gebhart/patrepeval huggingface dataset:
Data from Molecular Profiling of Cohorts of Tumor Samples to Guide Clinical Development of Pembrolizumab as Monotherapy (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Molecular profiling of large databases of human tumor gene expression profiles offers novel opportunities for informing decisions in clinical development programs.&lt;/p&gt;Experimental Design:&lt;p&gt;Gene expression profile of programmed death ligand 1 (PD-L1) was explored in a dataset of 16,000 samples, including approximately 4,000 metastatic tumors, across &gt;25 tumor types prevalent in the United States, looking for new indications for the programmed death 1 (PD-1) inhibitor pembrolizumab. PD-L1 expression was highly concordant with several genomic signatures indicative of immune-inflamed tumor microenvironment. Prevalence of activated immune-inflamed tumors across all tumor types was explored and used to rank tumor types for potential response to pembrolizumab monotherapy.&lt;/p&gt;Results:&lt;p&gt;The analysis yielded 3 tiers of indications in which high levels of PD-L1 and immune-inflamed signatures were found in up to 40% to 60%, 20% to 40%, and 0% to 20% of tumors. Tier 1 contained novel indications known at the time of analysis to be responsive to PD-1 checkpoint blockade in the clinic (such as melanoma and non–small cell lung cancer), as well as indications not studied in the clinic previously, including microsatellite instability–high colorectal, head and neck, bladder, and triple-negative breast cancers. Complementary analysis of an Asian/Pacific cancer dataset (gastric cancer) revealed high prevalence of immune-inflamed tumors in gastric cancer. These data contributed to prioritization of these indications for clinical development of pembrolizumab as monotherapy.&lt;/p&gt;Conclusions:&lt;p&gt;Data highlight the value of molecular profiling in identifying populations with high unmet needs with potentially favorable response characteristics and accelerating development of novel therapies for these patients.&lt;/p&gt;&lt;p&gt;&lt;i&gt;See related commentary by Mansfield and Jen, p. 1443&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
Design of Density Clustering In Diabetic Retinopathy Based Eye Fundus Segmentation (2021)

Abstract In order to prevent further complications, we learned in this paper that earlier diagnosis is critical in Diabetic Retinopathy (DR). The disease can be classified into one of two stages (the early stage of non-proliferative and later stage of proliferative diabetic retinopathy) of Eye Fundus Images (EFI), diagnosed on the basis of the presence and quantities of a complex series of lesions such as microaneurysms, haemorrhages or exudates. Therefore it is important to properly segment regions of potential lesions to demonstrate and classify the lesions and the degree of DR. Density clustering approaches are promising candidates for the isolation of individual lesions, and can be used along with effective methods for vascular tree elimination, extraction and classification. In this article, our approach, findings, tradeoffs and assumptions for segmenting and detecting individual lesions are reported.
Gas-Liquid Flows Through Porous Media in Microgravity: The International Space Station Packed Bed Reactor Experiment (2020)

Experimental results on pressure drop and flow patterns for gas-liquid flow through packed beds obtained in the International Space Station with two types of packing are presented and analyzed. It is found that the pressure drop depends on the packing wettability in the viscous-capillary (V-C) regime and this dependence is compared with previously published results developed using short duration low-gravity aircraft tests. Within the V-C regime, the capillary contribution is the dominant force contributing to the pressure drop for the wetting case (glass) versus the viscous contribution dominating for the non-wetting case (Teflon). Outside of the V-C regime, it is also found that hysteresis effects that are often strong in normal gravity gas-liquid flows are greatly diminished in microgravity and pressure drop is nearly independent of packing wettability. A flow pattern transition map from bubble to pulse flow is also compared with the earlier aircraft data.
Identification of a CD40L gene mutation and genetic counselling in a family with immunodeficiency with hyperimmunoglobulinemia M (1995)

