gebhart/patrepeval huggingface dataset:
Very quick reverse transcription polymerase chain reaction for detecting 2009 H1N1 influenza A using wire-guide droplet manipulations (2010)

Reverse transcription polymerase chain reaction (RT-PCR) is currently a gold standard in identifying influenza A virus, especially H1N1 flu. Typical RT-PCR assays take about 1-2 h for thermocycling, and there is a growing need to further speed up the thermocycling to less than 30 min. Additionally, the PCR assay system should be made portable as a point-of-care detection tool. There have been attempts to further speed up the PCR assays by reducing its volume. There have also been attempts to use droplet microfluidics technology to PCR, primarily to automate the PCR enrichment processes and take advantage of its small volume. In all these attempts, heating and cooling is made by conduction heat transfer. Rapid movements of droplets (immersed in oil) over three different temperature zones make very quick PCR possible, as heating/cooling will be made by convection heat transfer, whose heat transfer coefficients are much higher than that of conduction. We used our newly-invented method of wire-guide droplet manipulations towards very quick RT-PCR. Computational fluid dynamics (CFD) simulation of our system revealed that heating/cooling for each temperature change takes 1-4 s for a 10 microL droplet, as compared to >30 s in the other quick PCRs. Theoretically a 30-cycle process can take as short as 13 s x 30 cycles = 6 min 30 s. The entire system was made as a single instrument, with the components made by a milling machine and a rapid prototyping device. No additional equipment and external computers are required. With this newly developed system, 160 bp gene sequence was amplified from 2009 H1N1 influenza A (human origin). The 30-cycle process took as short as 6 min 50 s for a 10 microL droplet (with additional 4 min for reverse transcription). Its product was confirmed by traditional gel electrophoresis, subsequent imaging as well as gene sequencing, which has been very difficult with the other stationary droplet/nanodrop approaches. The proposed system has a potential to become an extremely rapid, portable, point-of-care tool for detecting influenza A.
Tunneling Processes into Localized Subgap States in Superconductors (2015)

We combine scanning-tunneling-spectroscopy experiments probing magnetic impurities on a superconducting surface with a theoretical analysis of the tunneling processes between (superconducting) tip and substrate. We show that the current through impurity-induced Shiba bound states is carried by single-electron tunneling at large tip-substrate distances and Andreev reflections at smaller distances. The single-electron current requires relaxation processes, allowing us to extract information on quasiparticle transitions and lifetimes.
Reactivity of Titanium Oxo Ethoxo Cluster [Ti<sub>16</sub>O<sub>16</sub>(OEt)<sub>32</sub>]. Versatile Precursor of Nanobuilding Block-Based Hybrid Materials (2005)

Oxo alcoxo metallic clusters can be employed as inorganic nanobuilding blocks to obtain well-defined organic-inorganic hybrid materials. A better understanding of the surface reactivity of the clusters should allow optimization of the elaboration of hybrid materials through a better control of the hybrid interface. The oxo alcoxo cluster Ti(16)O(16)(OEt)32 presents a shell of labile ethoxy groups that can be selectively transalcoholyzed with preservation of the titanium oxo core, leading to new oxo alcoxo clusters Ti(16)O(16)(OEt)32-x(OR)x (R: alkyl, phenyl, styrenic, etc. groups). The reactivity of the Ti(16)O(16)(OEt)32 cluster toward aliphatic and aromatic alcohols is investigated to determine both the kinetics and the number of substituted titanium atoms, which are strongly dependent on the nature of the alcohol. Characterization of the organic modification of the cluster is performed in situ by liquid (13)C NMR measurements, using the molecular structures of two new clusters, Ti(16)O(16)(OEt)28(OnPr)4 and Ti(16)O(16)(OEt)(24)(OnPr)(8) (OnPr = propoxy groups), as references. The structures of these clusters have been established using single-crystal X-ray diffraction. Moreover, a complete spectroscopic assignment of each ethoxy group is proposed after combining crystallographic data, (13)C NMR T(1) relaxation measurements, and (1)H-(1)H, (1)H-(13)C 2D NMR experiments. Finally, the cluster is functionalized with polymerizable ligands via transalcoholysis and transesterification reactions using hydroxystyrene and acetoxystyrene.
Limited magnitude error locating parity check codes for flash memories (2012)

