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1. Validating the Galaxy and Quasar Catalog-Level Blinding Scheme for the DESI 2024 analysis

Author

Andrade, U., Mena-Fernández, J., Awan, H., Ross, A. J., Brieden, S., Pan, J., de Mattia, A., Aguilar, J., Ahlen, S., Alves, O., Brooks, D., Buckley-Geer, E., Chaussidon, E., Claybaugh, T., Cole, S., de la Macorra, A., Dey, Arjun, Doel, P., Fanning, K., Forero-Romero, J. E., Gaztañaga, E., Gil-Marín, H., Gontcho, S. Gontcho A, Guy, J., Hahn, C., Hanif, M. M. S, Honscheid, K., Howlett, C., Huterer, D., Juneau, S., Kremin, A., Landriau, M., Guillou, L. Le, Levi, M. E., Manera, M., Martini, P., Meisner, A., Miquel, R., Moustakas, J., Mueller, E., Muñoz-Gutiérrez, A., Myers, A. D., Nadathur, S., Newman, J. A., Nie, J., Niz, G., Palanque-Delabrouille, N., Percival, W. J., Pinon, M., Poppett, C., Prada, F., Rashkovetskyi, M., Rezaie, M., Rossi, G., Sanchez, E., Schlegel, D., Schubnell, M., Seo, H., Sprayberry, D., Tarlé, G., Vargas-Magaña, M., Verde, L., and Weaver, B. A.

Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

In the era of precision cosmology, ensuring the integrity of data analysis through blinding techniques is paramount -- a challenge particularly relevant for the Dark Energy Spectroscopic Instrument (DESI). DESI represents a monumental effort to map the cosmic web, with the goal to measure the redshifts of tens of millions of galaxies and quasars. Given the data volume and the impact of the findings, the potential for confirmation bias poses a significant challenge. To address this, we implement and validate a comprehensive blind analysis strategy for DESI Data Release 1 (DR1), tailored to the specific observables DESI is most sensitive to: Baryonic Acoustic Oscillations (BAO), Redshift-Space Distortion (RSD) and primordial non-Gaussianities (PNG). We carry out the blinding at the catalog level, implementing shifts in the redshifts of the observed galaxies to blind for BAO and RSD signals and weights to blind for PNG through a scale-dependent bias. We validate the blinding technique on mocks, as well as on data by applying a second blinding layer to perform a battery of sanity checks. We find that the blinding strategy alters the data vector in a controlled way such that the BAO and RSD analysis choices do not need any modification before and after unblinding. The successful validation of the blinding strategy paves the way for the unblinded DESI DR1 analysis, alongside future blind analyses with DESI and other surveys., Comment: Supporting publication of "DESI 2024 II: Sample definitions, characteristics, and two-point clustering statistics", "DESI 2024 III: Baryon Acoustic Oscillations from Galaxies and Quasars", and "DESI 2024 V: Analysis of the full shape of two-point clustering statistics from galaxies and quasars". (v2 - update DESI references)

Published
2024

2. Production of Alternate Realizations of DESI Fiber Assignment for Unbiased Clustering Measurement in Data and Simulations

Author

Lasker, J., Rosell, A. Carnero, Myers, A. D., Ross, A. J., Bianchi, D., Hanif, M. M. S, Kehoe, R., de Mattia, A., Napolitano, L., Percival, W. J., Staten, R., Aguilar, J., Ahlen, S., Bigwood, L., Brooks, D., Claybaugh, T., Cole, S., de la Macorra, A., Ding, Z., Doel, P., Fanning, K., Forero-Romero, J. E., Gaztañaga, E., Gontcho, S. Gontcho A, Gutierrez, G., Honscheid, K., Howlett, C., Juneau, S., Kremin, A., Landriau, M., Guillou, L. Le, Levi, M. E., Manera, M., Meisner, A., Miquel, R., Moustakas, J., Mueller, E., Nie, J., Niz, G., Oh, M., Palanque-Delabrouille, N., Poppett, C., Prada, F., Rezaie, M., Rossi, G., Sanchez, E., Schlegel, D., Schubnell, M., Seo, H., Sprayberry, D., Tarlé, G., Vargas-Magaña, M., Weaver, B. A., Wilson, Michael J., and Zheng, Y.

Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics
Abstract

A critical requirement of spectroscopic large scale structure analyses is correcting for selection of which galaxies to observe from an isotropic target list. This selection is often limited by the hardware used to perform the survey which will impose angular constraints of simultaneously observable targets, requiring multiple passes to observe all of them. In SDSS this manifested solely as the collision of physical fibers and plugs placed in plates. In DESI, there is the additional constraint of the robotic positioner which controls each fiber being limited to a finite patrol radius. A number of approximate methods have previously been proposed to correct the galaxy clustering statistics for these effects, but these generally fail on small scales. To accurately correct the clustering we need to upweight pairs of galaxies based on the inverse probability that those pairs would be observed (Bianchi \& Percival 2017). This paper details an implementation of that method to correct the Dark Energy Spectroscopic Instrument (DESI) survey for incompleteness. To calculate the required probabilities, we need a set of alternate realizations of DESI where we vary the relative priority of otherwise identical targets. These realizations take the form of alternate Merged Target Ledgers (AMTL), the files that link DESI observations and targets. We present the method used to generate these alternate realizations and how they are tracked forward in time using the real observational record and hardware status, propagating the survey as though the alternate orderings had been adopted. We detail the first applications of this method to the DESI One-Percent Survey (SV3) and the DESI year 1 data. We include evaluations of the pipeline outputs, estimation of survey completeness from this and other methods, and validation of the method using mock galaxy catalogs., Comment: 30 pages, 21 figures

