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BACKGROUND: Ovarian Cancer (OC) is a lethal malignant tumor with a poor prognosis. Disulfidptosis is a newly identified form of cell death caused by disulfide stress. Targeting disulfidptosis is a new metabolic therapeutic strategy in cancer treatment. We aimed to establish a disulfidptosis- related lncRNA signature for prognosis prediction and explore its treatment values in OC patients. METHOD: Data from the TCGA and GTEx databases and a disulfidptosis gene set were used to establish a disulfidptosis-related lncRNA signature for prognosis prediction in OC patients. Then, we internally and externally (PCR) validated our model. We also built a nomogram to improve our model's predictive power. Afterward, GSEA was employed to explore our model's potential functions. The ESTIMATE, CIBERSORT, TIMER, and ssGSEA were applied to estimate the immune landscape. Finally, the drug sensitivity of certain drugs for OC patients was analyzed. RESULTS: We built a prognosis model based on seven drlncRNAs, including AL157871.2, HCP5, AC027348.1, AL109615.3, AL928654.1, LINC02585, and AC011445.1. Our model performed well by internal validation. PCR data also confirmed the same trend in the lncRNA levels. Furthermore, the nomogram-integrated age, grade, stage, and risk score could accurately predict the survival outcomes of OC patients. Subsequently, GSEA unveiled that our model genes enriched the Hedgehog signaling pathway, a key regulator in OC tumorigenesis. Our predictive signature was associated with immune checkpoints, such as PD-1(P < 0.01), PD-L1(P < 0.001), and CTLA4 (P < 0.01), which might help screen out OC patients who are sensitive to immunotherapy. Small molecule drugs, such as AZD-2281, GDC-0449, imatinib, and nilotinib, might benefit OC patients with different risk scores. CONCLUSION: Our disulfidptosis-related lncRNA signature comprised of AL157871.2, HCP5, AC027348.1, AL109615.3, AL928654.1, LINC02585, and AC011445.1 could serve as a prognostic biomarker and guidance to therapy response for OC patients.
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Background and aims: Age-related cognitive impairment impacts a significant portion of the elderly population. Remnant cholesterol (RC) has attracted increased attention in relation to cardiovascular disease, diabetes, hypertension, and fatty liver disease. Nevertheless, its role in cognitive function is still enigmatic, prompting our exploration into the potential associations between them. Methods: A total of 1,331 participants from the NHANES (2011-2014) database, all aged over 60, were included in this investigation. Cognitive function was assessed using four widely applied tests, including the Consortium to Establish a Registry for Alzheimer's Disease Word Learning (CERAD-WL), CERAD Delayed Recall (CERAD-DR), Animal Fluency Test (AFT), as well as Digit Symbol Substitution test (DSST). Z-score is calculated by scores from the above four tests. The association between RC, total cholesterol (TC) to RC and cognitive performance was assessed by logistic regression analyses. In addition, restricted cubic spline (RCS) regression was performed to assess non-linearity between RC and cognitive function. Subgroup analysis was performed to evaluate the robustness of the results in populations with relevant covariate variables. Results: Those with Z-scores below the 25% quartile are defined as having cognitive impairment, totaling 498 individuals. Observationally, higher RC levels and a lower TC/RC were associated with an increased risk of cognitive impairment. After adjusting for confounding factors, the impact of RC levels on cognitive performance quartiles was consistent across various subgroups, except in individuals with trouble sleeping, no/unknown alcohol use, and no hypertension. Americans with high RC levels and trouble sleeping are more likely to develop cognitive impairment, with an odds ratio of 2.33 (95% CI: 1.18-4.59). Conclusion: This study suggests that higher RC levels and lower levels of TC/RC are associated with an increased likelihood of cognitive impairment, suggesting that RC can serve as a novel and convenient indicator for predicting the risk of cognitive impairment in the US population.
