Miracle-dz/UniFAR-FTUs huggingface dataset:
Application of Circulating Cell-Free Tumor DNA Profiles for Therapeutic Monitoring and Outcome Prediction in Genetically Heterogeneous Metastatic Melanoma.

PURPOSE Circulating cell-free tumor DNA (ctDNA) reflects the heterogeneous spectrum of tumor-specific mutations, especially in systemic disease. We validated plasma-based assays that allow the dynamic quantitative detection of ctDNA as a prognostic biomarker for tumor load and prediction of therapy response in melanoma. MATERIALS and METHODS We analyzed plasma-derived ctDNA from a large training cohort (n = 96) of patients with advanced-stage melanoma, with assays for the BRAF V600E and NRAS Q61 driver mutations as well as TERT C250T and TERT C228T promoter mutations. An independent patient cohort (n = 35) was used to validate the utility of ctDNA monitoring under mitogen-activated protein kinase-targeted or immune checkpoint therapies. RESULTS Elevated plasma ctDNA level at baseline was an independent prognostic factor of disease progression when compared with serum S100 and lactate dehydrogenase levels in multivariable analyses (hazard ratio [HR], 7.43; 95% CI, 1.01 to 55.19; P = .05). The change in ctDNA levels during therapy correlated with treatment response, where increasing ctDNA was predictive for shorter progression-free survival (eg, for BRAF V600E ctDNA, HR, 3.70; 95% CI, 1.86 to 7.34; P < .001). Increasing ctDNA levels predicted disease progression significantly earlier than did routine radiologic scans (P < .05), with a mean lead time of 3.5 months. NRAS-mutant ctDNA was detected in a significant proportion of patients with BRAF-mutant tumors under therapy, but unexpectedly also at baseline. In vitro sensitivity studies suggested that this represents higher-than-expected intratumoral heterogeneity. The detection of NRAS Q61 ctDNA in baseline samples of patients with BRAF V600E mutation who were treated with mitogen-activated protein kinase inhibitors significantly correlated with shorter progression-free survival (HR, 3.18; 95% CI, 1.31 to 7.68; P = .03) and shorter overall survival (HR, 4.08; 95% CI, 1.57 to 10.58; P = .01). CONCLUSION Our results show the potential role of ctDNA measurement as a sensitive monitoring and prediction tool for the early assessment of disease progression and therapeutic response in patients with metastatic melanoma.
Key issues on sediment quality assessment: A review of South American research with emphasis on Brazil

Conventional approaches to pollution prevention in South American countries have traditionally relied on scientists identifying potentially harmful substances and practices, and advising regulators concerning exposures and effects. Since the 1990s scientific knowledge and skills have contributed to the creation of pollution control legislation. However the extent, to which the legislation is effectively applied, is determined by government policies. To be effective, strategies for environmental protection must be firmly supported by political commitment. Sediment is recognized worldwide as a major repository for persistent contaminants in aquatic ecosystems. Contaminant dynamics promote changes in the overlying water quality, as well as in porewater and can affect the biota even though the overlying water may meet water quality criteria. It is recognized that traditional water quality-based controls are not enough to protect the aquatic environments in which sediment quality assessment is also required. Although chemical analysis of sediment provides information, which may allow for the estimation of potential biological effects, contaminant concentrations are not accurate predictors of biological responses. Sediment Quality Values can only be derived from a database of biological effects verified for different organisms by a variety of methods that show the relationship between effects and contaminants. Given the difficulties in establishing this database, Brazil, like other countries in South America, still does not have Sediment Quality Criteria (SQC) despite the existence of quality criteria for water. Although effluents are often controlled according to normalized standards, high levels of contamination in reservoirs, rivers, estuaries and coastal areas have been found; consequently sediments are receiving greater attention in South America. The principles and techniques globally accepted for sediment toxicity assessment are already in use in many South American countries, in an attempt to solve localized problems of environmental contamination. Most of the countries have chosen local test-species according to required criteria, and have already standardized protocols to establish the relationship between contamination and toxicity. Several integrative approaches for sediment quality evaluation such as; Apparent Effects Threshold (AET), Equilibrium Partitioning (EqP) and Sediment Quality Triad (SQT) are also being applied to hotspots to promote political measures for conservation and remediation.
Copper deficiency in Guizhou semi-fine wool sheep on pasture in south west China karst mountain area

