Miracle-dz/UniFAR-FTUs huggingface dataset:
The Mobilome; A Major Contributor to Escherichia coli stx2-Positive O26:H11 Strains Intra-Serotype Diversity

Shiga toxin-producing Escherichia coli of serotype O26:H11/H- constitute a diverse group of strains and several clones with distinct genetic characteristics have been identified and characterized. Whole genome sequencing was performed using Illumina and PacBio technologies on eight stx2-positive O26:H11 strains circulating in France. Comparative analyses of the whole genome of the stx2-positive O26:H11 strains indicate that several clones of EHEC O26:H11 are co-circulating in France. Phylogenetic analysis of the French strains together with stx2-positive and stx-negative E. coli O26:H11 genomes obtained from Genbank indicates the existence of four clonal complexes (SNP-CCs) separated in two distinct lineages, one of which comprises the “new French clone” (SNP-CC1) that appears genetically closely related to stx-negative attaching and effacing E. coli (AEEC) strains. Interestingly, the whole genome SNP (wgSNP) phylogeny is summarized in the cas gene phylogeny, and a simple qPCR assay targeting the CRISPR array specific to SNP-CC1 (SP_O26-E) can distinguish between the two main lineages. The PacBio sequencing allowed a detailed analysis of the mobile genetic elements (MGEs) of the strains. Numerous MGEs were identified in each strain, including a large number of prophages and up to four large plasmids, representing overall 8.7–19.8% of the total genome size. Analysis of the prophage pool of the strains shows a considerable diversity with a complex history of recombination. Each clonal complex (SNP-CC) is characterized by a unique set of plasmids and phages, including stx-prophages, suggesting evolution through separate acquisition events. Overall, the MGEs appear to play a major role in O26:H11 intra-serotype clonal diversification.
The expression of decorin in human ovarian tumors.

PURPOSE The purpose of this study was to examine ovarian cancer cells for the expression of decorin, a proteoglycan component of the cell matrix that can inhibit cancer cell growth. EXPERIMENTAL DESIGN Cultured ovarian cancer cells and surgically excised tumors were examined by immunohistochemistry and Western blot analysis for decorin expression. Reverse transcription-polymerase chain reaction analysis was used to analyze cultured cells for decorin transcripts. RESULTS We detected decorin transcripts in two ovarian cancer cell lines by reverse transcription-polymerase chain reaction analysis. However, no decorin was found in conditioned culture medium from those cell lines. Cells treated with the proteasome inhibitor MG132 showed strong perinuclear staining with a decorin-specific monoclonal antibody by immunohistochemistry. Also, Western blot analysis showed the presence of a ladder of decorin-specific bands that were intensified by treatment with MG132, suggesting that de novo synthesized decorin was degraded by the ubiquitination pathway. The decorin component of tumor stroma was previously shown to contain high levels of chondroitin sulfate as opposed to dermatan sulfate side chains, and those molecules contained unusually high levels of O- and 6-sulfate linkages. We provided immunohistochemical evidence that these chondroitin sulfate side chains may have been produced by myofibroblasts. CONCLUSIONS Decorin protein expression was not detected in ovarian cancer cells. Decorin transcripts were produced and probably translated, but the protein was probably degraded by the ubiquitination pathway. We present evidence that stromal decorin of ovarian tumors was made by myofibroblasts. We also propose that decorin may be a tumor suppressor gene that is inactivated during epithelial cell development.
Pathogenesis of Bolivian Hemorrhagic Fever in Guinea Pigs

Machupo virus, the cause of Bolivian hemorrhagic fever, is a highly lethal viral hemorrhagic fever with no Food and Drug Administration–approved vaccines or therapeutics. This study evaluated the guinea pig as a model using the Machupo virus–Chicava strain administered via aerosol challenge. Guinea pigs (Cavia porcellus) were serially sampled to evaluate the temporal progression of infection, gross and histologic lesions, and sequential changes in serum chemistry and hematology. The incubation period was 5 to 12 days, and complete blood counts revealed leukopenia with lymphopenia and thrombocytopenia. Gross pathologic findings included congestion and hemorrhage of the gastrointestinal mucosa and serosa, noncollapsing lungs with fluid exudation, enlarged lymph nodes, and progressive pallor and friability of the liver. Histologic lesions consisted of foci of degeneration and cell death in the haired skin, liver, pancreas, adrenal glands, lymph nodes, tongue, esophagus, salivary glands, renal pelvis, small intestine, and large intestine. Lymphohistiocytic interstitial pneumonia was also present. Inflammation within the central nervous system, interpreted as nonsuppurative encephalitis, was histologically apparent approximately 16 days postexposure and was generally progressive. Macrophages in the tracheobronchial lymph node, on day 5 postexposure, were the first cells to demonstrate visible viral antigen. Viral antigen was detected throughout the lymphoid system by day 9 postexposure, followed by prominent spread within epithelial tissues and then brain. This study provides insight into the course of Machupo virus infection and supports the utility of guinea pigs as an additional animal model for vaccine and therapeutic development.
Chapter 3 Ethanol Production and its Co-Products Front-End Fractionation and Back-End Oil Extraction Technologies

