gebhart/patrepeval huggingface dataset:
Abstract 1443: CHKing melanoma: CHK1 inhibitor +low dose hydroxyurea triggers immunogenic cell death and immunostimulatory cytokine expression to drive an anti-tumor immune response (2021)

Abstract About half of melanomas respond to immunotherapy, but we currently lack reliable markers to identify likely responders. Therefore, a large number of patients receive this expensive therapy for no benefit. We have previously shown that inhibition of the cell cycle regulator, Checkpoint kinase 1 (CHK1), with subclinical dose of the replication stress inducer hydroxyurea is cytotoxic in a high proportion of melanomas tested. We now report that CHK1 inhibitor + low dose hydroxyurea (LDHU) treatment triggers immunostimulatory cytokine and chemokine expression, and an immunogenic form of cell death. In xenograft models, the drug combination blocks tumor growth for extended periods after the completion of treatment. In syngeneic mouse melanoma models, the drug combination also effectively controls tumor growth and induces regression in a proportion of cases. It also increases immune cell infiltration and activation of a tumor directed cytotoxic T cell response. We also demonstrate that the drug combination does not adversely affect an adaptive immune response or rapidly proliferating human T cells. The mechanism by which drug treatment promotes cytokine expression is unlikely to involve the cGAS-STING signalling pathway which is commonly defective in melanomas. Using two engineered mouse melanoma models we have found that CHK1 inhibitor + LDHU increases cytotoxic CD8+ T cells and NK cell infiltration and activation, but we have also found increased CD4+ Treg tumor infiltration and increased CD8+ T cell PD-1 expression. We have also found increased expression of other immune checkpoint regulators. This indicates a strong anti-tumor immune response is initiated but immune suppression and T cell exhaustion have limited the extent of the response of the tumor infiltrating T cells. However, circulating T cells retained strong anti-tumor activity. The harvested tumors from the drug combination treated mice that do increase in size after treatment show strong evidence of cytotoxic activity. These data provide evidence that CHK1 inhibitors + LDHU is well tolerated and triggers a strong anti-cancer immune response that should combine with immune therapy, although the selection of the target of the immunotherapy will be critical for successfully overcoming the immune suppression triggered. Citation Format: Brian G. Gabrielli, Martina Proctor, Jazmina Gonzalez Cruz, Bijun Zeng, Riccardo Dolcetti, Colm Keane, Nikolas Haass, James Wells. CHKing melanoma: CHK1 inhibitor +low dose hydroxyurea triggers immunogenic cell death and immunostimulatory cytokine expression to drive an anti-tumor immune response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1443.
4D Ultrafast Ultrasound Imaging of Naturally Occurring Shear Waves in the Human Heart (2020)

The objectives were to develop a novel three-dimensional technology for imaging naturally occurring shear wave (SW) propagation, demonstrate feasibility on human volunteers and quantify SW velocity in different propagation directions. Imaging of natural SWs generated by valve closures has emerged to obtain a direct measurement of cardiac stiffness. Recently, natural SW velocity was assessed in two dimensions on parasternal long axis view under the assumption of a propagation direction along the septum. However, in this approach the source localization and the complex three-dimensional propagation wave path was neglected making the speed estimation unreliable. High volume rate transthoracic acquisitions of the human left ventricle (1100 volume/s) was performed with a 4D ultrafast echocardiographic scanner. Four-dimensional tissue velocity cineloops enabled visualization of aortic and mitral valve closure waves. Energy and time of flight mapping allowed propagation path visualization and source localization, respectively. Velocities were quantified along different directions. Aortic and mitral valve closure SW velocities were assessed for the three volunteers with low standard deviation. Anisotropic propagation was also found suggesting the necessity of using a three-dimensional imaging approach. Different velocities were estimated for the three directions for the aortic (3.4± 0.1 m/s, 3.5± 0.3 m/s, 5.4± 0.7 m/s) and the mitral (2.8± 0.5 m/s, 2.9± 0.3 m/s, 4.6± 0.7 m/s) valve SWs. 4D ultrafast ultrasound alleviates the limitations of 2D ultrafast ultrasound for cardiac SW imaging based on natural SW propagations and enables a comprehensive measurement of cardiac stiffness. This technique could provide stiffness mapping of the left ventricle.
Palladium/Stannic Oxide Interfacial Chemistry Promotes Hydrogen Oxidation Reactions in Alkaline Medium (2020)

