Miracle-dz/UniFAR-FTUs huggingface dataset:
Phase I/II trial of CCI-779 and bevacizumab in stage IV renal cell carcinoma: Phase I safety and activity results

5034 Background: The mammalian target of rapamicin (mTOR) and vascular endothelial growth factor (VEGF) pathways are critically involved in the pathogenesis and progression of clear cell renal cell carcinoma. Methods: The goal of the phase I portion of the trial was to determine the maximum tolerated dose (MTD) and dose limiting toxicity (DLT) of the combination of the mTOR inhibitor CCI-779 (C) and the anti-VEGF monoclonal antibody Bevacizumab (B). Patients with measurable stage IV clear cell RCC, performance status 0–2 and good organ function were eligible. Up to two prior treatment regimens were allowed. Treatment consisted of 25 mg IV weekly C and escalating IV doses of B (level 1= 5 mg/kg; level 2= 10 mg/kg) every other week. A cycle was defined as 4 weeks. Results: A total of 10 male and 2 female patients, median age 66 yrs (50–77) were enrolled to the phase I portion of the trial. PS: 0/1= 6/6; prior nephrectomy = 10; prior systemic therapy = 7 (prior cytokine therapy = 6); Number of metastatic sit.
Regulation of HIF-1α during Hypoxia by DAP5-Induced Translation of PHD2

Regulation of HIF-1α during Hypoxia by DAP5-Induced Translation of PHD2 by Jeffrey David Bryant Department of Molecular Genetics and Microbiology Duke University Date:_______________________ Approved: ___________________________ Matthias Gromeier, Supervisor ___________________________ Jack Keene ___________________________ Christopher Nicchitta ___________________________ Jen-Tsan Ashley Chi ___________________________ Christopher Counter An abstract of a thesis submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Molecular Genetics and Microbiology in the Graduate School of Duke University 2018 Copyright by Jeffrey David Bryant 2018
Pharmacological Properties of Herbal Oil Extracts Used In Iranian Traditional Medicine

Herbal oils also called oil extracts are traditional herbal remedies used to treat several conditions. Beneficial effects are achieved through the combination of nutrients, antioxidants and biostimulants obtained from herbs using gentle nondestructive oil extraction techniques. Therefore, all knowledge of healing effects of herbal oil, acquired over the centuries of trials and mistakes, are applicable only to oil extracts, until proven otherwise. In this study, the data collected by junior medical students divided into several groups from ethno-pharmacologists, herbal-drug sellers and rural native-healers, from different regions of Iran, especially Northwest, Central and Northern provinces. We report here, the herbal oil extract used in Iranian traditional herbal medicine. Thirtythree species, which are used as oil, extract found common in this study as Iranian traditional herbal medicine. According to the data collected in our study 33 percents of the herbal oils have been used for rheumatoid arthritis and joint diseases, arthralgia as anti-inflammatory. 22 percents of them used as analgesic and for sciatic or muscular pains. For hair fall 16 percent and for nourishing the hair roots one percent of the herbal oils have been used traditionally. Ten percent also used as neurotonics and for neurological conditions. Five percent of plant oils used for dermatological usages, skin moisturizing and skin care. The rest indications are 5 percent for internal diseases and 4 percents for miscellaneous and other usages, including gastrointestinal etc.
Population assessment of Western Gray Whales in 2006

(2005) which used data up to 2003, fitted to the same, individually-based population model. New median estimates of key population parameters (with 90% Bayesian confidence intervals) are 0.986 (0.975 - 0.995) for the adult survival rate; 0.72 (0.60 - 0.83) for the survival rate from calf to yearling; 3.0%
ANTIOXIDANT EFFECT OF THE STEM AND LEAVES OF SOLANUM XANTHOCARPUM

Solanum xanthocarpum L is used in the traditional medicine as diuretic. In the present study, the antioxidant activity of ethanol, chloroform and ethyl acetate extract of leaves and stem of Solanum xanthocarpum Lam was studied and the activity was compared with DPPH and BHT as standard. By employing DPPH (2,2-diphenyl-1picrylhydrazyl radical) scavenging assays, it was shown that all the ethanol extracts of leaves and stem show antioxidant activity.
Aspects of paediatric in-patient care: views of parents and school aged children

