gebhart/patrepeval huggingface dataset:
Collagen peptides enhance hippocampal neurogenesis and reduce anxietyrelated behavior in mice (2012)

The present study examined the effects of enzymatically hydrolyzed collagen peptides on the level of hippocampal neurogenesis and emotional behavior in adult mice. For this purpose, two kinds of enzymatically hydrolyzed collagen peptides, the lower or higher molecular weight peptides (LP: below 2,000, HP: about 30,000) were administered orally to C57BL/6 mice for 4 weeks. As a result, the density of proliferating cells in subgranular zone of hippocampus showed a 1.2-fold increase in LP mice as compared with HP mice. Additionally, LP mice spent less time in closed arms than HP mice in elevated plus maze test to examine anxiety-related behavior. These results suggest that oral administration of the lower molecular weight peptides derived from collagen enhanced the hippocampal neurogenesis and exerted emotional behavior in adult mice.
Jones, Thomas Rymer (1810–80) (2004)

Jones, Thomas Rymer Thomas Rymer Jones died on 10 December 1880; his father was a naval officer. Entering upon a medical career, he studied at Guy's Hospital and also in Paris, and qualified as a Member of the Royal College of Surgeons in 1833; but chronic deafness then prevented him from practising
Teflon granuloma presenting as an enlarging, gadolinium enhancing, posterior fossa mass with progressive hearing loss following microvascular decompression. (1995)

Deleterious effects of Teflon strand placement during microvascular decompression (MVD) for hemifacial spasm are rare. In this report, a patient who had previously undergone suboccipital MVD for hemifacial spasm presented 3 years postoperatively with a progressive asymmetric sensorineural hearing loss and magnetic resonance imaging evidence of an enlarging ipsilateral gadolinium enhancing 1-cm cerebellopontine angle lesion. At surgery a granuloma was found displacing the structures of the internal auditory canal. Histologically, evidence of a Teflon fiber-induced giant cell granuloma was identified. This paper reviews the literature of Teflon-induced histopathology as it relates to posterior fossa MVD surgery, as well as its relation to this previously unreported complication.
<title>Lossless volumetric medical image compression</title> (1999)

This paper focuses on lossless medical image compression methods for 3D volumetric medical images that operate on three-dimensional (3D) reversible integer wavelet transforms. We offer an application of the Set Partitioning in Hierarchical Trees (SPIHT) algorithm to volumetric medical images, using a 3D wavelet decomposition and a 3D spatial dependence tree. The wavelet decomposition is accomplished with integer wavelet filters implemented with the lifting method, where careful scaling and truncations keep the integer precision small and the transform unitary. We have tested our encoder on volumetric medical images using different integer filters and different coding unit sizes. The coding unit sizes of 16 and 8 slices save considerable memory and coding delay from full sequence coding units used in previous works. Results show that, even with these small coding units, our algorithm with certain filters performs as well and sometimes better in lossless coding than previously coding systems using 3D integer wavelet transforms on volumetric medical images.
Supplementary Table 5 from Deciphering the Impact of Common Genetic Variation on Lung Cancer Risk: A Genome-Wide Association Study (2023)

Supplementary Table 5 from Deciphering the Impact of Common Genetic Variation on Lung Cancer Risk: A Genome-Wide Association Study
Glucose-induced hyperaccumulation of cyclic AMP and defective glucose repression in yeast strains with reduced activity of cyclic AMP-dependent protein kinase. (1990)

