gebhart/patrepeval huggingface dataset:
Macrophage‐dependent induction of the Salmonella pathogenicity island 2 type III secretion system and its role in intracellular survival (1998)

Salmonella pathogenicity island 2 (SPI-2) encodes a putative type III secretion system necessary for systemic infection in animals. We have investigated the transcriptional organization and regulation of SPI-2 by creating gfp fusions throughout the entire gene cluster. These gfp fusions demonstrated that SPI-2 genes encoding structural, regulatory and previously uncharacterized putative secreted proteins are preferentially expressed in the intracellular environment of the host macrophage. Furthermore, the transcription of these genes within host cells was dependent on the two-component regulatory system SsrA/SsrB and an acidic phagosomal environment. Most SPI-2 mutants failed to replicate to the same level as wild-type strains in murine macrophages and human epithelial cells. In orally infected mice, SPI-2 mutants colonized the Peyer's patches but did not progress to the mesenteric lymph nodes. We conclude that SPI-2 genes are specifically expressed upon entry into mammalian cells and are required for intracellular growth in host cells in vivo and in vitro.
Optical Absorption Spectra of Electrically Gated Bilayer Graphene (2010)

The electronic structure and optical response of electrically gated bilayer graphene are studied by first-principles approaches. We have obtained the induced band gap that is in good agreement with experiment when the applied electric field is less than 1.5 V/nm. The infrared optical absorbance is calculated within the single-particle excitation picture and its fine structures are presented. In addition, the calculated infrared optical absorbance is found to be strongly depending on stacking styles of bilayer graphene and the polarization direction of the incident light, which provides efficient ways to identify the electric-field intensity and stacking styles in experiment. Finally, many-electron effects are discussed.
Point of care testing (2001)

Point of care testing, otherwise referred to as near patient, bedside, or extra laboratory testing, is not new. Many of the early “diagnostic tests” were first done at the bedside—for example, urine testing. Over the past few years, however, analytical systems have been developed that enable a wide range of tests to be done quickly and simply without the need for sophisticated laboratory equipment.1

The key objective of point of care testing is to generate a result quickly so that appropriate treatment can be implemented, leading to an improved clinical or economic outcome (figure). This article sets out the requirements for delivering an effective point of care testing service and reviews the evidence of the clinical and economic effectiveness of point of care testing.

#### Summary points

Point of care testing requires trained operators to ensure a good quality service

Testing is effective only if action taken on the result

Testing has been shown to reduce hospital stay, improve adherence to treatment, and reduce complications Although point of care testing is more expensive than laboratory testing, it produces wider economic benefits

I searched the literature with Medline and Embase using the key phrases “point of care testing,” “bedside testing,” “near patient testing,” and “extra laboratory testing.” I also hand searched relevant laboratory medicine and disease related journals (such as those on diabetes) and health technology assessment reports.

Two broad types of technology support point of care testing: small bench top analysers (for example, blood gas and electrolyte systems) and hand held, single use devices (such as urine albumin, blood glucose, and coagulation tests). The bench top systems are smaller versions of laboratory analysers in which vulnerable operator dependent steps have been automated—for example, automatic flushing of sample after analysis, calibration, and quality control. Hand held devices have been developed using microfabrication techniques. …
Immunotherapy for bladder cancer (2015)

It is nearly 40 years since Bacillus Calmette-Guérin (BCG) was first used as an immunotherapy to treat superficial bladder cancer. Despite its limitations, to date it has not been surpassed by any other treatment. As a better understanding of its mechanism of action and the clinical response to it have evolved, some of the questions around optimal dosing and treatment protocols have been answered. However, its potential for toxicity and failure to produce the desired clinical effect in a significant cohort of patients presents an ongoing challenge to clinicians and researchers alike. This review summarizes the evidence behind the established mechanism of action of BCG in bladder cancer, highlighting the extensive array of immune molecules that have been implicated in its action. The clinical aspects of BCG are discussed, including its role in reducing recurrence and progression, the optimal treatment regime, toxicity and, in light of new evidence, whether or not there is a superior BCG strain. The problems of toxicity and non-responders to BCG have led to development of new techniques aimed at addressing these pitfalls. The progress made in the laboratory has led to the identification of novel targets for the development of new immunotherapies. This includes the potential augmentation of BCG with various immune factors through to techniques avoiding the use of BCG altogether; for example, using interferon-activated mononuclear cells, BCG cell wall, or BCG cell wall skeleton. The potential role of gene, virus, or photodynamic therapy as an alternative to BCG is also reviewed. Recent interest in the immune check point system has led to the development of monoclonal antibodies against proteins involved in this pathway. Early findings suggest benefit in metastatic disease, although the role in superficial bladder cancer remains unclear.
Osajin and Pomiferin, Two Isoflavones Purified from Osage Orange Fruits, Tested for Repellency to the Maize Weevil (Coleoptera: Curculionidae) (2000)

