Miracle-dz/UniFAR-FTUs huggingface dataset:
Template Usage Is Responsible for the Preferential Acquisition of the K65R Reverse Transcriptase Mutation in Subtype C Variants of Human Immunodeficiency Virus Type 1

ABSTRACT We propose that a nucleotide template-based mechanism facilitates the acquisition of the K65R mutation in subtype C human immunodeficiency virus type 1 (HIV-1). Different patterns of DNA synthesis were observed using DNA templates from viruses of subtype B or C origin. When subtype C reverse transcriptase (RT) was employed to synthesize DNA from subtype C DNA templates, preferential pausing was seen at the nucleotide position responsible for the AAG-to-AGG K65R mutation. This did not occur when the subtype B RT and template were used. Template factors can therefore increase the probability of K65R development in subtype C HIV-1.
Surgery for elderly lung cancer.

OBJECTIVE There are still controversies about the surgical benefits for elderly lung cancer.The aims of this study were to assess impacts of aging for non-small cell lung cancer(NSCLC) following pulmonary resection. METHODS A retrospective study was undertaken for patients operated at a curative intent from January 1998 to October 2008. Patients were divided into two groups: Group 1 consisted of patients aged at least 75 years old, and group 2 were patients less than 75 years old. Perioperative characteristics and details, hospital courses, surgery-related morbidities, surgical mortality, and survival were compared between groups. RESULTS Of 442 eligible patients, 73 patients (16.5%) were in group 1 (mean age 78.3 years) and 369 (83.5%) patients were in group 2 (mean age 62.5 years). The following data were compared with statistical significance: hospital stay (17.8 vs. 8.9 days), mortality rate (8.2 vs. 2.2%), morbidity rate (26.0 vs. 13.3%), and length in intensive care unit (5.7 vs. 3.2 days). The main causes for morbidities in group 1 showed cardiopulmonary-related. Tumor stage without considering age had statistically significant influence on survival. Survivals of two groups were comparative. (p= 0.10) Intriguingly, the disease-related survival (28.3 months; p= 0.008) and progression-free survival (25.0 months; p<0.001) in group 1 were significantly better than group 2 (20.2 and 12.2 months). CONCLUSIONS Although operation for NSCLC in the elderly patients causes more complications, especially in the cardiopulmonary system, their outcome showed better than their younger counterparts. Pulmonary resection for elderly patients may get longer disease control. Elderly patients with physical fit for surgery should not be considered as a contraindication to pulmonary resection based on age alone.
Anemia may influence the outcome of patients undergoing neo-adjuvant treatment of rectal cancer.

BACKGROUND We hypothesized that anemia could represent one of the major factors influencing the outcome of patients undergoing neo-adjuvant treatment of rectal cancer. PATIENTS AND METHODS This analysis included all the consecutive patients who underwent neo-adjuvant treatment (chemotherapy and/or radiotherapy) before surgery for rectal cancer in three oncology/radiotherapy departments from June 1996 to December 2003. RESULTS Three hundred and seventeen patients were eligible for our analysis. Median age at diagnosis was 64 years (range 26-88 years); male/female ratio was 184/133. Two hundred and eighty-five patients (89.9%) were diagnosed with adenocarcinoma, while 32/317 (10.1%) with mucinous adenocarcinoma. Neo-adjuvant treatments carried out were as follows: radiotherapy alone in 75/317 patients (23.7%), radiotherapy plus chemotherapy in 242/317 patients (76.3%). At univariate and multivariate analysis, only the hemoglobin (Hb) level (group 1: < or=12 g/dl versus group 2: >12 g/dl) resulted in a significant factor for disease-free survival. The role of the Hb level seemed to be confirmed further by the clinical downstaging obtained in approximately 55% of patients in group 2, in comparison with 35% of the patients achieving a significant downstaging in group 1. CONCLUSION Our results indicated that anemia could represent an important parameter able to influence the outcome in patients receiving neo-adjuvant treatment of rectal cancer.
Variability of Precipitating Ion Fluxes During the September 2017 Event at Mars

