Miracle-dz/UniFAR-FTUs huggingface dataset:
Deep mutational scanning of Pneumocystis jirovecii dihydrofolate reductase reveals allosteric mechanism of resistance to an antifolate

Pneumocystis jirovecii is a fungal pathogen that causes pneumocystis pneumonia, a disease that mainly affects immunocompromised individuals. This fungus has historically been hard to study because of our inability to grow it in vitro. One of the main drug targets in P. jirovecii is its dihydrofolate reductase (PjDHFR). Here, by using functional complementation of the baker’s yeast ortholog, we show that PjDHFR can be inhibited by the antifolate methotrexate in a dose-dependent manner. Using deep mutational scanning of PjDHFR, we identify mutations conferring resistance to methotrexate. Thirty-one sites spanning the protein have at least one mutation that leads to resistance, for a total of 355 high-confidence resistance mutations. Most resistance-inducing mutations are found inside the active site, and many are structurally equivalent to mutations known to lead to resistance to different antifolates in other organisms. Some sites show specific resistance mutations, where only a single substitution confers resistance, whereas others are more permissive, as several substitutions at these sites confer resistance. Surprisingly, one of the permissive sites (F199) is without direct contact to either ligand or cofactor, suggesting that it acts through an allosteric mechanism. Modeling changes in binding energy between F199 mutants and drug shows that most mutations destabilize interactions between the protein and the drug. This evidence points towards a more important role of this position in resistance than previously estimated and highlights potential unknown allosteric mechanisms of resistance to antifolate in DHFRs. Our results offer unprecedented resources for the interpretation of mutation effects in the main drug target of an uncultivable fungal pathogen. Author summary The study of uncultivable microorganisms has always been a challenge. Such is the case of the human-specific pathogen Pneumocystis jirovecii, the causative agent of pneumocystis pneumonia. P. jirovecii is insensitive to classical antifungal drugs, making options for treatment and prophylaxis limited. In recent years, more and more cases of P. jirovecii infections have become resistant to treatment, highlighting the need to study and understand this pathogen’s mechanisms of resistance. Here, we use a yeast strain expressing P. jirovecii’s DHFR as a reporter for resistance to an antifolate, one of the drug families used to treat infections. We observed that this DHFR was sensitive to methotrexate, a powerful antifolate, in a quantitative manner. Then, by using a large-scale mutational assay, we identified virtually all single mutations that confer this protein resistance to methotrexate. While any of them have also been reported in other eukaryotes, we find new mutations at positions of the protein not previously known to confer resistance or to be in contact with this competitive inhibitor. Overall, our results are a comprehensive portrait of this DHFR’s resistance to methotrexate.
Cytoplasmic fluidization triggers breaking spore dormancy in fission yeast

The cytoplasm is a complex, crowded environment that influences myriad cellular processes including protein folding and metabolic reactions. Recent studies have suggested that changes in the biophysical properties of the cytoplasm play a key role in cellular homeostasis and adaptation. However, it still remains unclear how cells control their cytoplasmic properties in response to environmental cues. Here, we used fission yeast spores as a model system of dormant cells to elucidate the mechanisms underlying regulation of the cytoplasmic properties. By tracking fluorescent tracer particles, we found that particle mobility decreased in spores compared to vegetative cells, and rapidly increased at the onset of dormancy breaking upon glucose addition. This cytoplasmic fluidization depended on glucose sensing via the cAMP-PKA pathway. PKA activation led to trehalose degradation through trehalase Ntp1, thereby increasing particle mobility as the amount of trehalose decreased. In contrast, the rapid cytoplasmic fluidization did not require de novo protein synthesis, cytoskeletal dynamics, or cell volume increase. Furthermore, the measurement of diffusion coefficients with tracer particles of different sizes suggests that the spore cytoplasm impedes the movement of larger protein complexes (40–150 nm) such as ribosomes, while allowing free diffusion of smaller molecules (∼3 nm) such as second messengers and signaling proteins. Our experiments have thus uncovered a series of signaling events that enable cells to quickly fluidize the cytoplasm at the onset of dormancy breaking. Significance statement Cellular processes are influenced by the biophysical properties of the cytoplasm such as crowding and viscoelasticity. Although it has been suggested that cells tune the cytoplasmic properties in response to environmental changes, the molecular mechanisms remain unclear. Here, we used the dormant fission yeast spores and uncovered signaling pathways that facilitate cytoplasmic fluidization during dormancy breaking. Furthermore, we tracked the mobility of intracellular tracer particles, and found that the spore cytoplasm impedes the mobility of larger protein complexes, while allowing free diffusion of smaller molecules. These results suggest that small signaling proteins can diffuse relatively freely in the spore cytoplasm and have the ability to transmit dormancy breaking signals, while the motion of large complexes, such as ribosomes, is restricted.
Transforming traumatic intensity: Living with the uncertainty of terrifying symptoms

