Endy version

backend/app.py

@@ -39,7 +39,8 @@ def load_document(filename):
 # Load prompts at startup
 SYSTEM_PROMPT_TEMPLATE = load_prompt("system_prompt.txt")
 TRANSITION_PROMPT_TEMPLATE = load_prompt("transition_prompt.txt")
-DOCUMENT = load_document("patricia.txt")
+DOCUMENT = load_document("endy.txt")
+USER_GOAL = "Understand the new in situ doping strategy introduced here, how it changes precursor formation and cathode performance compared to conventional methods, and what generalizable materials insights and electrochemical improvements result from it."
 app = FastAPI()
 
 # Enable CORS
@@ -77,8 +78,8 @@ async def chat_endpoint(request: ChatRequest):
     current_chunk = request.currentChunk or request.chunk or "No specific chunk provided"
     next_chunk = request.nextChunk or ""
     action = request.action
-    user_goal = request.user_goal or "Understanding why these methods were used for the main question and how successful was the Apicomplexa treatment with herbicides?"
-    
+    user_goal = request.user_goal or USER_GOAL
+
     # Only include full document on first message or transitions to provide initial context
     include_document = len(request.messages) <= 1 or action in ['skip', 'understood']
     document = DOCUMENT if include_document else ""
@@ -181,7 +182,7 @@ async def chat_stream(request: ChatRequest):
     next_chunk = request.nextChunk or ""
     action = request.action
     
-    user_goal = request.user_goal or "Understanding GRPO (equation 3) and why does this make sense in contrast to PPO?"
+    user_goal = request.user_goal or USER_GOAL
     
     # Only include full document on first message or transitions to provide initial context
     # After that, the conversation history maintains context

frontend/src/components/DocumentViewer.jsx

@@ -46,7 +46,7 @@ const MyHighlightContainer = () => {
   return component;
 };
 
-const DocumentViewer = ({ selectedFile, documentData, onPageChange, preloadedHighlights = null, currentChunkIndex = null, onDocumentReady = null }) => {
+const DocumentViewer = ({ selectedFile, documentData, onPageChange, preloadedHighlights = null, currentChunkIndex = null, onDocumentReady = null, isChunkLoading = null }) => {
     const [highlights, setHighlights] = useState([]);
     const [pdfUrl, setPdfUrl] = useState(null);
     const [zoom, setZoom] = useState(1);
@@ -191,13 +191,18 @@ const DocumentViewer = ({ selectedFile, documentData, onPageChange, preloadedHig
     // Auto-scroll to current chunk when currentChunkIndex changes (only on navigation, not during streaming)
     useEffect(() => {
         // Only auto-scroll if we have highlighter utils and this is a valid chunk navigation
-        if (highlighterUtilsRef.current && currentChunkIndex !== null && currentChunkIndex !== undefined && currentChunkIndex >= 0) {
+        // Don't auto-scroll during streaming (when isChunkLoading is true for currentChunkIndex)
+        if (highlighterUtilsRef.current && 
+            currentChunkIndex !== null && 
+            currentChunkIndex !== undefined && 
+            currentChunkIndex >= 0 &&
+            (!isChunkLoading || !isChunkLoading(currentChunkIndex))) {
             // Small delay to ensure highlights are loaded
             setTimeout(() => {
                 scrollToChunk(currentChunkIndex);
             }, 200);
         }
-    }, [currentChunkIndex]); // Only depend on currentChunkIndex, not preloadedHighlights
+    }, [currentChunkIndex, isChunkLoading]); // Only depend on currentChunkIndex, not preloadedHighlights
 
