gebhart/patrepeval huggingface dataset:
Trapdoors for Lattices: Simpler, Tighter, Faster, Smaller. (2011)

We give new methods for generating and using “strong trapdoors ” in cryptographic lattices, which are simultaneously simple, efficient, easy to implement (even in parallel), and asymptotically optimal with very small hidden constants. Our methods involve a new kind of trapdoor, and include specialized algorithms for inverting LWE, randomly sampling SIS preimages, and securely delegating trapdoors. These tasks were previously the main bottleneck for a wide range of cryptographic schemes, and our techniques substantially improve upon the prior ones, both in terms of practical performance and quality of the produced outputs. Moreover, the simple structure of the new trapdoor and associated algorithms can be exposed in applications, leading to further simplifications and efficiency improvements. We exemplify the applicability of our methods with new digital signature schemes and CCA-secure encryption schemes, which have better efficiency and security than the previously known lattice-based constructions. 1
Hot Start PCR with heat-activatable primers: a novel approach for improved PCR performance (2008)

The polymerase chain reaction (PCR) is widely used for applications which require a high level of specificity and reliability, such as genetic testing, clinical diagnostics, blood screening, forensics and biodefense. Great improvements to PCR performance have been achieved by the use of Hot Start activation strategies that aim to prevent DNA polymerase extension until more stringent, higher temperatures are reached. Herein we present a novel Hot Start activation approach in PCR where primers contain one or two thermolabile, 4-oxo-1-pentyl (OXP) phosphotriester (PTE) modification groups at 3'-terminal and 3'-penultimate internucleotide linkages. Studies demonstrated that the presence of one or more OXP PTE modifications impaired DNA polymerase primer extension at the lower temperatures that exist prior to PCR amplification. Furthermore, incubation of the OXP-modified primers at elevated temperatures was found to produce the corresponding unmodified phosphodiester (PDE) primer, which was then a suitable DNA polymerase substrate. The OXP-modified primers were tested in conventional PCR with endpoint detection, in one-step reverse transcription (RT)-PCR and in real-time PCR with SYBR Green I dye and Taqman(R) probe detection. When OXP-modified primers were used as substitutes for unmodified PDE primers in PCR, significant improvement was observed in the specificity and efficiency of nucleic acid target amplification.
Activity of therapeutic JAK 1/2 blockade in graft-versus-host disease (2014)

Graft-versus-host-disease (GVHD) is a severe complication of allogeneic hematopoietic cell transplantation (allo-HCT) characterized by the production of high levels of proinflammatory cytokines. Activated Janus kinases (JAKs) are required for T-effector cell responses in different inflammatory diseases, and their blockade could potently reduce acute GVHD. We observed that inhibition of JAK1/2 signaling resulted in reduced proliferation of effector T cells and suppression of proinflammatory cytokine production in response to alloantigen in mice. In vivo JAK 1/2 inhibition improved survival of mice developing acute GVHD and reduced histopathological GVHD grading, serum levels of proinflammatory cytokines, and expansion of alloreactive luc-transgenic T cells. Mechanistically, we could show that ruxolitinib impaired differentiation of CD4(+) T cells into IFN-γ- and IL17A-producing cells, and that both T-cell phenotypes are linked to GVHD. Conversely, ruxolitinib treatment in allo-HCT recipients increased FoxP3(+) regulatory T cells, which are linked to immunologic tolerance. Based on these results, we treated 6 patients with steroid-refractory GVHD with ruxolitinib. All patients responded with respect to clinical GVHD symptoms and serum levels of proinflammatory cytokines. In summary, ruxolitinib represents a novel targeted approach in GVHD by suppression of proinflammatory signaling that mediates tissue damage and by promotion of tolerogenic Treg cells.
Deletion of a single N-linked glycosylation site from the transmembrane envelope protein of human immunodeficiency virus type 1 stops cleavage and transport of gp160 preventing env-mediated fusion (1994)

