gebhart/patrepeval huggingface dataset:
DNA Methylation Trajectories During Pregnancy (2019)

There is emerging evidence on DNA methylation (DNAm) variability over time; however, little is known about dynamics of DNAm patterns during pregnancy. We performed an epigenome-wide longitudinal DNAm study of a well-characterized sample of young women from the Swedish Born into Life study, with repeated blood sampling before, during and after pregnancy (n = 21), using the Illumina Infinium MethylationEPIC array. We conducted a replication in the Isle of Wight third-generation birth cohort (n = 27), using the Infinium HumanMethylation450k BeadChip. We identified 196 CpG sites displaying intra-individual longitudinal change in DNAm with a false discovery rate (FDR) <i>P</i> < .05. Most of these (91%) showed a decrease in average methylation levels over the studied period. We observed several genes represented by ⩾3 differentially methylated CpGs: <i>HOXB3, AVP, LOC100996291</i>, and MicroRNA 10a. Of 36 CpGs available in the replication cohort, 17 were replicated, all but 2 with the same direction of association (replication <i>P</i> < .05). Biological pathway analysis demonstrated that FDR-significant CpGs belong to genes overrepresented in metabolism-related pathways, such as adipose tissue development, regulation of insulin receptor signaling, and mammary gland fat development. These results contribute to a better understanding of the biological mechanisms underlying important physiological alterations and adaptations for pregnancy and lactation.
Identity-based protocol design patterns for machine-to-machine secure channels (2014)

In the classical design pattern for secure channel protocols, there is a first phase where the endpoints establish a shared secret and one or both endpoints authenticate by presenting a certificate and demonstrating knowledge of the associated private key; and a second phase where application data traffic between the endpoints is protected using symmetric keys for encryption and authentication derived from the shared secret. This classical pattern emerged in the nineties, when most secure channels were intended for human-to-machine (H2M) communications and the latency caused by roundtrips and transmission of bulky certificate chains resulted in no more than inconvenience to the human. In machine-to-machine (M2M) communication, on the other hand, excessive latency may be unacceptable for safety-critical and other applications. We describe a range of alternative protocol design patterns that use identity-based encryption to eliminate roundtrips and certificate transmission. These patterns can be used in the design of new secure channel protocols or retrofitted into existing protocols.
Summer pruning effects on fruit size, fruit quality, return bloom and fine root survival in apple trees (2003)

SummaryWhile many undesirable effects of summer pruning on apple (Malus domestica Borkh.) growth and development have been reported, the results are inconsistent and difficult to interpret. This study resolves the inconsistency by supplying a model that integrates pruning effects with tree physiological crop load, i.e. canopy net carbohydrate exchange rate per fruit. Our previous study suggests that the potential impact of reducing canopy photosynthesis after summer pruning depends on the balance of carbohydrate supply and demand. To test the hypothesis that summer pruning affects carbohydrate balance, we measured fruit growth, fruit quality, return bloom, and root growth in 20 year old slender spindle ‘Empire’/M.9 apple trees in response to different severities of summer pruning. Results were interpreted in relation to pruning severity, fruit number per tree, and the physiological crop load. Within commercial cropping ranges, light and moderate summer pruning had slight influences on fruit size and fresh weight. Summer pruning did not affect fruit colour, soluble solids content, starch, firmness, and internal breakdown after storage. Summer pruning alone did not affect return bloom or root growth. However, the potential negative effects of summer pruning on fruit growth, return bloom, and fine root survival can be predicted through their relationships with physiological crop load. This study suggests that the carbohydrate supply and demand balance model feasibly explains summer pruning influences. In addition, the impact of carbohydrate shortage after summer pruning is likely to be mediated by the reduction in canopy transpiration. However, the interaction between canopy carbon balance and water status after summer pruning is also likely to be manipulated by annual weather pattern.
Supramolecular Chemistry: Receptors, Catalysts, and Carriers (1985)

