Miracle-dz/UniFAR-FTUs huggingface dataset:
IFITM-2 and IFITM-3 but Not IFITM-1 Restrict Rift Valley Fever Virus

ABSTRACT We show that interferon-induced transmembrane protein 1 (IFITM-1), IFITM-2, and IFITM-3 exhibit a broad spectrum of antiviral activity against several members of the Bunyaviridae family, including Rift Valley fever virus (RVFV), La Crosse virus, Andes virus, and Hantaan virus, all of which can cause severe disease in humans and animals. We found that RVFV was restricted by IFITM-2 and -3 but not by IFITM-1, whereas the remaining viruses were equally restricted by all IFITMs. Indeed, at low doses of alpha interferon (IFN-α), IFITM-2 and -3 mediated more than half of the antiviral activity of IFN-α against RVFV. IFITM-2 and -3 restricted RVFV infection mostly by preventing virus membrane fusion with endosomes, while they had no effect on virion attachment to cells, endocytosis, or viral replication kinetics. We found that large fractions of IFITM-2 and IFITM-3 occupy vesicular compartments that are distinct from the vesicles coated by IFITM-1. In addition, although overexpression of all IFITMs expanded vesicular and acidified compartments within cells, there were marked phenotypic differences among the vesicular compartments occupied by IFITMs. Collectively, our data provide new insights into the possible mechanisms by which the IFITM family members restrict distinct viruses.
GMP-based CD133+ cells isolation maintains progenitor angiogenic properties and enhances standardization in cardiovascular cell therapy

The aim of the present study was to develop and validate a good manufacturing practice (GMP) compliant procedure for the preparation of bone marrow (BM) derived CD133+ cells for cardiovascular repair. Starting from available laboratory protocols to purify CD133+ cells from human cord blood, we implemented these procedures in a GMP facility and applied quality control conditions defining purity, microbiological safety and vitality of CD133+ cells. Validation of CD133+ cells isolation and release process were performed according to a two‐step experimental program comprising release quality checking (step 1) as well as ‘proofs of principle’ of their phenotypic integrity and biological function (step 2). This testing program was accomplished using in vitro culture assays and in vivo testing in an immunosuppressed mouse model of hindlimb ischemia. These criteria and procedures were successfully applied to GMP production of CD133+ cells from the BM for an ongoing clinical trial of autologous stem cells administration into patients with ischemic cardiomyopathy. Our results show that GMP implementation of currently available protocols for CD133+ cells selection is feasible and reproducible, and enables the production of cells having a full biological potential according to the most recent quality requirements by European Regulatory Agencies.
A 2-Stage Phase II Design with Direct Assignment Option in Stage II for Initial Marker Validation

Biomarkers are critical to targeted therapies, as they may identify patients more likely to benefit from a treatment. Several prospective designs for biomarker-directed therapy have been previously proposed, differing primarily in the study population, randomization scheme, or both. Recognizing the need for randomization, yet acknowledging the possibility of promising but inconclusive results after a stage I cohort of randomized patients, we propose a 2-stage phase II design on marker-positive patients that allows for direct assignment in a stage II cohort. In stage I, marker-positive patients are equally randomized to receive experimental treatment or control. Stage II has the option to adopt “direct assignment” whereby all patients receive experimental treatment. Through simulation, we studied the power and type I error rate of our design compared with a balanced randomized two-stage design, and conducted sensitivity analyses to study the effect of timing of stage I analysis, population shift effects, and unbalanced randomization. Our proposed design has minimal loss in power (<1.8%) and increased type I error rate (<2.1%) compared with a balanced randomized design. The maximum increase in type I error rate in the presence of a population shift was between 3.1% and 5%, and the loss in power across possible timings of stage I analysis was less than 1.2%. Our proposed design has desirable statistical properties with potential appeal in practice. The direct assignment option, if adopted, provides for an “extended confirmation phase” as an alternative to stopping the trial early for evidence of efficacy in stage I. Clin Cancer Res; 18(16); 4225–33. ©2012 AACR.
The Current Status of Somatostatin-Interneurons in Inhibitory Control of Brain Function and Plasticity

