Leveraging physics-based and explainable machine learning approaches to quantify the relative contributions of rain and air pollutants to wet deposition.

A quantitative understanding of the roles of rainfall and pollutant concentrations in wet deposition is important because they critically influence terrestrial and aquatic ecosystems. However, their relative contributions to wet deposition, which vary across regions, have not yet been identified. We propose two methods that quantitatively separate the contributions of rain and pollutant concentrations to wet deposition: one is based on simplified equations describing the wet scavenging of pollutants and the other is based on random forest models employing SHapley Additive exPlanations. Three-dimensional long-term air quality simulations from 2003 to 2019 are used as inputs for both the physics-based and machine learning models. Remarkably, the results drawn from the explainable machine learning model are consistent with those from the physics-based approach: overall, rain is a more important limiting factor than pollutant concentrations and the relative contribution of rain is larger than that of pollutants by up to a factor of 3-4 in polluted regions. In polluted regions, pollutant concentrations can remain relatively high even in the presence of precipitation owing to continuous and intense emissions; therefore, wet deposition is limited by rainfall. The contribution of rainfall is larger by 1.5-2.5 than that of pollutant concentrations in regions even with low emissions and this considerably large role of rain suggests that regional or transboundary pollutant transport plays a key role in modulating wet deposition. However, in very remote regions, once the rainfall amount exceeds a certain value, rainfall no longer contributes to increasing wet deposition because atmospheric pollutants are readily removed by rain. So, the contributions of the two factors are comparable in pristine regions. Our results can serve as a basis for explaining interannual variations in wet deposition and for future projections of wet deposition under emission control plans and climate change scenarios across regions.

Serial Circulating Tumor DNA Analysis with a Tumor-Naïve Next-Generation Sequencing Panel Detects Minimal Residual Disease and Predicts Outcome in Ovarian Cancer.

Circulating tumor DNA (ctDNA) may aid in personalizing ovarian cancer therapeutic options. Here, we aimed to assess the clinical utility of serial ctDNA testing using tumor-naïve, small-sized next-generation sequencing (NGS) panels. A total of 296 patients, including 201 with ovarian cancer and 95 with benign or borderline disease, were enrolled. Samples were collected at baseline (initial diagnosis or surgery) and every 3 months after that, resulting in a total of 811 blood samples. Patients received adjuvant therapy based on the current standard of care. Cell-free DNA was extracted and sequenced using an NGS panel of 9 genes: TP53, BRCA1, BRCA2, ARID1A, CCNE1, KRAS, MYC, PIK3CA, and PTEN. Pathogenic somatic mutations were identified in 69.2% (139/201) of patients with ovarian cancer at baseline but not in those with benign or borderline disease. Detection of ctDNA at baseline and/or at 6 months follow-up was predictive of progression-free survival (PFS). PFS was significantly poorer in patients with detectable pathogenic mutations at baseline that persisted at follow-up than in patients that converted from having detectable ctDNA at baseline to being undetectable at follow-up; survival did not differ between patients without pathogenic ctDNA mutations in baseline or follow-up samples and those that converted from ctDNA positive to negative. Disease recurrence was also detected earlier with ctDNA than with conventional radiologic assessment or CA125 monitoring. These findings demonstrate that serial ctDNA testing could effectively monitor patients and detect minimal residual disease, facilitating early detection of disease progression and tailoring of adjuvant therapies for ovarian cancer treatment. SIGNIFICANCE: In ovarian cancer, serial circulating tumor DNA testing is a highly predictive marker of patient survival, with a significantly improved recurrence detection lead time compared with conventional monitoring tools.

Anthropogenic fingerprints in daily precipitation revealed by deep learning.