Addition of glucose or related fermentable sugars to derepressed cells of the yeast Saccharomyces cerevisiae triggers a RAS-mediated cyclic AMP (cAMP) signal that induces a protein phosphorylation cascade. In yeast mutants (tpk1w1, tpk2w1, and tpk3w1) containing reduced activity of cAMP-dependent protein kinase, fermentable sugars, as opposed to nonfermentable carbon sources, induced a permanent hyperaccumulation of cAMP. This finding confirms previous conclusions that fermentable sugars are specific stimulators of cAMP synthesis in yeast cells. Despite the huge cAMP levels present in these mutants, deletion of the gene (BCY1) coding for the regulatory subunit of cAMP-dependent protein kinase severely reduced hyperaccumulation of cAMP. Glucose-induced hyperaccumulation of cAMP was also observed in exponential-phase glucose-grown cells of the tpklw1 and tpk2w1 strains but not the tpk3w1 strain even though addition of glucose to glucose-repressed wild-type cells did not induce a cAMP signal. Investigation of mitochondrial respiration by in vivo 31P nuclear magnetic resonance spectroscopy showed the tpk1w1 and tpk2w1 strains, to be defective in glucose repression. These results are consistent with the idea that the signal transmission pathway from glucose to adenyl cyclase contains a glucose-repressible protein. They also show that a certain level of cAMP-dependent protein phosphorylation is required for glucose repression. Investigation of the glucose-induced cAMP signal and glucose-induced activation of trehalase in derepressed cells of strains containing only one of the wild-type TPK genes indicates that the transient nature of the cAMP signal is due to feedback inhibition by cAMP-dependent protein kinase.
A highly selective long-wavelength fluorescent probe for the detection of human carboxylesterase 2 and its biomedical applications (2014)

A highly selective long-wavelength fluorescent probe TCFB has been developed for the detection of hCE2. The probe can be used for real-time monitoring of hCE2 activity in complex biological systems.
Novel Linear Quadrupole Ion Trap/FT Mass Spectrometer:  Performance Characterization and Use in the Comparative Analysis of Histone H3 Post-translational Modifications (2004)

We describe the design and performance of a prototype high performance hybrid mass spectrometer. This instrument consists of a linear quadrupole ion trap (QLT) coupled to a Fourier transform ion cyclotron resonance mass analyzer (FTMS). This configuration provides rapid and automated MS and MS/MS analyses, similar to the "data dependent scanning" found on standard 3-D Paul traps, but with substantially improved internal scan dynamic range, mass measurement accuracy, mass resolution, and detection limits. Sequence analysis of peptides at the zeptomole level is described. The recently released, commercial version of this instrument operates in the LC/MS mode (1 s/scan) with a mass resolution of 100 000 and is equipped with automatic gain control to provide mass measurement accuracy of 1-2 ppm without internal standard. Methodology is described that uses this instrument to compare the post-translational modifications present on histone H3 isolated from asynchronously growing cells and cells arrested in mitosis.
Genomic and Epigenomic Profile of Uterine Smooth Muscle Tumors of Uncertain Malignant Potential (STUMPs) Revealed Similarities and Differences with Leiomyomas and Leiomyosarcomas (2021)

Uterine smooth muscle tumors of uncertain malignant potential (STUMPs) represent a heterogeneous group of tumors that cannot be histologically diagnosed as unequivocally benign or malignant. For this reason, many authors are working to obtain a better definition of diagnostic and prognostic criteria. In this work, we analyzed the genomic and epigenomic profile of uterine smooth muscle tumors (USMTs) in order to find similarities and differences between STUMPs, leiomyosarcomas (LMSs) and leiomyomas (LMs), and possibly identify prognostic factors in this group of tumors. Array-CGH data on 23 USMTs demonstrated the presence of a more similar genomic profile between STUMPs and LMSs. Some genes, such as <i>PRKDC</i> and <i>PUM2</i>, with a potential prognostic value, were never previously associated with STUMP. The methylation data appears to be very promising, especially with regards to the divergent profile found in the sample that relapsed, characterized by an overall CGI hypomethylation. Finally, the Gene Ontology analysis highlighted some cancer genes that could play a pivotal role in the unexpected aggressive behavior that can be found in some of these tumors. These genes could prove to be prognostic markers in the future.
The Diagnostic Utility of Anti‐cyclic Citrullinated Peptide Antibodies, Matrix Metalloproteinase‐3, Rheumatoid Factor, Erythrocyte Sedimentation Rate, and C‐reactive Protein in Patients with Erosive and Non‐erosive Rheumatoid Arthritis (2005)

The results of our study suggest that the presence of elevated anti-CCP antibody titers have better diagnostic performance than MMP-3, RF, CRP and ESR in patients with erosive RA.
Sensitive Oligonucleotide Ligation Assay for Low-Level Detection of Nevirapine Resistance Mutations in Human Immunodeficiency Virus Type 1 Quasispecies (2007)