Abstract A nanostructured Pd/SnO 2 on metal‐organic‐framework‐derived carbon (Pd/SnO 2 /MOFDC) electrocatalyst and its monometallic catalyst (Pd/MOFDC) have been synthesized by microwave‐assisted strategies and investigated for the alkaline hydrogen oxidation reaction (HOR). Physical properties of the electrocatalysts are examined using X‐ray diffraction, thermogravimetric analysis, X‐ray photoelectron spectroscopy, Brunauer‐Emmett‐Teller analysis, transmission electron microscopy, and density functional theory. This study reveals that the Pd/SnO 2 /MOFDC possesses superior alkaline HOR activities (in terms of kinetic current, heterogeneous rate constant, diffusivity, exchange current density, and the mass activity) compared to those of the Pd/MOFDC and that are comparable to commercial Pt/C. The improved alkaline HOR activity on Pd/SnO 2 /MOFDC is attributed to the facile interfacial electrochemical processes arising from the multifunctional properties of SnO 2 with the thin Sn film: i) weakening of Pd‐H ads , confirmed by DFT simulation, and ii) oxophilic (thin Sn film) and spill‐over (SnO 2 ) effects that quickly transfer OH − ions to the desorbed H ads for facile reaction in the Volmer rate‐determining step (RDS). Tafel slope ( b a =52–102 mV dec −1 ) and activation energy ( E A ) values suggest the predominance of the Heyrovsky‐Volmer process. In addition to the improved HOR activity of Pd/SnO 2 /MOFDC, it also exhibits better stability than Pd/MOFDC. The good performance of Pd/SnO 2 /MOFDC toward the alkaline HOR promises potential development of low‐cost anode materials for alkaline membrane fuel cells.
Discussion of “A Wide-Band Lumped Circuit Model of Eddy Current Losses in a Coil With a Coaxial Insulation System and a Stranded Conductor” (2004)

For original article by P. Holmberg et al. see ibid., vol.18, p.50-60, Jan. 2003.
Insertion task in formation of rubber hose by robot (2021)

Many processes involve the manipulation of easily deformable objects such as food and cloth products, and the automation of such processes is required. However, there are still many challenges in pick-and-place, assembly and handling those objects using industrial robots. The insertion task involved in the formation of rubber hoses is an example of such a task. In this study, to automate the rubber hose insertion task, a preliminary investigation of friction force that affects the insertion task was examined and it was found that the air injection into the hose was effective to reduce the friction force. Based on the result, an air injection robotic hand (AIR-Hand) and a hose buckling preventing hand (HELP-Hand) were developed for a dual-arm robot. Furthermore, we integrated those two end effectors into one for a single-arm robot. The hose insertion task was successfully performed by both the dual-arm and single-arm robots, along with their corresponding manipulation plans.
Digital RF Processor (DRP&amp;#8482;) for Cellular Radios (2005)

RF circuits for multi-GHz frequencies have recently migrated to low-cost digital deep-submicron CMOS processes. Unfortunately, this process environment, which is optimized only for digital logic and SRAM memory, is extremely unfriendly for conventional analog and RF designs. We present fundamental techniques recently developed that transform the RF and analog circuit design complexity to digital domain for a wireless RF transceiver, so that it enjoys the benefits of digital approach, such as process node scaling and design automation. All-digital phase locked loop, all-digital control of phase and amplitude of a polar transmitter, and direct RF sampling techniques allow great flexibility in reconfigurable radio design. Digital signal processing concepts are used to help relieve analog design complexity, allowing one to reduce cost and power consumption in a reconfigurable design environment. The ideas presented have been used in Texas Instruments to develop two generations of commercial digital RF processors: a single-chip Bluetooth radio and a single-chip GSM radio.
Altered gene expression in the Werner and Bloom syndromes is associated with sequences having G-quadruplex forming potential (2009)