NAND multi-level cell (MLC) flash memories are widely used due to low cost and high capacity. However the increased number of levels in MLC results in larger interference and errors. The errors in MLC flash memories tend to be asymmetric and with limited-magnitude. To take advantage of the characteristics, we propose limited-magnitude parity check codes, which can reduce errors more effectively. A key advantage of the proposed method is that it has low complexity for encoding and decoding. Another useful feature of the proposed method is that the code rate and the block size can be chosen almost continuously unlike conventional error correcting codes.
Glucosepane Is a Major Protein Cross-link of the Senescent Human Extracellular Matrix (2005)

The extracellular matrix in most tissues is characterized by progressive age-related stiffening and loss of proteolytic digestibility that are accelerated in diabetes and can be duplicated by the nonenzymatic reaction of reducing sugars and extracellular matrix proteins. However, most cross-links of the Maillard reaction described so far are present in quantities too low to account for these changes. Here we have determined in human skin and glomerular basement membrane (GBM) collagen the levels of the recently discovered lysine-arginine cross-links derived from glucose, methylglyoxal, glyoxal, and 3-deoxyglucosone, i.e. glucosepane, MODIC, GODIC, and DOGDIC, respectively. Insoluble preparations of skin collagen (n = 110) and glomerular basement membrane (GBM, n = 28) were enzymatically digested, and levels were measured by isotope dilution technique using liquid chromatography/mass spectrometry. In skin, all cross-links increased with age (p < 0.0001) except DOGDIC (p = 0.34). In nondiabetic controls, levels at 90 years were 2000, 30, and 15 pmol/mg for glucosepane, MODIC, and GODIC, respectively. Diabetes, but not renal failure, increased glucosepane to 5000 pmol/mg (p < 0.0001), and for all others, increased it to <60 pmol/mg (p < 0.01). In GBMs, glucosepane reached up to 500 pmol/mg of collagen and was increased in diabetes (p < 0.0001) but not old age. In conclusion, glucosepane is the single major cross-link of the senescent extracellular matrix discovered so far, accounting for up to >120 mole% of triple helical collagen modification in diabetes. Its presence in high quantities may contribute to a number of structural and cell matrix dysfunctions observed in aging and diabetes.
Molecular Genetics of Emery–Dreifuss Muscular Dystrophy (2010)

Abstract Emery–Dreifuss muscular dystrophy (EDMD) is a rare neuromuscular disorder typically characterised by early contractures, slowly progressive muscular wasting, and life‐threatening heart conduction disturbances, which can develop into a cardiomyopathy. Some severe neonatal cases have also been identified. There is a wide intrafamilial and interfamilial clinical variability. Genetically, X‐linked recessive ( EMD1 and EDMD6 ), autosomal dominant ( EMD2 , EDMD4 and EDMD5 ) and autosomal recessive (EMD3) forms can be distinguished. By molecular genetic methods, EDMD can be associated with mutations in the STA (emerin gene symbol), LMNA (lamin A/C gene symbol), SYNE (nesprin gene symbol) 1 , SYNE2 and Four and a Half LIM Domain 1 ( FHL1 ) genes. Female carriers of the X‐linked forms may manifest with cardiac symptoms but heterozygous carriers of the autosomal forms do not show symptoms. Only approximately 46% of unrelated EDMD patients have a mutation in known genes pointing to further genetic heterogeneity in EDMD. The molecular pathogenesis is unresolved, but there is evidence for gene expression changes via altered nuclear signalling and for reduced resistance of muscles to physical damage during contraction. Key Concepts: Emery–Dreifuss muscular dystrophy (EDMD) is a neuromuscular disorder recognised clinically by three features: early contractures, a characteristic pattern of muscle wasting and cardiac conduction defects. EDMD was originally described as an X‐linked disorder, later found to be caused by mutations in the STA gene encoding a nuclear membrane protein, emerin. Molecular genetic analysis allows precise subtyping of EDMD into X‐linked forms ( STA and FHL1 associated), autosomal dominant forms ( LMNA , SYNE1/SYNE2 associated) and an autosomal recessive form ( LMNA associated). Wide clinical variability of EDMD and clinical overlap with other clinical entities frequently require consideration of patients not completely fulfilling the EDMD diagnostic criteria for molecular genetic differentiation in STA , LMNA , SYNE1/SYNE2 and FHL1 . Digenic pathogenesis has been observed including LMNA / STA , LMNA / DES and SYNE1/SYNE2 . In most cases, EDMD mutations affect proteins located in the nuclear membrane where they interact with each other. Many patients do not have mutations in genes identified so far, so further genes are expected to be involved in the pathogenesis of EDMD.
Blinded Contractility Analysis in hiPSC-Cardiomyocytes in Engineered Heart Tissue Format: Comparison With Human Atrial Trabeculae (2017)