Published
2024

3. DESI 2024 VI: Cosmological Constraints from the Measurements of Baryon Acoustic Oscillations

Author

DESI Collaboration, Adame, A. G., Aguilar, J., Ahlen, S., Alam, S., Alexander, D. M., Alvarez, M., Alves, O., Anand, A., Andrade, U., Armengaud, E., Avila, S., Aviles, A., Awan, H., Bahr-Kalus, B., Bailey, S., Baltay, C., Bault, A., Behera, J., BenZvi, S., Bera, A., Beutler, F., Bianchi, D., Blake, C., Blum, R., Brieden, S., Brodzeller, A., Brooks, D., Buckley-Geer, E., Burtin, E., Calderon, R., Canning, R., Rosell, A. Carnero, Cereskaite, R., Cervantes-Cota, J. L., Chabanier, S., Chaussidon, E., Chaves-Montero, J., Chen, S., Chen, X., Claybaugh, T., Cole, S., Cuceu, A., Davis, T. M., Dawson, K., de la Macorra, A., de Mattia, A., Deiosso, N., Dey, A., Dey, B., Ding, Z., Doel, P., Edelstein, J., Eftekharzadeh, S., Eisenstein, D. J., Elliott, A., Fagrelius, P., Fanning, K., Ferraro, S., Ereza, J., Findlay, N., Flaugher, B., Font-Ribera, A., Forero-Sánchez, D., Forero-Romero, J. E., Frenk, C. S., Garcia-Quintero, C., Gaztañaga, E., Gil-Marín, H., Gontcho, S. Gontcho A, Gonzalez-Morales, A. X., Gonzalez-Perez, V., Gordon, C., Green, D., Gruen, D., Gsponer, R., Gutierrez, G., Guy, J., Hadzhiyska, B., Hahn, C., Hanif, M. M. S, Herrera-Alcantar, H. K., Honscheid, K., Howlett, C., Huterer, D., Iršič, V., Ishak, M., Juneau, S., Karaçaylı, N. G., Kehoe, R., Kent, S., Kirkby, D., Kremin, A., Krolewski, A., Lai, Y., Lan, T. -W., Landriau, M., Lang, D., Lasker, J., Goff, J. M. Le, Guillou, L. Le, Leauthaud, A., Levi, M. E., Li, T. S., Linder, E., Lodha, K., Magneville, C., Manera, M., Margala, D., Martini, P., Maus, M., McDonald, P., Medina-Varela, L., Meisner, A., Mena-Fernández, J., Miquel, R., Moon, J., Moore, S., Moustakas, J., Mudur, N., Mueller, E., Muñoz-Gutiérrez, A., Myers, A. D., Nadathur, S., Napolitano, L., Neveux, R., Newman, J. A., Nguyen, N. M., Nie, J., Niz, G., Noriega, H. E., Padmanabhan, N., Paillas, E., Palanque-Delabrouille, N., Pan, J., Penmetsa, S., Percival, W. J., Pieri, M. M., Pinon, M., Poppett, C., Porredon, A., Prada, F., Pérez-Fernández, A., Pérez-Ràfols, I., Rabinowitz, D., Raichoor, A., Ramírez-Pérez, C., Ramirez-Solano, S., Ravoux, C., Rashkovetskyi, M., Rezaie, M., Rich, J., Rocher, A., Rockosi, C., Roe, N. A., Rosado-Marin, A., Ross, A. J., Rossi, G., Ruggeri, R., Ruhlmann-Kleider, V., Samushia, L., Sanchez, E., Saulder, C., Schlafly, E. F., Schlegel, D., Schubnell, M., Seo, H., Shafieloo, A., Sharples, R., Silber, J., Slosar, A., Smith, A., Sprayberry, D., Tan, T., Tarlé, G., Taylor, P., Trusov, S., Ureña-López, L. A., Vaisakh, R., Valcin, D., Valdes, F., Vargas-Magaña, M., Verde, L., Walther, M., Wang, B., Wang, M. S., Weaver, B. A., Weaverdyck, N., Wechsler, R. H., Weinberg, D. H., White, M., Yu, J., Yu, Y., Yuan, S., Yèche, C., Zaborowski, E. A., Zarrouk, P., Zhang, H., Zhao, C., Zhao, R., Zhou, R., Zhuang, T., and Zou, H.

Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

We present cosmological results from the measurement of baryon acoustic oscillations (BAO) in galaxy, quasar and Lyman-$\alpha$ forest tracers from the first year of observations from the Dark Energy Spectroscopic Instrument (DESI), to be released in the DESI Data Release 1. DESI BAO provide robust measurements of the transverse comoving distance and Hubble rate, or their combination, relative to the sound horizon, in seven redshift bins from over 6 million extragalactic objects in the redshift range $0.1-1$ and $w_a<0$. This preference is 2.6$\sigma$ for the DESI+CMB combination, and persists or grows when SN~Ia are added in, giving results discrepant with the $\Lambda$CDM model at the $2.5\sigma$, $3.5\sigma$ or $3.9\sigma$ levels for the addition of Pantheon+, Union3, or DES-SN5YR datasets respectively. For the flat $\Lambda$CDM model with the sum of neutrino mass $\sum m_\nu$ free, combining the DESI and CMB data yields an upper limit $\sum m_\nu < 0.072$ $(0.113)$ eV at 95% confidence for a $\sum m_\nu>0$ $(\sum m_\nu>0.059)$ eV prior. These neutrino-mass constraints are substantially relaxed in models beyond $\Lambda$CDM. [Abridged.], Comment: This DESI Collaboration Key Publication is part of the 2024 publication series using the first year of observations (see https://data.desi.lbl.gov/doc/papers). Typos corrected and a new figure and discussion added to Appendix A

Published
2024

4. DESI 2024 IV: Baryon Acoustic Oscillations from the Lyman Alpha Forest

Author

DESI Collaboration, Adame, A. G., Aguilar, J., Ahlen, S., Alam, S., Alexander, D. M., Alvarez, M., Alves, O., Anand, A., Andrade, U., Armengaud, E., Avila, S., Aviles, A., Awan, H., Bailey, S., Baltay, C., Bault, A., Bautista, J., Behera, J., BenZvi, S., Beutler, F., Bianchi, D., Blake, C., Blum, R., Brieden, S., Brodzeller, A., Brooks, D., Buckley-Geer, E., Burtin, E., Calderon, R., Canning, R., Rosell, A. Carnero, Cereskaite, R., Cervantes-Cota, J. L., Chabanier, S., Chaussidon, E., Chaves-Montero, J., Chen, S., Chen, X., Claybaugh, T., Cole, S., Cuceu, A., Davis, T. M., Dawson, K., de la Cruz, R., de la Macorra, A., de Mattia, A., Deiosso, N., Dey, A., Dey, B., Ding, J., Ding, Z., Doel, P., Edelstein, J., Eftekharzadeh, S., Eisenstein, D. J., Elliott, A., Fagrelius, P., Fanning, K., Ferraro, S., Ereza, J., Findlay, N., Flaugher, B., Font-Ribera, A., Forero-Sánchez, D., Forero-Romero, J. E., Garcia-Quintero, C., Gaztañaga, E., Gil-Marín, H., Gontcho, S. Gontcho A, Gonzalez-Morales, A. X., Gonzalez-Perez, V., Gordon, C., Green, D., Gruen, D., Gsponer, R., Gutierrez, G., Guy, J., Hadzhiyska, B., Hahn, C., Hanif, M. M. S, Herrera-Alcantar, H. K., Honscheid, K., Howlett, C., Huterer, D., Iršič, V., Ishak, M., Juneau, S., Karaçayli, N. G., Kehoe, R., Kent, S., Kirkby, D., Kremin, A., Krolewski, A., Lai, Y., Lan, T. -W., Landriau, M., Lang, D., Lasker, J., Goff, J. M. Le, Guillou, L. Le, Leauthaud, A., Levi, M. E., Li, T. S., Linder, E., Lodha, K., Magneville, C., Manera, M., Margala, D., Martini, P., Maus, M., McDonald, P., Medina-Varela, L., Meisner, A., Mena-Fernández, J., Miquel, R., Moon, J., Moore, S., Moustakas, J., Mueller, E., Muñoz-Gutiérrez, A., Myers, A. D., Nadathur, S., Napolitano, L., Neveux, R., Newman, J. A., Nguyen, N. M., Nie, J., Niz, G., Noriega, H. E., Padmanabhan, N., Paillas, E., Palanque-Delabrouille, N., Pan, J., Penmetsa, S., Percival, W. J., Pieri, M. M., Pinon, M., Poppett, C., Porredon, A., Prada, F., Pérez-Fernández, A., Pérez-Ràfols, I., Rabinowitz, D., Raichoor, A., Ramírez-Pérez, C., Ramirez-Solano, S., Rashkovetskyi, M., Ravoux, C., Rezaie, M., Rich, J., Rocher, A., Rockosi, C., Roe, N. A., Rosado-Marin, A., Ross, A. J., Rossi, G., Ruggeri, R., Ruhlmann-Kleider, V., Samushia, L., Sanchez, E., Saulder, C., Schlafly, E. F., Schlegel, D., Schubnell, M., Seo, H., Sharples, R., Silber, J., Sinigaglia, F., Slosar, A., Smith, A., Sprayberry, D., Tan, T., Tarlé, G., Trusov, S., Vaisakh, R., Valcin, D., Valdes, F., Vargas-Magaña, M., Verde, L., Walther, M., Wang, B., Wang, M. S., Weaver, B. A., Weaverdyck, N., Wechsler, R. H., Weinberg, D. H., White, M., Yu, J., Yu, Y., Yuan, S., Yèche, C., Zaborowski, E. A., Zarrouk, P., Zhang, H., Zhao, C., Zhao, R., Zhou, R., and Zou, H.

Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

We present the measurement of Baryon Acoustic Oscillations (BAO) from the Lyman-$\alpha$ (Ly$\alpha$) forest of high-redshift quasars with the first-year dataset of the Dark Energy Spectroscopic Instrument (DESI). Our analysis uses over $420\,000$ Ly$\alpha$ forest spectra and their correlation with the spatial distribution of more than $700\,000$ quasars. An essential facet of this work is the development of a new analysis methodology on a blinded dataset. We conducted rigorous tests using synthetic data to ensure the reliability of our methodology and findings before unblinding. Additionally, we conducted multiple data splits to assess the consistency of the results and scrutinized various analysis approaches to confirm their robustness. For a given value of the sound horizon ($r_d$), we measure the expansion at $z_{\rm eff}=2.33$ with 2\% precision, $H(z_{\rm eff}) = (239.2 \pm 4.8) (147.09~{\rm Mpc} /r_d)$ km/s/Mpc. Similarly, we present a 2.4\% measurement of the transverse comoving distance to the same redshift, $D_M(z_{\rm eff}) = (5.84 \pm 0.14) (r_d/147.09~{\rm Mpc})$ Gpc. Together with other DESI BAO measurements at lower redshifts, these results are used in a companion paper to constrain cosmological parameters., Comment: This DESI Collaboration Key Publication is part of the 2024 publication series using the first year of observations (see https://data.desi.lbl.gov/doc/papers). Minor changes in v4, version accepted for publication in JCAP

Published
2024

5. Optimal Reconstruction of Baryon Acoustic Oscillations for DESI 2024

Author

Paillas, E., Ding, Z., Chen, X., Seo, H., Padmanabhan, N., de Mattia, A., Ross, A. J., Nadathur, S., Howlett, C., Aguilar, J., Ahlen, S., Alves, O., Andrade, U., Brooks, D., Buckley-Geer, E., Burtin, E., Chen, S., Claybaugh, T., Cole, S., Dawson, K., de la Macorra, A., Dey, Arjun, Doel, P., Fanning, K., Ferraro, S., Forero-Romero, J. E., Garcia-Quintero, C., Gaztañaga, E., Gil-Marín, H., Gontcho, S. Gontcho A, Gutierrez, G., Hahn, C., Hanif, M. M. S, Honscheid, K., Ishak, M., Kehoe, R., Kremin, A., Landriau, M., Guillou, L. Le, Levi, M. E., Manera, M., Martini, P., Medina-Varela, L., Meisner, A., Mena-Fernández, J., Miquel, R., Moustakas, J., Mueller, E., Muñoz-Gutiérrez, A., Myers, A. D., Newman, J. A., Nie, J., Niz, G., Palanque-Delabrouille, N., Percival, W. J., Poppett, C., Prada, F., Pérez-Fernández, A., Rashkovetskyi, M., Rezaie, M., Rosado-Marin, A., Rossi, G., Ruggeri, R., Sanchez, E., Saulder, C., Schlafly, E. F., Schlegel, D., Schubnell, M., Sprayberry, D., Tarlé, G., Valcin, D., Vargas-Magaña, M., Yu, J., Yuan, S., Zhou, R., and Zou, H.

Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

Baryon acoustic oscillations (BAO) provide a robust standard ruler to measure the expansion history of the Universe through galaxy clustering. Density-field reconstruction is now a widely adopted procedure for increasing the precision and accuracy of the BAO detection. With the goal of finding the optimal reconstruction settings to be used in the DESI 2024 galaxy BAO analysis, we assess the sensitivity of the post-reconstruction BAO constraints to different choices in our analysis configuration, performing tests on blinded data from the first year of DESI observations (DR1), as well as on mocks that mimic the expected clustering and selection properties of the DESI DR1 target samples. Overall, we find that BAO constraints remain robust against multiple aspects in the reconstruction process, including the choice of smoothing scale, treatment of redshift-space distortions, fiber assignment incompleteness, and parameterizations of the BAO model. We also present a series of tests that DESI followed in order to assess the maturity of the end-to-end galaxy BAO pipeline before the unblinding of the large-scale structure catalogs., Comment: Supporting publication of DESI 2024 III: Baryon Acoustic Oscillations from Galaxies and Quasars

Published
2024

6. DESI 2024 III: Baryon Acoustic Oscillations from Galaxies and Quasars

Author

DESI Collaboration, Adame, A. G., Aguilar, J., Ahlen, S., Alam, S., Alexander, D. M., Alvarez, M., Alves, O., Anand, A., Andrade, U., Armengaud, E., Avila, S., Aviles, A., Awan, H., Bailey, S., Baltay, C., Bault, A., Behera, J., BenZvi, S., Beutler, F., Bianchi, D., Blake, C., Blum, R., Brieden, S., Brodzeller, A., Brooks, D., Buckley-Geer, E., Burtin, E., Calderon, R., Canning, R., Rosell, A. Carnero, Cereskaite, R., Cervantes-Cota, J. L., Chabanier, S., Chaussidon, E., Chaves-Montero, J., Chen, S., Chen, X., Claybaugh, T., Cole, S., Cuceu, A., Davis, T. M., Dawson, K., de la Macorra, A., de Mattia, A., Deiosso, N., Dey, A., Dey, B., Ding, Z., Doel, P., Edelstein, J., Eftekharzadeh, S., Eisenstein, D. J., Elliott, A., Fagrelius, P., Fanning, K., Ferraro, S., Ereza, J., Findlay, N., Flaugher, B., Font-Ribera, A., Forero-Sánchez, D., Forero-Romero, J. E., Garcia-Quintero, C., Gaztañaga, E., Gil-Marín, H., Gontcho, S. Gontcho A, Gonzalez-Morales, A. X., Gonzalez-Perez, V., Gordon, C., Green, D., Gruen, D., Gsponer, R., Gutierrez, G., Guy, J., Hadzhiyska, B., Hahn, C., Hanif, M. M. S, Herrera-Alcantar, H. K., Honscheid, K., Howlett, C., Huterer, D., Iršič, V., Ishak, M., Juneau, S., Karaçaylı, N. G., Kehoe, R., Kent, S., Kirkby, D., Kremin, A., Krolewski, A., Lai, Y., Lan, T. -W., Landriau, M., Lang, D., Lasker, J., Goff, J. M. Le, Guillou, L. Le, Leauthaud, A., Levi, M. E., Li, T. S., Linder, E., Lodha, K., Magneville, C., Manera, M., Margala, D., Martini, P., Maus, M., McDonald, P., Medina-Varela, L., Meisner, A., Mena-Fernández, J., Miquel, R., Moon, J., Moore, S., Moustakas, J., Mudur, N., Mueller, E., Muñoz-Gutiérrez, A., Myers, A. D., Nadathur, S., Napolitano, L., Neveux, R., Newman, J. A., Nguyen, N. M., Nie, J., Niz, G., Noriega, H. E., Padmanabhan, N., Paillas, E., Palanque-Delabrouille, N., Pan, J., Penmetsa, S., Percival, W. J., Pieri, M., Pinon, M., Poppett, C., Porredon, A., Prada, F., Pérez-Fernández, A., Pérez-Ràfols, I., Rabinowitz, D., Raichoor, A., Ramírez-Pérez, C., Ramirez-Solano, S., Rashkovetskyi, M., Rezaie, M., Rich, J., Rocher, A., Rockosi, C., Roe, N. A., Rosado-Marin, A., Ross, A. J., Rossi, G., Ruggeri, R., Ruhlmann-Kleider, V., Samushia, L., Sanchez, E., Saulder, C., Schlafly, E. F., Schlegel, D., Schubnell, M., Seo, H., Sharples, R., Silber, J., Slosar, A., Smith, A., Sprayberry, D., Swanson, J., Tan, T., Tarlé, G., Trusov, S., Vaisakh, R., Valcin, D., Valdes, F., Vargas-Magaña, M., Verde, L., Walther, M., Wang, B., Wang, M. S., Weaver, B. A., Weaverdyck, N., Wechsler, R. H., Weinberg, D. H., White, M., Yu, J., Yu, Y., Yuan, S., Yèche, C., Zaborowski, E. A., Zarrouk, P., Zhang, H., Zhao, C., Zhao, R., Zhou, R., and Zou, H.

Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

We present the DESI 2024 galaxy and quasar baryon acoustic oscillations (BAO) measurements using over 5.7 million unique galaxy and quasar redshifts in the range 0.1

Published
2024

7. Baryon Acoustic Oscillation Theory and Modelling Systematics for the DESI 2024 results

Author

Chen, Shi-Fan, Howlett, Cullan, White, Martin, McDonald, Patrick, Ross, Ashley J., Seo, Hee-Jong, Padmanabhan, Nikhil, Aguilar, J., Ahlen, S., Alam, S., Alves, O., Andrade, U., Blum, R., Brooks, D., Chen, X., Cole, S., Davis, T. M., Dawson, K., de la Macorra, A., Dey, Arjun, Ding, Z., Doel, P., Ferraro, S., Font-Ribera, A., Forero-Sánchez, D., Forero-Romero, J. E., Garcia-Quintero, C., Gaztañaga, E., Gontcho, S. Gontcho A, Hanif, M. M. S, Honscheid, K., Kisner, T., Kremin, A., Lambert, A., Landriau, M., Levi, M. E., Manera, M., Meisner, A., Mena-Fernández, J., Miquel, R., Muñoz-Gutiérrez, A., Paillas, E., Palanque-Delabrouille, N., Percival, W. J., Prada, F., Pérez-Fernández, A., Rashkovetskyi, M., Rezaie, M., Rosado-Marin, A., Rossi, G., Ruggeri, R., Sanchez, E., Schlegel, D., Silber, J., Tarlé, G., Vargas-Magaña, M., Weaver, B. A., Yu, J., Yuan, S., Zhou, R., and Zhou, Z.

Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

This paper provides a comprehensive overview of how fitting of Baryon Acoustic Oscillations (BAO) is carried out within the upcoming Dark Energy Spectroscopic Instrument's (DESI) 2024 results using its DR1 dataset, and the associated systematic error budget from theory and modelling of the BAO. We derive new results showing how non-linearities in the clustering of galaxies can cause potential biases in measurements of the isotropic ($\alpha_{\mathrm{iso}}$) and anisotropic ($\alpha_{\mathrm{ap}}$) BAO distance scales, and how these can be effectively removed with an appropriate choice of reconstruction algorithm. We then demonstrate how theory leads to a clear choice for how to model the BAO and develop, implement and validate a new model for the remaining smooth-broadband (i.e., without BAO) component of the galaxy clustering. Finally, we explore the impact of all remaining modelling choices on the BAO constraints from DESI using a suite of high-precision simulations, arriving at a set of best-practices for DESI BAO fits, and an associated theory and modelling systematic error. Overall, our results demonstrate the remarkable robustness of the BAO to all our modelling choices and motivate a combined theory and modelling systematic error contribution to the post-reconstruction DESI BAO measurements of no more than $0.1\%$ ($0.2\%$) for its isotropic (anisotropic) distance measurements. We expect the theory and best-practices laid out to here to be applicable to other BAO experiments in the era of DESI and beyond., Comment: 30 pages, 18 figures, 1 table, updated to match version accepted by MNRAS

Published
2024

9. The Early Data Release of the Dark Energy Spectroscopic Instrument

Author

DESI Collaboration, Adame, A. G., Aguilar, J., Ahlen, S., Alam, S., Aldering, G., Alexander, D. M., Alfarsy, R., Prieto, C. Allende, Alvarez, M., Alves, O., Anand, A., Andrade-Oliveira, F., Armengaud, E., Asorey, J., Avila, S., Aviles, A., Bailey, S., Balaguera-Antolínez, A., Ballester, O., Baltay, C., Bault, A., Bautista, J., Behera, J., Beltran, S. F., BenZvi, S., Silva, L. Beraldo e, Bermejo-Climent, J. R., Berti, A., Besuner, R., Beutler, F., Bianchi, D., Blake, C., Blum, R., Bolton, A. S., Brieden, S., Brodzeller, A., Brooks, D., Brown, Z., Buckley-Geer, E., Burtin, E., Cabayol-Garcia, L., Cai, Z., Canning, R., Cardiel-Sas, L., Rosell, A. Carnero, Castander, F. J., Cervantes-Cota, J. L., Chabanier, S., Chaussidon, E., Chaves-Montero, J., Chen, S., Chen, X., Chuang, C., Claybaugh, T., Cole, S., Cooper, A. P., Cuceu, A., Davis, T. M., Dawson, K., de Belsunce, R., de la Cruz, R., de la Macorra, A., Della Costa, J., de Mattia, A., Demina, R., Demirbozan, U., DeRose, J., Dey, A., Dey, B., Dhungana, G., Ding, J., Ding, Z., Doel, P., Doshi, R., Douglass, K., Edge, A., Eftekharzadeh, S., Eisenstein, D. J., Elliott, A., Escoffier, S., Fagrelius, P., Fan, X., Fanning, K., Fawcett, V. A., Ferraro, S., Ereza, J., Flaugher, B., Font-Ribera, A., Forero-Sánchez, D., Forero-Romero, J. E., Frenk, C. S., Gänsicke, B. T., García, L. Á., García-Bellido, J., Garcia-Quintero, C., Garrison, L. H., Gil-Marín, H., Golden-Marx, J., Gontcho, S. Gontcho A, Gonzalez-Morales, A. X., Gonzalez-Perez, V., Gordon, C., Graur, O., Green, D., Gruen, D., Guy, J., Hadzhiyska, B., Hahn, C., Han, J. J., Hanif, M. M. S, Herrera-Alcantar, H. K., Honscheid, K., Hou, J., Howlett, C., Huterer, D., Iršič, V., Ishak, M., Jacques, A., Jana, A., Jiang, L., Jimenez, J., Jing, Y. P., Joudaki, S., Jullo, E., Juneau, S., Kizhuprakkat, N., Karaçaylı, N. G., Karim, T., Kehoe, R., Kent, S., Khederlarian, A., Kim, S., Kirkby, D., Kisner, T., Kitaura, F., Kneib, J., Koposov, S. E., Kovács, A., Kremin, A., Krolewski, A., L'Huillier, B., Lahav, O., Lambert, A., Lamman, C., Lan, T. -W., Landriau, M., Lang, D., Lange, J. U., Lasker, J., Leauthaud, A., Guillou, L. Le, Levi, M. E., Li, T. S., Linder, E., Lyons, A., Magneville, C., Manera, M., Manser, C. J., Margala, D., Martini, P., McDonald, P., Medina, G. E., Medina-Varela, L., Meisner, A., Mena-Fernández, J., Meneses-Rizo, J., Mezcua, M., Miquel, R., Montero-Camacho, P., Moon, J., Moore, S., Moustakas, J., Mueller, E., Mundet, J., Muñoz-Gutiérrez, A., Myers, A. D., Nadathur, S., Napolitano, L., Neveux, R., Newman, J. A., Nie, J., Nikutta, R., Niz, G., Norberg, P., Noriega, H. E., Paillas, E., Palanque-Delabrouille, N., Palmese, A., Zhiwei, P., Parkinson, D., Penmetsa, S., Percival, W. J., Pérez-Fernández, A., Pérez-Ràfols, I., Pieri, M., Poppett, C., Porredon, A., Pothier, S., Prada, F., Pucha, R., Raichoor, A., Ramírez-Pérez, C., Ramirez-Solano, S., Rashkovetskyi, M., Ravoux, C., Rocher, A., Rockosi, C., Ross, A. J., Rossi, G., Ruggeri, R., Ruhlmann-Kleider, V., Sabiu, C. G., Said, K., Saintonge, A., Samushia, L., Sanchez, E., Saulder, C., Schaan, E., Schlafly, E. F., Schlegel, D., Scholte, D., Schubnell, M., Seo, H., Shafieloo, A., Sharples, R., Sheu, W., Silber, J., Sinigaglia, F., Siudek, M., Slepian, Z., Smith, A., Soumagnac, M. T., Sprayberry, D., Stephey, L., Suárez-Pérez, J., Sun, Z., Tan, T., Tarlé, G., Tojeiro, R., Ureña-López, L. A., Vaisakh, R., Valcin, D., Valdes, F., Valluri, M., Vargas-Magaña, M., Variu, A., Verde, L., Walther, M., Wang, B., Wang, M. S., Weaver, B. A., Weaverdyck, N., Wechsler, R. H., White, M., Xie, Y., Yang, J., Yèche, C., Yu, J., Yuan, S., Zhang, H., Zhang, Z., Zhao, C., Zheng, Z., Zhou, R., Zhou, Z., Zou, H., Zou, S., and Zu, Y.

Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

The Dark Energy Spectroscopic Instrument (DESI) completed its five-month Survey Validation in May 2021. Spectra of stellar and extragalactic targets from Survey Validation constitute the first major data sample from the DESI survey. This paper describes the public release of those spectra, the catalogs of derived properties, and the intermediate data products. In total, the public release includes good-quality spectral information from 466,447 objects targeted as part of the Milky Way Survey, 428,758 as part of the Bright Galaxy Survey, 227,318 as part of the Luminous Red Galaxy sample, 437,664 as part of the Emission Line Galaxy sample, and 76,079 as part of the Quasar sample. In addition, the release includes spectral information from 137,148 objects that expand the scope beyond the primary samples as part of a series of secondary programs. Here, we describe the spectral data, data quality, data products, Large-Scale Structure science catalogs, access to the data, and references that provide relevant background to using these spectra., Comment: 43 pages, 7 figures, 17 tables, accepted for publication in the Astronomical Journal

Published
2023
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10. Validation of the Scientific Program for the Dark Energy Spectroscopic Instrument

Author

DESI Collaboration, Adame, A. G., Aguilar, J., Ahlen, S., Alam, S., Aldering, G., Alexander, D. M., Alfarsy, R., Prieto, C. Allende, Alvarez, M., Alves, O., Anand, A., Andrade-Oliveira, F., Armengaud, E., Asorey, J., Avila, S., Aviles, A., Bailey, S., Balaguera-Antolínez, A., Ballester, O., Baltay, C., Bault, A., Bautista, J., Behera, J., Beltran, S. F., BenZvi, S., Silva, L. Beraldo e, Bermejo-Climent, J. R., Berti, A., Besuner, R., Beutler, F., Bianchi, D., Blake, C., Blum, R., Bolton, A. S., Brieden, S., Brodzeller, A., Brooks, D., Brown, Z., Buckley-Geer, E., Burtin, E., Cabayol-Garcia, L., Cai, Z., Canning, R., Cardiel-Sas, L., Rosell, A. Carnero, Castander, F. J., Cervantes-Cota, J. L., Chabanier, S., Chaussidon, E., Chaves-Montero, J., Chen, S., Chuang, C., Claybaugh, T., Cole, S., Cooper, A. P., Cuceu, A., Davis, T. M., Dawson, K., de Belsunce, R., de la Cruz, R., de la Macorra, A., de Mattia, A., Demina, R., Demirbozan, U., DeRose, J., Dey, A., Dey, B., Dhungana, G., Ding, J., Ding, Z., Doel, P., Doshi, R., Douglass, K., Edge, A., Eftekharzadeh, S., Eisenstein, D. J., Elliott, A., Escoffier, S., Fagrelius, P., Fan, X., Fanning, K., Fawcett, V. A., Ferraro, S., Ereza, J., Flaugher, B., Font-Ribera, A., Forero-Sánchez, D., Forero-Romero, J. E., Frenk, C. S., Gänsicke, B. T., García, L. Á., García-Bellido, J., Garcia-Quintero, C., Garrison, L. H., Gil-Marín, H., Golden-Marx, J., Gontcho, S. Gontcho A, Gonzalez-Morales, A. X., Gonzalez-Perez, V., Gordon, C., Graur, O., Green, D., Gruen, D., Guy, J., Hadzhiyska, B., Hahn, C., Han, J. J., Hanif, M. M. S, Herrera-Alcantar, H. K., Honscheid, K., Hou, J., Howlett, C., Huterer, D., Iršič, V., Ishak, M., Jana, A., Jiang, L., Jimenez, J., Jing, Y. P., Joudaki, S., Joyce, R., Jullo, E., Juneau, S., Kizhuprakkat, N., Karaçaylı, N. G., Karim, T., Kehoe, R., Kent, S., Khederlarian, A., Kim, S., Kirkby, D., Kisner, T., Kitaura, F., Kneib, J., Koposov, S. E., Kovács, A., Kremin, A., Krolewski, A., L'Huillier, B., Lahav, O., Lambert, A., Lamman, C., Lan, T. -W., Landriau, M., Lang, D., Lange, J. U., Lasker, J., Guillou, L. Le, Leauthaud, A., Levi, M. E., Li, T. S., Linder, E., Lyons, A., Magneville, C., Manera, M., Manser, C. J., Margala, D., Martini, P., McDonald, P., Medina, G. E., Medina-Varela, L., Meisner, A., Mena-Fernández, J., Meneses-Rizo, J., Mezcua, M., Miquel, R., Montero-Camacho, P., Moon, J., Moore, S., Moustakas, J., Mueller, E., Mundet, J., Muñoz-Gutiérrez, A., Myers, A. D., Nadathur, S., Napolitano, L., Neveux, R., Newman, J. A., Nie, J., Niz, G., Norberg, P., Noriega, H. E., Paillas, E., Palanque-Delabrouille, N., Palmese, A., Zhiwei, P., Parkinson, D., Penmetsa, S., Percival, W. J., Pérez-Fernández, A., Pérez-Ràfols, I., Pieri, M., Poppett, C., Porredon, A., Prada, F., Pucha, R., Raichoor, A., Ramírez-Pérez, C., Ramirez-Solano, S., Rashkovetskyi, M., Ravoux, C., Rocher, A., Rockosi, C., Ross, A. J., Rossi, G., Ruggeri, R., Ruhlmann-Kleider, V., Sabiu, C. G., Said, K., Saintonge, A., Samushia, L., Sanchez, E., Saulder, C., Schaan, E., Schlafly, E. F., Schlegel, D., Scholte, D., Schubnell, M., Seo, H., Shafieloo, A., Sharples, R., Sheu, W., Silber, J., Sinigaglia, F., Siudek, M., Slepian, Z., Smith, A., Sprayberry, D., Stephey, L., Suárez-Pérez, J., Sun, Z., Tan, T., Tarlé, G., Tojeiro, R., Ureña-López, L. A., Vaisakh, R., Valcin, D., Valdes, F., Valluri, M., Vargas-Magaña, M., Variu, A., Verde, L., Walther, M., Wang, B., Wang, M. S., Weaver, B. A., Weaverdyck, N., Wechsler, R. H., White, M., Xie, Y., Yang, J., Yèche, C., Yu, J., Yuan, S., Zhang, H., Zhang, Z., Zhao, C., Zheng, Z., Zhou, R., Zhou, Z., Zou, H., Zou, S., and Zu, Y.

Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

The Dark Energy Spectroscopic Instrument (DESI) was designed to conduct a survey covering 14,000 deg$^2$ over five years to constrain the cosmic expansion history through precise measurements of Baryon Acoustic Oscillations (BAO). The scientific program for DESI was evaluated during a five month Survey Validation (SV) campaign before beginning full operations. This program produced deep spectra of tens of thousands of objects from each of the stellar (MWS), bright galaxy (BGS), luminous red galaxy (LRG), emission line galaxy (ELG), and quasar target classes. These SV spectra were used to optimize redshift distributions, characterize exposure times, determine calibration procedures, and assess observational overheads for the five-year program. In this paper, we present the final target selection algorithms, redshift distributions, and projected cosmology constraints resulting from those studies. We also present a `One-Percent survey' conducted at the conclusion of Survey Validation covering 140 deg$^2$ using the final target selection algorithms with exposures of a depth typical of the main survey. The Survey Validation indicates that DESI will be able to complete the full 14,000 deg$^2$ program with spectroscopically-confirmed targets from the MWS, BGS, LRG, ELG, and quasar programs with total sample sizes of 7.2, 13.8, 7.46, 15.7, and 2.87 million, respectively. These samples will allow exploration of the Milky Way halo, clustering on all scales, and BAO measurements with a statistical precision of 0.28% over the redshift interval $z<1.1$, 0.39% over the redshift interval $1.1

Published
2023
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13. Development of Tutorial Video Learning Media on Food Dehydration to Increase Learning Outcomes of Students of Culinary Arts Program

Author

Mutiara, Erli, AnuGerah, Ajeng Inggit, Sutanti, Siti, Agustina, Dian, Hanif, M., Striełkowski, Wadim, Editor-in-Chief, Black, Jessica M., Series Editor, Butterfield, Stephen A., Series Editor, Chang, Chi-Cheng, Series Editor, Cheng, Jiuqing, Series Editor, Dumanig, Francisco Perlas, Series Editor, Al-Mabuk, Radhi, Series Editor, Scheper-Hughes, Nancy, Series Editor, Urban, Mathias, Series Editor, Webb, Stephen, Series Editor, Kusumastuti, Adhi, editor, Anis, Samsudin, editor, Hidayanto, Achmad Nizar, editor, Nurmasitah, Sita, editor, Atika, Atika, editor, Utomo, Aryo Baskoro, editor, Apriyani, Delta, editor, Fitriyana, Deni Fajar, editor, Bahatmaka, Aldias, editor, Rachmawati, Rina, editor, and Ihsani, Ade Novi Nurul, editor

Published
2024
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14. Ubo Rampe of Covid-19 Tolak Balak : A Meaning Study on Symbolic Forms of Covid-19 Traditional Ritual Prevention in Kampung Buddha Sodong Ponorogo

Author

Hanif, M., Chasanatun, F., Rudyanto, H. E., Striełkowski, Wadim, Editor-in-Chief, Black, Jessica M., Series Editor, Butterfield, Stephen A., Series Editor, Chang, Chi-Cheng, Series Editor, Cheng, Jiuqing, Series Editor, Dumanig, Francisco Perlas, Series Editor, Al-Mabuk, Radhi, Series Editor, Scheper-Hughes, Nancy, Series Editor, Urban, Mathias, Series Editor, Webb, Stephen, Series Editor, Rahman, Abdul, editor, Dwiputrianti, Septiana, editor, and Afandi, Muhamad Nur, editor

Published
2024
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17. Immuno-surveillance and protection of the human cochlea

Author

Wei Liu, Hao Li, Charlotta Kämpfe Nordström, Niklas Danckwardt-Lillieström, Sumit Agrawal, Hanif M. Ladak, and Helge Rask-Andersen

Subjects
human cochlea, IBA1, immuno-surveillance, super resolution microscopy, synchrotron phase-contrast imaging, Neurology. Diseases of the nervous system, RC346-429
Abstract

BackgroundDespite its location near infection-prone areas, the human inner ear demonstrates remarkable resilience. This suggests that there are inherent instruments deterring the invasion and spread of pathogens into the inner ear. Here, we combined high-resolution light microscopy, super-resolution immunohistochemistry (SR-SIM) and synchrotron phase contrast imaging (SR-PCI) to identify the protection and barrier systems in the various parts of the human inner ear, focusing on the lateral wall, spiral ganglion, and endolymphatic sac.Materials and methodsLight microscopy was conducted on mid-modiolar, semi-thin sections, after direct glutaraldehyde/osmium tetroxide fixation. The tonotopic locations were estimated using SR-PCI and 3D reconstruction in cadaveric specimens. The sections were analyzed for leucocyte and macrophage activity, and the results were correlated with immunohistochemistry using confocal microscopy and SR-SIM.ResultsLight microscopy revealed unprecedented preservation of cell anatomy and several macrophage-like cells that were localized in the cochlea. Immunohistochemistry demonstrated IBA1 cells frequently co-expressing MHC II in the spiral ganglion, nerve fibers, lateral wall, spiral limbus, and tympanic covering layer at all cochlear turns as well as in the endolymphatic sac. RNAscope assays revealed extensive expression of fractalkine gene transcripts in type I spiral ganglion cells. CD4 and CD8 cells occasionally surrounded blood vessels in the modiolus and lateral wall. TMEM119 and P2Y12 were not expressed, indicating that the cells labeled with IBA1 were not microglia. The round window niche, compact basilar membrane, and secondary spiral lamina may form protective shields in the cochlear base.DiscussionThe results suggest that the human cochlea is surveilled by dwelling and circulating immune cells. Resident and blood-borne macrophages may initiate protective immune responses via chemokine signaling in the lateral wall, spiral lamina, and spiral ganglion at different frequency locations. Synchrotron imaging revealed intriguing protective barriers in the base of the cochlea. The role of the endolymphatic sac in human inner ear innate and adaptive immunity is discussed.

Published
2024
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18. Development and validation of a surgical planning tool for bone-conduction implants

Author

Evan S. Simpson, Carlos D. Salgado, Seyed Alireza Rohani, Sumit K. Agrawal, and Hanif M. Ladak

Subjects
Image analysis, BONEBRIDGE, Temporal bone, Surgical planning, Computed tomography, Bone conduction devices, Science (General), Q1-390, Social sciences (General), H1-99
Abstract

Background: The BONEBRIDGE® (Med-El GmbH) is a bone-conduction device comprising an external audio processor and an internal Bone Conduction-Floating Mass Transducer (BC-FMT) surgically anchored to the temporal bone. Due to the implant's size, its placement may be challenging in certain anatomies, necessitating thorough surgical planning. Manual planning methods are laborious, time-intensive, and prone to errors. This study aimed to develop and validate an automated algorithm for determining skull thickness, aiding in the surgical planning of the BONEBRIDGE and other devices requiring similar bone thickness estimations. Materials and methods: Twelve cadaveric temporal bones underwent clinical computed tomography (CT). A custom Python algorithm was developed to automatically segment bone from soft tissue, generate 3D models, and perform ray-tracing to estimate bone thickness. Two thickness colormaps were generated for each sample: the cortical thickness to the first air cell and the total thickness down to the dura. The algorithm was validated against expert manual measurements to achieve consensus interpretation. Results: The algorithm estimated bone-to-air thicknesses (mean = 4.7 mm, 95% Confidence Interval [CI] of 4.3–5.0 mm) that closely matched the expert measurements (mean = 4.7 mm, CI of 4.4–5.0 mm), with a mean absolute difference (MAD) of 0.3 mm. Similarly, the algorithm's estimations to the dura (6.0 mm, CI of 5.4–6.5 mm) were comparable to the expert markings (5.9 mm, CI of 5.4–6.5 mm), with a MAD of 0.3 mm. Conclusions: The first automated algorithm to calculate skull thickness to both the air cells and dura in the temporal bone was developed. Colormaps were optimized to aid with the surgical planning of BONEBRIDGE implantation, however the tool can be generalized to aid in the surgical planning of any bone thickness application. The tool was published as a freely available extension to the open-source 3D Slicer software program (www.slicer.org).

