Capture 168 PDFs locally; rewrite publication links; underline-only-in-quotes

PDFs:
- Mirrored 168 of 169 publication PDFs from
  daslab.stanford.edu/site_data/pub_pdf/ into assets/pdfs/ so they
  survive the AWS decommission. Total ~1.0 GB.
- One file (Balch_NatComm_2026.pdf, 142 MB) exceeds GitHub's 100 MB
  hard per-file limit; left it pointing to the AWS URL for now and
  stashed a copy at /tmp/dasbackup/. We can move that one to GitHub
  Releases or LFS later.
- Rewrote 168 _publications/*.md pdf: fields from the absolute
  https://daslab.stanford.edu/... URLs to local /assets/pdfs/<name>.

Underline only-the-inner-text:
- publications.md: wrap publication titles in
  <span class='pub-title-text'> inside the surrounding quote marks.
- style.scss: target .pub-title-text (instead of .pub-title) for the
  text-decoration: underline rule on no-thumbnail entries, so the
  underline now stops at the quote marks.

Author: rhiju

.gitattributes

@@ -0,0 +1,2 @@
+/assets/pdfs/Kretsch_Nature_ComplexWaterNetworks_2025.pdf filter=lfs diff=lfs merge=lfs -text
+/assets/pdfs/Kretsch_OrnateRNA_2025.pdf filter=lfs diff=lfs merge=lfs -text

_publications/0004-2025-compact-rna-sensors-for-increasingly-complex-functions-of-mu.md

@@ -4,7 +4,7 @@ year: 2025
 authors: Choe, C.A.*, Andreasson, J.O.L.*, Melaine, F., Kladwang, W., Wu, M.J., Portela, F., Wellington-Oguri, R., Nicol, J.J., Wayment-Steele, H.K., Gotrik, M., Eterna Participants, Khatri, P., Greenleaf, W.J., and Das, R. (*Co-lead authors)
 journal: Nature Chemistry
 thumb: /assets/images/publications/opentb_thumbnail.png
-pdf: "https://daslab.stanford.edu/site_data/pub_pdf/ChoeAndreasson_NatureChemistry_2025.pdf"
+pdf: /assets/pdfs/ChoeAndreasson_NatureChemistry_2025.pdf
 doi: "https://doi.org/10.1038/s41557-025-01907-8"
 featured: True
 order: 4

_publications/0005-2025-blind-prediction-of-complex-water-and-ion-ensembles-around-r.md

@@ -4,7 +4,7 @@ year: 2025
 authors: Kretsch, R.C., Posani, E., Baulin, E.F., Bujnicki, J.M. Bussi, G. Cheatham III, T.E., Chen, S.-J., Elofsson, A. Farsani, M.A., Fisher, O.N., Gromiha, M.M., Gupta, A., Hamada, M., Harini, K.., Hu, G., Huang, D., Iwakiri, J. Jain, A. Kagaya, Y., Kihara, D., Kmiecik, S. Krishnan, S.R., Kurisaki, I., Languin-Cattoën, O., Li, J., Li, S., Malekzadeh, K., Nakamura, T., Ni, W., Nithin, C., Palo, M.Z., Park, J.H., Pilla, S.P., Poblete, S., Pucci, F., Punuru, P., Saha, A., Sato, K., Srivastava, A., Terashi, G., Tugolukova, E., Verburgt, J., Wuyun, Q., Zerze, G.H., Zhang, K., Zhang, S., Zheng, W., Zhou, Y., Chiu, W., Case, D.A., Das, R.
 journal: Proteins
 thumb: /assets/images/publications/R1260_paper_thumbnail_portrait.png
-pdf: "https://daslab.stanford.edu/site_data/pub_pdf/Proteins_-_2025_-_Kretsch_-_Blind_Prediction_of_Complex_Water_and_Ion_Ensembles_Around_RNA_in_CASP16.pdf"
+pdf: /assets/pdfs/Proteins_-_2025_-_Kretsch_-_Blind_Prediction_of_Complex_Water_and_Ion_Ensembles_Around_RNA_in_CASP16.pdf
 doi: "https://dx.doi.org/10.1002/prot.70079"
 featured: True
 order: 5

_publications/0006-2025-assessment-of-nucleic-acid-structure-prediction-in-casp16.md

@@ -4,7 +4,7 @@ year: 2025
 authors: Kretsch R.C., Hummer, A.M., He, S., Yuan, R., Zhang, J., Karagianes, T., Cong, Q., Kryshtafovych, A., Das, R.
 journal: Proteins
 thumb: /assets/images/publications/CASP16_OLE.png
-pdf: "https://daslab.stanford.edu/site_data/pub_pdf/Proteins_-_2025_-_Kretsch_-_Assessment_of_Nucleic_Acid_Structure_Prediction_in_CASP16.pdf"
+pdf: /assets/pdfs/Proteins_-_2025_-_Kretsch_-_Assessment_of_Nucleic_Acid_Structure_Prediction_in_CASP16.pdf
 doi: "https://doi.org/10.1002/prot.70072"
 featured: True
 order: 6

_publications/0008-2025-functional-relevance-of-casp16-nucleic-acid-predictions-as-e.md

