gebhart/patrepeval huggingface dataset:
Fibrous capsule formation around titanium and copper (2007)

Previous studies suggest that implant material properties influence the quality and quantity of fibrous capsule around the implant. However, the precise relation between material surface chemistry, early inflammatory response, and fibrous subsequent repair outcome is still unknown. Titanium (Ti) and copper (Cu), surfaces with different inflammatory potential, were implanted subcutaneously in rats and retrieved fibrous capsules were analyzed after 28 and 56 days. Histological examinations show pronounced differences in capsule morphology. The fibrous capsule around Ti was thinner than that around Cu, with less number of the inflammatory cells in the layer close to the implant surface, and less and smaller blood vessels. The capsule around Cu was thick, with a large number of the inflammatory cells, particularly macrophages and giant cells, and increased number of blood vessels. Our study suggests that material surface properties, which initiate early, multiple cellular inflammatory events, are also associated with increased fibrosis and angiogenesis during repair phase.
Purification and Properties of Glycine Oxidase from <i>Pseudomonas putida</i> KT2440 (2015)

Glycine oxidase, encoded by the thiO gene, participates in the biosynthesis of thiamin by providing glyoxyl imine to form the thiazole moiety of thiamin. We have purified and characterized ThiO from Pseudomonas putida KT2440. It has a monomeric structure that is distinct from the homotetrameric ThiOs from Bacillus subtilis and Geobacillus kaustophilus. The P. putida ThiO is unique in that glycine is its preferred substrate, which differs markedly from the B. subtilis and G. kaustophilus enzymes that use D-proline as the preferred substrate.
Hepatic Very Low Density Lipoprotein-ApoB Overproduction Is Associated with Attenuated Hepatic Insulin Signaling and Overexpression of Protein-tyrosine Phosphatase 1B in a Fructose-fed Hamster Model of Insulin Resistance (2002)

A fructose-fed hamster model of insulin resistance was previously documented to exhibit marked hepatic very low density lipoprotein (VLDL) overproduction. Here, we investigated whether VLDL overproduction was associated with down-regulation of hepatic insulin signaling and insulin resistance. Hepatocytes isolated from fructose-fed hamsters exhibited significantly reduced tyrosine phosphorylation of the insulin receptor and insulin receptor substrates 1 and 2. Phosphatidylinositol 3-kinase activity as well as insulin-stimulated Akt-Ser473 and Akt-Thr308 phosphorylation were also significantly reduced with fructose feeding. Interestingly, the protein mass and activity of protein-tyrosine phosphatase-1B (PTP-1B) were significantly higher in fructose-fed hamster hepatocytes. Chronic ex vivo exposure of control hamster hepatocytes to high insulin also appeared to attenuate insulin signaling and increase PTP-1B. Elevation in PTP-1B coincided with marked suppression of ER-60, a cysteine protease postulated to play a role in intracellular apoB degradation, and an increase in the synthesis and secretion of apoB. Sodium orthovanadate, a general phosphatase inhibitor, partially restored insulin receptor phosphorylation and significantly reduced apoB secretion. In summary, we hypothesize that fructose feeding induces hepatic insulin resistance at least in part via an increase in expression of PTP-1B. Induction of hepatic insulin resistance may then contribute to reduced apoB degradation and enhanced VLDL particle assembly and secretion.
Novel Microbial-Based Immunotherapy Approach for Crohn's Disease (2019)

