Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling Gene Regulatory Subnetworks from Time Course Gene Expression Data

Identifying gene regulatory network (GRN) from time course gene expression data has attracted more and more attentions. Due to the computational complexity, most approaches for GRN econstruction are limited on a small number of genes and low connectivity of the underlying networks. These approaches can only identify a single network for a given set of genes. However, for a large-scale gene network, there might exist multiple potential sub-networks, in which genes are only functionally related to thers in the sub-networks. In this paper, we propose an efficient algorithm for identifying multiple sub-networks from gene expression data by incorporating community structure information into GRN inference. The proposed algorithm iteratively solves two optimization problems, and thus promisingly applies to large-scale GRNs. Experimental studies on synthetic datasets validate the effectiveness of the proposed algorithm in the inference of sub-networks.
'Bridging worlds': meeting the emotional needs of dying patients.

AIM This paper is a report of a study to develop a grounded theory to explain how district nurses meet the emotional needs of dying patients in the community. BACKGROUND There has been a policy commitment internationally to improve community services and enable people with terminal illnesses to die in their own homes. This increasing trend towards home deaths in the United Kingdom (UK) makes more demand on district nurses to provide emotional support for dying patients. METHODS A 'classic' grounded theory study was conducted in the UK between 2002 and 2005. Unstructured observations and semi-structured interviews were conducted with a purposive sample of nine district nurses, nine patients and four family carers. A further theoretical sample of five books of authors' accounts of their dying experiences and three district nurses who were advanced practitioners were selected. FINDINGS Five categories were identified in the data: 'outside world', 'dying world', 'entering dying world', 'maintaining connections' and the core category 'bridging worlds'. The theory of 'bridging worlds' indicated that dying patients experienced 'dying world' and 'outside world'. District nurses met dying patients' emotional needs by acting as a bridge between their two worlds, encouraging them to maintain connections with the outside world so that they did not become isolated in their dying world. CONCLUSION District nurses should ensure that they meet both the physical and emotional needs of dying patients. Nursing education and literature need to concentrate on raising awareness of nurses' role in providing emotional support.
Impacts and Risks to Public Health and Welfare : Human Health and Air Quality

Copies of all comment letters submitted and transcripts of the public hearings are available at the EPA Docket Center Public Reading Room, or electronically through http://www.regulations. gov by searching Docket ID EPA-HQ-OAR-2009-0171. This document accompanies the Administrator's final Endangerment and Cause or Contribute Findings for Greenhouse Gases Under Section 202(a) of the Clean Air Act (Findings) and the Technical Support Document (TSD), which contains the underlying science and greenhouse gas emissions data. EPA prepared this document in multiple volumes, with each volume focusing on a different broad category of comments on the Proposed Findings. This volume of the document provides responses to public comments regarding human health and air quality. In light of the very large number of comments received and the significant overlap between many comments, this document does not respond to each comment individually. Rather, EPA summarized and provided a single response to each significant argument, assertion, and question contained within the totality of comments. Within each comment summary, EPA provides in parentheses one or more lists of Docket ID numbers for commenters who raised particular issues; however, these lists are not meant to be exhaustive and EPA does not individually identify each and every commenter who made a certain point in all instances, particularly in cases where multiple commenters expressed essentially identical arguments. Several commenters provided additional scientific literature to support their arguments. EPA's general approach for taking such literature into consideration is described in Volume 1, Section 1.1, of this Response to Comments document. As with the comments, there was overlap in the literature received. EPA identified the relevant literature related to the significant comments, and responded to the significant issues raised in the literature. EPA does not individually identify each and every piece of literature (submitted or incorporated by reference) that made a certain point in all instances. Throughout this document, we provide a list of references at the end of each volume for additional literature cited by EPA in our responses; however, we do not repeat the full citations of literature cited in the TSD. EPA's responses to comments are generally provided immediately following each comment summary. In some cases, EPA has discussed responses to specific comments or groups of similar comments in the Findings. In such cases, EPA references the Findings rather than repeating those responses in this document. Comments were assigned to specific volumes of this Response to Comments document based on an …
Synergy and Mode of Action of Ceftazidime plus Quercetin or Luteolin on Streptococcus pyogenes

