gebhart/patrepeval huggingface dataset:
Dynamics of Gray Matter Loss in Alzheimer's Disease (2003)

We detected and mapped a dynamically spreading wave of gray matter loss in the brains of patients with Alzheimer's disease (AD). The loss pattern was visualized in four dimensions as it spread over time from temporal and limbic cortices into frontal and occipital brain regions, sparing sensorimotor cortices. The shifting deficits were asymmetric (left hemisphere > right hemisphere) and correlated with progressively declining cognitive status (p < 0.0006). Novel brain mapping methods allowed us to visualize dynamic patterns of atrophy in 52 high-resolution magnetic resonance image scans of 12 patients with AD (age 68.4 +/- 1.9 years) and 14 elderly matched controls (age 71.4 +/- 0.9 years) scanned longitudinally (two scans; interscan interval 2.1 +/- 0.4 years). A cortical pattern matching technique encoded changes in brain shape and tissue distribution across subjects and time. Cortical atrophy occurred in a well defined sequence as the disease progressed, mirroring the sequence of neurofibrillary tangle accumulation observed in cross sections at autopsy. Advancing deficits were visualized as dynamic maps that change over time. Frontal regions, spared early in the disease, showed pervasive deficits later (>15% loss). The maps distinguished different phases of AD and differentiated AD from normal aging. Local gray matter loss rates (5.3 +/- 2.3% per year in AD v 0.9 +/- 0.9% per year in controls) were faster in the left hemisphere (p < 0.029) than the right. Transient barriers to disease progression appeared at limbic/frontal boundaries. This degenerative sequence, observed in vivo as it developed, provides the first quantitative, dynamic visualization of cortical atrophic rates in normal elderly populations and in those with dementia.
Laboratory evaluation of temperature effects on the germination and growth of entomopathogenic fungi and on their pathogenicity to two aphid species (2003)

As part of an approach to select potential mycoinsecticides for aphid biocontrol, we investigated the effects of temperature on the growth, germination and pathogenicity of some hyphomycete fungi. Commercially available mycoinsecticides (based on Beauveria bassiana (Balsamo) Vuillemin and Verticillium lecanii (Zimmermann) Viegas) and other isolates of B bassiana, V lecanii, Metarhizium anisopliae (Metschnikoff) Sorokin and Paecilomyces fumosoroseus (Wize) Brown & Smith were evaluated. The rate of in vitro conidial germination of all isolates was slower at 10 and 15 degrees C than at 20 and 25 degrees C. Similarly, in vitro growth of most isolates was adversely affected at 10 and 15 degrees C. The greatest reduction at 10 degrees C in rates of conidial germination and colony growth, compared with other temperatures, was for M anisopliae isolates. Germination of V lecanii (isolate HRI 1.72) was fastest at 10 degrees C compared with the other fungi. It was also the most pathogenic of three isolates tested against Aphis fabae Scopoli and Myzus persicae Sulzer at 10, 18 and 23 degrees C. Generally, A fabae was more susceptible than M persicae to infection by the fungal isolates tested. A significant interaction between aphid species and temperature indicated that the pathogenic nature of an isolate was dependent not only on the target aphid species but also the temperature conditions of the bioassay. The series of studies, detailed above, allowed a temperature profile to be formed for the different isolates. Verticillium lecanii isolate HRI 1.72 (commercialised as Vertalec) was the most promising isolate selected from results of the series of experiments. Temperature profiles in conjunction with infectivity assays can be useful in selecting appropriate isolates for a particular thermal environment.
Crystal structures of B-DNA with incorporated 2'-deoxy-2'-fluoro-arabino-furanosyl thymines: Implications of conformational preorganization for duplex stability (1998)

