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1.
Urolithiasis ; 52(1): 57, 2024 Apr 02.
Artigo em Inglês | MEDLINE | ID: mdl-38563829

RESUMO

Calcium oxalate kidney stones, the most prevalent type of kidney stones, undergo a multi-step process of crystal nucleation, growth, aggregation, and secondary transition. The secondary transition has been rather overlooked, and thus, the effects on the disease and the underlying mechanism remain unclear. Here, we show, by periodic micro-CT images of human kidney stones in an ex vivo incubation experiment, that the growth of porous aggregates of calcium oxalate dihydrate (COD) crystals triggers the hardening of the kidney stones that causes difficulty in lithotripsy of kidney stone disease in the secondary transition. This hardening was caused by the internal nucleation and growth of precise calcium oxalate monohydrate (COM) crystals from isolated urine in which the calcium oxalate concentrations decreased by the growth of COD in closed grain boundaries of COD aggregate kidney stones. Reducing the calcium oxalate concentrations in urine is regarded as a typical approach for avoiding the recurrence. However, our results revealed that the decrease of the concentrations in closed microenvironments conversely promotes the transition of the COD aggregates into hard COM aggregates. We anticipate that the suppression of the secondary transition has the potential to manage the deterioration of kidney stone disease.


Assuntos
Líquidos Corporais , Cálculos Renais , Litotripsia , Humanos , Oxalato de Cálcio , Dureza
2.
Surg Case Rep ; 10(1): 102, 2024 Apr 25.
Artigo em Inglês | MEDLINE | ID: mdl-38662187

RESUMO

BACKGROUND: Intraoperative parathyroid hormone (IOPTH) monitoring is a critical surgical adjunct for determining the extent of surgery for primary hyperparathyroidism (PHPT), with reported false-positive and false-negative rates of up to 10%. Surgeons must understand the parathyroid hormone (PTH) dynamics and select the appropriate IOPTH protocol and interpretation criteria for curative surgery. CASE PRESENTATION: We present the case of a 64-year-old woman with a large cystic parathyroid tumor and PHPT who experienced a significant delay in IOPTH decrease but was cured without additional surgery. The patient's basal intact PTH was 96.2 pg/mL, which decreased to 93.3 pg/mL at 25 min and 72.4 pg/mL at 55 min after removal of the parathyroid tumor. In an attempt to elucidate its pathophysiology, 1-84 PTH levels were measured in stored serum. These results can also be attributed to the relatively low basal PTH levels, intact PTH spike, and high ratio of large carboxyl-terminal PTH fragments present. The patient had normal intact PTH and calcium levels at the 9-month postoperative visit. CONCLUSIONS: As detailed reports on these phenomena are scarce, we discuss the causes of false-negative IOPTH results in terms of PTH production, secretion, metabolism, and differences in measurement methods to avoid unnecessary surgery.

3.
Surg Today ; 2024 Apr 18.
Artigo em Inglês | MEDLINE | ID: mdl-38635056

RESUMO

PURPOSE: To investigate the parathyroid function and calcium (Ca) levels in the secondary hyperparathyroidism (SHPT) state in patients with Graves' disease. METHODS: We examined 31 consecutive patients with Graves' disease without chronic kidney disease, who were treated with total thyroidectomy. The patients were divided into a normal parathyroid hormone (PTH) group (NPTH group; n = 19) with a PTH level ≤ 65 pg/mL, and a secondary hyperparathyroidism group (SHPT group; n = 12), with a PTH level > 65 pg/mL. The PTH and Ca-related parameters were examined and the risk factors for postoperative hypocalcemia were analyzed. RESULTS: The preoperative Ca level was significantly lower (2.24 ± 0.06 vs. 2.31 ± 0.07 mmol/L, p < 0.05) in the SHPT group than in the NPTH group. The reduction in PTH, 1,25-dihydroxyvitamin D (1,25(OH)2D), and Ca levels from the preoperative day to the next morning was significantly greater in the SHPT group than in the NPTH group (p < 0.05). When intraoperative factors were included, the decrease in the PTH level alone was significant. SHPT was a significant factor in determining the extent of PTH reduction. CONCLUSIONS: Hyperfunctioning parathyroid glands in the SHPT state were more susceptible to postoperative PTH reduction, which, combined with low preoperative Ca levels, increased the risk of postoperative hypocalcemia in patients with Graves' disease.

