bluuebunny/crossref_metadata_2025_split huggingface dataset:
THE METAPHYSICS OF DOWNWARD CAUSATION: REDISCOVERING THE FORMAL CAUSE
Authors: Tabaczek Mariusz 
Published: May 2013

AbstractThe methodological nonreductionism of contemporary biology opens an interesting discussion on the level of ontology and the philosophy of nature. The theory of emergence (EM), and downward causation (DC) in particular, bring a new set of arguments challenging not only methodological, but also ontological and causal reductionism. This argumentation provides a crucial philosophical foundation for the science/theology dialogue. However, a closer examination shows that proponents of EM do not present a unified and consistent definition of DC. Moreover, they find it difficult to prove that higher‐order properties can be causally significant without violating the causal laws that operate at lower physical levels. They also face the problem of circularity and incoherence in their explanation. In our article we show that these problems can be overcome only if DC is understood in terms of formal rather than physical (efficient) causality. This breakdown of causal monism in science opens a way to the retrieval of the fourfold Aristotelian notion of causality.
Muscle metaboreflex and autonomic regulation of heart rate in humans
Authors: Fisher James P. , Adlan Ahmed M. , Shantsila Alena , Secher J. Frederik , Sørensen Henrik , Secher Niels H. 
Published: May 2013

Key points
Heart rate increases during exercise due to withdrawal of cardiac parasympathetic tone and increased cardiac sympathetic nerve activity.
We investigated the autonomic mechanisms whereby heart rate is regulated by the activation of metabolically sensitive skeletal muscle afferents (muscle metaboreflex).
Heart rate responses elicited by partial flow restriction during leg cycling (enhanced metaboreflex activation) and post‐exercise muscle ischemia following leg cycling and handgrip (isolated metaboreflex activation) were evaluated under control (no drug), β‐adrenergic blockade and parasympathetic blockade conditions.
We show that the muscle metaboreflex principally elevates heart rate by increasing cardiac sympathetic activity, and only following dynamic exercise with a large muscle mass (post‐exercise muscle ischemia following leg cycling) does the partial withdrawal of cardiac parasympathetic tone make a contribution to this heart rate response.
These findings may have implications for patient populations in which alterations in skeletal muscle afferent sensitivity have been identified.
Abstract  We elucidated the autonomic mechanisms whereby heart rate (HR) is regulated by the muscle metaboreflex. Eight male participants (22 ± 3 years) performed three exercise protocols: (1) enhanced metaboreflex activation with partial flow restriction (bi‐lateral thigh cuff inflation) during leg cycling exercise, (2) isolated muscle metaboreflex activation (post‐exercise ischaemia; PEI) following leg cycling exercise, (3) isometric handgrip followed by PEI. Trials were undertaken under control (no drug), β1‐adrenergic blockade (metoprolol) and parasympathetic blockade (glycopyrrolate) conditions. HR increased with partial flow restriction during leg cycling in the control condition (Δ11 ± 2 beats min−1; P < 0.05). The magnitude of this increase in HR was similar with parasympathetic blockade (Δ11 ± 2 beats min−1), but attenuated with β‐adrenergic blockade (Δ4 ± 1 beats min−1; P < 0.05 vs. control and parasympathetic blockade). During PEI following leg cycling exercise, HR remained similarly elevated above rest under all conditions (Δ11 ± 2, Δ13 ± 3 and Δ9 ± 4 beats min−1, for control, β‐adrenergic and parasympathetic blockade; P > 0.05 between conditions). During PEI following handgrip, HR was similarly elevated from rest under control and parasympathetic blockade (Δ4 ± 1 vs. Δ4 ± 2 beats min−1; P > 0.05 between conditions) conditions, but attenuated with β‐adrenergic blockade (Δ0.2 ± 1 beats min−1; P > 0.05 vs. rest). Thus muscle metaboreflex activation‐mediated increases in HR are principally attributable to increased cardiac sympathetic activity, and only following exercise with a large muscle mass (PEI following leg cycling) is there a contribution from the partial withdrawal of cardiac parasympathetic tone.
Comparison of Pyrosequencing, Sanger Sequencing, and Melting Curve Analysis for Detection of Low-Frequency Macrolide-Resistant Mycoplasma pneumoniae Quasispecies in Respiratory Specimens
Authors: Chan Kwok-Hung , To Kelvin K. W. , Chan Betsy W. K. , Li Clara P. Y. , Chiu Susan S. , Yuen Kwok-Yung , Ho Pak-Leung 
Published: May 2013