<b>Background:</b> Current Crohn's disease (CD) therapies focus on suppressing immune function and come with consequent risk, such as infection and cancer. Notwithstanding, most CD patients still experience disease progression. There is a need for new CD treatment strategies that offer better health outcomes for patients. <b>Aims:</b> To assess safety, efficacy, and tolerability of a novel microbial-derived immunotherapy, QBECO, that aims to restore rather than suppress immune function in CD. <b>Methods:</b> A randomized, double-blind, placebo-controlled trial was conducted in 68 patients with moderate-to-severe CD. Primary endpoints: safety and Week 8 clinical improvement. Secondary endpoints: Week 8 clinical response and remission. Week 8 responders continued blinded treatment through Week 16; non-responders received open-label QBECO from Weeks 9-16. Exploratory analyses included immune biomarker and genotype assessments. <b>Results:</b> QBECO was well-tolerated. Mean reduction in Crohn's Disease Activity Index (CDAI) score was -68 for QBECO vs. -31 for placebo at Week 8. Improvement with QBECO continued through Week 16 (-130 CDAI reduction). Week 8 QBECO clinical response, improvement and remission rates were 41.2%, 32.4%, 29.4% vs. 26.5%, 23.5%, 23.5% for placebo. TNFα inhibitor-naïve subjects achieved higher response rates at Week 8 with QBECO (64%) vs. placebo (26%). Specific immune biomarkers were identified that linked to QBECO response. <b>Conclusion:</b> This proof-of-concept study supports further investigation for the use of QBECO as a novel immunotherapy approach for CD. Biomarker analyses suggests it may be feasible to personalize CD treatment with QBECO. Larger trials are now needed to confirm clinical improvement and the unique biological findings. <b>Clinical Trial Number:</b> NCT01809275 (https://clinicaltrials.gov/ct2/show/NCT01809275).
POP promotions for alcolhol: increasing brand loyalty or just increasing binge drinking? (2006)

The consumption of alcohol by young Australians in general, and at risky levels has increased. University students, as part of this group, display consistent and increasing risky drinking patterns. One key area of interest in understanding this situation is the use of alcohol advertising and marketing. Of particular interest to this research is the use of point-of-purchase promotions in licensed venues and the impact they may have on consumption. In order to help understand these promotions, focus groups were conducted with male university students between the age of 18 and 24 years from the University of Wollongong. Overall, the perception of these promotions was that they encouraged male university students to drink at risky levels. Many respondents reported increasing their own personal drinking levels to participate in a promotion and participants would generally consume the desired amount in the one sitting, rather than over several.
Successful expansion of functional and stable regulatory T cells for immunotherapy in liver transplantation (2016)

Strategies to prevent organ transplant rejection whilst minimizing long-term immunosuppression are currently under intense investigation with regulatory T cells (Tregs) nearing clinical application. The clinical trial, ThRIL, recently commenced at King's College London, proposes to use Treg cell therapy to induce tolerance in liver transplant recipients, the success of which has the potential to revolutionize the management of these patients and enable a future of drug-free transplants. This is the first report of the manufacture of clinical grade Tregs from prospective liver transplant recipients via a CliniMACS-based GMP isolation technique and expanded using anti-CD3/CD28 beads, IL-2 and rapamycin. We report the enrichment of a pure, stable population of Tregs (>95% CD4(+)CD25(+)FOXP3(+)), reaching adequate numbers for their clinical application. Our protocol proved successful in, influencing the expansion of superior functional Tregs, as compared to freshly isolated cells, whilst also preventing their conversion to Th17 cells under pro-inflammatory conditions. We conclude with the manufacture of the final Treg product in the clinical research facility (CRF), a prerequisite for the clinical application of these cells. The data presented in this manuscript together with the much-anticipated clinical results from ThRIL, will undoubtedly inform the improved management of the liver transplant recipient.
α1-Antitrypsin Determines the Pattern of Emphysema and Function in Tobacco Smoke–exposed Mice: Parallels with Human Disease (2002)