Supramolecular chemistry is the study of the structures and functions of the supermolecules that result from binding substrates to molecular receptors. Macropolycyclic receptors and coreceptors have been designed that form cryptate inclusion complexes and display molecular recognition towards spherical, tetrahedral, and linear substrates of various kinds (metal cations, inorganic anions, and organic or biological cations or anions). Anion binding has led to the development of anion coordination chemistry. Metalloreceptors simultaneously bind organic molecules and metal ions; speleands combine polar and nonpolar binding subunits. Receptors bearing reactive functional groups may act as molecular reagents or catalysts, performing a chemical transformation on the bound substrates (by such reactions as hydrogen transfer, ester cleavage, and protoadenosinetriphosphatase and protokinase activities). Receptors fitted with lipophilic groups can operate as molecular carriers, translocating bound species through a membrane; this transport can be coupled to chemical potentials (proton and redox gradients).
Preferential processing of tactile events under conditions of divided attention (2009)

Differences in transduction and transmission latencies of visual, auditory and tactile events cause corresponding differences in simple reaction time. As reaction time is usually measured in unimodal blocks, it is unclear whether such latency differences also apply when observers monitor multiple sensory channels. We investigate this by comparing reaction time when attention is focused on a single modality, and when attention is divided between multiple modalities. Results show that tactile reaction time is unaffected by dividing attention, whereas visual and auditory reaction times are significantly and asymmetrically increased. These findings show that tactile information is processed preferentially by the nervous system under conditions of divided attention, and suggest that tactile events may be processed preattentively.
Optically Stable Biocompatible Flame-Made SiO2-Coated Y2O3:Tb3+ Nanophosphors for Cell Imaging (2012)

Nanophosphors are light-emitting materials with stable optical properties that represent promising tools for bioimaging. The synthesis of nanophosphors, and thus the control of their surface properties, is, however, challenging. Here, flame aerosol technology is exploited to generate Tb-activated Y(2)O(3) nanophosphors (∼25 nm) encapsulated in situ by a nanothin amorphous inert SiO(2) film. The nanocrystalline core exhibits a bright green luminescence following the Tb(3+) ion transitions, while the hermetic SiO(2)-coating prevents any unspecific interference with cellular activities. The SiO(2)-coated nanophosphors display minimal photobleaching upon imaging and can be easily functionalized through surface absorption of biological molecules. Therefore, they can be used as bionanoprobes for cell detection and for long-term monitoring of cellular activities. As an example, we report on the interaction between epidermal growth factor (EGF)-functionalized nanophosphors and mouse melanoma cells. The cellular uptake of the nanophosphors is visualized with confocal microscopy, and the specific activation of EGF receptors is revealed with biochemical techniques. Altogether, our results establish SiO(2)-coated Tb-activated Y(2)O(3) nanophosphors as superior imaging tools for biological applications.
Core Analysis for the Development and Constraint of Physical Models of Geothermal Reservoirs (2003)

Effective reservoir exploration, characterization, and engineering require a fundamental understanding of the geophysical properties of reservoir rocks and fracture systems. Even in the best of circumstances, spatial variability in porosity, fracture density, salinity, saturation, tectonic stress, fluid pressures, and lithology can all potentially produce and/or contribute to geophysical anomalies. As a result, serious uniqueness problems frequently occur when interpreting assumptions based on a knowledge base founded in validated rock physics models of reservoir material.
Baseline correction of vibration acceleration signals with inconsistent initial velocity and displacement (2016)

This study improves upon the traditional polynomial detrending method in order to correct the vibration acceleration signals with inconsistent initial velocity and displacement more rationally and efficiently. When numerical integration of recorded acceleration signals using assumed initial velocity and displacement values (which are generally inconsistent with real values) is performed, baseline shift or drift phenomenon can arise in velocity and displacement curves obtained. Baseline correction must be performed if an inconsistent acceleration signal is to be used in dynamic analyses. Polynomial detrending is generally used to remove unreasonable trends in time series, but the consistency among acceleration, velocity, and displacement has not received sufficient attention. The traditional polynomial detrending method is improved by purposefully removing the shifted trends in velocity and displacement. Two inconsistent vibration signals are selected to be corrected using both the traditional method and the improved method. It was found that the traditional method does not give a satisfactory correction result, but the improved method can correct the signal to be consistent. The improved detrending method is effective in making vibration signals have consistent acceleration, velocity, and displacement.
Synbiotic synthesis of oligosaccharides during milk fermentation by addition of leuconostoc starter and sugars. (2007)