Although the majority of corn co-products produced by the dry-grind ethanol industry are dried distiller’s grains with solubles, limited quantities of new corn co-products are being produced, most notably high-protein DDG. Interest by the U.S. ethanol industry in implementing front-end fractionation technologies has decreased dramatically from a few years ago, and this can be attributed to the high capital investment required and disappointing improvements in ethanol production efficiency. There are several reasons why fractionation technologies were being considered a few years ago in the U.S. ethanol industry. Some of these reasons include increased ethanol yield, less enzyme use during fermentation, lower production of co-product mass that requires drying, reduced drying costs and heat damage to proteins in co-products, less energy and water use, reduced need for frequent cleaning of the system to remove oil, ability to market or use the corn oil for other high value applications, and increased number of fractionated co-products to potentially add value and create new markets for corn co-products. Unfortunately, many of these potential advantages were never realized.
Analysis of singing voice for epoch extraction using Zero Frequency Filtering method

Epoch is the instant of significant excitation of the vocal tract system during the production of voiced speech. Estimation of epochs or Glottal closure instants (GCIs) is a well studied topic in the speech analysis. From the recent studies on GCI detection from singing voice with state-of-art methods proposed for speech, there exist a clear gap in accuracy between speech and singing voice. This is because of source-filter interaction in singing voice compared to speech. Performance of existing algorithms deteriorates as most of the techniques depends on the ability to model the vocal tract system in order to emphasize the excitation characteristics in the residual. The objective of this paper is to analyze the singing voice for the estimation of epochs by studying the characteristics of the source-filter interaction and the effect of wider range of pitch using the Zero Frequency Filtering (ZFF) method. It is observed that high source-filter interaction can be captured in the form of the impulse-like excitation by passing the signal through three ideal digital resonators having poles at zero frequency, and the effect of wider range of pitch can be controlled by processing short segment (0.4-0.5 sec) signal.
Cortisol, Chromogranin A, and Pupillary Responses Evoked by Speech Recognition Tasks in Normally Hearing and Hard-of-Hearing Listeners: A Pilot Study

Pupillometry is one method that has been used to measure processing load expended during speech understanding. Notably, speech perception (in noise) tasks can evoke a pupil response. It is not known if there is concurrent activation of the sympathetic nervous system as indexed by salivary cortisol and chromogranin A (CgA) and whether such activation differs between normally hearing (NH) and hard-of-hearing (HH) adults. Ten NH and 10 adults with mild-to-moderate hearing loss (mean age 52 years) participated. Two speech perception tests were administered in random order: one in quiet targeting 100% correct performance and one in noise targeting 50% correct performance. Pupil responses and salivary samples for cortisol and CgA analyses were collected four times: before testing, after the two speech perception tests, and at the end of the session. Participants rated their perceived accuracy, effort, and motivation. Effects were examined using repeated-measures analyses of variance. Correlations between outcomes were calculated. HH listeners had smaller peak pupil dilations (PPDs) than NH listeners in the speech in noise condition only. No group or condition effects were observed for the cortisol data, but HH listeners tended to have higher cortisol levels across conditions. CgA levels were larger at the pretesting time than at the three other test times. Hearing impairment did not affect CgA. Self-rated motivation correlated most often with cortisol or PPD values. The three physiological indicators of cognitive load and stress (PPD, cortisol, and CgA) are not equally affected by speech testing or hearing impairment. Each of them seem to capture a different dimension of sympathetic nervous system activity.
The cultural politics of queer theory in education research

This special issue was born from the idea that there are certain habits of thought and boundaries drawn around the use and perceived place of queer theory in education research. Our intention in this special issue is to disrupt these habits of thinking by opening up dialogue about (1) the objects and subjects of queer research; (2) the forms of politics incited by the use of queer theory in education; and (3), the methodological approaches used by scholars when queer(y)ing/queering. As editors, we invited contributions from those who found queer theory problematic, and/or past its use-by date, as well as from those who continue to see a productive place for queer research in education, however that may be defined. The first paper in this issue is an interview we conducted with Raewyn Connell, a recipient of the American Sociological Association’s award for her distinguished contribution to the study of sex and gender. She is also on record as being a critic of queer politics and theory. For instance, in the article entitled Kartini’s Children (2010), she writes:
EFFECTS OF TEXTUAL ENHANCEMENT AND TOPIC FAMILIARITY ON KOREAN EFL STUDENTS READING COMPREHENSION AND LEARNING OF PASSIVE FORM

