Miracle-dz/UniFAR-FTUs huggingface dataset:
Downstream effects of beaver ponds on the water quality of New England first‐ and second‐order streams

Beaver, as allogenic ecosystem engineers, are capable of extensively altering surrounding habitats resulting in significant effects on stream water quality. This paper presents insight into downstream effects of beaver impoundments (both actively maintained and abandoned by beaver) and accumulated sediments on water quality, especially in protected watersheds serving as a drinking water supply. In a tributary un‐inhabited by beaver compared to those with active beaver ponds, we found significantly (p < 0·001) lower concentrations of NO3N (respectively: mean (standard error)) without beaver 0·11 (0·005) mg/l and with beaver 0·14 (0·002) mg/l), NH4N (0·007 (0·002) and 0·24 (0·002) mg/l), dissolved organic carbon (DOC) (3·47 (0·081) and 8·37 (0·203) mg/l), chlorophyll (2·38 (0·066) and 6·96 (0·203) µg/l), and temperature (16·43 (0·101) and 19·85 (0·123) °C), but higher pH (7·17 (0·02) and 6·72 (0·022)), PO4 (0·20 (0·01) and 0·17 (0·014) mg/l) concentration, and dissolved oxygen (DO) saturation (100·8 (0·708) and 67·6 (1·74)%). Within the beaver ponds, we observed a high abundance of predatory zooplankton, which help to control algae and feed on detritus within the pond ecosystem. We intentionally breached an abandoned beaver dam in the field and conducted a sediment resuspension experiment in the laboratory to assess the potential for increases in turbidity and nutrients from beaver pond sediments as would be expected in the event of a catastrophic dam breach. We found that abandoned beaver ponds have a stronger influence on downstream water quality than actively maintained ponds owing to higher turbidity with finer sediments and sharply increased stream water temperature during a dam failure. Copyright © 2010 John Wiley & Sons, Ltd.
Global Megathrust Earthquake Hazard—Maximum Magnitude Assessment Using Multi-Variate Machine Learning

Megathrust subduction faults have caused the largest earthquakes ever recorded in human history. In addition, they are often associated with devastating tsunamis. Thus, assessing their potential maximum magnitude and respective return periods is vital for seismic-tsunami hazard assessment. However, empirical data is limited, owing to their very-long recurrence period that can be several centuries or millennia. To bridge this gap of empirical data with seismotectonic observations, a combined assessment of maximum magnitudes and return periods was undertaken applying a variety of machine learning and conventional methods. For this purpose, 76 subduction zone segments have been assessed worldwide. This includes a 3D modelling of subduction slab geometries on the basis of earthquake hypocentres and a collection of various relevant parameters e.g. those of local geology, geodesy or seismicity. These parameters have been used to assess the potential maximum magnitudes using machine learning classification and other statistical methods. The results have been combined with a tapered Gutenberg-Richter seismicity model and plate tectonic modelling to quantify earthquake return periods and their uncertainties. They show that almost all major subduction zones have the potential to produce earthquakes $M_w\ge8.5$ and that the maximum magnitude highly correlates with the subduction zone geometry. The results also highlight the potential of large megathrust earthquakes in regions where no large or significant events have been recorded during human written history. It is hoped that the results of this study support the development of tail-end hazard and risk studies for long return period events and the quantification of tsunami hazard and risk.
Intradermal ras peptide vaccination with granulocyte‐macrophage colony‐stimulating factor as adjuvant: Clinical and immunological responses in patients with pancreatic adenocarcinoma