The objectives of this project were to investigate the idea of family-centred care from the parents' and children's perspectives, to find out the difference between theory and practice, and to seek parents' views on methods for improving hospital environment and its facilities for children and parents. This study was conducted in a junior school in County Durham using qualitative and quantitative research methods. The data were obtained via surveying parents and children, interviewing parents whose children had been in hospital and collecting drawings from children. The facilities for families, parents and children in hospital might have shown some improvement, however there are several aspects that still need to be achieved. Some parents asserted that their basic needs were not being met during their hospital stay with their children. The mothers argued that having a sick child in hospital has an impact on the whole family and hospitals need to give some attention to their concerns. Although many professionals presume that they are working with a family-centred care approach, it is not clear to what extent this concept has been put into practice. The mothers reported the need for adequate communication and negotiation with health professionals to facilitate mutual collaboration and to avoid the anxiety that the participation in care might cause to parents and children. It has been proposed by some parents that home care could replace hospital-based care. The concern was that support for home care might be inadequate. Mothers in this study also proposed that the practice of home care could be facilitated by having direct communication with named nurses and doctors, using dedicated phone lines. Community nurses have also a part to play in home care. It would be important to consider innovations more proactive to health promotion such as parenting advice about healthy and unhealthy behaviour.
Health Literacy Skills in Relatives Ã¢Â€Â™ Speech: A Canadian Case-Study

Objective: Exploring how health literacy skills are expressed by relatives of two first stroke survivors and the influence of such skills on their participation in the rehabilitation process. Methods: This case study consists of a secondary analysis of qualitative material focusing on perceived health services received by relatives post-stroke. Two cases were purposively selected for their contrast in educational attainment. Results: Four core concepts, in accordance with current HL conceptualization, emerged from the analysis. Themes related to understanding and communicating health-related information was prominent. More specifically, comprehension and linguistic skills, and particularly the use of medical terminology, as well as self-confidence appear to be conducive to a better dialogue with health professionals and lead to more satisfactory answers. Conclusion: The relatives’ speech provided indications about health literacy skills and confirmed their importance in developing self-determination. Fostering an open dialogue with relatives represents an opportunity to consider their skills when establishing a partnership and thus contributes to the development of greater health literacy and participation.
A review of reported seaweed diseases and pests in aquaculture in Asia

Department of Life Sciences, Natural History Museum, London, UK Aquaculture Department, Southeast Asian Fisheries Development Center, Iloilo, Philippines Scottish Association for Marine Science, Scottish Marine Institute, Oban, UK University of the Philippines Visayas, College of Fisheries and Ocean Sciences Institute of Aquaculture, Iloilo, Philippines Marine Biotechnology Unit, Institute of Ocean and Earth Sciences (IOES), University of Malaya, Kuala Lumpur, Malaysia Botany Department, University of Dar es Salaam, Dar es Salaam, Tanzania Cefas, Dorset, UK
Genetic diversity of Cedrela fissilis (Meliaceae) in the Brazilian Atlantic Forest reveals a complex phylogeographic history driven by Quaternary climatic fluctuations

Quaternary climatic fluctuations have shaped the geographic distribution of lineages, potentially affecting the demography, genetic structure, and patterns of genetic diversity of extant species. Different phylogeographic scenarios have been proposed for plants in neotropical cloud forests during the Last Glacial Maximum based on paleoecological data: the dry refugia hypothesis (DRH) and the moist forest hypothesis. We specifically focus on the Brazilian Atlantic Forest (BAF) range of Cedrela fissilis (Meliaceae), sampling 410 specimens from 50 localities. Our study combines analyses of the genetic diversity, phylogeographic patterns, and past geographic distributions with a particular focus on highland populations. We identified 283 alleles across the 11 microsatellite loci, ranging from 18 to 33 alleles per locus, distributed across five genetic groups. Most populations of C. fissilis from the BAF exhibited a diffuse genetic structure, reflected in low pairwise FST values, which could be the consequence of high gene flow. In addition, the plastid data showed a connection between the western, southern, and eastern populations in the North‐East of Brazil, but no association between genetic data and elevation was observed. Habitat suitability projections over the past 140 000 years showed less fragmentation relative to the present, indicating a higher connectivity and gene flow. Our results provide support for both the moist forest as well as the DRH, suggesting that most likely, a mixture of these processes has acted through space and time.
Use of testicular tone and echogenicity in identifying boars with low sperm quality