The mammalian neocortex contains many distinct inhibitory neuronal populations to balance excitatory neurotransmission. A correct excitation/inhibition equilibrium is crucial for normal brain development, functioning, and controlling lifelong cortical plasticity. Knowledge about how the inhibitory network contributes to brain plasticity however remains incomplete. Somatostatin- (SST-) interneurons constitute a large neocortical subpopulation of interneurons, next to parvalbumin- (PV-) and vasoactive intestinal peptide- (VIP-) interneurons. Unlike the extensively studied PV-interneurons, acknowledged as key components in guiding ocular dominance plasticity, the contribution of SST-interneurons is less understood. Nevertheless, SST-interneurons are ideally situated within cortical networks to integrate unimodal or cross-modal sensory information processing and therefore likely to be important mediators of experience-dependent plasticity. The lack of knowledge on SST-interneurons partially relates to the wide variety of distinct subpopulations present in the sensory neocortex. This review informs on those SST-subpopulations hitherto described based on anatomical, molecular, or electrophysiological characteristics and whose functional roles can be attributed based on specific cortical wiring patterns. A possible role for these subpopulations in experience-dependent plasticity will be discussed, emphasizing on learning-induced plasticity and on unimodal and cross-modal plasticity upon sensory loss. This knowledge will ultimately contribute to guide brain plasticity into well-defined directions to restore sensory function and promote lifelong learning.
Bulk diffusion of 1d exclusion process with bond disorder.

Given a doubly innite sequence of positive numbers fck : k 2 Zg such that fc 1 k : k 2 Zg satises a LLN with limit 2 (0;1), we consider the nearest-neighbor simple exclusion process on Z where ck is the probability rate of jumps between k and k + 1. If = 1 we require an additional minor technical condition. By extending a method developed in (11) we show that the diusiv ely rescaled process has hydrodynamic behavior described by the heat equation with diusion constant 1= . In particular, the process has diusiv e behavior for < 1 and subdiusiv e behavior for = 1.
Effect of Hachimijiogan against Renal Dysfunction and Involvement of Hypoxia-Inducible Factor-1α in the Remnant Kidney Model

In chronic renal failure, hypoxia of renal tissue is thought to be the common final pathway leading to end-stage renal failure. In this study the effects of hachimijiogan, a Kampo formula, were studied with respect to hypoxia-inducible factor (HIF). Using remnant kidney rats, we studied the effects of hachimijiogan on renal function in comparison with angiotensin II receptor blocker. The result showed that oral administration of hachimijiogan for seven days suppressed urinary protein excretion and urinary 8-OHdG, a marker of antioxidant activity, equally as well as oral administration of candesartan cilexetil. In contrast, the protein volume of HIF-1α in the renal cortex was not increased in the candesartan cilexetil group, but that in the hachimijiogan group was increased. In immunohistochemical studies as well, the expression of HIF-1α of the high-dose hachimijiogan group increased compared to that of the control group. Vascular endothelial growth factor and glucose transporter 1, target genes of HIF-1α, were also increased in the hachimijiogan group. These results suggest that hachimijiogan produces a protective effect by a mechanism different from that of candesartan cilexetil.
Detection and characterization of novel sequence insertions using paired-end next-generation sequencing

MOTIVATION In the past few years, human genome structural variation discovery has enjoyed increased attention from the genomics research community. Many studies were published to characterize short insertions, deletions, duplications and inversions, and associate copy number variants (CNVs) with disease. Detection of new sequence insertions requires sequence data, however, the 'detectable' sequence length with read-pair analysis is limited by the insert size. Thus, longer sequence insertions that contribute to our genetic makeup are not extensively researched. RESULTS We present NovelSeq: a computational framework to discover the content and location of long novel sequence insertions using paired-end sequencing data generated by the next-generation sequencing platforms. Our framework can be built as part of a general sequence analysis pipeline to discover multiple types of genetic variation (SNPs, structural variation, etc.), thus it requires significantly less-computational resources than de novo sequence assembly. We apply our methods to detect novel sequence insertions in the genome of an anonymous donor and validate our results by comparing with the insertions discovered in the same genome using various sources of sequence data. AVAILABILITY The implementation of the NovelSeq pipeline is available at http://compbio.cs.sfu.ca/strvar.htm CONTACT eee@gs.washington. edu; cenk@cs.sfu.ca
Misresponse to Reversed and Negated Items in Surveys: A Review

