gebhart/patrepeval huggingface dataset:
Measurements of water vapor adsorption on The Geysers rocks (1996)

One of the goals of this project is to determine the dependence of the water retention capacity of the rocks as a function of temperature. The results show a significant dependence of the adsorption and desorption isotherms on the grain size of the sample. The increase in the amount of water retained with temperature observed previously between 90 and 30{degrees}C for various reservoir rocks from The Geysers may be due to the contribution of slow chemical adsorption and may be dependent on the time allowed for equilibration. In contrast with the results of Shang, some closed and nearly closed hysteresis loops on the water adsorption/desorption isotherms were obtained in this study. In these cases the effects of activated processes were not present, and no increase in water adsorption with temperature was observed.
A proactive approach to wound infection (2001)

The management and treatment of infection is a complex and important area in tissue viability nursing. Andrew Kingsley discusses the value of microbiology to clinical practice and the importance of adopting a proactive approach to the management of infected wounds using an infection continuum and algorithm to help promote effective care.
Structural and Functional Impairments of Polysialic Acid by a Mutated Polysialyltransferase Found in Schizophrenia (2011)

Polysialic acid (polySia), a unique acidic glycan modifying neural cell adhesion molecule (NCAM), is known to regulate embryonic neural development and adult brain functions. Polysialyltransferase STX is responsible for the synthesis of polySia, and two single nucleotide polymorphisms (SNPs) of the coding region of STX are reported from schizophrenic patients: SNP7 and SNP9, respectively, giving STX(G421A) with E141K and STX(C621G) with silent mutations. In this study, we focused on these mutations and a binding activity of polySia to neural materials, such as brain-derived neurotrophic factor (BDNF). Here we describe three new findings. First, STX(G421A) shows a dramatic decrease in polySia synthetic activity on NCAM, whereas STX(C621G) does not. The STX(G421A)-derived polySia-NCAM contains a lower amount of polySia with a shorter chain length. Second, polySia shows a dopamine (DA) binding activity, which is a new function of polySia as revealed by frontal affinity chromatography for measuring the polySia-neurotransmitter interactions. Interestingly, the STX(G421A)-derived polySia-NCAM completely loses the DA binding activity, whereas it greatly diminishes but does not lose the BDNF binding activity. Third, an impairment of the polySia structure with an endosialidase modulates the DA-mediated Akt signaling. Taken together, impairment of the amount and quality of polySia may be involved in psychiatric disorders through impaired binding to BDNF and DA, which are deeply involved in schizophrenia and other psychiatric disorders, such as depression and bipolar disorder.
Cover Picture: Eur. J. Immunol. 6/10 (2010)

Abstract The cover image of this issue consists of confocal images of cytomegalovirus‐infected human fibroblast cells stained for HLA‐A2/pp65 complexes, taken from Makler et al. ( pp . 1552–1565). In this article, the authors use antibodies that mimic TCR specificity to directly visualize the dynamics of antigen presentation in these cells. The authors show that, following infection, large intracellular pools of HLA‐A2/pp65 complexes are localized to the Golgi. Interestingly, these large pools are sequestered inside infected cells and only a small portion of them are exported to the cell surface.
Nanoporous metals for biodegradable implants: Initial bone mesenchymal stem cell adhesion and degradation behavior (2016)

Nanostructured Fe-Mn and Fe-Mn-Zn metal scaffolds were generated through a well-controlled selective leaching process in order to fulfill the growing demand for adjustable degradation rates and improved cellular response of resorbable materials. Mouse bone marrow mesenchymal stem cells (D1 ORL UVA) were seeded onto eleven, carefully chosen nanoporous surfaces for 24 h in vitro. Using a combination of fluorescence microscopy, scanning electron microscopy (SEM), and an MTS assay, it was discovered that scaffolds with nanoscale roughened surfaces had increased cell attachment by up to 123% compared to polished smooth Fe-Mn surfaces. Significant cell spreading and construction of cell multilayers were also apparent after 24 h, suggesting better adhesion. Additionally, static electrochemical polarization experiments revealed an improvement of up to 26% in the actual rate of biodegradation for Fe-Mn surface-modified materials. However, any residual concentration of zinc after leaching was shown to slightly increase corrosion resistance. The results demonstrate that selectively leached, nanostructured Fe-Mn surfaces have the potential of being tailored to a diverse set of transient implant scenarios, while also effectively boosting overall biocompatibility, initial cell attachment, and degradation rate. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1747-1758, 2016.
Threshold voltage (1998)