ABSTRACT This study aimed to evaluate the use of some testicular traits to identify boars with low sperm morphological quality. The consistency (scores from 1 to 5), tone with tonometry (mm), parenchyma echogenicity and heterogeneity with ultrasound (pixel) were assessed in 402 mature boars (18.5 months on average). Sperm abnormality thresholds (≤ 25% of total sperm abnormalities, ≤ 5% of heads, acrosome, neck or midpiece defects, ≤ 10% tail defects, and 15% cytoplasmic droplets) were used to classify boars as approved or disapproved. Three classes of testicular traits were formed (extremely low and high values, approximately 15% each, were kept in separated classes). When the traits were individually evaluated, fewer boars were approved if the echogenicity or heterogeneity were high, or if the tone was rigid. When evaluated in combination, the interaction between heterogeneity and tone, and between heterogeneity and echogenicity were significant. The high heterogeneity combined with soft tone or with hypo-echogenicity resulted in lower approval of boars. Tonometry and ultrasonography have a moderate potential to be included in breeding soundness examination of boars. When combined, they provide more reliable information about the impact of testicular parenchymal alterations on morphology of sperm cells.
Hormonal Basis for Low Light Intensity-induced Flower Bud Abscission of Pepper

A series of field and greenhouse experiments was conducted with three cultivars of bell pepper (Capsicum annuum L.) to determine the hormonal basis for flower bud and flower abscission as induced by low light intensity (LLI). Imposition of 80% shade for 6 days increased abscission of reproductive structures by 38% and resulted in an increase in bud ethylene production. Concomitantly, bud reducing sugars and sucrose decreased and these were negatively correlated with ethylene levels and those of its precursor, ACC. Infusion of ACC into the pedicel resulted in flower bud abscission within 48 hr. The results indicate that ethylene is the primary causal agent of pepper flower bud abscission. Production of auxin by the bud plays a role in prevention of abscission. The abscission of disbudded pedicels was prevented by infusion of NAA. Although the three cultivars had similar responses to ACC, they differed in the amount of abscission under stress, bud sugar levels, and the time of onset of ACC and ethylene production. Chemical names used: 1-aminocyclopropane-1-carboxylic acid (ACC); α-napthaleneacetic acid (NAA); (2-chloro-ethyl)phosphonic acid (ethephon).
Development of blue stain in mechanically harvested Scots pine (Pinus sylvestris) logs during storage

Blue stain is a type of discoloration that considerably lowers the aesthetic qualities of wood. During harvesting, fungal inoculum finds its way into the wood through places of cutting, delimbing, and damage to the tree stem. The development of peripheral blue stain in the logs of Scots pine (Pinus sylvestris L.) due to damage by a harvester head was investigated, using logs felled and delimbed with a chainsaw as reference. The development of blue stain was related to the age class of the stand, the date of felling, and the microclimatic conditions of the wood storage place. The mean surface area of blue stain in logs produced with the harvester was almost 35 cm2, approximately 30% larger than that of the reference logs. In stands of the fourth age class (diameter at breast height 32 cm), the surface of blue stain was more than two times larger than that of stands of the third age class (diameter at breast height 24 cm). The mean area of blue stain in wood stored after spring felling (19.3 cm2) was about 50% of that after summer felling (38.2 cm2). In particular, the development of blue stain in logs obtained with a harvester was visible between weeks 6 and 9 after spring felling and between weeks 3 and 6 after summer felling. For both felling dates, the range of blue stain depended less on air temperature around the wood stack and depended more on the duration of storage.
How do we segment text? Two-stage chunking operation in reading

