gebhart/patrepeval huggingface dataset:
Basic microbiology and metabolism (2023)

1. Describe the microbiology and metabolisms of BNR microorganisms. 2. Conceptualise a BNR microbial ecosystem by linking their metabolisms. 3. Define their growth systems with appropriate C source, N source, e-donor couple, e-acceptor couple, and partner compounds. 4. Formulate their anabolic, catabolic, and metabolic reactions, by deriving stoichiometries by elemental, charge, electron, and/or Gibbs free energy balances. 5. Implement thermodynamic relations to estimate stoichiometric and kinetic parameters. 6. Formulate a volumetric growth process rate using saturation/inhibition switching functions. 7. Use Herbert-Pirt kinetic relations to predict material allocations to maintenance and growth. 8. Simulate simple mathematical models to predict their growth, selection, and interactions in ideal (dis)continuous bioreactors such as batch, sequencing batch, and chemostat. 9. Propose methods to measure microbial selection and conversions.
Fluid sorption of orthopedic grade ultrahigh molecular weight polyethylene in a serum environment is affected by the surface area and sterilization method (2000)

It is shown in this work that lubricant sorption in ultrahigh molecular weight polyethylene (UHMWPE) increases with available surface area of the component. This has clinical relevance, because sliding and articulation experienced in simulator studies can result in changes in surface roughness and the creation of new surfaces. This study compares the fluid sorption of orthopedic grade UHMWPE with different surface areas (but equivalent volume) for different sterilization methods. For both the gamma radiation and nonsterile control samples, the gain in total fluid absorbed scaled proportionately with surface area. For the EtO sterilization treatment, the fluid gain was nonlinear and substantially less than the radiated and control groups. The findings from this study clearly indicate that the sterilization and surface area affect the fluid uptake and weight gain of UHMWPE.
Prediction of blood levels following oral administration of weakly acidic drug particles such as sulfa drugs in rabbits from the in vitro dissolution behavior. (1984)

Prediction of blood levels following oral administration of weakly acidic drug particles such as sulfa drugs from data obtained in in vitro dissolution tests of drug suspensions was studied in the rabbit. The relationship between in vivo and in vitro dissolution rates or between absorption rate and in vitro dissolution rate was investigated. The drug absorption from aqueous solution was suggested to be rate-limited by the gastric emptying rate because the initial absorption rate constant in a biexponential time course of aqueous solution for the amount unabsorbed vs. time plot was almost the same among 9 of the 10 drugs tested, except for sulfacetamide. This indicated that when the in vivo dissolution rate constant is much slower than the initial absorption rate constant of aqueous solution, the time course of blood levels for the solid drug will deviate from that of aqueous solution. Based on the consideration, the critical in vitro dissolution rate constant corresponding to the initial absorption rate constants of aqueous solution was calculated by means of statistical analysis using the relationship between in vivo and in vitro parameters. The validity of this prediction was examined using four high-solubility drugs, and it was found that the prediction could be done whether the in vitro dissolution medium was distilled water or 0.1 N HCl solution. Although in the present study, the experiment was done using an aqueous suspension form in the rabbit, the applicability of this prediction method to other dosage forms and to the case of humans is discussed.
Protein Phosphorylation and The Regulation of Cation Cotransport (1980)

The turkey erythrocyte is a useful system in which to investigate the relationship between protein phosphorylation and membrane transport. This cell possesses a catecholamine- and cyclic AMP-stimulated Na+-K+ 'cotransport' system in its plasma membrane, and the physiological properties of this system have been partially elucidated. It is distinct from the Na+-K+ 'pump' and is insensitive to ouabain, but can be blocked by certain diuretic agents such as furosemide and bumetanide. A plasma membrane protein of MW 230000, called goblin, has been identified as the major protein whose state of phosphorylation increases upon incubation of turkey erythrocytes with catecholamines or cyclic AMP. The kinetics of phosphorylation of goblin at its cyclic AMP-sensitive sites correlate well with the kinetics of Na+-K+ cotransport activation under various conditions. This protein may play a role in the regulation of the Na+-K+ cotransport system by catecholamines and cyclic AMP.
Parallel in vitro expansion of human hepatitis C virus specific FoxP3- effector memory and FoxP3+ regulatory CD8+ T cells on recognition of the same antigen (2007)