K‐RAS mutations are frequently found in adenocarcinomas of the pancreas, and induction of immunity against mutant ras can therefore be of possible clinical benefit in patients with pancreatic cancer. We present data from a clinical phase I/II trial involving patients with adenocarcinoma of the pancreas vaccinated by i.d. injection of synthetic mutant ras peptides in combination with granulocyte‐macrophage colony‐stimulating factor. Forty‐eight patients (10 surgically resected and 38 with advanced disease) were treated on an outpatient basis. Peptide‐specific immunity was induced in 25 of 43 (58%) evaluable patients, indicating that the protocol used is very potent and capable of eliciting immune responses even in patients with end‐stage disease. Patients followed‐up for longer periods showed evidence of induction of long‐lived immunological memory against the ras mutations. CD4+ T cells reactive with an Arg12 mutation also present in the tumor could be isolated from a tumor biopsy, demonstrating that activated, ras‐specific T cells were able to selectively accumulate in the tumor. Vaccination was well tolerated in all patients. Patients with advanced cancer demonstrating an immune response to the peptide vaccine showed prolonged survival from the start of treatment compared to non‐responders (median survival 148 days vs. 61 days, respectively; p = 0.0002). Although a limited number of patients were included in our study, the association between prolonged survival and an immune response against the vaccine suggests that a clinical benefit of ras peptide vaccination may be obtained for this group of patients. © 2001 Wiley‐Liss, Inc.
Uncemented or cemented revision stems? Analysis of 2,296 first-time hip revision arthroplasties performed due to aseptic loosening, reported to the Swedish Hip Arthroplasty Register

Background and purpose — Uncemented stems are increasingly used in revision hip arthroplasty, but only a few studies have analyzed the outcomes of uncemented and cemented revision stems in large cohorts of patients. We compared the results of uncemented and cemented revision stems. Patients and methods — 1,668 uncemented and 1,328 cemented revision stems used in first-time revisions due to aseptic loosening between 1999 and 2016 were identified in the Swedish Hip Arthroplasty Register. Kaplan–Meier analysis was used to investigate unadjusted implant survival with re-revision for any reason as the primary outcome. Hazard ratios (HR) for the risk of re-revision were calculated using a Cox regression model adjusted for sex, age, head size, concomitant cup revision, surgical approach at primary and at index revision surgery, and indication for primary total hip arthroplasty. Results — Unadjusted 10-year survival was 85% (95% CI 83–87) for uncemented and 88% (CI 86–90) for cemented revision stems. The adjusted HR for re-revision of uncemented revision stems during the first year after surgery was 1.3 (CI 1.0–1.6), from the second year the HR was 1.1 (CI 0.8–1.4). Uncemented stems were most often re-revised early due to infection and dislocation, whereas cemented stems were mostly re-revised later due to aseptic loosening. Interpretation — Both uncemented and cemented revision stems had satisfactory long-term survival but they differed in their modes of failure. Our conclusions are limited by the fact that femoral bone defect size could not be investigated within the setting of the current study.
Thyroid Hormone Action on Innate Immunity

The interplay between thyroid hormone action and the immune system has been established in physiological and pathological settings. However, their connection is complex and still not completely understood. The thyroid hormones (THs), 3,3′,5,5′ tetraiodo-L-thyroxine (T4) and 3,3′,5-triiodo-L-thyronine (T3) play essential roles in both the innate and adaptive immune responses. Despite much research having been carried out on this topic, the available data are sometimes difficult to interpret or even contradictory. Innate immune cells act as the first line of defense, mainly involving granulocytes and natural killer cells. In turn, antigen presenting cells, macrophages and dendritic cells capture, process and present antigens (self and foreign) to naïve T lymphocytes in secondary lymphoid tissues for the development of adaptive immunity. Here, we review the cellular and molecular mechanisms involved in T4 and T3 effects on innate immune cells. An overview of the state-of-the-art of TH transport across the target cell membrane, TH metabolism inside these cells, and the genomic and non-genomic mechanisms involved in the action of THs in the different innate immune cell subsets is included. The present knowledge of TH effects as well as the thyroid status on innate immunity helps to understand the complex adaptive responses achieved with profound implications in immunopathology, which include inflammation, cancer and autoimmunity, at the crossroads of the immune and endocrine systems.
Neoadjuvant Trastuzumab Emtansine and Pertuzumab in Human Epidermal Growth Factor Receptor 2–Positive Breast Cancer: Three-Year Outcomes From the Phase III KRISTINE Study