The Guizhou semi-fine sheep in the Weining County, Guizhou province, south west China karst mountain area were affected by an ailment characterized by pica, emaciation, dyskinesia, depressed appetites, unsteady gait and anemia. We found that concentrations of copper (Cu) in soil and forage from affected and unaffected areas were within the normal ranges, but concentrations of sulfur (S) and molybdenum (Mo) in soil and forage were significantly higher (P<0.01) in affected areas than in unaffected areas. Concentrations of Cu in blood, wool and liver from the affected Guizhou semi-fine sheep were significantly lower (P<0.01) than those in healthy animals. Affected Guizhou semi-fine sheep showed a hypochromic microcytic anemia and a low level of ceruloplasmin. Oral administration of CuSO 4 prevented and cured the disease. We conclude that the disorder of Guizhou semi-fine sheep is caused by secondary Cu deficiency, mainly due to high S and Mo content in forage.
In vivo release of aflatoxin B1 bound to different sequestering agents in dairy cows

Abstract Nine lactating dairy cows, producing 31.08±5.00 kg of milk/cow/day and fed with a Total Mixed Ration (TMR) with an intake of 22.3±0.8 Kg s.s. /cow, were used to investigate the resistance of the AFs-SA complex in the rumen and in the gastro-intestinal tract. Two commercial sequestering agents Atox® and Mycosorb® were used. The AFB1 was also mixed to a rumen fluid (R-SA). AFB1 sequestered by Atox®, Mycosorb® and by R-SA were then fed to cows before the morning meal. Milk samples were collected for 6 consecutive milkings and analyzed for AFM1 content. The in vitro binding capacity of the two SA were 94.2% for Atox®, 84.3% for Mycosorb® and 71.86% for the R-SA. Both Atox® and Mycosorb® released some of the sequestered AFB1 determining an increase of the AFM1 in milk as soon as in the 1st milking from oral drenching (4.23±7.33; 23.60±8.23 and 46.06±39.84 ppt for Atox®, Mycosorb® and R-SA respectively). The AFM1 (ng/cow) in milk at the 4th milking was lower (66.04, 661.77 and 1613.04; P<0.05) in Atox® and Mycosorb® than R-SA, respectively. The percentage release of bound AFB1 were 1.63% for Atox®, 20.27% for Mycosorb® and 50.48% for R-SA.
Abundance and distribution of Salmincola edwardsii (Copepoda) on anadromous brook trout, Salvelinus fontinalis, (Mitchill) in the Moisie River system, Quebec

Riviere a la Truite, a tributary of the Moisie River, is probably a focus of Salmincola edwardsii transmission within the system. Differences in prevalence of the copepod on fish between Riviere a la Truite and the main river suggested that up to 41% of anadromous brook trout, Salvelinus fontinalis, in the Moisie River system overwinter in the tributary. Infected fish were generally less than 200 mm long and copepods were attached almost exclusively to the fins and their bases. The primary site of copepod attachment at low intensities of infection was the adipose fin but at high intensities the dorsal fin was most frequently infected. This displacement in attachment location with increased intensity may result in density-dependent mortality of copepods. Copepods were overdispersed on the host population at each major sampling time and data fit a negative binomial distribution (k ranged from 0.2 to 0.8).
Life history of Gambusia vittata (Pisces: Poeciliidae)