According to twenty-first century climate-model projections, greenhouse warming will intensify rainfall variability and extremes across the globe1-4. However, verifying this prediction using observations has remained a substantial challenge owing to large natural rainfall fluctuations at regional scales3,4. Here we show that deep learning successfully detects the emerging climate-change signals in daily precipitation fields during the observed record. We trained a convolutional neural network (CNN)5 with daily precipitation fields and annual global mean surface air temperature data obtained from an ensemble of present-day and future climate-model simulations6. After applying the algorithm to the observational record, we found that the daily precipitation data represented an excellent predictor for the observed planetary warming, as they showed a clear deviation from natural variability since the mid-2010s. Furthermore, we analysed the deep-learning model with an explainable framework and observed that the precipitation variability of the weather timescale (period less than 10 days) over the tropical eastern Pacific and mid-latitude storm-track regions was most sensitive to anthropogenic warming. Our results highlight that, although the long-term shifts in annual mean precipitation remain indiscernible from the natural background variability, the impact of global warming on daily hydrological fluctuations has already emerged.

Exploring the Characteristics of Circulating Tumor DNA in Pt1a Clear Cell Renal Cell Carcinoma: A Pilot Study.

Circulating tumor DNA (ctDNA) is a promising biomarker for clear cell renal cell carcinoma (ccRCC); however, its characteristics in small renal masses of ccRCC remain unclear. In this pilot study, we explored the characteristics of ctDNA in pT1a ccRCC. Plasma samples were collected preoperatively from 53 patients with pT1a ccRCC. The ctDNA of pT1a ccRCC was profiled using next-generation sequencing and compared with that of higher-stage ccRCC. The association of ctDNA in pT1a ccRCC with clinicopathological features was investigated. The positive relationship of mutations between ctDNA and matched tissues was evaluated. In pT1a ccRCC, the ctDNA detection rate, cell-free DNA concentration, and median variant allele frequency were 20.8%, 5.8 ng/mL, and 0.38%, respectively, which were significantly lower than those in metastatic ccRCC. The ctDNA gene proportions in pT1a samples differed from those in metastatic ccRCC samples. The relationships between ctDNA and tumor size, tumor grade, and patient age were not elucidated. The positive concordance between ctDNA and matched tissues was poor for pT1a ccRCC. Strategies are needed to increase sensitivity while eliminating noise caused by clonal hematopoiesis to increase the clinical utility of ctDNA analysis in small renal masses of ccRCC.

Hemispherically asymmetric Hadley cell response to CO2 removal.

A poleward shift of the Hadley cell (HC) edge in a warming climate, which contributes to the expansion of drought-prone subtropical regions, has been widely documented. The question addressed here is whether this shift is reversible with CO2 removal. By conducting large-ensemble experiments where CO2 concentrations are systematically increased and then decreased to the present-day level, we show that the poleward-shifted HC edge in a warming climate does not return to its present-day state when CO2 concentrations are reduced. While the Southern Hemisphere HC edge remains poleward of its present-day state, the Northern Hemisphere HC edge ends up farther equatorward of its present-day state. Such hemispherically asymmetric HC edge changes are closely associated with the changes in vertical wind shear in the subtropical atmosphere, which result from the long adjustment time of the ocean response to CO2 removal. Our findings suggest that CO2 removal may not guarantee the recovery of the subtropical dryness associated with the HC changes.

Increase in convective extreme El Niño events in a CO2 removal scenario.

Convective extreme El Niño (CEE) events, characterized by strong convective events in the eastern Pacific, are known to have a direct link to anomalous climate conditions worldwide, and it has been reported that CEE will occur more frequently under greenhouse warming. Here, using a set of CO2 ramp-up and ramp-down ensemble experiments, we show that frequency and maximum intensity of CEE events increase further in the ramp-down period from the ramp-up period. These changes in CEE are associated with the southward shift of the intertropical convergence zone and intensified nonlinear rainfall response to sea surface temperature change in the ramp-down period. The increasing frequency of CEE has substantial impacts on regional abnormal events and contributed considerably to regional mean climate changes to the CO2 forcings.

Observationally-constrained projections of an ice-free Arctic even under a low emission scenario.

The sixth assessment report of the IPCC assessed that the Arctic is projected to be on average practically ice-free in September near mid-century under intermediate and high greenhouse gas emissions scenarios, though not under low emissions scenarios, based on simulations from the latest generation Coupled Model Intercomparison Project Phase 6 (CMIP6) models. Here we show, using an attribution analysis approach, that a dominant influence of greenhouse gas increases on Arctic sea ice area is detectable in three observational datasets in all months of the year, but is on average underestimated by CMIP6 models. By scaling models' sea ice response to greenhouse gases to best match the observed trend in an approach validated in an imperfect model test, we project an ice-free Arctic in September under all scenarios considered. These results emphasize the profound impacts of greenhouse gas emissions on the Arctic, and demonstrate the importance of planning for and adapting to a seasonally ice-free Arctic in the near future.

