gebhart/patrepeval huggingface dataset:
Calcium isotope fractionation by osteoblasts and osteoclasts, across endothelial and epithelial cell barriers, and with binding to proteins (2021)

Timely and accurate diagnosis of osteoporosis is essential for adequate therapy. Calcium isotope ratio (δ<sup>44/42</sup>Ca) determination has been suggested as a sensitive, noninvasive, and radiation-free biomarker for the diagnosis of osteoporosis, reflecting bone calcium balance. The quantitative diagnostic is based on the calculation of the δ<sup>44/42</sup>Ca difference between blood, urine, and bone. The underlying cellular processes, however, have not been studied systematically. We quantified calcium transport and δ<sup>44/42</sup>Ca fractionation during in vitro bone formation and resorption by osteoblasts and osteoclasts and across renal proximal tubular epithelial cells (HK-2), human vein umbilical endothelial cells (HUVECs), and enterocytes (Caco-2) in transwell systems and determined transepithelial electrical resistance characteristics. δ<sup>44/42</sup>Ca fractionation was furthermore quantified with calcium binding to albumin and collagen. Calcified matrix formed by osteoblasts was isotopically lighter than culture medium by -0.27 ± 0.03‰ within 5 days, while a consistent effect of activated osteoclasts on δ<sup>44/42</sup>Ca could not be demonstrated. A transient increase in δ<sup>44/42</sup>Ca in the apical compartment by 0.26‰ occured across HK-2 cells, while δ<sup>44/42</sup>Ca fractionation was small across the HUVEC barrier and absent with Caco-2 enterocytes, and with binding of calcium to albumin and collagen. In conclusion, δ<sup>44/42</sup>Ca fractionation follows similar universal principles as during inorganic mineral precipitation; osteoblast activity results in δ<sup>44/42</sup>Ca fractionation. δ<sup>44/42</sup>Ca fractionation also occurs across the proximal tubular cell barrier and needs to be considered for in vivo bone mineralization modeling. In contrast, the effect of calcium transport across endothelial and enterocyte barriers on blood δ<sup>44/42</sup>Ca should be low and is absent with physiochemical binding of calcium to proteins.
Reduced adherence of micro‐organisms to human mucosal epithelial cells following treatment with Taurolin, a novel antimicrobial agent (1987)

Taurolin, a non-antibiotic antimicrobial agent, significantly reduced the adherence of buccal and vaginal strains of Candida albicans blastospores and urine isolates of Escherichia coli and Staphylococcus saprophyticus to epithelial cells. Light microscopy and radio-isotopic counting methods were used to quantify the adherence of the micro-organisms to either uroepithelial or buccal epithelial cells. A maximum reduction in adherence of approximately 65% was obtained. The anti-adherence capacity was time-dependent, requiring a contact time of 30 min to achieve maximum effect. Taurolin at sub-minimum inhibitory concentrations (MIC) significantly reduced the adherence of Candida and E. coli. A concentration slightly higher than the MIC was required for Staph. saprophyticus. Treatment of either epithelial cells or micro-organisms with Taurolin resulted in reduced adherence of microorganisms.
Repeated stenting of recurrent in-stent restenotic lesions: intravascular ultrasound analysis and clinical outcome. (2007)

While serial restenting a recurrent ISR lesion was not associated with progressive decrease in MSA, it was still associated with chronic stent underexpansion and a high rate of adverse events. Attention should be directed to achieving better stent expansion to minimize subsequent recurrences.
Exogenous Surfactants in a Piglet Model of Acute Respiratory Distress Syndrome (1996)

