gebhart/patrepeval huggingface dataset:
Phototroph-heterotroph interactions during growth and long-term starvation across Prochlorococcus and Alteromonas diversity (2021)

Abstract Microbial interactions such as those between phytoplankton and bacteria been studied intensively using specific model organisms, due to their potential impact on ecosystems and biogeochemistry. Yet, to what extent interactions differ between closely related organisms, or how these interactions change over time or culture conditions, remains unclear. Here, we characterize the interactions between five strains each of two globally abundant marine microorganisms, Prochlorococcus (a phototroph) and Alteromonas (a heterotroph), from the first encounter between individual strains and over more than a year of repeated cycles of exponential growth and long-term nitrogen starvation. Prochlorococcus - Alteromonas interactions had little effect on traditional growth parameters such as Prochlorococcus growth rate, maximal fluorescence or lag phase, affecting primarily the dynamics of culture decline, which we interpret as representing cell mortality and lysis. The shape of the Prochlorococcus decline curve and the carrying capacity of the co-cultures were determined by the phototroph and not the heterotroph strains involved. Comparing various mathematical models of culture mortality suggests that Prochlorococcus death rate increases over time in mono-cultures but decreases in co-cultures, with cells potentially becoming more resistant to stress. Our results demonstrate intra-species differences in ecologically-relevant co-culture outcomes. These include the recycling efficiency of N and whether the interactions are mutually synergistic or competitive. They also highlight the information-rich growth and death curves as a useful readout of the interaction phenotype. Significance Statement Interactions between phytoplankton and marine bacteria impact global ecosystems and biogeochemistry. Here, we explore how intra-species variability affects the interactions between Prochlorococcus , a globally abundant photosynthetic cyanobacetrium and Alteromonas , a heterotrophic bacterium that lives off and recycles organic matter. Under nitrogen starvation, Prochlorococcus growing alone increasingly accumulate damage and die, whereas in co-culture with Alteromonas they become increasingly resilient. The specific Prochlorococcus strain had a much larger effect on co-culture behavior than the Alteromonas strain, determining whether the interactions are mutually synergistic or potentially competitive. These results show how ecologically relevant outcomes of interactions may vary between closely related microorganisms, and highlight growth and death curves from laboratory (co)-cultures as information-rich views of microbial growth and death.
Habitual physical activity improves vagal cardiac modulation and carotid baroreflex function in elderly women (2023)

The impact of habitual physical activity on vagal-cardiac function and baroreflex sensitivity in elderly women is poorly characterized. This study compared vagal-cardiac modulation and carotid baroreflex (CBR) function in eight physically active (67.6 ± 1.9 years; peak O<sub>2</sub> uptake 29.1 ± 2.5 mL/min/kg) versus eight sedentary (67.3 ± 1.8 years; peak O<sub>2</sub> uptake 18.6 ± 0.9 mL/min/kg) elderly women. Heart rate (HR) variabilities and maximal changes of HR and mean arterial pressure (MAP) elicited by 5-s pressure pulses between +40 and -80 mmHg applied to the carotid sinus were measured at rest and during carotid baroreceptor unloading effected by -15 mmHg lower-body negative pressure (LBNP). HR variability was greater in active than sedentary women in both low (0.998 ± 0.286 versus 0.255 ± 0.063 bpm<sup>2</sup>; <i>P</i> = 0.036) and high (0.895 ± 0.301 versus 0.156 ± 0.045 bpm<sup>2</sup>; <i>P</i> = 0.044) frequency domains. CBR-HR gains (bpm/mmHg) were greater (fitness factor <i>P</i> < 0.001) in active versus sedentary women at rest (-0.146 ± 0.014 versus -0.088 ± 0.011) and during LBNP (-0.105 ± 0.014 versus -0.065 ± 0.008). CBR-MAP gains (mmHg/mmHg) tended to be greater (fitness factor <i>P</i> = 0.077) in active versus sedentary women at rest (-0.132 ± 0.013 versus -0.110 ± 0.011) and during LBNP (-0.129 ± 0.015 versus -0.113 ± 0.013). However, LBNP did not potentiate CBR-MAP gains in either sedentary or active women (LBNP factor <i>P</i> = 0.94), and it depressed CBR-HR gains in both groups (LBNP factor <i>P</i> = 0.003). CBR-HR gains in the sedentary women did not differ (sex factor <i>P</i> = 0.65) from gains reported in age-matched sedentary men, although CBR-MAP gains tended to be greater (sex factor <i>P</i> = 0.109) in the men. Thus, tonic vagal modulation indicated by HR variability and dynamic vagal responses assessed by CBR-HR gain were augmented in physically active women. Enhanced vagal-cardiac function may protect against senescence-associated cardiac electrical and hemodynamic instability in elderly women.
Computing the Field in Proteins and Channels (2010)