There is growing consensus that regulatory T cells contribute to regulation of T cell responses to tumors and microbes. FoxP3 has been shown to be the most specific marker for regulatory CD4+ T cells, however, itrsquor;s significance in the CD8+ T cell population is less understood. Here we show that the in vitro stimulation of PBMC from chronically HCV infected patients with specific peptides gives rise to two distinct antigen-specific T populations, FoxP3- and FoxP3+ CD8+ T cells. The FoxP3+ virus-specific CD8+ T cells share phenotypical markers of regulatory T cells, such as CTLA–4 and GITRI expression. They do not produce Interleukin (IL)–2 or IL–10, but moderate amounts of IFNg after peptide specific stimulation and have a suppressive, cell-contact dependent suppressive activity. Interleukin (IL)–2 and IL–10 are critical cytokines since the expansion of virus-specific FoxP3+ CD8+ T cells is blocked by the addition of anti-IL–2- or IL–10- neutralizing monoclonal antibodies. Taken together, our results indicate that stimulation with the same viral antigen leads to the expansion of both, FoxP3- memory/ effector as well as FoxP3+ regulatory virus-specific CD8+ T cells that regulate immune responses antigen-specifically. These results may also have therapeutic consequences since the antigen-specific induction of regulatory CD8+ T cells may be used to achieve a fine tuning of antigen-specific suppression in various clinical settings.
Optimal energy-efficient relay selection in cooperative cellular networks (2013)

In this paper, we consider relay selection technique in a cooperative cellular network where user terminals act as relays to help the communications between a base station (BS) and cell-edge users (CEUs). We firstly build cooperative sets for source mobile users according to their transmission radius. Then, transmission power sets are built for all mobile users according to SNR thresholds. Finally, Energy Efficient Cooperative-Sets-based Maximum Weighted Matching (EECS-MWM) algorithm is proposed to select the optimal relay for source users to maximize the system energy efficiency. The performance of proposed scheme is evaluated and compared with existing methods in terms of system energy efficiency, capacity, and the number of successful matched user pairs, which show that EECS-MWM can improve the performance of the cooperative cellular networks.
Investigation of gelation behavior of polyvinyl alcohol‐glutaraldehyde system (1997)

The polyvinyl alcohol-glutaraldehyde gel system was investigated in this work. The gelation kinetics under oil field environments and effects on the structures and properties of the gels formed were discussed. The basic characteristics of this gel system were determined. The fundamental data during gelation were obtained and application of the gel system for the tertiary oil recovery was evaluated. Under the experimental condition, among the gelation time t, initial pH of the system, and glutaraldehyde concentration x, there exists the relation ln t(pH, x) = 2.35pH - 0.85 ln x - 10.91 It is conspicuous that the gelation of this gel system is less sensitive to hardness and salt contents; the gels formed under the relevant condition were quite stable. Thus, the application of this gel system for tertiary oil recovery under hostile environments is very promising. © 1997 John Wiley & Sons, Inc.
SABER engaging the private sector in education country report : Swaziland 2016 (2017)