Abstract Viviparous fishes of the family Poeciliidae have been model systems in the study of life histories because of their remarkable variation in life-history traits both within and among species, and because of the diversity of selective environments that they occupy. However, the life histories of several poeciliids remain unknown. In this study, we describe the life history of Gambusia vittata, a poorly known poeciliid endemic to eastern Mexico. We analyze variation in number of embryos per reproductive female, size of individual embryos, size at maturity, reproductive effort, the amount of maternal transfer of nutrients to developing embryos, and the relationship between female size and life-history traits. We collected individuals from three sites across 3 months. We found that brood size varied significantly across sites and that brood size, embryo mass, and reproductive allotment varied across months within sites. Brood size, embryo mass, and reproductive allotment all increased with female size. We found that this species exhibits moderate matrotrophy, meaning that females transfer small amounts of nutrients to embryos during development. We compare our results to other poeciliid species and provide tentative explanations for the patterns of intraspecific variation that we observed in the life history of G. vittata.
The low‐expression programming of 11β‐HSD2 mediates osteoporosis susceptibility induced by prenatal caffeine exposure in male offspring rats

Prenatal caffeine exposure (PCE) can cause developmental toxicity of long bones in offspring, but the long‐term effects and the underlying mechanism have not been fully clarified. Here, we investigated the effects of PCE peak bone mass accumulation and osteoporosis susceptibility in offspring and its intrauterine programming mechanism.
Clinical Course and Mortality of Stroke Patients With Coronavirus Disease 2019 in Wuhan, China

Supplemental Digital Content is available in the text. Background and Purpose: No studies have reported the effect of the coronavirus disease 2019 (COVID-19) epidemic on patients with preexisting stroke. We aim to study the clinical course of COVID-19 patients with preexisting stroke and to investigate death-related risk factors. Methods: We consecutively included 651 adult inpatients with COVID-19 from the Central Hospital of Wuhan between January 2 and February 15, 2020. Data on the demography, comorbidities, clinical manifestations, laboratory findings, treatments, complications, and outcomes (ie, discharged or death) of the participants were extracted from electronic medical records and compared between patients with and without preexisting stroke. The association between risk factors and mortality was estimated using a Cox proportional hazards regression model for stroke patients infected with severe acute respiratory syndrome coronavirus 2. Results: Of the 651 patients with COVID-19, 49 with preexisting stroke tended to be elderly, male, had more underlying comorbidities and greater severity of illness, prolonged length of hospital stay, and greater hospitalization expenses than those without preexisting stroke. Cox regression analysis indicated that the patients with stroke had a higher risk of developing critical pneumonia (adjusted hazard ratio, 2.01 [95% CI, 1.27–3.16]) and subsequent mortality (adjusted hazard ratio, 1.73 [95% CI, 1.00–2.98]) than the patients without stroke. Among the 49 stroke patients, older age and higher score of Glasgow Coma Scale or Sequential Organ Failure Assessment were independent risk factors associated with in-hospital mortality. Conclusions: Preexisting stroke patients infected with severe acute respiratory syndrome coronavirus 2 were readily predisposed to death, providing an important message to individuals and health care workers that preventive measures must be implemented to protect and reduce transmission in stroke patients in this COVID-19 crisis.
Efficient Production of Uniform Plants from Cotyledon Explants of Sugarbeet (Beta vulgaris L.)

In order to improve regenerative potential in Beta vulgaris L. cultural conditions were established for efficient plant regeneration from cotyledon-derived calli. Organogenic calli were initiated at frequencies of 8–59 % with six sugarbeet lines. N6-benzyl-ammopurine (1 mg/1) associated with 2,3,5 triiodobenzoic acid (0.5 mg/1) was found to be the best combination to alter the endogenous phytohormonal balance in 21 ± 1 day-old seedlings. Flow cytometry was used to determine nuclear DNA Content (ploidy) in cotyledons, calli and regenerated plants, and suggested that 88 % of the regenerants were diploids. The relatively high cytological stability of the regenerants was attributed to the rapid cell differentiation within initiated calli. The problem of vitrification was overcome by using phloridzin and high agar concentration.
Reproducible Machine Learning Methods for Lung Cancer Detection Using Computed Tomography Images: Algorithm Development and Validation