ABSTRACTMacrolide-resistantMycoplasma pneumoniae(MRMP) is emerging worldwide and has been associated with treatment failure. In this study, we used pyrosequencing to detect low-frequency MRMP quasispecies in respiratory specimens, and we compared the findings with those obtained by Sanger sequencing and SimpleProbe PCR coupled with a melting curve analysis (SimpleProbe PCR). Sanger sequencing, SimpleProbe PCR, and pyrosequencing were successfully performed for 96.7% (88/91), 96.7% (88/91), and 93.4% (85/91) of theM. pneumoniae-positive specimens, respectively. The A-to-G transition at position 2063 was the only mutation identified. Pyrosequencing identified A2063G MRMP quasispecies populations in 78.8% (67/88) of the specimens. Only 38.8% (26/67) of these specimens with the A2063G quasispecies detected by pyrosequencing were found to be A2063G quasispecies by Sanger sequencing or SimpleProbe PCR. The specimens that could be detected by SimpleProbe PCR and Sanger sequencing had higher frequencies of MRMP quasispecies (51% to 100%) than those that could not be detected by those two methods (1% to 44%). SimpleProbe PCR correctly categorized all specimens that were identified as wild type or mutant by Sanger sequencing. The clinical characteristics of the patients were not significantly different when they were grouped by the presence or absence of MRMP quasispecies, while patients with MRMP identified by Sanger sequencing more often required a switch from macrolides to an alternativeM. pneumoniae-targeted therapy. The clinical significance of mutant quasispecies should be investigated further with larger patient populations and with specimens obtained before and after macrolide therapy.
ON MODELS FOR VISCOELASTIC MATERIALS THAT ARE MECHANICALLY INCOMPRESSIBLE AND THERMALLY COMPRESSIBLE OR EXPANSIBLE AND THEIR OBERBECK–BOUSSINESQ TYPE APPROXIMATIONS
Authors: PRUŠA VÍT , RAJAGOPAL K. R. 
Published: May 2013

Viscoelastic fluid like materials that are mechanically incompressible but are compressible or expansible with respect to thermal stimuli are of interest in various applications ranging from geophysics and polymer processing to glass manufacturing. Here we develop a thermodynamical framework for the modeling of such materials. First we illustrate the basic ideas in the simpler case of a viscous fluid, and after that we use the notion of natural configuration and the concept of the maximization of the entropy production, and we develop a model for a Maxwell type viscoelastic fluid that is mechanically incompressible and thermally expansible or compressible. An important approximation in fluid mechanics that is frequently used in modeling buoyancy driven flows is the Oberbeck–Boussinesq approximation. Originally, the approximation was used for studying the flows of viscous fluids in thin layers subject to a small temperature gradient. However, the approximation has been used almost without any justification even for flows of non-Newtonian fluids induced by strong temperature gradients in thick layers. Having a full system of the governing equations for a Maxwell type viscoelastic mechanically incompressible and thermally expansible or compressible fluid, we investigate the validity of the Oberbeck–Boussinesq type approximation for flows of this type of fluids. It turns out that the Oberbeck–Boussinesq type approximation is in general not a good approximation, in particular if one considers "high Rayleigh number" flows. This indicates that the Oberbeck–Boussinesq type approximation should not be used routinely for all buoyancy driven flows, and its validity should be thoroughly examined before it is used as a mathematical model.
Synergistic Interactions between Urban Heat Islands and Heat Waves: The Impact in Cities Is Larger than the Sum of Its Parts
Authors: Li Dan , Bou-Zeid Elie 
Published: May 2013