The transmembrane envelope glycoprotein (gp41) of human immunodeficiency virus type 1 possesses four consensus sites (Asn-X-Ser/Thr) for the incorporation of N-linked sugars situated on the extracellular domain of the molecule. The purpose of this investigation was to determine the significance of each of these sites in relation to the structure and function of the viral envelope glycoprotein. Each of the four sites was removed by in vitro mutagenesis of gp160 sequence in the non-infectious viral clone pEVd1443, so that amino acids 616, 621, 642 and 679 were each changed from asparagine to serine. The effects of mutagenesis were assessed by syncytium assay after wild-type or mutant envelope clones had been transfected into CD4+ HeLa cells. Removal of the glycosylation site at position 642 resulted in the synthesis of precursor gp160 that was neither cleaved, to give gp120 and gp41, nor transported to the plasma membrane of transfected cells. A consequence of these events was that envelope mutant 642 failed to induce syncytia between neighbouring cells in which it had been expressed. The results of this study indicate that N-linked glycosylation of Asn-642 in the glycoprotein produced by the pEVd1443 expression system is necessary for the correct intracellular processing of gp160 to yield surface-expressed, fusogenic gp41.
Photodynamic therapy enhanced by hyperbaric oxygen in acute endoluminal palliation of malignant bronchial stenosis (Clinical pilot study in 40 patients) (2001)

Although the small number of patients does not allow to draw definitive conclusions, the results suggest that combined PDT/HBO represents a new, safe and technically feasible approach. It enables efficient and rapid reduction of the endoluminal tumor load and helps conditioning the patient for further treatment procedures.
Fibroblast Growth Factor 21 Corrects Obesity in Mice (2008)

Fibroblast growth factor 21 (FGF21) is a metabolic regulator that provides efficient and durable glycemic and lipid control in various animal models. However, its potential to treat obesity, a major health concern affecting over 30% of the population, has not been fully explored. Here we report that systemic administration of FGF21 for 2 wk in diet-induced obese and ob/ob mice lowered their mean body weight by 20% predominantly via a reduction in adiposity. Although no decrease in total caloric intake or effect on physical activity was observed, FGF21-treated animals exhibited increased energy expenditure, fat utilization, and lipid excretion, reduced hepatosteatosis, and ameliorated glycemia. Transcriptional and blood cytokine profiling studies revealed effects consistent with the ability of FGF21 to ameliorate insulin and leptin resistance, enhance fat oxidation and suppress de novo lipogenesis in liver as well as to activate futile cycling in adipose. Overall, these data suggest that FGF21 exhibits the therapeutic characteristics necessary for an effective treatment of obesity and fatty liver disease and provides novel insights into the metabolic determinants of these activities.
Pericytes and periendothelial cells of brain parenchyma vessels co-express aminopeptidase N, aminopeptidase A, and nestin (1999)

Within the parenchyma of the CNS, the endothelium of all vessels is surrounded by a layer of cells, pericytes in capillaries and periendothelial or intima smooth muscle cells in other vessels. The origin of these cell types, their relationship, and their role are unclear. However, it has been recently shown that genetically engineered mice that lack pericytes develop microaneurysms at late gestation and die before birth (Lindahl et al. [1997] Science 277:242-245). The goal of this study was to identify in situ molecular markers that would be common to pericytes and periendothelial cells of adult mouse brain. Immunocytochemistry experiments were carried out at the optical and electron-microscopic levels on mouse brain sections with antibodies specific for aminopeptidase N, aminopeptidase A, and the intermediate filament nestin. The results of our experiments show that in all brain parenchyma vessels of all sizes, pericytes and periendothelial cells are immunoreactive for aminopeptidase N, essentially at the plasma membrane level, and are also labeled by nestin specific antibodies, which decorate typical intermediate filaments. In addition, brain pericytes and periendothelial cells are also immunoreactive to monoclonal antibodies to aminopeptidase A. In contrast, pericytes and periendothelial cells do not express microglial markers. Taken together these data show that pericytes and periendothelial intima smooth muscle cells share common markers, suggesting a common origin or function, and are distinct from microglia.
Unifying the Video and Question Attentions for Open-Ended Video Question Answering (2017)

