Miracle-dz/UniFAR-FTUs huggingface dataset:
Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle

Significance Members of the diatom family Rhopalodiaceae possess a cyanobacterial endosymbiont called a “spheroid body. ” The spheroid body evolved much more recently than did mitochondria or plastids and is predicted to fix nitrogen. Here we present what is, to our knowledge, the first completely sequenced spheroid body genome from a rhopalodiacean diatom. Comparative analyses revealed that the endosymbiont is metabolically reduced, confirming its status as an obligate endosymbiont. The genome possesses genes for nitrogen fixation, and, to our surprise, no essential genes for photosynthesis. Thus, the spheroid body is, to our knowledge, the first known example of a nonphotosynthetic cyanobacterium, free-living or symbiotic. Rhopalodiacean diatoms have the potential to provide unique insight into the evolution of bacterial endosymbionts and their hosts. The evolution of mitochondria and plastids from bacterial endosymbionts were key events in the origin and diversification of eukaryotic cells. Although the ancient nature of these organelles makes it difficult to understand the earliest events that led to their establishment, the study of eukaryotic cells with recently evolved obligate endosymbiotic bacteria has the potential to provide important insight into the transformation of endosymbionts into organelles. Diatoms belonging to the family Rhopalodiaceae and their endosymbionts of cyanobacterial origin (i.e., “spheroid bodies”) are emerging as a useful model system in this regard. The spheroid bodies, which appear to enable rhopalodiacean diatoms to use gaseous nitrogen, became established after the divergence of extant diatom families. Here we report what is, to our knowledge, the first complete genome sequence of a spheroid body, that of the rhopalodiacean diatom Epithemia turgida. The E. turgida spheroid body (EtSB) genome was found to possess a gene set for nitrogen fixation, as anticipated, but is reduced in size and gene repertoire compared with the genomes of their closest known free-living relatives. The presence of numerous pseudogenes in the EtSB genome suggests that genome reduction is ongoing. Most strikingly, our genomic data convincingly show that the EtSB has lost photosynthetic ability and is metabolically dependent on its host cell, unprecedented characteristics among cyanobacteria, and cyanobacterial symbionts. The diatom–spheroid body endosymbiosis is thus a unique system for investigating the processes underlying the integration of a bacterial endosymbiont into eukaryotic cells.
Encapsulating peritoneal sclerosis in the new millennium: a national cohort study.

BACKGROUND AND OBJECTIVES The study aim was to establish the incidence and characterize all encapsulating peritoneal sclerosis (EPS) cases in patients treated by peritoneal dialysis (PD). DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS The patient cohort, which started PD from January 1, 2000, to December 31, 2007, was identified from the Scottish Renal Registry (n = 1238). Possible EPS cases were identified by the ten adult Scottish renal units. Patient records were examined to ensure cases met diagnostic criteria. RESULTS Forty-six cases were identified; 19 had their first PD exposure after January 1, 2000. The rate was 1.5%, an incidence of 4.9 per 1000 person-years. The incidence increased with PD duration, with rates of 0, 0.6, 2.0, 3.5, 8.1, 8.8 and 5% at <1, 1 to 2, >2 to 3, >3 to 4, >4 to 5, >5 to 6 and >6 yr PD exposure, respectively. The median PD duration of EPS cases was 5.1 yr (interquartile range [IQR] 3.4 to 6.1 yr). At diagnosis, 12 (26%) were on PD and 33 (72%) were diagnosed <2 yr after PD stopped. The cases had a median of 3.3 episodes of peritonitis (range 0 to 20, IQR 1 to 4.5). Thirty (65%) had used 3.86% dextrose dialysate and 45 (98%) had used Extraneal. The mortality was 42% at 1 yr postdiagnosis with a median survival of 149 d (IQR 61 to 408 d). CONCLUSIONS The incidence reported in this study may be used to inform patients of the minimum risk of developing EPS on PD.
Time Will Tell: Leveraging Temporal Expressions in IR

