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feat(xml-jats): parse XML JATS documents (#967)

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* chore(xml-jats): separate authors and affiliations

In XML PubMed (JATS) backend, convert authors and affiliations as they
are typically rendered on PDFs.

Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com>

* fix(xml-jats): replace new line character by a space

Instead of removing new line character from text, replace it by a space character.

Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com>

* feat(xml-jats): improve existing parser and extend features

Partially support lists, respect reading order, parse more sections, support equations, better text formatting.

Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com>

* chore(xml-jats): rename PubMed objects to JATS

Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com>

---------

Signed-off-by: Cesar Berrospi Ramis <75900930+ceberam@users.noreply.github.com>
This commit is contained in:
Cesar Berrospi Ramis
2025-02-17 10:43:31 +01:00
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commit 428b656793
35 changed files with 13688 additions and 30671 deletions
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item-0 at level 0: unspecified: group _root_
item-1 at level 1: title: The coreceptor mutation CCR5Δ32 ... V epidemics and is selected for by HIV
item-2 at level 2: paragraph: Amy D. Sullivan, Janis Wigginton, Denise Kirschner
item-3 at level 2: paragraph: Department of Microbiology and I ... dical School, Ann Arbor, MI 48109-0620
item-4 at level 2: section_header: Abstract
item-5 at level 3: text: We explore the impact of a host ... creasing the frequency of this allele.
item-6 at level 2: text: Nineteen million people have die ... factors such as host genetics (4, 5).
item-7 at level 2: text: To exemplify the contribution of ... follow the CCR5Δ32 allelic frequency.
item-8 at level 2: text: We hypothesize that CCR5Δ32 limi ... g the frequency of this mutant allele.
item-9 at level 2: text: CCR5 is a host-cell chemokine re ... iral strain (such as X4 or R5X4) (30).
item-10 at level 2: section_header: The Model
item-11 at level 3: text: Because we are most concerned wi ... t both economic and social conditions.
item-12 at level 3: picture
item-12 at level 4: caption: Figure 1 A schematic representation of the basic compartmental HIV epidemic model. The criss-cross lines indicate the sexual mixing between different compartments. Each of these interactions has a positive probability of taking place; they also incorporate individual rates of transmission indicated as λ, but in full notation is λ î,,→i,j, where i,j,k is the phenotype of the infected partner and î, is the phenotype of the susceptible partner. Also shown are the different rates of disease progression, γ i,j,k , that vary according to genotype, gender, and stage. Thus, the interactions between different genotypes, genders, and stages are associated with a unique probability of HIV infection. M, male; F, female.
item-13 at level 3: table with [6x5]
item-13 at level 4: caption: Table 1 Children's genotype
item-14 at level 3: section_header: Parameter Estimates for the Model.
item-15 at level 4: text: Estimates for rates that govern ... d in Fig. 1 are summarized as follows:
item-16 at level 4: formula: \frac{dS_{i,j}(t)}{dt}={\chi}_{ ... ,\hat {k}{\rightarrow}i,j}S_{i,j}(t),
item-17 at level 4: formula: \hspace{1em}\hspace{1em}\hspace ... j,A}(t)-{\gamma}_{i,j,A}I_{i,j,A}(t),
item-18 at level 4: formula: \frac{dI_{i,j,B}(t)}{dt}={\gamm ... j,B}(t)-{\gamma}_{i,j,B}I_{i,j,B}(t),
item-19 at level 4: formula: \frac{dA(t)}{dt}={\gamma}_{i,j, ... \right) -{\mu}_{A}A(t)-{\delta}A(t),
item-20 at level 4: text: where, in addition to previously ... on of the infected partner, and j ≠ .
item-21 at level 4: table with [14x5]
item-21 at level 5: caption: Table 2 Transmission probabilities
item-22 at level 4: table with [8x3]
item-22 at level 5: caption: Table 3 Progression rates
item-23 at level 4: table with [20x3]
item-23 at level 5: caption: Table 4 Parameter values
item-24 at level 4: text: The effects of the CCR5 W/Δ32 an ... nting this probability of infection is