A 13-year-old boy with immunodeficiency with hyper-IgM was analyzed for mutations in the CD40L gene. An insertional mutation of an extra T in a run of four T's was found in the second exon of the gene, leading to a premature translation stop. Genetic counselling of the family was performed, based on mutation detection by PCR/oligohybridization.
Is reconfigurable computing commercially viable (panel)? (1997)

Article Is reconfigurable computing commercially viable (panel)? Share on Author: Herman Schmit Carnegie Mellon Univ. Carnegie Mellon Univ.View Profile Authors Info & Claims FPGA '97: Proceedings of the 1997 ACM fifth international symposium on Field-programmable gate arraysFebruary 1997 https://doi.org/10.1145/258305.258318Online:09 February 1997Publication History 0citation263DownloadsMetricsTotal Citations0Total Downloads263Last 12 Months1Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Electro-Thermal Imaging Of Breast Phantom: An Experimental Study (2016)

To increase the temperature contrast in thermal<br> images, the characteristics of the electrical conductivity and thermal<br> imaging modalities can be combined. In this experimental study, it is<br> objected to observe whether the temperature contrast created by the<br> tumor tissue can be improved just due to the current application<br> within medical safety limits. Various thermal breast phantoms are<br> developed to simulate the female breast tissue. In vitro experiments<br> are implemented using a thermal infrared camera in a controlled<br> manner. Since experiments are implemented in vitro, there is no<br> metabolic heat generation and blood perfusion. Only the effects and<br> results of the electrical stimulation are investigated. Experimental<br> study is implemented with two-dimensional models. Temperature<br> contrasts due to the tumor tissues are obtained. Cancerous tissue is<br> determined using the difference and ratio of healthy and tumor<br> images. 1 cm diameter single tumor tissue causes almost 40 °mC<br> temperature contrast on the thermal-breast phantom. Electrode<br> artifacts are reduced by taking the difference and ratio of background<br> (healthy) and tumor images. Ratio of healthy and tumor images show<br> that temperature contrast is increased by the current application.
Antiplatelet and Antithrombotic Activities of Non-Steroidal Anti-Inflammatory Drugs Containing an N-Acyl Hydrazone Subunit (2014)

Nonsteroidal anti-inflammatory drugs (NSAIDs) 1-5 containing an N-acyl hydrazone subunit were prepared and their antiplatelet and antithrombotic activities assessed in vitro and in vivo. Compounds 1-5 inhibited the platelet aggregation induced by adenosine diphosphate and/or arachidonic acid, with inhibition rates of 18.0%-61.1% and 65.9%-87.3%, respectively. Compounds 1 and 5 were the most active compounds, inhibiting adenosine-diphosphate-induced platelet aggregation by 57.2% and 61.1%, respectively. The inhibitory rates for arachidonic-acid-induced platelet aggregation were similar for compound 2 (80.8%) and acetylsalicylic acid (ASA, 80%). After their oral administration to mice, compounds 1, 3, and 5 showed shorter mean bleeding times than ASA. Compounds 1 and 5 also protected against thromboembolic events, with survival rates of 40% and 33%, respectively, compared with 30% for ASA. In conclusion, these results indicate that these novel NSAIDs containing an NAH subunit may offer better antiplatelet and antithrombotic activities than ASA.
Human chromosome 7 circa 2004: a model for structural and functional studies of the human genome (2004)