Temporal expressions, such as between 1992 and 2000, are frequent across many kinds of documents. Text retrieval, though, treats them as common terms, thus ignoring their inherent semantics. For queries with a strong temporal component, such as U.S. president 1997, this leads to a decrease in retrieval effectiveness, since relevant documents (e.g., a biography of Bill Clinton containing the aforementioned temporal expression) can not be reliably matched to the query. We propose a novel approach, based on language models, to make temporal expressions first-class citizens of the retrieval model. In addition, we present experiments that show actual improvements in retrieval effectiveness.
Broadcasting through UDG in Manets by GPS Assistance

Adhocnetworks are useful in many Application Environments and do not need any infrastructure support. Collaborative computing and communication in smaller areas can be setup by using Adhoc networking technologies. Broadcast protocols play an important role in building wireless multihop Adhoc networks . Because of high mobility in the network, rapid topological changes occurs, message passing in between the network occurs collision, so to avoid collision and maximum utilization of bandwidth we are using cross layer interaction. Some parameters (eg: radio propagation, hostile interference, traffic demands etc)may dynamically change ,the protocol must be adaptively tuned. so proper tuning requires exchange of information across layers, and protocol uses the unit disk graph model with FDMA And TDMA mechanisms.
A retrofit for asbestos-based brake pad employing palm kernel fiber as the base filler material

The development of automobile brake pad using locally sourced palm kernel fiber was carried out. Asbestos, a carcinogenic material, has been used for decades as a friction material. This development has thus prompted a couple of research efforts geared towards its replacement for brake pad manufacture. Palm kernel fiber was used as an alternative filler material in conjunction with various quantities of epoxy resin as the matrix. Three sets of compositions were made, and the resulting specimens subjected to physical and mechanical tests using standard materials, procedures, and equipment. The essence is to determine their suitability and hence possible performance in service. The result showed that sample C with 40% palm kernel fiber content having hardness, compressive strength, abrasion resistance, specific gravity, water absorption, and oil absorption of 178 MPa, 96.2 MPa, 1.67 mg/m, 1.8 g/cm3, 1.86%, and 0.89%, respectively, had an optimum performance rating. It was equally ascertained that increase in the filler content had the effect of increase in hardness, wear resistance, and specific gravity of the composite brake pad, while water and oil absorption got decreased when compared with results obtained by other researchers using conventional brake pads made of other friction materials including asbestos. This is an indicator that palm kernel fiber is a possible and effective retrofit for asbestos as a filler material in automotive brake pad manufacture.
Does Python Smell Like Java? Tool Support for Design Defect Discovery in Python

The context of this work is specification, detection and ultimately removal of detectable harmful patterns in source code that are associated with defects in design and implementation of software. In particular, we investigate five code smells and four antipatterns previously defined in papers and books. Our inquiry is about detecting those in source code written in Python programming language, which is substantially different from all prior research, most of which concerns Java or C-like languages. Our approach was that of software engineers: we have processed existing research literature on the topic, extracted both the abstract definitions of nine design defects and their concrete implementation specifications, implemented them all in a tool we have programmed and let it loose on a huge test set obtained from open source code from thousands of GitHub projects. When it comes to knowledge, we have found that more than twice as many methods in Python can be considered too long (statistically extremely longer than their neighbours within the same project) than in Java, but long parameter lists are seven times less likely to be found in Python code than in Java code. We have also found that Functional Decomposition, the way it was defined for Java, is not found in the Python code at all, and Spaghetti Code and God Classes are extremely rare there as well. The grounding and the confidence in these results comes from the fact that we have performed our experiments on 32'058'823 lines of Python code, which is by far the largest test set for a freely available Python parser. We have also designed the experiment in such a way that it aligned with prior research on design defect detection in Java in order to ease the comparison if we treat our own actions as a replication. Thus, the importance of the work is both in the unique open Python grammar of highest quality, tested on millions of lines of code, and in the design defect detection tool which works on something else than Java.
The liver‐specific tumor suppressor STAT5 controls expression of the reactive oxygen species–generating enzyme NOX4 and the proapoptotic proteins PUMA and BIM in mice

