Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequence Stratigraphic Significance of Organic Matter Variations: Example from the Upper Cretaceous Mancos Shale of the San Juan Basin, New Mexico: Chapter 14

Study of a portion of the Upper Cretaceous Mancos Shale in the San Juan Basin of New Mexico shows that organic facies deposited on the shelf change noticeably at surfaces that have sequence stratigraphic significance. Shelf sediments below transgressive surfaces contain abundant, well-preserved terrestrial organic matter (phytoclasts) whereas sediments above transgressive surfaces contain sparse and highly degraded phytoclasts and more hydrogen-rich organic matter. Shelf sediments associated with the maximum flooding surface typically contain the least terrestrial organic matter. These results indicate that the type and preservation of organic matter is related to both the rate of terrigenous sediment supply to the shelf and the bottom water oxygen conditions present on t e shelf. Variations in the amount and type of organic matter (organic facies) preserved in shelf sediments are predictable within a sequence stratigraphic framework. Each systems tract has a distinctive depositional style that affects the amount of terrigenous sediment influx to the shelf and, consequently, the type and preservation of organic matter that is deposited on the shelf. Fine-grained marine sediments in transgressive systems tracts possess high total organic carbon and yield relatively high amounts of hydrocarbons during pyrolysis. Petrographically, this organic matter is composed primarily of amorphous nonstructured protistoclasts. Phytoclasts in the transgressive systems tract are highly degraded. In contrast, progradational marine depositional systems of both the lowstand and hig stand systems tracts contain End_Page 221------------------------ less total organic carbon and less pyrolyzable hydrocarbons. Petrographic analysis of organic matter in these rocks reveals abundant macerals of terrestrial origin. Phytoclasts are especially well preserved in the lowstand systems tract. Integration of data from the characterization of organic matter with sedimentologic and regional stratigraphic information provides greater precision in locating surfaces that bound systems tracts within the depositional sequence. An example of this approach is presented for a part of the Upper Cretaceous Mancos Shale of the San Juan Basin, New Mexico. Organic matter data not only improve systems tract identification in fine-grained, basinward facies but also demonstrate that the predictive capabilities of sequence stratigraphy are applicable to marine petroleum source rocks. These results indicate that optimum source rock potential is found in the transgressive systems tract below the condensed section facies that contains the downlap surface.
Suppression of Kynurenine 3-Monooxygenase as a Treatment for Triple-negative Breast Carcinoma

Kynurenine 3-monooxygenase (KMO), a key enzyme within the kynurenine (KYN) pathway of tryptophan (TRY) metabolism, enables the excess production of toxic metabolites (such as 3-hydroxykynurenine, xanthurenic acid, 3-hydroxyanthranilic acid and quinolinic acid), and modulates the balance between these toxic molecules and the protective metabolite, kynurenic acid (KYNA). Despite its importance, KMO suppression as a treatment for cancer has not been fully explored. Instead, researchers have focused on prevention of KYN pathway activity by inhibition of enzymes indoleamine 2,3-dioxygenase (IDO1 and IDO2) or tryptophan 2,3-dioxygenase (TDO, also known as TDO2). However, studies using IDO/TDO inhibitors against cancer have not yet shown that this type of treatment can be successful. We argue that KMO suppression can be an effective strategy for treatment of cancer by 1) decreasing toxic metabolites within the KYN pathway and 2) increasing levels of KYNA, which has important protective and anticancer properties. This strategy may be beneficial in the treatment of aggressive breast cancer, particularly in patients with triple-negative breast cancer. A major challenge to this strategy, when searching for an effective treatment for tumors, especially tumors like breast carcinoma that often metastasize to the brain, is finding KMO inhibitors that adequately cross the blood-brain barrier.
lncRNA SEMA3B-AS1 Inhibits miR-513c-5p to Regulate the Progression of Triple-negative Breast Cancer

