gebhart/patrepeval huggingface dataset:
Association of response to programmed death 1 receptor or ligand (PD1/PDL1) blockade with immune-related gene expression profiling across three cancer-types. (2016)

3038 Background: Anti-PD1/PDL1 drugs show consistent activity across various solid tumors. However, a substantial proportion of patients show primary resistance, and those who benefit do not benefit to the same extend. Here, we explored the predictive ability of immune-related gene expression in advanced lung cancer, head and neck and melanoma. Methods: Treatment-naive (n = 45) or pre-treated (n = 31) tumor samples from 76 patients with lung non-squamous (n = 28), squamous cell lung cancer (n = 20), head and neck (n = 5) and melanoma (n = 23) were evaluated. RNA from formalin-fixed paraffin-embedded tissue sections was analyzed using the NanoString PanCancer Immune Panel (730 genes). Patients were treated with pembrolizumab (n = 35), nivolumab (n = 28) or atezolizumab (n = 13). All genes, and 16 immune cell-type signatures, were linked to response and progression-free survival (PFS). Logistic regression models for overall response rate (ORR; defined as partial or complete response at 6-8 weeks) and non-progressive rate (NPR; non-progressive vs. progressive disease at 6-8 weeks), and Cox models for PFS, were used. Results: The ORR and NPR were 32.9% and 61.8%, respectively. Median PFS was 5.57 months (3.20-7.67). No gene was found significantly associated with ORR (False Discovery Rate [FDR] < 5%). Expression of 374 genes, including PD1 and PDL1, was found significantly associated with NPR (FDR = 0%). Six signatures (T-cells, CD8-T cells, NK-cells, CD4-activated, T-regulated and Th1-cells) showed significant associations with both NPR and PFS. The median PFS of the Th1-cells high-tertile group was 12.3 months compared to 2.6 months of the Th1-cells low-tertile group (hazard ratio = 0.26, 0.10-0.65,P= 0.004). These associations were independent of sample timing, drug used or cancer-type. Conclusions: Expression of immune-related genes in tumor samples identifies patients likely to have primary resistance to anti-PD1/PDL1 monotherapy. Results are consistent with the hypothesis that identification of a preexisting and stable adaptive immune response predicts clinical outcome regardless of cancer-type or anti-PD1/PDL1 inhibitor.
Nonlinear optical absorption of antimony and lead oxyhalide glasses (2002)

Nonlinear optical properties and optical limiting behavior of antimony and lead oxyhalide glasses were studied using laser pulses of 80 ps at 532 nm. The standard Z-scan technique was used to determine large nonlinear absorption coefficients which range from 11 to 20 cm/GW, using intensities of 100 MW/cm2. Photodarkening was observed when intensities larger than ≈200 MW/cm2 were incident on the samples.
The Captured Retroviral Envelope syncytin-A and syncytin-B Genes Are Conserved in the Spalacidae Together with Hemotrichorial Placentation1 (2014)

Syncytins are fusogenic envelope (env) genes of retroviral origin that have been captured for a function in placentation. Multiple independent events of syncytin gene capture were found to have occurred in primates, rodents, lagomorphs, carnivores, and ruminants. In the mouse, two syncytin-A and -B genes are present, which trigger the formation of the two-layered placental syncytiotrophoblast at the maternal-fetal interface, a structure classified as hemotrichorial. Here, we identified syncytin-A and -B orthologous genes in the genome of all Muroidea species analyzed, thus dating their capture back to about at least 40 million years ago, with evidence that they evolved under strong purifying selection. We further show, in the divergent Spalacidae lineage (blind mole rats [Spalax]), that both syncytins have conserved placenta-specific expression, as revealed by RT-PCR analysis of a panel of Spalax galili tissues, and display fusogenic activity, using ex vivo cell-cell fusion assays. Refined analysis of the placental architecture and ultrastructure revealed that the Spalax placenta displays a hemotrichorial organization of the interhemal membranes, as similarly observed for other Muroidea species, yet with only one trophoblastic cell layer being clearly syncytialized. In situ hybridization experiments further localized syncytin transcripts at the level of these differentiated interhemal membranes. These findings argue for a role of syncytin gene capture in the establishment of the original hemotrichorial placenta of Muroidea, and more generally in the diversity of placental structures among mammals.
Phylogenetic position of Petrospongium rugosum (Ectocarpales, Phaeophyceae) : insights from the protein-coding plastid rbcL and psaA gene sequences (2006)