This is an early but comprehensive review of the PNP Poisson Nernst Planck theory of ion channels. Extensive reference is made to the earlier literature. The starting place for this theory of open channels is a theory of electrodiffusion rather like that used previously to describe membranes. The theory uses Poisson's equation to describe how charge on ions and the channel protein creates electrical potential; it uses the Nernst-Planck equations to describe migration and diffusion of ions in gradients of concentration and electrical potential. Combined, these are also the "drift-diffusion equations" of solid state physics, which are widely, if not universally used to describe the flow of current and the behavior of semiconductors.
Crucifijos en las aulas: ¿lesión a los derechos fundamentales? (2010)

El 3 de noviembre de 2009, la Sala Segunda del Tribunal Europeo de Derechos Humanos (TEDH) decidio que la existencia de un crucifijo en las aulas escolares lesiona la libertad religiosa (negativa) de aquellos padres que no desean una educacion religiosa (cristiana, catolica) para sus hijos. Esta decision del Tribunal ha generado, tanto en Italia, como en Europa, criticas y polemicas (a veces intensas). El analisis de esa sentencia revela paralelos notables con la resolucion sobre los crucifijos del Tribunal Constitucional aleman de 1995. Ambas decisiones se basan en un entendimiento erroneo de la dimension negativa de los derechos fundamentales. Igualmente problematicas resultan, tanto las consideraciones sobre la existencia de una intromision en el derecho fundamental, como aquellas sobre la solucion del conflicto de los intereses afectados. Esta solucion que se ha dado al problema es unilateral y desventajosa para la libertad religiosa positiva. Ha sido la Sala del TEDH en particular la que ignora el margen de apreciacion del Estado contra la reiterada jurisprudencia del propio Tribunal. Particularmente en una materia tan sensible como lo es la relacion entre el Estado y la Iglesia, valdria mas para un Tribunal supranacional comportarse en forma mas moderada en la imposicion de su propia opinion juridica.
An overview of genetic rust resistance: From broad to specific mechanisms (2017)

Global agriculture is under threat due to the rapid evolution and spread of pathogenic fungi that cause rust diseases. For instance, the recently evolved races of wheat stem rust (Puccinia graminis f. sp. tritici) and stripe rust (P. striiformis f. sp. tritici) fungus in parts of Africa, Asia, and Europe are a menace to food security due to their ability to spread rapidly and overcome resistance in common wheat varieties Similarly, new variants of Asian soybean rust (Phakopsora pachyrhizi) detected in Brazil and the United States pose a major constraint to soybean cultivation Since genetic resistance can provide effective and chemical-free disease control, many efforts are directed towards isolating rust-resistance genes in crop plants and understanding how to best deploy them for durable resistance [3]. In addition, related nonhost species are increasingly being utilised to identify new sources of resistance Here, we summarise current knowledge of rust resistance, focussing on race-specific, non-race-specific, and nonhost resistance mechanisms.
Hextend[registered sign] (hetastarch solution) decreases multiple organ injury and xanthine oxidase release after hepatoenteric ischemia-reperfusion in rabbits (1997)

We conclude that multiple organ injury and xanthine oxidase release after hepatoenteric ischemia-reperfusion are decreased by colloid administration.
Octogenarian patients with colorectal cancer: Characterizing an emerging clinical entity (2017)

Octogenarians presented with several distinct characteristics and had worse outcome. Further research is warranted to better define this growing population.
Probing Electronic Communication in Covalently Linked Multiporphyrin Arrays. A Guide to the Rational Design of Molecular Photonic Devices (2001)

