gebhart/patrepeval huggingface dataset:
Efficient<i>in vivo</i>gene transfection by stable DNA/PEI complexes coated by hyaluronic acid (2008)

Plasmid DNA was mixed with polyethyleneimine (PEI) and hyaluronic acid (HA) to afford ternary complexes with negative surface charge regardless of the mixing order. They showed reduced non-specific interactions with blood components. When DNA and PEI were mixed at a high concentration such as that used in in vivo experiments, they soon aggregated, and large particles were formed. On the other hand, pre-addition of HA to DNA prior to PEI effectively diminished the aggregation, and 10% (in volume) of the complexes remained as small particles with a diameter below 80 nm. Those negatively charged small ternary complexes induced a much stronger extra-gene expression in tumor than binary DNA/PEI complex after intratumoral or intravenous injection into the mice bearing B16 cells.
Lattice sizes, crystallinities, and spacing between amorphous chains - characterization of ethene-/ɑ-olefin copolymers with various comonomers and comonomer contents measured by wide angle X-ray scattering (2009)

Abstract Ethene-/ɑ-olefin copolymers having a wide range of comonomer contents with comonomers between 4 and 26 carbon atoms in length were characterized by wide angle X-ray scattering (WAXS). It was found that the crystallinities matched fairly well with the crystallinities from DSC and volumetric measurements. An increase of the crystal lattice size was found with increasing comonomer content and comonomer length. Both are attributed to the formation of defects around these short-chain branches in the crystal lattice, which widen it. Increasing the cooling time will lead to a more densely packed crystal structure, if the quenched structure is distorted, i.e. if the sample contains comonomer. A higher molar mass M w widens the average space between chains in the amorphous phase as well as the addition of comonomer. The latter finding is explained by the increasing number of chain ends introduced by the comonomer which increases the free volume in the sample because of the worse amorphous packing of the chain ends.
Conversion of B DNA between solution and fiber conformations. (1981)

At low salt and high DNA concentration, rodlike DNA molecules form specific aggregates containing about seven parallel DNA molecules packed in a bundle. Bundle formation can be reversed by addition of small amounts of EDTA, and formation of the specific aggregates can be induced at higher salt concentration by addition of trivalent ions. In contrast to monomeric DNA, the aggregated species has the optical anisotropy expected for the B form as observed in fibers.
Mortality for Newborns of Birthweight less Than 1500 g in Spanish Neonatal Units (2002-2005) (2007)

The purpose of this study was to analyze the mortality and its prognostic factors in a Spanish cohort of very low birthweight (VLBW) infants during the period 2002 to 2005. Using the Spanish Society of Neonatology database (SEN 1500), 8942 infants with a birthweight < 1500 g were recruited. The overall mortality was 17.3%. However, this incidence underwent a significant decrease over the study period, from 19.4% in 2002 to 15.2% in 2005 ( P = 0.003). Mortality ranged from 12.4% in 25% of the participating neonatal units to 19.4% in a further 25%. Mortality was higher in outborn infants (25.8%) than in inborn infants (16.6%) ( P < 0.001). The mortality rates of these neonates are also presented by 100-g intervals (401 to 1500) and for the different hospitalization times: in the delivery room, within 24 hours and 28 days of birth, at 36 weeks of postmenstrual age, and on discharge. Of note was that mortality was greatest within 24 hours and 28 days of birth in each of the weight groups ( P < 0.001). In conclusion, in the cohort of infants < 1500 g examined, mortality in the period from 2002 to 2005 was still high, especially among newborns weighing < 1000 g. We did, however, observe a decreasing trend in mortality rates for the participating neonatal units over the 4 study years. Our findings highlight the need to promote intrauterine transport and improve neonatal transport as well as the management of these infants in the delivery room and within the first 28 days of life.
PairGP: Gaussian process modeling of longitudinal data from paired multi-condition studies (2022)