L'algue brune crustacee et spongieuse Petrospongium rugosum (Okamura) Setchell et Gardner est presente en Coree, au Japon, en Australie, en Nouvelle-Zelande et le long de la cote Pacifique de l'Amerique du Nord. Bien que cette espece ait ete placee dans les Chordariaceae, au sein des Ectocarpales sensu lato, ou dans la famille des Leathesiaceae, dans les Chordariales sensu stricto, ses relations avec les autres lignees d'algues brunes a ete peu etudiee en termes d'ultrastructure plastidiale et de phylogenie moleculaire. Nous avons examine la morphologie de P. rugosum et determine les sequences des genes psaA et rbcL a partir de quatre recoltes provenant de differentes localites. Nous avons compare les sequences avec celles, homologues, d'especes supposees proches et nouvellement sequencees (Leathesia difformis et Spermatochnus paradoxus), ainsi qu'avec des sequences publiees d'autres algues brunes. L'espece croit dans la zone interdidale superieure des cotes du sud de la Coree, de novembre a juin. Les thalles sont nettement rugueux et formes de filaments haplostiques, disposes en couches corticales et medullaires. Les sporocystes uniloculaires sont produits lateralement a partir des cellules inferieures des couches corticales. Un gros pyrenoide pedoncule, recouvert d'un sac pyrenoidien, est present dans les plastes parietaux discoides. Les sequences rbcL et psaA des specimens provenant des quatre localites differentes sont presque identiques ; ces specimens forment un groupe monophyletique. Toutes les analyses phylogenetiques des deux genes montrent que P. rugosum est nettement separe de Leathesia et des autres membres des Chordariaceae. Petrospongium est taxon frere d'Ectocarpus mais cette relation n'est soutenue ni par les valeurs de bootstrap ni par les analyses bayesiennes.
1357. Intraperitoneal Therapy of Ovarian Cancer Using an Engineered Measles Virus (2002)

The use of replicating viruses for cancer therapy (virotherapy) holds much promise. We reported previously that the live attenuated Edmonston B vaccine strain of measles virus (MV-Edm) had antineoplastic efficacy against hematological malignancies. In this study, we demonstrate that a recombinant MV-Edm, genetically engineered to express an inert soluble marker peptide (MV-hCEA), is potent against human epithelial ovarian cancer cells in vitro and in vivo. The virus was selectively oncolytic for ovarian tumor cells but caused minimal cytopathic damage on nontransformed ovarian surface epithelium and mesothelium. In contrast to nontransformed cells, the ovarian tumor cells expressed high levels of the measles virus receptor CD46. When injected directly into large established s.c. SKOV3ip.1 human epithelial ovarian xenografts in athymic mice, the virus induced complete regression of 80% of the tumors. i.p. administration of virus enhanced the median survival of mice with advanced i.p. SKOV3ip.1 tumors by >50 days. In addition, we could easily follow the kinetic profile of viral gene expression in the treated mice by determining serum levels of the virally encoded marker peptide (soluble human carcinoembryonic antigen). Trackable recombinant measles viruses warrant further investigation for therapy of ovarian cancer.
Microbial ureases: significance, regulation, and molecular characterization (1989)

