Miracle-dz/UniFAR-FTUs huggingface dataset:
Yield of bone marrow culture in the diagnosis of infectious diseases in patients with acquired immunodeficiency syndrome

The yield in cultures of bone marrow aspirations or biopsies was determined in 50 patients with acquired immunodeficiency syndrome. Most patients were febrile and had no identifiable source of infection. Concurrent stool, urine, and blood samples were also cultured. The bone marrow aspiration and biopsy procedures produced no complications and enabled a microbiological diagnosis to be made in 42% of the cases. Granuloma formation was not seen in any of the infected bone marrow specimens despite the fact that mycobacteria were seen in abundance in some. Bone marrow culture is a valuable low-morbidity invasive procedure in the evaluation of febrile patients with acquired immunodeficiency syndrome.
Determinants of Capital Structure: Case of Companies Listed on Zagreb Stock Exchange

In this article we sought to analyze some factors influencing companies’ leverage. To examine such factors, we have selected a sample of companies registered on Zagreb Stock Exchange. The sample is from non-financial companies covering the period of 2002-2006 and comprised 89 listed companies. Tangibility, profitability, size, and growth were confirmed as relevant determinants, and only the non-debt tax shield was confirmed as irrelevant determinant in capital structure decisions. Companies’ features as capital origin structure, business industry, and company age were confirmed to play roles in capital structure composition.
Characterization and behaviour of α‐glucan synthase in Schizosaccharomyces pombe as revealed by electron microscopy

α‐1,3‐Glucan is a cell wall component in Schizosaccharomyces pombe and is exclusive to budding yeast. We analysed the ultrastructure of the cell wall in the α‐glucan synthase mutant mok1 and determined the role of α‐1,3‐glucan in cell wall formation of Sz. pombe. The mok1 mutant cell has an abnormal shape, with swelling at the tip or at the site of the septum. The cell wall is thicker and looser than that of wild‐type cells, and the layered structure of the cell wall is broken. The glucan fibrils forming the protoplast retain a fine fibril structure, although their development into bundles is abnormal. We also report the localization of Mok1p by immunoelectron microscopy using high‐pressure freeze substitution and SDS‐digested freeze‐fracture replica labelling methods. The Mok1p is localized on the cell membrane and moves from the cell tip to the medial region during the cell cycle. These results confirm that Mok1p plays an important role in the normal construction of the cell wall and in the primary step of glucan bundle formation, and that it is required for new cell wall synthesis during vegetative growth. These findings suggest that α‐1,3‐glucan is an essential component for cell wall formation in fission yeast. Copyright © 2003 John Wiley & Sons, Ltd.
Autologous transplantation for relapsed or primary refractory peripheral T‐cell lymphoma

Autologous transplantation (ASCT) is the standard of care for chemosensitive relapsed or primary refractory aggressive lymphoma, but little is known about its efficacy in the subset of patients with peripheral T‐cell lymphoma (PTCL). We undertook a retrospective review of patients with PTCL who underwent ASCT for relapsed or refractory disease after responding to second‐line therapy, excluding patients with indolent histologies and those with anaplastic lymphoma kinase (ALK) expressing anaplastic large cell lymphoma. The results of 24 patients with PTCL were compared with those of 86 consecutive patients with chemosensitive relapsed or primary refractory diffuse large B‐cell lymphoma (DLBCL). With a median follow‐up time of 6 years for surviving patients with PTCL and DLBCL, the 5‐year progression‐free survival (PFS) rates for PTCL and DLBCL patients were 24% and 34% respectively (P = 0·14); the corresponding overall survival (OS) rates were 33% and 39% respectively. There were no significant differences between the two groups with respect to time to disease progression or survival after progression. The second‐line age‐adjusted international prognostic index was the only variable prognostic for PFS and OS in a multivariate analysis. The outcome of ASCT for patients with chemosensitive relapsed or primary refractory PTCL is similar to that for patients with DLBCL.
Evidence for the role of cognitive resources in flavour–flavour evaluative conditioning

