gebhart/patrepeval huggingface dataset:
Activation of RNase L in Egyptian Rousette Bat-Derived RoNi/7 Cells Is Dependent Primarily on OAS3 and Independent of MAVS Signaling (2019)

Bats are reservoirs for many RNA viruses that are highly pathogenic in humans yet relatively apathogenic in the natural host. It has been suggested that differences in innate immunity are responsible. The antiviral OAS-RNase L pathway is well characterized in humans, but there is little known about its activation and antiviral activity in bats. During infection, OASs, upon sensing double-stranded RNA (dsRNA), produce 2'-5' oligoadenylates (2-5A), leading to activation of RNase L which degrades viral and host RNA, limiting viral replication. Humans encode three active OASs (OAS1 to -3). Analysis of the Egyptian Rousette bat genome combined with mRNA sequencing from bat RoNi/7 cells revealed three homologous OAS proteins. Interferon alpha treatment or viral infection induced all three OAS mRNAs, but RNase L mRNA is constitutively expressed. Sindbis virus (SINV) or vaccinia virus (VACVΔE3L) infection of wild-type (WT) or <i>OAS1-</i>KO (knockout), <i>OAS2</i>-KO, or <i>MAVS-</i>KO RoNi/7 cells, but not <i>RNase L</i>-KO or <i>OAS3</i>-KO cells, induces robust RNase L activation. SINV replication is 100- to 200-fold higher in the absence of RNase L or OAS3 than in WT cells. However, <i>MAVS</i>-KO had no detectable effect on RNA degradation or replication. Thus, in RoNi/7 bat cells, as in human cells, activation of RNase L during infection and its antiviral activity are dependent primarily on OAS3 while MAVS signaling is not required for the activation of RNase L and restriction of infection. Our findings indicate that OAS proteins serve as pattern recognition receptors (PRRs) to recognize viral dsRNA and that this pathway is a primary response to virus rather than a secondary effect of interferon signaling.<b>IMPORTANCE</b> Many RNA viruses that are highly pathogenic in humans are relatively apathogenic in their bat reservoirs, making it important to compare innate immune responses in bats to those well characterized in humans. One such antiviral response is the OAS-RNase L pathway. OASs, upon sensing dsRNA, produce 2-5A, leading to activation of RNase L which degrades viral and host RNA, limiting viral replication. Analysis of Egyptian Rousette bat sequences revealed three OAS genes expressing OAS1, OAS2, and OAS3 proteins. Interferon treatment or viral infection induces all three bat OAS mRNAs. In these bat cells as in human cells, RNase L activation and its antiviral activity are dependent primarily on OAS3 while MAVS signaling is not required. Importantly, our findings indicate the OAS-RNase L system is a primary response to virus rather than a secondary effect of interferon signaling and therefore can be activated early in infection or while interferon signaling is antagonized.
Electrochemical Incineration in the Presence of Halides (2005)

The influence of different halides on electrochemical incineration of oxalic acid was studied. Experiments were initially carried out&#13;\nat a Pt electrode in alkaline media, in which case, in the absence of mediating effects, a slow electroxidation was observed.&#13;\nHowever, with halides, the rate of the electrochemical incineration was increased significantly, following the order F- &gt; Br- &gt; Cl-, and the rate of the mediated process was practically independent of applied current density. An explanation has been&#13;\nattempted for the role of halides, in relation with the oxygen evolution reaction, concomitant with the electrochemical incineration.
Strong current arc discharges of alternating current (2002)

Summary form only given. The review of experimental investigation results of strong current (I=10-10/sup 4/A) quasistationary alternating current discharges in high pressure gases (P/spl ges/10/sup 5/Pa) is given. Structural and alternating current are properties in vortex, turbulent flows of air, argon, nitrogen and hydrogen were investigated. The existence of two arc discharge column regimes-contracted and diffusional-was determined experimentally. Processes of arc heat exchange with the surrounding gas for these regimes were studied. Together with the volume processes, mechanisms of discharge shorting on the electrodes surface and their erosion in the spot and without spot regimes in dependence of current quantity, gas pressure and electrodes material were investigated. Powerful (N=10-10/sup 3/ kW) alternating current plasma generators were designed and created on the basis of these investigations.
Lower bound of sample word length in bit/digit serial architectures (1992)

