gebhart/patrepeval huggingface dataset:
Mechanisms Involved in BACE Upregulation Associated to Stress (2012)

The objective of the present work was to study a purported involvement of stress in amyloid pathology through the modulation of BACE expression. Early-life stressed rats (maternal separation, MS) showed significant increases in corticosterone levels, BACE expression and Aβ levels. The CpG7 site of the BACE promoter was significantly hypomethylated in MS, and corticosterone levels negatively correlated to the methylation status of CpG7. The activation of the stress-activated protein kinase JNK was also increased in MS rats. In SHSY-5Y neuroblastoma cells, corticosterone induced a rapid increase in BACE expression that was abolished by specific inhibiton of JNK activation or by spironolactone, a mineralocorticoid receptor antagonist, but not by mifepristone, a glucocorticoid receptor antagonist. Corticosterone was also able to increase pJNK expression and this effect was fully reverted by spironolactone. Mice chronically treated with corticosterone showed increased BACE and pJNK expression. These increases were reverted by treatment with spironolactone or with a JNK inhibitor. It is suggested that increased corticosterone levels associated to stress lead to increase BACE transcription both through epigenetic mechanisms and activation of JNK.
Suppression of serum IgE response and systemic anaphylaxis in a food allergy model by orally administered high-dose TGF-β (2005)

Some epidemiological or association studies suggest that transforming growth factor-beta (TGF-beta) in breast milk may be a decisive factor in diminishing the risk of allergic diseases during infancy. The observations have prompted us to investigate whether TGF-beta, when taken orally, can affect allergic immune responses. Repeated high-dose ovalbumin peptide (OVA) feeding was previously reported to induce OVA-specific IgE production and an anaphylactic reaction after intravenous challenge of OVA in OVA-TCR transgenic mice, which might represent a model for food allergy. By using this model, we showed here that oral administration of high-dose TGF-beta simultaneously with OVA feeding significantly inhibited the OVA-specific IgE elevation and anaphylactic reaction in OVA-TCR transgenic DO11.10 mice. These effects were associated with suppression of OVA-specific IL-4 production and GATA-3 expression and with up-regulation of IFN-gamma production and T-bet expression by splenocytes. Intra-peritoneal injection of anti-TGF-beta-neutralizing antibody abolished the inhibitory effects of orally administered TGF-beta on the serum IgE response and anaphylactic reaction after OVA feeding in DO11.10 mice. Interestingly, oral administration of high-dose TGF-beta suppressed activation-induced T cell death induced by OVA feeding in DO11.10 mice. We thus conclude that TGF-beta, when taken orally at high dose, has the capacity to modulate a food allergy-related reaction, at least in part, through its systemic activity.
Enhanced Expression of Transgenes from Adeno-Associated Virus Vectors with the Woodchuck Hepatitis Virus Posttranscriptional Regulatory Element: Implications for Gene Therapy (1999)

The woodchuck hepatitis virus posttranscriptional regulatory element (WPRE) evolved to stimulate the expression of intronless viral messages. To determine whether this ability to enhance expression could be useful in nonviral and heterologous viral gene delivery systems, we analyzed the ability of the WPRE to elevate the expression of a cDNA encoding the green fluorescent protein (GFP) in these contexts. We find that the WPRE can stimulate the expression of GFP when the gene is delivered by transfection or transduction with recombinant adeno-associated virus (AAV). Enhancement occurred both during transient expression and when the gene is stably incorporated into the genome of target cells. This enhancement required that the WPRE be located in cis within the GFP message, and was observed in both transformed cell lines and primary human fibroblasts. These results demonstrate that the WPRE will be an effective tool for increasing the long-term expression of transgenes in gene therapy.
Non-invasive assessment of Alzheimer’s disease neurofibrillary pathology using 18F-THK5105 PET (2014)