     // Handle selection - log coordinates and add debugging
     const handleSelection = (selection) => {

frontend/src/components/ProgressBar.jsx

@@ -5,7 +5,7 @@ const ProgressBar = ({
     totalChunks, 
     onChunkClick = null // Optional: allow clicking on progress bar segments
 }) => {
-    const progressPercentage = totalChunks > 0 ? ((currentChunkIndex) / totalChunks) * 100 : 0;
+    const progressPercentage = totalChunks > 0 ? ((currentChunkIndex +1) / totalChunks) * 100 : 0;
     
     return (
         <div className="w-full">

frontend/src/components/SimpleChat.jsx

@@ -44,9 +44,10 @@ const SimpleChat = ({ messages, currentChunkIndex, onSend, isLoading }) => {
   const scrollAfterLayout = () => {
     requestAnimationFrame(() => {
       requestAnimationFrame(() => {
-        if (anchorRef.current) {
-          // Scroll the anchor to the top of the nearest scrollable ancestor (your container).
-          anchorRef.current.scrollIntoView({ behavior: 'smooth', block: 'start', inline: 'nearest' });
+        if (anchorRef.current && containerRef.current) {
+          // Calculate position relative to container instead of using scrollIntoView
+          const anchorTop = anchorRef.current.offsetTop;
+          containerRef.current.scrollTo({ top: anchorTop, behavior: 'smooth' });
         } else if (containerRef.current) {
           // fallback: go to top
           containerRef.current.scrollTo({ top: 0, behavior: 'smooth' });