ABSTRACT In this case, presentation of a patient who experienced severe sexual abuse in childhood and attempted to manage his traumatic dreams and flashbacks with autoerotic asphyxiation, the author describes how she tolerated the anxiety of a life-threatening symptom while engaging in a deep and transformative treatment. She writes about her understanding of the symptoms, how she bore the accompanying anxiety, and what the mutative forces were that led to the patient relinquishing the symptom and progressing forward. Mutative factors included the creation of a relational home, ongoing awareness of forward edge meanings of the patient’s behaviors (including the potentially lethal symptom) and the establishment of deep mutual trust, both generally and specifically in the patient’s capacity to know what he needed in order to grow. These factors helped the patient integrate his sense of shame and self-loathing. The therapist’s deep trust in the patient’s sense of what he needed as she guided the treatment deepened the bond between them and created the paradoxical sense of both intensity and calm that the patient longed for. This paper details dreams that illustrate the nature of the therapeutic relationship and the patient’s internal experience. The therapist details her own experience in the co-transference in this highly charged case. Overall, this paper will help therapists to recognize, connect with, and protect traumatized patients, while not being distracted by the frightening symptoms themselves.
Genesis of flood basalts from eclogite‐bearing mantle plumes

On the basis of the geochemistry of flood basalts, we investigate the hypothesis that the source material for these magmas includes a significant eclogite component derived from ancient subducted oceanic crust entrained into mantle plumes at the core-mantle boundary. We present finite element models of the melting in starting plumes (plume heads) in both continental and oceanic regions. Starting plume models in which the plume heads are composed solely of pyrolite mantle are incapable of generating sufficient volumes of melt, or any melt at all, for reasonable plume head temperatures (1400–1600°C) or lithosphere ages (6.25–100 m.y.). This result is in contrast to the results of Farnetani and Richards [1994] whose models require higher plume head temperatures (1600–1700°C) and a weak, mobile lithosphere in order to generate volumes of melt similar to flood basalts. Plumes composed of 15 wt % eclogite yield volumes of melt comparable to flood basalts in both oceanic and continental settings. The maximum extent of melting in these models is about 10–30%. This agrees with the model of Hofmann and White [1982], who argued that ocean island basalts are derived from subducted oceanic crust. If the embedded eclogite thermally reequilibrates with the surrounding plume material, then melt volumes and total extents of melting increase by a additional factor of 2–3. A simple two-dimensional rifting model for a slow spreading ocean basin underlain by a lens of hot plume material shows that plume-related melting occurs over 50–60 m.y. , a much longer period than for flood basalts.
Methane and carbon dioxide exchanges between the atmosphere and northern boreal forest soils