Background/Aim: Triple-negative breast cancer (TNBC) is the most malignant breast cancer subtype with a short survival time and high morality. There is an urgent need for effective indicators able to predict tumor progression and provide reference for adjusting the therapeutic strategy of TNBC. lncRNA semaphorin 3B antisense RNA1-AS1 (SEMA3B-AS1) was previously identified to be correlated with the stemness and autophagy of breast cancer. SEMA3B-AS1’s role in TNBC was investigated in the present study, aiming to explore a novel biomarker for the development and prognosis of TNBC. Materials and Methods: SEMA3B-AS1 expression was detected in tissue samples from 113 TNBC patients using PCR. The clinical significance of SEMA3B-AS1 was assessed by the Chi-square test and Cox analysis. The in vitro function of SEMA3B-AS1 was investigated by CCK8 and Transwell assay. Study of molecular mechanism, correlation analysis and dual-luciferase reporter assay were employed to assess the correlation of SEMA3B-AS1 with miR-513c-5p. Results: A significant down-regulation of SEMA3B-AS1 was observed in TNBC, which was related to patient TNM stage, lymph node metastasis, and Ki67 levels. SEMA3B-AS1 down-regulation indicated patients’ adverse prognoses and served as an independent prognostic factor. In vitro, SEMA3B-AS1 suppressed the stemness, proliferation, and metastasis of TNBC cells. Moreover, SEMA3B-AS1 negatively regulated miR-513c-5p, which could reverse the inhibitory effects of SEMA3B-AS1 on TNBC cells. Conclusion: SEM3B-AS1 indicates the severity of TNBC patients and regulates tumor progression via modulating miR-513c-5p.
Prediction of Oncotype DX Recurrence Score by Evaluating the Peritumoral Tumor Budding in Early-stage Breast Carcinoma

Background/Aim: The Oncotype DX Recurrence Score (ORS) predicts the likelihood of recurrence and the benefit of chemotherapy in patients with estrogen receptor (ER)-positive, human epidermal growth factor receptor 2 (HER2)-negative early-stage breast carcinoma (ESBC). Tumor budding (TB) is a poor prognostic factor in breast carcinoma. This study aimed to determine the clinicopathological significance of TB in predicting ORS in patients with ESBC. Patients and Methods: We included 359 patients with ER-positive, HER2-negative ESBC. The number of peritumoral TB was assessed, and the cases were categorized into TB-low (<10 buds) and TB-high (≥10 buds) groups. Results: Patients with TB-high ESBC (170/359; 47.4%) showed a significantly higher median ORS (15.0 vs. 13.0) than those with TB-low tumors (189/359; 52.6%). Multivariate analysis revealed that high TB level was an independent predictive factor for higher ORS in patients with ESBC. Conclusion: High TB in ESBC independently predicted higher ORS. TB may serve as a surrogate marker for predicting ORS in patients with ESBC.
Technological Diffusion, Spatial Spillovers and Regional Convergence in Europe

In this paper we study two closely related issues. First, the role of technology heterogeneity and diffusion in the convergence of GDP per worker observed across the European regions, in the absence of data on regional TFP. Second, the spatial pattern of the observed regional heterogeneity in technology and the relevance of this pattern for the econometric analysis of regional convergence in Europe. As for the first issue, our aim is to assess whether the convergence observed across European regions is due to convergence in technology as well as to convergence in capital-labor ratios. We first develop a growth model where technology accumulation in lagging regions depends on their own propensity to innovate and on technology diffusion from the leading region, and convergence in GDP per worker is due to both capital deepening and catch-up. We use data (1978-97) on 131 European regions. Propensities to innovate are computed by assigning each patent collected by the European Patent Office to its region of origin. Our findings are consistent with the hypothesis that technology differs across regions and that convergence is partly due to technological catch-up. As for the second empirical issue, we study to what extent each region s propensity to innovate is correlated with that of the surrounding regions. Our results show, first, that the performance of each region does depend on that of the surrounding areas. Second, that the intensity of such spillovers fades with distance. Taken together, these findings suggest the existence of significant localized spillovers of technological knowledge. Finally, we show that these spillovers are strong enough to play a role that cannot be ignored in the econometric analysis of the convergence process in Europe.
FOLFIRI Chemotherapy for Patients With Metastatic Urachal Carcinoma

