gebhart/patrepeval huggingface dataset:
Plasma membrane fractions from rat liver contain a phosphatidate phosphohydrolase distinct from that in the endoplasmic reticulum and cytosol. (1991)

Assays for two distinct phosphatidate phosphohydrolase activities were established based upon a differential inhibition by N-ethylmaleimide (NEM). The activity that is insensitive to this reagent in rat liver is predominantly in the plasma membrane fraction, whereas the NEM-sensitive activity is in the cytosolic and microsomal fractions. The NEM-insensitive activity is further distinguished from the NEM-sensitive phosphohydrolase by: (a) being relatively stable to heat; (b) not being inhibited by phenylglyoxal, butane-2,3-dione, cyclohexane-1,2-dione, 2,4-dinitrofluorobenzene, 7-chloro-4-nitrobenz-2-oxa-1,3-diazole, and diethyl pyrocarbonate; (c) being inhibited by NaF and phosphatidylcholine; and (d) not being stimulated by Mg2+. The NEM-insensitive activity was specific for phosphatidate. Both phosphohydrolase activities could be inhibited by chlorpromazine, propranolol, sphingosine, and spermine. The NEM-sensitive phosphatidate phosphohydrolase activity was increased by incubating hepatocytes for 12 h with glucagon and dexamethasone, and this effect was antagonized by insulin. The NEM-sensitive phosphohydrolase is concluded to be involved in glycerolipid synthesis. The activity of the NEM-insensitive phosphohydrolase was not altered by preincubation of rat hepatocytes in the short or long term with vasopressin, glucagon, insulin, triiodothyronine, or dexamethasone, but it might be modulated indirectly by sphingosine. The NEM-insensitive enzyme of the plasma membranes could be involved in signal transduction via the agonist-stimulated degradation of phosphatidylcholine through the phospholipase D pathway.
Using web information for author name disambiguation (2009)

In digital libraries, ambiguous author names may occur due to the existence of multiple authors with the same name (polysemes) or different name variations for the same author (synonyms). We proposed here a new method that uses information available on the Web to deal with both problems at the same time. Our idea consists of gathering information from input citations and submitting queries to a Web search engine, aiming at finding curricula vitae and Web pages containing publications of the ambiguous authors. From the content of documents in the answer sets returned by the Web search engine, useful information that can help in the disambiguation process is extracted. Using this information, author names are disambiguated by leveraging a hierarchical clustering method that groups citations in the same document together in a bottom-up fashion. Experimental results show that the our method yields results that outperform those of two state-of-the-art unsupervised methods and are statistically comparable with those of a supervised one, but requiring no training. We observe gains of up to 65.2% in the pairwise F1 metric when compared with our best unsupervised baseline method.
The Biology of Pichia membranifaciens Killer Toxins (2017)

The killer phenomenon is defined as the ability of some yeast to secrete toxins that are lethal to other sensitive yeasts and filamentous fungi. Since the discovery of strains of Saccharomyces cerevisiae capable of secreting killer toxins, much information has been gained regarding killer toxins and this fact has substantially contributed knowledge on fundamental aspects of cell biology and yeast genetics. The killer phenomenon has been studied in Pichia membranifaciens for several years, during which two toxins have been described. PMKT and PMKT2 are proteins of low molecular mass that bind to primary receptors located in the cell wall structure of sensitive yeast cells, linear (1→6)-β-d-glucans and mannoproteins for PMKT and PMKT2, respectively. Cwp2p also acts as a secondary receptor for PMKT. Killing of sensitive cells by PMKT is characterized by ionic movements across plasma membrane and an acidification of the intracellular pH triggering an activation of the High Osmolarity Glycerol (HOG) pathway. On the contrary, our investigations showed a mechanism of killing in which cells are arrested at an early S-phase by high concentrations of PMKT2. However, we concluded that induced mortality at low PMKT2 doses and also PMKT is indeed of an apoptotic nature. Killer yeasts and their toxins have found potential applications in several fields: in food and beverage production, as biocontrol agents, in yeast bio-typing, and as novel antimycotic agents. Accordingly, several applications have been found for P. membranifaciens killer toxins, ranging from pre- and post-harvest biocontrol of plant pathogens to applications during wine fermentation and ageing (inhibition of Botrytis cinerea, Brettanomyces bruxellensis, etc.).
SD-6DoF-ICLK: Sparse and Deep Inverse Compositional Lucas-Kanade Algorithm on SE(3) (2021)