Evidence for surfactant dysfunction in acute respiratory distress syndrome (ARDS) suggests a role for exogenous surfactant which contains apoprotein for resistance to protein inhibition. We compared the effects of KL-4-Surfactant, an artificial preparation containing a synthetic 21 amino acid peptide with SP-B-like activity, with Exosurf, an artificial protein-free surfactant, and Survanta, a bovine protein-containing surfactant, in a saline lung lavage model of ARDS in neonatal piglets. Two sequential series of lung lavages were performed to lower PaO2 < 100 mm Hg, each followed by administration of surfactant or air and a 90-min observation period. Progressive lung injury was demonstrated by deterioration in pulmonary function, increasing bronchoalveolar lavage protein, and changes in histopathology. All surfactants improved oxygenation, although oxygenation was generally better with Survanta and KL-4-Surfactant. Further, Survanta and KL-4-Surfactant groups showed improvement in ventilation, with decreases in PaCO2 and increases in FRC. Only KL-4-Surfactant demonstrated greater pressure-volume characteristics and lower bronchoalveolar protein than those of Controls. We conclude that the physiologic effects of KL-4-Surfactant are more like Survanta in this model. We speculate that KL-4-Surfactant may improve pulmonary function, reduce alveolar protein leak, and thus be efficacious in the treatment of ARDS.
Collective aspects of privacy in the Twitter social network (2018)

Preserving individual control over private information is one of the rising concerns in our digital society. Online social networks exist in application ecosystems that allow them to access data from other services, for example gathering contact lists through mobile phone applications. Such data access might allow social networking sites to create shadow profiles with information about non-users that has been inferred from information shared by the users of the social network. This possibility motivates the shadow profile hypothesis: the data shared by the users of an online service predicts personal information of non-users of the service. We test this hypothesis for the first time on Twitter, constructing a dataset of users that includes profile biographical text, location information, and bidirectional friendship links. We evaluate the predictability of the location of a user by using only information given by friends of the user that joined Twitter before the user did. This way, we audit the historical prediction power of Twitter data for users that had not joined Twitter yet. Our results indicate that information shared by users in Twitter can be predictive of the location of individuals outside Twitter. Furthermore, we observe that the quality of this prediction increases with the tendency of Twitter users to share their mobile phone contacts and is more accurate for individuals with more contacts inside Twitter. We further explore the predictability of biographical information of non-users, finding evidence in line with our results for locations. These findings illustrate that individuals are not in full control of their online privacy and that sharing personal data with a social networking site is a decision that is collectively mediated by the decisions of others.
A soluble form of the glycolipid‐anchored receptor for urokinase‐type plasminogen activator is secreted from peripheral blood leukocytes from patients with paroxysmal nocturnal hemoglobinuria (1992)

The cellular urokinase-type plasminogen-activator (uPA) receptor (uPAR) is a glycolipid-anchored membrane protein thought to be involved in pericellular proteolysis during cell migration and tumor invasion. In the present study, we have identified and characterized two soluble forms of uPAR which have retained their ligand-binding capability. One variant was generated in vitro by treatment of intact normal cells with either a phosphatidylinositol-specific phospholipase C (PLC) or endoproteinase Asp-N. The other soluble uPAR variant was secreted in vivo from peripheral blood leukocytes affected by the stem-cell disorder paroxysmal nocturnal hemoglobinuria (PNH), and was found in the plasma from these PNH patients as well as in the conditioned medium from cultured PNH leukocytes. Under normal conditions, we find no evidence for any shedding or secretion of a soluble uPA-binding counterpart to human uPAR in plasma. Unlike normal leukocytes, the PNH-affected cells do not express uPAR on the cell surface, although they do contain apparently normal levels of uPAR-specific mRNA. The secreted uPAR derived from PNH cells has a mobility in SDS/PAGE that is slightly higher than that of uPAR solubilized by PtdIns-specific PLC or detergent, but resembles that of a truncated, recombinant uPAR variant, which has its C-terminus close to the proposed glycolipid-attachment site, suggesting that the secreted protein has been proteolytically processed for glycolipid attachment. The presence in plasma from PNH patients of such a secreted, hydrophilic form of uPAR lends support to the hypothesis that the lesion underlying the PNH disorder resides either in glycolipid biosynthesis or in the function of an as-yet-unidentified transamidating enzyme assumed to cleave and assemble the truncated uPAR with the preformed glycolipid moiety.
The trouble with domestic violence (1996)

I am a community nurse and today I visited a new family - a 79 year old woman and her principal carer, a frail 83 year old sister with whom she shares a bedroom.
Polyethylene Glycol Rapidly Restores Axonal Integrity and Improves the Rate of Motor Behavior Recovery After Sciatic Nerve Crush Injury (2010)