In bit/digit-serial architectures the allowable sample word length is lower-bounded to synchronise the feedback loops (the cycles) correctly. A systematic procedure for finding this lower bound and the critical cycle that achieves the bound are described. From this information a successful schedule can be guaranteed for all cases, which has been difficult using previous approaches.
Improving Performance of Dynamic Programming via Parallelism and Locality on Multicore Architectures (2008)

Dynamic programming (DP) is a popular technique which is used to solve combinatorial search and optimization problems. This paper focuses on one type of DP, which is called nonserial polyadic dynamic programming (NPDP). Owing to the nonuniform data dependencies of NPDP, it is difficult to exploit either parallelism or locality. Worse still, the emerging multi/many-core architectures with small on-chip memory make these issues more challenging. In this paper, we address the challenges of exploiting the fine grain parallelism and locality of NPDP on multicore architectures. We describe a latency-tolerant model and a percolation technique for programming on multicore architectures. On an algorithmic level, both parallelism and locality do benefit from a specific data dependence transformation of NPDP. Next, we propose a parallel pipelining algorithm by decomposing computation operators and percolating data through a memory hierarchy to create just-in-time locality. In order to predict the execution time, we formulate an analytical performance model of the parallel algorithm. The parallel pipelining algorithm achieves not only high scalability on the 160-core IBM Cyclops64, but portable performance as well, across the 8-core Sun Niagara and quad-cores Intel Clovertown.
&lt;title&gt;Space-based forest fire detection concept&lt;/title&gt; (1995)

Small, incipient wildfires in the boreal forest can be detected with a space-based infrared sensor that uses currently available technology. At night, wildfires with a temperature of 700 K or more and an area of 1 m<SUP>2</SUP> should be visible if there is a clear line of sight to the sensor. Sensor refinements and signal processing could enhance this level of detection. Clouds, topographical variations and the forest canopy may obscure the line of sight, so that multiple looks would significantly improve the probability of detection of a small fire. The relatively long revisit time of a satellite-based sensor is a constraint of the fire management application. Although the cost and revisit time of a spaceborne sensor are currently too high for it to replace airborne sensors, there is an important role as an adjunct sensor operating at night. Many of the specifications of an infrared sensor for wildfire detection are similar to those for space-based surveillance applications, so that useful infrared imagery from space may become available to the forest management community at relatively low cost.
Adaptive and Move Making Auxiliary Cuts for Binary Pairwise Energies (2017)

Many computer vision problems require optimization of binary non-submodular energies. In this context, iterative submodularization techniques based on trust region (LSA-TR) and auxiliary functions (LSA-AUX) have been recently proposed [9]. They achieve state-of-the-art-results on a number of computer vision applications. In this paper we extend the LSA-AUX framework in two directions. First, unlike LSA-AUX which selects auxiliary functions based solely on the current solution, we propose to incorporate several additional criteria. This results in tighter bounds for configurations that are more likely or closer to the current solution. Second, we propose move-making extensions of LSA-AUX which achieve tighter bounds by restricting the search space. Finally, we evaluate our methods on several applications. We show that for each application at least one of our extensions significantly outperforms the original LSA-AUX. Moreover, the best extension of LSA-AUX is comparable to or better than LSA-TR on five out of six applications, achieving state-of-the-arts results on four out of six applications.
Role of CD133 Molecule in Wnt Response and Renal Repair (2018)

Renal repair after injury is dependent on clonal expansion of proliferation-competent cells. In the human kidney, the expression of CD133 characterizes a population of resident scattered cells with resistance to damage and ability to proliferate. However, the biological function of the CD133 molecule is unknown. By RNA sequencing, we found that cells undergoing cisplatin damage lost the CD133 signature and acquired metanephric mesenchymal and regenerative genes such as SNAIL1, KLF4, SOX9, and WNT3. CD133 was reacquired in the recovery phase. In CD133-Kd cells, lack of CD133 limited cell proliferation after injury and was specifically correlated with deregulation of Wnt signaling and E-cadherin pathway. By immunoprecipitation, CD133 appeared to form a complex with E-cadherin and β-catenin. In parallel, CD133-Kd cells showed lower β-catenin levels in basal condition and after Wnt pathway activation and reduced TCF/LEF promoter activation in respect to CD133<sup>+</sup> cells. Finally, the lack of CD133 impaired generation of nephrospheres while favoring senescence. These data indicate that CD133 may act as a permissive factor for β-catenin signaling, preventing its degradation in the cytoplasm. Therefore, CD133 itself appears to play a functional role in renal tubular repair through maintenance of proliferative response and control of senescence. Stem Cells Translational Medicine 2018;7:283-294.
Carbon nanotubes suspended in ethylene glycol yield nanofluids with enhanced heat transfer properties (2014)