MOSFET threshold voltage (VT) is the most important parameter governing sub-0.25 μm MOS device operation. Critical device performance issues such as speed, off state current and active power depend on VT (1). The primary components that influence VT are oxide thickness (Wox), oxide charge (Qox), interface trap charge (Qit), and channel dopant profile. Although conventional based CV methods have led many to believe that CV cannot be used for ultra-thin oxides, accurate methods for measuring VT and its components using both a hard probe and a high repeatability mercury probe are described in this paper.
Immunoproteomic Approach to Elucidating the Pathogenesis of Cryptococcosis Caused by Cryptococcus gattii (2010)

Cryptococcosis caused by Cryptococcus gattii is a devastating disease of immunocompetent hosts with an incompletely understood pathogenesis. Utilizing an immunoproteomic approach in a naturally occurring koala model of disease, a number of key proteins and pathways are identified in the early and late pathogenesis of cryptococcosis for the first time. In particular, the thioredoxin system appears important in the pathogenesis of cryptococcosis caused by C. gattii VGII.
Storability research with starch potato cultivars. (1987)

Studies over 4 years with 10 commercial or commercially promising cultivars grown on peat soils in the Netherlands revealed significant differences with respect to susceptibility to damage, weight loss and starch loss during storage at 6 or 20 degrees C and development of rotting at 20 degrees C. Astarte had high weight losses, and Elkana and Prominent low losses. Astarte showed a high susceptibility to internal and external damage. Erlkana, Atrela and Prominent were highly susceptible to conversion of starch to sugar at 6 degrees C, reducing processing quality; Astarte and Promesse were much less susceptible. (Abstract retrieved from CAB Abstracts by CABI’s permission)
Oncogenic EGFR Represses the TET1 DNA Demethylase to Induce Silencing of Tumor Suppressors in Cancer Cells (2016)

Oncogene-induced DNA methylation-mediated transcriptional silencing of tumor suppressors frequently occurs in cancer, but the mechanism and functional role of this silencing in oncogenesis are not fully understood. Here, we show that oncogenic epidermal growth factor receptor (EGFR) induces silencing of multiple unrelated tumor suppressors in lung adenocarcinomas and glioblastomas by inhibiting the DNA demethylase TET oncogene family member 1 (TET1) via the C/EBPα transcription factor. After oncogenic EGFR inhibition, TET1 binds to tumor suppressor promoters and induces their re-expression through active DNA demethylation. Ectopic expression of TET1 potently inhibits lung and glioblastoma tumor growth, and TET1 knockdown confers resistance to EGFR inhibitors in lung cancer cells. Lung cancer samples exhibited reduced TET1 expression or TET1 cytoplasmic localization in the majority of cases. Collectively, these results identify a conserved pathway of oncogenic EGFR-induced DNA methylation-mediated transcriptional silencing of tumor suppressors that may have therapeutic benefits for oncogenic EGFR-mediated lung cancers and glioblastomas.
In Vitro Activity of Riboflavin against the Human Malaria Parasite Plasmodium falciparum (2000)