The human Werner and Bloom syndromes (WS and BS) are caused by deficiencies in the WRN and BLM RecQ helicases, respectively. WRN, BLM and their Saccharomyces cerevisiae homologue Sgs1, are particularly active in vitro in unwinding G-quadruplex DNA (G4-DNA), a family of non-canonical nucleic acid structures formed by certain G-rich sequences. Recently, mRNA levels from loci containing potential G-quadruplex-forming sequences (PQS) were found to be preferentially altered in sgs1Delta mutants, suggesting that G4-DNA targeting by Sgs1 directly affects gene expression. Here, we extend these findings to human cells. Using microarrays to measure mRNAs obtained from human fibroblasts deficient for various RecQ family helicases, we observe significant associations between loci that are upregulated in WS or BS cells and loci that have PQS. No such PQS associations were observed for control expression datasets, however. Furthermore, upregulated genes in WS and BS showed no or dramatically reduced associations with sequences similar to PQS but that have considerably reduced potential to form intramolecular G4-DNA. These findings indicate that, like Sgs1, WRN and BLM can regulate transcription globally by targeting G4-DNA.
Targeted Next‐Generation Sequencing Analysis of 1,000 Individuals with Intellectual Disability (2015)

To identify genetic causes of intellectual disability (ID), we screened a cohort of 986 individuals with moderate to severe ID for variants in 565 known or candidate ID-associated genes using targeted next-generation sequencing. Likely pathogenic rare variants were found in ∼11% of the cases (113 variants in 107/986 individuals: ∼8% of the individuals had a likely pathogenic loss-of-function [LoF] variant, whereas ∼3% had a known pathogenic missense variant). Variants in SETD5, ATRX, CUL4B, MECP2, and ARID1B were the most common causes of ID. This study assessed the value of sequencing a cohort of probands to provide a molecular diagnosis of ID, without the availability of DNA from both parents for de novo sequence analysis. This modeling is clinically relevant as 28% of all UK families with dependent children are single parent households. In conclusion, to diagnose patients with ID in the absence of parental DNA, we recommend investigation of all LoF variants in known genes that cause ID and assessment of a limited list of proven pathogenic missense variants in these genes. This will provide 11% additional diagnostic yield beyond the 10%-15% yield from array CGH alone.
Supporting Data Analytics Applications Which Utilize Cognitive Services (2017)

A wide variety of services are available over the Web which can dramatically improve the functionality of applications. These services include information retrieval (including data lookups from a variety of sources and Web searches), natural language understanding, visual recognition, and data storage. A key problem is how to provide support for applications which use these services. This paper presents a rich software development kit (SDK) which accesses these services and provides a variety of features applications need to use these services, optimize performance, and compare them. A key aspect of our SDK is its support for natural language understanding services. We also present a personalized knowledge base built on top of our rich SDK that uses publically available data sources as well as private information. The knowledge base supports data analysis and reasoning over data.
SQL-on-hadoop systems (2015)

Enterprises are increasingly using Apache Hadoop, more specifically HDFS, as a central repository for all their data; data coming from various sources, including operational systems, social media and the web, sensors and smart devices, as well as their applications. At the same time many enterprise data management tools (e.g. from SAP ERP and SAS to Tableau) rely on SQL and many enterprise users are familiar and comfortable with SQL. As a result, SQL processing over Hadoop data has gained significant traction over the recent years, and the number of systems that provide such capability has increased significantly. In this tutorial we use the term SQL-on-Hadoop to refer to systems that provide some level of declarative SQL(-like) processing over HDFS and noSQL data sources, using architectures that include computational or storage engines compatible with Apache Hadoop.
Élaboration et étude des propriétés d'un bioréacteur multi-membranaire (2007)

Ce travail concerne l'elaboration et l'etude des proprietes des materiaux multimembranaires a base d'hydrogels physiques de chitosane, utilises comme pour des applications en medecine regenerative. Les systemes multimembranaires, sont elabores a partir de gels physiques a l'alcool sans aucun agent reticulant externe. L'architecture de type oignon est obtenue apres l'optimisation de l'etape de neutralisation. L'etude systematique des parametres physico-chimiques mis en jeu au cours de la formation des membranes a permis de proposer un mecanisme de neutralisation. L'influence des conditions de neutralisation sur la morphologie a differentes echelles a ete observee par diffusion / diffraction des rayons X et microscopie electronique, permettant d'identifier au moins 3 morphologies caracteristiques. Les proprietes mecaniques des membranes d'hydrogel ont ete etudiees a l'aide de tests de traction. Enfin l'etude du comportement de differents types cellulaires mis en culture dans les hydrogels multimembranaires a permis de valider la bioactivite et le fort potentiel de cette architecture comme bioreacteurs
Dietary Whey Protein Enhances Liver Glycogen Restoration after Exercise in Rats (2006)