4.
J Phys Chem Lett ; 15(1): 180-186, 2024 Jan 11.
Artigo em Inglês | MEDLINE | ID: mdl-38153689

RESUMO

Spatiotemporal control of the polymorphic phase transition of glycine crystals was demonstrated by three-dimensional (3D) processing with a focused femtosecond laser pulse as an external stimulus. We found that the transition from a metastable form (ß-form) to more stable ones (α- or γ-form) could be triggered from the irradiated area of not only the surface but also inside of glycine crystals. This 3D processing with a focused femtosecond laser pulse enabled us to precisely monitor the transition dynamics from a targeted position to the entire part of crystals. The systematic study with the space-selective phase transition method revealed that the phase transition inside of glycine crystals was significantly slower (e.g., ∼50 times) than that at the crystal surface, which indicates the crucial role of water molecules in air on the phase transition dynamics. We foresee that this laser method can be a practical tool for monitoring spatiotemporal dynamics of phase transition.

5.
Surg Today ; 2023 Dec 05.
Artigo em Inglês | MEDLINE | ID: mdl-38052742

RESUMO

PURPOSE: This study investigated the effects of ice cream consumption on chyle leakage after left lateral neck dissection in patients with thyroid cancer. METHODS: A total of 491 patients with thyroid cancer underwent left lateral neck dissection with identification of the thoracic duct following ice cream consumption. Before closing the wound, the anesthesiologist increased the intrathoracic pressure to observe chyle leakage. If chyle leakage occurred postoperatively, the drain was removed using the drain negative pressure release test. RESULTS: Postoperative chyle leakage was observed in 18 of the 491 patients who underwent left lateral neck dissection. We treated 17 patients conservatively and 1 patient surgically. Drains were removed within five days in all patients. After the drain negative pressure release test had been performed in eight patients, the drainage volume significantly decreased from an average of 175 ml to 31 ml per day. The average number of days until the removal of the drainage tube was 3.2 days. No perioperative complications were associated with ice cream consumption. CONCLUSIONS: In left lateral neck dissection for thyroid cancer, performing surgery following ice cream consumption does not completely prevent chyle leakage; however, early drain removal is possible because there is only mild leakage.

6.
Nucleic Acids Res ; 51(14): 7480-7495, 2023 08 11.
Artigo em Inglês | MEDLINE | ID: mdl-37439353

RESUMO

The 3243A > G in mtDNA is a representative mutation in mitochondrial diseases. Mitochondrial protein synthesis is impaired due to decoding disorder caused by severe reduction of 5-taurinomethyluridine (τm5U) modification of the mutant mt-tRNALeu(UUR) bearing 3243A > G mutation. The 3243A > G heteroplasmy in peripheral blood reportedly decreases exponentially with age. Here, we found three cases with mild respiratory symptoms despite bearing high rate of 3243A > G mutation (>90%) in blood mtDNA. These patients had the 3290T > C haplotypic mutation in addition to 3243A > G pathogenic mutation in mt-tRNALeu(UUR) gene. We generated cybrid cells of these cases to examine the effects of the 3290T > C mutation on mitochondrial function and found that 3290T > C mutation improved mitochondrial translation, formation of respiratory chain complex, and oxygen consumption rate of pathogenic cells associated with 3243A > G mutation. We measured τm5U frequency of mt-tRNALeu(UUR) with 3243A > G mutation in the cybrids by a primer extension method assisted with chemical derivatization of τm5U, showing that hypomodification of τm5U was significantly restored by the 3290T > C haplotypic mutation. We concluded that the 3290T > C is a haplotypic mutation that suppresses respiratory deficiency of mitochondrial disease by restoring hypomodified τm5U in mt-tRNALeu(UUR) with 3243A > G mutation, implying a potential therapeutic measure for mitochondrial disease associated with pathogenic mutations in mt-tRNAs.


Assuntos
Síndrome MELAS , Doenças Mitocondriais , Humanos , Síndrome MELAS/genética , Síndrome MELAS/metabolismo , RNA de Transferência de Leucina/metabolismo , Taurina , Haplótipos , Mutação , DNA Mitocondrial/genética , Doenças Mitocondriais/genética
7.
J Phys Chem Lett ; 14(19): 4394-4402, 2023 May 18.
Artigo em Inglês | MEDLINE | ID: mdl-37154425

RESUMO

Focused irradiation with ultrashort laser pulses realized the fine spatiotemporal control of ice crystallization in supercooled water. An effective multiphoton excitation at the laser focus generated shockwaves and bubbles, which acted as an impulse for inducing ice crystal nucleation. The impulse that was localized close to the laser focus and accompanied by a small temperature elevation allowed the precise position control of ice crystallization and its observation with spatiotemporal resolution of micrometers and microseconds using a microscope. To verify the versatility of this laser method, we also applied it using various aqueous systems (e.g., plant extracts). The systematic study of crystallization probability revealed that laser-induced cavitation bubbles play a crucial role in inducing ice crystal nucleation. This method can be used as a tool for studying ice crystallization dynamics in various natural and biological phenomena.