High-throughput technologies produce gene expression time-series data that need fast and specialized algorithms to be processed. While current methods already deal with different aspects, such as the non-stationarity of the process and the temporal correlation, they often fail to take into account the pairing among replicates. We propose PairGP, a non-stationary Gaussian process method to compare gene expression time-series across several conditions that can account for paired longitudinal study designs and can identify groups of conditions that have different gene expression dynamics. We demonstrate the method on both simulated data and previously unpublished RNA sequencing (RNA-seq) time-series with five conditions. The results show the advantage of modeling the pairing effect to better identify groups of conditions with different dynamics. The pairing effect model displays good capabilities of selecting the most probable grouping of conditions even in the presence of a high number of conditions. The developed method is of general application and can be applied to any gene expression time series dataset. The model can identify common replicate effects among the samples coming from the same biological replicates and model those as separate components. Learning the pairing effect as a separate component, not only allows us to exclude it from the model to get better estimates of the condition effects, but also to improve the precision of the model selection process. The pairing effect that was accounted before as noise, is now identified as a separate component, resulting in more accurate and explanatory models of the data.
Rote Liste und Gesamtartenliste der Röhrlinge s. l. (Boletales) (2017)

Aus Berlin sind bis heute 87 Boletales-Arten bekannt. Davon werden 26 Arten (30 %) in die Rote Liste aufgenommen. Dies ist die erste Rote Liste von Großpilzgattungen für Berlin. Auf eine Eingruppierung in die Kategorie „Ausgestorben oder verschollen“ wird verzichtet, da eine systematische Nachsuche bisher nicht stattgefunden hat. Diese Liste dient gleichzeitig als Pilotprojekt zur Prüfung, ob die Datenmenge und die gewählte Rastergröße der Artkartierung ausreichen, um statistisch signifikante Aussagen über Gefährdungen von Großpilzen in Berlin zu treffen.
Palmitic Acid-Modified Poly-<scp>l</scp>-Lysine for Non-Viral Delivery of Plasmid DNA to Skin Fibroblasts (2007)

Palmitic acid conjugates of poly-L-lysine (PLL-PA) were prepared, and their ability to deliver plasmid DNA into human skin fibroblasts was evaluated in vitro. The conjugates were capable of condensing a 4.7 kb plasmid DNA into 50-200 nm particles (mean +/- SD = 112 +/- 34 nm), which were slightly smaller than the particles formed by PLL (mean +/- SD = 126 +/- 51 nm). Both PLL and PLL-PA were readily taken up by the cells, but PLL-PA delivered the plasmid DNA into a higher proportion of cells. DNA delivery was found to be reduced by endocytosis inhibitor Brefeldin A, suggesting an active mechanism of particle uptake. Using enhanced green fluorescent protein (EGFP) as a reporter gene, PLL-PA was found to give the highest number of EGFP-positive cells among several carriers tested, including polyethyleneimine, Lipofectamine-2000, and an adenovirus. Although some carriers gave a higher percentage of EGFP-positive cells than PLL-PA, they were also associated with higher toxicities. We conclude that PLL-PA is a promising gene carrier for non-viral modification of human fibroblasts.
On serializability of multidatabase transactions through forced local conflicts (2002)

A multidatabase transaction management mechanism called the optimistic ticket method (OTM) is introduced for enforcing global serializability. It permits the commitment of multidatabase transactions only if their relative serialization order is the same in all participating local database systems (LDBSs). OTM requires the LDBSs to guarantee only local serializability. The basic idea in OTM is to create direct conflicts between multidatabase transactions at each LDBS in order to determine the relative serialization order of their subtransactions. A refinement of OTM, called the implicit ticket method (ITM), is also introduced that uses implicit tickets and eliminates ticket conflicts but works only when the participating LDBSs use rigorous transaction scheduling mechanisms. ITM uses the local commitment order of each subtransaction to determine its implicit ticket value. It achieves global serializability by controlling the commitment (execution order) and thus the serialization order of multidatabase transactions. Both OTM and ITM do not violate the autonomy of the LDBSs and can be combined in a single comprehensive mechanism.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Magnetic anomalies and the possibilities of continental drifting in the Gulf of Mexico (1971)