CH4 and CO2 fluxes were measured in upland boreal forest soils near Thompson, Manitoba, from May 16 to September 16, 1994. Most sites consumed atmospheric CH4, fluxes ranging from +0.6 to −2.6 mg CH4 m−2 d−1, and emitted CO2 at rates between 0.2 and 26.8 g CO2 m−2 d−1. There was some evidence of episodic CH4 emissions after heavy rainfall from soils which normally consumed CH4. There were two distinct groups: sites in which both CO2 and CH4 exchange was strong (mean 5.2 g CO2 m−2 d−1, −1.0 mg CH4 m−2 d−1); and those which had a weak exchange of both gases (mean 2.5 g CO2 m−2 d−1, −0.2 mg CH4 m−2 d−1). The presence of black spruce trees, a Sphagnum spp. ground cover and a thick organic layer (20–50 cm) characterized the weak exchange group. These characteristics were indicative of colder, wetter conditions with slower N cycling and longer path lengths to the zone of CH4 oxidation. The strong exchange group had either aspen, jack pine, or birch trees; a vascular plant cover; and a thin organic layer (1–5 cm). These characteristics were indicative of warmer, drier conditions with faster N cycling and shorter path lengths to the zone of CH4 oxidation. The seasonal average of both CO2 and CH4 flux from 11 sites could be predicted by regressions involving the amount of soil organic matter (0–5 cm depth) and seasonal temperature at a depth of 20 cm (r2=0.69 and 0.82, respectively). Using these vegetation characteristics and a Landsat image of the Boreal Ecosystem-Atmosphere Study (BOREAS) northern study area for areal weighting, net gas fluxes were calculated for the upland soils, estimated to be −0.4 mg CH4 m−2 d−1 and 4 g CO2 m−2 d−1.
Multiple Jets of the Antarctic Circumpolar Current South of Australia

Abstract Maps of the gradient of sea surface height (SSH) and sea surface temperature (SST) reveal that the Antarctic Circumpolar Current (ACC) consists of multiple jets or frontal filaments. The braided and patchy nature of the gradient fields seems at odds with the traditional view, derived from hydrographic sections, that the ACC is made up of three continuous circumpolar fronts. By applying a nonlinear fitting procedure to 638 weekly maps of SSH gradient (∇SSH), it is shown that the distribution of maxima in ∇SSH (i.e., fronts) is strongly peaked at particular values of absolute SSH (i.e., streamlines). The association between the jets and particular streamlines persists despite strong topographic and eddy–mean flow interactions, which cause the jets to merge, diverge, and fluctuate in intensity along their path. The SSH values corresponding to each frontal branch are nearly constant over the sector of the Southern Ocean between 100°E and 180°. The front positions inferred from SSH agree closely with .
Influencia del acceso abierto en las revistas de América Latina en el contexto internacional de la ciencia

Los ultimos anos han sido testigos de la emergencia del Acceso Abierto en la comunicacion academica. Este movimiento puede ser agrupado en dos grandes areas: la ruta verde y la ruta dorada. Existen varios estudios que muestran cual ha sido la extension y la magnitud de este fenomeno pero pocos muestran los efectos en terminos de impacto y visibilidad de las revistas teniendo en cuenta tanto la distribucion tematica como la distribucion por regiones geograficas. Este estudio pretende mostrar esta extension y presencia desde la perspectiva de las revistas contenidos en la base de datos Scopus de Elsevier, asi como sus efectos sobre la visibilidad, sobre todo centrada en la region latinoamericana. Los resultados preliminares muestran que a nivel internacional, en todas las disciplinas tematicas la presencia de las revistas ruta verde sobrepasan ampliamente el porcentaje de las revistas ruta dorada. Sin embargo, en las regiones perifericas y en las emergentes en el campo de la ciencia y la tecnologia, la ruta dorada es la que mas predomina y ademas estas revistas suelen aparecer en los ultimas posiciones de las distribuciones de impacto. Con estos datos de contexto, este estudio pretende caracterizar y describir cual es la presencia del acceso abierto en la region latinoamericana a nivel tematico y cuales son sus efectos sobre la visibilidad
Realistic use of two‐error regression treatments as applied to rubidium‐strontium data

Four two-error linear regression treatments have been reported in the literature for use in Rb-Sr geochronology. We have made a general comparison of these treatments and have examined some of the assumptions and concepts implied in their use. For certain cases we show that analytical errors involved in Rb-Sr measurement are normally distributed and uncorrelated and may thus be regressed with any of the four published treatments. Furthermore, by the use of simulated test data, we show that all treatments provide essentially identical regression parameters (slope, intercept, and associated error estimates), provided that the observed scatter can be accounted for solely in terms of the experimental error. Such data are said to define an isochron. Data that possess scatter in excess of experimental error (i.e., geological error) are said to define an errorchron, and for such data the existing treatments may not furnish reliable regression parameters. One of the most important provisions of several of the treatments is a statistical index for distinguishing between isochrons and errorchrons. Use of this index requires an allowance for small-sample statistics based both on the number of samples regressed and on the number of replicates used in calculating the experimental error. As the value chosen for the experimental error also directly affects the final isochron error estimate, a Student's t multiplier (derived from the number of replicates used in calculating the experimental errors) should be applied to the final isochron error estimates.
Investigating Recharge in Arid Alluvial Basin Aquifers: The Pecos Valley Aquifer, Texas