There are important advantages to including reversed items in questionnaires (e.g., control of acquiescence, disruption of nonsubstantive responding, better coverage of the domain of content of a construct), but reversed items can also lead to measurement problems (e.g., low measure reliability, complex factor structures). The authors advocate the continued use of reversed items in measurement instruments but also argue that they should be used with caution. To help researchers improve their scale construction practices, the authors provide a comprehensive review of the literature on reversed and negated items and offer recommendations about their use in questionnaires. The theoretical discussion is supplemented with data on 1330 items from measurement scales that have appeared in Journal of Marketing Research and Journal of Consumer Research.
ERP implementation framework for Malaysian private institution of higher learning

Enterprise Resource Planning (ERP) systems are widely used by many multinational companies throughout the world. Recently, many institutions of higher learning have replaced their legacy systems to ERP systems as a means for integration advantages. Investments with this ERP system are representing the largest investment for institutions of higher learning. They invest millions of dollars and the time taken for the implementation sometimes takes two to three years, or even more. Without a solid history of successes and failures, implementers are at a disadvantage in knowing how best to implement ERP systems so that they will provide operational and strategic benefits to their owners. Due to these problems, this research is carried out in order to establish an ERP implementation framework for Malaysian private institutions of higher learning. The framework has four phases; project initiation, project implementation, realization and operation and maintenance. Every phase will be having a combination of critical success factors (CSF's), deliverables and responsibilities and this combination as unique features for the private institution of higher learning in Malaysia environment.
Irreversibilities and the Timing of Environmental Policy

The standard framework in which economists evaluate environmental policies is cost-benefit analysis, so policy debates usually focus on the expected flows of costs and benefits, or on the choice of discount rate. But this can be misleading when there is uncertainty over future outcomes, when there are reversibilities, and when policy adoption can be delayed. This paper shows how two kinds of uncertainty over the future costs and benefits of reduced environmental degradation, and over the evolution of an ecosystem interact with two kinds of irreversibilities - sunk costs associated with an environmental regulation, and "sunk benefits" of avoided environmental degradation - to affect optimal policy timing and design.
Avoiding negative depth in inverse depth bearing-only SLAM

In this paper we consider ways to alleviate negative estimated depth for the inverse depth parameterisation of bearing-only SLAM. This problem, which can arise even if the beacons are far from the platform, can cause catastrophic failure of the filter.We consider three strategies to overcome this difficulty: applying inequality constraints, the use of truncated second order filters, and a reparameterisation using the negative logarithm of depth. We show that both a simple inequality method and the use of truncated second order filters are successful. However, the most robust performance is achieved using the negative log parameterisation.
Nontuberculous Mycobacterial Disease in Children – Epidemiology, Diagnosis & Management at a Tertiary Center

Background There are limited data on the epidemiology, diagnosis and optimal management of nontuberculous mycobacterial (NTM) disease in children. Methods Retrospective cohort study of NTM cases over a 10-year-period at a tertiary referral hospital in Australia. Results A total of 140 children with NTM disease, including 107 with lymphadenitis and 25 with skin and soft tissue infections (SSTIs), were identified. The estimated incidence of NTM disease was 0.6–1.6 cases / 100,000 children / year; no increasing trend was observed over the study period. Temporal analyses revealed a seasonal incidence cycle around 12 months, with peaks in late winter/spring and troughs in autumn. Mycobacterium-avium-complex accounted for most cases (77.8%), followed by Mycobacterium ulcerans (14.4%) and Mycobacterium marinum (3.3%). Polymerase chain reaction testing had higher sensitivity than culture and microscopy for acid-fast bacilli (92.0%, 67.2% and 35.7%, respectively). The majority of lymphadenitis cases underwent surgical excision (97.2%); multiple recurrences in this group were less common in cases treated with clarithromycin and rifampicin compared with clarithromycin alone or no anti-mycobacterial drugs (0% versus 7.1%; OR:0.73). SSTI recurrences were also less common in cases treated with two anti-mycobacterial drugs compared with one or none (10.5% versus 33.3%; OR:0.23). Conclusions There was seasonal variation in the incidence of NTM disease, analogous to recently published observations in tuberculosis, which have been linked to seasonal variation in vitamin D. Our finding that anti-mycobacterial combination therapy was associated with a reduced risk of recurrences in patients with NTM lymphadenitis or SSTI requires further confirmation in prospective trials.
Helicobacter pylori Seropositivity and Risk of Lung Cancer