This report presents an analysis of how effectively the current policies in Swaziland engage the private sector in basic (primary and secondary) education. The analysis draws on the engaging the private sector (EPS) framework, a product of the World Bank’s systems approach for better education results (SABER). SABER-EPS research in Swaziland has found that at both the primary and secondary levels, quality, and equity are challenges. The private sector plays an increasingly significant role in education at both levels. Based on a review of existing policies, SABER-EPS offers the following recommendations for Swaziland to enhance private sector engagement in education in order to meet the challenges of access, quality, and equity: (1) empower parents to make informed educational choices, while providing additional support to disadvantaged groups; (2) strengthen accountability mechanisms to ensure that all students receive a quality education; and (3) strengthen the policy environment for the non-state sector to promote transparency and an adequate supply of school places. The report provides an overview of SABER-EPS findings, followed by a description of the basic education system in Swaziland that focuses on the private sector and government policies related to the private provision of education. The report then benchmarks Swaziland’s policy environment utilizing the SABER-EPS Framework and offers policy options to enhance access and learning for all children in primary and secondary school.
Effect of guarana (Paullinia cupana) on fatigue in breast cancer patients undergoing systemic chemotherapy. (2010)

9007 Background: In breast cancer (BC) patients undergoing systemic chemotherapy, cancer-related fatigue (CRF) is a common problem that can negatively impact quality of life. Guarana Paullinia cupana is a plant native to the Amazon basin that has been used as a stimulant since pre-Columbian times. Purpose: To evaluate the effectiveness of guarana extract on fatigue, sleep quality, anxiety, depression symptoms, and menopause in a group of BC chemotherapy patients. Methods: Patients with progressive fatigue after their first cycle of chemotherapy were randomized to receive either guarana 50 mg by mouth twice daily (32 patients) or placebo (43 patients) for 21 days. After a 7-day wash-out period, patients were crossed over to the opposite experimental arm. All patients were evaluated on days 1, 21, and 49 using the FACIT F, FACIT-ES, Brief Fatigue Inventory (BFI), Pittsburgh Sleep Quality Index, Chalder Fatigue Scale, and Hospital Anxiety and Depression Scale (HADS). Results: Guarana significantly improved the FACIT-F, FACIT-ES and BFI global scores compared to placebo on days 21 and 49 (p < 0.01). The Chalder Scale improved significantly on day 21 (p = 0.002) but not on day 49 (p = 0.26). Guarana did not produce any CTCAE grades 3 or 4 toxicities and did not worsen sleep quality or cause anxiety or depression. Conclusions: Guarana is an effective, cheap and nontoxic alternative for the treatment of fatigue in BC patients receiving systemic chemotherapy. Further studies are needed to confirm our results and to evaluate their generalizability to other types of cancer. No significant financial relationships to disclose.
Combining different biochemical markers of myocardial ischemia does not improve risk stratification in chest pain patients compared to troponin I alone (2005)

The combinations of different markers were prognostically non-superior compared to TnI, which thus, should be preferred as a biochemical marker for risk stratification in patients with chest pain.
Unambiguous video pipeline description motivated by HDR (2016)

The transition to High Dynamic Range (HDR) requires new standards for video. Existing standards for SDR have tacitly assumed the CRT's native response characteristics for the Electro-Optical Transfer Function or EOTF, often referred to as `gamma'. Since the EOTF was universal and fixed by the physics of the CRT, SDR standards have been typically expressed in terms of the complementary Opto-Electrical Transfer Function or OETF. Unfortunately, viewing the video pipeline solely in terms of the OETF (e.g., BT.709) and EOTF (e.g., BT.1886) is somewhat ambiguous. The resolution of this ambiguity requires the inclusion of the Opto-Optical Transfer Function or OOTF. This paper explains this ambiguity and why it is important for HDR. It closes with a description of an OOTF for HDR that is compatible with the OOTF of existing SDR standards.
Placental neurosteroids shape cerebellar development and social behaviour (2019)