The fundamental conformational states of right-handed double helical DNA, the A- and B-forms, are associated with distinct puckers of the sugar moieties. The furanose conformation itself is affected by the steric and electronic nature of the ring substituents. For example, a strongly electronegative substituent at the C2' position, such as in the 2'-deoxy-2'-fluoro ribo furanosyl analogue, will drive the conformational equilibrium towards the C3'- endo type (north). Conversely, the 2'-deoxy-2'-fluoro arabino furanosyl modification with opposite stereochemistry at C2' appears to have a preference for a C2'- endo type pucker (south). Incorporation of 2'-fluoroarabinofuranosyl thymines was previously shown to enhance the thermodynamic stability of B-DNA duplexes. We have determined the crystal structures of the B-DNA dodecamer duplexes [d(CGCGAASSCGCG)]2and [d(CGCGAASTCGCG)]2with incorporated 2'-deoxy-2'-fluoroarabinofuranosyl thymines S (south) at 1.55 A resolution. In the crystal structures, all S residues adopt an O4'- endo conformation (east), well compatible with an overall B-form duplex geometry. In addition to the increased rigidity of S nucleosides, a clathrate-like ordered water structure around the 2'-fluorines may account for the observed larger thermodynamic stability of DNA duplexes containing 2'-deoxy-2'-fluoroarabino thymidines.
Insulin and insulin-like growth factor-I (IGF-I) receptor overexpression in breast cancers leads to insulin/IGF-I hybrid receptor overexpression: evidence for a second mechanism of IGF-I signaling. (1999)

The insulin receptor (IR) form hybrids with the closely related insulin-like growth factor-I (IGF-I) receptor (IGF-I-R). Because most human breast carcinomas overexpress both the IR and the IGF-I-R, we evaluated whether the insulin/IGF-I hybrid receptor (Hybrid-R) is also overexpressed in these tumors and what role it plays in breast cancer biology. Using specific ELISAs and Western blots, we measured Hybrid-R content and function in 8 human cultured breast cancer cell lines and 39 human breast cancer specimens. Hybrid-R content and function were also compared to the content and function of the IR and the IGF-I-R. Hybrid-R content exceeded the IGF-I-R content in >75% of breast cancer specimens and was directly related to the molar ratio of both the IR and IGF-I-R content, suggesting that Hybrid-R formation occurred by random assembly of IR and IGF-I-R half-receptors. Hybrid-Rs became tyrosine autophosphorylated when breast cancer cells were exposed to IGF-I but not when they were exposed to insulin. In cells with an elevated Hybrid-R content, Hybrid-R autophosphorylation in response to IGF-I exceeded IGF-I-R autophosphorylation, suggesting that most of the IGF-I effect occurred via the Hybrid-R. Furthermore, Hybrid-Rs mediated growth in response to IGF-I, as indicated by experiments with blocking antibodies to the IGF-I-R. These data indicated therefore that: (a) Hybrid-Rs are present and play a major role in mediating the IGF-I signal in breast cancer; (b) their expression is directly related to IR overexpression; and (c) potential therapies designed to block IGF-I actions in breast cancer must take into account the role of these Hybrid-Rs.
Role of the Vagus Nerve in Mediating Proximal Nutrient-Induced Glucagon-Like Peptide-1 Secretion* (1999)

Plasma levels of glucagon-like peptide-1 (GLP-1) rise rapidly after nutrient ingestion, suggesting the existence of a proximal gut signal regulating GLP-1 release from the L cells of the distal small intestine. Glucose-dependent insulinotropic peptide (GIP) has been shown to be one such proximal signal; however, the dependence of GIP on gastrin-releasing peptide, a neuromodulator, suggested a role for the nervous system in this proximal-distal loop. Investigations into the nature of this proximal signal were therefore conducted in an in situ model of the rat gastrointestinal system. Infusions of corn oil into a 10-cm segment of duodenum that was isolated by loose ligation (to ensure that the luminal contents did not progress to the ileal L cell) increased the secretion of GLP-1 in parallel with that of gut glucagon-like immunoreactivity (gGLI; r = 0.85; P < 0.05). Infusion of fat into a transected segment of duodenum also significantly raised gGLI secretion compared with saline infusion, reaching a peak value of 132 +/- 37 pg/ml above basal (P < 0.05). However, peak secretion was significantly delayed when the gut was transected compared with that after ligation alone (19 +/- 4 vs. 6 +/- 1 min, respectively; P < 0.05). Furthermore, bilateral subdiaphragmatic vagotomy in conjunction with gut transection completely abolished the fat-induced rise in gGLI secretion (P < 0.001). Consistent with a role for the vagus in the regulation of the L cell, stimulation of the distal end of the celiac branch of the subdiaphragmatic vagus nerve significantly stimulated the secretion of gGLI to a level of 71 +/- 14 pg/ml above basal (P < 0.05). As found previously, supraphysiological infusion of GIP significantly increased gGLI secretion in control animals by 123 +/- 32 pg/ml (P < 0.05); this was not prevented by hepatic branch vagotomy (96 +/- 25 pg/ml; P < 0.05). In contrast, although infusion of GIP at physiological levels into sham-vagotomized animals also increased gGLI secretion, by 40 +/- 6 pg/ml (P < 0.05), selective hepatic branch vagotomy abolished GIP-induced gGLI secretion (P < 0.05). The results of these experiments therefore demonstrate that the secretion of GLP-1 and gGLI from the ileal L cell in response to fat is regulated by a complex neuroendocrine loop, involving the enteric nervous system, the afferent and efferent vagus nerves, as well as the duodenal hormone GIP.
Client behavior and feed characteristics of RSS, a publish-subscribe system for web micronews (2005)