One way that dis/likes are formed is through evaluative conditioning (EC). In two experiments we investigated the role of cognitive resources in flavour–flavour conditioning. Both experiments employed an EC procedure in which three novel flavoured conditioned stimuli (CSs) were consumed. One was consumed with a pleasant unconditioned stimulus (US; CS+ sugar), one with an aversive US (CS+ saline), and a third with plain water (CS–). Half of participants in each experiment performed a cognitive load task during conditioning. We measured EC using self-reported measures of liking (Experiments 1 and 2) and an indirect measure of liking: drink pick-up latency (Experiment 2). In both experiments, differential EC was observed in the no cognitive load condition but not in the cognitive load condition. This pattern of results was observed in self-reported measures of liking as well as in the drink pick-up latency data. Results from both experiments show that EC occurs only when there are sufficient cognitive resources available. The fact that this was observed using both self-reported and indirect measures suggests that insufficient cognitive resources affect learning itself rather than merely obstructing reporting.
Retracing the footsteps of H.H. Thomas: a review of his Stonehenge bluestone provenancing study

Abstract The long-distance transport of the Stonehenge bluestones from the Mynydd Preseli area of north Pembrokeshire was first proposed by geologist H.H. Thomas in 1923. For over 80 years, his work on the provenancing of the Stonehenge bluestones from locations in Mynydd Preseli in south Wales has been accepted at face value. New analytical techniques, alongside transmitted and reflected light microscopy, have recently prompted renewed scrutiny of Thomas's work. While respectable for its time, the results of these new analyses, combined with a thorough checking of the archived samples consulted by Thomas, reveal that key locations long believed to be sources for the Stonehenge bluestones can be discounted in favour of newly identified locations at Craig-Rhos-y-felin and Carn Goedog.
Susceptibility to Paget's Disease of Bone Is Influenced by a Common Polymorphic Variant of Osteoprotegerin

To clarify the role of the TNFRSF11B gene encoding osteoprotegerin (OPG), in Paget's disease of bone (PDB) we studied TNFRSF11B polymorphisms in an association study of 690 UK subjects and in a worldwide familial study of 66 kindreds. We found that the G1181 allele of TNFRSF11B, encoding lysine at codon 3 of the OPG protein, predisposes to both sporadic and familial PDB.
Bloodstream infections among children with juvenile idiopathic arthritis: a prospective study from the onset of disease.

OBJECTIVES To describe the incidence and nature of bloodstream infections (BSI) among children with juvenile idiopathic arthritis (JIA) followed-up prospectively from disease onset. METHODS The Social Insurance Institution's (SII) national register on individuals with reimbursement for medication of chronic diseases was used to identify children with JIA from 2004 through 2011 and their medications. The National Infectious Disease Register (NIDR) collects data of all blood culture positive samples from all microbiology laboratories in Finland. We combined the NIDR and SII registers to identify JIA patients with BSI. Clinical and laboratory data of each JIA-BSI patient were collected from hospital records. RESULTS There were 1604 JIA patients and 6630 person-years of follow-up. Five patients had BSI. During the first 5 years after diagnosis the cumulative emergence of BSI was 0.38% [95% confidence interval (CI) 0.16% to 0.92%]. The incidence rates were 7.5/10 000 follow-up years for JIA (95% CI 2.4-17.6) and 2.8/10 000 follow-up years for the age-matched general population (95% CI 2.7-2.9). The standardised incidence ratio was 3.0 (95% CI 1.2 to 7.2). The causative bacteria were Streptococcus pneumoniae, Staphylococcus aureus, Escherichia coli and Fusobacterium necrophorum. Three patients were on anti-rheumatic drugs, including two on TNF inhibitors. All patients responded rapidly to antimicrobial therapy and recovered uneventfully. CONCLUSIONS Although BSI is rare among children with JIA, the incidence is 3-fold higher than among the general population.
Activation of the Akt/mTOR signaling pathway: a potential response to long-term neuronal loss in the hippocampus after sepsis