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Accurate sampling of protein conformations is pivotal for advances in biology and medicine. Although there has been tremendous progress in protein structure prediction in recent years due to deep learning, models that can predict the different stable conformations of proteins with high accuracy and structural validity are still lacking. Here, we introduce UFConf, a cutting-edge approach designed for robust sampling of diverse protein conformations based solely on amino acid sequences. This method transforms AlphaFold2 into a diffusion model by implementing a conformation-based diffusion process and adapting the architecture to process diffused inputs effectively. To counteract the inherent conformational bias in the Protein Data Bank, we developed a novel hierarchical reweighting protocol based on structural clustering. Our evaluations demonstrate that UFConf outperforms existing methods in terms of successful sampling and structural validity. The comparisons with long-time molecular dynamics show that UFConf can overcome the energy barrier existing in molecular dynamics simulations and perform more efficient sampling. Furthermore, We showcase UFConf's utility in drug discovery through its application in neural protein-ligand docking. In a blind test, it accurately predicted a novel protein-ligand complex, underscoring its potential to impact real-world biological research. Additionally, we present other modes of sampling using UFConf, including partial sampling with fixed motif, Langevin dynamics, and structural interpolation.
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ZrTe_{5} has recently attracted much attention due to the observation of intriguing nonreciprocal transport responses which necessitate the lack of inversion symmetry (I). However, there has been debate on the exact I-asymmetric structure and the underlying I-breaking mechanism. Here, we report a spontaneous I breaking in ZrTe_{5} films, which initiates from interlayer sliding and is stabilized by subtle intralayer distortion. Moreover, we predict significant nonlinear anomalous Hall effect (NAHE) and kinetic magnetoelectric effect (KME), which are attributed to the emergence of Berry curvature and orbital magnetization in the absence of I symmetry. We also explicitly manifest the direct coupling between sliding ferroelectricity, NAHE, and KME based on a sliding-dependent k·p model. By studying the subsurface sliding in ZrTe_{5} multilayers, we speculate that surface nonlinear Hall current and magnetization would emerge on the natural cleavage surface. Our findings elucidate the sliding-induced I-broken mechanism in ZrTe_{5} films and open new avenues for tuning nonreciprocal transport properties in Van der Waals layered materials.
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The respective unique merit of antiferromagnets and two-dimensional (2D) materials in spintronic applications inspires us to exploit 2D antiferromagnetic spintronics. However, the detection of the Néel vector in 2D antiferromagnets remains a great challenge because the measured signals usually decrease significantly in the 2D limit. Here we propose that the Néel vector of 2D antiferromagnets can be efficiently detected by the intrinsic nonlinear Hall (INH) effect which exhibits unexpected significant signals. As a specific example, we show that the INH conductivity of the monolayer manganese chalcogenides MnX (X=S, Se, Te) can reach the order of nm·mA/V^{2}, which is orders of magnitude larger than experimental values of paradigmatic antiferromagnetic spintronic materials. The INH effect can be accurately controlled by shifting the chemical potential around the band edge, which is experimentally feasible via electric gating or charge doping. Moreover, we explicitly demonstrate its 2π-periodic dependence on the Néel vector orientation based on an effective k·p model. Our findings enable flexible design schemes and promising material platforms for spintronic memory device applications based on 2D antiferromagnets.