AbstractCities are well known to be hotter than the rural areas that surround them; this phenomenon is called the urban heat island. Heat waves are excessively hot periods during which the air temperatures of both urban and rural areas increase significantly. However, whether urban and rural temperatures respond in the same way to heat waves remains a critical unanswered question. In this study, a combination of observational and modeling analyses indicates synergies between urban heat islands and heat waves. That is, not only do heat waves increase the ambient temperatures, but they also intensify the difference between urban and rural temperatures. As a result, the added heat stress in cities will be even higher than the sum of the background urban heat island effect and the heat wave effect. Results presented here also attribute this added impact of heat waves on urban areas to the lack of surface moisture in urban areas and the low wind speed associated with heat waves. Given that heat waves are projected to become more frequent and that urban populations are substantially increasing, these findings underline the serious heat-related health risks facing urban residents in the twenty-first century. Adaptation and mitigation strategies will require joint efforts to reinvent the city, allowing for more green spaces and lesser disruption of the natural water cycle.
A Revised Conceptual Model of the Tropical Marine Boundary Layer. Part III: Bragg Scattering Layer Statistical Properties
Authors: Davison Jennifer L. , Rauber Robert M. , Di Girolamo Larry , LeMone Margaret A. 
Published: May 2013

Abstract
This paper examines the structure and variability of the moisture field in the tropical marine boundary layer (TMBL) as defined by Bragg scattering layers (BSLs) observed with S-band radar. Typically, four to five BSLs were present in the TMBL, including the transition layer at the top of the surface-based mixed layer. The transition-layer depth (~350 m) exhibited a weak diurnal cycle because of changes in the mixed-layer depth. BSLs and the “clear” layers between them each had a median thickness of about 350 m and a lifetime over the radar of 8.4 h, with about 25% having lifetimes longer than 20 h. More (fewer) BSLs were present when surface winds had a more southerly (northerly) component. Both BSLs and clear layers increased in depth with increasing rain rates, with the rainiest days producing layers that were about 100 m thicker than those on the driest days. The analyses imply that the relative humidity (RH) field in the TMBL exhibits layering on scales observable by radar. Satellite and wind profiler measurements show that the layered RH structure is related, at least in part, to detraining cloudy air.
Based on analyses in this series of papers, a revised conceptual model of the TMBL is presented that emphasizes moisture variability and incorporates multiple moist and dry layers and a higher TMBL top. The model is supported by comparing BSL tops with satellite-derived cloud tops. This comparison suggests that the layered RH structure is related, in part, to cloud detrainment at preferred altitudes within the TMBL. The potential ramifications of this change in TMBL conceptualization on modeling of the TMBL are discussed.
Improving major amputation rates in the multicomplex diabetic foot patient: focus on the severity of peripheral arterial disease
Authors: Brechow Andrej , Slesaczeck Torsten , Münch Dirk , Nanning Thomas , Paetzold Hartmut , Schwanebeck Uta , Bornstein Stefan , Weck Matthias 
Published: May 2013

Objective: Peripheral arterial disease (PAD), as well as diabetic neuropathy, is a risk factor for the development of diabetic foot ulcers. The aim of this study was to evaluate differences and predictors of outcome parameters in patients with diabetic foot by stratifying these subjects according to the severity of PAD. Research design and methods: In a prospective study, patients with new diabetic foot ulcers have been treated and investigated by structured healthcare. Subjects were recruited between 1 January 2000 and 31 December 2007. All study participants underwent a 2-year follow-up observation period. The patients underwent a standardized examination and classification of their foot ulcers according to a modification of the University of Texas Wound Classification System. The severity of PAD was estimated by measurement of the ankle brachial index (ABI) and the continuous wave Doppler flow curve into undisturbed perfusion (0.9 < ABI < 1.3), compensated perfusion (0.5 < ABI < 0.9), decompensated perfusion (ABI < 0.5) and medial arterial calcification. Results: A total of 678 patients with diabetic foot were consecutively included into the study (69% male, mean age 66.3 ± 11.0 years, mean diabetes duration 15.8 ± 10.2 years). Major amputations (above the ankle) were performed in 4.7% of the patients. 22.1% of these subjects had decompensated PAD. These subjects had delayed ulcer healing, higher risk for major amputation [odds ratio (OR) 7.7, 95% confidence interval (CI) 2.8–21.2, p < 0.001] and mortality (OR 4.9, 95 % CI 1.1–22.1, p < 0.05). Conclusion: This prospective study shows that the severity of PAD significantly influences the outcome of diabetic foot ulcers regarding to wound healing, major amputation and mortality.
Positive selection of mC46-expressing CD4+ T cells and maintenance of virus specific immunity in a primate AIDS model
Authors: Younan Patrick M. , Polacino Patricia , Kowalski John P. , Peterson Christopher W. , Maurice Nicholas J. , Williams Nathaniel P. , Ho On , Trobridge Grant D. , Von Laer Dorothee , Prlic Martin , Beard Brian C. , DeRosa Stephen , Hu Shiu-Lok , Kiem Hans-Peter 
Published: May 2013