Human chromosome 7 is arguably amongst the most comprehensively characterized segments of the human genome. By microscopic examination, it belongs to the medium-sized group C submetacentric class, and historical studies involving chromosome-length measurements estimated that it accounts for approximately 5.3% of the human genome (or 160 Mb). Early successes in molecular genetics led to the identification of some of its biomedically important genes, including the T-cell receptor and homeobox families as well as the erythropoietin and cystic fibrosis genes. The Human Genome Project brought chromosome 7-specific and genome-wide initiatives, generating a wealth of genomic resources that have revealed the presence of over 350 disease-associated genes. Two distinct assemblies of the chromosome 7 sequence have been generated-one based largely on mapped large-insert clones and the other based on an integrated whole-genome shotgun sequencing strategy. These two sequences are mainly identical (<1% difference), and both estimate the unit length of chromosome 7 to be just over 158 Mb, remarkably similar to the originally predicted size. Systematic annotation efforts have anchored to the sequence, amongst many features, over 900 known genes and some 1000 other gene structures, as well as over 650 chromosomal breakpoints identified in patients with characterized phenotypic differences. Chromosome 7 has also been shown to contain the highest content of intra-autosomal segmental duplications in the human genome. The orthologous regions of roughly 22 Mb of chromosome 7 are currently being sequenced in multiple other vertebrate species. Examining these comparative sequence data, in conjunction with the other accumulating genomic information about these regions and the rest of the chromosome, should provide a model for the next generation of structural and functional analyses of the human genome.
(s|qu)eries (2015)

Many different domains collect event sequence data and rely on finding and analyzing patterns within it to gain meaningful insights. Current systems that support such queries either provide limited expressiveness, hinder exploratory workflows or present interaction and visualization models which do not scale well to large and multi-faceted data sets. In this paper we present (s|qu)eries (pronounced "Squeries"), a visual query interface for creating queries on sequences (series) of data, based on regular expressions. (s|qu)eries is a touch-based system that exposes the full expressive power of regular expressions in an approachable way and interleaves query specification with result visualizations. Being able to visually investigate the results of different query-parts supports debugging and encourages iterative query-building as well as exploratory work-flows. We validate our design and implementation through a set of informal interviews with data scientists that analyze event sequences on a daily basis.
Optical fiber transmission for QPSK, 16QAM, and Frequency-modulated IF signals (1981)

In microwave radio links, intermediate frequency (IF) signals are used as a signal for intrastation and interequipment connections. As usual, several modulated IF signals are used as shown in Table I, and so the IF signal optical transmission using a laser diode and an LED has been enabled.
FEM Analysis of Friction for Pressing Dies Controlled by Shot Treatment FEM-Analyse der Reibung von kugelgestrahlten Schmiedegesenken (2015)

Kurzfassung The finite element method (FEM) analysis of elastic-plastic deformation was applied to examine the effect of surface tex- ture controlling of dies by means of hybrid-shot (double shot by two different kinds of particles) treatment on the galling property applied to high tensile strength steel sheets. The FEM analysis results showed that the apparent friction coefficient, which was calculated from pressing load and the drawing force, increased with each increase in the pressing load. The experimental results from the drawing tests with lubricant oil showed that the friction coefficient of the die after hybrid-shot treatment decreased slightly with the increase of the pressing load. On the other hand, the friction coefficient of the die wit- hout shot treatment, (i.e. nearly flat surface), slightly increased with the increase of the pressing load due to the digging effect. These findings reveal that the effect of surface texture of dies was caused not only by the elastic-plastic deformation but also by the oil lubrication condition. The FEM analysis was therefo- re performed by taking into account the digging effect as well as the micro-oil pool effect. The experimental result in the case of hybrid-shot dies corresponds well to the FEM result by ad- opting the virtual oil model where the oil segment was defined as an elastic solid body. n
Contrasting effects of Symbiodinium identity on coral host transcriptional profiles across latitudes (2018)