Cigarette smoking in humans is associated with various patterns of emphysema and functional consequences. We tested the hypothesis that variations in alpha1-antitrypsin expression modulate the pattern of emphysema and functional consequences in cigarette smoke-exposed mice. We compared the effects of up to 6 months of cigarette smoke exposure in C57BL/6J (C57) mice and in low-alpha1-antitrypsin, C57BL/6J pa+/pa+ (pallid) mice. At the end of the experiment, we determined lung mechanical properties, the extent (mean linear intercept) and type of emphysema, and the cellular inflammatory response. After 4 months of cigarette smoking, pallid smoking mice, but not C57 smoking mice, had a significant increase in mean linear intercept. After 6 months of smoke exposure, C57 smoking mice and pallid smoking mice had similar degrees of emphysema. The pattern of emphysema in pallid smoking mice was more diffuse than in C57 smoking mice, affecting all airspaces. Pallid mice, but not C57 mice, developed a T cell inflammation in the alveolar wall after 6 months of smoking (p < 0.01). Although lung compliance was not changed in C57 smoking mice after smoke exposure, it increased significantly in pallid smoking mice over the 6 months of exposure (p < 0.0082). In summary, cigarette smoking induces emphysema in C57 and pallid mice, but the emphysema, inflammatory infiltrate, and resulting physiologic abnormalities were substantially different in the two strains, with the C57 and pallid mice exhibiting features similar to centrilobular and panlobular emphysema, respectively.
The Significance of C16 Fatty Acids in the <i>sn</i>-2 Positions of Glycerolipids in the Photosynthetic Growth of <i>Synechocystis</i> sp. PCC6803 (2006)

Most extant cyanobacteria contain C16 fatty acids in the sn-2 positions of glycerolipids, which are regulated by lysophosphatidic acid acyltransferase (LPAAT; EC 2.3.1.51). Synechocystis sp. PCC6803 contains sll1848, sll1752, and slr2060 as putative acyltransferase genes. sll1848 was recently reported to encode an indispensable palmitoyl-specific LPAAT; however, here we show that each of the three genes is dispensable. Delta1848 and Delta1848 Delta2060 cells had markedly higher contents of stearate (18:0), oleate (18:1), and linoleate (18:2) in place of palmitate (16:0) in the sn-2 positions, suggesting that Delta1848 Delta2060 cells incorporate 18:0 and 18:1 in the sn-2 positions. The levels of sll1752 transcripts increased in Delta1848 Delta2060 cells. This was accompanied by increased LPAAT activity toward 18:0 coenzyme A and its derivative in the membrane fraction. From these findings, together with the activity of a recombinant sll1752 protein and complementation of the Escherichia coli LPAAT mutant plsC, we conclude that sll1752 encodes a second LPAAT that prefers stearoyl and oleoyl substrates. Delta1848 Delta2060 cells grew slowly at 30 degrees C at lower cell density, and exhibited more severe damage at 20 degrees C than wild-type cells. Furthermore, Delta1848 Delta2060 cells exhibited photoinhibition more severely than wild-type cells. A phycobilisome core-membrane linker protein (slr0335) was also found to be susceptible to protein extraction under our conditions; its content decreased in the membrane fractions of Delta1848 Delta2060 cells. We conclude that C16 fatty acids in sn-2 positions are preferred in the photosynthetic growth of this cyanobacterium, despite sll1752 orthologs being conserved in most cyanobacteria. However, no sll1752 ortholog is conserved among photosynthetic eukaryotes including Cyanidioschyzon merolae.
Human Pose Estimation Using Convolutional Neural Networks (2019)

Human pose estimation has always been a challenging problem that holds great attention, it has the widespread and extensive variety of uses from the classification of images to activity acknowledgment, main challenge is the detection and localization of the key points in the variation of several body poses. To resolve this issue, substantial research work have been done in this area. This paper discusses the issues in human pose estimation and gives the overview of considerable research work in pose estimation, including deep learning approach and customary image-based techniques. After analyzing several results and detecting the restrictions, the author has reconstructed a simple model using convolutional neural network that estimates the poses and demonstrates the potential of CNN's. The author concludes with a few promising bearings and directions that have to be explored for future research.
Common Gate Transformer Feedback LNA in a High IIP3 Current Mode RF CMOS Front-End (2006)

A new topology of transformer based low noise amplifier is presented. The structure realizes a low noise input match and a current gain greater than one by a current to current positive feedback closed around a common gate stage. The amplifier is inserted in a high linearity current mode RF front-end receiver working between 4.15-4.4GHz with a NF of 4.2dB, a gain of 24.2dB and an IIP3 of -2dBm
Structural studies of of "active complex" of bleomycin: assignment of ligands to the ferrous ion in a ferrous-bleomycin-carbon monoxide complex. (1979)