The human malaria parasite Plasmodium falciparum digests hemoglobin and polymerizes the released free heme into hemozoin. This activity occurs in an acidic organelle called the food vacuole and is essential for survival of the parasite in erythrocytes. Since acidic conditions are known to enhance the auto-oxidation of hemoglobin, we investigated whether hemoglobin ingested by the parasite was oxidized and whether the oxidation process could be a target for chemotherapy against malaria. We released parasites from their host cells and separately analyzed hemoglobin ingested by the parasites from that remaining in the erythrocytes. Isolated parasites contained elevated amounts (38.5% +/- 3.5%) of oxidized hemoglobin (methemoglobin) compared to levels (0.8% +/- 0.2%) found in normal, uninfected erythrocytes. Further, treatment of infected cells with the reducing agent riboflavin for 24 h decreased the parasite methemoglobin level by 55%. It also inhibited hemozoin production by 50% and decreased the average size of the food vacuole by 47%. Administration of riboflavin for 48 h resulted in a 65% decrease in food vacuole size and inhibited asexual parasite growth in cultures. High doses of riboflavin are used clinically to treat congenital methemoglobinemia without any adverse side effects. This activity, in conjunction with its impressive antimalarial activity, makes riboflavin attractive as a safe and inexpensive drug for treating malaria caused by P. falciparum.
Assertion-Based QA With Question-Aware Open Information Extraction (2018)

We present assertion based question answering (ABQA), an open domain question answering task that takes a question and a passage as inputs, and outputs a semi-structured assertion consisting of a subject, a predicate and a list of arguments. An assertion conveys more evidences than a short answer span in reading comprehension, and it is more concise than a tedious passage in passage-based QA. These advantages make ABQA more suitable for human-computer interaction scenarios such as voice-controlled speakers. Further progress towards improving ABQA requires richer supervised dataset and powerful models of text understanding. To remedy this, we introduce a new dataset called WebAssertions, which includes hand-annotated QA labels for 358,427 assertions in 55,960 web passages. To address ABQA, we develop both generative and extractive approaches. The backbone of our generative approach is sequence to sequence learning. In order to capture the structure of the output assertion, we introduce a hierarchical decoder that first generates the structure of the assertion and then generates the words of each field. The extractive approach is based on learning to rank. Features at different levels of granularity are designed to measure the semantic relevance between a question and an assertion. Experimental results show that our approaches have the ability to infer question-aware assertions from a passage. We further evaluate our approaches by incorporating the ABQA results as additional features in passage-based QA. Results on two datasets show that ABQA features significantly improve the accuracy on passage-based QA.
Heterotrimers Formed by Tumor Necrosis Factors of Different Species or Muteins (2001)

Incubation of murine tumor necrosis factor (mTNF) at subnanomolar concentrations results in partial dissociation of the trimers, coinciding with a decrease in bioactivity. Using size-exclusion chromatography, we observed that the conversion of labeled mTNF to monomers is not only prevented by coincubation with an excess of unlabeled mTNF but also with unlabeled human TNF (hTNF). Moreover, after coincubation of mTNF and hTNF four different TNF complexes were revealed by native polyacrylamide gel electrophoresis, viz. homotrimeric mTNF and hTNF, as well as two complexes with an intermediate migration pattern. Analytical gel filtration in combination with native polyacrylamide gel electrophoresis and Western blot immunodetection indicated that these new complexes consisted of heterotrimeric TNF molecules. We conclude that an exchange of monomers takes place during coincubation of two different species of TNF, which results in homotrimeric and heterotrimeric TNF. To assess receptor interaction in vitro, TNF heterotrimeric molecules were used as obtained after incubation of mTNF with labeled hTNF (which only binds to mTNF receptor I) or with labeled mutein mTNF75 (specific for mTNF receptor II). These heterotrimers were retained by both mTNF receptors, which means that the mTNF subunits incorporated in heterotrimeric complexes still can bind to both types of TNF receptor. In addition, the gradual decrease in mTNF bioactivity during preincubation at subnanomolar concentrations was prevented by the presence of mutein mTNF75, which is inactive in an L929 cytotoxicity assay, indicating that heterotrimerization can influence the overall bioactivity.
Determination of carboxylic acids by high-performance liquid chromatography with 2-(2,3-anthracenedicarboximido)ethyl trifluoromethanesulfonate as a highly sensitive fluorescent labelling reagent (1993)

