gebhart/patrepeval huggingface dataset:
Autogenous regulation of histone mRNA decay by histone proteins in a cell-free system. (1987)

We tested the hypothesis that histone mRNA turnover is accelerated in the presence of free histone proteins. In an in vitro mRNA decay system, histone mRNA was degraded four- to sixfold faster in reaction mixtures containing core histones and a cytoplasmic S130 fraction than in reaction mixtures lacking these components. The decay rate did not change significantly when histones or S130 was added separately, suggesting either that the histones were modified and thereby activated by S130 or that additional factors besides histones were required. RecA, SSB (single-stranded binding), and histone proteins all formed complexes with histone mRNA, but only histones induced accelerated histone mRNA turnover. Therefore, the effect was not the result of random RNA-protein interactions. Moreover, histone proteins did not induce increased degradation of gamma globin mRNA, c-myc mRNA, or total poly(A)- or poly(A)+ polysomal mRNAs. This autoregulatory mechanism is consistent with the observed accumulation of cytoplasmic histone proteins in cells after DNA synthesis stops, and it can account, in part, for the rapid disappearance of histone mRNA at the end of S phase.
Cardiac Findings during Uncomplicated Acute Influenza in Ambulatory Adults (2005)

Most ambulatory young adults with acute influenza have clinically insignificant abnormal electrocardiogram findings early during the illness. These abnormalities resolve promptly and are not associated with changes in cardiac markers or echocardiogram findings.
A new PCR-based seroneutralization assay in cell culture for diagnosis of hepatitis E (1997)

A new method for the serological diagnosis of hepatitis E virus (HEV) infection based on neutralization of the virus in cell culture was developed. The test involves a short incubation of the virus in the presence of the serum sample to be tested and permissive cells. With viral replication being limited and without a cytopathic effect, viral growth in cells is evaluated by reverse transcription and PCR. The specificity of the test was established by studying sera from healthy individuals and patients with hepatitis living in France, where autochthonous hepatitis E is unknown. The kinetics and sensitivity of antibody detection were evaluated during the experimental infection of monkeys. Neutralizing antibodies were found in 79% of patients during an outbreak of hepatitis E and in 43% of patients with sporadic, acute non-A, non-B (without anti-hepatitic C virus antibodies) hepatitis. This neutralization assay is proposed as a confirmatory test for the available enzyme-linked immunosorbent assay (ELISA), which is now recognized as giving many false-positive reactions, and to improve identification of new hepatitis viruses since false-negative reactions with HEV ELISA are also encountered.
Expression of vascular endothelial growth factor (VEGF) and its two receptors (VEGF-R1-Flt1 and VEGF-R2-Flk1/KDR) in non-small cell lung carcinomas (NSCLCs): correlation with angiogenesis and survival (1999)

The formation of new vessels (angiogenesis) is essential for primary tumour growth and metastasis and is induced by several angiogenic factors, including vascular endothelial growth factor (VEGF). The microvascular density (MVD) in tumours was assessed and the expression of VEGF and its receptors VEGF-R1-Flt1 and VEGF-R2-KDR/Flk1 was investigated in the different cellular compartments in vivo, in order to establish their interrelationship and their prognostic influence. Immunohistochemical study of 69 stage I-II non-small cell lung carcinomas (NSCLCs) was performed on paraffin sections with CD34 antibody to estimate MVD, using a Chalkley eye-piece graticule and VEGF, VEGF-R1, and VEGF-R2 antibodies. There was strong expression of VEGF and its receptors in tumour cells, endothelial cells, and stromal fibroblasts. In tumour cells, the level of VEGF was correlated with that of VEGF-R1 ( p = 0. 018) but not that of VEGF-R2. In fibroblasts, high expression of VEGF was correlated with that of VEGF-R1 ( p = 0.0001) and VEGF-R2 ( p = 0.0001). In endothelial cells, expression of VEGF was correlated with that of VEGF-R1 ( p < 0.0001) and VEGF-R2 ( p = 0.04). The level of VEGF in fibroblasts was correlated with that of VEGF-R1 ( p = 0.0028) and VEGF-R2 ( p = 0.01) in endothelial cells. There was no correlation between the level of MVD and that of VEGF or VEGF-R1 or VEGF-R2. Neither the level of MVD, nor the level of expression of VEGF and VEGF receptors in any compartment influenced the patient's survival. In conclusion, although angiogenesis is essential for tumour growth, this study failed to demonstrate that MVD, VEGF, VEGF-R1, and VEGF-R2 are prognostic markers for stage I-II NSCLC. VEGF, however, might act as a direct autocrine growth factor for tumour cells via VEGF-R1 and angiogenesis could be promoted in a paracrine loop, where VEGF is produced by fibroblasts and tumour cells and then binds to endothelial cells via induced VEGF receptors. VEGF and its receptors thus appear as relevant therapeutic targets in NSCLC.
Changes in the Composition of the Human Fecal Microbiome After Bacteriotherapy for Recurrent Clostridium difficile-associated Diarrhea (2010)