Understanding electronic communication among the constituents in multicomponent macromolecular architectures is essential for the rational design of molecular devices for photonic, electronic, or optoelectronic applications. This Account describes studies aimed at understanding the mechanisms of electronic communication in porphyrin-based architectures that undergo excited-state energy migration and ground-state hole/electron hopping. Porphyrins are ideal building blocks for such constructs owing to their attractive and versatile physical properties and amenability to synthetic control. These properties have permitted the creation of covalently linked multiporphyrin arrays wherein the rates of excited-state energy migration and ground-state hole/electron hopping can be tuned over a wide range.
ras Oncogene Proteins: Three-dimensional Structures, Functional Implications, and a Model for Signal Transducer (1988)

ras oncogene products (for review, see Barbacid 1987) are of interest for at least two reasons: First, the most commonly found oncogenes isolated from human tumors or transformed human cell lines belong to the ras gene family (for a survey, see Nishimura and Sekiya 1987); second, ras gene products are thought to belong to the family of signal transducer proteins, G proteins (for review, see Stryer and Bourne 1986; Gilman 1987; Neer and Clapham 1988). In the human genome, there are three distinct cellular ras genes: c-Ha-ras, c-Ki-ras, and N-ras. Proteins encoded by these genes, p21 proteins, have a molecular weight of 21,000 with 188 or 189 amino acid residues, bind GDP/GTP (Scolnick et al. 1979), and have practically identical amino acid sequences, with the exception of the carboxy-terminal 25 residues. The difference between the normal ras proto-oncogenes and the activated (transforming) ras oncogenes is usually a single base change...
Preparation of (5S)-5-C-methyl-β-L-lyxo-hexofuranose derivative as(+)-lactacystin precursors (2010)

We present here the preparation of the precursor for stereoselective synthesis of (+)-lactacystin starting from D-glucose. The first step is conversion of D-glucose to 1,2:5,6-di-O-isopropylidene-α-D-gulofuranose. The second step is introduction of a methyl group at C5 and preparation of compound 9. This compound can be used as a precursor of target molecule of (+)-lactacystin
Relations between allometric scalings and fluctuations in complex systems: The case of Japanese firms (2012)

To elucidate allometric scaling in complex systems, we investigated the underlying scaling relationships between typical three-scale indicators for approximately 500,000 Japanese firms; namely, annual sales, number of employees, and number of business partners. First, new scaling relations including the distributions of fluctuations were discovered by systematically analyzing conditional statistics. Second, we introduced simple probabilistic models that reproduce all these scaling relations, and we derived relations between scaling exponents and the magnitude of fluctuations.
Test for a correlation between Vλ and the +y opponent spectral sensitivity (1985)

Rushton and Baker 1 have shown that the ratio of R to G cones varies between observers. We use this variability to ask if observers who are rich, say, in R-cone input to the V λ or flicker channel are also likely to be rich in R-cone input to the r-g and y-b opponent-color channels. Results for the r-g channel (eight observers): Although the R/G flicker ratio varied considerably across observers, the spectral position of unique yellow varied little and did not correlate with the R/G ratio. Conclusions are similar for the y-b channel; there is no correlation between the amounts of a B primary required to cancel yellowness from long- and middle-wavelength test lights and amounts of these lights required in a flicker match.
Identification of a Novel TGFβ/PKA Signaling Transduceome in Mediating Control of Cell Survival and Metastasis in Colon Cancer (2011)

This work impacts our understanding of the possible mechanisms that are critical to the growth and maintenance of metastases as well as understanding of a novel TGFβ function as a metastatic suppressor. These results raise the possibility that regeneration of attenuated TGFβ signaling would be an effective target in the treatment of metastasis. Our work indicates the clinical potential for developing anti-metastasis therapy based on inhibition of this very important aberrant cell survival mechanism by the multifaceted TGFβ/PKA transduceome induced pathway. Development of effective treatments for metastatic disease is a pressing need since metastases are the major cause of death in solid tumors.
A secreted endoribonuclease ENDU-2 from the soma protects germline immortality in C. elegans (2020)

