gebhart/patrepeval huggingface dataset:
Doxycycline in Mitochondrial Mediated Pathway of Apoptosis: A Systematic Review (2010)

Tetracyclines have been long known for their antimicrobial role. They are one of the most widely used antibiotics in clinical practice since last 5 decades. Recently their role as matrix metalloproteinase inhibitor and in apoptosis has widely attracted attention in biological field. Of them, doxycycline is one with long duration of actions and has recently been shown to have various anti-cancer properties, especially cytotoxic and anti-proliferative activities. Here, we systematically reviewed the role of doxycycline in the mitochondrial mediated apoptosis in various tissues. MEDLINE and EMBASE databases were searched using a formal search strategy with definite inclusion and exclusion criteria. Data extraction was performed for each included study using a custom designed data extraction form. A total of 81 references were identified through MEDLINE and 5 were identified through EMBASE. 74 references from MEDLINE and all 5 in EMBASE were excluded through reading titles, abstracts and full text. In total, 7 studies fulfilled inclusion criteria. Following systematic review of these studies, we concluded that doxycycline induces apoptosis through mitochondrial mediated pathway in different tissue cells however it may be cell specific. The caspase independent apoptosis as one of the mechanisms of actions of doxycycline needs further studies for better understanding.
Earlier and higher dosing of alglucosidase alfa improve outcomes in patients with infantile-onset Pompe disease: Evidence from real-world experiences (2020)

Low CK and uGlc4 levels were correlated with favorable response to ERT in IOPD patients, although CK may be more fluctuated than uGlc4. High-dose ERT instituted immediately at newborn screening seems to give the best outcome, and a dosage increase is necessary upon - or, even better, before - a rise in biomarker levels.
The Volume of Saliva in the Mouth Before and After Swallowing (1984)

In 20 male and 20 female adult subjects, the volume of saliva in the mouth before (VMAX) and after (RESID) swallowing was determined. RESID could be computed by measuring the potassium and chloride concentrations in unstimulated saliva and in the expectorate after a five-second rinse with 5 ml of water immediately following a swallow. The mean value of RESID after a normal swallow was significantly higher in males (0.87 ml) than in females (0.66 ml). After a forced swallow, RESID was only slightly but significantly reduced, being 0.82 ml and 0.60 ml in males and females, respectively. The volume of saliva normally swallowed was calculated from the unstimulated salivary flow rate and the normal swallowing frequency. The mean value of VMAX (RESID plus volume normally swallowed) in males was 1.19 ml, which was slightly but not significantly higher than that in females (0.96 ml). When water was infused into the mouth at increasing flow rates, there was an increase in VMAX and in both the volume of fluid swallowed and the swallowing frequency.
Noninvasively Imaging pH at the Surface of Implanted Orthopedic Devices with X-ray Excited Luminescence Chemical Imaging (2019)

Implanted medical device-associated infections are a leading cause of fixation failure, and early diagnosis is the key to successful treatment. During infection, acidosis near the implant plays a role in antibiotic resistance and low pH is a potential infection indicator. Herein, we describe a pH sensor which attaches to the implants to noninvasively image local pH with high spatial resolution. The sensor has two layers: a scintillator layer which emits 620 and 700 nm light upon X-ray irradiation and a pH indicator layer containing bromocresol green dye that absorbs 620 nm luminescence in neutral/basic pH and passes 700 nm light at all pHs. We also developed a dedicated imaging system capable of scanning relatively large specimens through thick tissues. A focused X-ray beam irradiates one spot on the sensor, and the 620 to 700 nm peak ratio is measured to determine the local pH; images are acquired by scanning the X-ray beam across the surface and measuring the pH point-by-point. The sensor was covered with varying thickness slices of chicken breast tissue (0-19 mm) to evaluate how the tissue affects the peak intensity and ratio. Thick tissues attenuated both 620 and 700 nm light, with more attenuation at 620 nm than 700 nm. Although this spectral distortion shifted the pH calibration curve, the effect could be corrected for using a scintillator film region with no pH indicator layer as a spectral reference. The sensor was attached to an orthopedic plate affixed to a human cadaveric tibia and imaged through tissue. This approach provides both high spatial resolution from focused X-ray excitation and surface chemical specificity from the indicator dye, providing a tool for imaging local pH through tissue.
DNA extraction replicates improve diversity and compositional dissimilarity in metabarcoding of eukaryotes in marine sediments (2017)