Clostridium difficile-associated disease (CDAD) is the major known cause of antibiotic-induced diarrhea and colitis, and the disease is thought to result from persistent disruption of commensal gut microbiota. Bacteriotherapy by way of fecal transplantation can be used to treat recurrent CDAD, which is thought to reestablish the normal colonic microflora. However, limitations of conventional microbiologic techniques have, until recently, precluded testing of this idea. In this study, we used terminal-restriction fragment length polymorphism and 16S rRNA gene sequencing approaches to characterize the bacterial composition of the colonic microflora in a patient suffering from recurrent CDAD before and after treatment by fecal transplantation from a healthy donor. Although the patient's residual colonic microbiota, prior to therapy was deficient in members of the bacterial divisions-Firmicutes and Bacteriodetes, transplantation had a dramatic impact on the composition of the patient's gut microbiota. By 14 days posttransplantation, the fecal bacterial composition of the recipient was highly similar to that of the donor and was dominated by Bacteroides spp. strains and an uncharacterized butyrate producing bacterium. The change in bacterial composition was accompanied by resolution of the patient's symptoms. The striking similarity of the recipient's and donor's intestinal microbiota following after bacteriotherapy suggests that the donor's bacteria quickly occupied their requisite niches resulting in restoration of both the structure and function of the microbial communities present.
Intravascular photoacoustic imaging of atherosclerotic plaques: ex-vivo study using a rabbit model of atherosclerosis (2007)

Diagnosis and treatment of atherosclerosis necessitates the detection and differentiation of rupture prone plaques. In principle, intravascular photoacoustic (IVPA) imaging has the ability to simultaneously visualize the structure and composition of atherosclerotic plaques by utilizing the difference in optical absorption. Extensive studies are required to validate the utility of IVPA imaging in detecting vulnerable plaques and address issues associated with the clinical implementation of the technique. In this work, we performed <i>ex vivo </i>imaging studies using a rabbit model of atherosclerosis. The intravascular photoacoustic (IVPA) and ultrasound (IVUS) images of the normal aorta and aorta with plaque were obtained and compared with histological slices of the tissue. The results indicate that IVPA imaging is capable of detecting plaques and showed potential in determining the composition. Furthermore, we initially addressed several aspects of clinical implementation of the IVPA imaging. Specifically, the configuration of combined IVPA and IVUS catheter was investigated and the effect of the optical absorption of the luminal blood on the IVPA image quality was evaluated. Overall, this study suggests that IVPA imaging can become a unique and important clinical tool.
Analogs of substance P. Peptides containing D-amino acid residues in various positions of substance P and displaying agonist or receptor selective antagonist effects (1986)

Agonist and antagonist analogues of substance P were synthesized by replacing at least two of the amino acid residues with D-Trp, D-Phe, D-Val, or D-Pro residues. The syntheses of these compounds were achieved by solid-phase methodology using the hydroxymethyl resin. The analogues were tested for agonist and antagonist activity on guinea pig ileum and rat spinal cord preparations. Two types of antagonists were obtained. The first type of compounds, e.g., [N alpha-Z-Arg1,N epsilon-Z-Lys3,D-Trp7,8,D-Met11]-SP-OMe (1), antagonized SP and SP(6-11)-hexapeptide on the ileum but only SP(6-11)-hexapeptide on the spinal cord. The second type of antagonists, e.g., [N alpha-Z-Arg1,N epsilon-Z-Lys3,D-Pro9,10]-SP-OMe (17), were inactive on the ileum but were potent antagonists of the hexapeptide on the spinal cord. Two of the antagonists, [N alpha-Z-Arg1,N epsilon-Z-Lys3,D-Trp7,8,D-Met11]-SP (3) and [D-Trp7,8,9]-SP (43), were also tested in vivo. Both of these depressed hypotensive responses to SP and SP(6-11)-hexapeptide in rabbits.
A wettability switchable surface by microscale surface morphology change (2007)