Microbial ureases hydrolyze urea to ammonia and carbon dioxide. Urease activity of an infectious microorganism can contribute to the development of urinary stones, pyelonephritis, gastric ulceration, and other diseases. In contrast to these harmful effects, urease activity of ruminal and gastrointestinal microorganisms can benefit both the microbe and host by recycling (thereby conserving) urea nitrogen. Microbial ureases also play an important role in utilization of environmental nitrogenous compounds and urea-based fertilizers. Urease is a high-molecular-weight, multimeric, nickel-containing enzyme. Its cytoplasmic location requires that urea enter the cell for utilization, and in some species energy-dependent urea uptake systems have been detected. Eucaryotic microorganisms possess a homopolymeric urease, analogous to the well-studied plant enzyme composed of six identical subunits. Gram-positive bacteria may also possess homopolymeric ureases, but the evidence for this is not conclusive. In contrast, ureases from gram-negative bacteria studied thus far clearly possess three distinct subunits with Mrs of 65,000 to 73,000 (alpha), 10,000 to 12,000 (beta), and 8,000 to 10,000 (gamma). Tightly bound nickel is present in all ureases and appears to participate in catalysis. Urease genes have been cloned from several species, and nickel-containing recombinant ureases have been characterized. Three structural genes are transcribed on a single messenger ribonucleic acid and translated in the order gamma, beta, and then alpha. In addition to these genes, several other peptides are encoded in the urease operon of some species. The roles for these other genes are not firmly established, but may involve regulation, urea transport, nickel transport, or nickel processing.
Ageing fears and concerns of gay men aged 60 and over (2016)

Purpose – In light of the fact that the “baby boomer” generation is moving into early old age, the purpose of this paper is to examine what aspects of ageing and old age concerned an age cohort of 25 gay men aged 60 plus. Design/methodology/approach – The primary data for this paper came from interviews with 25 men aged 60 and older who were recruited in Auckland, London, Manchester, Melbourne, and New York. Interviewees were contacted by a variety of means, such as by e-mail introductions, advertisements placed on social media, and recommendations of mutual friends or acquaintances. Once contacted, the men were sent a plain-language statement outlining the purpose of the study and the intention to publish the results and were asked to sign and return a consent form. Narrative identity was central to understandings of the men’s lives got from analysing their interview transcripts. Findings – Analysis of extracts from their life stories showed the men interviewed for this paper drew on two principal narratives when discussing their apprehensions about growing old. The first related to general fears or concerns about old age that would be fairly common among members of the general population. The second narrative related to gay-specific fears or concerns. Significant claims: that class affects gay men’s experience of old age just as it does for everyone else; and that fears of being ostracised because of their sexuality were strongest when the men spoke about aged-accommodation settings. Research limitations/implications – More research is needed on gay men’s experience of in-home supported care and residential care to see if the reality of the heterosexism and/or homophobia matches the fears of some in this sample. Originality/value – This is a relatively new field and there is a growing number of researchers examining the ageing concerns and experiences of the GLBT population. The originality of this paper lies in the international sample on which it is based, its use of narrative analysis, and its relevance to policy makers as well as to members of the GLBT population, carers, and owners/managers of aged-care accommodation facilities.
An architecture for flexible auto-tuning: The Periscope Tuning Framework 2.0 (2016)

Due to the complexity and diversity of new parallel architectures, automatic tuning of parallel applications has become increasingly important for achieving acceptable performance levels, as well as performance portability. The European AutoTune project developed a tuning framework that closely integrates and automates performance analysis and performance tuning. The Periscope Tuning Framework (PTF) relies on a flexible plugin mechanism and provides tuning plugins for various different tuning aspects. Each plugin provides codified expert knowledge for performance or energy efficiency tuning. PTF is able to tune serial and parallel codes for homogeneous and heterogeneous target hardware. The output of the framework is tuning recommendations that can be integrated into the production version of the code. In this paper, we present the latest development in the design of PTF aiming at (1) achieving higher portability and scalability by using the Score-P measurement infrastructure, (2) extending Score-P with tuning capabilities, (3) increasing analysis capabilities by providing new analysis strategies, and (4) increasing tuning capabilities by providing new plugins.
Estimating the environmental profile of early design concepts for an electric fruit juicer using the Eco-PaS methodology (2005)

status: Published
Methods of Optimal Lyapunov Function Generation with Application to Power Electronic Converters and Systems (2007)