Human impact on marine benthic communities has traditionally been assessed using visible morphological traits and has focused on the macrobenthos, whereas the ecologically important organisms of the meio- and microbenthos have received less attention. DNA metabarcoding offers an alternative to this approach and enables a larger fraction of the biodiversity in marine sediments to be monitored in a cost-efficient manner. Although this methodology remains poorly standardised and challenged by biases inherent to rRNA copy number variation, DNA extraction, PCR, and limitations related to taxonomic identification, it has been shown to be semi-quantitative and useful for comparing taxon abundances between samples. Here, we evaluate the effect of replicating genomic DNA extraction in order to counteract small scale spatial heterogeneity and improve diversity and community structure estimates in metabarcoding-based monitoring. For this purpose, we used ten technical replicates from three different marine sediment samples. The effect of sequence depth was also assessed, and in silico pooling of DNA extraction replicates carried out in order to maintain the number of reads constant. Our analyses demonstrated that both sequencing depth and DNA extraction replicates could improve diversity estimates as well as the ability to separate samples with different characteristics. We could not identify a "sufficient" replicate number or sequence depth, where further improvements had a less significant effect. Based on these results, we consider replication an attractive alternative to directly increasing the amount of sample used for DNA extraction and strongly recommend it for future metabarcoding studies and routine assessments of sediment biodiversity.
One year experience with the Chronicle® implantable hemodynamic monitor in patients on the heart transplant waiting list (2007)

Aims: The vast majority of heart transplants is performed in patients in HU status. Close monitoring of patients waiting at home is now essential to identify those who deteriorate.
CS-07 * mTORC2/Akt SIGNALING IS MODULATED BY NONCANONICAL MITOCHONDRIAL NOTCH-PINK1 INTERACTION IN MEDULLOBLASTOMA (GROUP III) TUMORIGENESIS (2014)

MYC-amplified medulloblastoma is a lethal pediatric tumor lacking effective treatment options. Targeting of mitochondrial activity through inhibition of a novel, noncanonical Notch/PINK1 signaling pathway was recently shown to attenuate the viability of human glioblastoma as performed by our laboratory (Lee KS et al., Genes and Development, 2013). As such, we set out to investigate the role of such the same pathway trafficking mechanisms in medulloblastoma (group III) tumorigenesis and its impact on mTORC2/Akt signaling. Our results suggest both Notch1 and Notch2 involvement in noncanonical mitochondrial Notch/PINK1 signaling in human MYC-amplified medulloblastoma. In vitro inhibition of this axis targets cell viability in a tumor-selective manner. In vivo replication of such trends in currently pending in established murine models. Such preclinical findings highlight the promise of an increased focus on mitochondrial-specific therapies in the development of novel agents for MYC-amplified medulloblastoma.
Abstract W P351: Plasma Interleukin-6 and C-reactive Protein Are Associated With Acute Diffusion Hyperintensity After Transient Ischemic Attack (2014)

Background: In suspected TIA, DWI hyperintensity confirms the diagnosis of brain ischemia and identifies those with 3-fold risk of early recurrent stroke. However, immediate MRI is expensive and may not be available in many healthcare settings. A simple validated blood test to objectively support the diagnosis of cerebral ischaemia after transient symptoms might have utility in clinical practice. We hypothesised that blood markers of inflammation may be associated with abnormal DWI following TIA. Methods: BIO-TIA was a multi-centre prospective study of consecutive patients with clinically-defined TIA, confirmed by a stroke physician. Phlebotomy and stroke protocol MRI were performed within 72 hours of symptoms. Patients with malignancy, active infection, trauma, surgery, definite transient non-ischaemic symptoms or recurrent stroke before phlebotomy/MRI were excluded. Plasma high-sensitivity CRP and interleukin-6 (IL-6) were measured by mass spectrometry. Results: In 201 included patients, mean age was 68 years (59% male). Carotid stenosis was present in 26.4% and atrial fibrillation in 29.1%. Mean ABCD2 score was 4.2 (SD 1.3). Acute DWI hyperintensity was observed in 37.8% (76/201). Median hsCRP was 1.78mg/L in DWI-negative, compared with 3.01mg/L in DWI-positive TIA (p=0.04). Median IL-6 was 3.76pg/ml (DWI-negative) versus 4.91pg/ml (DWI-positive) (p=0.04). When the highest quartiles of CRP and IL-6 distributions were compared with quartiles 1-3, the prevalence of DWI hyperintensity was 61.5% (Q4) versus 32.9% (Q1-3) for CRP (p=0.001), and 56.4% (Q4) versus 34.9% [Q1-3) for IL-6 (p=0.02). Thresholds of 4.78mg/L for CRP or 6.21pg/ml for IL-6 had at least 80% specificity for identification of abnormal DWI signal. IL-6 was associated with CRP (rho 0.58), age (rho 0.36), and ABCD2 score (rho 0.18) and carotid stenosis (p≤0.01 for all), but not statin use. Conclusion: Our preliminary findings require validation, but suggest that inexpensive, rapidly-measured blood markers are associated with acute DWI hyperintensity after TIA. If validated, blood markers may have utility to support the diagnosis of cerebral ischemia or select patients for early MRI.
MODUS-COVID Vorhersage vom 8.4.2020 (2020)

