gebhart/patrepeval huggingface dataset:
Chemical nature of nitric oxide storage forms in rat vascular tissue (2002)

Endothelial NO production results in local formation of adducts that may act as storage forms of NO. Because little is known about their chemical nature, concentrations, and possible role in vascular biology, we sought to characterize those species basally present in rat aorta, using two independent approaches. In the first approach, tissue homogenates were analyzed by using chemiluminescence- and ion-chromatography-based techniques that allow trace-level quantification of NO-related compounds in complex biological matrices. In the second approach, NO stores were characterized by their ability to release NO when illuminated with light and subsequently relax vascular smooth muscle (photorelaxation). The latter included a careful assessment of action spectra for photorelaxation, taking into account the light-scattering properties of the tissue and the storage depletion rates induced by exposure to controlled levels of light. Biochemical analyses revealed that aortic tissues contained 10 +/- 1 microM nitrite, 42 +/- 7 microM nitrate, 40 +/- 6 nM S-nitroso, and 33 +/- 6 nM N-nitroso compounds (n = 4-8). The functional data obtained suggest that the NO photolytically released in the tissue originated from species with photophysical properties similar to those reported for low-molecular-weight S-nitrosothiols, as well as from nitrite. The relative contribution of these potential NO stores to the extent of photorelaxation was consistent with their concentrations detected biochemically in vascular tissue when their photoactivity was taken into account. We conclude that intravascular nitroso species and nitrite both have the potential to release physiologically relevant quantities of NO independent of enzymatic control by NO synthase.
A natural language bipolar argumentation approach to support users in online debate interactions† (2013)

With the growing use of the Social Web, an increasing number of applications for exchanging opinions with other people are becoming available online. These applications are widely adopted with the consequence that the number of opinions about the debated issues increases. In order to cut in on a debate, the participants need first to evaluate the opinions of the other users to detect whether they are in favour or against the debated issue. Bipolar argumentation proposes algorithms and semantics to evaluate the set of accepted arguments, given the support and the attack relations among them. Two main problems arise. First, an automated framework to detect the relations among the arguments represented by the natural language (NL) formulation of the users’ opinions is needed. Our paper addresses this open issue by proposing and evaluating the use of NL techniques to identify the arguments and their relations. In particular, we adopt the textual entailment (TE) approach, a generic framework for applied semantics, where linguistic objects are mapped by means of semantic inferences at a textual level. TE is then coupled together with an abstract bipolar argumentation system which allows to identify the arguments that are accepted in the considered online debate. Second, we address the problem of studying and comparing the different proposals put forward for modelling the support relation. The emerging scenario shows that there is not a unique interpretation of the support relation. In particular, different combinations of additional attacks among the arguments involved in a support relation are proposed. We provide an NL account of the notion of support based on online debates, by discussing and evaluating the support relation among arguments with respect to the more specific notion of TE in the NL processing field. Finally, we carry out a comparative evaluation of four proposals of additional attacks on a sample of NL arguments extracted from Debatepedia. The originality of the proposed framework lies in the following point: NL debates are analysed and the relations among the arguments are automatically extracted.
Enhanced pulmonary histopathology induced by respiratory syncytial virus (RSV) challenge of formalin-inactivated RSV-immunized BALB/c mice is abrogated by depletion of interleukin-4 (IL-4) and IL-10 (1994)