frontend/src/hooks/useDocumentProcessor.js

@@ -47,44 +47,36 @@ export const useDocumentProcessor = () => {
             // Use hardcoded chunks for the document
             const hardcodedChunks = [
   {
-    "topic": "The Rationale: Why Target a Plant-Like Organelle in the Malaria Parasite?",
-    "text": "With *P. falciparum* containing a plant-like plastid apicoplast, the membranes surrounding the apicoplast suggested that glycerolipids that are unique to algae and plant plastids might also be present in the apicoplast membranes. As such, MGDG and DGDG may be present in Apicomplexa like *P. falciparum* and *T. gondii*. Investigations of galactolipid biosynthesis and content in membranes of these Apicomplexa have indicated that radioactively labelled UPD-galactose is incorporated into both MGDG and DGDG. The latter was also immunologically detected in parasite lysates (Figure 1.10). Distinct enzymatic processes or amino acid derivation of the synthases were involved since no clear identification of MGDG or DGDG synthase orthologues could be identified in the *P. falciparum* genome utilising only bioinformatic searches (119)."
+    "topic": "The Core Problem: Instability in Advanced Single-Crystal Cathodes",
+    "text": `INTRODUCTION\nWith the aim to establish a low-carbon and environmentally\nfriendly society, next-generation lithium-ion batteries (LIBs)\nare urgently required to promote the large-scale application of\nelectric vehicles. 1,2 Since Ni element dominates the reversible\ncapacity, Ni-rich layered oxides receive great expectations due\nto their exceptional advantages in energy density and\nproduction cost, especially for ultrahigh-nickel Li-\nNixCo,Mn1-x-yO2 (NCM, x ≥ 0.9).3−8 However, the conven-\ntional spherical NCM cathodes formed by agglomeration of\nprimary particles always suffer from severe structural\ndegradation with the generation of intergranular microcracks\nand detrimental phase transitions during cycling.9–12 Recently,\nthe NCM fabrication with quasi single-crystal morphology\n(SNCM) has attracted enormous research attention both in industry and laboratory, which is widely considered as a\npromising modification strategy. 13,14 The SNCM cathode\nconsists of single dispersed particles of 2−5 μm with an\nenhanced crystalline structure and internal boundary-free\nconfiguration. 15,16 Benefiting from its exceptional morphology,\nSNCM can significantly alleviate the accumulation of\nanisotropic stresses and intergranular microcrack formation,\nleading to a considerable enhancement in capacity retention and cycled particle integrity.17,18 Meanwhile, its excellent\nmechanical strength is beneficial in further increasing the\ncompaction density of cathodes to achieve higher specific\nenergy density with relative low cost.19,20\nWhile the transformation of agglomerated nanoparticles into\nseparate micron-sized single-crystals presents numerous\nadvantages, it also unveils some inherent challenges.21 The\nlower specific surface area and prolonged Li+ diffusion distance\nin single-crystal particles can contribute to the sluggish Li+\ndiffusion kinetics, resulting in poor capacity and inferior rate\nperformance of SNCM.22−24 This will further trigger\ninhomogeneous distribution of Li+ concentration during\ncycling, causing the coexistence of multiple phases with severe\nlattice strain within single-crystals.25 As a result, lattice strain\nexacerbates planar gliding and intragranular cracks generation\nof microsized single-crystals, which has been considered as the\nroot cause of surface degradation and structural damage.26,27\nTherefore, the poor Li+ diffusion kinetics is the origin of various degradation mechanisms in SNCM and urgently needs\nto be improved to advance its application potential.`
   },
   {
-    "topic": "The Strategy: Using Herbicides as a Starting Point for Antimalarials",
-    "text": "MGDG synthase has been shown to be essential to plant cell growth, with knock-outs of MGD1 in *Arabidopsis* as a member of the multigene MGDG synthase family, leading to a complete lack of chlorophyll, chloroplast ultrastructure disruption and severe plant growth inhibition (118). This data provides support for galactolipid biosynthesis as a valid growth inhibition strategy. As this process is unique in *P. falciparum* and not found in humans, it is an enticing strategy for the development of novel antimalarials."
+    "topic": "The Conventional Solution and Its Limitations: Dry Doping",