Streptococcus pyogenes causes streptococcal toxic shock syndrome. The recommended therapy has been often failure through the interfering of beta-lactamase-producing bacteria (BLPB). The present study was to investigate antibacterial activity, synergy, and modes of action of luteolin and quercetin using alone and plus ceftazidime against S. pyogenes. The MICs of ceftazidime, luteolin, and quercetin against all S. pyogenes were 0.50, 128, and 128 µg mL−1, respectively. A synergistic effect was exhibited on luteolin and quercetin plus ceftazidime against these strains at fractional inhibitory concentration indices 0.37 and 0.27, respectively, and was confirmed by the viable count. These combinations increased cytoplasmic membrane (CM) permeability, caused irregular cell shape, peptidoglycan, and CM damage, and decreased nucleic acid but increased proteins in bacterial cells. Enzyme assay demonstrated that these flavonoids had an inhibitory activity against β-lactamase. In summary, this study provides evidence that the inhibitory mode of action of luteolin and quercetin may be mediated via three mechanisms: (1) inhibiting of peptidoglycan synthesis, (2) increasing CM permeability, and (3) decreasing nucleic acid but increasing the protein contents of bacterial cells. So, luteolin and quercetin propose the high potential to develop adjunct to ceftazidime for the treatment of coexistence of the BLPB and S. pyogenes infections.
The role of sanctions in Australia's residential aged care quality assurance system.

OBJECTIVE To assess the role of sanctions as the highest level of enforcement in Australia's residential aged care quality assurance (QA) system. DESIGN ANALYSIS of secondary data on accreditation activities and outcomes from 1999-2000 to 2007-08, extracted from the Annual Report on the Aged Care Act 1997. SETTING A total of 138 sanctioned homes among all aged care homes in Australia (n = 2830 in 2007-08). MAIN OUTCOME MEASURES Chi-square test of differences between sanctioned and non-sanctioned homes, and z scores to identify variables underlying differences. RESULTS Sanctions are a rare event as more frequent enforcement actions at lower levels of regulatory action mean that a diminishing number of homes are subject to higher levels of action. Relationships between the risk of sanctions and characteristics of homes (state, size, sector and level of care) were evident. Sanctions provide only limited signals on quality to potential users and do not reflect the full scope of the QA process and the range of quality of care found. CONCLUSIONS The effectiveness of sanctions in contributing to quality improvement has to be seen within the wider regulatory framework, which in turn has to be set in the context of other factors driving quality of care. Quality improvement in Australia and elsewhere will depend on further development of QA systems but will also require attention to wider contextual factors that contribute to quality outcomes, including quality of the aged care workforce.
The Effect of Extrusion Conditions on Water-extractable Arabinoxylans from Corn Fiber

The effect of feed moisture contents (30%, 40%, and 50%) and screw speed (200 rpm, 250 rpm, and 300 rpm) on the corn fiber gum (CFG) yield and soluble arabinoxylans (SAX) content of destarched corn fiber was investigated. The CFG yields and SAX contents of extruded, destarched corn fiber were higher than that of destarched corn fiber. In extruded, destarched corn fiber, increased screw speed and decreased feed moisture contents resulted in a higher SAX contents. The maximum yields of CFG obtained from extruded, destarched corn fiber were 79.1±19.0 g/kg (30% feed moisture content) and 82.3±11.30 g/kg (300 rpm screw speed). The highest SAX content was also observed at a screw speed of 300 rpm. The results of the present study show that water extraction and extrusion combined have the potential to increase CFG and SAX yields from corn fiber.
Collaborative investigation of variables in susceptibility testing of yeasts

A multicenter study was performed to evaluate the effect of medium, incubation time (24 and 48 h), and temperature (30 and 35 degrees C) on intra- and interlaboratory variations in MICs of flucytosine, amphotericin B, and ketoconazole for yeasts. Testing was performed on coded isolates of Candida species (11 strains) and Cryptococcus neoformans (2 strains) by using a standard macrodilution protocol 11 laboratories. Four chemically defined media buffered to pH 7.0 with morpholinepropanesulfonic acid were evaluated, including buffered yeast nitrogen base, synthetic amino acid medium-fungal, RPMI 1640 medium, and high-resolution antifungal assay medium. Intralaboratory variability was less than or equal to fourfold for 97% of the replicate sets of data. The highest level of interlaboratory agreement, irrespective of antifungal agent or incubation conditions, was observed with RPMI 1640 medium. Intralaboratory variability was less than or equal to fourfold for 93% of the determinations with ketoconazole and 100% with flucytosine tested in RPMI 1640 medium at 35 degrees C for 24 h. Variability in amphotericin B results was less than or equal to fourfold for 81% of the determinations in RPMI 1640 medium at 35 degrees C for 48 h. The rank order of MICs within each antifungal test group was similar among the various laboratories and was generally in agreement with the reference rank order regardless of the test medium that we used.
Endothelial precursors and mature endothelial cells are increased in the peripheral blood of myelodysplastic syndromes