8.
Opt Express ; 31(9): 14705-14714, 2023 Apr 24.
Artigo em Inglês | MEDLINE | ID: mdl-37157329

RESUMO

We report the generation of picosecond pulsed light at a 266 nm wavelength with an average power of 53 W. We developed a picosecond pulsed 1064 nm laser source with an average power of 261 W, a repetition rate of 1 MHz, and a pulse duration of 14 ps, using a gain-switched DFB laser diode as a seed laser and a 914 nm laser-diode-pumped Nd-doped YVO4 power amplifier. We achieved stable generation of 266 nm light with an average power of 53 W from frequency quadrupling using an LBO and a CLBO crystals. The amplified power of 261 W and the 266 nm average power of 53 W from the 914 nm pumped Nd:YVO4 amplifier are the highest ever reported, to the best of our knowledge.

9.
PLoS One ; 18(3): e0282743, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36893192

RESUMO

We sought to identify and quantitatively analyze calcium oxalate (CaOx) kidney stones on the order of micrometers, with a focus on the quantitative identification of calcium oxalate monohydrate (COM) and dihydrate (COD). We performed Fourier transform infrared (FTIR) spectroscopy, powder X-ray diffraction (PXRD), and microfocus X-ray computed tomography measurements (microfocus X-ray CT) and compared their results. An extended analysis of the FTIR spectrum focusing on the 780 cm-1 peak made it possible to achieve a reliable analysis of the COM/COD ratio. We succeeded in the quantitative analysis of COM/COD in 50-µm2 areas by applying microscopic FTIR for thin sections of kidney stones, and by applying microfocus X-ray CT system for bulk samples. The analysis results based on the PXRD measurements with micro-sampling, the microscopic FTIR analysis of thin sections, and the microfocus X-ray CT system observation of a bulk kidney stone sample showed roughly consistent results, indicating that all three methods can be used complementarily. This quantitative analysis method evaluates the detailed CaOx composition on the preserved stone surface and provides information on the stone formation processes. This information clarifies where and which crystal phase nucleates, how the crystals grow, and how the transition from the metastable phase to the stable phase proceeds. The phase transition affects the growth rate and hardness of kidney stones and thus provides crucial clues to the kidney stone formation process.


Assuntos
Oxalato de Cálcio , Cálculos Renais , Humanos , Oxalato de Cálcio/química , Cálculos Renais/diagnóstico por imagem , Cálculos Renais/química , Espectroscopia de Infravermelho com Transformada de Fourier , Tomografia Computadorizada por Raios X , Raios X
10.
J Hand Surg Asian Pac Vol ; 28(1): 61-68, 2023 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-36803469

RESUMO

Background: This multicenter retrospective study aimed to compare clinical outcomes and cost-effectiveness with bone substitutes on volar locking plate (VLP) fixation of unstable distal radial fractures (DRF) in the elderly. Methods: The data of 1,980 patients of ≥65 years of age who underwent surgery for the DRF with a VLP in 2015-2019 were extracted from a database (named TRON). Patients lost to follow-up or who received autologous bone grafting were excluded. The patients (n = 1,735) were divided into the VLP fixation alone (Group VLA) and VLP fixation with bone substitutes (Group VLS). Propensity score matching of background characteristics (ratio, 4:1) was performed. The modified Mayo wrist scores (MMWS) were evaluated as clinical outcomes. The implant failure rate, bone union rate, volar tilt (VT), radial inclination (RI), ulnar variance (UV) and distal dorsal cortical distance (DDD) were evaluated as radiologic parameters. We also compared the initial surgery cost and total cost for each group. Results: After matching, the backgrounds of Groups VLA (n = 388) and VLS (n = 97) were not significantly different. The MMWS values of the groups were not significantly different. Radiographic evaluation revealed no implant failure in either group. Bone union was confirmed in all patients in both groups. The VT, RI, UV and DDD values of the groups were not significantly different. The initial surgery cost and total cost in the VLS group were significantly higher than those in the VLA group ($3,515 vs. $3,068, p < 0.001). Conclusions: In patients of ≥65 years of age with DRF, the clinical and radiological outcomes of VLP fixation with bone substitutes did not differ from those of VLP fixation alone, yet the additional use of bone augmentation was associated with higher medical costs. The indications for bone substitutes should be more strictly considered in the elderly with DRF. Level of Evidence: Level IV (Therapeutic).