This study has adapted the oligonucleotide ligation assay (OLA) to probe for low-level nevirapine (NVP) resistance mutations K103N and Y181C in the human immunodeficiency virus type 1 (HIV-1) population of infected mother-infant pairs from Uganda. When NVP is used to prevent perinatal transmission, NVP-resistant HIV-1 clones may be rapidly selected due to a low barrier for mutation and a relatively high level of fitness (compared to that of other drug-resistant HIV-1 clones). Monitoring for even a low frequency of NVP resistance mutations may help predict the success of subsequent treatment or warrant the use of another regimen to prevent transmission in a subsequent pregnancy. The standard OLA was optimized by using nonstandard bases in oligonucleotides to allow promiscuous base pairing and accommodate significant HIV-1 heterogeneity. Radiolabeled as opposed to fluorescently tagged oligonucleotides increased the sensitivity, whereas alteration of the template, oligonucleotides, salt, and thermostable DNA ligase concentrations increased the specificity for the detection of minority codons. This modified OLA is now capable of detecting mutants with the K103N or the Y181C mutation present in an HIV-1 population at a frequency of approximately 0.4% and is at least 10- to 30-fold more sensitive than the original protocol. A cohort of 19 Ugandan mothers who received NVP treatment perinatally were sampled 6 weeks postdelivery. Ten of 19 HIV-1 DNA samples extracted from peripheral blood mononuclear cells had a detectable K103N (0.5 to 44%) or Y181C (0.8 to 92.5%) mutation, but only one plasma HIV-1 RNA sample had a viral population with the Y181C mutation. These findings suggest that OLA is a robust, sensitive, and specific method for the detection of low-frequency drug resistance mutations in an intrapatient HIV-1 population.
Identification of Motility and Autoagglutination Campylobacter jejuni Mutants by Random Transposon Mutagenesis (2002)

Campylobacter jejuni has been identified as the leading cause of acute bacterial diarrhea in the United States, yet compared with other enteric pathogens, considerably less is understood concerning the virulence factors of this human pathogen. A random in vivo transposon mutagenesis system was recently developed for the purpose of creating a library of C. jejuni transformants. A total of 1,065 C. jejuni transposon mutants were screened for their ability to swarm on motility agar plates and autoagglutinate in liquid cultures; 28 mutants were subsequently identified. The transposon insertion sites were obtained by using random-primed PCR, and the putative genes responsible for these phenotypes were identified. Of these mutants, all 28 were found to have diminished motility (0 to 86% that of the control). Seventeen motility mutants had insertions in genes with strong homology to functionally known motility and chemotaxis genes; however, 11 insertions were in genes of unknown function. Twenty motility mutants were unable to autoagglutinate, suggesting that the expression of flagella is correlated with autoagglutination (AAG). However, four mutants expressed wild-type levels of surface FlaA, as indicated by Western blot analysis, yet were unable to autoagglutinate (Cj1318, Cj1333, Cj1340c, and Cj1062). These results suggest that FlaA is necessary but not sufficient to mediate the AAG phenotype. Furthermore, two of the four AAG mutants (Cj1333 and Cj1062) were unable to invade INT-407 intestinal epithelial cells, as determined by a gentamicin treatment assay. These data identify novel genes important for motility, chemotaxis, and AAG and demonstrate their potential role in virulence.
Testosterone/cortisol ratio in response to acute stress: A possible marker of risk for marital violence (2013)

Testosterone to cortisol (T/C) ratios could be associated with feelings and expression of anger as high testosterone and low cortisol levels indicate a predisposition to violence. The basal T/C ratio has recently been proposed as a marker for proneness to social aggression; so far, however, only its value as an indicator of state anger or violence has been investigated. Given this, we aimed to establish whether the T/C ratio response to acute stress was a specific psychobiological feature in individuals with a history of violence, namely, perpetrators of intimate partner violence (IPV). T/C ratio and anger responses were compared in men jailed for IPV and controls using the Trier Social Stress Test. IPV perpetrators had higher T/C ratios than controls, during the preparation period, and 15 and 30 minutes post-task. In IPV perpetrators, high T/C ratios were linked to better self-esteem and good mental health. An increase in anger may increase proneness to violence by altering hormones and, thereby, increasing T/C ratios. The basal T/C ratio together with acute stress responses and other indicators could serve as a marker to identify men at high risk of reacting violently to their partners.
Augmentation Enterocystoplasty for the Management of Voiding Dysfunction in Spinal Cord Injury Patients (1990)