+    "text": "Element doping has been widely confirmed as a promising\napproach to enhance the Li+ diffusion kinetics and structural\nstability of SNCM.28−34 However, most current research has\npredominantly focused on the dry-doping method, where\ndopants are added during the mixing stage between lithium\nand SNCM precursors.16,35 For this approach, certain\nsubstitution elements face challenges in incorporating into\nthe cathode lattice due to their large atomic mass and limited\nsolid solubility,31 resulting in an inhomogeneous distribution\nwithin the bulk and causing internal structural degradation in\nSNCM. Moreover, the dopants tend to react with the lithium\nsource at the surface to generate a nonuniformly distributed\nimpurity layer that obstructs Li+ diffusion channels. Overly\nincreasing the sintering time and temperature to promote the\ndiffusion of doping ions may lead to severe Li/Ni disorder-\ning.36"
   },
   {
-    "topic": "The Specific Compound: Introducing A51B1C1_1",
-    "text": "Due to the presence of MGDG and DGDG in the plant-derived apicoplast of  $P.$  falciparum, an interesting speculation is that Galvestine-1 and its derivatives might have growth-inhibitory capacity against the malaria parasite by targeting lipid biosynthesis processes in the apicoplast. This study therefore presents the determination of the antimalarial property of one of the lead MGDG synthase inhibitors from the Botté study, A51B1C1_1 (Figure 1.13).\n\nOne major advantage of this strategy would be that these compounds are herbicidederived and could therefore, if they are active against *P. falciparum*, prove to be highly selective to the parasite without targeting any metabolic process in humans. This compound furthermore provides a novel chemical scaffold unrelated to any current antimalarials, which would be a novel action in the parasite compared to currently used antimalarials, and be able to overcome the resistance mechanisms against current antimalarials. Thus, if these compounds prove to be active against the malaria parasite, they may be developed into new antimalarial drugs."
+    "topic": "The Innovation: An 'Inside-Out' In Situ Doping Strategy",
+    "text": "In contrast, the in situ doping method, where dopants\nand the main elements (Ni, Co, and Mn) are simultaneously added during the coprecipitation reaction for precursor\npreparation, can result in a homogeneous modification effect\nfrom the inside out and effectively address aforementioned\nproblems.9,37 Although the in situ doping possesses obvious\nmerits for holistically enhancing the Li+ diffusion kinetics of\nSNCM, there is a high threshold for attaining the desired\neffect. The choice of dopant needs to take into account its\nsolubility and thermodynamic diffusion properties. Meanwhile,\nthe amount of dopant addition requires precise regulation to\nprevent affecting the supersaturation within the reaction\nsystem and thus producing low-quality precursors.\nIn this work, we thoroughly investigated the in situ doping\ntechnology to achieve the optimal dopant element (Nb, Zr, W,\netc), doping amount and reaction conditions, enabling precise\ncontrol over the preparation of in situ doped single-crystal\nLiNi0.92Co0.03Mn0.05O2 (SNCM). It is confirmed that in situ\ndoping offers distinct advantages in the successful incorpo-\nration and uniform dispersion of dopants into the precursor\nlattice, resulting in modulated precursor primary particle\nmorphology."
   },
   {
-    "topic": "The Research Aims: A Multi-Faceted Approach",
-    "text": "The primary objective of this study was to determine the antimalarial potential of compound A51B1C1_1 as well as the physiological response of *P. falciparum* after treatment with this compound by employing a comprehensive functional genomics approach.\n\nChapter 2 focuses on determining the antimalarial activity of A51B1C1_1 through morphological investigation of *P. falciparum* after treatment with this compound. This is followed by a complete transcriptome analysis employing DNA microarray to identify responsive transcripts in *P. falciparum* that were differentially regulated upon treatment with this compound.\n\nChapter 3 introduces the use of higher-level functional genomics analyses of the response of *P. falciparum* to A51B1C1 1 treatment by investigating the proteome of the parasites after perturbation with this herbicide-derived compound."
+    "topic": "Mechanism: How In Situ Doping Engineers a Better Precursor",