Non-invasive imaging of tau pathology in the living brain would be useful for accurately diagnosing Alzheimer's disease, tracking disease progression, and evaluating the treatment efficacy of disease-specific therapeutics. In this study, we evaluated the clinical usefulness of a novel tau-imaging positron emission tomography tracer 18F-THK5105 in 16 human subjects including eight patients with Alzheimer's disease (three male and five females, 66-82 years) and eight healthy elderly controls (three male and five females, 63-76 years). All participants underwent neuropsychological examination and 3D magnetic resonance imaging, as well as both 18F-THK5105 and 11C-Pittsburgh compound B positron emission tomography scans. Standard uptake value ratios at 90-100 min and 40-70 min post-injection were calculated for 18F-THK5105 and 11C-Pittsburgh compound B, respectively, using the cerebellar cortex as the reference region. As a result, significantly higher 18F-THK5105 retention was observed in the temporal, parietal, posterior cingulate, frontal and mesial temporal cortices of patients with Alzheimer's disease compared with healthy control subjects. In patients with Alzheimer's disease, the inferior temporal cortex, which is an area known to contain high densities of neurofibrillary tangles in the Alzheimer's disease brain, showed prominent 18F-THK5105 retention. Compared with high frequency (100%) of 18F-THK5105 retention in the temporal cortex of patients with Alzheimer's disease, frontal 18F-THK5105 retention was less frequent (37.5%) and was only observed in cases with moderate-to-severe Alzheimer's disease. In contrast, 11C-Pittsburgh compound B retention was highest in the posterior cingulate cortex, followed by the ventrolateral prefrontal, anterior cingulate, and superior temporal cortices, and did not correlate with 18F-THK5105 retention in the neocortex. In healthy control subjects, 18F-THK5105 retention was ∼10% higher in the mesial temporal cortex than in the neocortex. Notably, unlike 11C-Pittsburgh compound B, 18F-THK5105 retention was significantly correlated with cognitive parameters, hippocampal and whole brain grey matter volumes, which was consistent with findings from previous post-mortem studies showing significant correlations of neurofibrillary tangle density with dementia severity or neuronal loss. From these results, 18F-THK5105 positron emission tomography is considered to be useful for the non-invasive assessment of tau pathology in the living brain. This technique would be applicable to the longitudinal evaluation of tau deposition and allow a better understanding of the pathophysiology of Alzheimer's disease.
Carbohydrate preferences of Bifidobacterium species isolated from the human gut. (2003)

The growth of nine species of Bifidobacterium on media containing glucose, xylose, xylooligosaccharides (XOS), xylan or fructooligosaccharides (FOS) as the sole carbon source were compared in pure culture. The bifidobacteria differed in fermentation profiles when tested on different carbohydrates. All species grew to their highest final optical density (OD) on a glucose containing medium, with the exception of B. catenulatum which demonstrated a preference for xylose over glucose, and XOS over FOS. B. bifidum grew to the highest OD on XOS compared to xylose suggesting a specific transport system for the oligosaccharide over the monomer. This is consistent with a lack of beta-xylosidase activity present in the culture medium. Lactate, formate and acetate levels were determined and the ratios of these metabolites altered between and within species growing on different carbohydrates. In general, high lactate production correlated with low formate production and low lactate concentrations were obtained at higher levels of formate. Bifidobacteria may alter their metabolic pathways based upon the carbohydrates that are available for their use.
Femtosecond laser microstructuring: an enabling tool for optofluidic lab‐on‐chips (2011)

Abstract This paper provides an overview of the rather new field concerning the applications of femtosecond laser microstructuring of glass to optofluidics. Femtosecond lasers have recently emerged as a powerful microfabrication tool due to their unique characteristics. On the one hand, they enable to induce a permanent refractive index increase, in a micrometer‐sized volume of the material, allowing single‐step, three‐dimensional fabrication of optical waveguides. On the other hand, femtosecond‐laser irradiation of fused silica followed by chemical etching enables the manufacturing of directly buried microfluidic channels. This opens the intriguing possibility of using a single laser system for the fabrication and three‐dimensional integration of optofluidic devices. This paper will review the state of the art of femtosecond laser fabrication of optical waveguides and microfluidic channels, as well as their integration for high sensitivity detection of biomolecules and for cell manipulation.
Optimization of T-cell Reactivity by Exploiting TCR Chain Centricity for the Purpose of Safe and Effective Antitumor TCR Gene Therapy (2015)