2-(2,3-Anthracenedicarboximido)ethyl trifluoromethanesulfonate (AE-OTf) is a highly sensitive fluorescent labelling reagent for carboxylic acids for use in liquid chromatography. The labelling reaction of carboxylic acids with AE-OTf was completed within 10 min at room temperature in acetonitrile in the presence of tetraethylammonium carbonate as a base. The 2-(2,3-anthracenedicarboximido)ethyl esters of 18 kinds of fatty acids including polyunsaturated fatty acids were separated from each other on an ODS column with an isocratic solvent system within 30 min. The relative standard deviations of their peak areas were within 2%(n= 8, 1.4–3.3 pmol on-column). Their relative peak areas were almost 1.0 and their detection limits were 0.8–2.7 fmol (signal-to-noise ratio = 3). These fatty acids were successfully determined at least over the range 20 fmol-6 pmol (correlation coefficient r >0.999 for all fatty acids tested).
Patterns of mortality in a surgical intensive care unit. (1981)

Mortalities in a surgical intensive care unit during a three year period were reviewed. The over-all mortality was 8.2 per cent. Sixty-four per cent of the deaths followed nontraumatic surgical illness and 36 per cent followed trauma. Eighty-one per cent of patients died as a direct result of traumatic injuries, while only 19 per cent died of sepsis or multiple organ failure. On the other hand, 62 per cent of the nontrauma related deaths were a consequence of sepsis or multiple organ failure. Further research into cellular support is needed to reverse the problem of sepsis related organ failure.
Activity of the mTOR inhibitor sirolimus and HDAC inhibitor vorinostat in heavily pretreated refractory Hodgkin lymphoma patients. (2014)

8508 Background: Preclinical models suggested synergistic antineoplastic activity of HDAC and mTOR inhibitors in Hodgkin lymphoma by reducing the activity of AKT, mTOR and HDAC. Methods: We designed a phase I study to determine the safety of the mTOR inhibitor sirolimus (1mg-5mg PO daily q 28 days) and HDAC inhibitor vorinostat (100mg-400mg PO daily q 28 days) in advanced cancers with an expansion cohort at the recommended phase 2 dose (RP2D) of sirolimus 4mg and vorinostat 300mg for patients with refractory classical Hodgkin lymphoma. The expansion cohort included optional pre- and post-treatment tumor biopsies, peripheral blood mononuclear cells (PBMCs), plasma/serum collections for pharmacodynamic (PD) and pharmacokinetic (PK) endpoints. Upon identification of R2PD patients were allowed to be treated and registered off label if protocol spots were not available. Results: A total of 28 patients (men, n=15; women, n=13), median age 34 years, median of 6 prior therapies (including autologous SCT [n=23], autologous and allogeneic SCT [n=6]) were enrolled in dose escalation (n=1), RP2D (n=19) or registered off label (n=8). Per Cheson 2007 criteria the overall response rate was 57% with 9 CRs (32%) and 7 PRs (25%). At the median follow-up of 5.4 months, the median progression-free survival has not been reached. Also given successful induction of remissions 5 (18%) patients were referred for allogeneic SCT. Major grade 3-4 treatment-related toxicities included grade 3 thrombocytopenia (9 patients, 32%), grade 4 thrombocytopenia (8, 29%), grade 3 anemia (4, 14%), and grade 3 transaminitis (3, 11%). Treatment interruptions and/or dose modifications were needed in 19 (68%) patients. Ten (36%) patients had archival tissue available for targeted next-generation sequencing and one patient had a loss of TSC2, an abnormality that putatively activates mTOR (PR -56% for 8.4+ months). PD studies in pre- and post-treatment tumor biopsies, PBMCs and plasma as well as PK analysis are pending. Conclusions: The combination of sirolimus and vorinostat is well tolerated with encouraging activity in very heavily pretreated patients with Hodgkin lymphoma refractory to standard therapies. Clinical trial information: NCT01087554.
CO 2 laser with 65MW pulses and 100kW power: concept and first steps of development (2008)