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BACKGROUND: Metabolism dysfunction can affect the biological behavior of tumor cells and result in carcinogenesis and the development of various cancers. However, few thoughtful studies focus on the predictive value and efficacy of immunotherapy of metabolism-related gene signatures in endometrial cancer (EC). This research aims to construct a predictive metabolism-related gene signature in EC with prognostic and therapeutic implications. METHODS: We downloaded the RNA profile and clinical data of 503 EC patients and screened out different expressions of metabolism-related genes with prognosis influence of EC from The Cancer Genome Atlas (TCGA) database. We first established a metabolism-related genes model using univariate and multivariate Cox regression and Lasso regression analysis. To internally validate the predictive model, 503 samples (entire set) were randomly assigned into the test set and the train set. Then, we applied the receiver operating characteristic (ROC) curve to confirm our previous predictive model and depicted a nomogram integrating the risk score and the clinicopathological feature. We employed a gene set enrichment analysis (GSEA) to explore the biological processes and pathways of the model. Afterward, we used ESTIMATE to evaluate the TME. Also, we adopted CIBERSORT and ssGSEA to estimate the fraction of immune infiltrating cells and immune function. At last, we investigated the relationship between the predictive model and immune checkpoint genes. RESULTS: We first constructed a predictive model based on five metabolism-related genes (INPP5K, PLPP2, MBOAT2, DDC, and ITPKA). This model showed the ability to predict EC patients' prognosis accurately and performed well in the train set, test set, and entire set. Then we confirmed the predictive signature was a novel independent prognostic factor in EC patients. In addition, we drew and validated a nomogram to precisely predict the survival rate of EC patients at 1-, 3-, and 5-years (ROC1-year = 0.714, ROC3-year = 0.750, ROC5-year = 0.767). Furthermore, GSEA unveiled that the cell cycle, certain malignant tumors, and cell metabolism were the main biological functions enriched in this identified model. We found the five metabolism-related genes signature was associated with the immune infiltrating cells and immune functions. Most importantly, it was linked with specific immune checkpoints (PD-1, CTLA4, and CD40) that could predict immunotherapy's clinical response. CONCLUSION: The metabolism-related genes signature (INPP5K, PLPP2, MBOAT2, DDC, and ITPKA) is a valuable index for predicting the survival outcomes and efficacy of immunotherapy for EC in clinical settings.
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Neoplasias do Endométrio , Humanos , Feminino , Carcinogênese , Ciclo Celular , Mineração de Dados , Bases de Dados FactuaisRESUMO
The ability to design and control the chemical characteristics of covalent organic frameworks (COFs) offers a new avenue for the development of functional materials, especially with respect to topological properties. Based on density functional theory calculations, by varying the core units through the choice of bridging groups [O, CâO, CH2, or C(CH3)2] and the linker units [acetylene, diacetylene, or benzene], we have designed heterotriangulene-based COFs that are predicted to be two-dimensional higher-order topological insulators (TIs). The higher-order TI characteristics of these COFs are identified via their topological invariants and the presence of in-gap topological corner modes and gapped edge states. The frontier molecular orbital energies of the building moieties play an important role in determining the size of the higher-order TI gap, which we find to be highly dependent on linker units. We also examined the deposition of the COFs on a boron nitride substrate to assess the feasibility of experimental observation of a higher-order TI phase in the organic layer. This work thus provides new insights into heterotriangulene-based COFs and guidance for the exploration of purely organic topological materials.
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Electronic devices based on two-dimensional materials are promising for application in space instrumentation because of their small size and low power consumption, and irradiation tolerance of these devices is required because of the existence of energetic particles in aerospace conditions. We investigate the performance degradation of graphene field effect transistors (GFETs) with 3 MeV protons by using an in situ irradiation facility. Our results indicate that GFET performance degraded severely at the ion fluence of 8 × 1011 cm-2. Surprisingly, although the performance of the proton-irradiated GFETs is difficult to recover in vacuum, it can nearly completely recover within hours when the GFET is moved into an air environment, indicating that the performance change is due to the charge accumulation in SiO2 under proton irradiation rather than the lattice damage of graphene. Our results have great importance for the application of 2D devices in aerospace and other radiative environments.
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BACKGROUND: Although lower limb lymphedema (LLL) is more or equally as frequent and harmful as upper limb lymphedema after cancer treatment, there are only a few studies on this topic. Cancer-related secondary LLL not only has physical implications, but also affects quality of life among patients who underwent gynecological cancer treatment. Despite numerous studies of various therapies, the optimal treatment for cancer-related LLL is still unknown. OBJECTIVES: We aimed to investigate the efficacy of lumbar sympathetic ganglion block (LSGB) in patients with secondary LLL in the present study. STUDY DESIGN: This study is a retrospective study. SETTING: A single academic hospital, outpatient setting. METHODS: A total of 30 patients with secondary unilateral LLL and failed complex decongestive treatment, from January 2017 through May 2021, were reviewed for inclusion in this study. The patients underwent fluoroscopy-guided LSGB 2 times with the help of digital subtraction angiography at 3-day intervals. Leg circumference was measured, and the volume of the leg was calculated before surgery, on the first day after the first surgery, on the first day after the second surgery, and on the seventh day after the second surgery. The World Health Organization Quality of Life Instrument Questionnaire scores were monitored before and after LSGB. RESULTS: The leg circumference and volume decreased significantly from baseline after the treatment (P < 0.001). One week after 2 rounds of LSGB, the physical health score, psychological score, and social relationships score were higher than those before treatment (all P < 0.05). There was no difference in the environmental health score (P = 0.2731). LIMITATIONS: This study was limited by its sample size and retrospective observational design. CONCLUSIONS: LSGB can be a safe and effective treatment option for patients with secondary LLL after gynecological cancer treatment.