ABSTRACT Compromised placental function or premature loss has been linked to diverse neurodevelopmental disorders 1,2 . The placenta is the first functional foetal endocrine organ, but the direct impact of placental hormone loss on foetal brain in late gestation has not been empirically tested. Allopregnanolone (ALLO) is a non-glucocorticoid, progesterone derivative that acts as a positive modulator of GABA-A receptor activity 3 with the potential to alter critical GABA-mediated developmental processes 4,5 . To directly test the role of placental ALLO, we generated a novel mouse model in which the gene encoding the synthetic enzyme for ALLO ( Akr1c14 ) is specifically deleted in trophoblasts using a tissue-specific Cre-Lox strategy. ALLO concentrations are significantly decreased in late gestation in placenta and brain when placental Akr1c14 is removed, indicating placenta as the primary gestational ALLO source. We now demonstrate that targeted placental ALLO loss leads to permanent changes in brain development in a sex- and regionally-specific manner. Placental ALLO insufficiency led to male-specific cerebellar white matter (WM) abnormalities characterized by excess myelination with increased myelin protein expression, similar to changes reported in boys with autism spectrum disorders (ASD) 6,7 . Behavioural testing of these mice revealed increased repetitive behaviour and sociability deficits, two hallmarks of ASD, only in male offspring with placental ALLO insufficiency. Notably, a strong positive correlation was seen between the cerebellar contents of myelin basic protein (MBP) and the severity of ASD-like behaviours. A single injection of ALLO during gestation was sufficient to rescue both cerebellar MBP levels and aberrant behaviours. This study reveals a new role for a placental hormone in shaping specific brain structures and behaviours, and suggests that identifying placental hormone insufficiency or preterm loss may offer novel therapeutic opportunities to prevent later neurobehavioural disorders.
Academic Leadership: Gatekeeping or Groundskeeping? (2020)

Common approaches to academic leadership include serving as assessors of the progress of individuals towards organizationally determined milestones and markers of success. Likewise, leadership development often focuses on leadership skills and tactics, rather than on cultivation and enactment of leadership philosophies and progressive vision. Here, I discuss the importance of cultivating leadership for progressive faculty and academic staff development through strategically tending the cultures and systems that one leads, in addition to tactical supervision of people. I describe this as systems-engaged leadership manifested as groundskeeping, or as attending to the individuals in an organization while simultaneously actively tending the ecosystems in which the work of the organization occurs. Groundskeeping contrasts with more traditional approaches of leading, which function as gatekeeping, or primarily via guarding who gains access and who advances based on conceptualizations and assumptions about who can function and thrive.
Immunization with Glucose-6-Phosphate Isomerase Induces T Cell-Dependent Peripheral Polyarthritis in Genetically Unaltered Mice (2004)

Rheumatoid arthritis is a chronic inflammatory disease primarily affecting the joints. The search for arthritogenic autoantigens that trigger autoimmune responses in rheumatoid arthritis has largely focused on cartilage- or joint-specific Ags. In this study, we show that immunization with the ubiquitously expressed glycolytic enzyme glucose-6-phosphate isomerase (G6PI) induces severe peripheral symmetric polyarthritis in normal mice. In genetically unaltered mice, T cells are indispensable for both the induction and the effector phase of G6PI-induced arthritis. Arthritis is cured by depletion of CD4(+) cells. In contrast, Abs and FcgammaR(+) effector cells are necessary but not sufficient for G6PI-induced arthritis in genetically unaltered mice. Thus, the complex pathogenesis of G6PI-induced arthritis in normal mice differs strongly from the spontaneously occurring arthritis in the transgenic K/B x N model where Abs against G6PI alone suffice to induce the disease. G6PI-induced arthritis demonstrates for the first time the induction of organ-specific disease by systemic autoimmunity in genetically unaltered mice. Both the induction and effector phase of arthritis induced by a systemic autoimmune response can be dissected and preventive and therapeutic strategies evaluated in this model.
Radiation‐induced malignant and atypical peripheral nerve sheath tumors (1980)