Background/Aim: Urachal carcinoma is a rare cancer, with limited evidence regarding systemic chemotherapy for metastatic urachal carcinoma. This study aimed to evaluate the efficacy and safety of a combination therapy of 5-fluorouracil and irinotecan (FOLFIRI) in patients with metastatic urachal carcinoma. Patients and Methods: Patients with metastatic urachal carcinoma treated with FOLFIRI between March 2008 and April 2023 at the Department of Medical Oncology, Tohoku University Hospital, were retrospectively analyzed using medical records. Results: Six patients with urachal carcinoma received FOLFIRI. The histological type was adenocarcinoma in all patients. The metastatic or recurrent sites were the peritoneum, lungs, lymph nodes, and local relapse sites. Three patients received FOLFIRI as first-line chemotherapy, and the other three received FOLFIRI as second-line chemotherapy. Two patients had only non-measurable lesions as the targets of tumor response. The best response was the stable disease or non-complete response/non-progressive disease in four patients, with a disease control rate of 67%. The median progression-free survival was 7.5 months. In two patients with ascites only as the site of metastasis, the amount of ascites and serum tumor marker levels decreased after FOLFIRI was initiated. Grade 3/4 toxicities included grade 3 neutropenia in one patient and grade 3 diarrhea in one patient. Conclusion: FOLFIRI has modest efficacy and good tolerability for the treatment of metastatic urachal carcinoma.
Generating New Musical Preferences from Hierarchical Mapping of Predictions to Reward

Prediction learning is considered a fundamental feature of biological systems that underlies perception, action, and reward. For cultural artifacts like music, isolating the genesis of reward from prediction is challenging, since predictions are acquired implicitly throughout life. Here, we examined the trajectory of listeners’ preferences for melodies in a novel musical scale, where local and global predictions were independently manipulated. Across seven studies (n = 842 total) in two cultures, participants preferred melodies that were presented more during exposure (globally predictable) and that followed schematic expectations (locally predictable). Learning trajectories depended on music reward sensitivity. Furthermore, fMRI showed that while auditory cortical activation reflects predictions, functional connectivity between auditory and reward areas encodes preference. The results are the first to show a hierarchical, relatively culturally-independent process by which predictions map onto reward. Collectively, our findings propose a novel mechanism by which the human brain links predictions with reward value.
Test research on influence of vegetation on mechanical parameters of soils

By using vane shear test,portable sounding test,water content test and direct shear test,the strengthening effect of vegetation on the soil slope of an expressway,i.e.the influence of vegetation on mechanical parameters of slope soil is researched.The tests are done in two kinds of vegetation areas.The result indicates that the vegetation has potential influence on the stability of shallow slope.Through tests the quantitative influence of the vegetation on the shallow slope is analyzed.
Biochemical markers of renal function and maternal hypothyroidism in early pregnancy

Objective The physiological adaptations during a normal pregnancy affect renal and thyroid function and levels of associated biochemical markers. An association between cystatin C (CysC), creatinine, and thyroid function has been considered in nonpregnant individuals but not in pregnant women specifically. Methods Cohort study within the North Denmark Region Pregnancy Cohort (2011–2015) with assessment of thyroid function and autoantibodies (ADVIA Centaur XPT, Siemens Healthineers) in serum residues from the early pregnancy. Consecutive samples (n = 1112) were selected for measurement of CysC and creatinine (Atellica CH 930, Siemens Healthineers), and results were linked to information in Danish nationwide registers for (i) establishment of pregnancy-specific reference intervals for CysC and creatinine and (ii) evaluation of the prevalence of maternal hypothyroidism in early pregnancy according to levels of CysC and creatinine. Results The established reference intervals (2.5–97.5 percentiles) differed by week of pregnancy (week 4–8, 9–11, 12–15) and were CysC: 0.58–0.92 mg/L; 0.54–0.91 mg/L; 0.52–0.86 mg/L; creatinine: 46.9–73.0 µmol/L; 42.0–68.4 µmol/L; 38.8–66.4 µmol/L. The prevalence of maternal autoimmune hypothyroidism in early pregnancy differed by the level of CysC and creatinine (<25th percentile; 25th–75th percentile; >75th percentile) and was for CysC 1.7%, 3.8%, 7.4% and for creatinine 2.5%, 4.1%, 7.1%. Conclusions Reference intervals for CysC and creatinine were dynamic in early pregnancy and decreased with increasing gestational age. Furthermore, higher levels of CysC and creatinine associated with a higher prevalence of maternal autoimmune hypothyroidism. Results encourage considerations on the underlying mechanisms for the association between markers of renal and thyroid function.
Prevalence, Diagnostic Utility and Associated Characteristics of Bronchodilator Responsiveness