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Linfedema , Neoplasias , Humanos , Estudos Retrospectivos , Qualidade de Vida , Extremidade Inferior , Linfedema/psicologia , Linfedema/terapia , Gânglios SimpáticosRESUMO
Devices based on two-dimensional (2D) materials such as graphene and molybdenum disulfide have shown extraordinary potential in physics, nanotechnology, and electronics. The performances of these applications are heavily affected by defects in utilized materials. Although great efforts have been spent in studying the formation and property of various defects in 2D materials, the long-term evolution of vacancies is still unclear. Here, using a designed program based on the kinetic Monte Carlo method, we systematically investigate the vacancy evolution in monolayer graphene on a long-time and large spatial scale, focusing on the variation of the distribution of different vacancy types. In most cases, the vacancy distribution remains nearly unchanged during the whole evolution, and most of the evolution events are vacancy migrations with a few being coalescences, while it is extremely difficult for multiple vacancies to dissolve. The probabilities of different categories of vacancy evolutions are determined by their reaction rates, which, in turn, depend on corresponding energy barriers. We further study the influences of different factors such as the energy barrier for vacancy migration, coalescence, and dissociation on the evolution, and the coalescence energy barrier is found to be dominant. These findings indicate that vacancies (also subnanopores) in graphene are thermodynamically stable for a long period of time, conducive to subsequent characterizations or applications. Besides, this work provides hints to tune the ultimate vacancy distribution by changing related factors and suggests ways to study the evolution of other defects in various 2D materials.
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Higher-order topological insulator (HOTI) states, such as two-dimension (2D) HOTI featured with topologically protected corner modes at the intersection of two gapped crystalline boundaries, have attracted much recent interest. However, the physical mechanism underlying the formation of HOTI states is not fully understood, which has hindered our fundamental understanding and discovery of HOTI materials. Here we propose a mechanistic approach to induce higher-order topological phases via structural buckling of 2D topological crystalline insulators (TCIs). While in-plane mirror symmetry is broken by structural buckling, which destroys the TCI state, the combination of mirror and rotation symmetry is preserved in the buckled system, which gives rise to the HOTI state. We demonstrate that this approach is generally applicable to various 2D lattices with different symmetries and buckling patterns, opening a horizon of possible materials to realize 2D HOTIs. The HOTIs so generated are also shown to be robust against buckling height fluctuation and in-plane displacement. A concrete example is given for the buckled [Formula: see text]-Sb monolayer from first-principles calculations. Our finding not only enriches our fundamental understanding of higher-order topology, but also opens a new route to discovering HOTI materials.
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High-order topological insulators (HOTIs), as generalized from topological crystalline insulators, are characterized with lower-dimensional metallic boundary states protected by spatial symmetries of a crystal, whose theoretical framework based on band inversion at special k points cannot be readily extended to quasicrystals because quasicrystals contain rotational symmetries that are not compatible with crystals, and momentum is no longer a good quantum number. Here, we develop a low-energy effective model underlying HOTI states in 2D quasicrystals for all possible rotational symmetries. By implementing a novel Fourier transform developed recently for quasicrystals and approximating the long-wavelength behavior by their large-scale average, we construct an effective k·p Hamiltonian to capture the band inversion at the center of a pseudo-Brillouin zone. We show that an in-plane Zeeman field can induce mass kinks at the intersection of adjacent edges of a 2D quasicrystal topological insulators and generate corner modes (CMs) with fractional charge, protected by rotational symmetries. Our model predictions are confirmed by numerical tight-binding calculations. Furthermore, when the quasicrystal is proximitized by an s-wave superconductor, Majorana CMs can also be created by tuning the field strength and chemical potential. Our work affords a generic approach to studying the low-energy physics of quasicrystals, in association with topological excitations and fractional statistics.