Human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) may serve as a new assay for drug testing in a human context, but their validity particularly for the evaluation of inotropic drug effects remains unclear. In this blinded analysis, we compared the effects of 10 indicator compounds with known inotropic effects in electrically stimulated (1.5 Hz) hiPSC-CM-derived 3-dimensional engineered heart tissue (EHT) and human atrial trabeculae (hAT). Human EHTs were prepared from iCell hiPSC-CM, hAT obtained at routine heart surgery. Mean intra-batch variation coefficient in baseline force measurement was 17% for EHT and 49% for hAT. The PDE-inhibitor milrinone did not affect EHT contraction force, but increased force in hAT. Citalopram (selective serotonin reuptake inhibitor), nifedipine (LTCC-blocker) and lidocaine (Na+ channel-blocker) had negative inotropic effects on EHT and hAT. Formoterol (beta-2 agonist) had positive lusitropic but no inotropic effect in EHT, and positive clinotropic, lusitropic, and inotropic effects in hAT. Tacrolimus (calcineurin-inhibitor) had a negative inotropic effect in EHTs, but no effect in hAT. Digoxin (Na+-K+-ATPase-inhibitor) showed a positive inotropic effect only in EHTs, but no effect in hAT probably due to short incubation time. Ryanodine (ryanodine receptor-inhibitor) reduced contraction force in both models. Rolipram and acetylsalicylic acid showed noninterpretable results in hAT. Contraction amplitude and kinetics were more stable over time and less variable in hiPSC-EHTs than hAT. HiPSC-EHT faithfully detected cAMP-dependent and -independent positive and negative inotropic effects, but limited beta-2 adrenergic or PDE3 effects, compatible with an immature CM phenotype.
In vivo immune responses to Candida albicans modified by treatment with recombinant murine gamma interferon (1989)

The immunologic effects of in vivo administration of recombinant murine gamma interferon (rMuIFN-gamma) were determined in a murine model of candidiasis. Naive mice were given graded doses of rMuIFN-gamma and then challenged intravenously with Candida albicans. Increased morbidity and mortality were noted in four different strains of mice, viz., BALB/c, A/J, Swiss Webster, and CBA/J, providing the mice had not been immunized with C. albicans before challenge. Quantitative culture of selected organs of Swiss Webster and CBA/J mice surviving treatment with rMuIFN-gamma revealed elevated numbers of C. albicans cells, particularly in the kidneys, but also in the liver, lungs, and spleen. The lungs, livers, and spleen of female CBA/J mice were more protected from increased multiplication of the fungus than were those of males of the same species or female Swiss Webster mice. On the basis of these initial findings, the effect of treatment with 5,000 U of rMuIFN-gamma on immune responses in a gastrointestinal model of candidiasis was determined. CBA/J mice that had been colonized with C. albicans as infants were boosted with a cutaneous inoculation of the fungus when 6 to 10 weeks old; development of delayed hypersensitivity (DH), antibodies, and protective responses was assayed at intervals thereafter. Daily treatment with rMuIFN-gamma (beginning 1 day before cutaneous inoculation) suppressed weak immune responses but had little effect on responses which were strong. For example, DH and anti-C. albicans antibody production were suppressed in animals colonized with C. albicans but not boosted by cutaneous inoculation, and DH was suppressed in uncolonized animals that had been inoculated once cutaneously with the fungus as well. There was no rMuIFN-gamma-induced suppressive effect of DH in mice which had been stimulated maximally with C. albicans, i.e., colonized animals that had been boosted cutaneously with the organisms. Collectively, these data indicate that naive mice or mice with minimal levels of anti-C. albicans sensitivity, females somewhat more so than males, were sensitive to suppressive effects of in vivo treatment with rMuIFN-gamma when challenged with C. albicans. In contrast, under conditions similar to those of humans, in whom underlying immunity to C. albicans is usually present, suppression of host responses to C. albicans was not observed in immunized mice in response to treatment with rMuIFN-gamma.
Hypoxia-Induced Down-regulation of <i>BRCA1</i> Expression by E2Fs (2005)