Lung cancer is the leading cause of cancer mortality worldwide. Helicobacter pylori (H. pylori) is a risk factor for distal stomach cancer, and a few small studies have suggested that H. pylori may be a potential risk factor for lung cancer. To test this hypothesis, we conducted a study of 350 lung adenocarcinoma cases, 350 squamous cell carcinoma cases, and 700 controls nested within the Alpha-Tocopherol, Beta-Carotene Cancer Prevention Study (ATBC) cohort of male Finnish smokers. Controls were one-to-one matched by age and date of baseline serum draw. Using enzyme-linked immunosorbent assays to detect immunoglobulin G antibodies against H. pylori whole-cell and cytotoxin-associated gene (CagA) antigens, we calculated odds ratios (ORs) and 95% confidence intervals (95% CIs) for associations between H. pylori seropositivity and lung cancer risk using conditional logistic regression. H. pylori seropositivity was detected in 79.7% of cases and 78.5% of controls. After adjusting for pack-years and cigarettes smoked per day, H. pylori seropositivity was not associated with either adenocarcinoma (OR: 1.1, 95% CI: 0.75–1.6) or squamous cell carcinoma (OR: 1.1, 95% CI: 0.77–1.7). Results were similar for CagA-negative and CagA-positive H. pylori seropositivity. Despite earlier small studies suggesting that H. pylori may contribute to lung carcinogenesis, H. pylori seropositivity does not appear to be associated with lung cancer.
Cells with haematopoietic stem cell phenotype in adult human endometrium: relevance to infertility?

BACKGROUND Uterine lymphoid cell repertoires are specialized in order to meet the twin demands of successful pregnancy and local immunosurveillance. The possibility that some of these populations might differentiate locally from progenitor cells has been proposed. METHODS Endometrial tissue from women with a history of infertility as well as fertile controls was examined for haematopoietic stem cells (HSCs) and lymphoid progenitors using three-colour flow cytometry. RESULTS Significant populations of phenotypic HSCs (CD34+ CD45+ ) were detected in all samples, a high proportion of which co-expressed the differentiation marker CD45RA (45.7%), indicating ongoing differentiation. Almost 30% of uterine HSCs co-expressed CD56 and 44% co-expressed CD7, suggesting the presence of lymphoid progenitors. Small proportions expressed CD127 and CD122, receptors for interleukin (IL)-7 and IL-15, respectively. HSC numbers were similar in the endometrial samples from fertile and infertile women. However, the proportion co-expressing the natural killer (NK) antigen CD56 was significantly increased compared with HSCs found in the endometrium of fertile controls (P = 0.002). CONCLUSIONS This is the first demonstration of cells with an HSC phenotype in the human endometrium, and increased proportions of NK progenitors in endometrium of women with infertility suggests a dysregulation of this pathway that may contribute to infertility.
Reduce memory requirements by handling efficient move only in haar transform

With the increasing growth of technology and the entrance into the digital age, we have to handle a vast amount of information every time which often presents difficulties. So, the digital information must be stored and retrieved in an efficient and effective manner, in order for it to be put to practical use. Wavelet Transform has been proved to be a very useful tool for image processing in recent years. Wavelets are mathematical tools for hierarchically decomposing functions. Wavelets provide a mathematical way of encoding information in such a way that it is layered according to level of detail. This layering facilitates approximations at various intermediate stages. These approximations can be stored using a lot less space than the original data. The most distinctive feature of Haar Wavelet Transform lies in the fact that it lends itself easily to simple manual calculations. The present paper attempts to reduce memory requirements by handling efficient move only in Haar Wavelet transform. The algorithm or procedure proposed allows certain calculation in the process decomposition be ignored without affecting the results.
ANALISIS PENGARUH CASH RATIO, DEBT TO EQUITY RATIO, RETURN ON ASSEST, DAN FIRM SIZE TERHADAP DIVIDEND PAYOUT RATIO PADA PERUSAHAAN MANUFAKTUR YANG TERDAFTAR DI BEI PERIODE 2009-2011

