gebhart/patrepeval huggingface dataset:
The PERK Arm of the Unfolded Protein Response Negatively Regulates Transmissible Gastroenteritis Virus Replication by Suppressing Protein Translation and Promoting Type I Interferon Production (2018)

Coronavirus replication is closely associated with the endoplasmic reticulum (ER), the primary cellular organelle for protein synthesis, folding, and modification. ER stress is a common consequence in coronavirus-infected cells. However, how the virus-induced ER stress influences coronavirus replication and pathogenesis remains controversial. Here, we demonstrated that infection with the alphacoronavirus transmissible gastroenteritis virus (TGEV) induced ER stress and triggered the unfolded protein response (UPR) <i>in vitro</i> and <i>in vivo</i>, and ER stress negatively regulated TGEV replication <i>in vitro</i> Although TGEV infection activated all three UPR pathways (activating transcription factor 6 [ATF6], inositol-requiring enzyme 1 [IRE1], and protein kinase R-like ER kinase [PERK]), the virus-triggered UPR suppressed TGEV replication in both swine testicular (ST) and IPEC-J2 cells primarily through activation of the PERK-eukaryotic initiation factor 2α (eIF2α) axis, as shown by functional studies with overexpression, small interfering RNA (siRNA), or specific chemical inhibitors. Moreover, we demonstrated that PERK-eIF2α axis-mediated inhibition of TGEV replication occurs through phosphorylated eIF2α-induced overall attenuation of protein translation. In addition to direct inhibition of viral production, the PERK-eIF2α pathway activated NF-κB and then facilitated type I IFN production, resulting in TGEV suppression. Taken together, our results suggest that the TGEV-triggered PERK-eIF2α pathway negatively regulates TGEV replication and represents a vital aspect of host innate responses to invading pathogens.<b>IMPORTANCE</b> The induction of ER stress is a common outcome in cells infected with coronaviruses. The UPR initiated by ER stress is actively involved in viral replication and modulates the host innate responses to the invading viruses, but these underlying mechanisms remain incompletely understood. We show here that infection with the alphacoronavirus TGEV elicited ER stress <i>in vitro</i> and <i>in vivo</i>, and the UPR PERK-eIF2α branch was predominantly responsible for the suppression of TGEV replication by ER stress. Furthermore, the PERK-eIF2α axis inhibited TGEV replication through direct inhibition of viral proteins due to global translation inhibition and type I IFN induction. These findings highlight a critical role of the UPR PERK-eIF2α pathway in modulating host innate immunity and coronavirus replication.
Accurate atomic momentum integrals and Compton profiles (2020)

Abstract Analytical expressions for integrals involving momentum density have been developed, and an algorithm for the efficient computation of Compton profiles (CPs) based in those equations is reported. The performance of the algorithm is tested by computing the CPs of atoms from helium to xenon for a wide range of incident photon energies. Calculations have been made at Hartree–Fock level (HF), using three different Slater basis sets, showing a good agreement with the experimental results.
Chlorpropamide-induced pure white cell aplasia (1987)

We investigated the mechanism for isolated agranulocytosis and marrow pure white cell aplasia in an elderly man receiving 0.5 to 1.0 g per day of chlorpropamide (Chl) without other toxic drug exposure or overt systemic illness. Patient marrow revealed an absence of recognizable granulocytic precursors; megakaryocytes and erythroid precursors were normal. The WBC count was 1800/mm3 on admission with only 2% neutrophils; the absolute neutrophil count first exceeded 500/mm3 on the 17th day following cessation of Chl. A serum Chl level on admission was 100 micrograms/mL (acute phase, AP); no Chl was detected in serum (convalescent phase, CP) assessed on the 22nd hospital day. Antineutrophil antibodies were not detected, and T cell depletion failed to augment patient in vitro granulopoiesis. Patient AP serum produced potent complement-mediated inhibition (87% +/- 7%) of autologous granulocyte progenitors (CFU-GM) with minimal inhibition of erythroid (11% +/- 5%) or multipotent (5% +/- 4%) progenitor cells. Selective inhibition by patient AP serum of CFU-GM (74% +/- 11%) was also seen against two allogeneic marrows. Patient CP serum no longer inhibited (6% +/- 4%) autologous CFU-GM. Addition of Chl (5 to 120 micrograms/mL) to CP serum but not to control serum resulted in potent drug concentration-dependent complement-mediated inhibition of autologous and allogeneic CFU-GM. Inhibition of CFU-GM in the presence of Chl was no longer demonstrable following immunoabsorbent removal of IgG from patient serum. Patient serum in the presence of Chl had limited activity against morphologically recognizable marrow granulocytic precursors in a microimmunofluorescence assay. These results are most consistent with the development of Chl-dependent, selective antibody-mediated immune inhibition of granulopoiesis.
Contextualized Sparse Representations for Real-Time Open-Domain Question Answering (2020)