Loss of signal transducer and activator of transcription 5 (STAT5) from liver tissue results in steatosis and enhanced cell proliferation. This study demonstrates that liver‐specific Stat5‐null mice develop severe hepatic steatosis as well as hepatocellular carcinomas at 17 months of age, even in the absence of chemical insults. To understand STAT5′s role as a tumor suppressor, we identified and investigated new STAT5 target genes. Expression of Nox4, the gene encoding the reactive oxygen species (ROS)‐generating enzyme NOX4, was induced by growth hormone through STAT5. In addition, the genes encoding the proapoptotic proteins PUMA and BIM were induced by growth hormone through STAT5, which bound to GAS motifs in the promoter regions of all three genes. We further show that STAT5‐induced activation of Puma and Bim was dependent on NOX4. Treatment of mice with transforming growth factor‐β, an inducer of apoptosis, resulted in cleaved caspase‐3 in control but not in liver‐specific Stat5‐null mice. This study demonstrates for the first time that cytokines through STAT5 regulate the expression of the ROS‐generating enzyme NOX4 and key proapoptotic proteins. Conclusion: STAT5 harnesses several distinct signaling pathways in the liver and thereby functions as a tumor suppressor. Besides suppressing the activation of STAT3, STAT5 induces the expression of proapoptotic genes and the production of ROS. (HEPATOLOGY 2012;56:2375–2386)
An Algorithm for VP Ellipsis

An algorithm is proposed to determine antecedents for VP ellipsis. The algorithm eliminates impossible antecedents, and then imposes a preference ordering on possible antecedents. The algorithm performs with 94% accuracy on a set of 304 examples of VP ellipsis collected from the Brown Corpus. The problem of determining antecedents for VP ellipsis has received little attention in the literature, and it is shown that the current proposal is a significant improvement over alternative approaches.
PLANT ECOLOGY: Plant‐soil feedback and the maintenance of diversity in Mediterranean‐climate shrublands

&NA; Soil biota influence plant performance through plant‐soil feedback, but it is unclear whether the strength of such feedback depends on plant traits and whether plant‐soil feedback drives local plant diversity. We grew 16 co‐occurring plant species with contrasting nutrient‐acquisition strategies from hyperdiverse Australian shrublands and exposed them to soil biota from under their own or other plant species. Plant responses to soil biota varied according to their nutrient‐acquisition strategy, including positive feedback for ectomycorrhizal plants and negative feedback for nitrogen‐fixing and nonmycorrhizal plants. Simulations revealed that such strategy‐dependent feedback is sufficient to maintain the high taxonomic and functional diversity characterizing these Mediterranean‐climate shrublands. Our study identifies nutrient‐acquisition strategy as a key trait explaining how different plant responses to soil biota promote local plant diversity.
Nanobiomaterials in Cancer Therapy : Applications of Nanobiomaterials

Nanobiomaterials in Cancer Therapy presents the major applications of nanobiomaterials in oncology, offering an up-to-date overview of the latest research in this field. Utilizing nanobiomaterials, novel therapeutic approaches enable significant improvements in drug-loading capacity, formulation stability and drug efficiency. In this book, leading researchers from around the world share their expertise and unique insights. The book covers the fabrication methods of platforms for multimodal and combinatorial therapeutic options, along with simultaneous and real-time cancer imaging, and innovative approaches for oncology by passive or active pathways of multifunctional nanocarriers. The work also classifies and discusses engineered nanobiosystems for cancer therapy, prevention, and low cancer recurrence or relapse. This book will be of interest to postdoctoral researchers, professors and students engaged in the fields of materials science, biotechnology and applied chemistry. It will also be highly valuable to those working in industry, including pharmaceutics and biotechnology companies, medical researchers, biomedical engineers and advanced clinicians.A comprehensive resource for researchers, practitioners and students working in biomedical, biotechnological and engineering fields.A valuable guide to recent scientific progress and the latest application methods.Discusses novel opportunities and ideas for developing or improving technologies in nanomedicine and nanobiology.
Contextual Determinants for Users ’ Acceptance of Personal Data Processing : A Multinational Analysis