A total of 12 spinal cord injury adults underwent augmentation enterocystoplasty for treatment of a high pressure neurogenic bladder. These patients suffered from urinary incontinence, recurrent urinary tract infection, upper tract deterioration and severe autonomic dysreflexia. A sigmoid colon segment fashioned into a cup-patch was used in 11 patients and detubularized cecum was used in 1. The artificial urinary sphincter was implanted in 3 patients at augmentation enterocystoplasty and in 1 after enterocystoplasty. After a mean followup of 15 months all patients were continent on clean intermittent self-catheterization, the upper tract had remained stable or had improved and the symptoms of autonomic dysreflexia had disappeared. A third of the patients are on maintenance antibiotic therapy to control bacteriuria.
Development of a Bioactive Sauce Based on Oriental Mustard Flour with Antifungal Properties for Pita Bread Shelf Life Improvement (2019)

Ochratoxin A (OTA) is a mycotoxin produced in the secondary metabolism of fungus belonging to the genus <i>Aspergillus</i> and <i>Penicillium</i>. In this study, the employment of oriental mustard flour (OMF) as an ingredient in a packaged sauce was evaluated for the generation in situ of the antimicrobial compound allyl isothiocyanate (AITC) in order to preserve pita bread contaminated with <i>Penicillium verrucosum</i> VTT D-01847, an OTA producer, in an active packaging system. Four different concentrations (8, 16, 33 and 50 mg/g) were tested. Mycelium formation, mycotoxin production, AITC absorbed by the food matrix, and volatilization kinetics were studied for each concentration. The results obtained were compared with bread treated with the commercial additive calcium propionate (E-282). The results showed a shelf life increase of two and three days with the employment of 33 and 50 mg/g of OMF, with a significant reduction of the fungal population (3.1 and 5.7 logs, respectively) in comparison with the control experiment. The use of 16 and 33 mg/g of OMF in the sauce formulation decreased the concentration of OTA in the bread samples while no OTA production was detected employing 50 mg/g of OMF.
Increased formation of ursodeoxycholic acid in patients treated with chenodeoxycholic acid. (1974)

The formation of ursodeoxycholic acid, the 7 beta-hydroxy epimer of chenodeoxycholic acid, was investigated in three subjects with cerebrotendinous xanthomatosis and in four subjects with gallstones. Total biliary bile acid composition was analyzed by gas-liquid chromatography before and after 4 months of treatment with 0.75 g/day of chenodeoxycholic acid. Individual bile acids were identified by mass spectrometry. Before treatment, bile from cerebrotendinous xanthomatosis (CTX) subjects contained cholic acid, 85%; chenodeoxycholic acid, 7%; deoxycholic acid, 3%; allocholic acid, 3%; and unidentified steroids, 2%; while bile from gallstone subjects contained cholic acid, 45%; chenodeoxycholic acid, 43%; deoxycholic acid, 11%, and lithocholic acid, 1%. In all subjects, 4 months of chenodeoxycholic acid therapy increased the proportion of this bile acid to approximately 80% and decreased cholic acid to 3% of the total biliary bile acids, the remaining 17% of bile acids were identified as ursodeoxycholic acid. After the intravenous injection of [3H]chenodeoxycholic acid, the specific activity of biliary ursodeoxycholic acid exceeded the specific activity of chenodeoxycholic acid, and the resulting specific activity decay curves suggested precursor-product relationships. When [3H]7-ketolithocholic acid was administrated to another patient treated with chenodeoxycholic acid, radioactivity was detected in both the ursodeoxycholic acid and chenodeoxycholic acid fractions. These results indicate that substantial amounts of ursodeoxycholic acid are formed in patients treated with chenodeoxycholic acid. The ursodeoxycholic acid was synthesized from chenodeoxycholic acid presumably via 7-ketolithocholic acid.
Interference management and performance analysis of UMTS/HSPA+ femtocells (2009)