Survivors of sepsis may suffer chronic cognitive impairment as a long-term sequela. However, the precise mechanisms of cognitive dysfunction after sepsis are not well understood. We employed the cecal ligation-and-puncture-induced septic mouse model. We observed elevated phosphorylation of Akt, mammalian target of rapamycin (mTOR) and p70S6K on days 14 and 60, progressive neuronal loss in the cornu ammonis 1 region, and abnormal neuronal morphology in the hippocampus in the sepsis mouse model. These findings indicate that changes in neuronal morphology and number in the hippocampus after sepsis were associated with strong activation of the Akt/mTOR signaling pathway, and may reflect a “self-rescuing” feedback response to neuronal loss after sepsis.
The large resolvase TnpX is the only transposon‐encoded protein required for transposition of the Tn4451/3 family of integrative mobilizable elements

Chloramphenicol resistance in Clostridium perfringens and Clostridium difficile is often encoded by catP genes located within the 6.3 kb integrative mobilizable elements Tn4451 and Tn4453 respectively. This family of transposons is capable of being mobilized into a recipient cell in the presence of another conjugative element. Transposition is mediated by the large resolvase TnpX, which excises the element to produce a circular molecule that is the integrative intermediate. In this study, in vivo deletion analysis of the transposon‐encoded tnpV and tnpY genes showed that they are not essential for excision or integration of this group of elements. Similar studies on tnpW suggested either that this gene is not essential for these functions or that TnpW does not function when provided in trans. Development and use of an in vivo insertion assay showed that TnpX is the only transposon‐encoded protein required for the integration reaction. Subsequently, a TnpXLEH6 protein was purified and shown to catalyse excision in vitro in the absence of any other protein and preferentially to excise a supercoiled DNA substrate. In summary, these studies have shown that TnpX is the only transposon protein required in vivo and in vitro for the excision process and that, like excision, integration also occurs by a serine recombinase‐mediated site‐specific recombination mechanism.
Intracytoplasmic tagging of cells with ferumoxides and transfection agent for cellular magnetic resonance imaging after cell transplantation: methods and techniques

Background. Superparamagnetic iron oxides (SPIO) are being used to label cells for in vivo monitoring by magnetic resonance imaging (MRI). The purpose of this study is to present protocols using SPIO and a polycationic transfection agent for magnetic labeling of cells as a basis for cellular MRI. Methods. Various concentrations of ferumoxides (FE)–poly-l-lysine (PLL) complexes were used to magnetically label cells. Iron incorporation into cells along with cell viability and short- and long-term toxicity were evaluated. Results. Rapidly growing cell suspension and adherent cells were effectively labeled by means of endocytosis into endosomes at low concentrations of FE (25 &mgr;g/mL media) and PLL (0.75 &mgr;g/mL media). Hematopoietic stem cells and lymphocytes required higher concentrations of PLL (1.5 &mgr;g/mL) in serum-free media during initial FE-PLL complex formation before labeling the cells in culture. Total iron concentration in cells depended on the cell type, concentration of FE-PLL complexes in media, cellular density, and incubation time. Iron concentrations after overnight incubation with given FE at 25 &mgr;g/mL media resulted in, for example, T cells being labeled with 1 to 3 pg/cell of intracytoplasmic endosomal iron and 15 to 20 pg/cell of intracytoplasmic iron in mesenchymal stem cells compared with 0.01 to 0.1 pg/cell for unlabeled cells. Protocols developed for this study demonstrated no adverse effect on the cell viability, functional capacity, or toxicity. Conclusion. This technique can be used to label cells for in vivo MRI tracking of stem cells and lymphocytes. FE at a concentration of 25 to 50 &mgr;g/mL with a ratio of SPIO to PLL of 1:0.03 to 1:0.06 would be sufficient to label cells for cellular MRI.
A Transactional Approach to Associative XML Classification by Content and Structure

We proposeXCCS, which is short for XML Classification by Content and Structure, a new approach for the induction of intelligible classification models for XML data, that are a valuable support for more effective and efficient XML search, retrieval and filtering. The idea behind XCCS is to represent each XML document as a transaction in a space of boolean features, that are informative of its content and structure. Suitable algorithms are developed to learn associative classifiers from the transactional representation of the XML data.XCCS induces very compact classifiers with outperforming effectiveness compared to several established
Improvements in hierarchical phrase-based Statistical Machine Translation