Abstract Multicellular organisms coordinate tissue specific response to environmental information via both cell-autonomous and non-autonomous mechanisms. In addition to secreted ligands, secreted small RNAs have recently been reported to regulate gene expression across tissue boundaries. Here we show that the conserved poly-U specific endoribonuclease ENDU-2 is secreted from the soma and taken-up by the germline to ensure germline immortality at elevated temperature in C. elegans . ENDU-2 binds to mature mRNAs and negatively regulates mRNA abundance both in the soma and the germline. While ENDU-2 promotes RNA decay in the soma directly via its endoribonuclease activity, ENDU-2 prevents misexpression of soma-specific genes in the germline and preserves germline immortality independent of its RNA-cleavage activity. In summary, our results suggest that the secreted RNase ENDU-2 transmits environmental information across tissue boundaries and contributes to maintenance of stem cell immortality probably via retaining a stem cell specific program of gene expression.
Purification and comparative studies of dihydrolipoamide dehydrogenases from the anaerobic, glycine-utilizing bacteria Peptostreptococcus glycinophilus, Clostridium cylindrosporum, and Clostridium sporogenes (1990)

Three different dihydrolipoamide dehydrogenases were purified to homogenity from the anaerobic glycine-utilizing bacteria Clostridium cylindrosporum, Clostridium sporogenes, and Peptostreptococcus glycinophilus, and their basic properties were determined. The enzyme isolated from P. glycinophilus showed the properties typical of dihydrolipoamide dehydrogenases: it was a dimer with a subunit molecular mass of 53,000 and contained 1 mol of flavin adenine dinucleotide and 2 redox-active sulfhydryl groups per subunit. Only NADH was active as a coenzyme for reduction of lipoamide. Spectra of the oxidized enzyme exhibited maxima at 230, 270, 353, and 453 nm, with shoulders at 370, 425, and 485 nm. The dihydrolipoamide dehydrogenases of C. cylindrosporum and C. sporogenes were very similar in their structural properties to the enzyme of P. glycinophilus except for their coenzyme specificity. The enzyme of C. cylindrosporum used NAD(H) as well as NADP(H), whereas the enzyme of C. sporogenes reacted only with NADP(H), and no reaction could be detected with NAD(H). Antibodies raised against the dihydrolipoamide dehydrogenase of C. cylindrosporum reacted with extracts of Clostridium acidiurici, Clostridium purinolyticum, and Eubacterium angustum, whereas antibodies raised against the enzymes of P. glycinophilus and C. sporogenes showed no cross-reaction with extracts from 42 organisms tested.
Electrocardiographic Findings in Acute Coronary Syndrome (2012)

This chapter contains sections titled: Introduction The 12-lead electrocardiogram in ST segment elevation myocardial infarction – evolution of electrocardiogram abnormalities The 12-lead electrocardiogram in non-ST segment elevation myocardial infarction presentations Electrocardiogram ST segment elevation myocardial infarctionmimickers and confounders
Streamlining amine synthesis (2015)

Bulky amine groups that help make many drugs more bioavailable can be added readily to organic compounds [Also see Research Article by Gui et al. ]
Abstract 10486: Single-Beat Estimation Right Ventricular End Diastolic Pressure Relationship (2021)

Introduction: An abnormal right ventricular (RV) end-diastolic pressure-volume relationship (EDPVR) is an early marker of poor prognosis in pulmonary arterial hypertension (PAH). Prior studies assessing RV diastolic impairment utilized pressure (P) measured at right heart catheterization (RHC) and non-simultaneous volume (V) measured by cardiac magnetic resonance imaging (cMRI), which serves as the current reference standard for V. Our aims were: (a) to validate a single-beat (SB) method to assess RV EDPVR in an animal model against multi-beat (MB) measurements during preload variation, and (b) to use V obtained via transthoracic 3D echocardiography (3DE) during simultaneous RHC. Methods: In six anesthetized swine under an Institutional Animal Care &amp; Use Committee-approved protocol, a SB method was used to derive EDPVR as V 15 , the previously described predicted ventricular V at a theoretical EDP of 15 mmHg. A multi-beat (MB) reference EDPVR was defined using conductance/micromanometer catheter-measured RVP and V during preload variation. The V 15 value derived from the SB method was compared by Bland-Altman analysis to that defined by the reference EDPVR. Clinically, the SB method was applied to 13 patients with PAH and 10 age- and gender-matched controls who underwent RHC with simultaneous transthoracic 3DE. V 15 values between groups were compared by t-test. Results: In the animal model there was strong correlation between MB and SB estimates of V 15 (r=0.95; p&lt;0.0001) with acceptable accuracy and precision (bias -4.2±6.1 mL, overall error 8.4%). Consistent with previous reports using cMRI, PAH patients exhibited greater V 15 (166±43 mL vs. 131±30 mL; p=0.04) (Figure 1) . Conclusion: This study demonstrates validity of a SB assessment of RV EDPVR using data obtained from transthoracic 3DE performed during RHC, obviating the need for non-simultaneous cMRI. Further studies are needed to examine SB assessment of RV EDPVR across the spectrum of PH phenotypes.
Laser energy levels for trabecular meshwork damage in the primate eye. (1983)