The probable arrangement of the continents of the Americas, Europe, and Africa before the opening of the Atlantic was determined by Bullard et al. [1965]. This is the well-known ‘Bullard fit,’ which has been reproduced in many articles. On this fit the most anomalous region is that which comprises Mexico, Central America, the Gulf of Mexico, and the Caribbean Sea. On the Bullard fit, the distance from the shores of Venezuela to the shores of Texas is about 1100 km. At present this distance is about 3300 km. It appears that North America moved northwestward with respect to South America by about 2200 km since the time shown by Bullard. However, this extension cannot be explained at present in terms of known sea-floor spreading.
The Anti-Inflammatory Effects of the Methanolic Extract and Fractions from Davilla elliptica St. Hil. (Dilleniaceae) on Bothrops jararaca Envenomation (2015)

Inflammation and haemorrhage are the main characteristics of tissue injury in botropic envenomation. Although some studies have shown that anti-venom prevents systemic reactions, it is not efficient in preventing tissue injury at the site of the bite. Therefore, this work was undertaken to investigate the anti-inflammatory effects of the methanolic extract and fractions from D. elliptica and to evaluate the role of matrix metalloproteinases (MMPs) in this process. Effects of the extract and fractions from D. elliptica were evaluated using a carrageenan-induced paw oedema model in rats, and leukocyte rolling was visualized by intravital. The quantification of MMPs activities (MMP-2 and MMP-9) extracted from the dermis of mice treated with extract and fractions alone or incubated with venom was determined by zymographic analyses. Our results show that intraperitoneal (i.p.) injection of fractions significantly reduced paw oedema after the carrageenan challenge. Treatment with the tannins fraction also resulted in considerable inhibition of the rolling of leukocytes and this fraction was able to decrease the activation of MMP-9. These results confirmed the anti-inflammatory activity of the methanolic extract and tannins fraction of D. elliptica and showed that the dermonecrosis properties of B. jararaca venom might be mediated through the inhibition of MMP-9 activity.
Hormonal And Immunological Changes in Mice after Spinal Cord Injury (2007)

Spinal cord injury (SCI) is associated with immune deficiencies and life-threatening infections. However, the specific mechanisms underlying this pathological condition remain unclear. In recent years, increasing evidence has suggested that anabolic hormones may be involved in immunological complications. Here, we monitored candidate hormone concentrations and immune cell counts, in CD1 mice, for 4 weeks after low-thoracic transection of the spinal cord (Tx). Serum dihydroepiandrosterone (DHEA), insulin, and parathyroid hormone (PTH) levels decreased throughout the time period studied compared with control, non-Tx mice. In turn, testosterone and growth hormone (GH) levels were only transiently changed, with a decrease of testosterone during the first 2 weeks and an increase of GH at 1 week post-Tx. A complete blood count revealed either unchanged or moderately decreased erythrocyte, platelet, hemoglobin and hematocrit levels. Total leukocyte, lymphocyte, and eosinophil counts also decreased, whereas neutrophils and monocytes did not change significantly. In the bone marrow, lymphocyte numbers decreased and neutrophils increased, whereas monocytes, eosinophils, and megakariocytes did not change significantly. These results revealed significant changes occurring rapidly (<1-2 weeks) after Tx in both hormonal and immunological systems, providing compelling evidence of a role for anabolic hormones in SCI-related immune deficiencies.
A novel variable optical reflection standard to implement 16-term optical calibration (2002)

