Gradient Descent: The Ultimate Optimizer

Working with any gradient-based machine learning algorithm involves the tedious task of tuning the optimizer's hyperparameters, such as the learning rate. There exist many techniques for automated hyperparameter optimization, but they typically introduce even more hyperparameters to control the hyperparameter optimization process. We propose to instead learn the hyperparameters themselves by gradient descent, and furthermore to learn the hyper-hyperparameters by gradient descent as well, and so on ad infinitum. As these towers of gradient-based optimizers grow, they become significantly less sensitive to the choice of top-level hyperparameters, hence decreasing the burden on the user to search for optimal values

A model for the formation energies of alanates and boranates

We develop a simple model for the formation energies (FEs) of alkali and lkaline earth alanates and boranates, based upon ionic bonding between metal cations and (AlH4)- or (BH4)- anions. The FEs agree well with values obtained from first principles calculations and with experimental FEs. The model shows that details of the crystal structure are relatively unimportant. The small size of the (BH4)- anion causes a strong bonding in the crystal, which makes boranates more stable than alanates. Smaller alkali or alkaline earth cations do not give an increased FE. They involve a larger ionization potential that compensates for the increased crystal bonding.Comment: 3 pages, 2 figure

W-Nb-O oxides with tunable acid properties as efficient catalysts for the transformation of biomass-derived oxygenates in aqueous systems