Asymmetrical response of summer rainfall in East Asia to CO2 forcing.

Understanding the regional hydrological response to varying CO2 concentration is critical for cost-benefit analysis of mitigation and adaptation polices in the near future. To characterize summer monsoon rainfall change in East Asia in a changing CO2 pathway, we used the Community Earth System Model (CESM) with 28 ensemble members in which the CO2 concentration increases at a rate of 1% per year until its quadrupling peak, i.e., 1468 ppm (ramp-up period), followed by a decrease of 1% per year until the present-day climate conditions, i.e., 367 ppm (ramp-down period). Although the CO2 concentration change is symmetric in time, the amount of summer rainfall anomaly in East Asia is increased 42% during a ramp-down period than that during a ramp-up period when the two periods of the same CO2 concentration are compared. This asymmetrical rainfall response is mainly due to an enhanced El Niño-like warming pattern as well as its associated increase in the sea surface temperature in the western North Pacific during a ramp-down period. These sea surface temperature patterns enhance the atmospheric teleconnections and the local meridional circulations around East Asia, resulting in more rainfall over East Asia during a ramp-down period. This result implies that the removal of CO2 does not guarantee the return of regional rainfall to the previous climate state with the same CO2 concentration.

Analytical and Clinical Validation of Cell-Free Circulating Tumor DNA Assay for the Estimation of Tumor Mutational Burden.

BACKGROUND: Ultra-deep sequencing to detect low-frequency mutations in circulating tumor-derived DNA (ctDNA) increases the diagnostic value of liquid biopsy. The demand for large ctDNA panels for comprehensive genomic profiling and tumor mutational burden (TMB) estimation is increasing; however, few ctDNA panels for TMB have been validated. Here, we designed a ctDNA panel with 531 genes, named TMB500, along with a technical and clinical validation. METHODS: Synthetic reference cell-free DNA materials with predefined allele frequencies were sequenced in a total of 92 tests in 6 batches to evaluate the precision, linearity, and limit of detection of the assay. We used clinical samples from 50 patients with various cancers, 11 healthy individuals, and paired tissue samples. Molecular barcoding and data analysis were performed using customized pipelines. RESULTS: The assay showed high precision and linearity (coefficient of determination, r2 =0.87) for all single nucleotide variants, with a limit of detection of 0.24%. In clinical samples, the TMB500 ctDNA assay detected most variants present and absent in tissues, showing that ctDNA could assess tumor heterogeneity in different tissues and metastasis sites. The estimated TMBs correlated well between tissue and blood, except in 4 cases with extreme heterogeneity that showed very high blood TMBs compared to tissue TMBs. A pilot evaluation showed that the TMB500 assay could be used for disease monitoring. CONCLUSIONS: The TMB500 assay is an accurate and reliable ctDNA assay for many clinical purposes. It may be useful for guiding the treatment of cancers with diverse genomic profiles, estimating TMB in immune therapy, and disease monitoring.

Greenhouse warming and anthropogenic aerosols synergistically reduce springtime rainfall in low-latitude East Asia.

Low-latitude East Asia, particularly southern China, has experienced a markedly decreasing springtime rainfall in recent years whereas rainfall trends are weak in mid-latitude East Asia. Details of human influences on this contrasting feature remain uncertain. This study provides a quantification of the relative roles of greenhouse warming and aerosols in the observed spring rainfall trends over East Asia using a state-of-the-art numerical model. Greenhouse warming drives more rapid temperature increases over high-latitude East Asia potentially associated with reduced spring snow than the western North Pacific, which induces an anomalous anticyclone over the East China Sea. This circulation change results in a northwestward extension of the western North Pacific subtropical high, reducing rainfall at low latitudes while moderately increasing rainfall at mid-latitudes. In contrast, anthropogenic aerosols reduce rainfall in both low- and mid-latitude East Asia. Hence, the two anthropogenic factors synergistically reduce rainfall at low latitudes, with a stronger contribution of greenhouse warming (~34%) than aerosols (~17%). In mid-latitude East Asia, their contributions are offset, resulting in weak rainfall trends. Further, the anthropogenic influences are found to be relatively larger under drier conditions, suggesting that a more severe drought can occur in low-latitude East Asia under future drought-conducive conditions.