In previous studies, children immunized with a formalin-inactivated respiratory syncytial virus vaccine (FI-RSV) developed severe pulmonary disease with greater frequency than did controls during subsequent natural RSV infection. In earlier efforts to develop an animal model for this phenomenon, extensive pulmonary histopathology developed in FI-RSV-immunized cotton rats and mice subsequently challenged with RSV. In mice, depletion of CD4+ T cells at the time of RSV challenge completely abrogated this histopathology. Furthermore, the predominant cytokine mRNA present in lungs of FI-RSV-immunized mice during subsequent infection with RSV was that characteristically secreted by Th2 T cells, namely interleukin-4 (IL-4). In the present studies, we sought to determine the relative contributions of gamma interferon (IFN-gamma), IL-2, IL-4, and IL-10 to the lymphocytic infiltration into the lungs observed following RSV challenge of mice previously immunized with FI-RSV. Mice previously immunized with FI-RSV or infected with RSV were depleted of IFN-gamma, IL-2, IL-4, or IL-10 immediately before RSV challenge, and the magnitude of inflammatory cell infiltration around bronchioles and pulmonary blood vessels was quantified. The phenomenon of pulmonary-histopathology potentiation by FI-RSV was reproduced in the present study, thereby allowing us to investigate the effect of cytokine depletion on the process. Simultaneous depletion of both IL-4 and IL-10 completely abrogated pulmonary histopathology in FI-RSV-immunized mice. Depletion of IL-4 alone significantly reduced bronchiolar, though not perivascular, histopathology. Depletion of IL-10 alone had no effect. Depletion of IFN-gamma, IL-2, or both together had no effect on the observed histopathology. These data indicate that FI-RSV immunization primes for a Th2-, IL-4-, and IL-10-dependent inflammatory response to subsequent RSV infection. It is possible that this process played a role in enhanced disease observed in infants and children immunized with FI-RSV.
Dissecting Multistep Tumorigenesis in Transgenic Mice (1988)

Orthologs and paralogs are two fundamentally different types of homologous genes that evolved, respectively, by vertical descent from a single ancestral gene and by duplication. Orthology and paralogy are key concepts of evolutionary genomics. A ...Read More
Amyloid β Protein Modulates Glutamate-Mediated Neurotransmission in the Rat Basal Forebrain: Involvement of Presynaptic Neuronal Nicotinic Acetylcholine and Metabotropic Glutamate Receptors (2007)

Amyloid beta (Abeta) protein, a 39-43 amino acid peptide deposited in brains of individuals with Alzheimer's disease (AD), has been shown to interact directly with a number of receptor targets including neuronal nicotinic acetylcholine receptors (nAChRs) and glutamate receptors. In this study, we investigated the synaptic effects of Abeta(1-42) on glutamate-mediated neurotransmission in the diagonal band of Broca (DBB), a cholinergic basal forebrain nucleus. Glutamatergic miniature EPSCs (mEPSCs) were recorded using whole-cell patch-clamp recordings from identified cholinergic DBB neurons in rat forebrain slices. In 54% of DBB neurons, bath application of Abeta(1-42) (100 nM), but not Abeta(42-1) (inverse fragment), significantly increased the frequency of mEPSCs without affecting amplitude or kinetic parameters (rise or decay time). In 32% of DBB neurons, bath application of Abeta(1-42) significantly decreased only the frequency but not amplitude of mEPSCs. Application of dihydro-beta-erythroidine (DHbetaE) (an antagonist for the alpha4beta2 subtype of nAChRs) but not alpha-bungarotoxin (an antagonist for the alpha7 subtype of nAChRs) blocked Abeta(1-42)-mediated increases in mEPSC frequency. The Abeta(1-42)-mediated increase in glutamatergic transmission is thus presynaptic and mediated via non-alpha7 AChRs. In contrast, Abeta(1-42)-mediated decreases in mEPSC frequency could not be antagonized by either DHbetaE or alpha-bungarotoxin. However, the Abeta(1-42)-evoked depression in mEPSC frequency was antagonized by (RS)-alpha-methyl-4-carboxyphenyglycine, a nonselective group I/II metabotropic glutamate receptor antagonist. These observations provide further insight into the mechanisms whereby Abeta affects synaptic function in the brain and may be relevant in the context of synaptic failure observed in AD.
Improving the bioconversion of plant biomass to biofuels: A multidisciplinary approach (2011)

In 2010 our group reported the discovery of two cellodextrin transporter families, and soon after demonstrated the utility of these transporters in the production of lignocellulosic biofuel. These discoveries required diverse insights from multiple research groups, highlighting the need for multidisciplinary teams to tackle the most pressing research problems in bioenergy.
Enhanced Humoral Immune Response Correlates With Improved Disease-Free and Overall Survival in American Joint Committee on Cancer Stage II Melanoma Patients Receiving Adjuvant Polyvalent Vaccine (2002)

These findings suggest that an increased IgM response in patients receiving PV therapy for stage II melanoma is associated with decreased recurrence and improved survival.
Cryptotanshinone Induces Inhibition of Breast Tumor Growth by Cytotoxic CD4+ T Cells through the JAK2/STAT4/ Perforin Pathway (2014)