While publish-subscribe systems have attracted much research interest since the last decade, few established benchmarks have emerged, and there has been little characterization of how publish-subscribe systems are used in practice.This paper examines RSS, a newly emerging, widely used publish-subscribe system for Web micronews.Based on a trace study spanning 45 days at a medium-size academic department and periodic polling of approximately 100,000 RSS feeds, we extract characteristics of RSS content and usage.We find that RSS workload resembles the Web in content size and popularity; feeds are typically small (less than 10KB), albeit with a heavy tail, and feed popularity follows a power law distribution.The update rate of RSS feeds is widely distributed; 55% of RSS feeds are updated hourly, while 25% show no updates for several days.And, only small portions of RSS content typically change during an update; 64% of updates involve less than three lines of the RSS content.Overall, this paper presents an analysis of RSS, the first widely deployed publish-subscribe system, and provides insights for the design of next generation publish-subscribe systems.
High-power erbium-doped fiber laser mode locked by a semiconductor saturable absorber (1995)

Using an erbium-doped fiber laser (EDFL) passively mode locked by a semiconductor saturable absorber, we generate 5.5-ps pulses of a 2.3-nJ/pulse, which are more than three times higher in energy than for other reported EDFL's. We show that, by introduction of a linear loss element within the cavity, multiple pulsing behavior at high pump powers can be suppressed. We also determine the saturable-absorber characteristics-absorbance versus wavelength near band gap-that are necessary to produce short mode-locked pulses.
Bromodomain-peptide displacement assays for interactome mapping and inhibitor discovery (2011)

Histone lysine acetylation is a key component of epigenetic regulation of gene transcription. Bromodomains, found in histone acetyl transferases and other chromatin-associated proteins, bind selectively to acetylated lysines, acting as "readers" of the histone code, and have recently been shown to contain a druggable binding pocket. Here we report the development of high-throughput assays that quantify the binding of bromodomains to acetylated histone peptides. We have used these assays to screen for histone binding partners of as yet uncharacterized bromodomains, adding to current knowledge of the histone code and expanding the repertoire of assays for chemical probe discovery. We have also demonstrated that these assays can be used to detect small molecule binding from the very weak to the nanomolar range. This assay methodology is thereby anticipated to provide the basis both for broader interactome profiling and for small molecule inhibitor discovery.
Shotgun DNA microarrays and stage‐specific gene expression in Plasmodium falciparum malaria (2000)

Malaria infects over 200 million individuals and kills 2 million young children every year. Understanding the biology of malarial parasites will be facilitated by DNA microarray technology, which can track global changes in gene expression under different physiological conditions. However, genomes of Plasmodium sp. (and many other important pathogenic organisms) remain to be fully sequenced so, currently, it is not possible to construct gene-specific microarrays representing complete malarial genomes. In this study, 3648 random inserts from a Plasmodium falciparum mung bean nuclease genomic library were used to construct a shotgun DNA microarray. Through differential hybridization and sequencing of relevant clones, large differences in gene expression were identified between the blood stage trophozoite form of the malarial parasite and the sexual stage gametocyte form. The present study lengthens our list of stage-specific transcripts in malaria by at least an order of magnitude above all previous studies combined. The results offer an unprecedented number of leads for developing transmission blocking agents and for developing vaccines directed at blood stage antigens. A significant fraction of the stage-selective transcripts had no sequence homologues in the current genome data bases, thereby underscoring the importance of the shotgun approach. The malarial shotgun microarray will be useful for unravelling additional important aspects of malaria biology and the general approach may be applied to any organism, regardless of how much of its genome is sequenced.
On the Relationship Between Feature‐Recognizing MRI and MRI Encoded by Singular Value Decomposition (1995)