Open-domain question answering can be formulated as a phrase retrieval problem, in which we can expect huge scalability and speed benefit but often suffer from low accuracy due to the limitation of existing phrase representation models. In this paper, we aim to improve the quality of each phrase embedding by augmenting it with a contextualized sparse representation (SPARC). Unlike previous sparse vectors that are term-frequencybased (e.g., tf-idf) or directly learned (only few thousand dimensions), we leverage rectified self-attention to indirectly learn sparse vectors in n-gram vocabulary space. By augmenting the previous phrase retrieval model Our CuratedTREC score is even better than the best known retrieve & read model with at least 45x faster inference speed. 1
Performance of Electro-Active Papers Made with Cellulose and Multi-Walled Carbon Nanotubes (2006)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
X-Ray reflectivity of fibonacci multilayers (1995)

We have numerically computed the reflectivity of X-rays incident normally onto Fibonacci multilayers, and compared the results with those obtained in periodic approximant multilayers. The constituent layers are of low and high refractive indices with the same thickness. Whereas the reflectivity of periodic approximant multilayers changes only slightly with increasing the number of layers, Fibonacci multilayers present a completely different behaviour. In particular, we have found a highly fragmented and self-similar reflectivity pattern in Fibonacci systems. The behaviour of the fragmentation pattern on increasing the number of layers is quantitatively described using multifractal techniques. We end with a brief discussion on possible practical applications of our results in the design of new X-ray devices.
Pillared Smectite Clay Coatings for Ceramic‐Matrix Composites (1995)

This paper describes a novel route for the low‐temperature formation of mullite, from pillared smectite clay precursors, for use as fiber coatings in ceramic‐matrix composites. In particular, alumina‐pillared bentonite converts in part to mullite at the unusually low temperature of about 800°C. The clay precursors display excellent film‐forming capability and have been coated onto silicon carbide fibers. Mechanical tests on composites of the coated fibers and a borosilicate glass demonstrate their success as debond coatings, suggesting that this approach is a viable and simple route to oxide coatings for fibers.
Characterizing the change from casual to careful style in spontaneous speech. (1991)

An examination has been carried out to determine which elements speakers use when changing style from casual to careful speech in a dialog situation. If automatic characterization of what an individual chooses to use to be more clearly understood can be achieved, benefits for speech synthesizers would include clearer and more natural speech. The present study uses data collected in a ‘‘spontaneous’’ situation, where 12 subjects each had two scenarios to act out with a ‘‘Wizard’’ partner guiding the course of the dialog. At two crucial points, the Wizard pretended not to be able to hear the subject, saying ‘‘comment?’’ (‘‘what?’’). The subject’s exchanges just before and after the Wizard’s interjection were compared. Acoustic (voicing and formants, for example), phonological (number of segments and reduction phenomena), and prosodic (especially intensity and duration) elements have been examined. Results show which of these are modified when the change of style occurs. The study underlines the fact that the choice of elements is not the same for all speakers; individuals and groups of individuals use different strategies to arrive at their own versions of careful speech.
ChemInform Abstract: FRIEDEL‐CRAFTS SUBSTITUTION OF 3H‐PYRROLIZINE AND THE RING OPENING OF 5‐(TRICHLOROACETYL)‐3H‐PYRROLIZINE (1982)