The inability to rapidly (within minutes to hours) improve behavioral function after severance of peripheral nervous system axons is an ongoing clinical problem. We have previously reported that polyethylene glycol (PEG) can rapidly restore axonal integrity (PEG-fusion) between proximal and distal segments of cut- and crush-severed rat axons in vitro and in vivo. We now report that PEG-fusion not only reestablishes the integrity of crush-severed rat sciatic axons as measured by the restored conduction of compound action potentials (CAPs) and the intraaxonal diffusion of fluorescent dye across the lesion site, but also produces more rapid recovery of appropriate hindlimb motor behaviors. Improvement in recovery occurred during the first few postoperative weeks for the foot fault (FF) asymmetry test and between week 2 and week 3 for the Sciatic Functional Index (SFI) based on analysis of footprints. That is, the FF test was the more sensitive indicator of early behavioral recovery, showing significant postoperative improvement of motor behavior in PEG-treated animals at 24-48 h. In contrast, the SFI more sensitively measured longer-term postoperative behavioral recovery and deficits at 4-8 wk, perhaps reflecting the development of fine (distal) motor control. These and other data show that PEG-fusion not only rapidly restores physiological and morphological axonal continuity, but also more quickly improves behavioral recovery.
28 days of creatine nitrate supplementation is apparently safe in healthy individuals (2014)

Overall, CN appears to be safe in both 1 g and 2 g servings daily for up to a 28 day period. While those with previously elevated BUN levels may see additional increases resulting in post-supplementation values slightly beyond normal physiological range, these results have minor clinical significance and are not cause for concern. Otherwise, all hematological safety markers remained within normal range, suggesting that CN supplementation has no adverse effects in daily doses up to 2 g over 28 days and may be an alternative to creatine monohydrate supplementation.
Shape Constrained Automatic Segmentation of the Liver based on a Heuristic Intensity Model (2007)

Abstract. We present a fully automatic 3D segmentation method for the liver from contrast-enhanced CT data. It is based on a combination of a constrained free-form and statistical deformable model. The adaptation of the model to the image data is performed according to a simple model of the typical intensity distribution around the liver boundary and neighboring anatomical structures, considering the potential presence of tumors in the liver. All parameters of the deformation as well as the initial positioning of the model in the data are estimated automatically. 1
Fresh Approach for High-Throughput Studies of Ion-Selective Materials Using Reusable ChemFET Platform (2019)

Aqueous anions play an important role in our world, and the ability to continuously measure them provides both environmental and health benefits. Chemically-sensitive field effect transistors (ChemFETs) are becoming increasingly popular in the field of aqueous measurement due to their relatively low-cost capability for real-time, continuous sensing. Receptor molecules or mixtures displaying affinity for a particular ion can also be utilized in a ChemFET gate membrane. Receptors can be incorporated into the gate oxide membrane and the entire ChemFET can utilized in an aqueous environment, thus utilizing hydrophobic receptors in an aqueous anion-sensing application.\n\nDemonstrating the ability to reuse the sensors validates an important characteristic for ChemFET-based research. Additionally, numerous other receptor molecules are evaluated against an array of common anions. Selectivity coefficients are compared to the Hofmeister Series. Additional membranes are evaluated for suitability for incorporation of receptors on the ChemFET gate oxide surface. This thesis includes previously unpublished co-authored material.
Electroejaculation of Bulls Using Pulse Waves of Variable Frequency and Length (1975)

The effects of stimulation with the factorial combination of pulse waves of three wave lengths and three frequencies were compared to a modified sine wave for electroejaculation of the bull. The 4 msec pulse wave length and frequencies of 50 or 80 pulses/sec produced a higher incidence of penile protrusion and initiation and completion of ejaculation more quickly and at lower voltages. However, the sine wave treatment was equal or superior to any of the nine pulse wave treatments for all criteria studied. Seminal characteristics averaged over treatments were for first and second ejaculates, respectively; pre-sperm fluid volume, 2.71 and 3.49 ml; sperm-rich fluid volume, 5.24 and 6.00 ml; sperm-rich fluid spermatozoal concentration, 596 and 334 X 106/ml; and progressive motility 52.9 and 59.1%.
Rescue from anti-MHC class II antibody-mediated marrow graft failure by c-kit ligand (1994)