Key Points
Stem cell gene therapy results in enhanced virus-specific immunity and recovery of CD4+ T cells in a nonhuman primate model of AIDS. Gene therapy–mediated protection of stem cells results in a disease state similar to that observed in long-term nonprogressors.
Identifying Mendelian disease genes with the Variant Effect Scoring Tool
Authors: Carter Hannah , Douville Christopher , Stenson Peter D , Cooper David N , Karchin Rachel 
Published: May 2013

AbstractBackgroundWhole exome sequencing studies identify hundreds to thousands of rare protein coding variants of ambiguous significance for human health. Computational tools are needed to accelerate the identification of specific variants and genes that contribute to human disease.ResultsWe have developed the Variant Effect Scoring Tool (VEST), a supervised machine learning-based classifier, to prioritize rare missense variants with likely involvement in human disease. The VEST classifier training set comprised ~ 45,000 disease mutations from the latest Human Gene Mutation Database release and another ~45,000 high frequency (allele frequency>1%) putatively neutral missense variants from the Exome Sequencing Project. VEST outperforms some of the most popular methods for prioritizing missense variants in carefully designed holdout benchmarking experiments (VEST ROC AUC = 0.91, PolyPhen2 ROC AUC = 0.86, SIFT4.0 ROC AUC = 0.84). VEST estimates variant score p-values against a null distribution of VEST scores for neutral variants not included in the VEST training set. These p-values can be aggregated at the gene level across multiple disease exomes to rank genes for probable disease involvement. We tested the ability of an aggregate VEST gene score to identify candidate Mendelian disease genes, based on whole-exome sequencing of a small number of disease cases. We used whole-exome data for two Mendelian disorders for which the causal gene is known. Considering only genes that contained variants in all cases, the VEST gene score ranked dihydroorotate dehydrogenase (DHODH) number 2 of 2253 genes in four cases of Miller syndrome, and myosin-3 (MYH3) number 2 of 2313 genes in three cases of Freeman Sheldon syndrome.ConclusionsOur results demonstrate the potential power gain of aggregating bioinformatics variant scores into gene-level scores and the general utility of bioinformatics in assisting the search for disease genes in large-scale exome sequencing studies. VEST is available as a stand-alone software package athttp://wiki.chasmsoftware.organd is hosted by the CRAVAT web server athttp://www.cravat.us
Gene expression in human fungal pathogen Coccidioides immitis changes as arthroconidia differentiate into spherules and mature
Authors: Viriyakosol Suganya , Singhania Akul , Fierer Joshua , Goldberg Jonathan , Kirkland Theo N , Woelk Christopher H 
Published: May 2013

Abstract

Background

Coccidioides immitis is a dimorphic fungus that causes disease in mammals, including human beings. It grows as a mycelium containing arthroconidia in the soil and in the host arthroconidia differentiates into a unique structure called a spherule. We used a custom open reading frame oligonucleotide microarray to compare the transcriptome of C. immitis mycelia with early (day 2) and late stage (day 8) spherules grown in vitro. All hybridizations were done in quadruplicate and stringent criteria were used to identify significantly differentially expressed genes.

Results
22% of C. immitis genes were differentially expressed in either day 2 or day 8 spherules compared to mycelia, and about 12% of genes were differentially expressed comparing the two spherule time points. Oxireductases, including an extracellular superoxide dismutase, were upregulated in spherules and they may be important for defense against oxidative stress. Many signal transduction molecules, including pleckstrin domain proteins, protein kinases and transcription factors were downregulated in day 2 spherules. Several genes involved in sulfur metabolism were downregulated in day 8 spherules compared to day 2 spherules. Transcription of amylase and α (1,3) glucan synthase was upregulated in spherules; these genes have been found to be important for differentiation to yeast in Histoplasma. There were two homologs of 4-hydroxyphenylpyruvate dioxygenase (4-HPPD); transcription of one was up- and the other downregulated. We tested the effect of a 4-HPPD inhibitor, nitisinone, on mycelial and spherule growth and found that it inhibited mycelial but not spherule growth.