@@ -3,7 +3,7 @@ title: Functional relevance of CASP16 nucleic acid predictions as evaluated by s
 year: 2025
 authors: Kretsch, R.C., Albrecht, R., Andersen, E.S., Chen, H., Chiu, W., Das, R., Gezelle, J.G., Hartmann, M.D., Höbartner, C., Hu, Y., Jadhav, S., Johnson, P.E., Jones, P., Koirala, D., Kristoffersen, E.L., Largy, E., Lewicka, A., Mackereth, C.D., Marcia, M., Nigro, M., Ojha, M., Piccirilli, J.A., Rice, P.A., Shin, H., Steckelberg, A., Su, Z., Srivastava, Y., Wang, L., Wu, Y., Xie, J., Zwergius, N.H., Moult, J., Kryshtafovych, A.
 journal: Proteins
-pdf: "https://daslab.stanford.edu/site_data/pub_pdf/Proteins_-_2025_-_Kretsch_-_Functional_Relevance_of_CASP16_Nucleic_Acid_Predictions_as_Evaluated_by_Structure_Providers.pdf"
+pdf: /assets/pdfs/Proteins_-_2025_-_Kretsch_-_Functional_Relevance_of_CASP16_Nucleic_Acid_Predictions_as_Evaluated_by_Structure_Providers.pdf
 doi: "https://doi.org/10.1002/prot.70043"
 order: 8
 ---

_publications/0009-2025-cryo-em-structure-of-human-telomerase-dimer-reveals-haca-rnp.md

@@ -3,7 +3,7 @@ title: Cryo-EM structure of human telomerase dimer reveals H/ACA RNP-mediated di
 year: 2025
 authors: Balch S., Sekne Z., Franco-Echevarría E., Ludzia P., Kretsch R.C., Sun W., Yu H., Ghanim G.E., Thorkelsson S., Ding Y., Das R., Nguyen T.H.D.
 journal: Science
-pdf: "https://daslab.stanford.edu/site_data/pub_pdf/Balch_Science_2025.pdf"
+pdf: /assets/pdfs/Balch_Science_2025.pdf
 doi: "https://dx.doi.org/10.1126/science.adr5817"
 order: 9
 ---

_publications/0010-2025-comprehensive-analysis-of-saccharomyces-cerevisiae-intron-st.md

@@ -3,7 +3,7 @@ title: Comprehensive analysis of Saccharomyces cerevisiae intron structures in v
 year: 2025
 authors: Rangan, R., Huang, R., Hunter O., Pham P., Ares, Jr., M., Das, R.
 journal: Nature Structural & Molecular Biology
-pdf: "https://daslab.stanford.edu/site_data/pub_pdf/Rangan_NSMB_2025.pdf"
+pdf: /assets/pdfs/Rangan_NSMB_2025.pdf
 doi: "https://doi.org/10.1038/s41594-025-01565-x"
 order: 10
 ---

_publications/0011-2025-openaso-rna-rescue-designing-splice-modulating-antisense-oli.md

@@ -3,7 +3,7 @@ title: "OpenASO: RNA Rescue - designing splice-modulating antisense oligonucleot
 year: 2025
 authors: Tse V., Guiterrez M., Townley J., Romano J., Pearl J., Chacaltana G., Eterna Players, Das R., Sanford J.R., Stone M.D.
 journal: RNA
-pdf: "https://daslab.stanford.edu/site_data/pub_pdf/RNA-2025-Tse-rna.080288.124.pdf"
+pdf: /assets/pdfs/RNA-2025-Tse-rna.080288.124.pdf
 doi: "http://dx.doi.org/10.1261/rna.080288.124"
 order: 11
 ---

_publications/0012-2025-naturally-ornate-rna-only-complexes-revealed-by-cryo-em.md

@@ -4,7 +4,7 @@ year: 2025
 authors: Kretsch, R.C. Wu, Y. Shabalina, S.A. Lee, H. Nye, G. Koonin, E.V. Gao, A. Chiu, W. Das, R.
 journal: Nature
 thumb: /assets/images/publications/GOLLD.png
-pdf: "https://daslab.stanford.edu/site_data/pub_pdf/Kretsch_OrnateRNA_2025.pdf"
+pdf: /assets/pdfs/Kretsch_OrnateRNA_2025.pdf
 doi: "https://www.nature.com/articles/s41586-025-09073-0"
 featured: True
 order: 12

_publications/0013-2025-complex-water-networks-visualized-through-22-23-angstrom-cry.md

@@ -3,7 +3,7 @@ title: Complex water networks visualized through 2.2-2.3 Angstrom cryogenic elec
 year: 2025
 authors: Kretsch, R.C., Li, S., Pintilie, G., Palo, M.Z., Case, D.A., Das, R., Zhang, K., Chiu, W.
 journal: Nature
-pdf: "https://daslab.stanford.edu/site_data/pub_pdf/Kretsch_Nature_ComplexWaterNetworks_2025.pdf"
+pdf: /assets/pdfs/Kretsch_Nature_ComplexWaterNetworks_2025.pdf
 doi: "https://doi.org/10.1038/s41586-025-08855-w"
 order: 13
 ---