Video question answering is an important task toward scene understanding and visual data retrieval. However, current visual question answering works mainly focus on a single static image, which is distinct from the dynamic and sequential visual data in the real world. Their approaches cannot utilize the temporal information in videos. In this paper, we introduce the task of free-form open-ended video question answering. The open-ended answers enable wider applications compared with the common multiple-choice tasks in Visual-QA. We first propose a data set for open-ended Video-QA with the automatic question generation approaches. Then, we propose our sequential video attention and temporal question attention models. These two models apply the attention mechanism on videos and questions, while preserving the sequential and temporal structures of the guides. The two models are integrated into the model of unified attention. After the video and the question are encoded, the answers are generated wordwisely from our models by a decoder. In the end, we evaluate our models on the proposed data set. The experimental results demonstrate the effectiveness of our proposed model.
Association of the XBP1−116C/G polymorphism with schizophrenia in the Japanese population (2004)

Schizophrenia and bipolar disorder share some clinical features and linkage studies have shown that several loci are common. Recently, the authors found that the -116C-->G substitution in the promotor region of XBP1, a pivotal gene in endoplasmic reticulum (ER) stress response, causes the impairment of ER stress response, and that the -116C/C genotype is a protective factor; in other words the presence of the G allele increases the risk for bipolar disorder. The gene is located on 22q12.1, which is also linked with schizophrenia. The polymorphisms were investigated in 234 schizophrenic patients as compared with controls. Significant difference of genotype distribution was observed, which suggested that the -116C/C genotype is a protective factor for both of the major mental disorders.
Measurement of erythrocyte C4d and complement receptor 1 in systemic lupus erythematosus (2004)

This is the first report of abnormal levels of E-C4d in human disease. We found that abnormally high levels of E-C4d and low levels of E-CR1 are characteristic of SLE, and combined measurement of the 2 molecules has high diagnostic sensitivity and specificity for lupus. Determination of E-C4d/E-CR1 levels may be a useful addition to current tests and criteria for SLE diagnosis.
Optimization and Evaluation of a Belt Driven CVT for a 125 cc, 4 Stroke Scooter (1995)

&lt;div class="htmlview paragraph"&gt;This paper deals with optimization and evaluation of a rubber ‘V’ belt operated continuously variable transmission (CVT) used with a 125 cc,four stroke engine, on a scooter.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The paper consists of five parts. The first part describes the design and commissioning of a CVT Test Rig, where both the driving and driven pulleys are programmably controlled, giving details of its capabilities. The second part deals with Parameter Optimization of a CVT in order to obtain a good compromise between fuel economy and acceleration when used with a 125 cc, four stroke engine. Third part is devoted to determination of Transmission Efficiency of the CVT system and identification of those parameters which influence the efficiency. This aspect has not been dealt in previous publications. Experimental data on Temperature Measurements pertaining to the CVT under actual operating conditions in India, is presented in part four of the paper and this data is later used in the last part of the presentation which dwells on establishing a simulated test sequence to predict the Service Life of the Belt.&lt;/div&gt;
Identification of biosynthetic precursors for the endocannabinoid anandamide in the rat brain (2007)

Anandamide is an endogenous signaling lipid that binds to and activates cannabinoid receptors in the brain and peripheral tissues. The endogenous precursors of anandamide, N-arachidonoyl phosphatidylethanolamines (NArPEs), are a family of complex glycerophospholipids that derive from the exchange reaction of an arachidonoyl group between the sn-1 position of phosphatidylcholine and the primary amine of phosphatidylethanolamine catalyzed by N-acyl transferase activity. A precise characterization of the molecular composition of NArPE species generating anandamide has not yet been reported. In the present study, using liquid chromatography coupled to electrospray ionization ion-trap mass spectrometry, we identified the major endogenous NArPE species, which mainly contained sn-1 alkenyl groups (C16:0, C18:0, C18:1) and monounsaturated (C18:1) or polyunsaturated (C20:4, C22:4, C22:6) acyl groups at the sn-2 position of the glycerol backbone. Using rat brain particulate fractions, we observed a calcium-dependent increase in both NArPEs and anandamide formation after incubation at 37 degrees C for 30 min. Furthermore, a targeted lipidomic analysis showed that Ca(2+) specifically stimulated the formation of PUFA-containing NArPE species. These results reveal a previously unrecognized preference of brain N-acyl transferase activity for polyunsaturated NArPE and provide new insights on the physiological regulation of anandamide biosynthesis.
Nicotinic Agonists and Psychosis (2002)