This quasi-experimental study attempts to incorporate grammatical elements into meaning-focused reading classes by attracting learner attention to form with minimal interruption to meaning comprehension. Two hundred fifty-nine Korean English as a foreign language students underwent four different treatments—involving textual enhancement and topic familiarity conditions. The responses of the students were compared with respect to (a) their ability to identify and correct English passive errors and (b) their degree of reading comprehension. The results revealed that textual enhancement aided the learning of the target forms while having unfavorable effects on meaning comprehension. Topic familiarity, by contrast, aided the students' comprehension but was ineffective in terms of their learning of form. I discuss the findings in light of the theoretical relationship between acquisition and comprehension and conclude with implications for meaning-oriented lessons.
Transplanting kidneys from CMV-seropositive donors to CMV-seronegative recipients is not associated with poorer renal allograft function or survival.

BACKGROUND Cytomegalovirus (CMV)-seronegative recipients of renal allografts from CMV-seropositive donors (D+/R-) have a higher rate of acute rejection than other renal transplant recipients. A relationship between CMV infection/disease and chronic allograft nephropathy (CAN) has been proposed from animal studies, although human studies have been inconclusive. The objective of this study was to determine if CMV seromatching has an effect on renal allograft function and allograft survival. METHODS A retrospective single centre study was carried out in 333 first cadaveric transplant recipients from January 1, 1991 to December 31, 1997. The primary end-point was creatinine clearance at 3 years post-transplant in groups based on CMV seromatching. The secondary end-point was renal allograft survival. RESULTS Mean creatinine clearance 3 years post-transplant was 53.4 ml/min/1.73 m2 of body surface area. There was no significant difference in the mean creatinine clearance for groups formed on the basis of CMV seromatching. Delayed graft function and acute rejection were associated with a lower creatinine clearance at 3 years and reduced overall graft survival [hazard ratios 2.35 (1.56-3.54) (P<0.001) and 1.57 (1.0-2.46) (P = 0.046), respectively]. Considering the end-point of graft loss due to acute rejection (censoring for death with a functioning graft) identified the D+/R- group as having an increased hazard of graft loss due to acute rejection [hazard ratio 3.12 (1.16-8.57) (P = 0.024)]. CONCLUSIONS The D+/R- group does not appear to have poorer renal allograft function 3 years post-transplant. This group does, however, have an increased risk of early allograft loss due to acute rejection.
The Multidimensional View of Commitment and the Theory of Reasoned Action: A Comparative Evaluation

This study examined the relative ability of the multidimensional view of commitment and the theory of reasoned action to explain employee intentions and predict work behavior. Variables within the theory of reasoned action were superior to commitment in explaining employee intentions to be punctual and to engage in altruistic acts. However, the theory of reasoned action did not explain unique variance in either volitional behavior (altruism) or in less volitional behavior (tardiness). Finally, foci and bases of employee commitment accounted for significant variance in both altruism and tardiness, and explained variance in both behaviors over and above variables contained within the theory of reasoned action. Implications of these findings for the usefulness of the approaches are discussed.
Hematopoietic Stem-Cell Transplantation in the Developing World: Experience from a Center in Western India

We describe our experience of first 50 consecutive hematopoietic stem-cell transplants (HSCT) done between 2007 and 2012 at the Apollo Hospital, Gandhinagar, 35 autologous HSCT and 15 allogeneic HSCT. Indications for autologous transplant were multiple myeloma, non-Hodgkin lymphoma, Hodgkin lymphoma, and acute myeloid leukemia, and indications for allogeneic transplants were thalassemia major, aplastic anaemia, chronic myeloid leukemia, and acute lymphoblastic and myeloid leukaemia. The median age of autologous and allogeneic patient's cohort was 50 years and 21 years, respectively. Median follow-up period for all patients was 39 months. Major early complications were infections, mucositis, acute graft versus host disease, and venoocclusive disease. All of our allogeneic and autologous transplant patients survived during the first month of transplant. Transplant related mortality (TRM) was 20% (N = 3) in our allogeneic and 3% (N = 1) in autologous patients. Causes of these deaths were disease relapse, sepsis, hemorrhagic complications, and GVHD. 46% of our autologous and 47% of our allogeneic patients are in complete remission phase after a median follow-up of 39 months. 34% of our autologous patients and 13% of our allogeneic patients had disease relapse. Overall survival rate in our autologous and allogeneic patients is 65.7% and 57.1%, respectively. Our results are comparable to many national and international published reports.
An Evaluation and Ranking of Children’s Hospital Websites in the United States