PURPOSE The KRISTINE study compared neoadjuvant trastuzumab emtansine plus pertuzumab (T-DM1+P) with docetaxel, carboplatin, trastuzumab plus P (TCH+P) for the treatment human epidermal growth factor receptor 2–positive stage II to III breast cancer. T-DM1+P led to a lower pathologic complete response rate (44.4% v 55.7%; P = .016), but fewer grade 3 or greater and serious adverse events (AEs). Here, we present 3-year outcomes from KRISTINE. METHODS Patients were randomly assigned to neoadjuvant T-DM1+P or TCH+P every 3 weeks for six cycles. Patients who received T-DM1+P continued adjuvant T-DM1+P, and patients who received TCH+P received adjuvant trastuzumab plus pertuzumab. Secondary end points included event-free survival (EFS), overall survival, patient-reported outcomes (measured from random assignment), and invasive disease-free survival (IDFS; measured from surgery). RESULTS Of patients, 444 were randomly assigned (T-DM1+P, n = 223; TCH+P, n = 221). Median follow-up was 37 months. Risk of an EFS event was higher with TDM-1+P (hazard ratio [HR], 2.61 [95% CI, 1.36 to 4.98]) with more locoregional progression events before surgery (15 [6.7%] v 0). Risk of an IDFS event after surgery was similar between arms (HR, 1.11 [95% CI, 0.52 to 2.40]). Pathologic complete response was associated with a reduced risk of an IDFS event (HR, 0.24 [95% CI, 0.09 to 0.60]) regardless of treatment arm. Overall, grade 3 or greater AEs (31.8% v 67.7%) were less common with T-DM1+P. During adjuvant treatment, grade 3 or greater AEs (24.5% v 9.9%) and AEs leading to treatment discontinuation (18.4% v 3.8%) were more common with T-DM1+P. Patient-reported outcomes favored T-DM1+P during neoadjuvant treatment and were similar to trastuzumab plus pertuzumab during adjuvant treatment. CONCLUSION Compared with TCH+P, T-DM1+P resulted in a higher risk of an EFS event owing to locoregional progression events before surgery, a similar risk of an IDFS event, fewer grade 3 or greater AEs during neoadjuvant treatment, and more AEs leading to treatment discontinuation during adjuvant treatment.
Methods for Evaluating the Association Between Alcohol Outlet Density and Violent Crime.

BACKGROUND The objective of this analysis was to compare measurement methods-counts, proximity, mean distance, and spatial access-of calculating alcohol outlet density and violent crime using data from Baltimore, Maryland. METHODS Violent crime data (n = 11,815) were obtained from the Baltimore City Police Department and included homicides, aggravated assaults, rapes, and robberies in 2016. We calculated alcohol outlet density and violent crime at the census block (CB) level (n = 13,016). We then weighted these CB-level measures to the census tract level (n = 197) and conducted a series of regressions. Negative binomial regression was used for count outcomes and linear regression for proximity and spatial access outcomes. Choropleth maps, partial R2 , Akaike's Information Criterion, and root mean squared error guided determination of which models yielded lower error and better fit. RESULTS The inference depended on the measurement methods used. Eight models that used a count of alcohol outlets and/or violent crimes failed to detect an association between outlets and crime, and 3 other count-based models detected an association in the opposite direction. Proximity, mean distance, and spatial access methods consistently detected an association between outlets and crime and produced comparable model fits. CONCLUSIONS Proximity, mean distance, and spatial access methods yielded the best model fits and had the lowest levels of error in this urban setting. Spatial access methods may offer conceptual strengths over proximity and mean distance. Conflicting findings in the field may be in part due to error in the way that researchers measure alcohol outlet density.
Confounding effect of cyclosporine dosing when comparing horse and rabbit antithymocyte globulin in patients with severe aplastic anemia

We read the interesting paper recently published by Feng et al. [1][1] They found that double negative (CD3+CD4−CD8−) regulatory T cells (Tregs) where more frequent in the peripheral blood of rATG than hATG patients, despite no significant effect on the absolute number of these cells between the
The Karyology of Uraeotyphlus gansi, and Its Implications for the Systematics and Evolution of Uraeotyphlidae (Amphibia: Gymnophiona)