The importance of “context” in people’s privacy decisions is widely recognized, mostly in the area of inter-personal privacy. A comprehensive multinational analysis of what users consider to be the main contextual factors impacting their privacy decisions is still largely missing though, rendering it difficult to integrate context into data processing systems and privacy policy frameworks. We present a qualitative study in 4 countries followed by a largescale (N=9,625) quantitative study in 8 countries aimed at identifying the contextual, attitudinal and demographic determinants that influence individuals' acceptance of scenarios involving the use of their personal data, and at gauging the relative influence of these determinants globally and country-wise. We develop parsimonious regression models to analyze the relative importance of different factors in different countries. The implications of such models in developing context and privacy aware systems and privacy policy frameworks are discussed.
25-Hydroxyvitamin D and Peripheral Immune Mediators: Results from Two Nationwide Danish Pediatric Cohorts

(1) Background: We aimed to examine if 25-hydroxyvitamin D (25(OH)D) was related to the peripheral immunological and inflammatory signature both at birth, and in newly diagnosed patients with childhood type 1 diabetes (T1D) and their healthy controls; (2) Methods: The birth cohort consisted of 470 patients and 500 healthy controls. Dried blood samples were collected from the neonates in the period 1981–1999. The newly diagnosed cohort consisted of 460 patients and 453 siblings. Serum samples were collected in the period 1997–2005. A variety of peripheral immune mediators were measured and compared to total 25(OH)D levels (25(OH)D2 + 25(OH)D3). For each immune mediator, the relative change (RC) in the mean level was modeled by robust log-normal regression and correction for multiple testing was performed; (3) Results: Two associations were identified; there was a negative association between 25(OH)D (10 nmol/L increase) and leptin (RC (95% confidence interval (CI)), 0.98 (0.96; 1.00)), and a positive association between 25(OH)D (10 nmol/L increase) and the chemokine, chemokine (c-x-c motif) ligand (CXCL) 8 (RC (95% CI), 1.07 (1.01; 1.13)); (4) Conclusion: CXCL8 and leptin have significant associations with levels of 25(OH)D in the newly diagnosed cohort. These results do not indicate a strong influence of 25(OH)D on the peripheral immunological or inflammatory signature.
Pulse Wave Velocity as Index of Arterial Stiffness in HIV-Infected Patients Compared With a Healthy Population

Background:Chronic HIV infection leads to premature atherosclerosis. Arterial stiffness is considered a subclinical marker of cardiovascular disease. Methods:Pulse wave velocity (PWV) was determined in 254 individuals (174 HIV-infected patients and 80 healthy controls, 2:1 matched by age and gender) to compare the prevalence of arterial stiffness and to identify associated factors. PWV was determined using noninvasive automated device (Complior). Factors associated with impaired PWV were assessed among cardiovascular risk factors, HIV infection parameters, and laboratory data. Logistic regression analyses were performed to determine differences between groups and factors associated to arterial stiffness. Results:Overall, 81.4% of participants were male, median age was 46.54 [interquartile range (IQR): 41–52] years. Higher percentages of HIV-infected subjects showed dyslipemia (P = 0.012) and smoking habit (P = 0.002). The median time from HIV diagnosis was 13 (IQR: 6–18) years and the median time on antiretroviral therapy was 11 (IQR: 5–15) years. Nearly, all patients were virologically suppressed (89.7%) at the time of PWV. Arterial stiffness in the global population was 20.5%, 18.9% in HIV-infected group, and 23.8% in controls (P = 0.405). High diastolic blood pressure and high levels of triglycerides at time of PWV were associated with increased PWV (P = 0.009 and P = 0.023, respectively). Conclusions:Virologically suppressed HIV-infected patients showed similar arterial elasticity to non–HIV-infected patients. HIV-related conditions were not associated with arterial stiffness, probably because of the good immunologic and virological status of this group. However, high diastolic pressure at the time of PWV and high levels of triglycerides were associated risk factors.
The Multifaceted Role of T-Helper Responses in Host Defense against Aspergillus fumigatus