A novel wettability switchable surface which shields out any interference from driving energy is demonstrated. In this mechanism, a free-standing metal/polymer membrane with hydrophobic microposts is sustained by spacers, and electrostatic force is used to carry out the deflection of the metal/polymer membrane, hence changing the surface morphology as well as the fraction of a liquid/solid interface. Water contact angles under this mechanism can be manipulated from 131° to 152°, depending on the fraction of a liquid/solid interface. Since the driving energy of electrostatic action is shielded out by the ground electrode, the ingredients carried in the droplet can be thoroughly free from the interference and maintain functionality. Therefore, this mechanism has great potential to manipulate microdroplets for digital fluidic systems in bio-applications.
MNAzymes, a Versatile New Class of Nucleic Acid Enzymes That Can Function as Biosensors and Molecular Switches (2009)

To increase the versatility and utility of nucleic acid enzymes, we developed multicomponent complexes, known as MNAzymes, which produce amplified "output" signals in response to specific "input" signals. Multiple oligonucleotide partzymes assemble into active MNAzymes only in the presence of an input assembly facilitator such as a target nucleic acid. Once formed, MNAzymes catalytically modify a generic substrate, generating an amplified output signal that heralds the presence of the target while leaving the target intact. We demonstrated several applications including sensitive, isothermal target detection; discrimination of polymorphisms; and highly specific monitoring of real-time polymerase chain reaction (PCR). Furthermore, we showed their capacity to function as molecular switches and to work in series to create a molecular cascade. The modular nature of MNAzymes, together with the separation of input and output functionalities, provides potential for their integration into diverse devices such as diagnostic biosensors, molecular computers, and/or nanoscale machines.
Flexible-CMOS and biocompatible piezoelectric AlN material for MEMS applications (2013)

The development of a CMOS compatible flexible piezoelectric material is desired for numerous applications and in particular for biomedical MEMS devices. Aluminum nitride (AlN) is the most commonly used CMOS compatible piezoelectric material, which is typically deposited on Si in order to enhance the c-axis (002) crystal orientation which gives AlN its high piezoelectric properties. This paper reports on the successful deposition of AlN on polyimide (PI-2611) material. The AlN deposited has a FWHM (002) value of 5.1 and a piezoelectric d33 value of 1.12 pm V 1 , and SEM images show high quality columnar grains. The highly crystalline AlN material is due to the semi-crystalline properties of the polyimide film used. Cytotoxicity testing showed the AlN/polyimide material to be non-toxic to 3T3 cells and primary neurons. Surface properties of the AlN/polyimide film were evaluated as they have a significant effect on the adhesion of cells to the film. The results show neurons adhering to the AlN surface. The results of this paper show the characterization of a new flexible-CMOS and biocompatible AlN/polyimide material for MEMS devices with improved crystallinity and piezoelectric properties. (Some figures may appear in colour only in the online journal)
Development of chip-compatible sample preparation for diagnosis of infectious diseases (2012)

Diagnosis of infectious diseases in primary care is predominantly based on medical history and physical examination, as conventional laboratory investigations are often associated with delays that are unacceptable in medical practice. Point-of-care testing, and especially lab-on-a-chip (LoC) systems, are expected to result in a considerable reduction in associated healthcare costs and lead to fast, but appropriate and effective, personalized therapy. Although appropriate sample preparation is essential for final detection, most microfluidic-based approaches start from samples prepared by conventional laboratory procedures, therefore continuing to restrict the use of these systems to a laboratory setting. The lack of integrated sample preparation, especially for sample volumes in the milliliter range, is a major drawback of existing LoC systems. LoC systems that start with real samples and perform a full protocol from sample to result are still rare. In this article, the most recent advances in on-chip sample preparation are reviewed for microfluidic-based diagnosis of infectious diseases.
Supplementation with a combination of beta‐hydroxy‐beta‐methylbutyrate (HMB), arginine, and glutamine is safe and could improve hematological parameters (2004)