This paper introduces SD-6DoF-ICLK, a learning-based Inverse Compositional Lucas-Kanade (ICLK) pipeline that uses sparse depth information to optimize the relative pose that best aligns two images on SE(3). To compute this six Degrees-of-Freedom (DoF) relative transformation, the proposed formulation requires only sparse depth information in one of the images, which is often the only available depth source in visual-inertial odometry or Simultaneous Localization and Mapping (SLAM) pipelines. In an optional subsequent step, the framework further refines feature locations and the relative pose using individual feature alignment and bundle adjustment for pose and structure re-alignment. The resulting sparse point correspondences with subpixel-accuracy and refined relative pose can be used for depth map generation, or the image alignment module can be embedded in an odometry or mapping framework. Experiments with rendered imagery show that the forward SD-6DoF-ICLK runs at 145 ms per image pair with a resolution of 752 x 480 pixels each, and vastly outperforms the classical, sparse 6DoF-ICLK algorithm, making it the ideal framework for robust image alignment under severe conditions.
Plerixafor and G-CSF combination mobilizes hematopoietic stem and progenitors cells with a distinct transcriptional profile and a reduced <i>in vivo</i> homing capacity compared to plerixafor alone (2016)

Plerixafor and G-CSF combination mobilizes hematopoietic stem and progenitors cells with a distinct transcriptional profile and a reduced in vivo homing capacity compared to plerixafor alone
Antibacterial Activity of Sodium Phytate Against Salmonella typhimurium in Meats (2007)

The approval of use of certain food-grade phosphates as food additives in a wide variety of meat products greatly stimulated research on the applications of phosphates in foods. Phytic acid is a natural plant inositol hexaphosphate constituting 1-5% of most cereals, nuts, legumes, oil seeds, pollen, and spores. In this study, we inves- tigated antibacterial activity of sodium phytate (SPT) against Salmonella typhimurium in tryptic soy broth with differ- ent pHs and in chicken, pork and beef. In tryptic soy broth, SPT at the concentrations of 0.1, 0.5, and 1.0% effectively inhibited the growth of Salmonella typhymurium in a concentration-dependent manner. At pH 5.5-7.0 similar to meat pHs, 1% SPT almost completely inhibited the bacterial growth. The inhibitory effect of SPT was stronger at pH 7.0 than pH 5.5. In chicken, pork, and beef, SPT at the concentrations of 0.1, 0.5, and 1% significantly inhibited the growth of Salmonella typhimurium in a dose-dependant manner (p<0.01). The addition of 1% SPT in the meats sig- nificantly increased the meat pHs. These results indicate that SPT is very effective for inhibition of bacterial growth as a muscle food additive for increasing food safety and functions.
BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters (2021)

BiG-SLiCE opens up new possibilities to accelerate natural product discovery and offers a first step towards constructing a global and searchable interconnected network of BGCs. As more genomes are sequenced from understudied taxa, more information can be mined to highlight their potentially novel chemistry. BiG-SLiCE is available via https://github.com/medema-group/bigslice.
The use of crevicular fluid prostaglandin E<sub>2</sub> levels as a predictor of periodontal attachment loss (1986)