Reef-building corals can increase their resistance to heat-induced bleaching through adaptation and acclimatization and/or by associating with a more thermo-tolerant strain of algal symbiont (Symbiodinium sp.). Here, we show that these two adaptive pathways interact. We collected Acropora millepora corals from two contrasting thermal environments on the Great Barrier Reef: cooler, mid-latitude Orpheus Island, where all corals hosted a heat-sensitive clade C Symbiodinium, and warmer, low-latitude Wilkie Island, where corals hosted either a clade C or a more thermo-tolerant clade D. Corals were kept in a benign common garden to reveal differences in baseline gene expression, reflecting prior adaptation/long-term acclimatization. Model-based analysis identified gene expression differences between Wilkie and Orpheus corals that were negatively correlated with previously described transcriptome-wide signatures of heat stress, signifying generally elevated thermotolerance of Wilkie corals. Yet, model-free analyses of gene expression revealed that Wilkie corals hosting clade C were distinct from Wilkie corals hosting clade D, whereas Orpheus corals were more variable. Wilkie corals hosting clade C symbionts exhibited unique functional signatures, including downregulation of histone proteins and ion channels and upregulation of chaperones and RNA processing genes, putatively representing constitutive "frontloading" of stress response genes. Furthermore, clade C Symbiodinium exhibited constitutive expression differences between Wilkie and Orpheus, indicative of contrasting life history strategies. Our results demonstrate that hosting alternative Symbiodinium types is associated with different pathways of local adaptation for the coral host. These interactions could play a significant role in setting the direction of genetic adaptation to global warming in the two symbiotic partners.
A molecular simulation study of a cyclic siloxane with attached biphehylyl 4-allyloxybenzoate mesogens (1994)

Abstract A molecular simulation study of a cyclic siloxane macromolecule based on a pentamethylcyclosiloxane core and biphenylyl 4-allyloxybenzoate mesogenic units is reported. Molecular dynamics and semi-empirical calculations were used to provide insight into the conformation and the dielectric properties of the material. Out of three proposed conformations of the molecules, a cylindrical conformation was found to be the most probable. The intermolecular interactions were found to be optimized for the case where the mesogenic groups were planar and parallel to each other. The calculated mesogen length and inter-mesogen distances were consistent with available X-ray data. Electrostatic interactions were found to make a very significant contribution to the total energy. For the cylindrical model, the major component of the dipole was calculated to be along the long axis of the molecules. This is consistent with the alignment of the molecules parallel to a low frequency applied electric field as found experimentally.
Critical Evaluation of the Use of Extinction Paradigms for the Assessment of Opioid-Induced Conditioned Place Preference in Rats (2011)

The rewarding effects of drugs of abuse are often studied by means of the conditioned place preference (CPP) paradigm. CPP is one of the most widely used models in behavioral pharmacology, yet its theoretical underpinnings are not well understood, and there are very few studies on the methodological and theoretical aspects of this model. An important drawback of the classical CPP paradigm is that it often does not show dose-dependent results. The persistence of the conditioned response, i.e. the time required until the CPP effect is extinct, may be related to the strength of conditioning, which in turn may be related to the rewarding efficacy of a drug. Resistance to extinction may therefore be a useful additional measure to quantify the rewarding effect of drugs. In the present study we examined the persistence of drug-environment associations after conditioning with morphine (1, 3 and 10 mg/kg i.p.), oxycodone (0.3, 1 and 3 mg/kg i.p.) and heroin (0.05, 0.25 and 0.5 mg/kg i.p.) by repeated retesting in the CPP apparatus (15-min sessions, 5 days/week) until the rats reached extinction (i.e. less than 55% preference over 3 consecutive sessions). Following an unbiased CPP protocol, morphine, oxycodone and heroin induced CPP with minimal effective doses of 3, 1 and 0.25 mg/kg, respectively, and with similar effect sizes for each CPP-inducing dose. The number of sessions required for extinction was positively correlated with the dose of the drug (experiment 1: 18 and 45 sessions for 3 and 10 mg/kg morphine, and 19 and 27 sessions for 1 and 3 mg/kg oxycodone; experiment 2: 12 and 24 sessions for 3 and 10 mg/kg morphine, and 10 and 14 sessions for 0.25 and 0.5 mg/kg heroin). These findings suggest that the use of an extinction paradigm can extend the quantitative assessment of the rewarding effect of drugs - however, within certain limits only. The present paradigm appears to be less suited for comparing the rewarding efficacy of different drugs due to great test-retest variability. Finally, the additional potential gain of information using this paradigm has to be weighed against the considerably large amount of additional time and effort.
Ca 2+ -Induced Apoptosis Through Calcineurin Dephosphorylation of BAD (1999)