Chunking in language comprehension is a process that segments continuous linguistic input into smaller chunks that are in reader’s mental lexicon. Effective chunking during reading facilitates disambiguation and enhances efficiency for comprehension. However, the mechanisms of chunking remain elusive, especially in reading given that information arrives simultaneously yet the written systems may not have explicit cues for labeling boundaries such as Chinese. What are the mechanisms of chunking operation that mediates the reading of the text that normally contains hierarchical information? We investigated this question by manipulating the lexical status of the chunks at distinct levels of grain-size in four-character Chinese strings, including the two-character local chunk and four-character global chunk. Participants were asked to make lexical decision on these strings in a behavioral experiment, followed by a passive reading task when their electroencephalography (EEG) were recorded. The behavioral results showed that the lexical decision time of lexicalized two-character local chunks was influenced by the lexical status of four-character global chunk, but not vice versa, which indicated that the processing of global chunks possessed priority over the local chunks. The EEG results revealed that familiar lexical chunks were detected simultaneously at both levels and further processed in a different temporal order -- the onset of lexical access for the global chunks was earlier than that of local chunks. These consistent behavioral and EEG results suggest that chunking in reading occurs at multiple levels via a two-stage operation -- simultaneous detection and global-first recognition. Significance Statement The learners of a new language often read word by word. But why can proficient readers read multiple words at a time? The current study investigates how we efficiently segment a complicate text into smaller pieces and how we process these pieces. Participants read Chinese strings with different structures while their key-press responses and brain EEG signals were recorded. We found that texts were quickly (about 100 ms from their occurrences) segmented to varied sizes of pieces, and larger pieces were then processed earlier than small pieces. Our results suggest that readers can use existing knowledge to efficiently segment and process written information.
Engineered fibre enables targeted activation of butyrate-

22 Beneficial modulation of the gut microbiome has high-impact implications not only in humans, 23 but also in livestock that sustain our current societal needs. In this context, we have engineered an 24 acetylated galactoglucomannan (AcGGM) fibre from spruce trees to match unique enzymatic 25 capabilities of Roseburia and Faecalibacterium species, both renowned butyrate-producing gut 26 commensals. The accuracy of AcGGM was tested in an applied pig feeding trial, which resolved 355 27 metagenome-assembled genomes together with quantitative metaproteomes. In AcGGM-fed pigs, 28 both target populations differentially expressed AcGGM-specific polysaccharide utilization loci, 29 including novel, mannan-specific esterases that are critical to its deconstruction. We additionally 30 observed a “butterfly effect”, whereby numerous metabolic changes and interdependent cross31 feeding pathways were detected in neighboring non-mannolytic populations that produce short-chain 32 fatty acids. Our findings show that intricate structural features and acetylation patterns of dietary fibre 33 can be customized to specific bacterial populations, with the possibility to create greater modulatory 34 effects at large. 35
The complete chloroplast genome of Dipterocarpus turbinatus Gaertn. F

Abstract Dipterocarpus turbinatus Gaertn. F. , naturally distributes in Southern China, which is an elite natural tree with high economic and medicinal value. In study, all chloroplast (cp) genome of Dipterocarpus turbinatus Gaertn. F. was assembled and characterized based on Illumina pair-end sequencing data. The complete chloroplast genome length was 152,279 bp. It contained a large (LSC, 83,862 bp) and a small (SSC, 20,215 bp) single copy region, separated by a pair of inverted repeats of 24,101 bp (IRs). The overall GC content of genome was 37.3%, the corresponding values of LSC, SSC, and IR regions were 35.3, 31.6, and 43.2%, respectively. There were 128 genes in the genome including 84 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Among all genes, 14 genes contain a single intron and 1 gene has two introns. The result showed that Dipterocarpus turbinatus Gaertn. F. was closely related to Vatica mangachapoi.
Comparative genomics, phylogenomics and population genomics of New World Leishmania