Synthesis of oligosaccharides during milk fermentation was attempted by inoculating Leuconostoc citreum with Lactobacillus casei, Lb. delbrueckii subsp. bulgaricus, and Streptococcus thermophilus as starters. Dextransucrase of Ln. citreum worked as a catalyst for the transglycosylation reaction of sugars; sucrose was added as the glucose donor, and lactose or maltose acted as the acceptor compound for the reaction. When 4% sucrose was added in milk, glucosyl-lactose was synthesized (about 1%, w/v) after 1-2 days of fermentation at 15 or 25 degrees C. Alternatively, when sucrose and maltose (2% each, w/v) were added, panose (about 1%, w/v) and other isomaltooligosaccharides were made in a day at 15-35 degrees C. Growth patterns of lactobacilli and streptococci starters were not affected by the coculture of leuconostoc starter, but the rate of acid synthesis was slightly slowed at every temperature. Addition of sugars in milk did not give any adverse effect on the lactate fermentation. Accordingly, the use of leuconostoc starter and addition of sugars in milk allowed the production of oligosaccharides-containing fermented milk, and application of this method will facilitate the extensive development of synbiotic lactate foods.
A review on fast power diode development and modern novel structures (1996)

This work reviews the development of fast power diodes. It also includes a comparison of conventional and novel diode structures (SPEED, SSD, MPS, ESD, P-IN, CIC, ECPT, SFD, Buffer Layer Diodes, and the Hybrid Diode), analysed using the semiconductor device simulation package ETH/DESSIS/ise. Simulations were carried out for the forward and reverse I-V static characteristics, and for the forward and reverse recovery behaviour under the same operating conditions. The advantages and disadvantages of each design on the diode overall performance are outlined.
Autophagy in the Degenerating Human Intervertebral Disc (2015)

N/A.
Omentin Modulates Chronic Cardiac Remodeling After Myocardial Infarction (2023)

<b><i>Background:</i></b> Omentin, a circulating adipokine, is downregulated in complications of obesity, including heart disease. Here, we investigated whether omentin modulates adverse cardiac remodeling in mice after myocardial infarction (MI). <b><i>Methods and Results:</i></b> Transgenic mice expressing the human omentin gene in fat tissue (OMT-Tg) and wild-type (WT) mice were subjected to permanent ligation of the left anterior descending coronary artery (LAD) to induce MI. OMT-Tg mice had a higher survival rate after permanent LAD ligation than WT mice. Moreover, OMT-Tg mice had lower heart weight/body weight (HW/BW) and lung weight/body weight (LW/BW) ratios at 4 weeks after coronary artery ligation compared with WT mice. OMT-Tg mice also showed decreased left ventricular diastolic diameter (LVDd) and increased fractional shortening (%FS) following MI. Moreover, an increase in capillary density in the infarct border zone and a decrease in myocardial apoptosis, myocyte hypertrophy, and interstitial fibrosis in the remote zone following MI, were more prevalent in OMT-Tg than WT mice. Finally, intravenous administration of adenoviral vectors expressing human omentin to WT mice after MI resulted in decreases in HW/BW, LW/BW, and LVDd, and an increase in %FS. <b><i>Conclusions:</i></b> Our findings document that human omentin prevents pathological cardiac remodeling after chronic ischemia, suggesting that omentin represents a potential therapeutic molecule for the treatment of ischemic heart disease.
Domain-specific Web site identification: the CROSSMARC focused Web crawler (2003)

This paper presents techniques for identifying domain specific Web sites that have been implemented as part of the EC-funded R&amp;amp;D project, CROSSMARC. The project aims to develop technology for extracting interesting information from domain-specific Web pages. It is therefore important for CROSSMARC to identify Web sites in which interesting domain specific pages reside (focused Web crawling). This is the role of the CROSSMARC Web crawler. 1.
IODNE: An integrated optimization method for identifying the deregulated subnetwork for precision medicine in cancer (2017)