In this work, we study the influence of the September 2017 solar event on the precipitating heavy ion fluxes toward Mars' atmosphere as seen by Mars Atmosphere and Volatile EvolutioN/Solar Wind Ion Analyzer, an energy and angular ion spectrometer and by Mars Atmosphere and Volatile EvolutioN/Suprathermal and Thermal Ion Composition instrument, an energy, mass, and angular ion spectrometer. After a careful reconstruction of the background induced by the Solar Energetic Particle event in the Mars Atmosphere and Volatile EvolutioN/Solar Wind Ion Analyzer spectrometer, we investigate the precipitating ion flux responses to the space weather events that took place in September 2017. This period is a unique opportunity to analyze the respective role of various possible drivers of heavy ion precipitation into Mars' atmosphere with a wide range of different space weather events occurring during the same month. This study shows an increase in the precipitation flux by more than 1 order of magnitude during the arrival of the September Interplanetary Coronal Mass Ejection compared to the average flux during quiet solar conditions. We also showed that among the possible solar drivers, the solar wind dynamic pressure is the most significant during September 2017.
Back from the brink: potential for genetic rescue in a critically endangered tree

Rare plant species are vulnerable to genetic erosion and inbreeding associated with small population size and isolation due to increasing habitat fragmentation. The degree to which these problems undermine population viability remains debated. We explore genetic and reproductive processes in the critically endangered long‐lived tropical tree Medusagyne oppositifolia, an endemic to the Seychelles with a naturally patchy distribution. This species is failing to recruit in three of its four populations. We evaluate whether recruitment failure is linked to genetic problems associated with fragmentation, and if genetic rescue can mitigate such problems. Medusagyne oppositifolia comprises 90 extant trees in four populations, with only the largest (78 trees) having successful recruitment. Using 10 microsatellite loci, we demonstrated that genetic diversity is high (HE: 0.48–0.63; HO: 0.56–0.78) in three populations, with only the smallest population having relatively low diversity (HE: 0.26 and HO: 0.30). All populations have unique alleles, high genetic differentiation, and significant within population structure. Pollen and seed dispersal distances were mostly less than 100 m. Individuals in small populations were more related than individuals in the large population, thus inbreeding might explain recruitment failure in small populations. Indeed, inter‐population pollination crosses from the large donor population to a small recipient population resulted in higher reproductive success relative to within‐population crosses. Our study highlights the importance of maintaining gene flow between populations even in species that have naturally patchy distributions. We demonstrate the potential for genetic and ecological rescue to support conservation of plant species with limited gene flow.
The stratigraphic record of the Late Jurassic-Early Cretaceous rifting in the Alto Tajo-Serranía de Cuenca region (Iberian Ranges, Spain)

The Southwestern Iberian Domain (Southiberian Basin) corresponds to one of the five palaeogeographic domains into which the Iberian Basin was divided during the Late Jurassic-Early Cretaceous rifting stage. Although it was already known that this domain was clearly separated into two sub-basins, Cuenca and Valencia, the amelithostratigraphic scheme was assumed to be applicable to the whole domain. In the last decades, new data have been incorporated to the knowledge of the Serrania de Cuenca and the Alto Tajo region, showing that this area underwent a separated palaeogeographic evolution and developed a different stratigraphic record. Evidences of such independence are, among others, the development of a Late Jurassicearly Barremian unconformity with unique features in the Iberian Basin and herein described for the first time. Syn-rift sedimentation was controlled by an intricate extensional geometrical and kinematic pattern of multiple and small half-graben basins, and it is represented by just two unconformity-bounded units, late Barremian and Aptian in age respectively. This work reviews, clarifies, and simplifies old and confusing stratigraphic nomenclatures and proposes a specific lithostratigraphic scheme for the Alto Tajo-Serrania de Cuenca region. It includes the new upper Barremian Tragacete Formation and the redefinition of La Huerguina Formation in terms of lithofacies, lower boundary, age and environmental interpretation.
Investigation of seed germination of twelve Mediterranean wildflowers for evaluating their potential use on extensive green roofs.