Assuntos
Substitutos Ósseos , Fraturas do Rádio , Fraturas do Punho , Humanos , Idoso , Estudos Retrospectivos , Fraturas do Rádio/diagnóstico por imagem , Fraturas do Rádio/cirurgia , Substitutos Ósseos/uso terapêutico , Análise Custo-Benefício , Rádio (Anatomia)
11.
Sci Rep ; 13(1): 2436, 2023 Feb 10.
Artigo em Inglês | MEDLINE | ID: mdl-36765088

RESUMO

The electrical characteristics of Schottky contacts on individual threading dislocations (TDs) with a screw-component in GaN substrates and the structures of these TDs were investigated to assess the effects of such defects on reverse leakage currents. Micrometer-scale platinum/GaN Schottky contacts were selectively fabricated on screw- and mixed-TD-related etch pits classified based on the pit size. Current-voltage (I-V) data acquired using conductive atomic force microscopy showed that very few of the screw TDs generated anomalously large reverse leakage currents. An analysis of the temperature dependence of the I-V characteristics established that the leakage current conduction mechanisms for the leaky screw TDs differed from those for the other screw and mixed TDs. Specifically, anomalous current leakage was generated by Poole-Frenkel emission and trap-assisted tunneling via distinctive trap states together with Fowler-Nordheim tunneling, with the mechanism changing according to variations in temperature and applied voltage. The leaky TDs were identified as Burgers vector b = 1c closed-core screw TDs having a helical morphology similar to that of other screw TDs generating small leakage currents. Based on the results, we proposed that the atomic-scale modification of the dislocation core structure related to interactions with point defects via dislocation climbing caused different leakage characteristics of the TDs.

12.
J Biochem ; 173(2): 65-72, 2023 Feb 03.
Artigo em Inglês | MEDLINE | ID: mdl-36352502

RESUMO

Polyacrylamide gel electrophoresis (PAGE) with sodium dodecyl sulphate (SDS) and Coomassie brilliant blue (CBB) staining is widely used in protein research and requires time for electrophoresis, staining and destaining. Because the protein bands electrophoresed in the gel are invisible in most cases, the results cannot be observed until the whole process is complete. In this study, shadowgraph was applied to detect biomolecules such as proteins during electrophoresis. A simple optical system and camera-enabled real-time monitoring of migration and separation of individual protein bands in polyacrylamide gels without staining. The visibility was high enough that it was possible to visualize substances other than proteins, such as DNA. This method provides protein profiles instantly in the early stage of electrophoresis. The elimination of the staining and destaining steps will help save researchers' time. The method is also environmentally friendly and will help reduce the generation of waste solutions containing synthetic dyes.


Assuntos
Corantes , Proteínas , Corantes/análise , Corantes/química , Coloração e Rotulagem , Eletroforese em Gel de Poliacrilamida , Proteínas/química , Dodecilsulfato de Sódio
13.
J Phys Chem Lett ; 13(40): 9494-9500, 2022 Oct 13.
Artigo em Inglês | MEDLINE | ID: mdl-36201238

RESUMO

Cell-coupled field-effect transistor (FET) biosensors have attracted considerable attention because of their high sensitivity to biomolecules. The use of insect cells (Sf21) as a core sensor element is advantageous due to their stable adhesion to sensors at room temperature. Although visualization of the insect cell-substrate interface leads to logical amplification of signals, the spatiotemporal processes at the interfaces have not yet been elucidated. We quantitatively monitored the adhesion dynamics of Sf21 using interference reflection microscopy (IRM). Specific adhesion signatures with ring-like patches along the cellular periphery were detected. A combination of zeta potential measurements and lectin staining identified specific glycoconjugates with low electrostatic potentials. The ring-like structures were disrupted after cholesterol depletion, suggesting a raft domain along the cell periphery. Our results indicate dynamic and asymmetric cell adhesion is due to low electrostatic repulsion with fluidic sugar rafts. We envision the logical design of cell-sensor interfaces with an electrical model that accounts for actual adhesion interfaces.