Abstract Pyrrolizin (I) reagiert mit Acetyl‐ bzw. Trichloracetylchlorid in Gegenwart von Zn unter Bildung der Ketone (IIa) bzw. (IIb) und (III) [oder (IV); beim Ersatz von Zn durch K 2 CO 3 steigt die Ausb. an (IIb) auf 84%] und setzt sich mit Dichloracetylchlorid zu (V) um.
Bradykinin is a potent pruritogen in atopic dermatitis: A switch from pain to itch (2006)

Histamine, substance P, serotonin and bradykinin were applied by iontophoresis to lesional and visually non-lesional skin of 14 patients with atopic dermatitis, and normal skin of 15 healthy volunteers. Itch could be evoked by light stroking of skin with a cotton swab (alloknesis) in all lesional skin sites, but not in non-lesional or normal skin. Substances were applied in the same skin area before and 3 h after administration of placebo or antihistamine (olopatadine hydrochloride: H1-receptor-blocker). Intensities of itch and pain sensation and areas of flare and wheal were measured. All the substances induced significantly more intense itch in lesional skin than in non-lesional skin of patients. Even bradykinin, which evoked only weak itch and pain of similar intensities in non-lesional skin of patients and in healthy volunteers, induced intense itch in lesional skin, while the simultaneously increased pain did not suppress the itch sensation, indicating central sensitization. Histamine- and substance P-induced itch was almost completely suppressed by antihistamines, whereas bradykinin- and serotonin-induced itch was not. This suggests that substance P is a histamine-dependent pruritogen also in lesional skin under sensitized conditions but that bradykinin and serotonin are histamine-independent pruritogens in lesional skin. It is concluded that serotonin and bradykinin, classic endogenous algogens, can turn into potent histamine-independent pruritogens in lesional skin of atopic dermatitis.
The Partner Gene of AML1 in t(16;21) Myeloid Malignancies Is a Novel Member of the MTG8(ETO) Family (1998)

The t(16;21)(q24;q22) translocation is a rare but recurrent chromosomal abnormality associated with therapy-related myeloid malignancies and a variant of the t(8;21) translocation in which the AML1 gene on chromosome 21 is rearranged. Here we report the molecular definition of this chromosomal aberration in four patients. We cloned cDNAs from the leukemic cells of a patient carrying t(16;21) by the reverse transcription polymerase chain reaction using an AML1-specific primer. The structural analysis of the cDNAs showed that AML1 was fused to a novel gene named MTG16 (Myeloid Translocation Gene on chromosome 16) which shows high homology to MTG8 (ETO/CDR) and MTGR1. Northern blot analysis using MTG16 probes mainly detected 4.5 kb and 4.2 kb RNAs, along with several other minor RNAs in various human tissues. As in t(8;21), the t(16;21) breakpoints occurred between the exons 5 and 6 of AML1, and between the exons 1 and 2 or the exons 3 and 4 of MTG16. The two genes are fused in-frame, resulting in the characteristic chimeric transcripts of this translocation. Although the reciprocal chimeric product, MTG16-AML1, was also detected in one of the t(16;21) patients, its protein product was predicted to be truncated. Thus, the AML1-MTG16 gene fusion in t(16;21) leukemia results in the production of a protein that is very similar to the AML1-MTG8 chimeric protein.
A high resolution bathymetric map of Lake Kivu's northern basin: locating significant groundwater inflows through a geomorphologic interpretation (2012)

Keywords: - Abteilung_SURF_2012; - Abteilung_SURF Note: 06866 Reference EPFL-CONF-187306 URL: http://www.swisssed.ch; Record created on 2013-06-28, modified on 2016-08-09
Infectious subvirion particles of reovirus type 3 Dearing exhibit a loss in infectivity and contain a cleaved sigma 1 protein (1995)