Commercial lightwave analysers use advanced normalisation techniques to implement optical calibration. As integrated optical components gain wider usage, leakage effects cannot be neglected, and hence there will be an increasing need to perform 16-term calibration. One of the main constraints at present to implement optical 16-term or even 12-term calibration is the lack of enough optical reflection standards. Given the bandwidth limitation of the line standard, it is desirable to have at least three optical reflection standards in addition to the thru standard. In this work, a variable optical reflection standard which makes use of bulk optics is proposed. The structure consists of a fibre pigtail, a lens and a mirror all separated by air. The variation in optical reflection is produced by varying the distance between the lens and the other two elements.
Enhanced 3-methoxytyramine levels in crown gall tumours and other undifferentiated plant tissues (1984)

An amine, after dansylation, has been isolated from Nicotiana tabacum crown gall tumours for the first time and characterized as 4-hydroxy-3-methoxy-beta-phenylethylamine (3-methoxytyramine). The compound cannot be detected in differentiated N. tabacum tissues but appears in the corresponding callus controls. Its concentration is further increased 5-42-fold when N. tabacum is transformed with all strains of Agrobacterium tumefaciens so far tested.
Chemical Configuration of Osazones. III (1952)

Phenyl(1)-alkylphenyl(2)-glucosazones in which the alkyl was ethyl, allyl, and butyl, were prepared. These compounds required 3 moles of periodic acid to form 2 moles of formic acid and precipitated corresponding mesoxaldehyde-phenyl(1)-alkylphenyl(2)-osazones. The color of these crystals also changed by sunlight, that of ethyl derivative from yellow to orange yellow, that of allyl and butyl from yellow to red, without any change in their melting points. These changes were also found to be reversible, the original yellow crystals being obtained on recrystallization, and vice versa.
Production of durable and cost effective sewer pipes using petroleum and industrial waste by-products (2017)

The Arabian Gulf environment has an adverse impact on concrete structures because of the high ambient temperature, humidity, salt contaminated dust, sea water and underground salts. As an innovative solution, reinforced modified sulfur concrete (MSC) pipes are recognized as a durable and economical solution for deterioration of pipelines. This work describes the manufacture and characterization of new MSC based on a cost effective sulfur modification process. Bitumen, a by-product from crude oil refining process was used to modify elemental sulfur and enhance its physical, mechanical properties, and mostly to increase its corrosive resistivity. The study has focused on optimizing the proportions of an offered MSC mixes that are composed of modified sulfur (MS) as a binder, crushed sand, dune sand and ladle furnace (LF) slag as aggregates, and ground granulated blast furnace slag (GGFBS) as a filler. To maximize the physical and mechanical properties of MSC sewer pipes, different mixtures were prepared and investigated. The optimum mix of MSC has a maximum compressive strength of 64 MPa, maximum splitting tensile strength of 4.5 MPa, maximum flexural strength of 21 MP, with a high corrosion resistance in acidic and salty environments.
The Outcome of Pregnancies Complicated by Bleeding During the Second Trimester (1992)

Department of Obstetrics and Gynecology, University of Utah School of Medicine, Salt Lake City, Utah
SU‐FF‐T‐91: Automated Selection of Tradeoff Parameters in IMRT Prioritized Prescription Treatment Planning (2007)

Purpose: Prioritized prescription optimization is a method of IMRT treatment planning which solves the optimization problem step‐wise, first by determining the best performance of a high‐priority objective and then converting it to a constraint as lower priority goals are optimized in turn. This system is fully automated; however, there is a variable value we call ‘slip’ factor which determines the amount of degradation allowed after each priority is addressed. The purpose of this work is to investigate an approach to automating selection of the slip factor. Method and Materials: We propose a new version of prioritized prescription optimization that, after each step, estimates the desired value of the slip factor for the next step. We estimate, to first order, the rate of change of the objective function with respect to small perturbations in the slip. We then apply the Sensitivity Theorem to analyze the effect of the slip factor. In summary, after solving the first problem and obtaining the solution to the first step, w I , we plug the value of w I into a closed‐form expression of the Lagrange multiplier vector λ(0) to get λ(0), and then use the last element of λ(0) to compute the first‐order approximation model for the optimal objective value with variable slip. Results: We use the Sensitivity Theorem and Lagrange multipliers to derive a first‐order approximation model for the optimal objective function value for a given slip factor. On this basis, we propose to automatically select slip values based on the expected gain in the objective function. Conclusion: We have developed a mathematical theory and framework which allows us to automate the selection of the slip factor in prioritized prescription optimization, based on a local linear approximation. This proposal is the subject of ongoing tests.
The miracle of “sudden renal failure” (2005)