Assuntos
Colesterol , Lectinas , Animais , Adesão Celular , Glicoconjugados , Insetos , Açúcares , Temperatura
14.
Opt Express ; 30(11): 18628-18637, 2022 May 23.
Artigo em Inglês | MEDLINE | ID: mdl-36221660

RESUMO

A unique design of our ultracompact microcavity wavelength conversion device exploits the simple principle that the wavelength conversion efficiency is proportional to the square of the electric field amplitude of enhanced pump light in the microcavity, and expands the range of suitable device materials to include crystals that do not exhibit birefringence or ferroelectricity. Here, as a first step toward practical applications of all-solid-state ultracompact deep-ultraviolet coherent light sources, we adopted a low-birefringence paraelectric SrB4O7 crystal with great potential for wavelength conversion and high transparency down to 130 nm as our device material, and demonstrated 234 nm deep-ultraviolet coherent light generation, whose wavelength band is expected to be used for on-demand disinfection tools that can irradiate the human body.

15.
Artigo em Inglês | MEDLINE | ID: mdl-35973649

RESUMO

The growth rate of broiler chickens has increased by 400% over the past 50 years, and breast yields continue to increase. This has led to an increase in thoracic muscle abnormalities in broilers, with wooden breast becoming a major issue worldwide. The etiology and the mechanism underlying the etiology of wooden breasts have not yet been elucidated; however, it occurs due to oxidative stress. Reactive oxygen species, which cause oxidative stress, are mainly produced in mitochondria. Thus, in this study, we investigated the relationship between the severity of wooden breast in broilers and the characteristics of mitochondria as the source of reactive oxygen species. Sampling of the pectoralis major muscle at the ventral cranial position was conducted in 50-day-old broilers. The severity of wooden breast was classified into three groups based on the muscle fiber roundness and wing-wing contact test, with highest severity in severe wooden breast and lowest severity in normal breast. Nicotinamide adenine dinucleotide tetrazolium reductase staining revealed an increase in darkly stained muscle fibers, indicating high severity of wooden breast. The mitochondria were swollen in severe wooden breast cases, with highest swelling in severe wooden breast and lowest swelling in normal breast. The expression levels of the mitochondrial antioxidant enzyme genes superoxide dismutase 1 and superoxide dismutase 2 were significantly lower in wooden breast-severe tissue than in normal tissue. These results suggest that when the levels of reactive oxygen species in muscle fibers, which should be constant, are increased, mitochondrial homeostasis is not maintained and the damage levels increase in various membranes of the cell, leading to the disruption of normal physiological functions.


Assuntos
Doenças Musculares , Doenças das Aves Domésticas , Animais , Galinhas/metabolismo , Mitocôndrias/metabolismo , Doenças Musculares/genética , Doenças Musculares/metabolismo , Doenças Musculares/veterinária , Músculos Peitorais/metabolismo , Doenças das Aves Domésticas/metabolismo , Espécies Reativas de Oxigênio/metabolismo
16.
Cell Rep ; 40(9): 111292, 2022 08 30.
Artigo em Inglês | MEDLINE | ID: mdl-36044857

RESUMO

Cell competition is a process by which unwanted cells are eliminated from tissues. Apical extrusion is one mode whereby normal epithelial cells remove transformed cells, but it remains unclear how this process is mechanically effected. In this study, we show that autophagic and endocytic fluxes are attenuated in RasV12-transformed cells surrounded by normal cells due to lysosomal dysfunction, and that chemical manipulation of lysosomal activity compromises apical extrusion. We further find that RasV12 cells deficient in autophagy initiation machinery are resistant to elimination pressure exerted by normal cells, suggesting that non-degradable autophagic vacuoles are required for cell competition. Moreover, in vivo analysis revealed that autophagy-ablated RasV12 cells are less readily eliminated by cell competition, and remaining transformed cells destroy ductal integrity, leading to chronic pancreatitis. Collectively, our findings illuminate a positive role for autophagy in cell competition and reveal a homeostasis-preserving function of autophagy upon emergence of transformed cells.