Mammalian reoviruses exhibit differences in the capacity to grow in intestinal tissue: reovirus type 1 Lang (T1L), but not type 3 Dearing (T3D), can be recovered in high titer from intestinal tissue of newborn mice after oral inoculation. We investigated whether in vitro protease treatment of virions of T1L and T3D, using conditions to generate infectious subvirion particles (ISVPs) as occurs in the intestinal lumen of mice (D. K. Bodkin, M. L. Nibert, and B. N. Fields, J. Virol. 63:4676-4681, 1989), affects viral infectivity. Chymotrypsin treatment of T1L was associated with a 2-fold increase in viral infectivity, whereas identical treatment of T3D resulted in a 10-fold decrease in infectivity. Using sodium dodecyl sulfate-polyacrylamide gel electrophoresis, we found that loss of T3D infectivity was correlated with cleavage of its sigma 1 protein. We used reassortant viruses to identify viral determinants of infectivity loss and sigma 1 cleavage and found that both phenotypes segregate with the sigma 1-encoding S1 gene. Comparable results were obtained when trypsin treatment of virions of T1L and T3D was used. In experiments to determine the fate of sigma 1 fragments following cleavage, the capacity of anti-sigma 1 monoclonal antibody G5 to neutralize infectivity of T3D ISVPs was significantly decreased in comparison with its capacity to neutralize infectivity of virions, suggesting that a sigma 1 domain bound by G5 is lost from viral particles after proteolytic digestion. In contrast to the decrease in infectivity, chymotrypsin treatment of T3D virions leading to generation of ISVPs resulted in a 10-fold increase in their capacity to produce hemagglutination, indicating that a domain of sigma 1 important for binding to sialic acid remains associated with viral particles after sigma 1 cleavage. Neuraminidase treatment of L cells substantially decreased the yield of T3D ISVPs in comparison with the yield of virions, indicating that a sigma 1 domain important for binding sialic acid also can mediate attachment of T3D ISVPs to L cells and lead to productive infection. These results suggest that cleavage of T3D sigma 1 protein following oral inoculation of newborn mice is at least partly responsible for the decreased growth of T3D in the intestine and provide additional evidence that T3D sigma 1 contains more than a single receptor-binding domain.
Sketching and Layering Graffiti Primitives (2019)

We present a variant of the skeletal strokes algorithm aimed at mimicking the appearance of hand made graffiti art. It includes a unique fold-culling process that stylizes folds rather than eliminating them. We demonstrate how the stroke structure can be exploited to generate non-global layering and self-overlap effects like the ones that are typically seen in graffiti art and other related art forms like traditional calligraphy. The method produces vector output with no artificial artwork splits, patches or masks to render the non-global layering; each path of the vector output is part of the desired outline. The method lets users interactively generate a wide variety of stylised outputs.
EFFECT OF DONOR AGE ON OUTCOME OF KIDNEY TRANSPLANTATION (1994)

The shortage of cadaveric donors coupled with a rapidly growing number of potential recipients has resulted in an increased use of older donors. In 1992, 10.7% of all cadaveric kidney transplants were from donors above the age of 55 compared with 5.4% in 1988. The present investigation serves as a follow-up of a prior study of the effect of donor age on outcome with a 2-year analysis of more than 30,000 cadaveric kidney transplants performed in the United States between October 1, 1987, and December 31, 1991, that were reported to the United Network for Organ Sharing. There was no difference between the graft survival at 1 and 2 years comparing donors aged 56–65 versus 65 and older, but the older donors (aged 56 and greater) had a 1− and 2-year graft survival that was approximately 10% and 14% less than that for recipients from the ideal age group of donors (16–45 years). There was no practical adverse interaction between donor age and recipient age, gender, diabetic status, peak PRA (panel reactive antibody activity) level of mismatch, cold ischemia time, or recipient race on outcome. The kidneys from older donors had poorer graft survival than the kidneys from younger donors when transplanted into recipients of repeat transplants, though the impact of repeat transplant and donor age on graft survival are independent of one another. These data suggest that kidneys from donors over the age of 55 overall have reduced functional reserve, which has an adverse effect on long-term function. Thus, attempts should be made to better estimate functional reserve among the older age group, but age alone should not be the sole factor for exclusion of a potential donor. The use of older donors appears to present an increased but acceptable risk of graft loss 2 years after transplant.
Open mastoid procedures: Contemporary indications and surgical technique (1985)