The fruit of the osage orange tree, Maclura pomifera (Raf.) Schneid (Moraceae), has long been thought to be repellent to insects. A preliminary study reported here confirmed repellency of fruit extracts to the maize weevil, Sitophilus zeamais Motschulsky. Two isoflavones, osajin and pomiferin, were isolated from the mature fruit of M. pomifera in high purity (≥95%). Testing of purified osajin and pomiferin failed to show repellency. Repellency is likely caused by factors other than isoflavones in the fruit.
Adaptive bit allocation scheme in predictive coding of speech (2005)

An adaptive predictive coding with adaptive bit allocation (APC-AB) is presented for speech encoding at low to medium bit rates (6.4kb/s-24kb/s). In this system, a split-band predictive coding scheme and a bit allocation scheme are employed in order to remove the redundancies due to a periodic concentration of the prediction residual energy as well as nonuniform nature of the speech spectrum. Quantization bits are dynamically allocated both over the sub-bands(frequency domain) and over the subintervals(time domain) in accordance with the distribution of the residual energies in the time-frequency domain. Optimum bit allocation is derived based on the mean square error criterion on the speech waveform, and the SNR gain is presented in relation to the prediction gain of the full-band signal. This system is evaluated in terms of the segmental SNR and speech quality. The result shows that the APC-AB system has advantage over the conventional full-band APC system in the segmental SNR and the stability of the prediction loop. It was also shown that this system can provide speech quality subjectively equivalent to 7 bit Log-PCM at 16 kb/s, and to 6 bit Log-PCM at 9.6 kb/s.
Resistance to chemotherapy: new treatments and novel insights into an old problem (2008)

Resistance to cancer chemotherapeutic treatment is a common phenomenon, especially in progressive disease. The generation of cellular models of drug resistance has been pivotal in unravelling the main effectors of resistance to traditional chemotherapy at the molecular level (i.e. intracellular drug inactivation, detoxifying systems, defects in DNA repair, apoptosis evasion, membrane transporters and cell adhesion). The development of targeted therapies has also been followed by resistance, reminiscent of an evolutionary arms race, as exemplified by imatinib and other BCR-ABL inhibitors for the treatment of chronic myelogenous leukaemia. Although traditionally associated with the last stages of the disease, recent findings with minimally transformed pretumorigenic primary human cells indicate that the ability to generate drug resistance arises early during the tumorigenic process, before the full transformation. Novel technologies, such as genome profiling, have in certain cases predicted the outcome of chemotherapy and undoubtedly have tremendous potential for the future. In addition, the novel cancer stem cell paradigm raises the prospect of cell-targeted therapies instead of treatment directed against the whole tumour.
Determination of Gait Events Using an Externally Mounted Shank Accelerometer (2013)