Proton NMR studies at 360 MHz establish the binary Fe(II)-bleomycin complex to be paramagnetic with a spectrum covering 70 ppm. Addition of carbon monoxide generates a stable, diamagnetic Fe(II)-bleomycin-CO complex that is a putative structural analog of the "active" Fe(II)-bleomycin-O2 complex. The following six groups have been determined to be coordinated to the Fe(II) ion from analysis of the highly resolved 1H NMR spectra of this complex: CO, the primary and secondary amine nitrogens of the beta-aminoalanine moiety, the carbamoyl moiety on the 3-position of mannose, the pyrimidine N-1, and the imidazole N-1. The Fe(II)-bleomycin-CO complex binds to DNA, as shown by fluorescence quenching experiments, but Fe(II)-bleomycin-CO does not mediate thymine release. These results necessitate a major revision in the current model for metal coordination to bleomycin.
A Splice-Site Mutation in GABRG2 Associated With Childhood Absence Epilepsy and Febrile Convulsions (2002)

Our study identified a splice-donor-site mutation that was probably causing a nonfunctional GABRG2 subunit. This mutation occurred in heterozygosity in the affected members of a single nuclear family, exhibiting a phenotypic spectrum of childhood absence epilepsy and febrile convulsions. The GABRG2 gene seems to confer a rare rather than a frequent major susceptibility effect to common idiopathic absence epilepsy syndromes.
A National Human Neuroimaging Collaboratory Enabled by the Biomedical Informatics Research Network (BIRN) (2008)

The aggregation of imaging, clinical, and behavioral data from multiple independent institutions and researchers presents both a great opportunity for biomedical research as well as a formidable challenge. Many research groups have well-established data collection and analysis procedures, as well as data and metadata format requirements that are particular to that group. Moreover, the types of data and metadata collected are quite diverse, including image, physiological, and behavioral data, as well as descriptions of experimental design, and preprocessing and analysis methods. Each of these types of data utilizes a variety of software tools for collection, storage, and processing. Furthermore sites are reluctant to release control over the distribution and access to the data and the tools. To address these needs, the Biomedical Informatics Research Network (BIRN) has developed a federated and distributed infrastructure for the storage, retrieval, analysis, and documentation of biomedical imaging data. The infrastructure consists of distributed data collections hosted on dedicated storage and computational resources located at each participating site, a federated data management system and data integration environment, an Extensible Markup Language (XML) schema for data exchange, and analysis pipelines, designed to leverage both the distributed data management environment and the available grid computing resources.
Cascaded classifier approach based on Adaboost to increase detection rate of rare network attack categories (2012)

Network intrusion detection often finds a difficulty in creating classifiers that could handle unequal distributed attack categories. Generally R2L and U2R attacks are very rare attacks and even in KDD Cup99 dataset, these attacks are only 2% of overall datasets. So, these result in model not able to efficiently learn the characteristics of rare categories and this will result in poor detection rates of rare attack categories like R2L and U2R attacks. We introduce a new approach called cascading classification model based on AdaBoost and Bayesian Network Classifier that can improve the detection rate of rare network attack categories. In this approach we train two classifiers with two different training sets. The KDD Cup99 dataset was splitted into two training sets where one contains full of non rare attacks datasets and other contains datasets of rare attack categories. This cascaded classifier approach increases the detection rates of both rare network attack categories and also it increase overall detection rate of an IDS model. The higher detection rates are due to the mitigation of the influence from the dominant categories if the rare attack categories are separated from the dataset.
Genuine ARP (GARP) (2011)