In dem Bericht vom 08.04.2020 wird dem Bundesministerium für Bildung und Forschung (BMBF) über den aktuellen Stand des Projektes MODUS-COVID berichtet. Dieses Projekt beschäftigt sich mit der Infektionsdynamik von Covid 19 und der Simulation der Ausbreitung des Virus mit Hilfe der agentenbasierten Verkehrssimulation MATSim. Bestandteil dieses Berichtes sind erste Prognosen über die Entwicklung der Infektionszahlen ohne die Einführung von Gegenmaßnahmen, der Beibehaltung der aktuellen Maßnahmen und den Folgen der Wiederöffnung der Schulen zum 20.04.2020.
Characterization of a Naturally Occurring Class D β-Lactamase from Achromobacter xylosoxidans (2008)

A chromosomally encoded class D beta-lactamase, OXA-114, was characterized from Achromobacter xylosoxidans strain CIP69598. beta-Lactamase OXA-114 shared 56% amino acid identity with the naturally occurring class D beta-lactamase of Burkholderia cenocepacia and 42% identity with the acquired oxacillinases OXA-9 and OXA-18. OXA-114 has a narrow-spectrum hydrolysis profile, although it includes imipenem, at a very low level. PCR and sequencing revealed that bla(OXA-114)-like genes were identified in all A. xylosoxidans strains tested (n = 5), indicating that this beta-lactamase is naturally occurring in that species. Induction experiments with imipenem and cefoxitin did not show inducibility of bla(OXA-114) expression.
Regulation of the growth of Epstein-Barr virus-infected B cells. I. Growth regression by E rosetting cells from VCA-positive donors is a combined effect of autologous mixed leukocyte reaction and activation of T8+ memory cells. (1985)

Regression of B cell proliferation in co-cultures of EBV-infected B cells (BEBV) and autologous T cells at 1:4 ratio was studied. 3H-TdR incorporation was used to measure proliferation by the participating lymphocyte populations and a 51Cr release assay was used to document the generation of cells capable of killing autologous EBV-transformed B lymphoblastoid cell lines (LCLEBV). EBV-infected B cells cultured alone transformed to blasts by culture day 10, and continued to proliferate throughout the 22 day observation period. When EBV-infected B cells were co-cultured with E rosetted cells from VCA-positive donors, there was a characteristic proliferative response on day 10 (an augmented autologous mixed lymphocyte reaction; AMLR), followed by the development of T8+ cells capable of killing autologous LCLEBV, as well as over 90% suppression of EBV growth by day 22 as assessed by 3H-TdR incorporation, and confirmed in a visual outgrowth assay. Negative and positive selection techniques were used to define the regulatory components in the T cell population. Depletion of T8+ cells from the blood lymphocytes of VCA-positive donors did not significantly reduce the 10 day proliferative response, but the subsequent development of cytotoxic cells and the regression of BEBV outgrowth was not observed. Thus, the circulating T8+ cells are required for the subsequent appearance of autologous LCLEBV cytotoxicity and BEBV growth regulation. However, when the responder population consisted only of T8+ cells, the augmented AMLR response was absent, cytotoxic cell development was weak or absent, and there was no regression of EBV outgrowth. Therefore, the cells participating in the AMLR, as well as T8+ memory cells from VCA-positive donors, are necessary for the control of the in vitro EBV infection. Growth regression is dependent on the proliferation of the regulatory T cells. Mitomycin C treatment of fresh E rosetting cells or those exposed to BEBV for up to 10 days in culture abrogates growth regression and the subsequent appearance of LCLEBV killer cells. However, E rosetting cells exposed to BEBV for 14 days or more already have developed the ability to kill LCLEBV and no longer need to proliferate to induce growth regression when cultured with newly infected BEBV. These results lend additional support to the view that the control of EBV-induced B cell expansion requires a AMLR-dependent clonal amplification of EBV-specific, T8+ cytotoxic cells.
The ELI-ALPS MIR-HE laser system - design and status (2022)