Recent studies showed that combination of carbohydrate and protein was more effective than carbohydrate alone in the replenishment of muscle glycogen immediately after exercise. Furthermore, Morifuji et al. (British J Nutrition (2005) 93: 439–445) demonstrated that a daily intake of whey protein for two weeks increased glycogen contents in liver and skeletal muscle of exercise-trained rats. However, it is not clear if different types of dietary protein affect postexercise glycogen resynthesis in tissues. PURPOSE: The aim of the present study was to compare the effect of postexercise casein and whey protein feedings on the restoration of glycogen, and the activity of glycoregulatory enzymes in the liver and skeletal muscle of rats. METHODS: Male Sprague-Dawley rats (ca 100 g; n=6 per group) were used for this study. All rats were trained by using a 7-day swimming exercise program, during which rats swam 6 hr/day in two 3 hr bouts separated by 45 min of rest. Every training day, swimming training was finished before 8:30 PM. Rats were allowed free access to the standard diet (AIN-93) and water between 9:00 PM to 9:00 AM. After last training day, food was restricted to 18 g/rat. Between 4:00 PM and 5:00 PM on the next day of the last training, the rats performed 4 hr of swimming exercise with a weight equivalent to 2 % of their body weight to deplete muscle and liver glycogen. After gly cog en-depleting exercise, all the rats were allowed free access to a diet based on either casein or whey protein, and 5 % glucose water for 12 hr. Immediately after repletion period, arteriovenous blood was collected under ether anesthesia, centrifuged at 3000 g for 15 min and the serum then stored at −80°C. Triceps muscle and liver were quickly excised, washed and frozen at −80°C until assay. Triceps muscle and liver were used for the determination of both glycogen concentrations and glycoregulatory enzyme activities. RESULTS: Blood glucose and serum insulin levels were not different between the two groups. Glycogen concentration and the activities of hexokinase and total glycogen synthase in triceps muscle were not significantly different between casein and whey groups. On the other hand, liver glycogen concentration was significantly increased in the whey group as compared to the casein group (P<0.05). Liver glucokinase and total glycogen synthase activities were also higher in the whey group than those in the casein group (P<0.01). CONCLUSIONS: These results demonstrated that the whey protein diet enhanced liver glycogen repletion after exercise in rats, because of the increase in the glycoregulatory enzymes activity.
Uncertainties in estimates of lesion detectability in diagnostic ultrasound (1999)

Statistical properties of estimates of focal lesion detectability for medical ultrasonic imaging systems are investigated. Analytic forms for bias and variance of estimates of detectability of a lesion consisting of fully developed speckle embedded within a speckle background are derived. Bias and variance of estimates of detectability are investigated using a computer simulation and experiments on tissue-mimicking phantoms. This work offers a systematic methodology for interpreting measurements on phantoms in order to assess lesion detectability. In addition, it provides useful results which may be used to improve design of phantoms and experiments for imaging-system performance assessment.
Radiomic features predict local failure-free survival in stage III NSCLC adenocarcinoma treated with chemoradiation (2021)

Prognosis plays a crucial role in the customization of lung cancer care. The effective prediction of treatment response is essential to tailor treatment decisions to lung cancer patients. Molecular characterization of tumors using genomics-based approaches is important for personalized treatment planning, however, repeated tumor biopsies should be performed to capture their molecular heterogeneity, putting patients at risk of procedural complications such as a pneumothorax. Furthermore, the recent addition of immunotherapy after chemoradiotherapy for patients with unresectable stage III NSCLC can improve survival outcomes. The survival benefit achieved by stage III NSCLC patients undergoing chemoradiation is of interest since currently available biomarkers are inadequate to predict which patients are most likely to benefit from immunotherapy for first-line treatment along with chemoradiation. In this study, we investigate the association between local failure-free survival and radiomic features extracted from CT scans of stage III NSCLC adenocarcinoma patients. We retrospectively analyzed a well-curated cohort of 89 non-contrast enhanced CT scans from patients receiving homogeneous chemoradiation treatment. A set of 107 radiomic features was extracted using the pyradiomics package. In univariate analysis we performed log-rank tests per feature to predict risk of local failure. In multivariate analysis we applied principal component analysis to fit a Cox model to predict local failure-free survival. Univariate analysis showed that no individual radiomic feature can predict local failure-free survival, while multivariate analysis gave a C-index = 0.70, 95% CI = [0.56,0.85]. We conclude that radiomic features from CT scans, can predict local failure-free survival in stage III NSCLC.
Strain‐Induced Double Carbon–Carbon Bond Activations of Cycloparaphenylenes by a Platinum Complex: Application to the Synthesis of Cyclic Diketones (2018)