Published
2024
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23. Comparison of the Reliability Test of Semester Final Exam Scores for Graphic Media Courses Using Various Reliability Test Methods

Author

Setyaedhi, Hari Sugiharto, Ardianik, A., Hanif, M., Striełkowski, Wadim, Editor-in-Chief, Black, Jessica M., Series Editor, Butterfield, Stephen A., Series Editor, Chang, Chi-Cheng, Series Editor, Cheng, Jiuqing, Series Editor, Dumanig, Francisco Perlas, Series Editor, Al-Mabuk, Radhi, Series Editor, Scheper-Hughes, Nancy, Series Editor, Urban, Mathias, Series Editor, Webb, Stephen, Series Editor, Mustofa, Ali, editor, Widiyanah, Ima, editor, Prahani, Binar K., editor, Rahayu, Imami A. T., editor, Mudzakkir, Moh., editor, and Putri, Cicilia D. M., editor

Published
2023
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24. Kampung Budha Sodong’s Local Wisdom: The Symbolic Forms of Covid-19 Traditional Ritual, Its Internalization and Comparing to the Villagers’ Educational Backgrounds

Author

Hanif, M., Chasanatun, F., Rudyanto, H. E., Striełkowski, Wadim, Editor-in-Chief, Black, Jessica M., Series Editor, Butterfield, Stephen A., Series Editor, Chang, Chi-Cheng, Series Editor, Cheng, Jiuqing, Series Editor, Dumanig, Francisco Perlas, Series Editor, Al-Mabuk, Radhi, Series Editor, Scheper-Hughes, Nancy, Series Editor, Urban, Mathias, Series Editor, Webb, Stephen, Series Editor, Handhika, Jeffry, editor, Lukitasari, Marheny, editor, Ricahyono, Sigit, editor, and Nugraha, Dewanta Arya, editor

Published
2023
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29. Inelastic scattering of photoelectrons from He nanodroplets

Author

Shcherbinin, M. V., Westergaard, F. Vad, Hanif, M., Krishnan, S. R., LaForge, A. C., Richter, R., Pfeifer, T., and Mudrich, M.

Subjects
Physics - Atomic and Molecular Clusters
Abstract

We present a detailed study of inelastic energy-loss collisions of photoelectrons emitted from He nanodroplets by tunable extreme ultraviolet (XUV) radiation. Using coincidence imaging detection of electrons and ions, we probe the lowest He droplet excited states up to the electron impact ionization threshold. We find significant signal contributions from photoelectrons emitted from free He atoms accompanying the He nanodroplet beam. Furthermore, signal contributions from photoionization and electron impact excitation/ionization occurring in pairs of nearest-neighbor atoms in the He droplets are detected. This work highlights the importance of inelastic electron scattering in the interaction of nanoparticles with XUV radiation.

Published
2018
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32. Unlocking the human inner ear for therapeutic intervention

Author

Hao Li, Sumit Agrawal, Seyed Alireza Rohani, Ning Zhu, Daniela I. Cacciabue, Marcelo N. Rivolta, Douglas E. H. Hartley, Dan Jiang, Hanif M. Ladak, Gerard M. O’Donoghue, and Helge Rask-Andersen

Subjects
Medicine, Science
Abstract

Abstract The human inner ear contains minute three-dimensional neurosensory structures that are deeply embedded within the skull base, rendering them relatively inaccessible to regenerative therapies for hearing loss. Here we provide a detailed characterisation of the functional architecture of the space that hosts the cell bodies of the auditory nerve to make them safely accessible for the first time for therapeutic intervention. We used synchrotron phase-contrast imaging which offers the required microscopic soft-tissue contrast definition while simultaneously displaying precise bony anatomic detail. Using volume-rendering software we constructed highly accurate 3-dimensional representations of the inner ear. The cell bodies are arranged in a bony helical canal that spirals from the base of the cochlea to its apex; the canal volume is 1.6 μL but with a diffusion potential of 15 μL. Modelling data from 10 temporal bones enabled definition of a safe trajectory for therapeutic access while preserving the cochlea’s internal architecture. We validated the approach through surgical simulation, anatomical dissection and micro-radiographic analysis. These findings will facilitate future clinical trials of novel therapeutic interventions to restore hearing.

Published
2022
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38. Knowledge, Attitudes and Practices of Pharmacogenomics Among Senior Pharmacy Students: A Cross Sectional Study from Punjab, Pakistan

Author

Shah S, Hanif M, Khan HU, Khan FU, Abbas G, Khurram H, Khames A, Abdelgawad MA, Said AS, Abourehab MAS, Maheen S, Chand UR, and Haris M

Subjects
pharmacogenomics, knowledge, attitude, practice., Therapeutics. Pharmacology, RM1-950
Abstract

Shahid Shah,1 Muhammad Hanif,2 Hafeez Ullah Khan,3 Faiz Ullah Khan,4 Ghulam Abbas,5 Haris Khurram,6 Ahmed Khames,7 Mohamed A Abdelgawad,8 Amira SA Said,9,10 Mohammed AS Abourehab,11 Safirah Maheen,3 Usman Rashid Chand,1 Muhammad Haris1 1Department of Pharmacy Practice, Faculty of Pharmaceutical Sciences, Government College University Faisalabad, Faisalabad, Pakistan; 2Department of Pharmaceutics, Faculty of Pharmacy, Bahauddin Zakariya University Multan, Multan, Pakistan; 3College of Pharmacy, Department of Pharmaceutics, University of Sargodha, Sargodha, Pakistan; 4Department of Pharmacy Administration and Clinical Pharmacy, School of Pharmacy, Xi’an Jiaotong University, Xi’an, People’s Republic of China; 5Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Government College University Faisalabad, Faisalabad, Pakistan; 6National University of Computer and Emerging Sciences, Chiniot-Faisalabad Campus, Chiniot, Pakistan; 7Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Taif University, Taif, 21944, Saudi Arabia; 8Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Al Jouf, 72341, Saudi Arabia; 9Clinical Pharmacy Department, Faculty of Pharmacy, Beni-Suef, Egypt; 10Clinical Pharmacy Department, College of Pharmacy, Al Ain University, Al Ain, Abu Dhabi, United Arab Emirates; 11Department of Pharmaceutics, Faculty of Pharmacy, Umm Al-Qura University, Makkah, 21955, Saudi ArabiaCorrespondence: Shahid Shah; Ghulam Abbas, Email Shahid.waris555@gmail.com; ghulamabbas@gcuf.edu.pkBackground: Pharmacogenomics (PGx) is essential for optimizing drug therapy and reducing unwanted drug side effects. Our aim was to determine the knowledge, attitude and practice of senior pharmacy students in Punjab, Pakistan towards PGx.Methods: A cross-sectional study was conducted among 511 undergraduate pharmacy students from different universities in Punjab, Pakistan. A validated and pilot-tested structured questionnaire was administered to respondents to assess their knowledge, attitude, and practice regarding PGx. Descriptive statistics and multivariate logistic regression model were used to describe the results of the study. A p-value of less than 0.05 was considered statistically significant.Results: A total of 511 students (58.9% females and 41.1% males) responded to the survey. Most (87.7%) of the students knew that the drug response could be affected by genetic variations. Mean knowledge score of the students was 12.6. Good basic knowledge positively and significantly (p=0.01) affected students’ PGx test knowledge and attitudes. Most (> 70%) of students believed that human genetics affected the drug response due to interindividual variation and ethnic variation. Mean attitude score of the students was 5.23. The majority of students (> 92%) wanted to learn more about PGx and thought it could help them choose the right drug. Students’ knowledge was positively and significantly (p=0.01) affected by a good attitude. Mean practice score of the students was 11.95. When trying to solve a drug-related case study question, about 31.5% of students implemented the idea of human genetic variation. Only 28.8% of students attended a lecture related to the effects of genetic variations on drug therapy. Good practice positively and significantly (p=0.01) affected students’ knowledge of PGx tests.Conclusion: The senior pharmacy students had good knowledge and attitudes towards PGx. However, the practice of PGx needs to be improved to facilitate the application of PGx in clinical practice in Pakistan.Keywords: pharmacogenomics, knowledge, attitude, practice