Longitudinal data were collected over a period of at least 18 months and up to 3 years on 41 adult periodontitis patients (AAP Type III and IV). Ramfjord attachment level measurements and sampling of crevicular fluid (CF) at each tooth were repeated every 3 months. A mean full mouth CF prostaglandin E 2 (MCF‐PGE) value was determined for each patient at each visit. The three‐month monitoring was continued until a single site demonstrated a statistically and clinically significant attachment loss (ALOSS) episode. Results indicated that in ALOSS patients the MCF‐PGE was significantly elevated at the ALOSS visit as compared to previous levels. Furthermore, the sites which had the ALOSS had elevated levels as compared to the contralateral no ALOSS control sites (305.6±56.5 vs. 65.7±6.89 ng/ml, mean ± SEM). One month following treatment the CF‐PGE level dropped to 16.9±3.4 ng/ml at the ALOSS sites. Since the MCF‐PGE level increases preceding the attachment loss episode, reaches a maximum at the sites which actually undergo ALOSS, and subsides following treatment, the possibility of using the MCF‐PGE level to predict an oncoming future ALOSS episode was examined. The ALOSS patients had a MCF‐PGE level of 113.4±9.0 ng/ml 6 months prior to the ALOSS episode, which was significantly higher than the no ALOSS patients’MCF‐PGE level of 50.1±7.1. Analysis of MCF‐PGE levels as a screening test indicate that this measurement has a high degree of sensitivity, specificity, and a predictive value of 0.92–0.95. Thus, this method has significant merit as a diagnostic tool to determine if a patient is in a state of remission or about to undergo an attachment loss episode.
A comparative study of intraocular pressure and hemodynamic changes during general and regional anesthesia in abdominal and lower-limb surgeries (2022)

Context: In general anesthesia, intubation/extubation and use of succinylcholine elevate intraocular pressure (IOP). Elevation of IOP during anesthesia may be detrimental to patients with preexisting ocular conditions such as glaucoma and uveitis. Regional anesthesia (spinal) lowers mean arterial and may lead to hemodynamic changes. Aims: We aimed to study changes in IOP and mean arterial pressure (MAP) in patients undergoing abdominal and lower-limb surgery following general and regional anesthesia. Setting and Design: A prospective comparative nonrandomized study was done. One hundred and twenty patients were randomly allocated to receive either general (Group A, n = 60) or regional anesthesia (Group B, n = 60), respectively. An independent investigator recorded MAP and IOP (Perkins handheld tonometer). Statistics: A one-way repeated measures analysis of variance (ANOVA) was done to determine whether there are any significant differences between the means of three or more levels of a within-subject factor (IOP and MAP) over time. Results: In Group A, there was a significant rise in IOP (ANOVA, P = 0.007) after general anesthesia over time. In Group B, the change in IOP (ANOVA, P = 0.219) was not statistically significant over time. However, there was a significant reduction in MAP over time. Between the groups, the mean change in IOP was significantly higher in patients in Group A and mean MAP significantly lower in Group B, respectively. Conclusion: Patients with glaucoma, uveitis, and cardiovascular diseases should have IOP monitoring prior to deciding the type of anesthesia and after anesthesia for lower-limb and abdominal surgeries. Sudden loss of vision after anesthesia needs immediate attention.
Terahertz Electromagnetic Wave Transmission through Random Arrays of Single Rectangular Holes and Slits in Thin Metallic Sheets (2007)

We report on the observation of terahertz transparency in random arrays of the single rectangular holes and slits with the areal coverage of only 12%. The terahertz transparency occurs at the fundamental shape resonance of the rectangular holes and confirms the theoretical predictions of earlier works of García-Vidal et al. [Phys. Rev. Lett. 95, 103901 (2005)] on single rectangular holes and of Ruan and Qiu [Phys. Rev. Lett. 96, 233901 (2006)] on random arrays of holes.
Magnetic resonance nanoparticles for cardiovascular molecular imaging and therapy (2005)

Molecular vascular imaging represents a novel tool that promises to change the current medical paradigm of 'see and treat' to a 'detect and prevent' strategy. Nanoparticle agents, such as superparamagnetic nanoparticles and perfluorocarbon nanoparticle emulsions, have been developed for noninvasive imaging, particularly for magnetic resonance imaging. Designed to target specific epitopes in tissues, these agents are beginning to enter clinical trials for cardiovascular applications. The delivery of local therapy with these nanoparticles, using mechanisms such as contact-facilitated drug delivery, is in the advanced stages of preclinical research. Ultimately, combined diagnostic and therapeutic nanoparticle formulations may allow patients to be characterized noninvasively and segmented to receive custom-tailored therapy. This review focuses on recent developments of nanoparticle technologies with an emphasis on cardiovascular applications of magnetic resonance imaging.
Influenza Vaccines: Unmet Needs and Recent Developments (2013)

