Miracle-dz/UniFAR-FTUs huggingface dataset:
Life on carbon monoxide: X-ray structure of Rhodospirillum rubrum Ni-Fe-S carbon monoxide dehydrogenase

A crystal structure of the anaerobic Ni-Fe-S carbon monoxide dehydrogenase (CODH) from Rhodospirillum rubrum has been determined to 2.8-Å resolution. The CODH family, for which the R. rubrum enzyme is the prototype, catalyzes the biological oxidation of CO at an unusual Ni-Fe-S cluster called the C-cluster. The Ni-Fe-S C-cluster contains a mononuclear site and a four-metal cubane. Surprisingly, anomalous dispersion data suggest that the mononuclear site contains Fe and not Ni, and the four-metal cubane has the form [NiFe3S4] and not [Fe4S4]. The mononuclear site and the four-metal cluster are bridged by means of Cys531 and one of the sulfides of the cube. CODH is organized as a dimer with a previously unidentified [Fe4S4] cluster bridging the two subunits. Each monomer is comprised of three domains: a helical domain at the N terminus, an α/β (Rossmann-like) domain in the middle, and an α/β (Rossmann-like) domain at the C terminus. The helical domain contributes ligands to the bridging [Fe4S4] cluster and another [Fe4S4] cluster, the B-cluster, which is involved in electron transfer. The two Rossmann domains contribute ligands to the active site C-cluster. This x-ray structure provides insight into the mechanism of biological CO oxidation and has broader significance for the roles of Ni and Fe in biological systems.
Vibration-Induced Kinesthetic Illusions and Corticospinal Excitability Changes

ABSTRACT The authors' aim was to investigate the changes of corticospinal excitability during kinesthetic illusions induced by tendon vibration. Motor-evoked potentials in response to transcranial magnetic stimulation were recorded from the vibrated flexor carpi radialis and its antagonist, extensor carpi radialis. The illusions were evoked under vision conditions without feedback for the position of the wrist (open or closed eyes). In these two conditions motor-evoked potential changes during vibration in the antagonist were not identical. This discrepancy may be a result of 2 simultaneously acting, different and opposite influences and the balance between them depends on visual conditions. Thus, the illusion was accompanied by the facilitation of corticospinal excitability in both vibrated muscle and its antagonist.
Combinatorial patterns of histone modifications in Saccharomyces.cerevisiae

Histone modification is an important subject of epigenetics that plays an intrinsic role in transcriptional regulation. It has been suggested that multiple histone modifications act in a combinatorial fashion to form a ‘histone code’. In this study, the combinatorial patterns of histone modifications were studied by using a Bayesian network at the level of individual nucleosomes in S. cerevisiae. Our results indicated that there were 23 combinatorial patterns for 12 histone modifications investigated when a general Bayesian network was constructed. Meanwhile, different networks were also constructed for the genes with high transcript levels (H‐network) and low transcript levels (L‐network), respectively. Comparison among the general network, H‐network and L‐network illustrated four conserved combinations: H2BK16Ac → H3K4me3; H3K14Ac → H3K4me3; H2AK7Ac → H3K14Ac; and H4K12Ac → H3K18Ac. The detailed analysis for some combinations demonstrated that the combinations were ascribed to some histone‐modifying enzymes. Copyright © 2011 John Wiley & Sons, Ltd.
A CLINICAL DESCRIPTION OF A DISEASE RESEMBLING POLIOMYELITIS, SEEN IN ADELAIDE, 1949–1951

the "Dibenamine" hydrochloride and preparationof solutions, to Dr. Christina R. Trood (Baker Medical Research Institute) for valuable assistancein the infusion experiments, and to the staff of the Baker Medical Research Institute and Alfred Hospital Clinical ResearchUnit for help in many ways. A tribute of thanksand appreciation of their willing cooperation is due to the volunteers, without whose help the investigation could not have been carried out.
Quality of care in inflammatory bowel disease: A review and discussion