[EN] W-Nb-O oxide bronzes, prepared hydrothermally, have been characterized and studied as catalysts for both the gas-phase dehydration of glycerol and the liquid-phase selective condensation of light oxygenates derived from primary treatments of biomass (a mixture containing acetic acid, ethanol, propanal, hydroxyacetone and water). By controlling the nominal composition of the catalysts, it is possible to tune their textural and acid properties (concentration and nature of acid sites) to selectively produce acrolein from glycerol or C-5-C-10 hydrocarbons (with low O contents and with high yields) from light oxygenates. Interestingly, these catalysts are stable when working in gas phase reactions and they are re-usable, with high resistance to leaching, when working in aqueous media.Financial support by the Spanish Government (CTQ-2015-68951-C3-1, CTQ-2015-67592, MAT2016-78362-C4-4-R and SEV-2016-0683) and Generalitat Valenciana (GVA, PROMETEO/2018/006) is gratefully acknowledged. A. F.-A. and D. D. thank the "La Caixa-Severo Ochoa" Foundation and Severo Ochoa Excellence Program (SVP-2016-0683), respectively, for their fellowships. The authors thank the ICTS Centro Nacional de Microscopia Electronica (UCM) for instrumental facilities.Delgado-Muñoz, D.; Fernández-Arroyo, A.; Domine, ME.; García-González, E.; López Nieto, JM. (2019). W-Nb-O oxides with tunable acid properties as efficient catalysts for the transformation of biomass-derived oxygenates in aqueous systems. Catalysis Science & Technology. 9(12):3126-3136. https://doi.org/10.1039/c9cy00367cS31263136912Huber, G. W., Iborra, S., & Corma, A. (2006). Synthesis of Transportation Fuels from Biomass:  Chemistry, Catalysts, and Engineering. Chemical Reviews, 106(9), 4044-4098. doi:10.1021/cr068360dCorma, A., Iborra, S., & Velty, A. (2007). Chemical Routes for the Transformation of Biomass into Chemicals. Chemical Reviews, 107(6), 2411-2502. doi:10.1021/cr050989dTuck, C. O., Perez, E., Horvath, I. T., Sheldon, R. 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Catalysis Science & Technology, 7(1), 243-250. doi:10.1039/c6cy02198kLa Salvia, N., Delgado, D., Ruiz-Rodríguez, L., Nadji, L., Massó, A., & Nieto, J. M. L. (2017). V- and Nb-containing tungsten bronzes catalysts for the aerobic transformation of ethanol and glycerol. Bulk and supported materials. Catalysis Today, 296, 2-9. doi:10.1016/j.cattod.2017.04.009Chieregato, A., Basile, F., Concepción, P., Guidetti, S., Liosi, G., Soriano, M. D., … Nieto, J. M. L. (2012). Glycerol oxidehydration into acrolein and acrylic acid over W–V–Nb–O bronzes with hexagonal structure. Catalysis Today, 197(1), 58-65. doi:10.1016/j.cattod.2012.06.024Chieregato, A., Soriano, M. D., García-González, E., Puglia, G., Basile, F., Concepción, P., … Cavani, F. (2014). Multielement Crystalline and Pseudocrystalline Oxides as Efficient Catalysts for the Direct Transformation of Glycerol into Acrylic Acid. ChemSusChem, 8(2), 398-406. doi:10.1002/cssc.201402721Chieregato, A., Bandinelli, C., Concepción, P., Soriano, M. D., Puzzo, F., Basile, F., … Nieto, J. M. L. (2016). Structure-Reactivity Correlations in Vanadium-Containing Catalysts for One-Pot Glycerol Oxidehydration to Acrylic Acid. ChemSusChem, 10(1), 234-244. doi:10.1002/cssc.201600954Deleplanque, J., Dubois, J.-L., Devaux, J.-F., & Ueda, W. (2010). Production of acrolein and acrylic acid through dehydration and oxydehydration of glycerol with mixed oxide catalysts. Catalysis Today, 157(1-4), 351-358. doi:10.1016/j.cattod.2010.04.012Delgado, D., Chieregato, A., Soriano, M. D., Rodríguez-Aguado, E., Ruiz-Rodríguez, L., Rodríguez-Castellón, E., & López Nieto, J. M. (2018). Influence of Phase Composition of Bulk Tungsten Vanadium Oxides on the Aerobic Transformation of Methanol and Glycerol. European Journal of Inorganic Chemistry, 2018(10), 1204-1211. doi:10.1002/ejic.201800059Pham, T. N., Sooknoi, T., Crossley, S. 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Experimental and theoretical assessment of the mechanism and site requirements for ketonization of carboxylic acids on oxides. Journal of Catalysis, 345, 183-206. doi:10.1016/j.jcat.2016.11.006Wang, S., Goulas, K., & Iglesia, E. (2016). Condensation and esterification reactions of alkanals, alkanones, and alkanols on TiO2: Elementary steps, site requirements, and synergistic effects of bifunctional strategies. Journal of Catalysis, 340, 302-320. doi:10.1016/j.jcat.2016.05.026Fernández-Arroyo, A., Delgado, D., Domine, M. E., & López-Nieto, J. M. (2017). Upgrading of oxygenated compounds present in aqueous biomass-derived feedstocks over NbOx-based catalysts. Catalysis Science & Technology, 7(23), 5495-5499. doi:10.1039/c7cy00916jNakajima, K., Hirata, J., Kim, M., Gupta, N. K., Murayama, T., Yoshida, A., … Ueda, W. (2017). Facile Formation of Lactic Acid from a Triose Sugar in Water over Niobium Oxide with a Deformed Orthorhombic Phase. ACS Catalysis, 8(1), 283-290. doi:10.1021/acscatal.7b03003Goto, Y., Shimizu, K., Kon, K., Toyao, T., Murayama, T., & Ueda, W. (2016). NH3-efficient ammoxidation of toluene by hydrothermally synthesized layered tungsten-vanadium complex metal oxides. Journal of Catalysis, 344, 346-353. doi:10.1016/j.jcat.2016.10.013Omata, K., Matsumoto, K., Murayama, T., & Ueda, W. (2016). Direct oxidative transformation of glycerol to acrylic acid over Nb-based complex metal oxide catalysts. Catalysis Today, 259, 205-212. doi:10.1016/j.cattod.2015.07.016Blanch-Raga, N., Soriano, M. D., Palomares, A. E., Concepción, P., Martínez-Triguero, J., & Nieto, J. M. L. (2013). Catalytic abatement of trichloroethylene over Mo and/or W-based bronzes. Applied Catalysis B: Environmental, 130-131, 36-43. doi:10.1016/j.apcatb.2012.10.016BOTELLA, P. (2004). Selective oxidative dehydrogenation of ethane on MoVTeNbO mixed metal oxide catalysts. 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Molecular Evolution of HIV-1 CRF01_AE Env in Thai Patients