Increased angiogenesis has been demonstrated to be a significant prognostic factor in many solid tumors. In the oncohematological setting, it has been associated with myelodysplastic syndromes (MDS), chronic myeloid leukemia, acute lymphoid, and myeloid leukemias. Recently, increased circulating endothelial cells (CECs) have been associated with breast cancer and non-Hodgkin lymphoma (NHL). Based on these premises we analysed total and activated CECs, and endothelial precursors (CEPs) in 50 MDS patients and 20 healthy donors. CECs and CEPs were quantified by flow cytometry. CEC levels were compared with bone marrow (BM) microvessel density (MVD). In addition, some angiogenic factors, namely vascular endothelial growth factor (VEGF), basic fibroblast growth factor (bFGF) and soluble VEGF-Receptor2 (VEGFR2), were tested in the sera from 25 MDS patients. Total, activated CECs and CEPs were significantly increased in MDS when compared to control group (p<0.0001); whereas in the MDS cases no association was found with French--American--British (FAB), International Prognostic Scoring System (IPSS) subtypes or survival. Patients with higher CECs also showed higher MVD. Among the cytokines analysed, sVEGFR2 was significantly higher in the lower IPSS risk classes, while the levels of bFGF directly correlated with total and activated CECs. Taken together these data strengthen the hypothesis of a possible role of angiogenesis in MDS pathogenesis.
Microdissection and Chromosome Painting of the Alien Chromosome in an Addition Line of Wheat - Thinopyrum intermedium

In this study, chromosome painting was developed and used to identify alien chromosomes in TAi-27, a wheat - Thinopyrum intermedium addition line, and the chromosomes of the three different genomes of Th. Intermedium. The smallest alien chromosome of TAi-27 was microdissected and its DNA amplified by DOP-PCR was used as a probe to hybridize with metaphase chromosomes of TAi-27 and Th . intermedium . Results showed that hybridization signals were observed in all regions of a pair of the smallest alien chromosomes and the pericentromeric area of another pair of alien chromosomes in TAi-27, indicating that the probe from microdissected chromosome is species specific. In Th . intermedium , 14 chromosomes had wide and strong hybridization signals distributed mainly on the pericentromere area and 9 chromosomes with narrow and weak signals on the pericentromere area. The remaining chromosomes displayed a very weak or no signal. Sequential FISH/GISH on Th . intermedium chromosomes using the DNAs of microdissected chromosome, Pseudoroegneria spicata (St genome) and pDbH12 (a Js genome specific probe) as the probes indicated that the microdissected chromosome belonged to the St genome, three genomes (Js, J and St) in Th . intermedium could be distinguished, in which there is no hybridization signal on J genome that is similar to the genome of Th . bessarabicum . Our results showed that the smallest alien chromosomes may represent a truncated chromosome and the repetitive sequence distribution might be similar in different chromosomes within the St genome. However, the repetitive sequence distributions are different within the Js genome, within a single chromosome, and among different genomes in Th . intermedium . Our results suggested that chromosome painting could be feasible in some plants and useful in detecting chromosome variation and repetitive sequence distribution in different genomes of polyploidy plants, which is helpful for understanding the evolution of different genomes in polyploid plants.
A Unified Framework for Linear-Programming Based Communication Receivers

It is shown that a large class of communication systems which admit a sum-product algorithm (SPA) based receiver also admit a corresponding linear-programming (LP) based receiver. The two receivers have a relationship defined by the local structure of the underlying graphical model, and are inhibited by the same phenomenon, which we call pseudoconfigurations. This concept is a generalization of the concept of pseudocodewords for linear codes. It is proved that the LP receiver has the `maximum likelihood certificate' property, and that the receiver output is the lowest cost pseudoconfiguration. Equivalence of graph-cover pseudoconfigurations and linear-programming pseudoconfigurations is also proved. A concept of system pseudodistance is defined which generalizes the existing concept of pseudodistance for binary and nonbinary linear codes. It is demonstrated how the LP design technique may be applied to the problem of joint equalization and decoding of coded transmissions over a frequency selective channel, and a simulation-based analysis of the error events of the resulting LP receiver is also provided. For this particular application, the proposed LP receiver is shown to be competitive with other receivers, and to be capable of outperforming turbo equalization in bit and frame error rate performance.
Contemporary therapy of acute ST-elevation myocardial infarction.