Nanofluids (NFs) consisting of carbon nanotubes (CNTs) suspended in ethylene glycol (EG) were synthesized, and their stability and thermal conductivity enhancement rate were investigated. Stability of the CNT/EG-based NFs was enhanced by adding gum Arabic (GA). The increase in suspension stability was experimentally characterized using static and centrifugal testing processes. The mechanisms of GA in enhancing the fluid stability were characterized and the optimal mass ratio of GA to CNT was found to be about 11% by weight. Thermal conductivity was measured for varying CNT volume fraction under different fluid temperatures, and a nearly linear relationship between the thermal conductivity and the CNT volume fraction and temperature was observed.
Functional Analysis of the Twin-Arginine Translocation Pathway in <i>Corynebacterium glutamicum</i> ATCC 13869 (2006)

Compared to those of other gram-positive bacteria, the genetic structure of the Corynebacterium glutamicum Tat system is unique in that it contains the tatE gene in addition to tatA, tatB, and tatC. The tatE homologue has been detected only in the genomes of gram-negative enterobacteria. To assess the function of the C. glutamicum Tat pathway, we cloned the tatA, tatB, tatC, and tatE genes from C. glutamicum ATCC 13869 and constructed mutants carrying deletions of each tat gene or of both the tatA and tatE genes. Using green fluorescent protein (GFP) fused with the twin-arginine signal peptide of the Escherichia coli TorA protein, we demonstrated that the minimal functional Tat system required TatA and TatC. TatA and TatE provide overlapping function. Unlike the TatB proteins from gram-negative bacteria, C. glutamicum TatB was dispensable for Tat function, although it was required for maximal efficiency of secretion. The signal peptide sequence of the isomaltodextranase (IMD) of Arthrobacter globiformis contains a twin-arginine motif. We showed that both IMD and GFP fused with the signal peptide of IMD were secreted via the C. glutamicum Tat pathway. These observations indicate that IMD is a bona fide Tat substrate and imply great potential of the C. glutamicum Tat system for industrial production of heterologous folded proteins.
Platinum(100) hillock growth in a Pt/Ti electrode stack for ferroelectric random access memory (2003)

The Pt hillock in a Pt/Ti electrode stack has been the main concern in ferroelectric random access memory due to the reliability problem. The origin of the hillock formation is the compressive stress, and the main mass transport mechanism for hillock formation is the grain boundary diffusion for thin films with a columnar structure. However, the hillock growth orientation and mechanism have not been reported. In this study, we found that an orientation relationship of Pt(100)hillock//Pt(111)thin film existed between the Pt hillock and the thin film. The Pt hillock was a single crystal having facets with polyatomic steps. From these results, we suggest that the Pt hillock growth mechanism is the layer growth of flat faces, which shapes the hillock into a tetrahedron single crystal.
Transfection of Mammalian Cells Using Block Copolypeptide Vesicles (2013)

An arginine-leucine block copolypeptide (R60 L20 ) is synthesized, which is capable of forming vesicles with controllable sizes, able to transport hydrophilic cargo across the cell membrane, and exhibit relatively low cytotoxicity. The R60 L20 vesicles also possess the ability to deliver DNA into mammalian cells for transfection. Although the transfection efficiency is lower than that of the commercially available transfection agent Lipofectamine 2000, the R60 L20 vesicles are able to achieve transfection with significantly lower cytotoxicity and immunogenicity. This behavior is potentially due to its stronger interaction with DNA which subsequently provides better protection against anionic heparin.
DROWN: Breaking TLS using SSLv2 (2016)