One of the advantages of being a neonatologist is that former patients come to visit the clinic even many years after their initial stay, and I can follow up their development. However, sometimes a visiting patient can also bring a bad conscience back.

A few months ago, a lovely 8 year old boy visited our neonatal intensive care unit with his parents. He seemed impressed by the sight of the little babies and could not imagine that he, too, had once been as small. The parents were pleased to see me since, as they told their son, I was “the doctor who was in charge of you.” Only after talking to the parents for some time did I start to remember the family, but when the …
Class I Major Histocompatibility Complex, the Trojan Horse for Secretion of Amyloidogenic β2-Microglobulin (2013)

To form extracellular aggregates, amyloidogenic proteins bypass the intracellular quality control, which normally targets unfolded/aggregated polypeptides. Human D76N β2-microglobulin (β2m) variant is the prototype of unstable and amyloidogenic protein that forms abundant extracellular fibrillar deposits. Here we focus on the role of the class I major histocompatibility complex (MHCI) in the intracellular stabilization of D76N β2m. Using biophysical and structural approaches, we show that the MHCI containing D76N β2m (MHCI76) displays stability, dissociation patterns, and crystal structure comparable with those of the MHCI with wild type β2m. Conversely, limited proteolysis experiments show a reduced protease susceptibility for D76N β2m within the MHCI76 as compared with the free variant, suggesting that the MHCI has a chaperone-like activity in preventing D76N β2m degradation within the cell. Accordingly, D76N β2m is normally assembled in the MHCI and circulates as free plasma species in a transgenic mouse model.
Nematic Liquid Crystal Optical Channel Waveguides on Silicon (2006)

We demonstrate the first channel waveguides made of E7 nematic liquid crystal (LC) in SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> -Si V-grooves. The grooves have been obtained by wet etching n-Si substrates first and then by thermally growing an approximately 2-mum-thick SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> cladding layer. Propagation of infrared light at a wavelength of 1550 nm shows a good optical confinement in 10-mum-wide LC waveguides. Modal analysis and beam propagation simulations predict single mode propagation. This is experimentally confirmed by the acquired near field images. The optical waveguide acts as an integrated optic polarizer, since only vertical polarization can propagate due to the orientation of the LC molecules. The horizontal polarization state is suppressed by more than 25 dB.
Robotic melon harvesting (2000)

Intelligent sensing, planning, and control of a prototype robotic melon harvester is described. The robot consists of a Cartesian manipulator mounted on a mobile platform pulled by a tractor. Black and white image processing is used to detect and locate the melons. Incorporation of knowledge-based rules adapted to the specific melon variety reduces false detections. Task, motion and trajectory planning algorithms and their integration are described. The intelligent control system consists of a distributed blackboard system with autonomous modules for sensing, planning and control. Procedures for evaluating performance of the robot performing in an unstructured and changing environment are described. The robot was tested in the field on two different melon cultivars during two different seasons. Over 85% of the fruit were successfully detected and picked.
ChemInform Abstract: PHOTOLYSIS OF ORGANOPOLYSILANES, INSERTION OF SILYLENE SPECIES INTO A CONJUGATED DIENE (1975)

Abstract Die Photolyse eines Gemisches von 2,3‐Dimethylbutadien (I) und 2‐Phenylheptamethyltris?an (II) in Äther ergibt ein Gemisch der Verbindungen (III)‐(V),deren Bildung auf zwei möglichen Reaktionswegen eingehend diskutiert wird.