The ubiquitous opportunistic fungal pathogen Aspergillus fumigatus rarely causes infections in immunocompetent individuals. A healthy functional innate immune system plays a crucial role in preventing Aspergillus-infection. This pivotal role for the innate immune system makes it a main research focus in studying the pathogenesis of aspergillosis. Although sometimes overshadowed by the innate immune response, the adaptive immune response, and in particular T-helper responses, also represents a key player in host defense against Aspergillus. Virtually all T-helper subsets have been described to play a role during aspergillosis, with the Th1 response being crucial for fungal clearance. However; morbidity and mortality of aspergillosis can also be partly attributed to detrimental immune responses resulting from adaptive immune activation. Th2 responses benefit fungal persistence; and are the foundation of allergic forms of aspergillosis. The Th17 response has two sides; although crucial for granulocyte recruitment, it can be involved in detrimental immunopathology. Regulatory T-cells, the endogenous regulators of inflammatory responses, play a key role in controlling detrimental inflammatory responses during aspergillosis. The current knowledge of the adaptive immune response against A. fumigatus is summarized in this review. A better understanding on how T-helper responses facilitate clearance of Aspergillus-infection and control inflammation can be the fundamental basis for understanding the pathogenesis of aspergillosis and for the development of novel host-directed therapies.
The Real Role of Forearm Mixed Nerve Conduction Velocity in the Assessment of Proximal Forearm Conduction Slowing in Carpal Tunnel Syndrome

Summary: The decrease of forearm median motor conduction velocity (CV) in carpal tunnel syndrome (CTS) is a common electrodiagnostic finding in clinical practice and is possibly secondary to either conduction block at wrist or retrograde conduction slowing (RCS). This study is attempted to confirm the existence of RCS and to explore why this controversy occurs for a long time. Eighty CTS patients and controls were recruited. In addition to conventional electrodiagnosis, subjects received further electrodiagnostic protocol. First, a recording electrode was placed over the wrist and then at elbow with palm stimulation to calculate indirect forearm mixed nerve CV (forearm-mix CV) that represented real measurement of nerve fibers through the carpal tunnel. Then, direct measurement of forearm-mix CV was performed with recording at the elbow and stimulation at the wrist. CTS patients had markedly prolonged distal motor and sensory latencies and significantly prolonged wrist-palm sensory and motor conduction. There was a significant decrease in forearm median motor CV; however, there was no difference in ulnar distal motor latency and forearm motor CV. The mild decrease of forearm median motor CV was not proportional to the marked reduction of W-P MCV and there was no demonstrated conduction block at wrist, implying the reduction of forearm median motor CV is unlikely due to conduction blockage or slowing of the large myelinating fibers at the wrist and RCS really occurs over the forearm median nerve. In addition, the direct Forearm-mix CV was similar in CTS and controls; however, there was a significant decrease in indirect forearm-mix CV only in the CTS. Moreover, the difference between direct and indirect forearm-mix CV was significantly greater and poor consistency of direct and indirect forearm-mix CV in CTS, suggesting that direct and indirect forearm-mix CV represent CV from quite different nerve fibers. Therefore, we conclude that RCS really does occur in CTS and the direct forearm-mix CV reflects the CV of nerve fibers without damage in CTS. The misinterpretation and measurement of different components of forearm-mix CV results in the existence of this controversy till now.
Flow Network Models for Word Alignment and Terminology Extraction from Bilingual Corpora

This paper presents a new model for word alignments between parallel sentences, which allows one to accurately estimate different parameters, in a computationally efficient way. An application of this model to bilingual terminology extraction, where terms are identified in one language and gussed, through the alignment process, in the other one, is also described. An experiment conducted on a small English-French parallel corpus gave results with high precision, demonstrating the validity of the model.