Published
2022

39. Leveraging advanced AI algorithms with transformer-infused recurrent neural networks to optimize solar irradiance forecasting.

Author

Naveed, M. S., Hanif, M. F., Metwaly, M., Iqbal, I., Lodhi, E., Liu, X., Mi, J., Yuan, Ke, and Liu, Xin

Abstract

Solar energy (SE) is vital for renewable energy generation, but its natural fluctuations present difficulties in maintaining grid stability and planning. Accurate forecasting of solar irradiance (SI) is essential to address these challenges. The current research presents an innovative forecasting approach named as Transformer-Infused Recurrent Neural Network (TIR) model. This model integrates a Bi-Directional Long Short-Term Memory (BiLSTM) network for encoding and a Gated Recurrent Unit (GRU) network for decoding, incorporating attention mechanisms and positional encoding. This model is proposed to enhance SI forecasting accuracy by effectively utilizing meteorological weather data, handling overfitting, and managing data outliers and data complexity. To evaluate the model's performance, a comprehensive comparative analysis is conducted, involving five algorithms: Artificial Neural Network (ANN), BiLSTM, GRU, hybrid BiLSTM-GRU, and Transformer models. The findings indicate that employing the TIR model leads to superior accuracy in the analyzed area, achieving R2 value of 0.9983, RMSE of 0.0140, and MAE of 0.0092. This performance surpasses those of the alternative models studied. The integration of BiLSTM and GRU algorithms with the attention mechanism and positional encoding has been optimized to enhance the forecasting of SI. This approach mitigates computational dependencies and minimizes the error terms within the model. [ABSTRACT FROM AUTHOR]

Published
2024
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40. Determining the Effect of pH on Iron Oxidation Kinetics in Aquatic Environments: Exploring a Fundamental Chemical Reaction to Grasp the Significant Ecosystem Implications of Iron Bioavailability

Author

Kirby, Matthew E., Bullen, Jay C., Hanif, M. D., Heiba, Hany Fathy, Liu, Fengjie, Northover, George H. R., Resongles, Eleonore, and Weiss, Dominik J.

Abstract

Understanding the controls of the oxidation rate of iron (Fe) in oxygenated aquatic systems is fundamental for students of the Earth and Environmental Sciences as it defines the bioavailability of Fe, a trace metal essential for life. The laboratory experiment presented here was successfully developed and used during a third-year undergraduate lab course at Imperial College London for several years. It employs ultraviolet-visible (UV-vis) spectroscopy calibrated externally with 0 to 50 [mu]M Fe[superscript 2+] standards created in a 492 [mu]M ferrozine and 0.43 M acetate matrix. The students conducted the oxidation experiments in stirred batch reactors at equilibrium with atmospheric oxygen. The solution contained 40.5 [mu]M initial Fe[superscript 2+] concentration and a 5.1 mM imidazole buffer. The pH was adjusted to values between 7.22 and 7.77. The students observed a pseudo-first-order reaction with respect to Fe[superscript 2+] concentration. Plotting the logarithms of the apparent rate constants (k') at different pH values leads to a gradient of 2.2 ± 0.2 min[superscript -1] pH[superscript -1], indicating a second-order reaction with respect to OH[superscript -] concentration, in agreement with published literature. The oxidation reaction occurred rapidly (tens of seconds to tens of minutes) indicating that in oxygenated aquatic systems, Fe[superscript 3+] will be the dominant oxidation state, significantly reducing the bioavailability of Fe. The simple laboratory experiment presented here allows the students to learn about kinetic parameters for a fundamental chemical reaction. It allows the students to explore the significant implications this has for aquatic ecosystems.

Published
2020
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42. Nontuberculous Mycobacterial (NTM) Disease Among Pulmonary Tuberculosis Suspects in India: A Multicentre Study

Author

Sharma, S.K., primary, Upadhyay, V., additional, Solanki, R., additional, Patel, P., additional, Patel, M., additional, Dewan, R.K., additional, Verma, A.K., additional, Ranjan, A., additional, Yadav, R.N., additional, Hanif, M., additional, Chopra, K.K., additional, Dwivedi, K.K., additional, Mohan, A., additional, Jayaprada, R., additional, Ghewade, B., additional, Bhanushali, J., additional, and Hasnain, S.E., additional

Published
2024
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49. Immuno-surveillance and protection of the human cochlea

Author

Liu, Wei, Li, Hao, Kämpfe Nordström, Charlotta, Danckwardt-Lillieström, Niklas, Agrawal, Sumit, Ladak, Hanif M., Rask-Andersen, Helge, Liu, Wei, Li, Hao, Kämpfe Nordström, Charlotta, Danckwardt-Lillieström, Niklas, Agrawal, Sumit, Ladak, Hanif M., and Rask-Andersen, Helge

Abstract

Background: Despite its location near infection-prone areas, the human inner ear demonstrates remarkable resilience. This suggests that there are inherent instruments deterring the invasion and spread of pathogens into the inner ear. Here, we combined high-resolution light microscopy, super-resolution immunohistochemistry (SR-SIM) and synchrotron phase contrast imaging (SR-PCI) to identify the protection and barrier systems in the various parts of the human inner ear, focusing on the lateral wall, spiral ganglion, and endolymphatic sac. Materials and methods: Light microscopy was conducted on mid-modiolar, semi-thin sections, after direct glutaraldehyde/osmium tetroxide fixation. The tonotopic locations were estimated using SR-PCI and 3D reconstruction in cadaveric specimens. The sections were analyzed for leucocyte and macrophage activity, and the results were correlated with immunohistochemistry using confocal microscopy and SR-SIM. Results: Light microscopy revealed unprecedented preservation of cell anatomy and several macrophage-like cells that were localized in the cochlea. Immunohistochemistry demonstrated IBA1 cells frequently co-expressing MHC II in the spiral ganglion, nerve fibers, lateral wall, spiral limbus, and tympanic covering layer at all cochlear turns as well as in the endolymphatic sac. RNAscope assays revealed extensive expression of fractalkine gene transcripts in type I spiral ganglion cells. CD4 and CD8 cells occasionally surrounded blood vessels in the modiolus and lateral wall. TMEM119 and P2Y12 were not expressed, indicating that the cells labeled with IBA1 were not microglia. The round window niche, compact basilar membrane, and secondary spiral lamina may form protective shields in the cochlear base. Discussion: The results suggest that the human cochlea is surveilled by dwelling and circulating immune cells. Resident and blood-borne macrophages may initiate protective immune responses via chemokine signaling in the lateral wall, spiral

Published
2024
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