Cryptotanshinone (CPT), is a quinoid diterpene isolated from the root of the Asian medicinal plant, Salvia miotiorrhiza bunge. Numerous researchers have found that it could work as a potent antitumor agent to inhibit tumor growth in vitro, buith there has been much less emphasis on its in vivo role against breast tumors. Using a mouse tumor model of MCF7 cells, we showed that CPT strongly inhibited MCF7 cell growth in vivo with polarization of immune reactions toward Th1-type responses, stimulation of naive CD4+ T cell proliferation, and also increased IFN-γ and perforin production of CD4+ T cells in response to tumor-activated splenocytes. Furthermore, data revealed that the cytotoxic activity of CD4+ T cells induced by CPT was markedly abrogated by concanamycin A(CMA), a perforin inhibitor, but not IFN-γ Ab. On the other hand, after depletion of CD4+ T cells or blocked perforin with CMA in a tumor-bearing model, CPT could not effectively suppress tumor growth, but this phenomenon could be reversed by injecting naive CD4+ T cells. Thus, our results suggested that CPT mainly inhibited breast tumor growth through inducing cytotoxic CD4+ T cells to secrete perforin. We further found that CPT enhanced perforin production of CD4+ T cells by up-regulating JAK2 and STAT4 phosphorylation. These findings suggest a novel potential therapeutic role for CPT in tumor therapy, and demonstrate that CPT performs its antitumor functions through cytotoxic CD4+ T cells.
Expression of bcl-2 From a Defective Herpes Simplex Virus–1 Vector Limits Neuronal Death in Focal Cerebral Ischemia (1995)

These data indicate that bcl-2 expression protects neurons in vivo from ischemic injury and suggest the feasibility of gene therapy for stroke and perhaps other neurological diseases in which programmed cell death is involved.
Recurrent missense mutation in the protoporphyrinogen oxidase gene underlies variegate porphyria (1998)

The porphyrias represent a heterogeneous group of disorders of porphyrin or porphyrin-precursor metabolism, resulting from the inherited or acquired dysregulation of one of the eight enzymes in the porphyrin-heme biosynthetic pathway. Variegate porphyria, one of the acute hepatic porphyrias, is characterized by a partial reduction in the activity of the penultimate enzyme in the heme biosynthetic pathway, protoporphyrinogen oxidase (PPO). Recently, VP has been linked to the PPO gene on chromosome 1q22−23, and several disease-causing mutations have been described. In this study, we identified the underlying genetic lesion in two unrelated patients with VP and investigated all available family members by polymerase chain reaction, heteroduplex analysis, automated sequencing, and restriction enzyme digestion. Mutation analyses in both families revealed a G-to-A transition in exon 6 of the PPO gene resulting in the substitution of arginine by histidine at position 168 of the protein (R168H). This arginine residue is evolutionarily conserved in human, mouse, and Bacillus subtilis, indicating the importance of this residue in PPO function. Our study establishes a recurrent missense mutation as the underlying genetic defect in two unrelated patients with VP and explains the occurrence of the phenotype in their families. Am. J. Med. Genet. 79:22–26, 1998. © 1998 Wiley-Liss, Inc.
Vasorelaxation by New Hybrid Compounds Containing Dihydropyridine and Pinacidil-Like Moieties (1999)

The synthesis and pharmacological properties of a novel type of vasorelaxant hybrid compounds are described. The investigated compounds originate from fluorinated 4-aryl-1,4-dihydropyridines, which are known calcium channel blockers, and/or from fluorinated analogues of pinacidil, which is an opener of ATP-sensitive potassium channels. In particular, we studied the most potent hybrid, 2,6-dimethyl-3,5-dicarbomethoxy-4-(2-difluoromethoxy-5-N-(N' '-cyano-N'-1,2,2-trimethyl-propylguanidyl)-phenyl)-1, 4-dihydropyridine (4a), together with its parent compounds, the dihydropyridine 1b and the pinacidil analogue 3. In isolated rat mesenteric arteries, micromolar concentrations of 4a relaxed contractions exerted by K(+)-depolarization or by norepinephrine. The latter effect was sensitive to the potassium channel blocker glibenclamide. Micromolar 4a also inhibited [(3)H](+)-isradipine and [(3)H]P1075 binding to rat cardiac membranes, and it blocked L-type calcium channels expressed in a mammalian cell line. The respective parent compounds 1b and 3 were always more potent and more selective regarding calcium channel or potassium channel interaction, respectively. In contrast, 4a combined both effects within the same concentration range, indicating that it may represent a lead structure for a novel class of pharmacological hybrid compounds.
Prevalence and Impact of Posttraumatic Stress Disorder-Like Symptoms on Patients With Fibromyalgia Syndrome (2000)