Background Chest computed tomography (CT) is crucial for the detection of lung cancer, and many automated CT evaluation methods have been proposed. Due to the divergent software dependencies of the reported approaches, the developed methods are rarely compared or reproduced. Objective The goal of the research was to generate reproducible machine learning modules for lung cancer detection and compare the approaches and performances of the award-winning algorithms developed in the Kaggle Data Science Bowl. Methods We obtained the source codes of all award-winning solutions of the Kaggle Data Science Bowl Challenge, where participants developed automated CT evaluation methods to detect lung cancer (training set n=1397, public test set n=198, final test set n=506). The performance of the algorithms was evaluated by the log-loss function, and the Spearman correlation coefficient of the performance in the public and final test sets was computed. Results Most solutions implemented distinct image preprocessing, segmentation, and classification modules. Variants of U-Net, VGGNet, and residual net were commonly used in nodule segmentation, and transfer learning was used in most of the classification algorithms. Substantial performance variations in the public and final test sets were observed (Spearman correlation coefficient = .39 among the top 10 teams). To ensure the reproducibility of results, we generated a Docker container for each of the top solutions. Conclusions We compared the award-winning algorithms for lung cancer detection and generated reproducible Docker images for the top solutions. Although convolutional neural networks achieved decent accuracy, there is plenty of room for improvement regarding model generalizability.
Influence of Urban Form on Travel Behaviour in Four Neighbourhoods of Shanghai

Since the 1980s, much of the new urban development in China has departed significantly from the traditional pedestrian and bicycle-oriented urban form. This study examines the effects of the urban spatial transformation on travel, based on a travel survey of 1709 individuals from four selected neighbourhoods of Shanghai. Although pedestrian/ cyclist-friendly urban form may not avert the general trend of motorisation growth induced by rising income, it does help to slow down the pace of growth and reduces the need for high levels of motor vehicle ownership. In the pedestrian/cyclist-friendly neighbourhoods, residents travel shorter distances than in other neighbourhoods even though the same modes of travel are used. Pedestrian/cyclist-friendly urban form makes the non-motorised modes feasible options, which is essential to limit automobile dependence. These findings suggest that land use planning and urban design can effectively influence people's mobility demand and travel behaviour towards achieving `green transport' in urban China.
Forecasting Patent Growth by Combining Time-Series Signals Using Covariance Patterns

Bibliometrics has been employed previously with patents for technological forecasting. The primary challenge that technological forecasting faces is early-stage identification of technologies with the potential to have a significant impact on the socio-economic landscape. Bibliographic measures such as citations, are a good indicator of technological growth. With this intuition, we carry out an exploratory study using various time-series models and topic modeling over patent content to predict the growth or decline of various bibliographic measures for topics in the near future. Intu-itively, in order to effectively uncover these citation trends shortly after the patents are issued, we need to look beyond raw citation counts and take into account both the geographical and temporal information. We posit that, instead of using only citation counts for time-series prediction, judicious use of signals from topics generated from documents belonging to various geographical locations can help improve the performance. We carry out experiments on a large collection of patents and present some insightful results and observations.
Determination of Sowing Dates of Sweet Corn (Zea mays L. saccharata Sturt.) under Şanlıurfa Conditions