Conclusions
Transcription of many genes was differentially expressed in the process of arthroconidia to spherule conversion and spherule maturation, as would be expected given the magnitude of the morphologic change. The transcription profile of early stage (day 2) spherules was different than late stage (day 8) endosporulating spherules. In addition, very few genes that are important for spore to yeast conversion in other dimorphic fungi are differentially expressed in C. immitis mycelia and spherules suggesting that dimorphic fungi may have evolved different mechanisms to differentiate from mycelia to tissue invasive forms.
Clinical characteristics and risk factors of non-Candida fungaemia
Authors: Yamamoto Masaki , Takakura Shunji , Hotta Gou , Matsumura Yasufumi , Matsushima Aki , Nagao Miki , Ito Yutaka , Ichiyama Satoshi 
Published: May 2013

Abstract

Background
The incidence of fungaemia has been increasing worldwide. It is important to distinguish non-Candida fungaemia from candidaemia because of their different antifungal susceptibilities. The aims of this study were to investigate the clinical characteristics of non-Candida fungaemia and identify the clinical factors that differentiate it from candidaemia.

Methods
We investigated the clinical manifestations and mortality of non-Candida fungaemia in Kyoto University Hospital from 2004 to 2009.

Results
There were 110 episodes of fungaemia during the study period. There were 11 renal replacement therapy episodes of fungaemia due to non-Candida yeasts (10.0%), including 6 episodes with Cryptococcus neoformans, 4 with Trichosporon asahii, and 1 with Kodamaea ohmeri, in addition to 99 episodes of candidaemia (90.0%). The presence of collagen disease [odds ratio (OR) 9.00; 95% confidence interval (CI) 1.58-51.4; P = 0.01] or renal replacement therapy (OR 15.0; 95% CI 3.06-73.4; P < 0.01) was significantly more common in non-Candida fungaemia patients than in candidaemia patients. Prior colonisation by the species may be a predictor of non-Candida fungaemia. Non-Candida fungaemia had a higher mortality than candidaemia (54.5% versus 21.2%, P = 0.03).

Conclusions
Although Candida species frequently cause fungaemia, we should also be aware of non-Candida yeasts because of their high mortality, particularly among high-risk patients, such as those with collagen disease and those under renal replacement therapy. Prior colonisation by the causative organisms may be an important predictor of non-Candida fungaemia.
Is legal status impacting outcomes of group therapy for posttraumatic stress disorder with male asylum seekers and refugees from Iran and Afghanistan?
Authors: Drožđek Boris , Kamperman Astrid M , Tol Wietse A , Knipscheer Jeroen W , Kleber Rolf J 
Published: May 2013

Abstract

Background
Legal status and other resettlement stressors are known to impact mental health of asylum seekers and refugees. However, the ways in which they interact with treatment of posttraumatic stress disorder (PTSD) with these populations is still poorly understood. The aim of this study was to examine whether legal status and other resettlement stressors influence outcomes of a trauma-focused group PTSD treatment within a day-treatment setting with asylum seekers and refugees.

Methods
Sixty six male Iranian and Afghan patients with PTSD residing in the Netherlands were assessed with self-rated symptom checklists for PTSD, anxiety and depression, and a demographic questionnaire one week before and two weeks after the treatment. Multivariate linear regression analysis was used to examine the impact of legal status and living arrangements on the treatment outcomes per symptom domain.

Results
The results suggest that both asylum seekers and refugees can be helped with their mental health complaints with a trauma-focused group therapy for PTSD regardless of their legal status. Obtaining a refugee status in a course of the treatment appears to improve the treatment outcomes.

Conclusions
Legal status is impacting outcomes of group therapy for PTSD with male asylum seekers and refugees. Asylum seekers may benefit from group treatment regardless of unstable living conditions.