Rationale The prevalence and diagnostic utility of bronchodilator responsiveness (BDR) in a real-life setting is unclear. Objective To explore this uncertainty in patients aged ⩾12 years with physician-assigned diagnoses of asthma, asthma and chronic obstructive pulmonary disease (COPD), or COPD in NOVELTY, a prospective cohort study in primary and secondary care in 18 countries. Methods The proportion of patients with a positive BDR test in each diagnostic category was calculated using 2005 (ΔFEV1 or ΔFVC ⩾12% and ⩾200 ml) and 2021 (ΔFEV1 or ΔFVC >10% predicted) European Respiratory Society/American Thoracic Society criteria. Measurements and Main Results We studied 3,519 patients with a physician-assigned diagnosis of asthma, 833 with a diagnosis of asthma + COPD, and 2,436 with a diagnosis of COPD. The prevalence of BDR was 19.7% (asthma), 29.6% (asthma + COPD), and 24.7% (COPD) using 2005 criteria and 18.1%, 23.3%, and 18.0%, respectively, using 2021 criteria. Using 2021 criteria in patients diagnosed with asthma, BDR was associated with higher fractional exhaled nitric oxide; lower lung function; higher symptom burden; more frequent hospital admissions; and greater use of triple therapy, oral corticosteroids, or biologics. In patients diagnosed with COPD, BDR (2021) was associated with lower lung function and higher symptom burden. Conclusions BDR prevalence in patients with chronic airway diseases receiving treatment ranges from 18% to 30%, being modestly lower with the 2021 than with the 2005 European Respiratory Society/American Thoracic Society criteria, and it is associated with lower lung function and greater symptom burden. These observations question the validity of BDR as a key diagnostic tool for asthma managed in clinical practice or as a standard inclusion criterion for clinical trials of asthma and instead suggest that BDR be considered a treatable trait for chronic airway disease.
Further sounding rocket observations of structured whistler mode auroral emissions

[1] Two recent sounding rockets were launched into active auroral substorms from Poker Flat, Alaska: CHARM on 27 February 2007 and SIERRA on 14 January 2002. Both payloads included HF wave receivers. As previously reported, the SIERRA HF receiver recorded short-lived, periodic, time-dispersed features at 200-600 kHz ("stripes"), in which high-frequency components precede low frequencies, leading to a nearly linear frequency-time signature. These features coincided with a region identified as Alfvenic and dominated by suprathermal electron bursts and 10-110 eV downward going ions poleward of the main inverted V auroral arc. The CHARM experiment, using different electric field sensors, confirmed the occurrence of the stripe features with characteristics similar to those observed with SIERRA. The most promising mechanism to explain stripes is a cyclotron resonance between downgoing Z mode waves and upgoing electron conics in the topside ionosphere at altitudes of 3000-5000 km. These electron conics resonate with successively lower-frequency waves as they ascend, leading to emissions in which lower frequencies are delayed relative to higher frequencies; detailed modeling reproduces even fairly subtle nonlinear features of the stripes' frequency-time signature. The resulting structured Z mode waves then convert to whistler mode waves, which propagate to rocket altitudes. Previous simulations have shown that electron conics can be generated by Alfvenic acceleration and retain the periodicity of the driving Alfven wave. If this acceleration could be driven by Alfven waves at the frequency of the periodicity of the stripes, it could explain this periodicity and would be consistent with their correlation with an Alfvenic region.
Lipid-anchored proteasomes control membrane protein homeostasis