The gross karyotype of the uraeotyphlid caecilian Uraeotyphlus gansi is described as comprising 2n = 42 and fundamental number = 58. These are the first karyotype data for any species of malabaricus-group Uraeotyphlus, and the diploid number is the same as those ichthyophiids thus far studied and differs from the oxyurus-group Uraeotyphlus (2n = 36). These data support the recognition of two species groups within Uraeotyphlus, the monophyly of the oxyurus group, and the understanding that the ancestral diatriatan was more ichthyophiid- than uraeotyphlid-like.
Endocannabinoid signaling regulates spontaneous transmitter release from embryonic retinal amacrine cells

GABAergic amacrine cells, cultured from embryonic chick retina, display spontaneous mini frequencies ranging from 0–4.6 Hz as a result of the release of quanta of transmitter from both synapses and autapses. We show here that at least part of this variation originates from differences in the degree to which endocannabinoids, endogenously generated within the culture, are present at terminals presynaptic to individual cells. Though all cells examined scored positive for cannabinoid receptor type I (CB1R), only those showing a low initial rate of spontaneous minis responded to CB1R agonists with an increase in mini frequency, caused by a Gi/o-mediated reduction in [cAMP]. Cells displaying a high initial rate of spontaneous minis, on the other hand, were unaffected by CB1R agonists, but they did show a rate decrease with CB1R antagonists. Such a regulation of spontaneous transmitter release by endocannabinoids might be important in network maintenance in amacrine cells and other inhibitory interneurons.
Nanostructured polymer microcomposites: A distinct class of insulating materials

Experimental evidence was produced and gathered to demonstrate the distinct nature of nanostructured polymer microcomposites. The case of a polymer composite consisting of a high-content of micrometric quartz with a small adjunct of nanoclay is discussed. Emphasis is put on dielectric behavior studies while some results on thermal characteristics are presented. Overall results strongly support the potential of this class of insulating material for electrotechnical applications.
Aerobic Training and Green Tea Extract Protect against NMU-induced Prostate Cancer.

INTRODUCTION Aerobic training and green tea extract can be used to reduce the risk of prostate cancer. The goal of this study was to evaluate the effects of eight-week aerobic exercise training and administration of green tea extract on the level of nuclear factor kappa B (NF-kB), cyclooxygenase-2 (COX-2) and p53 tumor suppressor protein (p53) in prostate of rats which were stimulated by N-Methyl-N-nitrosourea (NMU) to induce the prostate cancer. METHODS 60 adult male Wistar rats were assigned into six groups including healthy control (HCt), cancer control (CCt), cancer training (CTr: 45 min/day at low-moderate intensity, 5 times/week, 8 weeks), cancer extract (CEx: 1.34 ml of green tea extract, 3 times/week, 8 weeks), cancer training+ cancer extract (CTr+CEx) and sham groups. Rats were sacrificed 48 hours after the last intervention session, and the prostate tissue was isolated to measure the levels of NF-kB, COX-2, and p53. RESULTS The NF- kB level in CCt group was increased significantly compared to the HCt (P=0.02). In the CTr group, NF-kB level was decreased significantly compared to the CCt and CEx groups (P=0.001 and 0.05, respectively). In addition, the levels of P53 protein were reduced in CTr, CEx and CTr+CEx groups compared to CCt group (P=0.001, 0.02 and 0.004, respectively). No significant changes were found in the level of COX-2 between groups. CONCLUSIONS These results suggest that a long-term exercise training combined with the intake of green tea extract may reduce levels of NF-kB and p53 in rats with prostate cancer. Given the importance of recognizing complementary therapies in this regard, future studies are warranted.
Dryas as a Model for Studying the Root Symbioses of the Rosaceae