The use of native plants in an urban context can have positive impacts, such as the reduction of water requirement, management costs, increasing urban biodiversity, and the safeguard of germplasm. This study evaluated the germination capacity of twelve native Mediterranean wildflowers aiming to be utilized for extensive green roofs. Some of the taxa (Antirrhinum majus subsp. tortuosum, Dianthus sylvestris, Lobularia maritima, Ruta chalepensis) have not been previously investigated. Seeds of native plants were collected in Italy, and quantitative analyses on seed germination in light or darkness conditions were carried out. For every taxa, mean germination time (MGT) and germination percentage were determined. The taxa differed markedly in their germination percentage and times. The results were generally concordant with previous research, and in particular for Armeria pungens, Clinopodium nepeta and A. majus. However, some differences were also observed for Helichrysum italicum subsp. microphyllum and Prasium majus, and distinct differences for Anthemis maritima and Glaucium flavum. Finally, A. majus, D. sylvestris and G. flavum (in darkness) showed high germination percentage, low MGT and limited requirement of pre-seeding treatments. Further research is needed to assess germination performances and success while scaling-up from laboratory to greenhouse to outdoor field conditions.
toward a Web Information System Benchmark

Evolving the database that is at the core of an Information System represents a difficult maintenance problem that has only been studied in the framework of traditional information systems. However, the problem is likely to be even more severe in web information systems, where open-source software is often developed through the contributions and collaboration of many groups and individuals. Therefore, in this paper, we present an indepth analysis of the evolution history of the Wikipedia database and its schema; Wikipedia is the best-known example of a large family of web information systems built using the open-source software MediaWiki. Our study is based on: (i) a set of Schema Modification Operators that provide a simple conceptual representation for complex schema changes, and (ii) simple software tools to automate the analysis. This framework allowed us to dissect and analyze the 4.5 years of Wikipedia history, which was short in time, but intense in terms of growth and evolution. Beyond confirming the initial hunch about the severity of the problem, our analysis suggests the need for developing better methods and tools to support graceful schema evolution. Therefore, we briefly discuss documentation and automation support systems for database evolution, and suggest that the Wikipedia case study can provide the kernel of a benchmark for testing and improving such systems.
Regulation of oxidative stress resistance in Campylobacter jejuni, a microaerophilic foodborne pathogen

Campylobacter jejuni is one of the leading bacterial causes of human gastroenteritis. Due to the increasing rates of human campylobacteriosis, C. jejuni is considered as a serious public health concern worldwide. C. jejuni is a microaerophilic, fastidious bacterium. C. jejuni must overcome a wide range of stress conditions during foodborne transmission to humans, such as food preservation and processing conditions, and even in infection of the gastrointestinal tracts of humans. Particularly, this microaerophilic foodborne pathogen must survive in the atmospheric conditions prior to the initiation of infection. C. jejuni possesses unique regulatory mechanisms for oxidative stress resistance. Lacking OxyR and SoxRS that are highly conserved in other Gram-negative foodborne pathogens, C. jejuni modulates the expression of genes involved in oxidative stress resistance mainly via the peroxide resistance regulator and Campylobacter oxidative stress regulator. Based on recent findings of ours and others, in this review, we described how C. jejuni regulates the expression of oxidative stress defense.
Influences of Centrifugation on Cells and Tissues in Liposuction Aspirates: Optimized Centrifugation for Lipotransfer and Cell Isolation