Biomechanical analysis requires the determination of specific foot contact events. This is typically achieved using force platform information; however, when force platforms are unavailable, alternative methods are necessary. A method was developed for the determination of gait events using an accelerometer mounted to the distal tibia, measuring axial accelerations. The aim of the investigation was to determine the efficacy of this method. Sixteen participants ran at 4.0 m/s ± 5%. Synchronized tibial accelerations and vertical ground reaction forces were sampled at 1000 Hz as participants struck a force platform with their dominant foot. Events determined using the accelerometer, were compared with the corresponding events determined using the force platform. Mean errors of 1.68 and 5.46 ms for average and absolute errors were observed for heel strike and of -3.59 and 5.00 ms for toe-off. Mean and absolute errors of 5.18 and 11.47 ms were also found for the duration of the stance phase. Strong correlations (r = .96) were also observed between duration of stance obtained using the two different methods. The error values compare favorably to other alternative methods of predicting gait events. This suggests that shank-mounted accelerometers can be used to accurately and reliably detect gait events.
Impact of education and provision of complementary feeding on growth and morbidity in children less than 2 years of age in developing countries: a systematic review (2013)

Complementary feeding interventions have a potential to improve the nutritional status of children in developing countries. However, large scale high quality randomized controlled trials are required to assess the actual impact of this intervention on growth and morbidity in children 6-24 months of age. Education should be combined with provision of complementary foods that are affordable, particularly for children in food insecure countries.
Compression and self-entanglement of single DNA molecules under uniform electric field (2011)

We experimentally study the effects of a uniform electric field on the conformation of single DNA molecules. We demonstrate that a moderate electric field (~200 V/cm) strongly compresses isolated DNA polymer coils into isotropic globules. Insight into the nature of these compressed states is gained by following the expansion of the molecules back to equilibrium after halting the electric field. We observe two distinct types of expansion modes: a continuous molecular expansion analogous to a compressed spring expanding, and a much slower expansion characterized by two long-lived metastable states. Fluorescence microscopy and stretching experiments reveal that the metastable states are the result of intramolecular self-entanglements induced by the electric field. These results have broad importance in DNA separations and single molecule genomics, polymer rheology, and DNA-based nanofabrication.
A Survey of Distributed Garbage Collection Techniques (1994)

This paper is organised as follows. Section 2 first introduces our object model. Section 3 describes the reference count-based approach. In particular, we compare those techniques according to their resilience to message failures. Such counting-based techniques are unable to collect cycles of garbage and must assume that they are rare enough to minimize memory leakage. A number of hybrid proposals as explained in 5 which combine counting-based techniques with a global (tracing-based) technique. Section (explained in Section 6) surveys some enhanced techniques well suited to distributed settings. Section (explained in Section 7) sums up our conclusions and proposes taxonomy of the reviewed techniques. 2 Model
Cytokine-dependent long-term culture of highly enriched precursors of hematopoietic progenitor cells from human bone marrow. (1990)

Human marrow cells positive for the CD34 antigen but not expressing HLA-DR, CD15, or CD71 antigens were isolated. In a liquid culture system supplemented with 48-hourly additions of recombinant interleukins IL-1 alpha, IL-3, IL-6, or granulocyte/macrophage colony-stimulating factor (GM-CSF), these cells were capable of sustaining in vitro hematopoiesis for up to eight weeks. The establishment of an adherent cell layer was never observed. Cultures containing no exogenous cytokine produced clonogenic cells for only 1 wk. IL-1 alpha and IL-6 were alone able to support hematopoiesis for 2 or 3 wk. Cells maintained with GM-CSF proliferated and contained assayable colony-forming cells for 3 or 4 wk, while maximal cellular expansion and generation of assayable progenitor cells occurred in the presence of IL-3 for 4-5 wk. When IL-3 was combined with IL-1 alpha or IL-6, hematopoiesis was sustained for 8 wks. Basophil numbers were markedly increased in the presence of IL-3. These studies indicate that marrow subpopulations can sustain hematopoiesis in vitro in the presence of repeated additions of cytokines. We conclude that a major function of marrow adherent cells in long-term cultures is that of providing cytokines which promote the proliferation and differentiation of primitive hematopoietic cells.
Impact of whole genome amplification on analysis of copy number variants (2008)