Dogs given 920 cGy of total body irradiation (TBI) followed by autologous marrow infusion uniformly achieve sustained hematopoietic reconstitution. We have previously shown that administration of the anti-MHC class II monoclonal antibody (MoAb) H81.98.21 (IgG2a) at 0.6 mg/kg/d immediately after transplantation results in delayed graft failure. A second noncrossblocking anti-MHC class II MoAb, B1F6, of the same isotype, at the same dose, did not interfere with sustained engraftment, suggesting that the observed effect was epitope dependent. Although higher concentrations of B1F6 were required, in the present study both MoAbs interfered with the propagation of long-term marrow cultures. When MoAb B1F6 was given in vivo at 1.2 mg/kg/d, ie, twice the dose used previously, dogs so treated also developed delayed marrow graft failure. Marrow failure with either MoAb involved myeloid, erythroid, and megakaryocytic lineages. Administration of recombinant canine c-kit ligand/stem cell factor (SCF) for 7 or 21 days posttransplant resulted in reversal of graft failure. Although the short course did induce a broad transient early peak of granulocytes, the longer course of SCF was accompanied by earlier sustained recovery than the short course. In conclusion, therefore, marrow graft failure induced by anti-MHC class II MoAb does not appear to be epitope dependent, involves all hematopoietic lineages, and is overcome by the administration of c-kit ligand.
Methylated BNIP3 gene in colorectal cancer prognosis (2010)

The DNA methylation of apoptosis-related genes in various cancers contributes to the disruption of the apoptotic pathway and results in resistance to chemotherapeutic agents. Irinotecan (CPT-11) is one of the key chemotherapy drugs used to treat metastatic colorectal cancer (CRC). However, a number of metastatic CRC patients do not benefit from this drug. Thus, the identification of molecular genetic parameters associated with the response to CPT-11 is of interest. To identify apoptosis-related genes that may contribute to CPT-11 resistance, microarray analysis was conducted using colon cancer cells in which 5-aza-2'deoxycytidine (DAC) enhanced sensitivity to CPT-11. Microarray analysis identified 10 apoptosis-related genes that were up-regulated following treatment with DAC. Among the genes, Bcl-2/adenovirus E1B 19 kDa protein interacting protein 3 (BNIP3), a Bcl-2 family pro-apoptotic protein, was identified as being involved in CPT-11 resistance following methylation of its promoter. An analysis of 112 primary CRC cases revealed that approximately 58% of cases showed BNIP3 methylation, and that patients with methylation exhibited a poorer outcome compared to those without methylation. In addition, in 30 patients who received first-line CPT-11 chemotherapy, patients with methylation exhibited resistance to chemotherapy compared to patients with no methylation. The results suggest that methylation of BNIP3 is a predictive factor in the prognosis and response to CPT-11 treatment in CRC patients.
Control and Synthesis of Non-Interferent Timed Systems (2012)

In this paper, we focus on the synthesis of secure timed systems which are modelled as timed automata. The security property that the system must satisfy is a non-interference property. Intuitively, non-interference ensures the absence of any causal dependency from a high-level domain to a lower-level domain. Various notions of non-interference have been defined in the literature, and in this paper we focus on Strong Non-deterministic Non-Interference (SNNI) and two (bi)simulation based variants thereof (CSNNI and BSNNI). We consider timed non-interference properties for timed systems specified by timed automata and we study the two following problems: (1) check whether it is possible to find a sub-system so that it is non-interferent; if yes (2) compute a (largest) sub-system which is non-interferent.
Optimising Selective Sampling for Bootstrapping Named Entity Recognition (2005)