Understanding recharge processes in arid alluvial basins is becoming increasingly important in light of drought and the increasing demand for groundwater as surface water resources become even more scarce. In this study, we investigate recharge to the Pecos Valley Aquifer, one of many alluvial basin aquifers that occur throughout western Texas as well as southwestern United States. The aim of this study is to gain greater understanding of factors controlling (1) spatial distribution of recharge and (2) sources of recharge water in these aquifers. These aims are achieved through investigation of (1) groundwater hydrology, (2) groundwater geochemistry, including isotopes, and (3) results of groundwater flow modeling. This study found that the common practice of using soil properties to predict recharge rates is potentially unreliable, especially in arid climates. These recharge rate predictions are unreliable because infiltration rate measurements are often based on fully saturated soils, which rarely occur naturally in arid climates. This results in a gross over-estimation of recharge rates. Groundwater isotopic compositions in the Pecos Valley Aquifer provide information about the source and spatial distribution of recharge to the aquifer. The isotopes analyzed as part of this study are stable deuterium, oxygen-18, and carbon-13, as well as carbon-14 and tritium. These groundwater isotopes indicate that in some parts of the alluvial basin, recharge water is locally-derived and infiltrates throughout the basin through playas. In other parts of the basin, recharge water is derived from adjacent mountains and recharge occurs along the margins of the basin from ephemeral streams.
Thyroid Nodule Segmentation and Classification in Ultrasound Images

This paper proposes, a novel computer based approach for benign or malignant assessment of thyroid nodules in ultrasound images. Ultrasound imaging is one of the frequently used diagnosis tool to detect and classify abnormalities of the thyroid gland. The proposed approach comprises of four important stages: pre-processing, segmentation, feature extraction and classification. Rayleigh trimmed anisotropic diffusion filter is used for pre-processing. A watershed algorithm is used to segment the nodule region. An artificial neural network (ANN) and support vector machine (SVM) classifiers are employed for the classification task, utilizing feature vectors derived from gray level co-occurrence (GLCM) features. The classification results are evaluated with the use of accuracy, sensitivity and specificity. It is derived that SVM classifier provides better result than ANN for discriminating benign and malignant nodules, obtaining accuracy 92.5%, sensitivity 96.66% and specificity 80%. Keywords— Thyroid Ultrasound; Anisotropic Diffusion; Computer Aided Diagnosis(CAD); Watershed Segmentation; GLCM; SVM; ANN;
A 2 D threshold-voltage model for small MOSFET with quantum-mechanical effects

A threshold condition different from the classical one is proposed for MOSFET with quantum effects, and is based on self-consistent numerical solution of the Schrödinger’s and Poisson’s equations. Furthermore, an accurate 1D threshold-voltage model including polysilicon-depletion effects is built by experimental fitting. Simulated results exhibit good agreement with measurement data. Based on this 1D model, a 2D quantum-modified threshold-voltage model for small MOSFET is developed by solving the quasi-2D Poisson’s equation and taking short-channel effects and quantum-mechanical effects into consideration. The model can also be used for deep-submicron MOSFET with high-k gate-dielectric and reasonable design of device parameters. 2007 Elsevier Ltd. All rights reserved.
True North: Discover Your Authentic Leadership

Acknowledgments. The Authors. Editor's Note (Warren Bennis). Foreword (David Gergen). Introduction: True North. Part One: Leadership Is a Journey. 1. The Journey to Authentic Leadership. 2. Why Leaders Lose Their Way. 3. Transformation From "I" to "We. " Part Two: Discover Your Authentic Leadership. 4. Knowing Your Authentic Self. 5. Practicing Your Values and Principles. 6. What Motivates You to Be a Leader? 7. Building Your Support Team. 8. Staying Grounded: Integrating Your Life. Part Three: Empowering People to Lead. 9. Leadership with Purpose and Passion. 10. Empowering People to Lead. 11. Honing Your Leadership Effectiveness. Epilogue: The Fulfillment of Leadership. Appendixes. A Research Study on Development of Authentic Leaders. B Authentic Leaders Interviewed for True North. C Leadership Exercises for Each Chapter. References. Index.
Oxide and sulphide isograds along a Late Archean, deep‐crustal profile in Tamil Nadu, south India