item-25 at level 4: formula: {\lambda}_{\hat {i},\hat {j},\h ... \hat {i},\hat {j},\hat {k}} \right] ,
item-26 at level 4: text: where j ≠  is either male or fe ... e those with AIDS in the simulations).
item-27 at level 4: text: The average rate of partner acqu ... owing the male rates to vary (36, 37).
item-28 at level 4: section_header: Transmission probabilities.
item-29 at level 5: text: The effect of a genetic factor i ... reported; ref. 42) (ref. 43, Table 2).
item-30 at level 5: text: Given the assumption of no treat ... ases during the end stage of disease).
item-31 at level 4: section_header: Disease progression.
item-32 at level 5: text: We assume three stages of HIV in ... ssion rates are summarized in Table 3.
item-33 at level 3: section_header: Demographic Setting.
item-34 at level 4: text: Demographic parameters are based ... [suppressing (t) notation]: χ1,j 1,j =
item-35 at level 4: formula: B_{r}\hspace{.167em}{ \,\substa ... }+I_{2,M,k})}{N_{M}} \right] + \right
item-36 at level 4: formula: p_{v} \left \left( \frac{(I_{1, ... ght] \right) \right] ,\hspace{.167em}
item-37 at level 4: text: where the probability of HIV ver ... heir values are summarized in Table 4.
item-38 at level 2: section_header: Prevalence of HIV
item-39 at level 3: section_header: Demographics and Model Validation.
item-40 at level 4: text: The model was validated by using ... 5% to capture early epidemic behavior.
item-41 at level 4: text: In deciding on our initial value ... n within given subpopulations (2, 49).
item-42 at level 4: text: In the absence of HIV infection, ... those predicted by our model (Fig. 2).
item-43 at level 4: picture
item-43 at level 5: caption: Figure 2 Model simulation of HIV infection in a population lacking the protective CCR5Δ32 allele compared with national data from Kenya (healthy adults) and Mozambique (blood donors, ref. 17). The simulated population incorporates parameter estimates from sub-Saharan African demographics. Note the two outlier points from the Mozambique data were likely caused by underreporting in the early stages of the epidemic.
item-44 at level 3: section_header: Effects of the Allele on Prevalence.
item-45 at level 4: text: After validating the model in th ... among adults for total HIV/AIDS cases.
item-46 at level 4: text: Although CCR5Δ32/Δ32 homozygosit ... frequency of the mutation as 0.105573.
item-47 at level 4: text: Fig. 3 shows the prevalence of H ... mic, reaching 18% before leveling off.
item-48 at level 4: picture
item-48 at level 5: caption: Figure 3 Prevalence of HIV/AIDS in the adult population as predicted by the model. The top curve (○) indicates prevalence in a population lacking the protective allele. We compare that to a population with 19% heterozygous and 1% homozygous for the allele (implying an allelic frequency of 0.105573. Confidence interval bands (light gray) are shown around the median simulation () providing a range of uncertainty in evaluating parameters for the effect of the mutation on the infectivity and the duration of asymptomatic HIV for heterozygotes.
item-49 at level 4: text: In contrast, when a proportion o ... gins to decline slowly after 70 years.
item-50 at level 4: text: In the above simulations we assu ... in the presence of the CCR5 mutation.
item-51 at level 4: text: Because some parameters (e.g., r ... s a major influence on disease spread.
item-52 at level 2: section_header: HIV Induces Selective Pressure on Genotype Frequency
item-53 at level 3: text: To observe changes in the freque ... for ≈1,600 years before leveling off.
item-54 at level 3: picture
item-54 at level 4: caption: Figure 4 Effects of HIV-1 on selection of the CCR5Δ32 allele. The Hardy-Weinberg equilibrium level is represented in the no-infection simulation (solid lines) for each population. Divergence from the original Hardy-Weinberg equilibrium is shown to occur in the simulations that include HIV infection (dashed lines). Fraction of the total subpopulations are presented: (A) wild types (W/W), (B) heterozygotes (W/Δ32), and (C) homozygotes (Δ32/Δ32). Note that we initiate this simulation with a much lower allelic frequency (0.00105) than used in the rest of the study to better exemplify the actual selective effect over a 1,000-year time scale. (D) The allelic selection effect over a 2,000-year time scale.