This study was conducted to determine optimum sowing dates for sweet corn in the Southeastern Anatolia region. The research was carried out at the Agricultural Research Station of Harran University in Şanliurfa during 2000 and 2001. Sowing dates were April 25, May 10, May 25, June 10, June 25, July 10, July 25 and August 10. Based on the sowing dates, fresh ear yield, duration of tasseling, ear diameter, kernel numbers per ear, single fresh ear weight and husk ratio parameters were statistically significant (**P < 0.01) in both years. The highest fresh ear yields were 177.51 and 172.30 kg ha-1 for the 25 July sowing date in 2000 and 2001, respectively. The lowest fresh ear yields were 18.24 and 15.53 kg ha-1 for the April 25 sowing date in 2000 and 2001, respectively. Fresh ear yield decreased with early sowing dates (from April 25 to June 25) in both years. The results indicate that optimal sowing dates for sweet corn could be from June 25 to July 25 in Şanliurfa and similar Southeastern Anatolia regions.
Effect of Graphene Family Materials on Multiple Myeloma and Non-Hodgkin’s Lymphoma Cell Lines

The interest around the graphene family of materials is constantly growing due to their potential application in biomedical fields. The effect of graphene and its derivatives on cells varies amongst studies depending on the cell and tissue type. Since the toxicity against non-adherent cell lines has barely been studied, we investigated the effect of graphene and two different graphene oxides against four multiple myeloma cell lines, namely KMS-12-BM, H929, U226, and MM.1S, as well as two non-Hodgkin lymphoma cells lines, namely KARPAS299 and DOHH-2. We performed two types of viability assays, MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide conversion) and ATP (adenosine triphosphate detection), flow cytometry analysis of apoptosis induction and cell cycle, cell morphology, and direct interaction analysis using two approaches—visualization of living cells by two different systems, and visualization of fixed and dyed cells. Our results revealed that graphene and graphene oxides exhibit low to moderate cytotoxicity against cells, despite visible interaction between the cells and graphene oxide. This creates possibilities for the application of the selected graphene materials for drug delivery systems or theragnostics in hematological malignancies; however, further detailed studies are necessary to explain the nature of interactions between the cells and the materials.
White and black spruce seedling development using the concept of relative addition rate

Ingestad's concept of relative addition rate was used to grow a range of seedling types, of both black (Picea mariana) (Mill.) B.S.P.), and white spruce (Picea glauca (Moench) Voss). Seedlings were grown for about 18 weeks in styrofoam containers under greenhouse conditions, and fertilized at exponentially increasing rates of either one, two, four or six per cent per day, following a one month pretreatment period. Pretreatment consisted of applying a nutrient solution proportionally low in nitrogen, but that had a relatively high conductivity compared to the initial solutions used in the exponentially increasing fertilizer treatments. Black spruce seedlings grew fastest, had significantly more root development or had a higher efficiency of nitrogen uptake when nutrients were applied at exponentially increasing amounts. In contrast, white spruce grew more rapidly when fertilized with a constant level of fertilizer (control treatment). Biomass allocation and nitrogen concentrations in seedlings of both spec.
Nature matrix: reconnecting people and nature

Many individuals and societies are no longer connected to the more-than-human world in such a way as to ensure a sustainable future. As such connection has diminished, environmental challenges have multiplied and influences for estrangement intensified. I review the importance of direct, intimate encounter with places and organisms on the attitudes of the young, as well as the significance of biophilia. The result of the loss of contact and subsequent alienation is the Extinction of Experience: an inexorable cycle of disconnection, apathy, and progressive depletion. I describe an effort to demonstrate this effect. Small, humble habitats, especially in urban settings, can be as important as big reserves in awakening biophilia. Biophobia, abetted by the loss of such habitats, the rise of the virtual in place of actual experience, economic inequalities, and overpopulation, further feeds the downward spiral of extinction and disaffection. The climate of global corporate growth that now prevails is inimical to sustainability, as is the current state of ecological illiteracy. Radical change is therefore necessary to address both economic disparity, in the direction of minimal ownership rather than maximum consumerism, and educational reform that places nature at the centre rather than the margin of the curriculum. I present a six-point programme, called Nature Matrix, for an alternative social and ethical paradigm. Rather than a pragmatic plan for the near future, Nature Matrix is a model for essential, incremental change, a dream whose eventual adoption may enhance chances for reconnection and for ecological survival itself: at present, a deeply uncertain prospect.