We report the design for a high-power optical parametric chirped-pulse amplifier (OPCPA) at 3200 nm central wavelength for the MIR-HE laser at ELI-ALPS, aiming to provide 20 mJ pulse energy and sub-2.5 cycles pulse length.
Distributed SDN architecture for NoC-based many-core SoCs (2019)

In the Software-Defined Networking (SDN) paradigm, routers are generic and programmable forwarding units that transmit packets according to a given policy defined by a software controller. Recent research has shown the potential of such a communication concept for NoC management, resulting in hardware complexity reduction, management flexibility, real-time guarantees, and self-adaptation. However, a centralized SDN controller is a bottleneck for large-scale systems.
The crucial role of metal ions in neurodegeneration: the basis for a promising therapeutic strategy (2005)

The variety of factors and events involved in neurodegeneration renders the subject a major challenge. Neurodegenerative disorders include a number of different pathological conditions, which share similar critical metabolic processes, such as protein aggregation and oxidative stress, both of which are associated with the involvement of metal ions. In this review, Alzheimer's disease, Parkinson's disease and prion disease are discussed, with the aim of identifying common trends underlying these devastating neurological conditions. Chelation therapy could be a valuable therapeutic approach, since metals are considered to be a pharmacological target for the rationale design of new therapeutic agents directed towards the treatment of neurodegeneration.
Potential noncataleptic neuroleptic agents: Synthesis and pharmacology of 7-chloro-4-[4-(2-hydroxyethyl)piperazino]-4,5-dihydrothieno[2,3-b]-1-benzothiepin (1983)

Heating of 2,5-dichloroacetophenone with 2-thiophenethiol, potassium carbonate and copper gave 5-chloro-2-(2-thienylthio)acetophenone ( V ) which was subjected to the Willgerodt reaction with sulphur and morpholine. The product was a mixture of the thiomorpholide VI and oxothiomorpholide VII . After a partial separation the predominanting product VI was hydrolyzed without characterization with ethanolic potassium hydroxide to give the acid VIII . Cyclization by treatment with phosphorus pentoxide in boiling toluene gave 7-chlorothieno[2,3- b ]-1-benzothiepin-4(5 H )-one ( X ) which was reduced with sodium borohydride to the alcohol XII . A reaction with hydrogen chloride in benzene led to the chloro derivative XIII whose substitution reaction with 1-(2-hydroxyethyl)piperazine afforded the title compound IV . The product has strong central depressant and discoordinating activity, a low cataleptic efficity but in a relatively high dose it does not influence the dopamine metabolism in the rat brain.
Selective nano-devices for the detection of nitroaromatic explosive compounds (2011)

In recent years, there is an increased threat of explosive attacks worldwide, as the explosive - based weapons are easy to make, obtain and deploy. Detecting traces of explosives is a challenging task because of the low vapor pressures of most explosives [1]. Protecting against explosive-based terrorism can be achieved by large-scale production of nano-sensor arrays that are inexpensive, highly sensitive and selective with low response and recovery times. In the present study, we demonstrated the selective response of GaN nanowire/ TiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> nanocluster hybrids to the nitroaromatic explosive, Trinitrotoluene at room temperature. The sensor detected between 0.5 ppb and 8 ppm TNT with good selectivity against interfering compounds like Toluene. The sensitivity of 1 ppm of TNT is ~10% with response and recovery times of ~30 s.
Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru (2006)