Adoptive transfer of T cells redirected by a high-affinity antitumor T-cell receptor (TCR) is a promising treatment modality for cancer patients. Safety and efficacy depend on the selection of a TCR that induces minimal toxicity and elicits sufficient antitumor reactivity. Many, if not all, TCRs possess cross-reactivity to unrelated MHC molecules in addition to reactivity to target self-MHC/peptide complexes. Some TCRs display chain centricity, in which recognition of MHC/peptide complexes is dominated by one of the TCR hemi-chains. In this study, we comprehensively studied how TCR chain centricity affects reactivity to target self-MHC/peptide complexes and alloreactivity using the TCR, clone TAK1, which is specific for human leukocyte antigen-A*24:02/Wilms tumor 1(235-243) (A24/WT1(235)) and cross-reactive with B*57:01 (B57). The TAK1β, but not the TAK1α, hemi-chain possessed chain centricity. When paired with multiple clonotypic TCRα counter-chains encoding TRAV12-2, 20, 36, or 38-2, the de novo TAK1β-containing TCRs showed enhanced, weakened, or absent reactivity to A24/WT1(235) and/or to B57. T cells reconstituted with these TCRα genes along with TAK1β possessed a very broad range (>3 log orders) of functional and structural avidities. These results suggest that TCR chain centricity can be exploited to enhance desired antitumor TCR reactivity and eliminate unwanted TCR cross-reactivity. TCR reactivity to target MHC/peptide complexes and cross-reactivity to unrelated MHC molecules are not inextricably linked and are separable at the TCR sequence level. However, it is still mandatory to carefully monitor for possible harmful toxicities caused by adoptive transfer of T cells redirected by thymically unselected TCRs.
Effect of one monolayer of surface gold atoms on the epitaxial growth of InAs nanowhiskers (1992)

This letter shows that selective heteroepitaxy of nanometer-scale InAs whiskers on SiO2-patterned GaAs substrates [Yazawa, Koguchi, and Hiruma, Appl. Phys. Lett. 58, 1080 (1991)] is induced by surface contamination with Au resulting from the fluorocarbon plasma etching process used to etch the SiO2 mask. We demonstrate that high densities (≂1010/cm2) of InAs nanowhiskers 20–30 nm in diameter can be epitaxially grown on InAs(111)B substrates onto which 1 monolayer of Au atoms had been deposited. This wirelike growth appears to be induced by ultrafine alloy droplets generated by the reactions between Au-clusters and InAs substrates.
Plant growth promotion byBacillus megateriuminvolves cytokinin signaling (2008)

Accumulating evidence indicates that plant growth promoting rhizobacteria (PGPR) influence plant growth and development by the production of phytohormones such as auxins, gibberellins, and cytokinins. Little is known on the genetic basis and signal transduction components that mediate the beneficial effects of PGPRs in plants. We recently reported the identification of a Bacillus megaterium strain that promoted growth of A. thaliana and P. vulgaris seedlings. In this addendum, the role of cytokinin signaling in mediating the plant responses to bacterial inoculation was investigated using A. thaliana mutants lacking one, two or three of the putative cytokinin receptors CRE1, AHK2 and AHK3, and RPN12 a gene involved in cytokinin signaling. We show that plant growth promotion by B. megaterium is reduced in AHK2-2 single and double mutant combinations and in RPN12. Furthermore, the triple cytokinin-receptor CRE1-12/AHK2-2/AHK3-3 knockout was insensitive to inoculation in terms of growth promotion and root developmental responses. Our results indicate that cytokinin receptors play a complimentary role in plant growth promotion by B. megaterium.
Signal Reconstruction From Noisy Random Projections (2006)

Recent results show that a relatively small number of random projections of a signal can contain most of its salient information. It follows that if a signal is compressible in some orthonormal basis, then a very accurate reconstruction can be obtained from random projections. This "compressive sampling" approach is extended here to show that signals can be accurately recovered from random projections contaminated with noise. A practical iterative algorithm for signal reconstruction is proposed, and potential applications to coding, analog-digital (A/D) conversion, and remote wireless sensing are discussed
Fetal endoderm primarily holds the temporal and positional information required for mammalian intestinal development. (1994)