Training a statistical named entity recognition system in a new domain requires costly manual annotation of large quantities of in-domain data. Active learning promises to reduce the annotation cost by selecting only highly informative data points. This paper is concerned with a real active learning experiment to bootstrap a named entity recognition system for a new domain of radio astronomical abstracts. We evaluate several committee-based metrics for quantifying the disagreement between classifiers built using multiple views, and demonstrate that the choice of metric can be optimised in simulation experiments with existing annotated data from different domains. A final evaluation shows that we gained substantial savings compared to a randomly sampled baseline. 1.
Identification of the Discrepancies between Pharmacist and Patient Perception of the Pharmacist’s Role as an Advisor on Drug Therapy Based on Social Science Theory (2015)

Article 25-2 of the Japanese Pharmacists' Act was revised in June 2014, establishing the position of pharmacists as "advisors on the use of pharmaceuticals." Prior to the Act's revision, we investigated the perceptions of patients and pharmacists about pharmacists' roles using a social science methodology. We also examined current opinions and necessary factors for the future growth and development of pharmacists. This questionnaire survey was conducted using an internet method. Patients and pharmacists answered 12 questions. Responses from 529 patients and 338 pharmacists were analyzed. For all items, pharmacists' awareness of their roles exceeded patients' awareness of the roles. In this study, the difference between pharmacist and patient awareness was larger than in similar research conducted in the United States. The greatest difference was observed in three items: "Understanding the effects of the drugs the patients are taking" (rate of high ratings: pharmacists 80.2%, patients 37.8%), "Understanding the health changes caused by the drugs dispensed to the patients" (pharmacists 80.2%, patients 28.4%), and "Consciously protecting patients from the adverse effects of drugs" (pharmacists 82.8%, patients 42.2%), indicating role discrepancy. Partition analysis indicated the three factors for a pharmacist to be regarded as a drug therapy or medication specialist: "The patient regards the pharmacist as his/her family or regular pharmacist," "The pharmacist is making it easy for a patient to talk with him/her" and "The pharmacist is aware of a patient's use of products other than prescribed drugs, such as over the counter (OTC) medications or health foods and nutritional supplements." Future efforts are necessary to resolve role discrepancy and implement ongoing monitoring.
Data from An Enhancer Demethylator Phenotype Converged to Immune Dysfunction and Resistance to Immune Checkpoint Inhibitors in Clear-Cell Renal Cell Carcinomas (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Immune checkpoint inhibitors (ICI) have revolutionized the treatment of patients with clear-cell renal cell carcinomas (ccRCC). Although analyses of transcriptome, genetic alterations, and the tumor microenvironment (TME) have shed light into mechanisms of response and resistance to these agents, the role of epigenetic alterations in this process remains fully unknown.&lt;/p&gt;Experimental Design:&lt;p&gt;We investigated the methylome of six ccRCC cohorts as well as one cell line dataset. Of note, we took advantage of the BIONIKK trial aiming to tailor treatments according to Paris Descartes 4-gene expression subgroups, and performed Illumina EPIC profiling for 46 samples related to patients treated with ipilimumab plus nivolumab, and 17 samples related to patients treated with sunitinib.&lt;/p&gt;Results:&lt;p&gt;A group of tumors associated with enhancer demethylation was discovered, namely &lt;i&gt;TED&lt;/i&gt;. &lt;i&gt;TED&lt;/i&gt; was associated with tumors with sarcomatoid differentiation and poor clinical outcome. &lt;i&gt;TED&lt;/i&gt; harbored &lt;i&gt;TET1&lt;/i&gt; promoter demethylation, activated the gene expression signature of epithelial–mesenchymal transition and IL6/JAK/STAT3 pathways, and displayed a TME characterized by both immune activation and suppressive populations, fibroblast infiltration, and endothelial depletion. In addition, &lt;i&gt;TED&lt;/i&gt; was a predictive factor of resistance to the combination of first-line ipilimumab-nivolumab in the BIONIKK clinical trial. Finally, &lt;i&gt;TED&lt;/i&gt; was associated with activation of specific regulons, which we also found to be predictive of resistance to immunotherapy in an independent cohort.&lt;/p&gt;Conclusions:&lt;p&gt;We report on the discovery of a novel epigenetic phenotype associated with resistance to ICIs that may pave the way to better personalizing patients’ treatments.&lt;/p&gt;&lt;/div&gt;