Protein degradation in eukaryotic cells is mainly carried out by the 26S proteasome, a macromolecular complex not only present in the cytosol and nucleus but also associated with various membranes. How proteasomes are anchored to the membrane and the biological meaning thereof have been largely unknown in higher organisms. Here, we show that N-myristoylation of the Rpt2 subunit is a general mechanism for proteasome-membrane interaction. Loss of this modification in the Rpt2-G2A mutant cells leads to profound changes in the membrane-associated proteome, perturbs the endomembrane system, and undermines critical cellular processes such as cell adhesion, endoplasmic reticulum–associated degradation and membrane protein trafficking. Rpt2G2A/G2A homozygous mutation is embryonic lethal in mice and is sufficient to abolish tumor growth in a nude mice xenograft model. These findings have defined an evolutionarily conserved mechanism for maintaining membrane protein homeostasis and underscored the significance of compartmentalized protein degradation by myristoyl-anchored proteasomes in health and disease.
DIML: Deep Interpretable Metric Learning via Structural Matching

In this paper, we present a new framework named DIML to achieve more interpretable deep metric learning. Unlike traditional deep metric learning method that simply produces a global similarity given two images, DIML computes the overall similarity through the weighted sum of multiple local part-wise similarities, making it easier for human to understand the mechanism of how the model distinguish two images. Specifically, we propose a structural matching strategy that explicitly aligns the spatial embeddings by computing an optimal matching flow between feature maps of the two images. We also devise a multi-scale matching strategy, which considers both global and local similarities and can significantly reduce the computational costs in the application of image retrieval. To handle the view variance in some complicated scenarios, we propose to use cross-correlation as the marginal distribution of the optimal transport to leverage semantic information to locate the important region in the images. Our framework is model-agnostic, which can be applied to off-the-shelf backbone networks and metric learning methods. To extend our DIML to more advanced architectures like vision Transformers (ViTs), we further propose truncated attention rollout and partial similarity to overcome the lack of locality in ViTs. We evaluate our method on three major benchmarks of deep metric learning including CUB200-2011, Cars196, and Stanford Online Products, and achieve substantial improvements over popular metric learning methods with better interpretability.
Can Lateral Viscosity Contrasts Explain Asymmetric Interseismic Deformation around Strike‐Slip Faults?

Abstract Geodetic studies have shown that deformation rates around several major strike‐slip faults are asymmetric. This asymmetry is often explained in terms of a crustal‐scale contrast in elastic properties across the fault. Motivated by the fact that elasticity variations for different rock types under similar ambient conditions are generally modest, whereas effective viscosity may vary over orders of magnitude, we have developed earthquake‐cycle models to evaluate whether contrasts in viscosity structure and effective plate thickness can explain observed asymmetric surface deformation. We find that an increased plate‐thickness contrast results in a more asymmetric surface‐velocity profile. Furthermore, for the same plate‐thickness contrast, asymmetry of the surface deformation is most pronounced in models with a low‐viscosity substrate. Initially, velocities relative to a point on the fault are higher on the side with the thin plate; however, late in the interseismic interval this reverses, and these velocities are higher on the side with the thick plate. Models with a contrast in the substrate viscosity on either side of the fault and a uniform plate thickness show behavior similar to that of the variable‐thickness plate models. In both suites of asymmetric models, the surface velocity at the fault varies through the earthquake cycle. This is necessary to reconcile symmetric coseismic deformation, asymmetric interseismic deformation, and the requirement of zero strain in the blocks on either side of the fault over an earthquake cycle. Given the modest asymmetry in surface deformation for models capable of producing localized interseismic deformation around the fault (i.e., models with high substrate viscosities), we conclude that lateral contrasts in viscosity or effective plate thickness cannot produce dramatic asymmetries in Global Positioning System surface‐velocity profiles across major strike‐slip faults.