The authors treated the trabecular meshwork of 17 primate eyes with the argon laser by a variety of protocols in an attempt to cause moderate, consistent intraocular pressure elevation. This was achieved most satisfactorily with deliveries of 0.5 to 1.0 seconds and a total energy of at least 50 joules. The method allows production of a satisfactory laser-induced model of chronic glaucoma with one treatment session in most eyes. This experience provides a measure of the upper limit of acceptable total laser energy for therapeutic procedures in humans with this instrument. Delivery durations longer than 0.1 sec should be used with caution in trabeculoplasty.
Estimation of Trapped Charge Density in SONOS Flash Memory Using a Parallel Capacitor Model (2011)

This paper proposes a model established using the parallel connection of MOS and floating-gate MOS capacitors to examine the electric properties of polysilicon-oxide-nitride-oxide-silicon (SONOS) Flash memory in both the fresh and programmed states. A linear relationship between threshold voltage shift and effective trapped charge density was revealed via the threshold electric field. The simulation of the channel current was given based on our model, being in agreement with the experimental results for both forward and reverse read modes. The model and theory make an easy and time-saving approach to comprehensively analyze the trapped charge and its effect on other electric properties, e.g., electric field, oxide capacitance, and charge distribution, contributing to the control of the write/erase operation, the optimization of the device structure, and the characteristics of the retention properties in SONOS Flash memory.
The Effects of Breed, Diet, Sex, Location and Slaughter Weight on Lamb Growth, Carcass Composition and Meat Flavor (1981)

The influence of breed, diet, sex, location fed and slaughter weight on carcass composition and quality and flavor of heavy lamb carcasses was examined. One-hundred and fifty-three Suffolk and Rambouillet-sired ram and wether lambs, fed a high or a low energy diet at the University of Wyoming (UWY) or the Roman L. Hruska US Meat Animal Research Center (MARC), were slaughtered at 62 or 76 kilograms. Suffolk-sired lambs grew faster (P<.01) than Rambouillet-sired lambs and increased their advantage (P<.05) in growth rate during the later periods of the trial. Suffolk-sired lambs had leaner carcasses (P<.01) but yellower fat (P<.05) and more pronounced secondary sex characteristics (P<.01) than Rambouillet-sired lambs. Breed did not influence the flavor of cooked ground meat. Ram lambs had higher (P<.01) rates of gain and trimmer carcasses than wether lambs. Ram lambs' superior potential for growth (P<.01) was more pronounced on the high energy diet than on the low energy diet. Ram lamb carcasses had softer, yellower fat and ram meat had more intense flavor scores (P<.01). Differences in fat softness between ram and wether carcasses became more apparent with increasing age and weight (P<.01). At similar slaughter weights, carcasses obtained from lambs fed the high energy diet had more (P<.01) kidney and pelvic fat than carcasses obtained from lambs fed the low energy diet. Carcasses from lambs fed the high energy diet had softer, yellower (P<.01) fat than carcasses from lambs fed the low energy diet. However, flavor scores were more intense (P<.01) for meat from lambs fed the low energy diet. Lambs fed at UWY were superior in growth rate to lambs fed at MARC. No differences in fat color, fat firmness or cooked meat flavor were observed between carcasses obtained from the two locations.
Multi-level Residual Networks from Dynamical Systems View (2017)

Deep residual networks (ResNets) and their variants are widely used in many computer vision applications and natural language processing tasks. However, the theoretical principles for designing and training ResNets are still not fully understood. Recently, several points of view have emerged to try to interpret ResNet theoretically, such as unraveled view, unrolled iterative estimation and dynamical systems view. In this paper, we adopt the dynamical systems point of view, and analyze the lesioning properties of ResNet both theoretically and experimentally. Based on these analyses, we additionally propose a novel method for accelerating ResNet training. We apply the proposed method to train ResNets and Wide ResNets for three image classification benchmarks, reducing training time by more than 40% with superior or on-par accuracy.