Studies of deeply buried, sedimentary microbial communities and associated biogeochemical processes during Ocean Drilling Program Leg 201 showed elevated prokaryotic cell numbers in sediment layers where methane is consumed anaerobically at the expense of sulfate. Here, we show that extractable archaeal rRNA, selecting only for active community members in these ecosystems, is dominated by sequences of uncultivated Archaea affiliated with the Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group, whereas known methanotrophic Archaea are not detectable. Carbon flow reconstructions based on stable isotopic compositions of whole archaeal cells, intact archaeal membrane lipids, and other sedimentary carbon pools indicate that these Archaea assimilate sedimentary organic compounds other than methane even though methanotrophy accounts for a major fraction of carbon cycled in these ecosystems. Oxidation of methane by members of Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group without assimilation of methane-carbon provides a plausible explanation. Maintenance energies of these subsurface communities appear to be orders of magnitude lower than minimum values known from laboratory observations, and ecosystem-level carbon budgets suggest that community turnover times are on the order of 100-2,000 years. Our study provides clues about the metabolic functionality of two cosmopolitan groups of uncultured Archaea.
Zeolitic imidazolate framework (ZIF-8) based polymer nanocomposite membranes for gas separation (2012)

As synthesised ZIF-8 nanoparticles (size ∼ 60 nm and specific surface area ∼ 1300–1600 m2 g−1) were directly incorporated into a model polymer matrix (Matrimid® 5218) by solution mixing. This produces flexible transparent membranes with excellent dispersion of nanoparticles (up to loadings of 30 wt%) with good adhesion within the polymer matrix, as confirmed by scanning electron microscopy, dynamic mechanical thermal analysis and gas sorption studies. Pure gas (H2, CO2, O2, N2 and CH4) permeation tests showed enhanced permeability of the mixed matrix membrane with negligible losses in selectivity. Positron annihilation lifetime spectroscopy (PALS) indicated that an increase in the free volume of the polymer with ZIF-8 loading together with the free diffusion of gas through the cages of ZIF-8 contributed to an increase in gas permeability of the composite membrane. The gas transport properties of the composite membranes were well predicted by a Maxwell model whilst the processing strategy reported can be extended to fabricate other polymer nanocomposite membranes intended for a wide range of emerging energy applications.
III-nitride transistors with capacitively coupled contacts (2006)

Al Ga N ∕ Ga N heterostructure field-effect transistor design using capacitively coupled contacts (C3HFET) is presented. Insulated-gate [C3 metal-oxide-semiconductor HFET (C3MOSHFET)] has also been realized. The capacitively coupled source, gate, and drain of C3 device do not require annealed Ohmic contacts and can be fabricated using gate alignment-free technology. For typical AlGaN∕GaN heterostructures, the equivalent contact resistance of C3 transistors is below 0.6Ωmm. In rf-control applications, the C3HFET and especially the C3MOSHFET have much higher operating rf powers as compared to HFETs. C3 design is instrumental for studying the two-dimensional electron gas transport in other wide band gap heterostructures such as AlN∕GaN, diamond, etc., where Ohmic contact fabrication is difficult.
Effects of Heat/Citric Acid Reprocessing on High-Flux Polysulfone Dialyzers (2002)

The surface features, morphology, and tensile properties of fibers obtained from pristine, reprocessed, and reused Fresenius Polysulfone High-Flux (Hemoflow F80A) hemodialyzers have been studied. Scanning electron microscopy of the dialyzer fibers revealed a dense skin layer on the inner surface of the membrane and a relatively thick porous layer on the outer surface. Transmission electron microscopy and atomic force microscopy showed an alteration in membrane morphology due to reprocessing and reuse, or to a deposition of blood-borne material on the membrane that is not removed with reprocessing. Fluorescent microscopy images also showed that a fluorescent material not removed by heat/citric acid reprocessing builds up with continued use of the dialyzers. The tensile properties of the dialyzer fibers were not affected by the heat/citric acid reprocessing procedure. The protein layers formed on pristine and reused hemodialyzer membranes during clinical use were also studied using sodium dodecyl sulfate polyacrylamide gel electrophoresis and immunoblotting. A considerable amount of protein was found on the blood side of single and multiple use dialyzers. Proteins adsorbed on the dialysate side of the membrane were predominantly in the molecular weight region below 30 kDa. Little protein was detected on the membranes of reprocessed hemodialyzers.
Thickness control of 3-dimensional mesoporous silica ultrathin films by wet-etching (2017)

The thickness of 3-dimensional (3D) mesoporous silica ultrathin films was controlled at a single-nanometer scale by wet-etching. A drop casting method with an aqueous etchant of ammonium fluoride was effective in etching the surfaces of films in the direction perpendicular to their substrates. The decrease in the film thickness depends on the interface tension of etching solutions. The wettability of thin films also influences the etching. CoPt nanodots were electrodeposited within ultrathin silica films on Ru substrates to form CoPt nanodot patterns.