item-55 at level 2: section_header: Discussion
item-56 at level 3: text: This study illustrates how popul ... pulations where the allele is present.
item-57 at level 3: text: We also observed that HIV can pr ... is) have been present for much longer.
item-58 at level 3: text: Two mathematical models have con ... ce of the pathogen constant over time.
item-59 at level 3: text: Even within our focus on host pr ... f a protective allele such as CCR5Δ32.
item-60 at level 3: text: Although our models demonstrate ... f the population to epidemic HIV (16).
item-61 at level 3: text: In assessing the HIV/AIDS epidem ... for education and prevention programs.
item-62 at level 2: section_header: Acknowledgments
item-63 at level 3: text: We thank Mark Krosky, Katia Koel ... ers for extremely insightful comments.
item-64 at level 2: section_header: References
item-65 at level 3: list: group list
item-66 at level 4: list_item: Weiss HA, Hawkes S. Leprosy Rev 72:92–98 (2001). PMID: 11355525
item-67 at level 4: list_item: Taha TE, Dallabetta GA, Hoover D ... AIDS 12:197–203 (1998). PMID: 9468369
item-68 at level 4: list_item: AIDS Epidemic Update. Geneva: World Health Organization1–17 (1998).
item-69 at level 4: list_item: D'Souza MP, Harden VA. Nat Med 2:1293–1300 (1996). PMID: 8946819
item-70 at level 4: list_item: Martinson JJ, Chapman NH, Rees D ... Genet 16:100–103 (1997). PMID: 9140404
item-71 at level 4: list_item: Roos MTL, Lange JMA, deGoede REY ... Dis 165:427–432 (1992). PMID: 1347054
item-72 at level 4: list_item: Garred P, Eugen-Olsen J, Iversen ... Lancet 349:1884 (1997). PMID: 9217763
item-73 at level 4: list_item: Katzenstein TL, Eugen-Olsen J, H ... rovirol 16:10–14 (1997). PMID: 9377119
item-74 at level 4: list_item: deRoda H, Meyer K, Katzenstain W ... ce 273:1856–1862 (1996). PMID: 8791590
item-75 at level 4: list_item: Meyer L, Magierowska M, Hubert J ... AIDS 11:F73–F78 (1997). PMID: 9302436
item-76 at level 4: list_item: Smith MW, Dean M, Carrington M, ... ence 277:959–965 (1997). PMID: 9252328
item-77 at level 4: list_item: Samson M, Libert F, Doranz BJ, R ... don) 382:722–725 (1996). PMID: 8751444
item-78 at level 4: list_item: McNicholl JM, Smith DK, Qari SH, ... ct Dis 3:261–271 (1997). PMID: 9284370
item-79 at level 4: list_item: Michael NL, Chang G, Louie LG, M ... at Med 3:338–340 (1997). PMID: 9055864
item-80 at level 4: list_item: Mayaud P, Mosha F, Todd J, Balir ... IDS 11:1873–1880 (1997). PMID: 9412707
item-81 at level 4: list_item: Hoffman IF, Jere CS, Taylor TE, ... li P, Dyer JR. AIDS 13:487–494 (1998).
item-82 at level 4: list_item: HIV/AIDS Surveillance Database. ... International Programs Center (1999).
item-83 at level 4: list_item: Anderson RM, May RM, McLean AR. ... don) 332:228–234 (1988). PMID: 3279320
item-84 at level 4: list_item: Berger EA, Doms RW, Fenyo EM, Ko ... (London) 391:240 (1998). PMID: 9440686
item-85 at level 4: list_item: Alkhatib G, Broder CC, Berger EA ... rol 70:5487–5494 (1996). PMID: 8764060
item-86 at level 4: list_item: Choe H, Farzan M, Sun Y, Sulliva ... ell 85:1135–1148 (1996). PMID: 8674119
item-87 at level 4: list_item: Deng H, Liu R, Ellmeier W, Choe ... don) 381:661–666 (1996). PMID: 8649511
item-88 at level 4: list_item: Doranz BJ, Rucker J, Yi Y, Smyth ... ell 85:1149–1158 (1996). PMID: 8674120
item-89 at level 4: list_item: Dragic T, Litwin V, Allaway GP, ... don) 381:667–673 (1996). PMID: 8649512
item-90 at level 4: list_item: Zhu T, Mo H, Wang N, Nam DS, Cao ... ce 261:1179–1181 (1993). PMID: 8356453
item-91 at level 4: list_item: Bjorndal A, Deng H, Jansson M, F ... rol 71:7478–7487 (1997). PMID: 9311827
item-92 at level 4: list_item: Conner RI, Sheridan KE, Ceradini ... Med 185:621–628 (1997). PMID: 9034141
item-93 at level 4: list_item: Liu R, Paxton WA, Choe S, Ceradi ... Cell 86:367–377 (1996). PMID: 8756719
item-94 at level 4: list_item: Mussico M, Lazzarin A, Nicolosi ... w) 154:1971–1976 (1994). PMID: 8074601
item-95 at level 4: list_item: Michael NL, Nelson JA, KewalRama ... rol 72:6040–6047 (1998). PMID: 9621067
item-96 at level 4: list_item: Hethcote HW, Yorke JA. Gonorrhea ... and Control. Berlin: Springer (1984).