Background: Although injective autologous fat transplantation is one of the most attractive options for soft-tissue augmentation, problems such as unpredictability and fibrosis resulting from fat necrosis limit its universal acceptance. Centrifugation is one of most common methods for overcoming these difficulties. This study was performed to investigate quantitatively the effects of centrifugation on liposuction aspirates to optimize centrifugal conditions for fat transplantation and isolation of adipose-derived stem cells. Methods: Liposuction aspirates, obtained from eight healthy female donors, were either not centrifuged or centrifuged at 400, 700, 1200, 3000, or 4200 g for 3 minutes. The volumes of the oil, adipose, and fluid portions and numbers of blood cells and adipose-derived cells in each portion were examined. The processed adipose tissues (1 ml) were injected into athymic mice, and grafts were harvested and weighed at 4 weeks. Morphologic alterations were observed using light and scanning electron microscopy. Results: Centrifugation concentrated adipose tissues and adipose-derived stem cells in the adipose portion and partly removed red blood cells from the adipose portion. Centrifugation at more than 3000 g significantly damaged adipose-derived stem cells. Centrifugation enhanced graft take per 1 ml centrifuged adipose but reduced calculated graft take per 1 ml adipose before centrifugation. Conclusions: Excessive centrifugation can destroy adipocytes and adipose-derived stem cells, but appropriate centrifugation concentrates them, resulting in enhanced graft take. The authors tentatively recommend 1200 g as an optimized centrifugal force for obtaining good short- and long-term results in adipose transplantation.
Activity Recognition of Assembly Tasks Using Body-Worn Microphones and Accelerometers

In order to provide relevant information to mobile users, such as workers engaging in the manual tasks of maintenance and assembly, a wearable computer requires information about the user's specific activities. This work focuses on the recognition of activities that are characterized by a hand motion and an accompanying sound. Suitable activities can be found in assembly and maintenance work. Here, we provide an initial exploration into the problem domain of continuous activity recognition using on-body sensing. We use a mock "wood workshop" assembly task to ground our investigation. We describe a method for the continuous recognition of activities (sawing, hammering, filing, drilling, grinding, sanding, opening a drawer, tightening a vise, and turning a screwdriver) using microphones and three-axis accelerometers mounted at two positions on the user's arms. Potentially "interesting" activities are segmented from continuous streams of data using an analysis of the sound intensity detected at the two different locations. Activity classification is then performed on these detected segments using linear discriminant analysis (LDA) on the sound channel and hidden Markov models (HMMs) on the acceleration data. Four different methods at classifier fusion are compared for improving these classifications. Using user-dependent training, we obtain continuous average recall and precision rates (for positive activities) of 78 percent and 74 percent, respectively. Using user-independent training (leave-one-out across five users), we obtain recall rates of 66 percent and precision rates of 63 percent. In isolation, these activities were recognized with accuracies of 98 percent, 87 percent, and 95 percent for the user-dependent, user-independent, and user-adapted cases, respectively
Statistical Forecasting of Current and Future Circum‐Arctic Ground Temperatures and Active Layer Thickness

Mean annual ground temperature (MAGT) and active layer thickness (ALT) are key to understanding the evolution of the ground thermal state across the Arctic under climate change. Here a statistical modeling approach is presented to forecast current and future circum‐Arctic MAGT and ALT in relation to climatic and local environmental factors, at spatial scales unreachable with contemporary transient modeling. After deploying an ensemble of multiple statistical techniques, distance‐blocked cross validation between observations and predictions suggested excellent and reasonable transferability of the MAGT and ALT models, respectively. The MAGT forecasts indicated currently suitable conditions for permafrost to prevail over an area of 15.1 ± 2.8 × 106 km2. This extent is likely to dramatically contract in the future, as the results showed consistent, but region‐specific, changes in ground thermal regime due to climate change. The forecasts provide new opportunities to assess future Arctic changes in ground thermal state and biogeochemical feedback.
Computing endomorphism rings of abelian varieties of dimension two

Generalizing a method of Sutherland and the author for elliptic curves, we design a subexponential algorithm for computing the endomorphism rings of ordinary abelian varieties of dimension two over finite fields. Although its correctness and complexity analysis rest on several assumptions, we report on practical computations showing that it performs very well and can easily handle previously intractable cases.
Long Terminal Repeat Retrotransposon Content in Eight Diploid Sunflower Species Inferred from Next-Generation Sequence Data