Large-scale copy number variants (CNVs) have recently been recognized to play a role in human genome variation and disease. Approaches for analysis of CNVs in small samples such as microdissected tissues can be confounded by limited amounts of material. To facilitate analyses of such samples, whole genome amplification (WGA) techniques were developed. In this study, we explored the impact of Phi29 multiple-strand displacement amplification on detection of CNVs using oligonucleotide arrays. We extracted DNA from fresh frozen lymph node samples and used this for amplification and analysis on the Affymetrix Mapping 500k SNP array platform. We demonstrated that the WGA procedure introduces hundreds of potentially confounding CNV artifacts that can obscure detection of bona fide variants. Our analysis indicates that many artifacts are reproducible, and may correlate with proximity to chromosome ends and GC content. Pair-wise comparison of amplified products considerably reduced the number of apparent artifacts and partially restored the ability to detect real CNVs. Our results suggest WGA material may be appropriate for copy number analysis when amplified samples are compared to similarly amplified samples and that only the CNVs with the greatest significance values detected by such comparisons are likely to be representative of the unamplified samples.
On the mechanism of inhibition of the veratryl alcohol oxidase activity of lignin peroxidase H2 by EDTA. (1992)

The mechanism of inhibition of the veratryl alcohol oxidase activity of lignin peroxidase H2 (LiPH2) by EDTA was investigated. It was found that EDTA was decarboxylated and that cytochrome c, nitro blue tetrazolium, ferric iron, and molecular oxygen were reduced in a reaction mixture containing LiPH2, H2O2, veratryl alcohol, and EDTA. The reductive activity observed with LiPH2 followed first order kinetics with respect to the concentration of EDTA. Stoichiometry studies showed that in the presence of sufficient EDTA, 1.7 mol of ferric iron were reduced per mole of H2O2 added to the reaction mixture. Superoxide- and EDTA-derived radicals were detected by ESR spin trapping upon incubation of LiPH2 with H2O2, veratryl alcohol, and EDTA. The Km values of veratryl alcohol and H2O2 remained the same for both the oxidative and reductive activities of LiPH2. Reductive activity was also observed with LiPH2 and EDTA using other free radical mediators in the place of veratryl alcohol, such as 1,4-dimethoxybenzene, 1,2,3- and 1,2,4-trimethoxybenzenes, and 1,2,4,5-tetramethoxybenzene. EDTA reduced the cation radical of 1,2,4,5-tetramethoxybenzene formed by LiPH2 in the presence of H2O2. Hence, it is proposed that the apparent inhibition of the veratryl alcohol oxidase activity of LiPH2 by EDTA is due to the reduction of the veratryl alcohol cation radical intermediate back to veratryl alcohol by EDTA. The reduction of cytochrome c, nitro blue tetrazolium, ferric ion, and molecular oxygen appears to be mediated by the EDTA radical formed by reduction of the veratryl alcohol cation radical.
Diels-Alder-based thermo-reversibly crosslinked polymers: Interplay of crosslinking density, network mobility, kinetics and stereoisomerism (2020)

Polymers crosslinked through thermo-reversible furan/maleimide Diels-Alder chemistry have been widely explored, since they stand as an ingenious design for reprocessable and self-healing thermosets and elastomers. For these polymeric products, crosslinking density plays a key role on the polymer thermo-reversibility. However, how this degree of network interconnectivity influences the kinetics of thermal reversibility has not yet been addressed. In order to tackle this problem, furan-grafted polyketones crosslinked by a bi-functional maleimide were prepared with different ratios between maleimide and furan groups. The thermo-reversible dynamics of the prepared polymers were then studied by rheology and differential scanning calorimetry. Here we show that, the thermo-reversible process occurs faster and at lower temperatures in polymers with lower crosslinking densities. Network mobility is responsible for this effect. It allows the formulations to rearrange their polymer network differently through the heating-cooling cycles. The results also indicate that the crosslinking density rather than the stereoisomerism of the Diels-Alder adducts plays a larger role in the reversible behavior of the system. Additionally, the thermo-reversible features of the polymer were shown to be dependent on its thermal history. This work impacts the development of reprocessable and self-healing crosslinked polymers, and the design of the corresponding reprocessing and healing procedures.
Tumour necrosis factor α inhibitors in the treatment of childhood uveitis (2006)

Anti-TNF-alpha treatment was beneficial in a high percentage of patients with childhood uveitis refractory to standard immunosuppressive treatment. Infliximab resulted in better clinical responses with less ocular complications than etanercept.
Evidence That Silencing of the HPRT Promoter by DNA Methylation Is Mediated by Critical CpG Sites (2001)