item-97 at level 4: list_item: Anderson RM, May RM. Nature (London) 333:514–522 (1988). PMID: 3374601
item-98 at level 4: list_item: Asiimwe-Okiror G, Opio AA, Musin ... IDS 11:1757–1763 (1997). PMID: 9386811
item-99 at level 4: list_item: Carael M, Cleland J, Deheneffe J ... AIDS 9:1171–1175 (1995). PMID: 8519454
item-100 at level 4: list_item: Blower SM, Boe C. J AIDS 6:1347–1352 (1993). PMID: 8254474
item-101 at level 4: list_item: Kirschner D. J Appl Math 56:143–166 (1996).
item-102 at level 4: list_item: Le Pont F, Blower S. J AIDS 4:987–999 (1991). PMID: 1890608
item-103 at level 4: list_item: Kim MY, Lagakos SW. Ann Epidemiol 1:117–128 (1990). PMID: 1669741
item-104 at level 4: list_item: Anderson RM, May RM. Infectious ... ol. Oxford: Oxford Univ. Press (1992).
item-105 at level 4: list_item: Ragni MV, Faruki H, Kingsley LA. ... ed Immune Defic Syndr 17:42–45 (1998).
item-106 at level 4: list_item: Kaplan JE, Khabbaz RF, Murphy EL ... virol 12:193–201 (1996). PMID: 8680892
item-107 at level 4: list_item: Padian NS, Shiboski SC, Glass SO ... nghoff E. Am J Edu 146:350–357 (1997).
item-108 at level 4: list_item: Leynaert B, Downs AM, de Vincenzi I. Am J Edu 148:88–96 (1998).
item-109 at level 4: list_item: Garnett GP, Anderson RM. J Acquired Immune Defic Syndr 9:500–513 (1995).
item-110 at level 4: list_item: Stigum H, Magnus P, Harris JR, S ... eteig LS. Am J Edu 145:636–643 (1997).
item-111 at level 4: list_item: Ho DD, Neumann AU, Perelson AS, ... don) 373:123–126 (1995). PMID: 7816094
item-112 at level 4: list_item: World Resources (1998–1999). Oxford: Oxford Univ. Press (1999).
item-113 at level 4: list_item: Kostrikis LG, Neumann AU, Thomso ... 73:10264–10271 (1999). PMID: 10559343
item-114 at level 4: list_item: Low-Beer D, Stoneburner RL, Muku ... at Med 3:553–557 (1997). PMID: 9142126
item-115 at level 4: list_item: Grosskurth H, Mosha F, Todd J, S ... . AIDS 9:927–934 (1995). PMID: 7576329
item-116 at level 4: list_item: Melo J, Beby-Defaux A, Faria C, ... AIDS 23:203–204 (2000). PMID: 10737436
item-117 at level 4: list_item: Iman RL, Helton JC, Campbell JE. J Quality Technol 13:174–183 (1981).
item-118 at level 4: list_item: Iman RL, Helton JC, Campbell JE. J Quality Technol 13:232–240 (1981).
item-119 at level 4: list_item: Blower SM, Dowlatabadi H. Int Stat Rev 62:229–243 (1994).
item-120 at level 4: list_item: Porco TC, Blower SM. Theor Popul Biol 54:117–132 (1998). PMID: 9733654
item-121 at level 4: list_item: Blower SM, Porco TC, Darby G. Nat Med 4:673–678 (1998). PMID: 9623975
item-122 at level 4: list_item: Libert F, Cochaux P, Beckman G, ... Genet 7:399–406 (1998). PMID: 9466996
item-123 at level 4: list_item: Lalani AS, Masters J, Zeng W, Ba ... e 286:1968–1971 (1999). PMID: 10583963
item-124 at level 4: list_item: Kermack WO, McKendrick AG. Proc R Soc London 261:700–721 (1927).
item-125 at level 4: list_item: Gupta S, Hill AVS. Proc R Soc London Ser B 260:271–277 (1995).
item-126 at level 4: list_item: Ruwende C, Khoo SC, Snow RW, Yat ... don) 376:246–249 (1995). PMID: 7617034
item-127 at level 4: list_item: McDermott DH, Zimmerman PA, Guig ... ncet 352:866–870 (1998). PMID: 9742978
item-128 at level 4: list_item: Kostrikis LG, Huang Y, Moore JP, ... at Med 4:350–353 (1998). PMID: 9500612
item-129 at level 4: list_item: Winkler C, Modi W, Smith MW, Nel ... ence 279:389–393 (1998). PMID: 9430590
item-130 at level 4: list_item: Martinson JJ, Hong L, Karanicola ... AIDS 14:483–489 (2000). PMID: 10780710
item-131 at level 4: list_item: Vernazza PL, Eron JJ, Fiscus SA, ... AIDS 13:155–166 (1999). PMID: 10202821
item-132 at level 1: caption: Figure 1 A schematic representat ... of HIV infection. M, male; F, female.
item-133 at level 1: caption: Table 1 Children's genotype
item-134 at level 1: caption: Table 2 Transmission probabilities
item-135 at level 1: caption: Table 3 Progression rates
item-136 at level 1: caption: Table 4 Parameter values
item-137 at level 1: caption: Figure 2 Model simulation of HIV ... g in the early stages of the epidemic.
item-138 at level 1: caption: Figure 3 Prevalence of HIV/AIDS ... of asymptomatic HIV for heterozygotes.
item-139 at level 1: caption: Figure 4 Effects of HIV-1 on sel ... n effect over a 2,000-year time scale.