Perkembangan pasar modal yang dikaitkan dengan pengaruh global, dan kondisi perekonomian Indonesia saat ini, serta tantangan yang di hadapi semakin berat dan prospek perusahaan yang semakin tidak jelas, secara langsung mempengaruhi perilaku pemodal dan kinerja emiten. Sehingga memberikan batas yang semakin sempit bagi peningkatan penanaman modal pada perusahaan yang terdaftar di Bursa Efek Indonesia (BEI). Penanaman modal perusahaan sebagai komoditas investasi yang tergolong beresiko tinggi karena sifat komoditasnya yang sangat peka terhadap perubahan-perubahan yang terjadi baik diluar maupun didalam negeri. Perubahan kondisi dibidang perekonomian, politik, moneter, maupun perubahan yang terjadi dalam perusahaan itu sendiri dapat berdampak positif dan dapat pula berdampak negatif. Tujuan dari penelitian ini adalah: (1) Untuk menganalisis Cash Ratio, Debt to Equity Ratio (DER), Returnon Assets (ROA), dan Firm Size berpengaruh bersama-samaterhadap Dividend Payout Ratio (DPR) pada perusahaan manufaktur yang listed di BEI pada periode 2009-2011. (2) Untuk menganalisis Cash Ratio, Debt to Equity Ratio (DER), Return on Assets (ROA), dan Firm Size berpengaruh secara parsialterhadap Dividend Payout Ratio (DPR) pada perusahaan manufaktur yang listed di BEI pada periode 2009-2011. Penelitian ini dilakukan pada perusahaan manufaktur yang terdaftar di BEI periode 2009-2011. Data yang digunakan dalam penelitian ini adalah data sekunder, metodeanalisis data yang digunakan adalah analisis regrasi berganda. Hasil analisis data diketahui bahwa Cash Ratio, Debt to Equity Ratio (DER), Return On Asset (ROA) dan Firm Zize secara bersama-sama berpengaruh terhadap Dividend Payout Ratio (DPR). Secara parsial variabel Cash Ratio, Debt to Equity Ratio (DER), Return On Asset (ROA) dan Firm Zize berpengaruh positif dan signifikan terhadap variabel Dividend Payout Ratio (DPR). Kata kunci: Cash Ratio, Debt To Equity Ratio, Return On As Set, Firm Size, Dividend Payout Ratio, dan Perusahaan Manufaktur.
Carbon acquisition of bloom‐forming marine phytoplankton

Carbon acquisition in relation to CO2 supply was investigated in three marine bloom‐forming microalgae, the diatom Skeletonema costatum, the flagellate Phaeocystis globosa, and the coccolithophorid Emiliania huxleyi. In vivo activities of extracellular (eCA) and intracellular (iCA) carbonic anhydrase activity, photosynthetic O2 evolution, CO2 and HCO3− uptake rates were measured by membrane inlet mass spectrometry in cells acclimated to pCO2 levels of 36, 180, 360, and 1,800 ppmv. Large differences were obtained between species both with regard to the efficiency and regulation of carbon acquisition. While eCA activity increased with decreasing CO2 concentration in S. costatum and P. globosa, consistently low values were obtained for E. huxleyi. No clear trends with pCO2 were observed in iCA activity for any of the species tested. Half saturation concentrations (K1/2) for photosynthetic O2 evolution, which were highest for E. huxleyi and lowest for S. costatum, generally decreased with decreasing CO2 concentration. In contrast, K1/2 values for P. globosa remained unaffected by pCO2 of the incubation. CO2 and HCO3− were taken up simultaneously by all species. The relative contribution of HCO3− to total carbon uptake generally increased with decreasing CO2, yet strongly differed between species. Whereas K1/2 for CO2 and HCO3− uptake was lowest at the lowest pCO2 for S. costatum and E. huxleyi, it did not change as a function of pCO2 in P. globosa. The observed taxon‐specific differences in CO2 sensitivity, if representative for the natural environment, suggest that changes in CO2 availability may influence phytoplankton species succession and distribution. By modifying the relative contribution of different functional groups, e.g., diatomaceous versus calcareous phytoplankton, to the overall primary production this could potentially affect marine biogeochemical cycling and air—sea gas exchange.