Hierarchical phrase-based translation (Hiero) is a statistical machine translation (SMT) model that encodes translation as a synchronous context-free grammar derivation between source and target language strings (Chiang, 2005; Chiang, 2007). Hiero models are more powerful than phrase-based models in capturing complex source-target reordering as well as discontiguous phrases, while being easier to estimate and decode with compared to their full syntax-based counterparts. In this thesis, we propose improvements to two broad aspects of the Hiero translation pipeline: i) learning Hiero translation model and estimating their parameters and ii) parameter tuning for discriminative log-linear models that are used to decode with such features. We use our own opensource implementation of Hiero called Kriya (Sankaran et al., 2012b) for all the experiments in this thesis. This thesis contains the following specific contributions: • We propose a Bayesian model for learning Hiero grammars as an alternative to the heuristic method usually used in Hiero. Our model learns a peaked distribution of grammars, which consistently performs better than the heuristically extracted grammars across several language pairs (Sankaran et al., 2013a). • We propose a novel unified-cascade framework for jointly learning alignments and the Hiero translation rules by removing the disconnect between the alignments and extracted synchronous context-free grammar. This is the first time a joint training framework is being proposed for Hiero, where we iterate the two step inference so that it learns in alternate iterations the phrase alignments and then the Hiero rules that are consistent with alignments. • We extend our Bayesian model for extracting compact Hiero translation rules using arity1 grammars, resulting in up to 57% reduction in model size while retaining the translation performance (Sankaran et al., 2011; Sankaran et al., 2012a). • We propose several novel approaches for parameter tuning of discriminative log-linear models
LAMA2 loss-of-function mutation in a girl with a mild congenital muscular dystrophy

The authors report a girl with autosomal recessive congenital muscular dystrophy linked to chromosome 6 (MDC1A) who carries a homozygous out-of-frame deletion in exon 56 of the LAMA2 gene but has a mild phenotype. She is still ambulant at age 13 years, shows white matter abnormalities on MRI, and traces of laminin α2 in her muscle biopsy with one of three antibodies used. This patient suggests that modulating factors can be associated with a less severe clinical phenotype in MDC1A.
The Effect of Restricting Residents' Duty Hours on Patient Safety, Resident Well-Being, and Resident Education: An Updated Systematic Review.

BACKGROUND Despite 25 years of implementation and a sizable amount of research, the impact of resident duty hour restrictions on patients and residents still is unclear. Advocates interpret the research as necessitating immediate change; opponents draw competing conclusions. OBJECTIVE This study updates a systematic review of the literature on duty hour restrictions conducted 1 year prior to the implementation of the Accreditation Council for Graduate Medical Education's 2011 regulations. METHODS The review draws on reports catalogued in MEDLINE and PreMEDLINE from 2010 to 2013. Interventions that dealt with the duty hour restrictions included night float, shortened shifts, and protected time for sleep. Outcomes were patient care, resident well-being, and resident education. Studies were excluded if they were not conducted in patient care settings. RESULTS Twenty-seven studies met the inclusion criteria. Most frequently, the studies concluded that the restrictions had no impact on patient care (50%) or resident wellness (47%), and had a negative impact on resident education (64%). Night float was the most frequent means of implementing duty hour restrictions, yet it yielded the highest proportion of unfavorable findings. CONCLUSIONS This updated review, including 27 recent applicable studies, demonstrates that focusing on duty hours alone has not resulted in improvements in patient care or resident well-being. The added duty hour restrictions implemented in 2011 appear to have had an unintended negative impact on resident education. New approaches to the issue of physician fatigue and its relationship to patient care and resident education are needed.
Identification of Clinical Aeromonas Species by rpoB and gyrB Sequencing and Development of a Multiplex PCR Method for Detection of Aeromonas hydrophila, A. caviae, A. veronii, and A. media

ABSTRACT Conventional identification of Aeromonas species based on biochemical methods is challenged by the heterogeneous nature of the species. Here, we present a new multiplex PCR method directed toward the gyrB and rpoB genes that identifies four Aeromonas species, A. hydrophila, A. media, A. veronii, and A. caviae, and we describe the application of this method on a Danish strain collection.
A stable and practical etoposide-containing intravenous long-/medium-chain triglycerides-based lipid emulsion formulation: pharmacokinetics, biodistribution, toxicity, and antitumor efficacy