Stability is an important design consideration in power electronics systems. To this end, it is often of interest to predict the region of attraction (ROA) associated with a stable equilibrium point. In the case of the presence of constraints that need to be satisfied, one is faced with the problem of estimating a restricted ROA (RROA). Recently practical methods for estimating RROAs have been proposed for relatively high order systems. In this paper, a proposal is set forth for the problem of finding a Lyapunov function that yields an estimated restricted region of attraction that is close to the true restricted region of attraction. Numerical examples illustrate the proposed methods.
Pteridines, LXXXIV. Synthesis, reactivity and properties of 1,3‐dimethyllumazine‐6‐ and 7‐carboxaldehyde derivatives (1987)

Abstract Convenient syntheses of 1,3‐dimethyllumazine‐6‐ (7) and ‐7‐carboxaldehyde ( 19 ) are described. The reactivity of the carboxaldehyde group has been investigated by oxidations, reductions and various carbonyl reactions forming a series of new derivatives. The newly synthesized compounds were characterized by elemental analysis, uv and 1 H‐nmr spectra.
Paying Attention to Descriptions Generated by Image Captioning Models (2017)

To bridge the gap between humans and machines in image understanding and describing, we need further insight into how people describe a perceived scene. In this paper, we study the agreement between bottom-up saliency-based visual attention and object referrals in scene description constructs. We investigate the properties of human-written descriptions and machine-generated ones. We then propose a saliency-boosted image captioning model in order to investigate benefits from low-level cues in language models. We learn that (1) humans mention more salient objects earlier than less salient ones in their descriptions, (2) the better a captioning model performs, the better attention agreement it has with human descriptions, (3) the proposed saliency-boosted model, compared to its baseline form, does not improve significantly on the MS COCO database, indicating explicit bottom-up boosting does not help when the task is well learnt and tuned on a data, (4) a better generalization is, however, observed for the saliency-boosted model on unseen data.
The role of co-infections and secondary infections in patients with COVID-19 (2021)

The current review describes varying rates of co-infections and/or superinfections in patients with COVID-19 infections, although often a clear distinction between the two is not clear in the literature. When they occur, these infections appear to be associated with both severity of COVID-19 as well as poorer outcomes.
Graphene nanosheet: synthesis, molecular engineering, thin film, hybrids, and energy and analytical applications (2011)

The emergence of graphene nanosheet (GN, 2010 Nobel Prize for Physics) has recently opened up an exciting new field in the science and technology of two-dimensional (2D) nanomaterials with continuously growing academic and technological impetus. GN exhibits unique electronic, optical, magnetic, thermal and mechanical properties arising from its strictly 2D structure and thus has many important technical applications. Actually, GN-based materials have enormous potential to rival or even surpass the performance of carbon nanotube-based counterparts, given that cheap, large-scale production and processing methods for high-quality GN become available. Therefore, the studies on GN in the aspects of chemistry, physical, materials, biology and interdisciplinary science have been in full flow in the past five years. In this critical review, from the viewpoint of chemistry and materials, we will cover recent significant advances in synthesis, molecular engineering, thin film, hybrids, and energy and analytical applications of the "star-material" GN together with discussion on its major challenges and opportunities for future GN research (315 references).
Recent advances in rechargeable zinc-air battery technology (2002)

AER Energy's battery development effort is focused on improving the zinc-air rechargeable battery system to serve the portable computer market. Therefore system attributes such as energy density, power, life, form factor, environmental impact and safety are areas of active investigation. The battery system consists of cells in series, an air manager housing and an electronic control system for battery charge termination. This paper reviews recent developments in each of these areas that have contributed to the enhanced performance of the zinc-air system for the target market.
Electrical stimulation enhances cellular/molecular functions of osteoblasts relevant to new bone formation in vitro (2005)

The present study applied electrical stimulation to osteoblasts in vitro and provided cellular/molecular evidence that alternating current electrical stimulation promotes various important, osteoblast functions, such as cell proliferation, expression of genes for collagenous and non-collagenous proteins, and calcium deposition in the extracellular matrix. These functions are responsible for the chemical composition of the organic and inorganic phases of the bone matrix and are required for new bone formation in vivo. Moreover, such functions have major consequences for bone repair, healing, and regeneration and may be responsible for the accelerated bone healing observed in animal models under electrical stimulation. The present in vitro research exemplifies the use of biophysical stimuli and alternative strategies for enhancing osteoblast functions which, although extremely promising, remain as yet unexplored for bone regeneration purposes in either clinical or tissue engineering applications.
SONIC DETERRENTS IN ANIMAL DAMAGE CONTROL: A REVIEW OF DEVICE TESTS AND EFFECTIVENESS (1990)