The most abundant transposable elements (TEs) in plant genomes are Class I long terminal repeat (LTR) retrotransposons represented by superfamilies gypsy and copia. Amplification of these superfamilies directly impacts genome structure and contributes to differential patterns of genome size evolution among plant lineages. Utilizing short-read Illumina data and sequence information from a panel of Helianthus annuus (sunflower) full-length gypsy and copia elements, we explore the contribution of these sequences to genome size variation among eight diploid Helianthus species and an outgroup taxon, Phoebanthus tenuifolius. We also explore transcriptional dynamics of these elements in both leaf and bud tissue via RT-PCR. We demonstrate that most LTR retrotransposon sublineages (i.e., families) display patterns of similar genomic abundance across species. A small number of LTR retrotransposon sublineages exhibit lineage-specific amplification, particularly in the genomes of species with larger estimated nuclear DNA content. RT-PCR assays reveal that some LTR retrotransposon sublineages are transcriptionally active across all species and tissue types, whereas others display species-specific and tissue-specific expression. The species with the largest estimated genome size, H. agrestis, has experienced amplification of LTR retrotransposon sublineages, some of which have proliferated independently in other lineages in the Helianthus phylogeny.
Jump Risk , Stock Returns , and Slope of Implied Volatility Smile

Under the jump-diffusion framework, expected stock return is dependent on the average jump size of stock price, which can be inferred from the slope of option implied volatility smile. This implies a negative relation between expected stock return and slope of implied volatility smile, which is strongly supported by the empirical evidence. For over 4,000 stocks ranked by slope of implied volatility smile during 1996 – 2005, the difference between average returns of the lowest and highest quintile portfolios is 22.2% per year. The findings cannot be explained by risk factors like RM −Rf , SMB, HML, and MOM; or by stock characteristics like size, book-to-market, leverage, volatility, skewness, and volume. ∗I thank Anurag Gupta, Michael Lemmon, Roger Loh, Francis Longstaff, Steve Mann, Pedro Santa-Clara, Dragon Tang, Sergey Tsyplakov, Hong Yan, Donghang Zhang, and seminar participants at the China International Conference in Finance in Dalian, Conference on Advances in the analysis of hedge fund strategies at Imperial College Business School, Second Singapore International Conference on Finance at NUS, Southern Finance Association Annual Meetings, University of South Carolina for helpful comments. I also would like to thank Anitha Manohar for research assistance. †Columbia, SC 29208, phone: (803) 777-4925, e-mail: syan@moore.sc. edu. Jump Risk, Stock Returns, and Slope of Implied Volatility Smile
Therapeutic Plasma Exchange Using the Spectra Optia Cell Separator Compared With the COBE Spectra

Background The Spectra Optia (SPO) is a novel continuous-flow centrifugal apheresis system based on the COBE Spectra (CSP) platform. There have been few attempts to validate the advantages of the SPO. We performed a retrospective study comparing the two cell separators for therapeutic plasma exchange (TPE) procedures in kidney transplant (KT) patients and seeing efficacy and safety. Methods We analyzed 720 TPE procedures performed between August 2012 and July 2014. Procedures included desensitization TPE before KT and TPE for the management of acute and chronic antibody-mediated graft rejection. Demographic characteristics, operational TPE variables, and laboratory data were analyzed. Results Demographic characteristics for the SPO (n=389) and CSP (n=331) groups did not differ significantly. The procedure time to exchange one plasma volume was 94.2±10.3 min in the SPO group and 100.4±11.2 min in the CSP group (P<0.001). The plasma removal efficiency (PRE) was 92.5±4.9% in the SPO group and 83.2±3.7% in the CSP group (P<0.001). There were no significant differences across the two apheresis systems for changes in hematologic parameters. Conclusions Compared with the CSP, the SPO was associated with an improved PRE and a shorter procedure time to exchange one plasma volume. Our results in KT patients show that the SPO is superior to the CSP in TPE procedures.