Volcanic-induced global monsoon drying modulated by diverse El Niño responses.

There remains large intersimulation spread in the hydrologic responses to tropical volcanic eruptions, and identifying the sources of diverse responses has important implications for assessing the side effects of solar geoengineering and improving decadal predictions. Here, we show that the intersimulation spread in the global monsoon drying response strongly relates to diverse El Niño responses to tropical eruptions. Most of the coupled climate models simulate El Niño-like equatorial eastern Pacific warming after volcanic eruptions but with different amplitudes, which drive a large spread of summer monsoon weakening and corresponding precipitation reduction. Two factors are further identified for the diverse El Niño responses. Different volcanic forcings induce systematic differences in the Maritime Continent drying and subsequent westerly winds over equatorial western Pacific, varying El Niño intensity. The internally generated warm water volume over the equatorial western Pacific in the pre-eruption month also contributes to the diverse El Niño development.

Second primary cancers in patients with oral cavity cancer included in the Korea Central Cancer Registry.

OBJECTIVES: The improved survival of patients with oral cavity cancer (OCC) has generated interest in factors affecting survivorship, particularly among second primary cancer (SPC) patients. This study aimed to assess the incidence, patterns, and risk factors for SPC after OCC treatment in the Korean population. MATERIALS AND METHODS: Data from 15,261 patients with OCC (ICD-O: C01-C06) identified between 1993 and 2014 were extracted from the Korean Central Cancer Registry. The standardized incidence ratio (SIR) for SPC after index OCC was calculated, and Poisson regression analysis was performed to evaluate the risk factors for SPC among survivors. RESULTS: The overall SIR for SPC among OCC survivors was 1.47 (95% confidence interval [CI] 1.39-1.56). SIR differed by sex (male: 1.51 vs. female: 1.37), age at diagnosis (<45 years: 2.47 vs. 45-64 years: 1.68 vs. ≥ 65 years: 1.10), index OCC subsite (floor of mouth: 1.95 vs. gum: 1.30), follow-up duration (6-23 months: 1.64 vs. 24-59 months: 1.51 vs. 60-119 months: 1.48 vs. ≥ 120 months: 1.24), histological OCC type (salivary gland malignancy: 1.77 vs. squamous cell carcinoma: 1.44 vs. others: 1.47), and radiation history (any: 1.94 vs. no radiation: 1.37). The risk factors for SPC development among OCC survivors included younger age at diagnosis and history of radiation therapy. CONCLUSION: OCC survivors have significantly increased risks of SPCs, exhibiting distinctive site distributions and chronological patterns. These patients would benefit from an SPC surveillance protocol.

Per-oral cross-facial sural nerve graft for facial reanimation.

BACKGROUND: Cross-facial nerve graft is considered the treatment of choice for facial reanimation in patients with unilateral facial palsy caused by central facial nerve damage. In most cases, a traditional parotidectomy skin incision is used to locate the buccal and zygomatic branches of the facial nerve. METHODS: In this study, cross-facial nerve graft with the sural nerve was planned for three patients with facial palsy through an intraoral approach. RESULTS: An incision was made on the buccal cheek mucosa, and the dissection was performed to locate the buccal branch of the facial nerve. The parotid papillae and parotid duct were used as anatomic landmarks to locate the buccal branch. CONCLUSIONS: The intraoral approach is more advantageous than the conventional extraoral approach because of clear anatomic marker (parotid papilla), invisible postoperative scar, reduced tissue damage from dissection, and reduced operating time.

Desmoplastic melanoma of the oral cavity: diagnostic pitfalls and clinical characteristics.