The reported peripheral nerve complications of therapeutic irradiation in humans include brachial and lumbar plexus fibrosis and cranial and peripheral nerve atrophy. We have encountered 9 patients with malignant (7) and atypical (2) peripheral nerve tumors occurring in an irradiated site suggesting that such tumors represent another delayed effect of radiation treatment on peripheral nerve. The neoplasms appeared 4 to 41 years following radio-therapy, at a time when the patients (6 females and 3 males) were 16 to 70 years old and cured of their original tumors. Eight patients had received irradiation to treat malignant disease; the ninth had a benign condition. The sites of peripheral nerve tumor were the brachial plexus in 5, cervical plexus in 1, lumbar plexus in 2, and retroperitoneum in 1. Eight patients presented with painful masses, and in 6 of the 8 there was a progressive neurological deficit. Seven patients died with metastases within two years of diagnosis. In all instances the radio-therapy was within an acceptable radiation dosage, yet 3 patients developed local radiation-induced skin and bony abnormalities. In 3 patients there were either clinical signs or a family history of von Recklinghausen disease, but the malignant peripheral nerve sheath tumors developed only in the radiation port. Animal studies support the clinical observation that malignant peripheral nerve sheath tumors can occur as a delayed effect of irradiation. Other etiological mechanisms, including an increased risk of second primaries in cancer patients and a genetic predisposition to peripheral nerve tumors, may also play a role.
Comparison of Acceleration Techniques for Selected Low-Level Bioinformatics Operations (2016)

Within the recent years clock rates of modern processors stagnated while the demand for computing power continued to grow. This applied particularly for the fields of life sciences and bioinformatics, where new technologies keep on creating rapidly growing piles of raw data with increasing speed. The number of cores per processor increased in an attempt to compensate for slight increments of clock rates. This technological shift demands changes in software development, especially in the field of high performance computing where parallelization techniques are gaining in importance due to the pressing issue of large sized datasets generated by e.g., modern genomics. This paper presents an overview of state-of-the-art manual and automatic acceleration techniques and lists some applications employing these in different areas of sequence informatics. Furthermore, we provide examples for automatic acceleration of two use cases to show typical problems and gains of transforming a serial application to a parallel one. The paper should aid the reader in deciding for a certain techniques for the problem at hand. We compare four different state-of-the-art automatic acceleration approaches (OpenMP, PluTo-SICA, PPCG, and OpenACC). Their performance as well as their applicability for selected use cases is discussed. While optimizations targeting the CPU worked better in the complex k-mer use case, optimizers for Graphics Processing Units (GPUs) performed better in the matrix multiplication example. But performance is only superior at a certain problem size due to data migration overhead. We show that automatic code parallelization is feasible with current compiler software and yields significant increases in execution speed. Automatic optimizers for CPU are mature and usually no additional manual adjustment is required. In contrast, some automatic parallelizers targeting GPUs still lack maturity and are limited to simple statements and structures.
DRAGON: FUEL ELEMENTS (1960)

The core zone of the Dragon 20-Mwh helium-cooled reactor consists of 37 elements with 7 fuel rcds in each, totaling 259 fuel rcds. A fuel rcd is thorium- uranium fuel surrounded by a graphite box; the assembly is restrained radially by the pressure drop in the coolant channels. For the purpose of keeping activity at low limits, the graphite box is impregnated sufficiently so that diffusion of gaseous fission products is delayed for at least 1 hour, and a gap is intrcduced between the fuel and the box for a small coolant purge. Details of fuel rod construction are given together with heat transfer and thermal stress equations and characteristics. (D.L.C.)
First-Principles Modeling of LaMnO3 SOFC Cathode Material (2008)

We present and discuss the results of first principles DFT plane-wave supercell calculations for atomic and molecular oxygen adsorption and diffusion on the LaMnO3 (001) surface which serves as a model material for a solid oxide fuel cell cathode. The dissociative adsorption of O2 molecules from the gas phase is energetically favorable on surface Mn ions even on a defect-free surface. We discuss optimal adsorption sites for oxygen, binding energies, electronic density redistribution as well as charge transfer. We also compare the surface migration energies for adsorbed O atoms and vacancies in the bulk and on the cathode surface