BACKGROUND: The envelope glycoproteins (Env), gp120 and gp41, are the most variable proteins of human immunodeficiency virus type 1 (HIV-1), and are the major targets of humoral immune responses against HIV-1. A circulating recombinant form of HIV-1, CRF01_AE, is prevalent throughout Southeast Asia; however, only limited information regarding the immunological characteristics of CRF01_AE Env is currently available. In this study, we attempted to examine the evolutionary pattern of CRF01_AE Env under the selection pressure of host immune responses. METHODOLOGY/PRINCIPAL FINDINGS: Peripheral blood samples were collected periodically over 3 years from 15 HIV-1-infected individuals residing in northern Thailand, and amplified env genes from the samples were subjected to computational analysis. The V5 region of gp120 showed highest variability in several samples over 3 years, whereas the V1/V2 and/or V4 regions of gp120 also showed high variability in many samples. In addition, the N-terminal part of the C3 region of gp120 showed highest amino acid diversity among the conserved regions of gp120. Chronological changes in the numbers of amino acid residues in gp120 variable regions and potential N-linked glycosylation (PNLG) sites are involved in increasing the variability of Env gp120. Furthermore, the C3 region contained several amino acid residues potentially under positive selection, and APOBEC3 family protein-mediated G to A mutations were frequently detected in such residues. CONCLUSIONS/SIGNIFICANCE: Several factors, including amino acid substitutions particularly in gp120 C3 and V5 regions as well as changes in the number of PNLG sites and in the length of gp120 variable regions, were revealed to be involved in the molecular evolution of CRF01_AE Env. In addition, a similar tendency was observed between CRF01_AE and subtype C Env with regard to the amino acid variation of gp120 V3 and C3 regions. These results may provide important information for understanding the immunological characteristics of CRF01_AE Env

Multi-messenger observations of a binary neutron star merger

On 2017 August 17 a binary neutron star coalescence candidate (later designated GW170817) with merger time 12:41:04 UTC was observed through gravitational waves by the Advanced LIGO and Advanced Virgo detectors. The Fermi Gamma-ray Burst Monitor independently detected a gamma-ray burst (GRB 170817A) with a time delay of ~1.7 s with respect to the merger time. From the gravitational-wave signal, the source was initially localized to a sky region of 31 deg2 at a luminosity distance of 40+8-8 Mpc and with component masses consistent with neutron stars. The component masses were later measured to be in the range 0.86 to 2.26 Mo. An extensive observing campaign was launched across the electromagnetic spectrum leading to the discovery of a bright optical transient (SSS17a, now with the IAU identification of AT 2017gfo) in NGC 4993 (at ~40 Mpc) less than 11 hours after the merger by the One- Meter, Two Hemisphere (1M2H) team using the 1 m Swope Telescope. The optical transient was independently detected by multiple teams within an hour. Subsequent observations targeted the object and its environment. Early ultraviolet observations revealed a blue transient that faded within 48 hours. Optical and infrared observations showed a redward evolution over ~10 days. Following early non-detections, X-ray and radio emission were discovered at the transient’s position ~9 and ~16 days, respectively, after the merger. Both the X-ray and radio emission likely arise from a physical process that is distinct from the one that generates the UV/optical/near-infrared emission. No ultra-high-energy gamma-rays and no neutrino candidates consistent with the source were found in follow-up searches. These observations support the hypothesis that GW170817 was produced by the merger of two neutron stars in NGC4993 followed by a short gamma-ray burst (GRB 170817A) and a kilonova/macronova powered by the radioactive decay of r-process nuclei synthesized in the ejecta

Narrowband Searches for Continuous and Long-duration Transient Gravitational Waves from Known Pulsars in the LIGO-Virgo Third Observing Run

Isolated neutron stars that are asymmetric with respect to their spin axis are possible sources of detectable continuous gravitational waves. This paper presents a fully coherent search for such signals from eighteen pulsars in data from LIGO and Virgo's third observing run (O3). For known pulsars, efficient and sensitive matched-filter searches can be carried out if one assumes the gravitational radiation is phase-locked to the electromagnetic emission. In the search presented here, we relax this assumption and allow both the frequency and the time derivative of the frequency of the gravitational waves to vary in a small range around those inferred from electromagnetic observations. We find no evidence for continuous gravitational waves, and set upper limits on the strain amplitude for each target. These limits are more constraining for seven of the targets than the spin-down limit defined by ascribing all rotational energy loss to gravitational radiation. In an additional search, we look in O3 data for long-duration (hours-months) transient gravitational waves in the aftermath of pulsar glitches for six targets with a total of nine glitches. We report two marginal outliers from this search, but find no clear evidence for such emission either. The resulting duration-dependent strain upper limits do not surpass indirect energy constraints for any of these targets. © 2022. The Author(s). Published by the American Astronomical Society