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Electronic properties of crystals are inherently pertained to crystalline symmetry, so that amorphization that lowers and breaks symmetry is detrimental. One important crystalline property is electron band topology which is known to be weakened and destroyed by structural disorder. Here, we report a counterintuitive theoretical discovery that atomic structural disorder by amorphization can in fact induce electronic order of topology in an otherwise topologically trivial crystal. The resulting nontrivial topology is characterized by a nonzero spin Bott index, associated with robust topological edge states and quantized conductance. The underlying topological phase transition (TPT) from a trivial crystal to a topological amorphous is analyzed by mapping out a phase diagram in the degree of structural disorder using an effective medium theory. The atomic disorder is revealed to induce topological order by renormalizing the spectral gap toward nontriviality near the phase boundary. As a concrete example, we further show such TPT in amorphous stanane by first-principles calculations. Our findings point to possible observation of an electronic ordering transition accompanied by a structural disorder transition.
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In addition to crystals, topological phases in quasicrystals and disorder systems have drawn increasing attention lately. Here, we propose a generic double band-inversion mechanism underlying the higher-order topological phase in quasicrystals, that is.,"higher-order topological quasicrystalline insulator" (HOTQI), which exploits local atomic orbital and lattice symmetries. It is generally applicable to both quasicrystals and crystals with either odd-rotational (OR) or even-rotational symmetry (ERS), different from previous HOTI mechanisms whose applicability is limited by symmetry types. The HOTQI is characterized by topological corner states at the nonordinary corners of pentagonal (octagonal) samples of five-fold (eight-fold) quasicrystals, which violate the translational invariance and ordinary crystalline symmetries. The role of quasicrystalline symmetry, the robustness against symmetry breaking, and possible experimental realizations are discussed. Our findings not only provide a concrete example of HOTQIs that is incompatible with classical crystallographic symmetry but also offer useful guidance to the search of higher-order topological materials and metamaterials.
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We develop a unified view of topological phase transitions (TPTs) in solids by revising the classical band theory with the inclusion of topology. Reevaluating the band evolution from an "atomic crystal" (a normal insulator (NI)) to a solid crystal, such as a semiconductor, we demonstrate that there exists ubiquitously an intermediate phase of topological insulator (TI), whose critical transition point displays a linear scaling between electron hopping potential and average bond length, underlined by deformation-potential theory. The validity of the scaling relation is verified in various two-dimensional (2D) lattices regardless of lattice symmetry, periodicity, and form of electron hoppings, based on a generic tight-binding model. Significantly, this linear scaling is shown to set an upper bound for the degree of structural disorder to destroy the topological order in a crystalline solid, as exemplified by formation of vacancies and thermal disorder. Our work formulates a simple framework for understanding the physical nature of TPTs with significant implications in practical applications of topological materials.
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Spin-orbit (SO) interaction is an indispensable element in the field of spintronics for effectively manipulating the spin of carriers. However, in crystalline solids, the momentum-dependent SO effective magnetic field generally results in spin randomization by a process known as the Dyakonov-Perel spin relaxation, leading to the loss of spin information. To overcome this obstacle, the persistent spin helix (PSH) state with a unidirectional SO field was proposed but difficult to achieve in real materials. Here, on the basis of first-principles calculations and tight-binding model analysis, we report for the first time a unidirectional SO field in monolayer transition metal dichalcogenides (TMDs, MX2, M = Mo, W; and X = S, Se) induced by two parallel chalcogen vacancy lines. By changing the relative positions of the two vacancy lines, the direction of the SO field can be tuned from x to y. Moreover, using k·p perturbation theory and group theory analysis, we demonstrate that the emerging unidirectional SO field is subject to both the structural symmetry and 1D nature of such defects engineered in 2D TMDs. In particular, through transport calculations, we confirm that the predicted SO states carry highly coherent spin current. Our findings shed new light on creating PSH states for high-performance spintronic devices.