Address Resolution Protocol (ARP) is used to map the network address (IP address) to a physical address (MAC address). Being a stateless protocol and lacking proper authentication mechanism in the ARP messages, ARP is vulnerable for cache poisoning attack. Attacker can perform Man-In-The-Middle (MITM) attack or Denial of Service (DoS) attack and can access sensitive information, modify the contents, or deny the host from getting services. Different techniques for the detection and prevention of ARP cache poisoning attack have been proposed. Detection techniques (such as ARPWatch and Intrusion Detection techniques) generate false positives. Some prevention technique makes change in the switch itself and some uses cryptographic techniques. Secure-ARP and Ticket based ARP (TARP) are cryptographic techniques but suffer from single point failure and ticket flooding attacks respectively. ARP is a stateless protocol and ARP messages lacks the address authentication mechanism. As an ARP reply is unicast, all host systems in the LAN are not aware of the attacker present in the LAN. In this paper, we have proposed a protocol known as "Genuine Address Resolution Protocol (GARP)". Two novel concepts, viz., broadcastbased reply, and the Certifier for proof of IP address ownership have been proposed in GARP. As a reply is broadcast, the host, whose IP the attacker is using for attack, is aware of the attacker and subsequently makes other hosts in the LAN also aware of the attacker. Thus, the protocol prevents possible attack from the same attacker in the future. Statefulness is achieved by two tables, viz., the pending table and the blacklist table. The pending table holds the reply till its genuineness is proved and the blacklist table holds the MAC of attacker. Furthermore, the Certificate Authority is responsible for monitoring the ARP activities, which intervenes with appropriate messages at appropriate instances. The Dynamic Host Configuration Protocol (DHCP) server could be loaded with the additional service of monitoring ARP activities. The protocol has been implemented on Linux operating system. GARP was tested for various possible cases of ARP cache poisoning attack. From the results, it could be inferred that the GARP provides security against ARP cache poisoning attacks.
Cross-stratum orchestration and flexgrid optical networks for data center federations (2013)

Current inter-data-center connections are configured as static big fat pipes, which entails large bit rate over-provisioning and thus high operational costs for DC operators. On the other hand, network operators cannot share such connections between customers, because DC traffic varies greatly over time. Those connections are used to perform virtual machine migration and database synchronization among federated DCs, allowing elastic DC operations. To improve resource utilization and save costs, dynamic inter-DC connectivity is currently being targeted from a research point of view and in standardization form. In this article, we show that dynamic connectivity is not enough to guarantee elastic DC operations and might lead to poor performance provided that not enough overprovisioning of network resources is performed. To alleviate it to some extent, we propose using the flexgrid optical technology that enables finer spectrum granularity adaptation and the ability to dynamically increase and decrease the amount of optical resources assigned to connections. DCs can be interconnected through a flexgrid-based network controlled using a centralized software defined network, based on the architecture currently being proposed by the IETF; a cross-stratum orchestrator architecture coordinates DC and network elastically. Illustrative results show that dynamic elastic connectivity provides benefits by reducing the amount of overprovisioned network resources and facilitating elastic DC operations.
Translation dynamics of single mRNAs in live cells and neurons (2016)

Translation is the fundamental biological process converting mRNA information into proteins. Single-molecule imaging in live cells has illuminated the dynamics of RNA transcription; however, it is not yet applicable to translation. Here, we report single-molecule imaging of nascent peptides (SINAPS) to assess translation in live cells. The approach provides direct readout of initiation, elongation, and location of translation. We show that mRNAs coding for endoplasmic reticulum (ER) proteins are translated when they encounter the ER membrane. Single-molecule fluorescence recovery after photobleaching provides direct measurement of elongation speed (5 amino acids per second). In primary neurons, mRNAs are translated in proximal dendrites but repressed in distal dendrites and display "bursting" translation. This technology provides a tool with which to address the spatiotemporal translation mechanism of single mRNAs in living cells.
SIZE CHARACTERISTICS OF TESTS FOR SAMPLE SELECTION BIAS: A MONTE CARLO COMPARISON AND EMPIRICAL EXAMPLE (2001)

The t-test of an individual coefficient is used widely in models of qualitative choice. However, it is well known that the t-test can yield misleading results when the sample size is small. This paper provides some experimental evidence on the finite sample properties of the t-test in models with sample selection biases, through a comparison of the t-test with the likelihood ratio and Lagrange multiplier tests, which are asymptotically equivalent to the squared t-test. The finite sample problems with the t-test are shown to be alarming, and much more serious than in models such as binary choice models. An empirical example is also presented to highlight the differences in the calculated test statistics.