Objectives: This work aimed to evaluate pharmacokinetics, biodistribution, toxicity, and antitumor activities of a highly stable long-/medium-chain triglycerides (LCT/MCT)-based etoposide parenteral emulsion (EPE) in comparison to etoposide parenteral solution (EPS). Methods: Using high-pressure homogenization method, EPE was prepared and sterilized at 121°C for 10 min by autoclaving. The biological samples were analyzed using the UPLC-ESI-MS/MS method. Results: Superior stability of EPE was verified with no significant changes in physicochemical properties in the accelerating and long-term stability tests. Similar pharmacokinetic behavior in beagle dogs was obtained and the AUC 0 – 12h values were 1196.73 ± 320.85 and 1505.56 ± 617.93 µg·h/L for EPE and EPS (p > 0.5), respectively. Likewise, no remarkable difference in biodistribution profiles in mice was found for both formulations. Safety assessment studies including hemolysis test, rabbit ear vein test and injection anaphylaxis were undertaken and the EPE was proven to be safe for intravenous administration. Specifically, after consecutive 12 weeks administration in rats, systematic and local toxicity induced by EPE were alleviated relative to that of EPS. Furthermore, significant and comparable antitumor activities to EPS were also demonstrated by EPE with tumor suppression rate (TSR) of 66.63, 55.94, and 60.16% against H460, Hep G2, and BCAP-37 human cancer cell lines in nude mice at the dose of 15 mg/kg, respectively. Conclusion: These results suggest that this LCT/MCT-based lipid emulsion is a promising alternative intravenous carrier for etoposide with high stability, improved convenience, alleviated toxicity, and noncompromised antitumor efficacy.
Successful cryoloop vitrification and subsequent in vitro maturation of mouse preantral follicles

The purpose of this study was to assess follicular viability and competence through in vitro maturation (IVM) of cryoloop vitrified mouse preantral follicles. Early mouse preantral follicles were isolated and vitrified using the cyroloop vitrification technique. After thawing, the preantral follicles and oocytes were cultured and in vitro matured for 10 d to the metaphase two stage (M2). Oocytes were assessed for viability at 2 and 10 d of IVM and compared to a control group of freshly isolated preantral follicles undergoing IVM. Of vitrified follicles, 94.0% (345/367) were recovered after thawing. The survival rate after the first two-days of IVM culture was 82.3% (284/345) for the cryoloop vitrified follicles and 100% for the control follicles (437/437). The percentage of oocytes in the cryoloop group that developed to M2 was 70.2% (174/248), comparable to that of the control group at 68.7% (241/351) (p value 0.12). Our results indicate that cyroloop vitrification is a viable and practical technique for cryopreservation of mouse preantral follicles. Human oocyte cypreservation by means of cryoloop vitrification may prove to be useful as a possible treatment modality for human fertility preservation.
Cross-breeding cattle for milk production in the tropics: achievements, challenges and opportunities

This paper reviews experiences with cross-breeding for milk production in the tropics. Data were compiled from 23 different studies evaluating the performance of different grades of cross-bred animals as well as local breeds. Relative performance of indigenous breeds compared with different grades of cross-breeds was calculated for three climatic zones. Traits considered were milk yield per lactation, age at first calving, services per conception, lifetime milk yield and total number of lactations completed. At 50 percent Bos taurus blood, lactation milk yields were 2.6, 2.4 and 2.2 times higher than those of local cattle in the highland, tropical wet and dry, and semi-arid climatic zones, respectively; lactation lengths increased by 1.2, 1.2 and 1.9 months in the above-mentioned climatic zones, respectively; there was a reduction in calving interval by 0.8 times and in age at first calving by 0.9 times. Similarly, cross-breds with 50 percent B. taurus genes had 1.8 times higher lifetime milk yields and a 1.2 times higher number of total lactations. Although cross-breeding faces a number of challenges such as better infrastructure, higher demand for health care, there are many advantages of using it. These are higher production per animal, higher income for the families and provision of high-value food. It is therefore likely to continue to be an important livestock improvement tool in the tropics in the future, where farmers can provide sufficient management for maintaining animals with higher input requirements and access to the milk market can be secured.