From theoretical considerations it is well known that pulsed CO<sub>2</sub> lasers with beam peak powers of 50 MW and a pulse length of 20 &mu;s should be able to launch small satellites. To overcome limitations from ultra high power densities in a single laser source, a new concept proposes a beam source which consists of several individual laser systems. Short laser pulses emitted by 16 Q-switched CO<sub>2</sub> laser sources with more than 50 MW power, as of coaxial electrode geometry with excellent beam power to volume ratio, will be combined on a common optical beam path to form a longer single pulse as required. Coaxial lasers have already been built successfully, although without Q-switching. As a main component of the above concept a new optical beam switching element - a "plasma mirror" - which can withstand ultra high power densities that must serve as a Q switch and as a beam path switch is proposed. From the literature it is well known that very dense plasmas are able to reflect an incoming laser beam totally if the plasma frequency, depending on the electron density, equals the laser radiation frequency. As a first step for the development of such a device the absorptivity and reflectivity of iron argon plasmas for CO<sub>2</sub> laser beams has been studied theoretically and experimentally by the authors with the result, that for plasma electron densities of 10<sup>17</sup> cm<sup>-3</sup> nearly 100% are absorbed due to "inverse bremsstrahlung", but that the plasma frequency and thus reflectivity can not be reached, since the electron density is too small in plasmas as contained in electrical arcs.
PaTre: A Method for Paralogy Trees Construction (2003)

Genomes can be described as a collection of clusters, the gene families, whose members are called paralogs. Paralogs are genes that most probably share duplication history and show a significant similarity in their sequences, even if they perform slightly different biological function. Among the different mechanisms that have led to an increase of the genomic information during biological evolution, gene duplication is probably the most important. To better understand duplication events, the first step is to investigate the history of the gene families in order to detect which duplication events have taken place, and in which relative (partial) order. Here we present a method, called PaTre, that, given a gene family, attempts to construct the paralogy tree of the family. We will work under the hypothesis that every family member derives from a duplication process of another member. By the term paralogy tree, we mean a directed tree in which the root represents the most ancient paralog of the family and each oriented arc (a, b) represents the existence of a duplication event from the template gene a to its copy b. Notice that gene a survives the event and can serve as a template of more than one duplication event; in fact, there can be more than one arc leaving a. PaTre uses new algorithmic techniques motivated by the specific application at hand. The reliability of the inferential process has been tested by means of a simulator that implements different hypotheses on the duplication-with-modification paradigm and on three examples of different biological gene families, belonging either to lower and higher organisms.
The gut bacterial microbiota of sea turtles differs between geographically distinct populations (2020)

The microbiota of metazoans can be influenced by a variety of factors including diet, environment and genetics. In this study we sampled multiple populations from 2 host species that do not overlap in distribution, in order to test whether their bacterial microbiotas are species-specific or more variable. Intestinal swabs were collected from loggerhead turtles originating from Florida, USA, and Queensland, Australia, as well as from flatback turtles from Crab Island, Queensland, and Port Hedland, Western Australia. We then manually extracted bacterial DNA and used 16S rRNA sequencing to explore bacterial microbial community composition and structure. Our investigation showed that the bacterial microbiota of sea turtles is heavily influenced by geography, with loggerhead turtles originating from the USA and Australia harbouring significantly different bacterial microbial populations in terms of composition. Similarly, we also found that flatback turtles from Crab Island had significantly less diverse microbiotas, with a predominance of the bacterial phylum Firmicutes , in comparison to their genetically similar counterparts from Port Hedland. Factors that may explain these observed differences between populations include host genetics, differences in foraging habitat quality and differences in migratory distance (and thus durations of inappetence) between foraging and breeding grounds. The mechanisms by which these factors may influence bacterial microbial composition of sea turtle gastrointestinal tracts warrants further investigation. The results of this study highlight the importance of interpreting microbiota data of wild animals in the context of geography.