Influenza is a worldwide public health concern. Since the introduction of trivalent influenza vaccine in 1978, vaccination has been the primary means of prevention and control of influenza. Current influenza vaccines have moderate efficacy, good safety, and acceptable tolerability; however, they have unsatisfactory efficacy in older adults, are dependent on egg supply for production, and are time-consuming to manufacture. This review outlines the unmet medical needs of current influenza vaccines. Recent developments in influenza vaccines are also described.
Potential of Casiopeínas® Copper Complexes and Antituberculosis Drug Combination against <b><i>Mycobacterium tuberculosis</i></b> (2016)

New compounds with antituberculosis activity and their combination with classic drugs have been evaluated to determine possible interactions and antagonism. The aim of this study was to evaluate the in vitro activity of Casiopeínas® copper-based compounds (CasIIIia, CasIIIEa, and CasIIgly) alone and combined with isoniazid (INH), rifampicin, or ethambutol (EMB) against resistant and susceptible Mycobacterium tuberculosis. Seventeen clinical M. tuberculosis isolates (5 multi-drug resistant and 2 resistant to INH and/or EMB) were subjected to determination of the minimal inhibitory concentration (MIC) by the resazurin microtiter assay and combination assessment by the resazurin drug combination microtiter assay. The Casiopeínas® alone showed a remarkable effect against resistant isolates with MIC values from 0.78 to 12.50 μg/ml. Furthermore, a synergistic effect mainly with EMB is shown for both resistant and susceptible clinical isolates. Casiopeínas® are promising candidates for future investigation into the development of antituberculosis drugs, being one of the first examples of essential metal-based drugs used in this field.
A surface-micromachined MEMS acoustic sensor with X-shape bottom electrode anchor (2009)

A surface-micromachined capacitive-type micro-electro-mechanical system (MEMS) acoustic sensor with X-shape bottom electrode anchor on a Si substrate is presented. As it is designed to be implemented on only one side of a substrate for a simple monolithic integrated process, this sensor has X-shape bottom electrode anchor fabricated. The anchor operates to remove the back side process of wafer for a conventional back chamber because the chamber is formed through Si surface etching by an isotropic dry etcher of XeF <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> . The Si MEMS acoustic sensor proposed in this paper has a diameter of 300 ¿m and a back chamber depth of 25 ¿m. It shows a pull down voltage of 9.1 V at 1 kHz and a zero-bias capacitance of 1.87 pF. Additionally, the sensor has an open-circuit sensitivity of 0.57 mV/Pa at 1 kHz on a bias of 5 V.
A Technique for Stable His‐Bundle Recording and Pacing: Electrophysiological and Hemodynamic Correlates (1995)

His-bundle electrograms recorded from intracardiac electrode catheters have been a mainstay of basic and clinical electrophysiology. However, consistent His-bundle pacing has not been as readily achieved. In 13 dogs anesthetized with sodium pentobarbital (30 mg/kg), we recorded leads II and aVR as well as the His-bundle electrogram from the aortic root. A deflectable tip multipolar catheter (4 rings, 5 mm apart) was introduced via the right jugular vein into the right ventricle (RV). In 7 dogs, using fluoroscopy, the tip was placed under the tricuspid septal leaflet. In the other 6, after thoracotomy, the same placement was made by palpation through the right atrial wall. Stable His-bundle and right bundle (Rb) branch recordings were made from distal and proximal electrode pairs, respectively. H-V intervals measured 35 +/- 6 ms from the aortic root and 33 +/- 5 ms from under the tricuspid leaflet (P = NS). Rb-V measured 25 +/- 4 ms. Consistent His-bundle pacing was accomplished from the aortic root with an average stimulus intensity of 6 +/- 10 mA and from the tricuspid leaflet at 16 +/- 8 mA (P < 0.05). In 7 anesthetized dogs we compared the hemodynamic effects of A-V sequential pacing at the same heart rates using the His-bundle recording site under the septal leaflet of the tricuspid valve (A-H pacing) or pacing from the RV apex (A-RV pacing). Under normal conditions there was a significant depression of mean blood pressure when A-RV pacing was compared with atrial pacing (AOO); but no difference was found between AOO and A-H pacing.(ABSTRACT TRUNCATED AT 250 WORDS)
The Sheep Grimace Scale as an indicator of post-operative distress and pain in laboratory sheep (2017)