Address for reprints: Paul W. Armstrong, MD, Department of Medicine, Division of Cardiology, 2-51 Medical Sciences Building, University of Alberta, Edmonton, Alberta T6G 2H7, Canada. E-mail: ac.atreblau@gnortsmra.luap Disclosures: Dr. Armstrong had research grants from Hoffmann LaRoche Canada, Sanofi-Aventis, Boehringer Ingelheim, Eli Lilly, and Portola Pharmaceuticals, and he has received honoraria from Sanofi-Aventis.
Health Insurance and Job Mobility: Evidence from Clinton's Second Mandate

In this paper we analyse data from the 1996 panel of the Survey of Income and Program Participation to investigate the effect of employer-provided health insurance (EPHI) on job mobility from 1996 to 2000. First, we estimate the effect of EPHI on four month job turnover. It is found that, after accounting for unobserved individual heterogeneity, holding EPHI induces substantial mobility reductions for all demographic groups, ranging from 31\% to 58\%. Second, we evaluate whether the 1996 Health Insurance Portability and Accountability Act succeeded in mitigating insurance induced mobility reductions and we find that it did not.
PM and hybrid excitation synchronous machines: Performances comparison

In this paper, a new topology of hybrid excitation synchronous machine (HESM) is presented. This kind of machine is well suited for hybrid vehicle applications. First of all, a summary description of the HESM is presented. A simplified analytic study based on reluctant network is presented. It is validated by finite element analysis and experimental measurements. The mechanical performances of the presented HESM are compared to a conventional permanent magnet synchronous machine (PMSM) designed for the same application.
Do neurobiological data help us to understand economic decisions better?

The contribution that neurobiological data provide us to comprehend the psychological aspects of economic decision-making is critically examined. First, different kinds of correspondences between neural events and mental activities are identified. On the basis of the distinctions made, some recent studies are selected, each of which focuses on a different stage of decision-making and employs a different set of neurobiological data. The thorough analysis of each study suggests that neuro-mental correspondences do not have an evidentiary function but rather a heuristic function, since they can point to the presence of specific differences between phenomena considered homogeneous or to the existence of a relationship between two mental activities which, however, have to be tested by psychological investigations.
IS STOCK PICKING DECLINING AROUND THE WORLD ? *

We do three things in this paper. We first develop a metric to measure the maximum fraction of volume explained by stock picking in a market. We then use our metric to measure stock picking around the world. We find that though there is more stock picking in emerging markets than in developed countries, it is declining everywhere. In the United States, for example, stock picking has secularly declined from a high of 60% in the 1960s to a low of 24% in the 2000s. Finally, as markets cannot be efficient if everyone believes that they are efficient and, therefore, do no stock picking – the Grossman and Stiglitz (1980) paradox – we ask what is the long-run steady state fraction of stock pickers? We develop a simple theoretical model, and calibrate this model to the United States economy to conclude that stock picking will eventually settle at 11% of trading volume in the United States.
Prevalent and Incident Bacterial Vaginosis Are Associated with Sexual and Contraceptive Behaviours in Young Australian Women

Background To determine prevalence and incidence of bacterial vaginosis (BV) and risk factors in young sexually-active Australian women. Methods 1093 women aged 16–25 years were recruited from primary-care clinics. Participants completed 3-monthly questionnaires and self-collected vaginal smears 6-monthly for 12-months. The primary endpoint was a Nugent Score = 7–10 (BV) and the secondary endpoint was a NS = 4–10 (abnormal flora [AF]). BV and AF prevalence estimates and 95% confidence intervals (95%CI) were derived, and adjusted odds ratios (AOR) calculated to explore epidemiological associations with prevalent BV and AF. Proportional-hazards regression models were used to examine factors associated with incident BV and AF. Results At baseline 129 women had BV [11.8% (95%CI: 9.4–14.2)] and 188 AF (17.2%; 15.1–19.5). Prevalent BV was associated with having a recent female partner [AOR = 2.1; 1.0–4.4] and lack of tertiary-education [AOR = 1.9; 1.2–3.0]; use of an oestrogen-containing contraceptive (OCC) was associated with reduced risk [AOR = 0.6; 0.4–0.9]. Prevalent AF was associated with the same factors, and additionally with >5 male partners (MSP) in 12-months [AOR = 1.8; 1.2–2.5)], and detection of C.trachomatis or M.genitalium [AOR = 2.1; 1.0–4.5]. There were 82 cases of incident BV (9.4%;7.7–11.7/100 person-years) and 129 with incident AF (14.8%; 12.5–17.6/100 person-years). Incident BV and AF were associated with a new MSP [adjusted rate ratio (ARR) = 1.5; 1.1–2.2 and ARR = 1.5; 1.1–2.0], respectively. OCC-use was associated with reduced risk of incident AF [ARR = 0.7; 0.5–1.0]. Conclusion This paper presents BV and AF prevalence and incidence estimates from a large prospective cohort of young Australian women predominantly recruited from primary-care clinics. These data support the concept that sexual activity is strongly associated with the development of BV and AF and that use of an OCC is associated with reduced risk.