This paper describes the similarity between two methods of non-Fourier MRI: feature-recognizing MRI (FR MRI) and MRI with encoding by singular value decomposition (SVD MRI). Both methods represented images as truncated expansions of non-Fourier basis functions; these basis images were derived from prior image data by using closely-related mathematical techniques: the Karhunen-Loeve decomposition (or principal components analysis) and singular value decomposition, respectively. We demonstrate that FR and SVD MRI are equivalent in the following sense: given the same prior image data, they lead to exactly the same basis functions. FR MRI utilized prior images of the same body part in many "training" subjects, thought to be similar to the "unknown" subject to be imaged. SVD MRI utilized a single prior image of one subject in order to perform dynamic imaging of that subject. We demonstrate that the basis function expansion derived from a single prior image may not be capable of representing new features (features not found in the prior image). Therefore, the SVD basis functions may be inappropriate for dynamic imaging.
Hepatic Gene Therapy: Persistent Expression of Human α1-Antitrypsin in Mice after Direct Gene Delivery In Vivo (1992)

The liver represents an excellent target organ for gene therapy. The current strategy for hepatic gene therapy involves the isolation of primary hepatocytes from a resected liver lobe, transduction of therapeutic genes in vitro followed by autologous hepatocellular transplantation. This ex vivo approach is a rather complex procedure in its entirety; thus, a simple method for direct gene delivery into hepatocytes in vivo has been developed. The procedure involves partial hepatectomy followed by the portal vein infusion of recombinant retroviral vectors. Histological analysis of hepatocytes after in vivo delivery of a recombinant retrovirus bearing the E. coli beta-galactosidase gene showed that 1-2% of the parenchymal cells were transduced. Direct hepatic transfer of human alpha 1-antitrypsin cDNA under the transcriptional direction of the albumin promoter-enhancer led to constitutive expression of the human protein in the sera of recipients at concentrations of 30-1,400 ng/ml for at least 6 months. The experimental animals showed no signs of illness and histologic analysis of the liver revealed no evidence of pathologic abnormalities. The results suggest that the in vivo approach is an attractive alternative for hepatic gene therapy.
Viral load as a predictor of the risk of cervical intraepithelial neoplasia (2002)

HPV infections are believed to be a necessary cause of cervical cancer. Viral burden, as a surrogate indicator for persistence, may help predict risk of subsequent SIL. We used results of HPV test and cytology data repeated every 4-6 months in 2,081 women participating in a longitudinal study of the natural history of HPV infection and cervical neoplasia in São Paulo, Brazil. Using the MY09/11 PCR protocol, 473 women were positive for HPV DNA during the first 2 visits. We retested all positive specimens by a quantitative, low-stringency PCR method to measure viral burden in cervical cells. Mean viral loads and 95% CIs were calculated using log-transformed data. RRs and 95% CIs of incident SIL were calculated by proportional hazards models, adjusting for age and HPV oncogenicity. The risk of incident lesions increased with viral load at enrollment. The mean number of viral copies/cell at enrollment was 2.6 for women with no incident lesions and increased (trend p = 0.003) to 15.1 for women developing 3 or more SIL events over 6 years of follow-up. Compared to those with <1 copy per cell in specimens tested during the first 2 visits, RRs for incident SIL increased from 1.9 (95% CI 0.8-4.2) for those with 1-10 copies/cell to 4.5 (95% CI 1.9-10.7) for those with >1,000 copies/cell. The equivalent RR of HSIL for >1,000 copies/cell was 2.6 (95% CI 0.5-13.2). Viral burden appears to have an independent effect on SIL incidence. Measurement of viral load, as a surrogate for HPV persistence, may identify women at risk of developing cervical cancer precursors.
Isolation and nucleotide sequence determination of a gene encoding a heat-stable enterotoxin of Escherichia coli (1983)