Decreased BRCA1 expression in the absence of genetic mutation is observed frequently in sporadic cancers of the breast and other sites, although little is known regarding the mechanisms by which the expression of this gene can be repressed. Here, we show that activating and repressive E2Fs simultaneously bind the BRCA1 promoter at two adjacent E2F sites in vivo, and that hypoxia induces a dynamic redistribution of promoter occupancy by these factors resulting in the transcriptional repression of BRCA1 expression. Functionally, we show that hypoxia is associated with impaired homologous recombination, whereas the nonhomologous end-joining (NHEJ) repair pathway is unaffected under these conditions. Repression of BRCA1 expression by hypoxia represents an intriguing mechanism of functional BRCA1 inactivation in the absence of genetic mutation. We propose that hypoxia-induced decreases in BRCA1 expression and consequent suppression of homologous recombination may lead to genetic instability by shifting the balance between the high-fidelity homologous recombination pathway and the error-prone NHEJ pathway of DNA repair. Furthermore, these findings provide a novel link between E2Fs and the transcriptional response to hypoxia and provide insight into the mechanisms by which the tumor microenvironment can contribute to genetic instability in cancer.
Interest of investigating p53 status in breast cancer by four different methods (2002)

Alterations in the p53 gene are among the most common molecular changes in breast cancer although its potential role as a prognostic and predictive factor of tumor response is controversial. All abnormalities of this tumor marker need to be detected with efficacy and practical technologies. In the present study, our aim was to compare four different analyses of p53 in order to determine how many and which techniques were necessary and sufficient to reflect the p53 status in breast cancer. We analyzed p53 at the molecular level with sequencing of total cDNA and allelic loss. Furthermore, we detected p53 protein accumulation by immunohistochemistry and presence of p53 antibodies by serological analysis. Nine patients (17%) had p53 gene alterations, 33% had allelic loss, 19% had positive p53 nuclear staining and p53 antibodies were detected in 12% of patients. We found p53 gene alterations associated with p53 nuclear protein expression (p=0.001). The single significant statistical correlation in this study suggested the need to define p53 status with more than one abnormality. The general view of a simultaneous multilevel analysis would make it possible to encompass the consequences of p53 abnormalities in breast cancer.
p38 Mitogen-Activated Protein Kinase-Dependent Transactivation of ErbB Receptor Family (2011)

Hepatic p38MAPK is activated following various stress stimuli. This event is upstream to ErbB receptors transactivation and plays an important role in stress-induced IRS-1 serine phosphorylation and insulin resistance.
Study on all-optical cross-band frequency conversion for communication satellite (2017)

A novel all-optical cross-band frequency conversion method for communication satellite is proposed and studied in this paper. An optical frequency comb (OFC) based on a Mach-Zehnder modulator (MZM) and a DFB laser is used as optical carrier and multi-wavelength local oscillators. The frequency conversion among C-band, Ku-band, K-band and Ka-band by feeding input signals of different frequency to the proposed scheme is demonstrated in the simulation. The proposed solution makes the cross-band frequency conversion possible and flexible, showing good application potential in the communication satellite systems of future.
Osteoporosis: Preventive practices and risk assessment among South Indian Women (2011)