Subnetwork analysis can explore complex patterns of entire molecular pathways for the purpose of drug target identification. In this article, the gene expression profiles of a cohort of patients with breast cancer are integrated with protein-protein interaction (PPI) networks using, simultaneously, both edge scoring and node scoring. A novel optimization algorithm, integrated optimization method to identify deregulated subnetwork (IODNE), is developed to search for the optimal dysregulated subnetwork of the merged gene and protein network. IODNE is applied to select subnetworks for Luminal-A breast cancer from The Cancer Genome Atlas (TCGA) data. A large fraction of cancer-related genes and the well-known clinical targets, ER1/PR and HER2, are found by IODNE. This validates the utility of IODNE. When applying IODNE to the triple-negative breast cancer (TNBC) subtype data, we identified subnetworks that contain genes such as ERBB2, HRAS, PGR, CAD, POLE, and SLC2A1.
Altered Mechanical Behavior of Epicardium Due to Isothermal Heating Under Biaxial Isotonic Loads (2003)

Recent isothermal biaxial isotonic tests suggest that increasing the temperature hastens the rate of denaturation of epicardium whereas increasing the mechanical load during heating delays this process, findings that are consistent with prior uniaxial tests on tendons. Yet, contrary to uniaxial reports, a clear time-temperature-load equivalency was not found in this multiaxial setting. There is, therefore, a need to delineate multiaxial thermomechanical behavior in greater detail, and ultimately, to correlate changes therein with the underlying microstructure. Toward this end, we describe a new experimental approach for quantifying heating-induced changes in the multiaxial mechanical response of thin sheet-like specimens. Illustrative results are presented for bovine epicardium subjected to nine different thermomechanical loading protocols. Among other results, it is shown that thermal damage tends to increase the stiffness at low strains and that overall changes in extensibility correlate well with the degree of thermal damage independent of the specific thermomechanical protocol. Multiaxial changes in behavior are nevertheless complex, and there is a need for significantly more testing before constitutive relations can be formulated.
Reactive Oxygen Species Scavengers Attenuate Endotoxin-induced Impairment of Hypoxic Pulmonary Vasoconstriction in Mice (2002)

Administration of N-acetylcysteine or EUK-8 1 h after endotoxin challenge in mice prevented the impairment of HPV after LMBO. Early therapy with ROS scavengers, either systemically or by inhalation, may provide a means to preserve HPV in sepsis-associated acute lung injury.
Triple compartment prolapse: sacrocolpopexy with anterior and posterior mesh extensions (2003)

Post-hysterectomy vault prolapse may be accompanied by anterior (cystocele) and posterior (rectocele) pelvic compartment prolapse. We describe our results with sacrocolpopexy with anterior and posterior polytetrafluoroethylene mesh (SCAPM) extensions. A prospective on-going study is presented of 12 consecutive, complicated patients referred to our tertiary referral unit with a median age of 60 years (range 39-69) who underwent SCAPM between April 1997 and June 1999. All patients had a history and physical examination, International Continence Society Prolapse Staging (ICS) and pre-operative multichannel urodynamics testing with their prolapse reduced. All patients had an ICS grade 2, triple compartment prolapse or worse for inclusion into this study. The operative results were assessed with a 10-point visual analogue scale (VAS) for personal satisfaction and the (non-validated) St George's Hospital symptom questionnaire assessing urgency, urge incontinence, stress incontinence, splinting, digitation, sexual activity and function. All patients were reviewed during February 2002 by an independent observer (B.G. gynaecologist) no longer associated with the Department of Urogynaecology. All patients were followed post-operatively for a median of 39 months (range 32-58). One patient had a recurrent grade 1 cystocele and another a grade 1 rectocele. The median VAS score for personal satisfaction with the operative results was 8 (range 6-10). There was one patient with de novo urgency and one with de novo stress incontinence. Four of the five patients who needed to splint or digitate to empty the rectum no longer required these measures post-operatively. There were no reports of de novo dyspareunia, and two patients had improved vaginal lubrication. Two patients, each with more than five prior vaginal procedures, had a total of three episodes of mesh erosion through the posterior vaginal wall. The SCAPM is an effective treatment for triple compartment prolapse and incomplete rectal emptying. Patient satisfaction is good.
Synthesis and characterization of zirconia-grafted SBA-15 nanocomposites (2011)