In rodents, the intestinal tract progressively acquires a functional regionalization during postnatal development. Using lactase-phlorizin hydrolase as a marker, we have analyzed in a xenograft model the ontogenic potencies of fetal rat intestinal segments taken prior to endoderm cytodifferentiation. Segments from the presumptive proximal jejunum and distal ileum grafted in nude mice developed correct spatial and temporal patterns of lactase protein and mRNA expression, which reproduced the normal pre- and post-weaning conditions. Segments from the fetal colon showed a faint lactase immunostaining 8-10 d after transplantation in chick embryos but not in mice; it is consistent with the transient expression of this enzyme in the colon of rat neonates. Heterotopic cross-associations comprising endoderm and mesenchyme from the presumptive proximal jejunum and distal ileum developed as xenografts in nude mice, and they exhibited lactase mRNA and protein expression patterns that were typical of the origin of the endodermal moiety. Endoderm from the distal ileum also expressed a normal lactase pattern when it was associated to fetal skin fibroblasts, while the fibroblasts differentiated into muscle layers containing alpha-smooth-muscle actin. Noteworthy, associations comprising colon endoderm and small intestinal mesenchyme showed a typical small intestinal morphology and expressed the digestive enzyme sucrase-isomaltase normally absent in the colon. However, in heterologous associations comprising lung or stomach endoderm and small intestinal mesenchyme, the epithelial compartment expressed markers in accordance to their tissue of origin but neither intestinal lactase nor sucrase-isomaltase. A thick intestinal muscle coat in which cells expressed alpha-smooth-muscle actin surrounded the grafts. The results demonstrate that: (a) the temporal and positional information needed for intestinal ontogeny up to the post-weaning stage results from an intrinsic program that is fixed in mammalian fetuses prior to endoderm cytodifferentiation; (b) this temporal and positional information is primarily carried by the endodermal moiety which is also able to change the fate of heterologous mesodermal cells to form intestinal mesenchyme; and (c) the small intestinal mesenchyme in turn may deliver instructive information as shown in association with colonic endoderm; yet this effect is not obvious with nonintestinal endoderms.
Use of cloned mtl genes of Escherichia coli to introduce mtl deletion mutations into the chromosome (1983)

The Escherichia coli mtl operon, which contains the cis-dominant regulatory region mtlC, the mannitol-specific enzyme II structural gene mtlA, and the D-mannitol-1-phosphate dehydrogenase structural gene mtlD, was cloned into plasmid pBR322. A 2-kilobase pair fragment of the mtl operon DNA containing the mtlA gene was subcloned into plasmid pACYC184. The direction of transcription of the cloned mtlA gene was determined. Localization of the mtlA gene on the cloned mtl operon DNA allowed in vitro construction of plasmid derivatives containing specific deletions in the mtl region. These plasmid derivatives were used to generate the corresponding mtl chromosomal deletions by homologous recombination at frequencies greater than 10(-4).
Four-port fiber frequency shifter with a null taper coupler (1994)

A prototype of a new design of fiber frequency shifter, based on a special four-port fused taper coupler with a null maximum coupling ratio, is reported. In this coupler the constituent fibers are so dissimilar that the maximum coupling is (ideally) zero. In the presence of a flexural acoustic wave, light is coupled between the fibers, acquiring a frequency shift in the process. Near 100% conversion with 30-dB sideband and carrier suppression is achieved, in an unoptimized device, for just 1 mW of electrical drive power.
EPIDEMIOLOGY OF ACROMEGALY IN THE NEWCASTLE REGION (1980)