Background: Estimated 25 million Indians are affected by Osteoporosis.1 It is eight times more common in women than in men.2
Objectives:To determine the preventive practice and assessing the risk status (KPR) on osteoporosis, find the association between selected variables and key variables, find the relationship between practice and risk status in each group of women; comparing the mean among the groups on same.
Methods:A cross-sectional survey on 110 women, selected by convenience sampling at Hiriadka, Karnataka. Demographic proforma, self reported practice scale and risk assessment tool were used.
Results:There was positive correlation between age and risk status (p<0.05) in group1, whereas in group 2 it was negatively correlated. Preventive practices and risk status was negatively correlated in both groups (p<0.05).
Farming as feedback control (2014)

This paper surveys a brief history of agriculture, demonstrating how advances in genetics, equipment, and management practices have resulted in the remarkable productivity experienced by today's agriculture industrial complex. We then show that progress in each of these areas is, in part, the result of new solutions to a feedback-control problem, whether it be for selective breeding, exploiting new sensor and actuation technology on a tractor or harvester, or using advanced crop and weather models to make better decisions about irrigation or pesticides. The paper concludes with an invitation for the controls community to explore the varied and important feedback-control problems in this area, emphasizing that sustainably feeding the exponentially growing global population, without harming the environment, will demand creative, careful thinking for years to come.
Studies in the enhancement of tumour immunity by coupling strong antigens to tumour cells ('heterogenization of tumours'). Helper T cell clones against PPD help other T cells mount anti-tumour responses to PPD-coupled tumour cells. (1984)

PPD-reactive T cell clones have been used to analyse the nature of T lymphocytes that are involved in the 'heterogenization' of tumour cells. This is a phenomenon where coupling tumour cells to a strong antigen (in this case PPD) causes an enhanced immune response to tumour-specific antigens to be elicited providing that the host shows T cell immunity to the strong antigen (in this case is BCG positive). Clones of T cells with the Lyt1+2- phenotype which were unable to mediate delayed-type hypersensitivity but which provided efficient help to hapten-primed B cells were found to potentiate anti-tumour immunity in BCG-negative syngeneic mice when immunized with Con-A-PPD coupled, X-irradiated MC6A tumour cells. There therefore appears to be a mechanism whereby a helper T cell response to one antigen can provide help for the generation of a T cell response to a linked antigen which is analogous to the well-known phenomenon of help to hapten primed B cells. Furthermore the clones of T cells that help B cells the best are those that give maximal augmentation of T cell immunity.
Automatic verification of active device drivers (2014)

We develop a practical solution to the problem of automatic verification of the interface between device drivers and the operating system. Our solution relies on a combination of improved driver architecture and verification tools. Unlike previous proposals for verification-friendly drivers, our methodology supports drivers written in C and can be implemented in any existing OS. Our Linuxbased evaluation shows that this methodology amplifies the power of existing model checking tools in detecting driver bugs, making it possible to verify properties that are beyond the reach of traditional techniques.
Oncolytic herpes simplex virus-based strategies: toward a breakthrough in glioblastoma therapy (2014)

Oncolytic viruses (OV) are a class of antitumor agents that selectively kill tumor cells while sparing normal cells. Oncolytic herpes simplex virus (oHSV) has been investigated in clinical trials for patients with the malignant brain tumor glioblastoma for more than a decade. These clinical studies have shown the safety of oHSV administration to the human brain, however, therapeutic efficacy of oHSV as a single treatment remains unsatisfactory. Factors that could hamper the anti-glioblastoma efficacy of oHSV include: attenuated potency of oHSV due to deletion or mutation of viral genes involved in virulence, restricting viral replication and spread within the tumor; suboptimal oHSV delivery associated with intratumoral injection; virus infection-induced inflammatory and cellular immune responses which could inhibit oHSV replication and promote its clearance; lack of effective incorporation of oHSV into standard-of-care, and poor knowledge about the ability of oHSV to target glioblastoma stem cells (GSCs). In an attempt to address these issues, recent research efforts have been directed at: (1) design of new engineered viruses to enhance potency, (2) better understanding of the role of the cellular immunity elicited by oHSV infection of tumors, (3) combinatorial strategies with different antitumor agents with a mechanistic rationale, (4) "armed" viruses expressing therapeutic transgenes, (5) use of GSC-derived models in oHSV evaluation, and (6) combinations of these. In this review, we will describe the current status of oHSV clinical trials for glioblastoma, and discuss recent research advances and future directions toward successful oHSV-based therapy of glioblastoma.