The Ca2+-activated protein phosphatase calcineurin induces apoptosis, but the mechanism is unknown. Calcineurin was found to dephosphorylate BAD, a pro-apoptotic member of the Bcl-2 family, thus enhancing BAD heterodimerization with Bcl-xL and promoting apoptosis. The Ca2+-induced dephosphorylation of BAD correlated with its dissociation from 14-3-3 in the cytosol and translocation to mitochondria where Bcl-xL resides. In hippocampal neurons, L-glutamate, an inducer of Ca2+ influx and calcineurin activation, triggered mitochondrial targeting of BAD and apoptosis, which were both suppressible by coexpression of a dominant-inhibitory mutant of calcineurin or pharmacological inhibitors of this phosphatase. Thus, a Ca2+-inducible mechanism for apoptosis induction operates by regulating BAD phosphorylation and localization in cells.
Bacterial survival, lymph node changes, and immunologic responses of cattle vaccinated with standard and mutant strains of Brucella abortus (1992)

Forty-eight cattle were used in 4 experiments; 6-week-old calves in experiments 1-3 (n = 24) and 10-month-old heifers in experiment 4 (n = 24). In experiments 1-3, 7 groups of 3 calves each were inoculated SC with 5 strains of Brucella abortus: virulent strain 2308 (2 groups), vaccine strain 19 (2 groups), and mutant strains RB51. 19 delta 31K, and 19 delta SOD. Sera and lymph node tissues were examined at 2-week intervals for evidence of infection. At postinoculation (PI) week 12, 2 calves in each group were given dexamethasone for 5 days. Calves were then euthanatized and lymphoid tissue, spleen, liver, and bone marrow were examined for evidence of B abortus. Calves given strain 2308 had large numbers of bacteria in their lymph nodes, marked granulomatous lymphadenitis in the deep cortex, and loss of lymphoid cells in superficial cortical areas. In addition, they had high serum antibody titers at PI week 16. Calves given strain 19, or genetic mutants derived from strain 19, cleared bacteria from lymph nodes more rapidly, had less lymphoid destruction, and developed antibody titers that did not persist for 16 weeks. The RB51 strain (rough) was cleared most rapidly from lymphoid tissues and induced serum antibody responses only to the core of the lipopolysaccharide molecule. Treatment of calves with dexamethasone did not cause B abortus to reappear in tissues of any calves, nor did serum antibody titers increase.(ABSTRACT TRUNCATED AT 250 WORDS)
Development of a Porcine Lymph Drainage Model to Study Particle Migration (2018)

<b><i>Background:</i></b> Intra-articular wear particulate migration from the knee joint has been studied in various animal models as well as postmortem in patients who received total knee joint replacement. However, there still exists a need for a simple, yet analogous animal model for tracking the migration of wear debris from the knee joint, especially through the draining lymph nodes. <b><i>Methods and Results:</i></b> To fill this need, a proof-of-concept porcine model was developed for particle migration from the knee joint into the surrounding lymphatic system. Vitreous carbon particles were deposited both intra-articularly and extracapsularly in a bilateral manner to the hind limbs in pigs (<i>n</i> = 6). The regional/draining lymph nodes were qualitatively assessed weekly by a veterinarian by manual palpation to detect any enlargement or change in consistency when compared to the initial assessment before the surgical procedure. At 6 weeks, the draining lymph nodes were harvested and processed for histology. Microscopic evaluation showed carbon particle migration from the knee into 100% of the iliac lymph nodes, 50% of the inguinal lymph nodes, and 0% of the popliteal lymph nodes. <b><i>Discussion:</i></b> Overall, this study established a needed animal model for evaluating carbon particle migration to the draining lymph nodes from the knee joint.