Background Children’s hospitals are faced with the rising need for technological innovation. Their prospective health care consumers, who increasingly depend on the Web and social media for communication and consumer engagement, drive this need. As patients and family members navigate the Web presence of hospitals, it is important for these specialized organizations to present themselves and their services efficiently. Objective The purpose of this study was to evaluate the website content of children’s hospitals in order to identify opportunities to improve website design and create benchmarks to judge improvement. Methods All websites associated with a children’s hospital were identified using a census list of all children’s hospitals in the United States. In March of 2014, each website and its social media were evaluated using a Web crawler that provided a 5-dimensional assessment that included website accessibility, marketing, content, technology, and usability. The 5-dimensional assessment was scored on a scale ranging from 0 to 10 with positive findings rated higher on the scale. Websites were ranked by individual dimensions as well as according to their average ranking across all dimensions. Results Mean scores of 153 websites ranged from 5.05 to 8.23 across all 5 dimensions. Results revealed that no website scored a perfect 10 on any dimension and that room exists for meaningful improvement. Conclusions Study findings allow for the establishment of baseline benchmarks for tracking future website and social media improvements and display the need for enhanced Web-based consumer engagement for children’s hospitals.
Self-anchoring in conversation: Why language users do not do what they 'should'

An old story about J. Edgar Hoover illustrates the miscommunication of intentions. When Hoover noticed that the text of a memo his secretary typed had spilled into the page margins, he scribbled a note to her: “Watch the borders. ” The next day agents were on high alert on the border with Mexico. The question we'd like to address in this paper is this: Why did Hoover miscommunicate? We propose that much miscommunication is systematic. It results from the nature of language use. We attempt to demonstrate our point by noting the similarities between the way people make decisions and the way they use language. As in decision making, uncertainty is inherent in the way people use language. The way language users overcome this uncertainty leads to systematic errors. When we attempt to understand what speakers mean, we must infer what they mean from what they say. This is because all utterances are ambiguous. “Borders” is lexically ambiguous, but ambiguity in language goes beyond lexical ambiguity. In fact, everything people say is ambiguous because it can convey more than one intention. To overcome this inherent ambiguity, we propose that language users rely on certain heuristics of language use. As with other heuristics, they are generally successful but they occasionally lead to systematic error. In this chapter, we propose that speakers, addressees, and overhearers reduce the uncertainty of linguistic utterances by using an anchoring and adjustment heuristic.
Defending Corner Kicks: Analysis from the English Premier League

The aim of this study was to explore tactical behaviour when defending corner kicks within the English Premier League. Specifically, the types of marking and defensive players positioned at the goalposts were investigated. A total of 436 corner kicks from 50 English Premier League games were analysed. The most commonly used marking system was one-to-one marking (90.1% of total corners), with zonal marking being used less often (9.9% of total corners). There was no significant association between the marking set-up and the number of attempts at goal conceded when defending corner kicks (p>0.05). However, teams who applied zonal marking conceded fewer goals and fewer attempts at goal than teams who used one-to-one marking. The most common set-up for defenders positioned at the goalposts was having a defender positioned only on the far post (47.3% of total corners). There was no significant association between the positioning of defensive players at goalposts and the number of attempts at goal conceded when defending corner kicks. A further detailed analysis of defending corner kicks is still required and suggestions have been made for future studies.
Reasons to Adopt ISO 50001 Energy Management System

Purpose: The main aim of this paper is to analyze the relationships between the corporate motivations that lead organizations to establish the ISO 50001 Energy Management System (EnMS) standard, and the difficulties and benefits derived from its adoption. Design/methodology/approach: Three independent exploratory factor analyses (EFA) were conducted in order to identify (i) sources of motivation: social requirements, ecology drivers, and competitive advantage; (ii) the difficulties of an ISO 50001 adoption: operational difficulties and organizational difficulty; and (iii) types of benefits: ecological benefits and operational benefits. In a second step, an exploratory path analysis, performed through Structural Equation Modeling (SEM), was used to analyze the relations among motivation, difficulties, and benefits related to the adoption of the ISO 50001 standard. Findings: Social requirements explain operational difficulties, which in turn impacts on operational benefits. Ecology drivers are directly related to ecological benefits. Organizational difficulties have an inverse relationship with operational and ecological benefits. Operational difficulties are related to operational benefits and ecological benefits. Research limitations/implications: The questionnaire was disseminated to 87 Spanish companies with ISO 50001 certification. Managers and other practitioners such as consultants, auditing companies, and official organizations in charge of developing standards might find useful implications. Originality/value: The standard was published in 2011 by the International Organization for Standardization (ISO). This paper contributes to assessment of the benefits of the standard by collecting information directly from the pioneer organizations that have adopted it, and provides clues on how to implement the standard and improve it in future.