Schizophrenia patients have insufficient inhibitory processing of identical paired auditory stimuli. This deficient "auditory gating" is thought to have physiological relevance, and its severity correlates with certain measures of both positive and negative symptoms. Schizophrenia patients also represent the heaviest smoking population subgroup. Because smoking temporarily normalizes their auditory gating deficit, this may represent a form of self-medication. Although this deficit is unresponsive to treatment with typical antipsychotic drugs, it does respond to the atypical antipsychotic clozapine. The normalization of this deficit by smoking may account for some of the intense drive to smoke that is experienced by schizophrenia patients. However, the normalizing effect of nicotine is transient and is not observed with repeated administration. Auditory gating is modulated by the alpha7 nicotinic receptor subtype, a rapidly desensitizing low-affinity nicotinic receptor. Agents that selectively activate the alpha7 receptor represent a novel class of therapeutic agents for use in the treatment of schizophrenia. Whether selective alpha7 agonists will have beneficial effects on symptoms other than the auditory gating deficit has not yet been established. The first developed alpha7-selective agonist, 3-2,4-dimethoxybenzylidene anabaseine (DMXB-A), normalizes auditory gating in three distinct animal models of the deficit. DMXB-A is a prototype for this potential new drug class, but proof-of-concept for this type of pharmacotherapy will not be available until the completion of planned clinical trials assessing DMXB-A's effects in schizophrenia patients. Additional avenues to the potential normalization of auditory gating deficits are also discussed, focusing on the novel efficacy of clozapine and the potential utility of allosteric modulators of nicotinic receptors.
SafetyNet: improving the availability of shared memory multiprocessors with global checkpoint/recovery (2003)

We develop an availability solution, called SafetyNet, that uses a unified, lightweight checkpoint/recovery mechanism to support multiple long-latency fault detection schemes. At an abstract level, SafetyNet logically maintains multiple, globally consistent checkpoints of the state of a shared memory multiprocessor, and it recovers to a pre-fault checkpoint of the system and re-executes if a fault is detected. SafetyNet efficiently coordinates checkpoints across the system in logical time and uses "logically atomic" coherence transactions to free checkpoints of transient coherence state. SafetyNet minimizes performance overhead by pipelining checkpoint validation with subsequent parallel execution. We illustrate SafetyNet avoiding system crashes due to either dropped coherence messages or the loss of an interconnection network switch. Using a full-system simulation of a 16-way multiprocessor running commercial workloads, we find that SafetyNet: 1) adds statistically insignificant runtime overhead in the common-case of fault-free execution, and 2) avoids a crash when tolerated faults occur.
Culture of Human Embryonic Stem Cells and the Extracellular Matrix Microenvironment (2005)

Among the major obstacles impeding successful derivation and continuous culture of human embryonic stem cells (hESC) for therapeutic purposes, are the presence of feeder cells and feeder-conditioned media of animal origin. The risk of contamination with xenopathogens makes hESC cultured in this way unsafe for future use in regenerative medicine. A holy grail for investigators in the field will be to establish and maintain new hESC lines in completely feeder-free and serum-free defined conditions. Recently, propagation of hESC has become possible, using mammalian- or human-derived extracellular matrix (ECM) and conditioned medium from feeder cells. In addition, providing a three-dimensional ECM environment can even support the derivation of new hESC. In this review, we examine recent advances in the use and development of substrates suitable for the derivation and maintenance of hESC, and our current understanding of the effects of a three-dimensional ECM milieu on cellular behavior.
An Enhanced CVD Approach to Extensive Nanotube Networks with Directionality (2000)