The strong correlation between promoter hypermethylation and gene silencing suggests that promoter methylation represses transcription. To identify methylation sites that may be critical for maintaining repression of the human HPRT gene, we treated human/hamster hybrid cells containing an inactive human X chromosome with the DNA demethylating agent 5-azadeoxycytidine (5aCdr), and we then examined the high resolution methylation pattern of the HPRT promoter in single cell-derived lines. Reactivation of HPRT correlated with complete promoter demethylation. In contrast, the 61 5aCdr-treated clones that failed to reactivate HPRT exhibited sporadic promoter demethylation. However, three specific CpG sites remained methylated in all unreactivated clones, suggesting these sites may be critical for maintaining transcriptional silencing of the HPRT gene. Re-treatment of partially demethylated (and unreactivated) clones with a second round of 5aCdr did not increase the frequency of HPRT reactivation. This is consistent with mechanisms of methylation-mediated repression requiring methylation at specific critical sites and argues against models invoking overall levels or a threshold of promoter methylation. Treatment of cells with the histone deacetylase inhibitor, trichostatin A, failed to reactivate HPRT on the inactive X chromosome, even when the promoter was partially demethylated by 5aCdr treatment, suggesting that transcriptional repression by DNA methylation is unlikely to depend upon a trichostatin A-sensitive histone deacetylase.
Th17 Response and Inflammatory Autoimmune Diseases (2011)

The proinflammatory activity of T helper 17 (Th17) cells can be beneficial to the host during infection. However, uncontrolled or inappropriate Th17 activation has been linked to several autoimmune and autoinflammatory pathologies. Indeed, preclinical and clinical data show that Th17 cells are associated with several autoimmune diseases such as arthritis, multiple sclerosis, psoriasis, and lupus. Furthermore, targeting the interleukin-17 (IL-17) pathway has attenuated disease severity in preclinical models of autoimmune diseases. Interestingly, a recent report brings to light a potential role for Th17 cells in the autoinflammatory disorder adult-onset Still's disease (AOSD). Whether Th17 cells are the cause or are directly involved in AOSD remains to be shown. In this paper, we discuss the biology of Th17 cells, their role in autoimmune disease development, and in AOSD in particular, as well as the growing interest of the pharmaceutical industry in their use as therapeutic targets.
Mechanisms of hypoxia‐induced periodic breathing during sleep in humans. (1983)

Ventilation was studied during wakefulness and sleep in six healthy humans in normoxia (mean barometric pressure (PB) = 740 torr), and in hypobaric hypoxia (PB = 455 torr). Hypoxia caused hyperventilation and hypocapnic alkalosis (delta Pa,CO2 = -7 torr) during wakefulness and in all sleep states. Periodic breathing was the predominant pattern of breathing in all stages of non-rapid eye movement (non-r.e.m.) sleep in hypoxia, but was rarely observed during wakefulness or r.e.m. sleep. Periodic breathing was composed of repetitive oscillations of reproducible cycle length characterized by clusters of breaths with augmented inspiratory effort (VT/TI) and highly variable distribution of breath-to-breath minute ventilation (VE) and tidal volume (VT), which alternated regularly with prolongations of the expiratory pause of the last breath of each cluster (apnea duration = 5-18 sec). Hypoxia-induced periodic breathing was eliminated by: (a) acute restoration of normoxia coincident with a 3-6 torr increase in Pa,CO2; and (b) augmented FI,CO2 (at constant arterial oxygen saturation) which rapidly and reversibly eliminated apneas and stabilized breathing pattern with a less than 2 torr increase in Pa,CO2. If hypocapnia was prevented (by augmented FI,CO2) during acute induction of hypoxia in non-r.e.m. sleep, periodic breathing was also prevented. We propose that the genesis of hypoxia-induced periodic breathing requires the combination of hypoxia and hypocapnia. Periodicity results from oscillations in CO2 about a CO2-apnea threshold whose functional expression is critically linked to sleep state.