Results suggest that PTSD-like symptoms are prevalent in FMS patients and may influence adaptation to this chronic illness. Clinicians should assess the presence of these symptoms, as the failure to attend to them in treatment may impede successful outcomes.
Characterization of Chloroplast Division Using the Arabidopsis Mutant arc5 (1996)

arc5 is a chloroplast division mutant of Arabidopsis thaliana. To identify the role of ARC5 in the chloroplast replication process we have followed the changes in arc5 chloroplasts during their perturbed division. ARC5 does not affect proplastid division but functions at a later stage in chloroplast development. Chloroplasts in developing mesophyll cells of arc5 leaves do not increase in number and all of the chloroplasts in mature leaf cells show a central constriction. Young arc5 chloroplasts are capable of initiating the division process but fail to complete daughter-plastid separation. Wild-type plastids increase in number to a mean of 121 after completing the division process, but in the mutant arc5 the approximately 13 plastids per cell are still centrally constricted but much enlarged. As the arc5 chloroplasts expand and elongate without dividing, the internal thylakoid membrane structure becomes flexed into an undulating ribbon. We conclude that the ARC5 gene is necessary for the completion of the last stage of chloroplast division when the narrow isthmus breaks, causing the separation of the daughter plastids.
Ablation of capsaicin sensitive afferent nerves impairs defence but not rapid repair of rat gastric mucosa. (1993)

Capsaicin sensitive afferent neurones have previously been reported to play a part in gastric mucosal protection. The aim of this study was to investigate whether these nociceptive neurones strengthen mucosal defence against injury or promote rapid repair of the damaged mucosa, or both. This hypothesis was examined in anaesthetised rats whose stomachs were perfused with ethanol (25 or 50% in saline, wt/wt) for 30 minutes. The gastric mucosa was inspected 0 and 180 minutes after ethanol had been given at the macroscopic, light, and scanning electron microscopic level. Rapid repair of the ethanol injured gastric mucosa (reduction of deep injury, partial re-epithelialisation of the denuded surface) took place in rats anaesthetised with phenobarbital, but not in those anaesthetised with urethane. Afferent nerve ablation as a result of treating rats with a neurotoxic dose of capsaicin before the experiment significantly aggravated ethanol induced damage as shown by an increase in the area and depth of mucosal erosions. Rapid repair of the injured mucosa, however, as seen in rats anesthetised with phenobarbital 180 minutes after ethanol was given, was similar in capsaicin and vehicle pretreated animals. Ablation of capsaicin sensitive afferent neurones was verified by a depletion of calcitonin gene related peptide from the gastric corpus wall. These findings indicate that nociceptive neurones control mechanisms of defence against acute injury but are not required for rapid repair of injured mucosa.
In vitro and in vivo resistance to cisplatin in cells that have lost DNA mismatch repair. (1997)

In vitro studies have shown that loss of DNA mismatch repair due to lack of either hMSH2 or hMLH1 activity results in low-level resistance to cisplatin but not to oxaliplatin, an analogue that produces a different type of DNA adduct. No information is currently available on whether this low-level resistance is sufficient to result in enrichment of mismatch repair-deficient cells during drug exposure in vitro or to account for clinical failure of treatment in vivo. Mixed populations of cells containing a minority of DNA mismatch repair-deficient cells constitutively expressing green fluorescence protein were exposed repeatedly in vitro to cisplatin and oxaliplatin. Treatment with cisplatin resulted in a gradual enrichment for DNA mismatch repair-deficient cells, whereas treatment with oxaliplatin did not. MSH2-/- and MSH2+/+ embryonic stem cells were established as xenografts in athymic nude mice. Animals were treated 48 h after tumor implantation with a single LD10 dose of either cisplatin or oxaliplatin. MSH2-/- tumors were significantly less responsive to cisplatin than MSH2+/+ tumors, whereas there was no difference in sensitivity to oxaliplatin. These results demonstrate that the degree of cisplatin resistance conferred by loss of DNA mismatch repair is sufficient to produce both enrichment of mismatch repair-deficient cells during treatment in vitro and a large difference in clinical responsiveness in vivo. The results identify loss of DNA mismatch repair as a mechanism of resistance to cisplatin but not oxaliplatin.
Xcel-RAM: Accelerating Binary Neural Networks in High-Throughput SRAM Compute Arrays (2019)