Extensive networks of oriented single-walled carbon nanotubes (SWNTs) suspended on elevated tower structures can be synthesized by the enhanced chemical vapor deposition (CVD) process described in this article (the experimental setup is shown in the Figure). It is demonstrated that high yields of continuous SWNTs with lengths up to 150 μm can be obtained (see also cover).
Software factories (2003)

The confluence of component based development, model driven development and software product lines forms an approach to application development based on the concept of software factories. This approach promises greater gains in productivity and predictability than those produced by incremental improvements to the current paradigm of object orientation, which have not kept pace with innovation in platform technology. Software factories promise to make application assembly more cost effective through systematic reuse, enabling the formation of supply chains and opening the door to mass customization.
Structure of the 68-kDa neurofilament gene and regulation of its expression. (1990)

The complete structure of the mouse 68-kDa neurofilament (NF-L) gene was elucidated. We cloned cDNAs corresponding to 3.5- and 2.3-kb NF-L mRNA, including their polyadenylation sites. Sequence analysis revealed that these NF-L mRNAs arose from the alternative use of two polyadenylation sites in exon 4. Promoter analysis using NF-L promoter-beta-galactosidase fusion plasmids determined regions responsible for its basic promoter activity, which were located between -328 and -36 base pairs from the transcription initiation site. These promoter fusion plasmids induced a significant level of beta-galactosidase in NF-nonproducing C6 cells as well as in NF-producing PC12h cells. The in vitro transcription assay using HeLa cell extract also showed that this promoter exhibited strong transcriptional activity. Little difference in NF-L mRNA stability was observed between the two cells. However, nuclear run-off assay revealed that the NF-L gene was not transcribed in NF-nonproducing C6 cells. These data suggest that the strong promoter activity of the NF-L gene is repressed in vivo at the transcription initiation level in a tissue-specific manner.
Cell-free mitochondrial DNA copy number variation in head and neck squamous cell carcinoma: A study of non-invasive biomarker from Northeast India (2017)

Head and neck squamous cell carcinoma is the most commonly diagnosed cancer worldwide. The lifestyle, food habits, and customary practices manifest the Northeast Indian population toward higher susceptibility to develop head and neck squamous cell carcinoma. Here, we have investigated the association of smoke and smokeless tobacco, and alcohol with copy number variation of cell-free mitochondrial DNA and cell-free nuclear DNA in cases and controls. Cell-free DNA from plasma was isolated from 50 head and neck squamous cell carcinoma cases and 50 controls with informed written consent using QIAamp Circulating Nucleic Acid Kit. Real-time polymerase chain reaction was done for copy number variation in cell-free mitochondrial DNA and cell-free nuclear DNA. Receiver operating characteristic curve analysis was performed to evaluate the diagnostic application between the two study groups using clinicopathological parameters. The levels of cell-free nuclear DNA and cell-free mitochondrial DNA of cases in association with smoke and smokeless tobacco, alcohol with smoking (p < 0.05) were significantly higher (p < 0.01 and p < 0.001, respectively) than controls. Using receiver operating characteristic curve analysis between head and neck squamous cell carcinoma cases and controls, we distinguished cell-free mitochondrial DNA (cutoff: 19.84 raw Ct; sensitivity: 84%; specificity: 100%; p < 0.001) and cell-free nuclear DNA (cutoff: 463,282 genomic equivalent/mL; sensitivity: 53%; specificity: 87%; p < 0.001). The copy number variation in cases (cell-free nuclear DNA: 5451.66 genomic equivalent/mL and cell-free mitochondrial DNA: 29,103,476.15 genomic equivalent/mL) and controls (cell-free nuclear DNA: 1650.9 genomic equivalent/mL and cell-free mitochondrial DNA: 9,189,312.54 genomic equivalent/mL), respectively. Our result indicates that the cell-free mitochondrial DNA content is highly associated with smoke and smokeless tobacco, betel quid chewing, and alcohol which shows greater promises, holding the key characteristics of diagnostic biomarkers, that is, minimal invasiveness, high specificity, and sensitivity.