Oxide–sulphide–Fe–Mg–silicate and titanite–ilmenite textures as well as their mineral compositions have been studied in felsic and intermediate orthogneisses across an amphibolite (north) to granulite facies (south) traverse of lower Archean crust, Tamil Nadu, south India. Titanite is limited to the amphibolite facies terrane where it rims ilmenite or occurs as independent grains. Pyrite is widespread throughout the traverse increasing in abundance with increasing metamorphic grade. Pyrrhotite is confined to the high‐grade granulites. Ilmenite is widespread throughout the traverse increasing in abundance with increasing metamorphic grade and occurring primarily as hemo‐ilmenite in the high‐grade granulite facies rocks. Magnetite is widespread throughout the traverse and is commonly associated with ilmenite. It decreases in abundance with increasing metamorphic grade. In the granulite facies zone, reaction rims of magnetite + quartz occur along Fe–Mg silicate grain boundaries. Magnetite also commonly rims or is associated with pyrite. Both types of reaction rims represent an oxidation effect resulting from the partial subsolidus reduction of the hematite component in ilmenite to magnetite. This is confirmed by the presence of composite three oxide grains consisting of hematite, magnetite and ilmenite. Magnetite and magnetite–pyrite micro‐veins along silicate grain boundaries formed over a wide range of post‐peak metamorphic temperatures and pressures ranging from high‐grade SO2 to low‐grade H2S‐dominated conditions. Oxygen fugacities estimated from the orthopyroxene–magnetite–quartz, orthopyroxene–hematite–quartz, and magnetite–hematite buffers average 2.5 log units above QFM. It is proposed that the trends in mineral assemblages, textures and composition are the result of an external, infiltrating concentrated brine containing an oxidizing component such as CaSO4 during high‐grade metamorphism later acted upon by prograde and retrograde mineral reactions that do not involve an externally derived fluid phase.
Sources of Eddy Energy Simulated by a Model of the Northeast Pacific Ocean

Abstract This paper examines the energy sources for eddy variability in the Gulf of Alaska using a numerical model and a novel form of data assimilation referred to as spectral nudging. Spectral nudging is distinguished from conventional nudging by its ability to operate only on specified frequency and wavenumber bands; in the present case, only the subannual variability is nudged, and only on spatial scales of 100 km or more. By using this approach, the broad-brush aspects of the model’s mean state are constrained to remain near the mean climatological conditions, while the simulated eddy field is determined by the model dynamics. Simulations of the North Pacific Ocean with a 0.25° horizontal resolution and spectral nudging have been previously shown to produce eddy fields that are significantly more energetic and more realistic than those produced by prognostic (i.e., not nudged) simulations. The analysis of the spectrally nudged model results undertaken here reveals the tendency of the circulation to b.
Heat flow and seismic observations in the northwestern Banda Arc

Results of heat flow measurements in the centers of three basins in the NW Banda Arc carried out during the Indonesian-Dutch Snellius II expedition in 1985 all show high heat flow values. The average heat flow in the north Buru basin, on the outside of the arc, is 161 mW/m2. Two small, NS to NW-SE elongated subbasins situated in the Lucipara basin show heat flow values of 175 and 134, mW/m2, respectively. The high heat flow measured in both the north Buru and Lucipara basins is interpreted to be the result of recent EW strike-slip movement in the northwestern Banda Arc.
An application of tramo-seats: changes in seasonality and current trend-cycle assessment

The paper details an application of programs TRAMO and SEATS to seasonal adjustment and trend-cycle estimation of the German Retail Trade Turnover series. When adjusting with X12-ARIMA, the Bundesbank identified two problems: heteroscedasticity in the seasonal component, associated with different moving patterns for some of the months, and unstability of the trend-cycle at the end of the series. It is seen how, starting with the fully automatic procedure and adding some simple modifications, TRAMO and SEATS deal properly with both problems, and provide good, stable, and robust results.