Assuntos
Competição entre as Células , Vacúolos , Autofagossomos , Autofagia , Células Epiteliais , Lisossomos
17.
Opt Express ; 30(7): 11797-11808, 2022 Mar 28.
Artigo em Inglês | MEDLINE | ID: mdl-35473115

RESUMO

We report 10,000-hour stable operation of a 266-nm picosecond laser with an average power of 20 W. We have developed a narrow-linewidth, high-peak-power 1064-nm laser source with a repetition rate of 600 kHz, an average power of 129 W, a linewidth of 0.15 nm, and a pulse duration of 14 ps using a gain-switched DFB-LD as a picosecond pulse seed source and a four-stage power amplifier with an Nd:YVO4 crystal. A 266-nm laser with a maximum average power of 25.4 W was generated by frequency conversion using LBO and CLBO crystals and had a pulse duration of 8 ps and beam quality factor of 1.5 at 20W. To the best of our knowledge, we also demonstrated that the average power and the beam quality can be maintained for 10,000 hours for the first time. We have confirmed the durability of the developed deep ultraviolet laser for industrial applications.

18.
Reprod Med Biol ; 21(1): e12454, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35414764

RESUMO

Purpose: To create and evaluate a machine-learning model for YOLOv3 that can simultaneously perform morphological evaluation and tracking in a short time, which can be adapted to video data under an inverted microscope. Methods: Japanese patients who underwent intracytoplasmic sperm injection at the Jikei University School of Medicine and Keiai Reproductive and Endosurgical Clinic from January 2019 to March 2020 were included. An AI model that simultaneously performs morphological assessment and tracking was created and its performance was evaluated. Results: For morphological assessment, the sensitivity and positive predictive value (PPV) of this model for abnormal sperm were 0.881 and 0.853, respectively. The sensitivity and PPV for normal sperm were 0.794 and 0.689, respectively. For tracking performance, among the 51 objects, 40 (78.4%) were mostly tracked, 11 (21.6%) were partially tracked, and 0 (0%) were mostly lost. Conclusions: This study showed that evaluating sperm morphology while tracking in a single model is possible by training YOLO v3. This model could acquire time-series data of one sperm, which will assist in acquiring and annotating sperm image data.

19.
Curr Biol ; 32(10): 2144-2159.e5, 2022 05 23.
Artigo em Inglês | MEDLINE | ID: mdl-35417667

RESUMO

For the maintenance of epithelial homeostasis, various aberrant or dysfunctional cells are actively eliminated from epithelial layers. This cell extrusion process mainly falls into two modes: cell-competition-mediated extrusion and apoptotic extrusion. However, it is not clearly understood whether and how these processes are governed by common molecular mechanisms. In this study, we demonstrate that the reactive oxygen species (ROS) levels are elevated within a wide range of epithelial layers around extruding transformed or apoptotic cells. The downregulation of ROS suppresses the extrusion process. Furthermore, ATP is extracellularly secreted from extruding cells, which promotes the ROS level and cell extrusion. Moreover, the extracellular ATP and ROS pathways positively regulate the polarized movements of surrounding cells toward extruding cells in both cell-competition-mediated and apoptotic extrusion. Hence, extracellular ATP acts as an "extrude me" signal and plays a prevalent role in cell extrusion, thereby sustaining epithelial homeostasis and preventing pathological conditions or disorders.


Assuntos
Apoptose , Competição entre as Células , Trifosfato de Adenosina/metabolismo , Células Epiteliais/metabolismo , Espécies Reativas de Oxigênio/metabolismo
20.
J Chem Phys ; 156(15): 154108, 2022 Apr 21.
Artigo em Inglês | MEDLINE | ID: mdl-35459300

RESUMO

A method for obtaining appropriate reaction coordinates is required to identify transition states distinguishing the product and reactant in complex molecular systems. Recently, abundant research has been devoted to obtaining reaction coordinates using artificial neural networks from deep learning literature, where many collective variables are typically utilized in the input layer. However, it is difficult to explain the details of which collective variables contribute to the predicted reaction coordinates owing to the complexity of the nonlinear functions in deep neural networks. To overcome this limitation, we used Explainable Artificial Intelligence (XAI) methods of the Local Interpretable Model-agnostic Explanation (LIME) and the game theory-based framework known as Shapley Additive exPlanations (SHAP). We demonstrated that XAI enables us to obtain the degree of contribution of each collective variable to reaction coordinates that is determined by nonlinear regressions with deep learning for the committor of the alanine dipeptide isomerization in vacuum. In particular, both LIME and SHAP provide important features to the predicted reaction coordinates, which are characterized by appropriate dihedral angles consistent with those previously reported from the committor test analysis. The present study offers an AI-aided framework to explain the appropriate reaction coordinates, which acquires considerable significance when the number of degrees of freedom increases.


Assuntos
Inteligência Artificial , Dipeptídeos , Alanina , Dipeptídeos/química , Isomerismo , Redes Neurais de Computação
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