These results show that HMB, arginine, and glutamine can be safely used to treat muscle wasting associated with AIDS and cancer.
From porous Si to patterned Si substrate: Can misfit strain energy in a continuous heteroepitaxial film be reduced? (1990)

The use of patterned Si substrates (specifically porous Si) for the reduction of heteroepitaxial film strain energy [S. Luryi and E. Suhir, Appl. Phys. Lett. 49, 140 (1986)] has been studied recently by several research groups. We report experimental studies and discuss the validity of the original concept. We studied molecular beam epitaxial growth of continuous GexSi1−x film on 〈100〉 porous Si substrates using Rutherford backscattering spectrometry, transmission electron microscopy, and x-ray rocking curves. The results show predominantly 60° dislocations with long misfit segments. There is no reduction in either strain in the films or dislocation density compared to the samples grown on regular Si substrates. In order to reduce defect densities, the stress fields from different growth areas of patterned substrate must not interfere. Arguments based on crystallographic considerations are presented which demonstrates that, first, the porous Si substrate is not suitable for such applications because of the nature of interconnected growth areas, and second, any kind of decaying stress field requires a certain degree of wafer warpage which does not always present in a realistic MBE-grown heterostructure. It is the conclusion of this discussion that the strain energy in a continuous heteroepitaxial film grown on patterned substrates does not reach a limiting value, but continues to increase with the film thickness.
The Case for Non-transparent Replication: Examples from Bayou. (1998)

Applications that rely on replicated data have different requirements for how their data is managed. For example, some applications may require that updates propagate amongst replicas with tight time constraints, whereas other applications may be able to tolerate longer propagation delays. Some applications only require replicas to interoperate with a few centralized replicas for data synchronization purposes, while other applications need communication between arbitrary replicas. Similarly, the type of update conflicts caused by data replication varies amongst applications, and the mechanisms to resolve them differ as well. The challenge faced by designers of replicated systems is providing the right interface to support cooperation between applications and their data managers. Application programmers do not want to be overburdened by having to deal with issues like propagating updates to replicas and ensuring eventual consistency, but at the same time they want the ability to set up appropriate replication schedules and to control how update conflicts are detected and resolved. The Bayou system was designed to mitigate this tension between overburdening and underempowering applications. This paper looks at two Bayou applications, a calendar manager and a mail reader, and illustrates ways in which they utilize Bayou’s features to manage their data in an application-specific manner. 1
Effects of Partial Hepatectomy on the Growth Characteristics and Hypoxic Fractions of Xenografted DLD-2 Human Colon Cancers (1992)

A recent publication by Leith et al. (Cancer Res. 51, 4111-4113, 1991) showed that administration of epidermal growth factor (EGF) (0.25 mg/kg; q.i.d. x 7) to mice bearing xenografted A431 human epidermoid cancers produced increased tumor growth and a reduction of the percentage of hypoxic cells within neoplasms. In contrast, sialoadenectomy, which removes the majority of circulating EGF in the mouse, resulted in slower tumor growth and increased hypoxic percentages. To investigate such homeostatic mechanisms further, we investigated the growth characteristics and hypoxic fractions of xenografted DLD-2 human colon tumors when tumor-bearing mice received partial hepatectomy (about 65%), unilateral nephrectomy, or nonspecific surgical trauma (laparotomy). Surgical procedures were performed when tumor volumes were about 375 mm3, and hypoxic percentages within tumors were measured by clonogenic excision assay procedures 72 h later. We found that partial hepatectomy increased the growth rates of the transplanted DLD-2 cancers by about a factor of 2.4. This increased growth rate was accompanied by an increase in the mitotic index from about 1.5 to 3.0%. Also, hypoxic fractions were decreased from 0.561 in control tumors to 0.235 in tumors from mice receiving partial hepatectomies. Unilateral nephrectomy and nonspecific surgery manipulations did not alter tumor growth rates, mitotic indices, or hypoxic percentages. These results indicate that partial hepatectomy produces significant alterations in tumor physiology. Results are consistent with a growth factor-mediated mechanism.
Über die Bildung und die Aufspaltung der symmetrischen Bisazoverbindungen der Bis‐acetessigester‐ [mesoxalyl‐arylhydrazon]‐dihydrazone und des Bis‐acetessigester‐[malonyldihydrazons] (1910)

