;1/h,1,2&gt; texture. On {100} pole figures, the recrystallisation textures were equivalently scattered around three &lt;100&gt; poles, therefore the rotation relationship around &lt;111&gt; axes with the original orientation was suggested.
RNA Interference Characterization of Proteins Discovered by Proteomic Analysis of Pancreatic Cancer Reveals Function in Cell Growth and Survival (2011)

By combining a mass spectrometry identification platform and an RNAi validation platform, we have identified a panel of cell surface glycoproteins that not only are overexpressed, but also play a functional role in pancreatic tumor cell survival.
Level of Sensing for Biomass Dryer Control and Optimization (2016)

<abstract> <b><sc>Abstract.</sc></b> Consistent and reliable operation of biomass dryers is problematic across existing pellet fuel producers and emerging advanced biofuel firms due to inexperience of operators, temporal variation in biomass moisture content, and lack of knowledge about drying characteristics of their feedstocks. The precision to which select parameters can be sensed at the research and commercial scale greatly affects both precision and the cost of automated control. Temperature and pressure are two of the key parameters which can be accurately sensed with relatively low cost components. Sensors for relative humidity, air flow rate and real-time mass are also needed. Forest Concepts has developed a Research Drying Apparatus to collect meaningful characteristics about select biomass feedstocks to inform the algorithms and sensor requirements of advanced model-predictive controls for optimal dryer efficiency and operation.
Dynamic Spectrum Management in Passive Optical Networks (2011)

Dynamic spectrum management is proposed as a simple and cost-effective way for smooth evolution of passive optical networks. Experimental testbed with dynamic spectrum management demonstrates 10Gb/s aggregated bandwidth in upstream using ONUs with 2.5Gb/s transmitters.
ChemInform Abstract: Evolution of a Synthetic Strategy: Total Synthesis of (.+‐.)‐Welwitindolinone A Isonitrile (I). (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Fragment-Based Discovery of Mexiletine Derivatives as Orally Bioavailable Inhibitors of Urokinase-Type Plasminogen Activator (2007)

Fragment-based lead discovery has been applied to urokinase-type plasminogen activator (uPA). The (R)-enantiomer of the orally active drug mexiletine 5 (a fragment hit from X-ray crystallographic screening) was the chemical starting point. Structure-aided design led to elaborated inhibitors that retained the key interactions of (R)-5 while gaining extra potency by simultaneously occupying neighboring regions of the active site. Subsequent optimization led to 15, a potent, selective, and orally bioavailable inhibitor of uPA.