In an attempt to derive estimates of the incidence and prevalence of acromegaly a survey of the population in the area served by the former Newcastle Regional Hospital Board has been conducted to detect cases of acromegaly alive after 1 January 1960 and diagnosed before 31 December 1971. Cases were detected by means of letters to general practitioners, hospital physicians, neurosurgeons and to hospital records officers, as well as from death certificates. From the population of 3.1 millions a firm diagnosis of acromegaly was made in 164 patients, in eighty-one on clinical grounds alone and in eighty-three with confirmation by assay of human growth hormone (hGH). The annual incidence of acromegaly appears to be close to three cases per million and the prevalence of diagnosed cases up to forty cases per million. In male acromegalics there was a significant increase in the risk of death from cardiovascular, cerebrovascular respiratory and malignant diseases but in females from cerebrovascular disease only.
Data memory organization and optimizations in application-specific systems (2001)

In application-specific designs, customized memory organization expands the search space for cost-optimized solutions. Several optimization strategies can be applied to embedded systems with several different memory architectures: data cache, scratch-pad memory, custom memory architectures, and dynamic random-access memory (DRAM).
A unified header compression framework for low-bandwidth links (2000)

Compressing protocol headers has traditionally been an attractive way of conserving bandwidth over low-speed links, including those in wireless systems. However, despite the growth in recent years in the number of end-to-end protocols beyond TCP/IP, header compression deployment for those protocols has not kept pace. This is in large part due to complexities in implementation, which often requires a detailed knowledge of kernel internals, and a lack of a common way of pursuing the general problem across a variety of end-to-end protocols. To address this, rather than defining several new protocol-specific standards, we present a unified framework for header compression. This framework includes a simple, platform-independent header description language that protocol implementors can use to describe high-level header properties, and a platform-specific code generation tool that produces kernel source code automatically from this header specification. Together, the high-level description language and code generator free protocol designers from having to understand any details of the target platform, enabling them to implement header compression with relatively little effort. We analyze the performance of compression produced using this framework for TCP/IP in the Linux 2.0 kernel and demonstrate that unified, automatically-generated header compression without significant performance penalty is viable.
Association of Antibody to GB Virus C (Hepatitis G Virus) with Viral Clearance and Protection from Reinfection (1998)

GB virus C (GBV-C) RNA and envelope antibody were assessed in a median of 4 samples collected over 6.5 years among injection drug users (IDUs). A marker of GBV-C infection was detected in 110 (94.8%) of 116 IDUs. GBV-C RNA was detected at all visits in 32, was never detected in 70, was acquired in 7, and was cleared in 8. The odds of detecting anti-GBV-C were 103-fold higher in participants without detectable RNA (64 of 70) than in IDUs with persistent RNA (3 of 32; P < 10(-7)). Anti-GBV-C was detected in all 8 instances of RNA clearance. GBV-C RNA never reappeared once it was cleared, and there were no new GBV-C infections among 61 anti-GBV-C-positive IDUs observed for 382 person-years, though all had ongoing drug use. Studies using RNA testing alone may significantly underestimate the occurrence of GBV-C infection. Anti-GBV-C is highly associated with viral clearance and protection from reinfection.
Sonographic size of uterus and ovaries in pre‐ and postmenopausal women (1996)

Uterine and ovarian size were measured in 765 pre- and postmenopausal women by transvaginal ultrasound. Of these, 263 (premenopausal, n = 155; postmenopausal, n = 108) were found to have neither uterine nor ovarian pathological findings. According to parity, premenopausal women were separated into three groups: nullipara, primipara and multipara. Postmenopausal women were separated into two groups according to years since menopause: < or = 5 years and > 5 years since menopause. In the premenopausal group, a parity-related enlargement in uterine size was observed between nulliparous and parous women. After the menopause, a significant reduction in uterine size and in the corpus-cervix ratio was observed. The reduction in uterine size was related to years since menopause. The endometrial thickness measured in the group of premenopausal women did not exceed 4 mm on day 4 and 8 mm on day 8 of the menstrual cycle; in the postmenopausal group, endometrial thickness did not exceed 5 mm (mean 3.6 mm). In the group of premenopausal women, no parity-related change in ovarian volume was observed. After menopause, there was an obvious reduction in ovarian volume. Between the two postmenopausal groups, there was a small but significant difference in ovarian volume.