+    "text": "A schematic diagram is provided to better understand the\nmechanism of coprecipitation reaction and the underlying\nreason for the morphological variation (Figure 1g). During the\npreparation of precursors, the main transition metal ions (Ni2+,\nMn2+, Co2+) in the system rapidly combine with hydroxide and\nprecipitate to form massive crystal nuclei.42,43 Subsequently,\nthe massive crystal nuclei promptly bind ions from the solution\nto form primary particles. In general, the {010} planes combine\nions faster than other planes due to its higher surface\nenergy,41,44 thus resulting in that the primary particles prefer\nto grow horizontally to obtain high exposure {001} planes.45\nMeanwhile, the {001} planes with lower surface energy can\nmerely agglomerate fewer stacked layers in the longitudinal\ndirection. However, when Nb-ions are continuously added into\nthe reaction system, the {010} planes will interact with doping\nions predominantly because Nb5+ are subjected to stronger\nelectrostatic adsorption force due to their more positive\ncharges than Ni2+, Co2+ and Mn2+. The substantial amounts of\nNb-ions accumulated on {010} planes exhibit an inhibiting\neffect on its horizontal growth, resulting in the morphology of\nhigh exposure {010} planes. Furthermore, the surface energy of\n{001} planes relatively get raised, thus tending to agglomerate\nmore longitudinal stacked layers. It is obvious that all these characterizations substantiate the controlled morphology\nmodulation and homogeneous Nb doping of NCMOH-Nb,\ndemonstrating the success of precursor engineering for in situ\ndoping. Notably, considering that the cathodes incline to well\ninherit the morphological structure of precursors, both the\nhigh exposure {010} planes and more longitudinal stacked\nlayers of NCMOH-Nb precursor are favorable to provide more\nLi+ channels and enhanced diffusion kinetics for SNCM-Nb-\nwet cathode.46,47"
   },
   {
-    "topic": "Method 1: Measuring Potency (IC50 Determination)",
-    "text": "#### 2.3.1 $IC_{50}$ determinations\n\nDose-response curves were established to determine the median inhibitory concentration ( $IC_{50}$ ) of the herbicide derivative A51B1C1_1 using a fluorescent SYBR Green I assay (MSF assay) on the chloroquine-sensitive *P. falciparum* strain 3D7. The average  $IC_{50}$  value of A51B1C1_1 determined in four individual experiments was found to be 447 ±16 nM (Figure 2.5)."
+    "topic": "Result 1: Improved Structural Stability and Phase Transition",
+    "text": "Effects of In Situ Doping on Structural Stability and\nLi+ Diffusion Kinetics. To comprehensively investigate the\neffects of dry and wet Nb doping on the structural evolution\nand phase transition reversibility during Li+ (de)intercalation,\nin situ XRD measurements were conducted with a potential\nrange of 2.5−4.5 V at 0.2 C. [...] Figure 3a exhibits a\nmagnified view of the (003) peak and the corresponding lattice\nparameter variations during the initial cycle. When charging\nfrom 2.5 to 4.18 V, the (003) diffraction peaks of all cathodes\nare slightly shifted to a smaller 2θ angle. With further charging\nto 4.5 V, the (003) diffraction peaks shift significantly to a\nlarger 2θ angle, illustrating that the cathodes encounter a\nsudden decay of c-axis parameters during the H2−H3 phase\ntransition.53,54 Because it is difficult to fully recover, H2−H3 is\ngenerally considered to be an irreversible phase transition. Its\nshift angle is a sign of structural stability for the SNCM\ncathode.55,56 In comparison, it is revealed that SNCM-Nb-wet\nfeatures the minimum H2−H3 phase transition angle of 1.11°,\noutperforming the 1.23° of SNCM-Nb-dry and 1.30° of\nSNCM-pure, which indicates the advantages of in situ doping\nfor suppressing the dramatic contraction of the lattice\nparameters. [...] In comparison, SNCM-Nb-wet experiences a\nsmooth H2−H3 phase transition accompanied by a confined\nwidth and intensity change during the entire charging/\ndischarging process (Figure 3d). Simultaneously, its structural\ntransition is fully reversible without residual phases. This\nphenomenon is due to that the internal homogeneous Nb5+\nmodification formed by in situ doping can effectively build\nstronger metal-oxygen bonds and stabilize the crystal\nstructure,48,58 thus alleviating the Li+ migration hindrance\nand hysteresis caused by the long transport distance inside the\nsingle-crystal particles. Thus, SNCM-Nb-wet obtained a\nsmoother phase transition and improved Li+ diffusion kinetics."
   },
   {
-    "topic": "Method 2: Observing the Physical Effects (Morphology Studies)",
-    "text": "#### 2.3.2 Morphology studies\n\nTwo independent *P. falciparum* (3D7) parasite cultures were treated at  $2xIC_{50}$ A51B1C1_1 and Galvestine-2 (Data for Galvestine-2 treated *P. falciparum* were obtained from a previous study by Mr J.C. Verlinden (166) and was included in this study as an additional analogue of the Galvestine-1 parent compound) and the effects on the morphology of the parasites were observed for 72 h. [...] In contrast *P. falciparum* parasites treated with A51B1C1_1 continued to show similarities to the control culture through the ring stage and early trophozoite stages. However, at 48 hpi, the control untreated parasites entered the merozoite stage, but the A51B1C1_1 treated parasites became pyknotic and remained so for the rest of the life cycle and was unable to progress to a new life cycle. These parasites could not invade new erythrocytes and form new rings, unlike the control culture."