The EU Directive 2010/63/EU changed the requirements regarding the use of laboratory animals and raised important issues related to assessing the severity of all procedures undertaken on laboratory animals. However, quantifiable parameters to assess severity are rare, and improved assessment strategies need to be developed. Hence, a Sheep Grimace Scale (SGS) was herein established by observing and interpreting sheep facial expressions as a consequence of pain and distress following unilateral tibia osteotomy. The animals were clinically investigated and scored five days before surgery and at 1, 3, 7, 10, 14 and 17 days afterwards. Additionally, cortisol levels in the saliva of the sheep were determined at the respective time points. For the SGS, video recording was performed, and pictures of the sheep were randomized and scored by blinded observers. Osteotomy in sheep resulted in an increased clinical severity score from days 1 to 17 post-surgery and elevated salivary cortisol levels one day post-surgery. An analysis of facial expressions revealed a significantly increased SGS on the day of surgery until day 3 post-surgery; this elevated level was sustained until day 17. Clinical severity and SGS scores correlated positively with a Pearson´s correlation coefficient of 0.47. Further investigations regarding the applicability of the SGS revealed a high inter-observer reliability with an intraclass correlation coefficient of 0.92 and an accuracy of 68.2%. In conclusion, the SGS represents a valuable approach for severity assessment that may help support and refine a widely used welfare assessment for sheep during experimental procedures, thereby meeting legislation requirements and minimizing the occurrence of unrecognized distress in animal experimentation.
Evaluation of LiF lenses as monochromators for inverse photoemission spectroscopy (1984)

A LiF lens followed by a pinhole can function as an efficient vacuum ultraviolet monochromator. The principles of such an instrument are described, and its limitations are determined using ray-tracing calculations. Two practical instruments for ultraviolet inverse photoemission with tunability in the 8–11.7-eV range are proposed: a biconvex singlet with good resolution (0.23 eV at 10.2 eV) but moderate collection angle ( f/5); and a planoconvex doublet with large collection angle ( f/1.5) but moderate resolution (0.38 eV at 10.2 eV). The main principles have been demonstrated using a prototype instrument.
An Efficient and Faithful in Vitro Replication System for Threose Nucleic Acid (2013)

The emerging field of synthetic genetics provides an opportunity to explore the structural and functional properties of synthetic genetic polymers by in vitro selection. Limiting this process, however, is the availability of enzymes that allow for the synthesis and propagation of genetic information present in unnatural nucleic acid sequences. Here, we report the development of a transcription and reverse-transcription system that can replicate unnatural genetic polymers composed of threose nucleic acids (TNA). TNA is a potential progenitor of RNA in which the natural ribose sugar found in RNA has been replaced with an unnatural threose sugar. Using commercial polymerases that recognize TNA, we demonstrate that an unbiased three-letter and two different biased four-letter genetic alphabets replicate in vitro with high efficiency and high overall fidelity. We validated the replication system by performing one cycle of transcription, selection, reverse transcription, and amplification on a library of 10(14) DNA templates and observed ∼380-fold enrichment after one round of selection for a biotinylated template. We further show that TNA polymers are stable to enzymes that degrade DNA and RNA. These results provide the methodology needed to evolve biologically stable aptamers and enzymes for exobiology and molecular medicine.
A Comprehensive Exploration on WikiSQL with Table-Aware Word Contextualization (2019)

We present SQLova, the first Natural-language-to-SQL (NL2SQL) model to achieve human performance in WikiSQL dataset. We revisit and discuss diverse popular methods in NL2SQL literature, take a full advantage of BERT {Devlin et al., 2018) through an effective table contextualization method, and coherently combine them, outperforming the previous state of the art by 8.2% and 2.5% in logical form and execution accuracy, respectively. We particularly note that BERT with a seq2seq decoder leads to a poor performance in the task, indicating the importance of a careful design when using such large pretrained models. We also provide a comprehensive analysis on the dataset and our model, which can be helpful for designing future NL2SQL datsets and models. We especially show that our model's performance is near the upper bound in WikiSQL, where we observe that a large portion of the evaluation errors are due to wrong annotations, and our model is already exceeding human performance by 1.3% in execution accuracy.