OBJECTIVES: Desmoplastic melanoma of the oral cavity is an extremely rare condition that is often confused on initial diagnosis with non-melanotic benign lesion or spindle cell tumors. The purpose of this article was to raise awareness of the disease using a literature review. MATERIALS AND METHODS: We analyzed 19 desmoplastic melanoma cases reported in the literature and added our experience. Data on clinical, histopathology, treatment, and survival were retrieved and analyzed. Survival analysis was by the Kaplan-Meier method. RESULTS: Initial clinical and histopathological features were indistinctive, and a definite diagnosis of desmoplastic melanoma at initial assessment was possible in only 23.5% of cases. Among tests, immunohistochemical studies for S-100 and vimentin were all positive. The 5-year disease-free survival rate for oral desmoplastic melanoma was 0%, and the 5-year overall survival rate was 55.0%. CONCLUSION: Oral desmoplastic melanoma has a high percentage of initial misdiagnosis and propensity for local recurrence. Thus, careful initial diagnosis and adequate surgery may result in improved overall survival.

A vitronectin-derived peptide reverses ovariectomy-induced bone loss via regulation of osteoblast and osteoclast differentiation.

Osteoporosis affects millions of people worldwide by promoting bone resorption and impairing bone formation. Bisphosphonates, commonly used agents to treat osteoporosis, cannot reverse the substantial bone loss that has already occurred by the time of diagnosis. Moreover, their undesirable side-effects, including osteonecrosis of the jaw, have been reported. Here, we demonstrated that a new bioactive core vitronectin-derived peptide (VnP-16) promoted bone formation by accelerating osteoblast differentiation and activity through direct interaction with ß1 integrin followed by FAK activation. Concomitantly, VnP-16 inhibited bone resorption by restraining JNK-c-Fos-NFATc1-induced osteoclast differentiation and αvß3 integrin-c-Src-PYK2-mediated resorptive function. Moreover, VnP-16 decreased the bone resorbing activity of pre-existing mature osteoclasts without changing their survival rate. Furthermore, VnP-16 had a strong anabolic effect on bone regeneration by stimulating osteoblast differentiation and increasing osteoblast number, and significantly alleviated proinflammatory cytokine-induced bone resorption by restraining osteoclast differentiation and function in murine models. Moreover, VnP-16 could reverse ovariectomy-induced bone loss by both inhibiting bone resorption and promoting bone formation. Given its dual role in promoting bone formation and inhibiting bone resorption, our results suggest that VnP-16 could be an attractive therapeutic agent for treating osteoporosis.

Functional diversity of miR-146a-5p and TRAF6 in normal and oral cancer cells.

Numerous studies implicate miR-146a as pleiotropic regulator of carcinogenesis; however, its roles in carcinogenesis are not fully understood. A clue from expression analyses of miR-146a-5p in all 13 oral squamous cell carcinoma (OSCC) cell lines examined and in OSCC tissues, whole blood and whole saliva of OSCC patients in vivo revealed that miR­146a-5p expression was highly upregulated. Particularly, we widened the view of its upregulation in saliva, implicating that high miR-146a-5p expression is not only correlated closely to the development of human oral cancer, but also to a possible candidate as a diagnostic marker of OSCC. Indeed, further examination showed that exogenous miR-146a-5p expression showed pleiotropic effects on cell proliferation and apoptosis which were partially based on the contextual responses of activation of JNK, downstream of TRAF6 that was targeted by miR-146a-5p in normal human keratinocytes and OSCC cell lines. TRAF6 suppression by a TRAF6-specific siRNA resulted in contradictory consequences on cellular processes in normal and OSCC cells. Notably, TRAF6 downregulation by both miR-146a-5p and TRAF6-specific siRNA deactivated JNK in SCC-9, but not in normal human keratinocytes. In support of the proliferation-promoting effect of miR-146a-5p, silencing of endogenous miR-146a-5p significantly reduced proliferation of SCC-9. Together, these results suggest that miR-146a-5p affects proliferation and apoptosis in a cellular context-dependent manner and selectively disarms the TRAF6-mediated branch of the TGF-ß signaling in OSCC cell lines by sparing Smad4 involvement.