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Avoiding horror autotoxicus: The importance of dendritic cells in peripheral T cell tolerance (2002)

The immune system generally avoids horror autotoxicus or autoimmunity, an attack against the body's own constituents. This avoidance requires that self-reactive T cells be actively silenced or tolerized. We propose that dendritic cells (DCs) play a critical role in establishing tolerance, especially in the periphery, after functioning T cells have been produced in the thymus. In the steady state, meaning in the absence of acute infection and inflammation, DCs are in an immature state and not fully differentiated to carry out their known roles as inducers of immunity. Nevertheless, immature DCs continuously circulate through tissues and into lymphoid organs, capturing self antigens as well as innocuous environmental proteins. Recent experiments have provided direct evidence that antigen-loaded immature DCs silence T cells either by deleting them or by expanding regulatory T cells. This capacity of DCs to induce peripheral tolerance can work in two opposing ways in the context of infection. In acute infection, a beneficial effect should occur. The immune system would overcome the risk of developing autoimmunity and chronic inflammation if, before infection, tolerance were induced to innocuous environmental proteins as well as self antigens captured from dying infected cells. For chronic or persistent pathogens, a second but dire potential could take place. Continuous presentation of a pathogen by immature DCs, HIV-1 for example, may lead to tolerance and active evasion of protective immunity. The function of DCs in defining immunologic self provides a new focus for the study of autoimmunity and chronic immune-based diseases.
Autism-like syndrome is induced by pharmacological suppression of BET proteins in young mice (2015)

Studies investigating the causes of autism spectrum disorder (ASD) point to genetic, as well as epigenetic, mechanisms of the disease. Identification of epigenetic processes that contribute to ASD development and progression is of major importance and may lead to the development of novel therapeutic strategies. Here, we identify the bromodomain and extraterminal domain-containing proteins (BETs) as epigenetic regulators of genes involved in ASD-like behaviors in mice. We found that the pharmacological suppression of BET proteins in the brain of young mice, by the novel, highly specific, brain-permeable inhibitor I-BET858 leads to selective suppression of neuronal gene expression followed by the development of an autism-like syndrome. Many of the I-BET858-affected genes have been linked to ASD in humans, thus suggesting the key role of the BET-controlled gene network in the disorder. Our studies suggest that environmental factors controlling BET proteins or their target genes may contribute to the epigenetic mechanism of ASD.
Standard for the format of ARPA network text messages (1977)

ARPA's Committee on Computer-Aided Human Communication (CAHCOM) wishes to promulgate a standard for the format of ARPA Network text message (mail) headers which will reasonably meet the needs of the various message service subsystems on the Network today. The authors of this document constitute the CAHCOM subcommittee charged with the task of developing this new standard.
Detecting data tampering attacks in synchrophasor networks using time hopping (2016)

Phasor Measurement Units (PMUs) and Wide Area Measurement Systems (WAMS) have emerged as the enabling technologies for the real time monitoring, control, and operation of future smart grids. However, this cyber-infrastructure is vulnerable to a wide range of cyber security threats. Among these, one of the major threats is data tampering or data modification attacks. In these attacks, the adversary can modify/change the data of PMU packets to cause significant damage to the grid's operation and equipment. To address this problem, this paper presents a method for detecting data tampering in synchrophasor networks. The proposed protocol uses a random time hopping sequence to detect data tampering. The PMU and phasor data concentrator (PDC) share a secret seed to generate a random time hopping sequence, while a hash value of the packets combined with a secret key is used to validate the integrity of PMU packets. Security analysis of the proposed protocol shows that it can detect data tampering attacks such as data modification, data injection, and replay attacks. Our performance analysis shows that the scheme has the efficiency and robustness required for real time applications in a smart grid.