We present DROWN, a novel cross-protocol attack on TLS that uses a server supporting SSLv2 as an oracle to decrypt modern TLS connections. We introduce two versions of the attack. The more general form exploits multiple unnoticed protocol flaws in SSLv2 to develop a new and stronger variant of the Bleichenbacher RSA padding-oracle attack. To decrypt a 2048-bit RSA TLS ciphertext, an attacker must observe 1,000 TLS handshakes, initiate 40,000 SSLv2 connections, and perform 250 offline work. The victim client never initiates SSLv2 connections. We implemented the attack and can decrypt a TLS 1.2 handshake using 2048-bit RSA in under 8 hours, at a cost of $440 on Amazon EC2. Using Internet-wide scans, we find that 33% of all HTTPS servers and 22% of those with browser-trusted certificates are vulnerable to this protocol-level attack due to widespread key and certificate reuse. For an even cheaper attack, we apply our new techniques together with a newly discovered vulnerability in OpenSSL that was present in releases from 1998 to early 2015. Given an unpatched SSLv2 server to use as an oracle, we can decrypt a TLS ciphertext in one minute on a single CPU—fast enough to enable man-in-the-middle attacks against modern browsers. We find that 26% of HTTPS servers are vulnerable to this attack. We further observe that the QUIC protocol is vulnerable to a variant of our attack that allows an attacker to impersonate a server indefinitely after performing as few as 217 SSLv2 connections and 258 offline work. We conclude that SSLv2 is not only weak, but actively harmful to the TLS ecosystem.
ChemInform Abstract: Antirheumatic Agents. Part 2. Novel Methotrexate Derivatives Bearing an Alkyl‐Substituted Benzene Ring. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Opioid Modulation of Recurrent Excitation in the Hippocampal Dentate Gyrus (2000)

kappa opioid receptor activation inhibits granule cell-mediated excitatory neurotransmission in the hippocampal formation via a decrease in glutamate release from both perforant path and mossy fiber terminals. We now report a third, anatomically and pharmacologically distinct site of such kappa opioid inhibition within the hippocampus. Granule cell population responses to selective stimulation of an excitatory hilar pathway were decreased by the kappa(1) opioid receptor agonist U69,593, an effect blocked by the kappa(1) antagonist norbinaltorphimine. U69,593 also inhibited hilar path induced long-term potentiation (LTP) of granule cell responses. LTP in this pathway was also blocked by the NMDA receptor antagonist d-2-amino-5-phosphonovalerate, unlike granule cell mossy fiber LTP in CA3. The kappa opioid peptide dynorphin is present in hilar mossy fiber collaterals. Ultrastructural analysis of these collaterals demonstrated dynorphin-containing vesicles in asymmetric synapses formed between axon terminals and granule cell dendrites, suggesting direct granule cell-granule cell connections. Evoked release of endogenous dynorphin within the hilus was effective in reducing hilar excitation of granule cells, although this release, in contrast to the release of dynorphin in the dentate molecular layer, was not dependent on L-type calcium channels. No hilar path excitation was observed in the absence of bicuculline, suggesting a strong GABA(A)-mediated inhibition of this pathway. However, hilar path activity could be seen after LTP, with or without bicuculline. Thus, kappa opioids can inhibit granule cell recurrent excitation, likely via effects on excitatory mossy fiber collaterals. Such collaterals are thought to be important in mediating temporal lobe epilepsy.
A novel optical biosensor for the early diagnosis of sepsis and severe COVID-19: the PROUD study (2020)

Abstract Background The accuracy of a new optical biosensor (OB) point-of-care device for the detection of severe infections is studied. Methods The OB emits different wavelengths and outputs information associated with heart rate, pulse oximetry, levels of nitric oxide and kidney function. At the derivation phase, recordings were done every two hours for three consecutive days after hospital admission in 142 patients at high-risk for sepsis by placing the OB on the forefinger. At the validation phase, single recordings were done in 54 patients with symptoms of viral infection; 38 were diagnosed with COVID-19. Results At the derivation phase, the cutoff value of positive likelihood of 18 provided 100% specificity and 100% positive predictive value for the diagnosis of sepsis. These were 87.5% and 91.7% respectively at the validation phase. OB diagnosed severe COVID-19 with 83.3% sensitivity and 87.5% negative predictive value. Conclusions The studied OB seems valuable for the discrimination of infection severity.
Serotonin Reuptake Inhibitor Increases Pseudarthrosis Rates in Anterior Cervical Discectomy and Fusions (2023)