Conditional relative survival of oral cavity cancer: Based on Korean Central Cancer Registry.

OBJECTIVES: Conditional relative survival (CRS) describes the survival chance of patients who have already survived for a certain period of time after diagnosis and treatment of cancer. Thus, CRS can complement the conventional 5-year relative survival, which does not consider the time patients have survived after their diagnosis. This study aimed to assess the 5-year CRS among Korean patients with oral cancer and the related risk factors. MATERIALS AND METHODS: We identified 15,329 oral cavity cancer cases with a diagnosis between 1993 and 2013 in the Korea Central Cancer Registry. The CRS rates were calculated according to sex, age, subsite, histology, and stage at diagnosis. RESULTS: The 5-year relative survival was 57.2%, and further analysis revealed that the 5-year CRS increased during the first 2years and reached a plateau at 86.5% after 5years of survival. Women had better 5-year CRS than men after 5years of survival (90.0% vs. 83.3%), and ≤45-year-old patients had better 5-year CRS than older patient groups (93.3% vs. 86.4% or 86.7%). Subsite-specific differences in 5-year CRS were observed (tongue: 91% vs. mouth floor: 73.9%). Squamous cell carcinoma had a CRS of 87.3%, compared to 85.5% for other histological types. Localized disease had a CRS of 95.7%, compared to 87.3% for regional metastasis. CONCLUSION: Patients with oral cavity cancer exhibited increasing CRS rates, which varied according to sex, age, subsite, histology, and stage at diagnosis. Thus, CRS analysis provides a more detailed perspective regarding survival during the years after the initial diagnosis or treatment.

Human-caused Indo-Pacific warm pool expansion.

The Indo-Pacific warm pool (IPWP) has warmed and grown substantially during the past century. The IPWP is Earth's largest region of warm sea surface temperatures (SSTs), has the highest rainfall, and is fundamental to global atmospheric circulation and hydrological cycle. The region has also experienced the world's highest rates of sea-level rise in recent decades, indicating large increases in ocean heat content and leading to substantial impacts on small island states in the region. Previous studies have considered mechanisms for the basin-scale ocean warming, but not the causes of the observed IPWP expansion, where expansion in the Indian Ocean has far exceeded that in the Pacific Ocean. We identify human and natural contributions to the observed IPWP changes since the 1950s by comparing observations with climate model simulations using an optimal fingerprinting technique. Greenhouse gas forcing is found to be the dominant cause of the observed increases in IPWP intensity and size, whereas natural fluctuations associated with the Pacific Decadal Oscillation have played a smaller yet significant role. Further, we show that the shape and impact of human-induced IPWP growth could be asymmetric between the Indian and Pacific basins, the causes of which remain uncertain. Human-induced changes in the IPWP have important implications for understanding and projecting related changes in monsoonal rainfall, and frequency or intensity of tropical storms, which have profound socioeconomic consequences.

Muscular invasion by oral squamous cell carcinoma of the posterior mandibular alveolar ridge is associated with cervical lymph node metastasis.

OBJECTIVES: To assess the association between muscle invasion by oral squamous cell carcinoma of the posterior mandibular alveolar ridge and cervical lymph node metastasis on the basis of preoperative magnetic resonance imaging (MRI). MATERIALS AND METHODS: Twenty-six patients with oral squamous cell carcinoma of the posterior mandibular alveolar ridge were evaluated by MRI. The associations between cervical lymph node metastasis and independent factors evaluated by MRI were analyzed. Overall survival was also analyzed in this manner. Representative biopsy specimens were stained with anti-podoplanin and anti-CD34 antibodies. RESULTS: Mylohyoid muscle invasion was associated with cervical lymph node metastasis. A combinational factor of mylohyoid and/or buccinator muscle invasion was also associated with cervical lymph node metastasis. Cervical lymph node metastasis and masticator space invasion had a negative effect on overall survival. No lymphatic vessels were identified near the tumor invasion front within the mandible. In contrast, lymphatic vessels were identified near the front of tumor invasion in the muscles. CONCLUSION: This study demonstrates an association between muscular invasion by oral squamous cell carcinoma of the posterior mandibular alveolar ridge and cervical lymph node metastasis.