A molecular analysis of desiccation tolerance mechanisms in the anhydrobiotic nematode Panagrolaimus superbus using expressed sequenced tags

<p>Abstract</p> <p>Background</p> <p>Some organisms can survive extreme desiccation by entering into a state of suspended animation known as anhydrobiosis. <it>Panagrolaimus superbus </it>is a free-living anhydrobiotic nematode that can survive rapid environmental desiccation. The mechanisms that <it>P. superbus </it>uses to combat the potentially lethal effects of cellular dehydration may include the constitutive and inducible expression of protective molecules, along with behavioural and/or morphological adaptations that slow the rate of cellular water loss. In addition, inducible repair and revival programmes may also be required for successful rehydration and recovery from anhydrobiosis.</p> <p>Results</p> <p>To identify constitutively expressed candidate anhydrobiotic genes we obtained 9,216 ESTs from an unstressed mixed stage population of <it>P. superbus</it>. We derived 4,009 unigenes from these ESTs. These unigene annotations and sequences can be accessed at <url>http://www.nematodes.org/nembase4/species_info.php?species=PSC</url>. We manually annotated a set of 187 constitutively expressed candidate anhydrobiotic genes from <it>P. superbus</it>. Notable among those is a putative lineage expansion of the <it>lea </it>(late embryogenesis abundant) gene family. The most abundantly expressed sequence was a member of the nematode specific <it>sxp/ral-2 </it>family that is highly expressed in parasitic nematodes and secreted onto the surface of the nematodes' cuticles. There were 2,059 novel unigenes (51.7% of the total), 149 of which are predicted to encode intrinsically disordered proteins lacking a fixed tertiary structure. One unigene may encode an exo-β-1,3-glucanase (GHF5 family), most similar to a sequence from <it>Phytophthora infestans</it>. GHF5 enzymes have been reported from several species of plant parasitic nematodes, with horizontal gene transfer (HGT) from bacteria proposed to explain their evolutionary origin. This <it>P. superbus </it>sequence represents another possible HGT event within the Nematoda. The expression of five of the 19 putative stress response genes tested was upregulated in response to desiccation. These were the antioxidants <it>glutathione peroxidase, dj-1 </it>and <it>1-Cys peroxiredoxin</it>, an <it>shsp </it>sequence and an <it>lea </it>gene.</p> <p>Conclusions</p> <p><it>P. superbus </it>appears to utilise a strategy of combined constitutive and inducible gene expression in preparation for entry into anhydrobiosis. The apparent lineage expansion of <it>lea </it>genes, together with their constitutive and inducible expression, suggests that LEA3 proteins are important components of the anhydrobiotic protection repertoire of <it>P. superbus</it>.</p

Tree diversity and above-ground biomass in the South America Cerrado biome and their conservation implications

Less than half of the original two million square kilometers of the Cerrado vegetation remains standing, and there are still many uncertainties as to how to conserve and prioritize remaining areas effectively. A key limitation is the continuing lack of geographically-extensive evaluation of ecosystem-level properties across the biome. Here we sought to address this gap by comparing the woody vegetation of the typical cerrado of the Cerrado–Amazonia Transition with that of the core area of the Cerrado in terms of both tree diversity and vegetation biomass. We used 21 one-hectare plots in the transition and 18 in the core to compare key structural parameters (tree height, basal area, and above-ground biomass), and diversity metrics between the regions. We also evaluated the effects of temperature and precipitation on biomass, as well as explored the species diversity versus biomass relationship. We found, for the first time, both that the typical cerrado at the transition holds substantially more biomass than at the core, and that higher temperature and greater precipitation can explain this difference. By contrast, plot-level alpha diversity was almost identical in the two regions. Finally, contrary to some theoretical expectations, we found no positive relationship between species diversity and biomass for the Cerrado woody vegetation. This has implications for the development of effective conservation measures, given that areas with high biomass and importance for the compensation of greenhouse gas emissions are often not those with the greatest diversity