Sonic devices are promoted as scientifically sound, humane, inexpensive, and simple to operate. The manufacture and sale of sonic devices intended to control damage by animals is a large industry, which included 51 manufacturers of ultrasonic devices and sales of $17 million in the United States in 1982 (Mix 1984). Consumer spending on sonic devices is increasing (Mix 1984), but the legality of selling untested devices is being questioned, and some companies in the United States have been ordered to refund consumers who purchased ineffective devices (W. D. Fitzwater. 1987. Natl. Anim. Damage Control Assoc., The Probe 71: 7). Frings and Frings (1967:397) noted, For every one of the noise-producing devices, there are experts offering it as the best available for bird control, and at the same time others finding it of low value. Their statement continues to accurately reflect the situation. Few experiments have been designed to test sonic devices and most publications on this subject describe field trials or demonstrations, rather than adequately controlled and replicated experiments. Our purposes are to review the mechanisms by which sonic devices may affect animals, review published evaluations and identify effective tests, discuss design requirements for effective tests of sonic devices, and draw conclusions about the efficacy of sonic devices for animal damage control.
Single-photon excitation ofKαin heliumlikeKr34+: Results supporting quantum electrodynamics predictions (2015)

We study two fundamental transitions from the ground state $^{1}S_{0}$ to $^{1}P_{1}$ ($w$ line) and $^{3}P_{1}$ ($y$ line) in heliumlike ${\mathrm{Kr}}^{34+}$ by resonant single-photon excitation using an electron-beam ion trap and monochromatic x rays at PETRA III. Our results for the transition energies $E(w)=13\phantom{\rule{0.16em}{0ex}}114.47(14)$ eV and $E(y)=13\phantom{\rule{0.16em}{0ex}}026.15(14)$ eV are in excellent agreement with quantum electrodynamics calculations, but disagree for $w$ with the average of the hitherto reported experimental results ${\overline{E}}_{\mathrm{Lit}}(w)=13\phantom{\rule{0.16em}{0ex}}115.15(17)$ eV. Independently of any energy calibration, we obtain a value $E(w)/E(y)=1.006\phantom{\rule{0.16em}{0ex}}780(7)$, also in consistency with predictions.
Comparison of weights in prestack amplitude-preserving Kirchhoff depth migration (1997)

Abstract Three different theoretical approaches to amplitude-preserving Kirchhoff depth migration are compared. Each of them suggests applying weights in the diffraction stack migration to correct for amplitude loss resulting from geometric spreading. The weight functions are given in different notations, but as is shown, all of these expressions are similar. A notation that is well suited for implementation is suggested: entirely in terms of Green's function quantities (amplitudes or point-source propagators). For the most common prestack configurations (common-shot and common-offset) and 3-D, 2.5-D, and 2-D migrations, expressions of the weights are given in this notation. The quantities needed for calculation of the weights can be computed easily, e.g., by dynamic ray tracing.
Grafted organic derivatives of kaolinite: II. Intercalation of primary n-alkylamines and delamination (2005)

Abstract Kaolinite was intercalated with n-hexylamine, n-octadecylamine and n-docosanamine, using methanol-kaolinite as the precursor. The intercalation compound with n-docosanamine presented the largest basal spacing for a kaolinite derivative thus far reported (64.2 Å). Five grafted derivatives of kaolinite were directly intercalated with n-hexyl- and n-octadecylamine. During intercalation, the grafted molecules rearrange from parallel to perpendicular orientation to the kaolinite surface, in order to maximize the interaction with the amine and minimize the interlayer expansion needed. The octadecylamine intercalation compounds were delaminated in toluene, accompanied by the deintercalation of the amine molecules. Thin kaolinite particles rolled into a halloysite-like morphology, but forming much smaller tubes, some of which possibly consist of single kaolinite layers. The delamination was more efficient with the grafted kaolinites than with raw kaolinite.