Patients taking serotonin reuptake-inhibiting antidepressants are at increased risk of worse postoperative outcome scores, including NDI and MCS-12, likely due to their underlying depression. This may contribute to their greater likelihood of having adjacent segment surgery. Additionally, preoperative use of serotonin reuptake inhibitors in patients undergoing an ACDF is a predictor of radiographic pseudarthrosis but not pseudarthrosis revision.
Vascularization of the Ciliary Body and Iridocorneal Angle in the Avian Eye (2005)

In experimental ophthalmology avian models play an important role in the investigation of the pathophysiology of glaucomas. One major problem in establishing new experimental designs is a deficiency in basic anatomical data of the avian eye bulb. The aim of this study was to give a detailed description of the vascularization of the ciliary body and the iridocorneal angle in the avian eye. The vascular anatomy of the avian eye was studied in 50 birds of different species and orders (Phasianiformes, Accipitriformes, Columbiformes) by light microscopy as well as by stereomicroscopy and scanning electron microscopy (SEM) of corrosion cast specimen. The comparison of the different species revealed that independently of the bird order the vessels were orientated in a similar way, thus enabling to establish a schematic diagram. There is a redundancy in the arterial blood supply of the ciliary body and iridocorneal angle, which is supplied by the circulus arteriosus iridis and the circulus arteriosus. For the first time we were able to create a corrosion cast of the complete avian sinus venosus sclerae by injection of a liquid plastic (Reckli®, Chemiewerkstatt GmbH, Herne, Germany) in the venous system. The sinus venosus sclerae is characterized by a double‐ring like structure. It drains into several vv. ciliares anteriores reaching the circulus venosus sclerae. A clearer understanding of the vascularization of the anterior eye segment, in particular of the sinus venosus sclerae, provides a step forward in experimental ophthalmology, especially regarding glaucoma research based on an avian model.
Kernel-Guided Training of Implicit Generative Models with Stability Guarantees (2019)

Modern implicit generative models such as generative adversarial networks (GANs) are generally known to suffer from issues such as instability, uninterpretability, and difficulty in assessing their performance. If we see these implicit models as dynamical systems, some of these issues are caused by being unable to control their behavior in a meaningful way during the course of training. In this work, we propose a theoretically grounded method to guide the training trajectories of GANs by augmenting the GAN loss function with a kernel-based regularization term that controls local and global discrepancies between the model and true distributions. This control signal allows us to inject prior knowledge into the model. We provide theoretical guarantees on the stability of the resulting dynamical system and demonstrate different aspects of it via a wide range of experiments.
Fibroblast Growth Factor Inhibits Insulin-Like Growth Factor-II (IGF-II) Gene Expression and Increases IGF-I Receptor Abundance in BC3H-1 Muscle Cells (1991)

Muscle is an important target tissue for insulin-like growth factor (IGF) action. We have previously reported that muscle cell differentiation is associated with down-regulation of the IGF-I receptor at the level of gene expression that is concomitant with an increase in the expression and secretion of IGF-II. Furthermore, treatment of myoblasts with IGF-II resulted in a similar decrease in IGF-I receptor mRNA abundance, suggesting an autocrine role of IGF-II in IGF-I receptor regulation. To explore further the role of IGF-II in IGF-I receptor regulation, BC3H-1 mouse muscle cells were exposed to differentiation medium in the presence of basic fibroblast growth factor (FGF), a known inhibitor of myogenic differentiation. FGF treatment of cells resulted in a 50% inhibition of IGF-II gene expression compared to that in control myoblasts and markedly inhibited IGF-II secretion. Concomitantly, FGF resulted in a 60-70% increase in IGF-I binding compared to that in control myoblasts. Scatchard analyses and studies of gene expression demonstrated that the increased IGF-I binding induced by FGF reflected parallel increases in IGF-I receptor content and mRNA abundance. These studies indicate that FGF may up-regulate IGF-I receptor expression in muscle cells through inhibition of IGF-II peptide expression and further support the concept of an autocrine role of IGF-II in IGF-I receptor regulation. In addition, these studies suggest that one mechanism by which FGF inhibits muscle cell differentiation is through inhibition of IGF-II expression.