The carbon-carbon (C-C) bond activation of [n]cycloparaphenylenes ([n]CPPs) by a transition-metal complex is herein reported. The Pt<sup>0</sup> complex Pt(PPh<sub>3</sub> )<sub>4</sub> regioselectively cleaves two C-C σ bonds of [5] CPP and [6]CPP to give cyclic dinuclear platinum complexes in high yields. Theoretical calculations reveal that the relief of ring strain drives the reaction. The cyclic complex was further transformed into a cyclic diketone by using a CO insertion reaction.
Electroslag Refining as a Clean Liquid Metal Source for Atomization and Spray Forming of Superalloys (1996)

A pilot plant has been constructed to demonstrate the concept of using a combination of electroslag refining (ESR) and an induction-heated, segmented, water-cooled copper guide tube (CIG) to melt, refine, and deliver a stream of liquid metal to a spray forming process. The basic ESR system consists of a consumable electrode of the alloy to be melted, a liquid slag, and a watercooled copper crucible. The liquid slag is heated by passing an ac-electric current from the electrode through the slag to the crucible. The liquid slag is maintained at a temperature high enough to melt the end of the electrode. As the electrode melts, a refining action takes place-oxide inclusions are exposed to the slag and are dissolved. Droplets of molten metal fall through the slag and are collected in a liquid metal pool contained in the crucible below. By the addition of the induction-heated, segmented, water-cooled copper guide tube (CIG) to the bottom of the crucible, a liquid metal stream can be extracted from the liquid metal pool. This stream makes an ideal liquid metal source for atomization and spray forming. The pilot plant has been operated at a melt rate of 15 to 25 kg/min with the Ni-base superalloys Alloy 718, Rene' 9.5 and Rene' 88. Process optimization and cleanliness evaluation studies are in progress.
Filters with inductance cancellation using printed circuit board transformers (2004)

Capacitor parasitic inductance often limits the high-frequency performance of filters for power applications. However, these limitations can be overcome through the use of specially-coupled magnetic windings that effectively nullify the capacitor parasitic inductance. This paper explores the use of printed circuit board (PCB) transformers to realize parasitic inductance cancellation of filter capacitors. Design of such inductance cancellation transformers is explored, and applicable design rules are established and experimentally validated. The high performance of the proposed inductance cancellation technology is demonstrated in an EMI filter design.
Signaling Mechanisms Induced by Endothelin Agonists in Human Adrenal Glomerulosa Cells (1998)

Endothelin-1 (ET-1) exhibits secretagogue and trophic actions on the adrenal zona glomerulosa (ZG). Little information is available on the intracellular signaling events that follow stimulation of ET receptors on ZG cells. This study examined the expression of ET receptor subtypes and their involvement in transduction mechanisms induced by ET agonists on human ZG cells in primary culture. RT-PCR allowed the detection of both ETA and ETB receptor mRNAs in these cells. ET-1 induced a concentration-dependent increase in inositol phosphate (IP) accumulation in the presence of LiCl, whereas ETB agonists were inactive. The ET-1-induced increase in IP accumulation was prevented by BQ-123. ET-1 evoked an increase in [Ca2+]i, which was partially prevented by BQ-788. IRL 1620 also delayed the rise in [Ca2+]i. These results show that in human adrenal ZG cells, ET-1 induces an increase in IP accumulation through ETA receptor activation and evokes a rise in [Ca2+]i via stimulation of both ETA and ETB receptors.