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Lieb lattice has been extensively studied to realize ferromagnetism due to its exotic flat band. However, its material realization has remained elusive; so far only artificial Lieb lattices have been made experimentally. Here, based on first-principles and tight-binding calculations, we discover that a recently synthesized two-dimensional sp2 carbon-conjugated covalent-organic framework (sp2c-COF) represents a material realization of a Lieb-like lattice. The observed ferromagnetism upon doping arises from a Dirac (valence) band in a non-ideal Lieb lattice with strong electronic inhomogeneity (EI) rather than the topological flat band in an ideal Lieb lattice. The EI, as characterized with a large on-site energy difference and a strong dimerization interaction between the corner and edge-center ligands, quenches the kinetic energy of the usual dispersive Dirac band, subjecting to an instability against spin polarization. We predict an even higher spin density for monolayer sp2c-COF to accommodate a higher doping concentration with reduced interlayer interaction.
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A symmetry-protected 2D Dirac semimetal has attracted intense interest for its intriguing material properties. Here, we report a 2D nonsymmorphic Dirac semimetal state in a chemically modified group-VA 2D puckered structure. Based on first-principles calculations, we demonstrate the existence of 2D Dirac fermions in a one-side modified phosphorene structure in two different types: one with a Dirac nodal line (DNL) structure for light elements with negligible spin-orbit coupling (SOC) and the other having an hourglass band protected by a nonsymmorphic symmetry for heavy elements with strong SOC. In the absence of SOC, the DNL exhibits an anisotropic behavior and unique electronic properties, such as constant density of states. The Dirac node is protected from gap opening by the nonsymmorphic space group symmetry. In the presence of SOC, the DNL states split and form an hourglass-shaped dispersion due to the broken inversion symmetry and the Rashba SOC interaction. Moreover, around certain high symmetry points in the Brillouin zone, the spin orientation is enforced to be along a specific direction. We construct an effective tight-binding model to characterize the 2D nonsymmorphic Dirac states. Our result provides a promising material platform for exploring the intriguing properties of essential nodal-line and nodal-point fermions in 2D systems.
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Despite the rapid progress in the field of the quantum spin Hall (QSH) effect, most of the QSH systems studied up to now are based on crystalline materials. Here we propose that the QSH effect can be realized in quasicrystal lattices (QLs). We show that the electronic topology of aperiodic and amorphous insulators can be characterized by a spin Bott index B_{s}. The nontrivial QSH state in a QL is identified by a nonzero spin Bott index B_{s}=1, associated with robust edge states and quantized conductance. We also map out a topological phase diagram in which the QSH state lies in between a normal insulator and a weak metal phase due to the unique wave functions of QLs. Our findings not only provide a better understanding of electronic properties of quasicrystals but also extend the search of the QSH phase to aperiodic and amorphous materials that are experimentally feasible.
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Herbertsmithite and Zn-doped barlowite are two compounds for experimental realization of two-dimensional kagome spin liquids. Theoretically, it has been proposed that charge doping a quantum spin liquid gives rise to exotic metallic states, such as high-temperature superconductivity. However, one recent experiment on herbertsmithite with successful Li-doping surprisingly showed an insulating state even under a heavily doped scenario, which cannot be explained by previous theories. Using first-principles calculations, we performed a comprehensive study on the Li intercalation doping effect of these two compounds. For the Li-doped herbertsmithite, we identified the optimized Li position at the Cl-(OH)3-Cl pentahedron site instead of the previously speculated Cl-(OH)3 tetrahedral site. With increasing Li doping concentration, saturation magnetization decreases linearly due to charge transfer from Li to Cu ions. Moreover, we found that Li forms chemical bonds with nearby (OH)- and Cl- ions, which lowers the surrounding chemical potential and traps electrons, as evidenced by the localized charge distribution, explaining the insulating behavior measured experimentally. Though a different structure from herbertsmithite, Zn-doped barlowite shows the same features upon Li doping. We conclude that Li doping this family of kagome spin liquids cannot realize exotic metallic states, and other methods should be further explored, such as element substitution with those having different valence electrons.