Abstract The history of the management of chronic ear disease with and without cholesteutoma is dominated by a canal wall down philosophy. The implication is that such an open procedure insures disease control and an uncomplicated future. In point of fact, problem canal wall down procedures can be fraught with as many seríous complications as their more controversial canal wall up counterpart is alleged to propagute. Such problem cavities most commonly result from poor execution of basic technique. The objective of this paper is to identify what constitutes a problem cavity and to describe the authors' techniques to avoid such difficulties. A technique has evolved which not only eradicates disease, but which is self‐cleansing and of minimal impact on the patient's lifestyle. The authors' experience with canal wall down procedures is reviewed.
Noise and distortion characteristics of semiconductor lasers in optical fiber communication systems (1982)

The distortion and noise characteristics of semiconductor lasers in connection with optical fibers are reviewed. In particular, the intrinsic distortions and noise of semiconductor lasers together with the partition noise are discussed followed by a discussion on the influence of reflections. Modal noise phenomena due to the interference pattern at the endface of optical fibers are treated with respect to noise and distortions. Finally, the influence of polarization coupling in single-mode fibers on the resulting transmission behavior is discussed.
A Second Look at the Fresh Frozen Plasma: Packed Red Blood Cell Ratio in Massive Transfusion Protocols (2009)

Vandromme, Marianne J. MD; Snyder, Christopher W. MD; McGwin, Gerald Jr MS, PhD; Weinberg, Jordan A. MD; Kerby, Jeffrey D. MD, PhD Author Information
Extending Graph Based Locking Protocols with Edge Locks (1983)

In recent years the introduction of target therapies with BRAF and MEK inhibitors (MAPKi) and of immunotherapy with anti-CTLA-4 and anti-PD-1 monoclonal antibodies have dramatically improved survival of metastatic melanoma patients. Despite these changes drug resistance remains a major hurdle. Several mechanisms are at the basis of drug resistance. Particular attention has been devoted over the last years to unravel mechanisms at the basis of adaptive/non genetic resistance occurring in BRAF mutated melanomas upon treatment with to MAPKi. In this paper we focus on the involvement of activation of ErbB3 receptor following early exposure of melanoma cells to BRAF or MEK inhibitors, and the following induction of PI3K/AKT pathway. Although different mechanisms have been invoked in the past at the basis of this activation we show here with a combination of approaches that autocrine production of neuregulin by melanoma cells is a major factor responsible for ErbB3 phosphorylation and downstream AKT activation. Interestingly the kinetic of neuregulin production and of the ensuing ErbB3 phosphorylation is different in different melanoma cell lines which underscores the high degree of tumor heterogeneity. Moreover, heterogeneity is further highlighted by the evidence that in different cell lines neuregulin upregulation can occur at the transcriptional or at the post-transcritpional level. Finally we complement our study by showing with a liquid biopsy assay that circulating tumor cells (CTCs) from melanoma patients undergo upregulation of ErbB3 phosphorylation in vivo shortly after initiation of therapy.
Two-Phase Sensor Decision: Machine-Learning for Bird Sound Recognition and Vineyard Protection (2021)

For a wireless sensor network consisting of numerous sensors, spread over a large area with no direct power supply, energy efficiency is of paramount importance. As most power is consumed by the communication module, special attention has to be paid to reduce communication needs as much as possible. The more data is sent, the larger the power requirement of the sensor module. Preprocessing can help in reducing the amount of data to send. However, it also consumes energy. This paper focuses on this tradeoff between preprocessing, pre-filtering and preselecting of sensor data on one hand, and uploading of unprocessed and unfiltered raw data on the other hand, for the special case of protecting vineyards from starlings. The paper proposes a two-phase decision mechanism based on machine learning: the less complex first phase is executed on the microcontroller of the sensor module, while the more complex, more accurate second phase is performed in the cloud. Individual noise sensors monitor the environment, and try to detect starling songs, using a simple, SVM-based classification. These sensors are grouped into clusters, through a mechanism similar to the well-known LEACH protocol, and signal to the current cluster-head the likelihood of starling presence. If several alerts are received to justify further investigation, the cluster-head asks the node with highest starling detection likelihood to upload a one second sound sample to the cloud. There, the more complex and more accurate second phase sound matching is performed, and the actuators deployed in the field are remotely triggered, if needed.