+    "topic": "Result 2: Superior Electrochemical Performance and Cycling Stability",
+    "text": "Comparison of Electrochemical Performances of Dry/\nIn Situ Doped Cathodes. After demonstrating that in situ\ndoping is beneficial in providing excellent structural stability and lithium-ion diffusion kinetics, we performed electro-\nchemical measurements under different operating temperatures\nin order to verify the advantages it brings to lithium storage\nperformance. As illustrated in Figure 4a, the initial discharge\ncapacities of Nb-doped cathodes at 1 C (SNCM-Nb-dry: 184.1\nmAh g−1, SNCM-Nb-wet: 182.7 mAh g−1) appear slightly\nlower than that of pristine cathode (SNCM-pure: 187.6 mAh\ng−1) due to the doping of inert Nb-ions.62 Whereas, SNCM-\nNb-wet displays the best cycling stability among these three\nsingle-crystal cathodes, with an excellent cycling retention of\n76.1% after 400 cycles. In comparison, SNCM-pure and\nSNCM-Nb-dry display a consistent capacity decay, showing\ncycling retentions of 56.8% and 65.1%, respectively. [...] Benefiting from the\nimproved Li+ diffusion kinetics inside the micron-sized\nsingle-crystal particles by in situ doping, SNCM-Nb-wet still\ncan exhibit enhanced cycling stability at high rate of 5 C with\n76.5% after 200 cycles, significantly superior to 64.6% of\nSNCM-Nb-dry and 44.2% of SNCM-pure (Figure 4c).\nFurthermore, increasing the operating temperature of Ni-\nrich SNCM is commonly regarded as an effective method to\nimprove the discharge specific capacities, but it generally\ncauses thermal safety issues during the practical application.69\nConsequently, the prepared samples are further evaluated at\nincreased temperatures up to 45 °C to demonstrate the\nadvantages of in situ doping. Figure 4d displays the cycling\nperformances of pristine and Nb-doped cathodes at 1 C and 45\n°C. SNCM-Nb-wet exhibits an outstanding capacity stability of\n75.5% after 200 cycles, obviously better than 63.6% of SNCM-\nNb-dry and 51.2% of SNCM-pure."
   },
   {
-    "topic": "Interpretation: The Compound Is Potent and Fast-Acting",
-    "text": "The IC<sub>50</sub> of compound A51B1C1 1 determined in a preliminary study in Grenoble, France (collaborator E. Maréchal), using the <sup>3</sup>H-hypoxanthine incorporation method, was found to be 180 nM (Personal communication, Eric Maréchal, Pretoria, 2009). The IC<sub>50</sub> value determined in this study using the SYBR Green I method was shown to be  $447 \\pm 16$  nM. The different values may be due to the techniques used to determine the  $IC_{50}$  as was previously observed (186, 191, 192). Values below 1  $\\mu$ M comply with the MMV requirements (www.mmv.org) and are an indication that a compound may have potential against *P. falciparum*."
+    "topic": "Visualizing the Mechanism: Uniform Li+ Distribution Prevents Cracks",
+    "text": "Simulation of Modified Mechanism in In Situ Doped\nCathodes. According to the aforementioned discussions, in\nsitu doped cathodes show a smoother phase transition process,\nwhich may lead to a more uniform internal Li+ concentration\ndistribution and superior Li+ diffusion kinetics. To visualize\nthis modification effect, COMSOL software is utilized to\nsimulate the internal Li+ concentration distribution [...]. Subsequently, along\nwith the detachment of Li+, SNCM-Nb-dry (Figure 5a) has an\naggravated Li+ concentration gradient distribution at all voltage\nstates. This corresponds to the severe two-phase coexistence\nobserved in the in situ XRD pattern, which will generate\ninhomogeneous intragranular stresses, eventually leading to\nstructural degradation. In contrast, SNCM-Nb-wet (Figure 5b)\ndisplays a relatively uniform and moderate Li+ concentration\nvariation during the whole charging/discharge process, which\nis beneficial for the single-crystal cathode to maintain the\nstructural stability throughout the long-term cycling. [...] To explore the modification mechanism of in\nsitu doping on structure stability, the morphology and\nmicrostructure evolution of SNCM-Nb-dry and SNCM-Nb-\nwet were detected by SEM and HRTEM after 100 cycles at 5\nC. As seen in Figure 6a, the internal cross-sectional structure of\nSNCM-Nb-dry is damaged after cycling and contains a\nmultitude of cracks and holes. [...] As for SNCM-Nb-\nwet, it can be discovered that after cycles the cross-sectional\nmorphology remains dense and integrated (Figure 6c). The\nHRTEM image of SNCM-Nb-wet (Figure 6d) also confirms\nthat the cathode maintains the intact R3m layered structure at\nthe particle surface[...]."