The nitrogen-fixing root nodule symbiosis is restricted to four plant orders: Fabales (legumes), Fagales, Cucurbitales and Rosales (Elaeagnaceae, Rhamnaceae, and Rosaceae). Interestingly all of the Rosaceae genera confirmed to contain nodulating species (i.e., Cercocarpus, Chamaebatia, Dryas, and Purshia) belong to a single subfamily, the Dryadoideae. The Dryas genus is particularly interesting from an evolutionary perspective because it contains closely related nodulating (Dryas drummondii) and non-nodulating species (Dryas octopetala). The close phylogenetic relationship between these two species makes Dryas an ideal model genus to study the genetic basis of nodulation by whole genome comparison and classical genetics. Therefore, we established methods for plant cultivation, transformation and DNA extraction for these species. We optimized seed surface sterilization and germination methods and tested growth protocols ranging from pots and Petri dishes to a hydroponic system. Transgenic hairy roots were obtained by adapting Agrobacterium rhizogenes-based transformation protocols for Dryas species. We compared several DNA extraction protocols for their suitability for subsequent molecular biological analysis. Using CTAB extraction, reproducible PCRs could be performed, but CsCl gradient purification was essential to obtain DNA in sufficient purity for high quality de novo genome sequencing of both Dryas species. Altogether, we established a basic toolkit for the culture, transient transformation and genetic analysis of Dryas sp.
Sunlight radiation as a villain and hero: 60 years of illuminating research

Abstract In the 60 years since the inaugural edition of the International Journal of Radiation Biology, much of our understanding of the biological effects of solar radiation has changed. Earlier in the century, sunlight played a ‘hero’s’ role in reducing disabling rickets, while today debate still continues on the amount of sun required before exposure reveals the ‘villainous’ side of solar radiation. Although knowledge of the ultra violet (UV) component of sunlight as a carcinogen has become widespread, skin cancer rates are still rising yearly. Twentieth century attitudes have seen an about-face in the field of dermatological sun protection, with sunscreens changing from recipes designed to promote a ‘healthy tan’ to formulations proven to block both ultraviolet B (UVB) and more recently, ultraviolet A (UVA), to minimize premature sun-aging and skin cancer risk. In the early 1960s, DNA was first found to exist within mitochondria, while recently the connections between mitochondrial changes and UV radiation exposure have been expanded. Sixty years ago, understanding of the endocrine systems of mammals was enjoying its infancy. Early discoveries that light, particularly natural light, could have profound effects on functions such as sleep patterns and hormonal balance were made, while today more advanced knowledge has led to lighting improvements having pronounced effects on human wellbeing. Photosensitization 60 years ago was a health concern for both humans and their domestic animals, while today chemically engineered photosensitizing drugs can be administered along with highly directed light to pinpoint delivery targets for drug action. Life on earth is inextricably bound up with solar radiation. This article attempts to outline many of the ways in which our opinions about solar radiation have changed since the journal’s inception.
Testing landmark redundancy for sex-based shape analysis of the adult human os coxa.

OBJECTIVES To test the individual effectiveness of common landmarks used in sex estimation of whole adult coxal bones in sex-based shape analysis and propose a method to determine how many principal components of sex-based shape to include for discriminant function analysis. METHODS Three-dimensional models (NextEngine desktop laser scanner) of left and right os coxae from 396 individuals (William Bass Skeletal Collection, Forensic Anthropology Centre, University of Tennessee, Knoxville, TN) were subjected to shape analysis using 32 landmarks (Landmark 3.6, Institute for Data Analysis and Visualization). Each landmark was individually removed and subjected to a new principal component analysis to identify the effect omitting a landmark has on PC1/PC2 ordination. Landmarks that poorly discriminated sex-based shape were considered redundant for analysis on sex estimation. RESULTS This study identified 17 landmarks that represent sex-based shape of right and left coxal bones most effectively, these are: the anterior superior iliac spine; posterior superior iliac spine; posterior inferior iliac spine; iliac crest; apex of the auricular surface; greater sciatic notch; ischial spine; superior, inferior and distal points on ischial tuberosity; superior, inferior and midpoint on the symphyseal face; arcuate eminence; ischiopubic ramus; posterosuperior and anterosuperior points on the acetabular rim. The first and second PCs of the 17-landmark configuration correctly predicted sex in 98.5% of cases; better than a 32-landmark configuration (96%) and better than previous landmark studies on whole coxal bone sex-based shape. CONCLUSIONS These 17 landmarks represent more meaningful data for sex-based shape analysis in PC1 and 2 and concentrate meaningful sex-based shape data to the first five PCs that make up over 50% of the total shape variance.