Visceral leishmaniasis is a major health problem in Brazil, being highly endemic in the State of Minas Gerais, in particular affecting people with limited resources and little access to adequate health care. The region of Governador Valadares is a reemerging focus of intense transmission of VL and TL with more than 127 cases reported since 2007 to 2013 and 30% of positive domestic dogs. In this subsection we will present the results of a study aimed at understanding the parasite population structure in the city using comparative genomic analysis of 36 samples from domestic dogs collected from 2008 to 2015. Analyses of this data were focused on the use of phylogenetic and population genetics methods to understand the evolution and the recent demographic history of parasites in this focus. Our results reveal the presence of two distinct sub-populations associated with two isolation periods and suggest a potential effect of climate on changes in the parasite population in this focus.
Egestion of plant propagules by turtles in a small Massachusetts river

ABSTRACT Evidence from flowing-water habitats has confirmed a role of turtles regarding the effective internal transport and viability of riparian plant seeds. We assessed potential propagule dispersal by Eastern painted turtles (Chrysemys picta) within a small river in Massachusetts and factors that may influence the diversity and abundance of egested propagules. From August–October 2015 and June–October 2016, we captured 69 turtles (28 male and 13 female), recorded standard measurements (sex, size, mass, BCI), and collected their faeces from which we isolated propagules. Propagules, mostly seeds, were observed in a small (28%) group of individuals. Overall, 4808 seeds of four taxa and 62 tubers were recovered. Most turtles (58%) defaecated propagules of just one taxon and number of seeds per turtle was highly variable (1–1506, 253.05 ± 414.55 seeds). Taxon richness, abundance, and Simpson Index of propagules varied significantly by sampling year. Sex-year interaction was also a significant predictor of propagule abundance. No turtle-specific features (sex or BCI) have any significant influence on any of the seeds egested. While our study suggests a minor role for C. picta as mobilisers of river plant propagules, these highly vagile animals may still create intermittent links between spatially isolated populations within and between waterbodies.
Winter river plumes shape community composition and activity of heterotrophic microorganisms on the Oregon Coast

Rivers and estuaries along the central Oregon margin transport large amounts of fluvialand terrestrial-derived materials into the coastal ocean during the winter season, which can become trapped in a nearshore coastal current by local density gradients and wind forcing. The influence of these substantial and persistent allochthonous inputs on wintertime biological activity in the Oregon coastal region is not well understood. We compared prokaryotic communities inside and outside of 2 buoyant coastal river plumes off the central Oregon coast in order to understand the relationship between plume conditions and the distributions of prokaryotic populations that form the base of the wintertime coastal food web by transforming carbon and nitrogen compounds. Both free-living and particle-associated communities inside nearshore plume zones were significantly different from communities outside the plume influence. Particulate organic matter concentrations correlated with the distribution of several Bacteroidetes populations with established roles in complex organic matter degradation in coastal ecosystems. Plume conditions also correlated with marine Gammaproteobacteria that are known to degrade terrestrially derived material. Peak heterotrophic respiration rates across sampling stations occurred at a local plume particle maximum, suggesting that particulate resources transported to coastal ocean waters by river plumes may be used or transformed by co-localized heterotrophic microorganisms. Taken together, the associations between river plume resources and prokaryotic populations implicated in organic matter turnover suggest that microbes in Oregon coastal ecosystems use allochthonous resources that are transported into the coastal ocean during winter, and that these resources help shape the coastal food web during the winter season.
Angiographic 3-D Blood Flow Measurement - Concept and Preliminary Experiments

Purpose In this article a new approach for determination of blood flow out of angiographic movies is proposed. The system is supposed to assist the radiologist/cardiologist during interventional therapy. It features intraoperative image acquisition, 2-dimensional flow determination, and 3-dimensional reconstruction. Potential application areas are angiography for radiology (peripheral vessels), cardiology (coronary imaging) und neurology (neurovascular imaging). Angiography is the gold standard to visualize vascular structures by contrast enhancement of the vessel. Additional flow measurements promise benefits to evaluate stenosis severity, end organ perfusion and the interventional strategy. Method