   },
   {
-    "topic": "Interpretation: A Lack of 'Delayed Death' Suggests a Non-Housekeeping Target",
-    "text": "Delayed death is a phenomenon where the perturbation only causes the death of the parasite in the next life cycle. [...] In contrast, drugs affecting non-housekeeping processes in the apicoplast of *P. falciparum* have been shown to not display delayed death phenomena (126). These drugs result in visible stress symptoms and growth arrest of the parasites within the first life cycle after exposure. Analyses of *P. falciparum* parasites treated with the herbicide derivative A51B1C1 1  $(2xIC_{50})$  revealed morphological signs of stress in the form of pyknotic parasites within the first 48 h. [...] Stressed forms of *P. falciparum* parasites under A51B1C1 1 pressure could indicate that either 1) this compound targets non-housekeeping processes of the apicoplast with no delayed death phenotype; or 2) the compound targets another biological process in the parasite not associated with the apicoplast."
-  },
-  {
-    "topic": "Method 3: Pinpointing the Target with Transcriptomics",
-    "text": "Using the information obtained from the morphological studies, the microarray study was designed and two time points were selected for the extraction of RNA from synchronised parasites. The background noise from multiple life stages is reduced in synchronised cultures enabling the detection of abundance differences in transcript levels above the normal levels in the IDC (158). [...] The time points selected for the sampling of RNA was 28 hpi and 36 hpi, which covers the life stages in which a morphological effect is seen after treatment with A51B1C1_1."
-  },
-  {
-    "topic": "Result: Transcript Data Confirms Lipid Metabolism as the Target",
-    "text": "The 1504 transcript data set includes ten transcripts (three with increased abundance and seven with decreased abundance, Table 2.6) involved in lipid biosynthesis or fatty acid biosynthesis. The presence of these transcripts (all have Log<sub>2</sub> FC of about 1) in the data set indicates the effect of the treatment on lipid biosynthesis (three in glycerophospholipid metabolism, Figure 2.20, and two in glycerolipid metabolism, Figure 2.21). In glycerophospholipid metabolism, three transcripts were affected of which one increased in abundance (PF14_0097, EC 2.7.7.41 – Cytidine-diphosphate-DAG synthase) and two with decreased abundance (PFI 1370, EC 4.1.1.65 -Phosphatidyl serine-decarboxylase and PF14 0020, EC 2.7.1.32 – Choline kinase) (Figure 2.20). In glycerolipid metabolism two transcripts (PFC0995c, EC 2.3.1.20 -DAG O-acyltransferase and PFI 1485, EC 2.7.1.107 – DAG kinase) both decreased in abundance (Figure 2.21)."
+    "topic": "Generalizing the Strategy and Summarizing the Mechanism",
+    "text": "In Situ Doping Promotion for Other Elements. More\nimportantly, we introduce dopants Zr4+ and W6+ in order to\nfurther demonstrate the advantages of in situ doping on the\ncathode properties. The dry and in situ doped cathodes are\nobtained by the same coprecipitation and two-stage calcination process. According to Figure 7a and Figure S24, the Zr-doped\nmaterials exhibit similar single-crystal particle morphology. [...] As\nseen in Figure 7g, SNCM-Zr-wet presents the best cycling\nretention with 90.8% after 100 cycles, obviously better than 80.5% of SNCM-Zr-dry and 69.9% of SNCM-pure. [...] Based\non the successful attempt of various doping ions, it is evident\nthat in situ doping achieves a uniform and consistent\nmodification effect within single-crystal particles and demon-\nstrates a certain applicability for different doping elements\n(Nb, Zr, W, etc).\nAnalysis of In Situ Doping Modification Mechanism.\n[...] In\ncomparison, the in situ doped cathodes benefited from the\nuniform distribution of doping ions and can substantially\naccelerate the Li+ diffusion kinetics and migration rate from the\ninside out. Furthermore, the fluent Li+ transportation results in\na uniform phase transition process and optimized Li+\nconcentration distribution, which can ensure the reversibility\nof the H2/H3 transition and alleviate the inner stress without\nthe formation of intragranular cracks. Hence, the in situ doped\ncathode maintains an integrated structure and excellent\nelectrochemical performances after long-term cycling."
   }
 ];