Deep neural networks are biologically inspired class of algorithms that have recently demonstrated the state-of-the-art accuracy in large-scale classification and recognition tasks. Hardware acceleration of deep networks is of paramount importance to ensure their ubiquitous presence in future computing platforms. Indeed, a major landmark that enables efficient hardware accelerators for deep networks is the recent advances from the machine learning community that have demonstrated the viability of aggressively scaled deep binary networks. In this paper, we demonstrate how deep binary networks can be accelerated in modified von Neumann machines by enabling binary convolutions within the static random access memory (SRAM) arrays. In general, binary convolutions consist of bit-wise exclusive-NOR (XNOR) operations followed by a population count (popcount). We present two proposals: one based on charge sharing approach to perform vector XNOR and approximate popcount and another based on bit-wise XNOR followed by a digital bit-tree adder for accurate popcount. We highlight the various tradeoffs in terms of circuit complexity, speed-up, and classification accuracy for both the approaches. Few key techniques presented as a part of the manuscript are the use of low-precision, low-overhead analog-to-digital converter (ADC), to achieve a fairly accurate popcount for the charge-sharing scheme and proposal for sectioning of the SRAM array by adding switches onto the read-bitlines, thereby achieving improved parallelism. Our results on benchmark image classification datasets for CIFAR-10 and SVHN on a binarized neural network architecture show energy improvements of up to 6.1× and 2.3× for the two proposals, compared to conventional SRAM banks. In terms of latency, improvements of up to 15.8× and 8.1× were achieved for the two respective proposals.
High-Strain Actuator Materials Based on Dielectric Elastomers (2000)

Dielectric elastomers are a new class of actuator materials that exhibit excellent performance. The principle of operation, as well as methods to fabricate and test these elastomers, is summarized here. The Figure is a sketch of an elastomer film (light gray) stretched on a frame (black) and patterned with an electrode (mid-gray). Upon applying a voltage, the active portion of the elastomer expands and the strain can easily be measured optically.
Expression Cloning of an Adenylate Cyclase-Coupled Calcitonin Receptor (1991)

A calcitonin receptor complementary DNA (cDNA) was cloned by expression of a cDNA library from a porcine kidney epithelial cell line in COS cells. The 482-amino acid receptor has high affinity for salmon calcitonin (dissociation constant Kd approximately 6 nM) and is functionally coupled to increases in intracellular cyclic adenosine monophosphate (cAMP). The receptor shows no sequence similarity to other reported G protein-coupled receptors but is homologous to the parathyroid hormone-parathyroid hormone-related peptide (PTH-PTHrP) receptor, indicating that the receptors for these hormones, which regulate calcium homeostasis, represent a new family of G protein-coupled receptors.
Targets of AtWRKY6 regulation during plant senescence and pathogen defense (2002)

In Arabidopsis, WRKY factors comprise a large gene family of plant-specific transcriptional regulators controlling several types of plant stress responses. To understand the regulatory role of WRKY proteins during such processes, we identified targets of the senescence- and defense-associated WRKY6 factor. WRKY6 was found to suppress its own promoter activity as well as that of a closely related WRKY family member, indicating negative autoregulation. On the other hand, WRKY6 positively influenced the senescence- and pathogen defense-associated PR1 promoter activity, most likely involving NPR1 function. One novel identified target gene, SIRK, encodes a receptor-like protein kinase, whose developmental expression is strongly induced specifically during leaf senescence. The transcriptional activation of SIRK is dependent on WRKY6 function. Senescing leaves of wrky6 knockout mutants showed a drastic reduction, and green leaves of WRKY6 overexpression lines showed clearly elevated SIRK transcript levels. Furthermore, the SIRK gene promoter was specifically activated by WRKY6 in vivo, functioning very likely through direct W-box interactions.