Femtocells are low-power cellular base stations that operate in licensed spectrum. They are typically deployed indoors to improve coverage and provide excellent user experience, including high data rates. Cellular operators benefit from reduced infrastructure and operational expenses for capacity upgrades and coverage improvements. Femtocells also bring unique challenges, such as unplanned deployment, user installation, restricted access, and interoperability with existing handsets and network infrastructure. Although femtocells may cause some interference to other users in the network, with the use of proper interference management techniques, this can be well controlled. We present interference management techniques for both downlink and uplink of femtocells operating based on 3GPP Release 7 standards (also known as HSPA+). Femtocell carrier selection and femtocell DL Tx power self-calibration are proposed as key interference management methods for downlink. For uplink interference management, adaptive attenuation at the femtocell and limiting the Tx power of the femtocell users are proposed. Different interference models and their analysis are presented. In addition, coverage performance and capacity results are presented to quantify the benefits of femtocells. We demonstrate that in addition to coverage enhancements, significant capacity improvements are achieved on both downlink and uplink when femtocells are deployed in 3G UMTS/HSPA+ networks.
Spatial relationship between soil hydraulic and soil physical properties in a farm field (2009)

The relationship between soil properties may vary with their spatial separation. Understanding this relationship is important in predicting hydraulic parameters from other soil physical properties. The objective of this study was to identify spatially dependent relationships between hydraulic parameters and soil physical properties. Regularly spaced (3-m) undisturbed soil samples were collected along a 384 m transect from a farm field at Smeaton, Saskatchewan. Saturated hydraulic conductivity, the soil water retention curve, and soil physical properties were measured. The scaling parameter, van Genuchten scaling parameter α (VGα), and curve shape parameter, van Genuchten curve shape parameter n (VGn), were obtained by fitting the van Genuchten model to measured soil moisture retention data. Results showed that the semivariograms of soil properties exhibited two different spatial structures at spatial separations of 20 and 120 m, respectively. A strong spatial structure was observed in organic carbon, saturated hydraulic conductivity (Ks), sand, and silt; whereas a weak structure was found for VGα and VGn. Correlation circle analysis showed strong spatially dependent relationships of Ks and VGα; with soil physical properties, but weak relationships of θs and VGn with soil physical properties. The spatially dependent relationships between soil physical and soil hydraulic parameters should be taken into consideration when developing pedotransfer functions. Key words: Spatial relationship, geostatistics, linear coregionalization model, principal component analysis, pedotransfer function
High Genetic Diversity and Implications for Determining Population Structure in the Blue CrabCallinectes sapidus (2017)

Understanding the population structure of a commercially fished species and how those populations change over time is essential for proper management. Although the blue crab Callinectes sapidus (Rathbun, 1896) covers a large geographic range spanning two continents and several distinct ecosystems, there are no clear morphological characters and a paucity of genetic data that can be used to distinguish populations within and among management areas. In this study, diversity indices were calculated for four loci in the mitochondrial genome of C. sapidus using specimens collected from the Rhode River in Maryland during the summers of 2003 to 2005. The locus with the highest diversity, which occurs within the open reading frame of the nad2 mitochondrial gene, was then used as a marker to determine population structure for samples collected from the Atlantic locations of the Chesapeake Bay; Raleigh, North Carolina; Meadowlands and Tuckerton, New Jersey; and Massachusetts, as well as locations in the Gulf of Mexico spanning the waters of Florida, Alabama, Mississippi, and Texas from 2003 to 2008. For the entire dataset, the genetic variation within each sample site accounted for 99.5%of the total diversity. Also, the Atlantic sampling sites could not be distinguished from the Gulf of Mexico sites using Bayesian inference. Interestingly, the sampling sites from Massachusetts did not show a reduction in their level of genetic diversity despite its location at the northern limit of C. sapidus habitat. There were significant differences looking temporally, however, with the 2003 samples, the year of hurricane Isabel, differing from the 2004 and 2005 samples. Using the nad2 marker along with four microsatellite loci on a sample of 28 megalopae entering the mouth of Chesapeake Bay also demonstrated extremely high diversity at all loci, and the megalopae were significantly different from an adult population of the same year at two of the microsatellite loci. This indicates that genetic diversity is high in adult as well as larval populations and that offshore mixing may be playing a large role in the observed diversity shared among geographically distant habitats. Seasonal weather patterns during larval development followed by selection during the multiple subsequent recruitment events may play a large role in shaping local populations, and larval transport and settling models will provide much more understanding of the population dynamics of this species.