A gene encoding a heat-stable enterotoxin (ST) from an Escherichia coli strain isolated from a human with diarrhea was cloned and characterized by nucleotide sequence analysis. The gene was found to be partially homologous to a previously characterized ST gene from an E. coli strain of bovine origin. Hybridization studies showed that most ST-producing strains of E. coli isolated from humans with diarrhea possess genes highly homologous to either the ST gene from the bovine strain or the ST gene characterized in the present study.
New fluorinated acrylic monomers for the surface modification of UV-curable systems (1999)

New fluorinated acrylates were synthesized and used as modifying additives for acrylic UV-curable systems. Their chemical structure is: CnF2n+1 R—OCO—CHCH2, where the linear perfluorinated chain contains from 4 to 10 carbon atoms, while R is a linear alkyl group containing or not a thioether group. Notwithstanding their very low concentration, the fluorinated monomers caused a dramatic change of the surface properties of the films, without changing their curing conditions and their bulk properties. X-ray photoelectron spectroscopy measurements showed that the monomers were able to concentrate selectively on the surfaces of the films, depending on their chemical structure and on the kind of substrate employed. The synthesis of the fluorinated monomers and the relationship between their chemical structure and the final surface properties of the UV-cured films will be discussed. © 1999 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 37: 77–87, 1999
Collagen–platelet interaction: Gly-Pro-Hyp is uniquely specific for platelet Gp VI and mediates platelet activation by collagen (1999)

Platelet activation by collagen involves the highly-specific recognition of the Gly-Pro-Hyp sequence by platelet glycoprotein VI. Recognition of alpha 2 beta 1 is insufficient to cause activation. Interaction between collagen and glycoprotein VI is unique since Gly-Pro-Hyp is common in collagens but occurs rarely in other proteins, and glycoprotein VI may be expressed solely by platelets. This sequence could provide a basis for a highly-specific anti-thrombotic reagent to control thrombosis associated with plaque rupture.
High performance In2O3 thin film transistors using chemically derived aluminum oxide dielectric (2013)

We report high performance solution-deposited indium oxide thin film transistors with field-effect mobility of 127 cm2/Vs and an Ion/Ioff ratio of 106. This excellent performance is achieved by controlling the hydroxyl group content in chemically derived aluminum oxide (AlOx) thin-film dielectrics. The AlOx films annealed in the temperature range of 250–350 °C showed higher amount of Al-OH groups compared to the films annealed at 500 °C, and correspondingly higher mobility. It is proposed that the presence of Al-OH groups at the AlOx surface facilitates unintentional Al-doping and efficient oxidation of the indium oxide channel layer, leading to improved device performance.
Prolonged Dexmedetomidine Infusion and Drug Withdrawal In Critically Ill Children (2017)

A withdrawal syndrome may occur after prolonged infusion of dexmedetomidine. As all our patients were also exposed to opioids this may be affected by the duration of opioid use. We identified a cumulative dose of 107 micrograms/kg of dexmedetomidine beyond which withdrawal symptoms were more likely (which equates to 4 days of use at a dose of 1 mcg/kg/hr). A protocol for weaning should be considered in this circumstance.
Routability of a rubber-band sketch (1991)

The SURF routing system employs a grid-less flexible
Vaccinia Virus B18R Gene Encodes a Type I Interferon-binding Protein That Blocks Interferon α Transmembrane Signaling (1995)

Poxviruses encode a large number of proteins that attenuate the inflammatory and immune responses to infection. In this report we demonstrate that a number of orthopoxviruses express a type I interferon (IFN)-binding protein, which is encoded by the B18R open reading frame in the WR strain of vaccinia virus. The B18R protein has significant regions of homology with the alpha subunits of the mouse, human, and bovine type I IFN receptors, bound human IFN alpha 2 with high affinity, and inhibited transmembrane signaling as demonstrated by inhibition of Fc receptor factor gamma 1/gamma 2 and interferon-stimulated gene factor-3 formation as well as inhibition of the IFN alpha antiviral response. Among viral host response modifiers, the B18R protein is unique inasmuch as it exists as a soluble extracellular as well as a cell surface protein and thus should effectively block both autocrine and paracrine functions of IFN.