The preparation of highly ordered mesoporous zirconia is of special interest when targeting applications in catalysis. Nevertheless, most of the previously reported attempts led to materials with a low hydrothermal stability. Herein, we accordingly report about the benefit of using mesoporous silica as a host support in which accessible zirconia crystallites are stabilized on the surface. The zirconia surface coverage could be tuned and optimized by playing on the most sensitive synthesis parameters, namely the quantity of zirconia, the calcination temperature and the pore diameter of the host support. The acid properties of the so-obtained materials were determined, showing a remarkable linear relationship between the amount of introduced zirconia and the number of acid sites, which evidenced a high accessibility of the acid sites in the nano-composite, due to a homogeneous dispersion of the zirconia phase in the pores of the silica host support.
Cycloaddition als Methode zur Glycosidierung (1996)

„… zu finden sind wirklich neue und andere Strategien zur Glycosidierung , die keine bimolekulare Reaktion zwischen einem entstehenden Oxocarbeniumion und einem sterisch gehinderten Alkohol geringer Nucleophilie erfordern.”︁ Eine der ersten Antworten auf diesen Appell von F. Barresi und O. Hindsgaul an alle Zuckerchemiker liefern die Versuche, die sich mit der unten gezeigten Reaktionssequenz beschreiben lassen. magnified image
Correlation between structure and function in phosphatidylinositol lipid-dependent Kir2.2 gating (2021)

Abstract Inward rectifier K + (Kir) channels regulate cell membrane potential. Different Kir channels respond to unique ligands, but all are regulated by phosphatidylinositol 4,5-bisphosphate (PI(4,5)P 2 ). Using planar lipid bilayers we show that Kir2.2 exhibits bursts of openings separated by long quiescent inter-burst periods. Increasing PI(4,5)P 2 concentration shortens the Kir2.2 inter-burst duration and lengthens the burst duration without affecting dwell times within a burst. From this, we propose that burst and inter-burst durations correspond to the CTD-docked and CTD-undocked conformations observed in the presence and absence of PI(4,5)P 2 in atomic structures. We also studied the effect of different phosphatidylinositol lipids on Kir2.2 activation and conclude that the 5’ phosphate is essential to Kir2.2 pore opening. Other phosphatidylinositol lipids can compete with PI(4,5)P 2 but cannot activate Kir2.2 without the 5’ phosphate. PI(4)P, which is directly interconvertible to and from PI(4,5)P 2 , might thus be a regulator of Kir channels in the plasma membrane.
Diffuse large B-cell non-Hodgkin's lymphoma in Gaucher disease (2020)

Gaucher disease type 1 (GD1) is the most common lysosomal storage disease and affects nearly 1 in 40,000 live births. In addition, it is the most common genetic disorder in the Ashkenazi Jewish population with phenotypic variation presenting in early childhood to asymptomatic nonagenarians. There have been a number of studies showing an increased risk of certain malignancies in patients, especially non- Hodgkin's lymphoma (NHL) and multiple myeloma. We describe a 66-year-old Ashkenazi Jewish male with GD1 who was first started on enzyme replacement therapy (ERT) with imiglucerase for GD1 at age 57 years, followed a year later by the diagnosis of diffuse large b-cell non-Hodgkin's lymphoma (DLBCL). He was treated with <i>R-CHOP</i> (cyclophosphamide, doxorubicin, vincristine, and prednisone, plus the monoclonal antibody rituximab), however relapsed and developed myelodysplasia necessitating an allo-stem-cell transplantation but succumbed to severe graft vs. host disease. In addition, we also describe a 38-year-old Ashkenazi Jewish male with GD1 who was diagnosed with DLBCL at age 22 years with Gaucher disease diagnosed on pre-treatment bone marrow biopsy which was confirmed by enzyme assay and genotyping. At age 24 years, he was started on ERT with imiglucerase and at age 35 years, he switched to eliglustat. He has remained in remission from the lymphoma. A meta-analysis of the literature will be elaborated upon and we will discuss the relationship of GD1 to NHL and discuss more recent information regarding lyso-GL1 and the development of NHL and multiple myeloma.