Abstract: The Institute of Medicine's publications To Err Is Human and Crossing the Quality Chasm publicized the widespread deficits in U.S. health care quality. Emerging studies continue to reveal deficits in the quality of adult and pediatric care, including subspecialty care. The inflammatory bowel diseases (IBD) Crohn's disease and ulcerative colitis require diligent, long‐term management and attention to their impact on intestinal and extraintestinal organ systems. Although the quality of IBD care has not been prospectively or comprehensively evaluated in the United States, several small studies have demonstrated significant variation in care. As variation may indicate underuse, overuse, or misuse of medical services, such variation suggests a clear need for translating evidence‐based practices into the actual practice and follow‐up provided for patients. This article reviews the history, rationale, and methods of quality measurement and improvement and identifies the unique challenges in adapting these general strategies to the care of the inflammatory bowel diseases. Inflamm Bowel Dis 2010
First-Degree Relatives of Breast-Cancer Patients: Cognitive Perceptions, Coping, and Adherence to Breast Self-Examination

Abstract The author assessed patterns of breast self-examination (BSE) related to cognitive appraisal, coping, and emotional distress in 80 women with first-degree relatives who were breast-cancer patients and 47 matched controls. Participants with first-degree relatives adhered to BSE better than did women with no family history of breast cancer, and women whose relatives had recurrent or metastatic disease performed more BSE than those whose relatives were currently disease free. Greater adherence to BSE was associated with lower levels of depression, more problem-focused coping, older age, and more education. In the women with first-degree relatives, BSE was also associated with higher perceptions of (a) control over prevention, (b) risk for breast cancer, and (c) higher levels of state anxiety. Perception of control, problem-focused coping, depression, and anxiety predicted 35% of the variance in adherence to BSE. The findings suggest that cognitive appraisal, coping strategies, and levels of emotional distress should be considered in designing programs for enhancing adherence to early detection procedures.
Emergency medical services provider perceptions of the nature of adverse events and near-misses in out-of-hospital care: an ethnographic view.

OBJECTIVES The objectives were to examine the perceptions of emergency medical services (EMS) providers regarding near-misses and adverse events in out-of-hospital care. METHODS This study uses qualitative methods (focus groups, interviews, event reporting) to examine the perceptions of EMS providers regarding near-misses and adverse events in out-of-hospital care. Results were reviewed by five researchers; analytic domains were assigned and emerging themes were identified. Descriptive statistics were calculated. RESULTS Fifteen in-depth interviews (73% advanced life support [ALS], 40% volunteer, and 87% male) resulted in 50 event descriptions. Eleven additional event reports were obtained from the anonymous reporting system. Of the 61 total events, 27 (44%) were near-misses and 34 (56%) were adverse events. Fourteen (23%) involved a child (< 19 years). Types of error included 33 clinical judgment (54%), 13 skill performance (21%), 9 medication event (15%), 3 destination choice (5%), and 3 others (5%). For the 21 cases where the provider discussed the event, 10 (48%) were reported to a physician, and 9 (43%) to a supervisor; 4 (19%) were not reported, and none were reported to the patient. Focus groups supported interview and event report data. Emerging themes included a focus on the errors of others and a "blame-and-shame" culture. CONCLUSIONS Adverse events and near-misses were common among the EMS providers who participated in this study, but the culture discourages sharing of this information. Participants attributed many events to systems issues and to inadequacies of other provider groups. Further study is necessary to investigate whether these hypothesis-generating themes are generalizable to the EMS community as a whole.
SERPENTS, SKELETONS, AND ANCESTORS?: THE TULA COATEPANTLI REVISITED

Abstract Since Acosta's work in the 1940s, relief carvings of serpents entwined with partially skeletonized personages on the coatepantli at Tula have frequently been identified as images of the Nahua Venus deity, Tlahuizcalpantecuhtli. Comparing these Toltec sculptures with this deity's iconography in Late Postclassic to Colonial period manuscripts, however, provides no support for this identification. Based on the northern Mesoamerican cultural connections of the Toltecs, the author suggests parallels between the coatepantli reliefs and the public display of ancestral and sacrificial human remains at Chalchihuites sites. Identification of the coatepantli figures as venerated ancestors from an ancestral cult is also supported by iconographic and archaeological evidence from Tula. Parallels to the coatepantli images in depictions of both living elites and ancestors juxtaposed with serpents from other Mesoamerican art traditions bolster this interpretation. On the basis of the evidence, the author hypothesizes that the skeletonized figures at Tula symbolize deceased kings and honored warriors rather than conquered foes.
Reassortants of H5N1 Influenza Viruses Recently Isolated from Aquatic Poultry in Hong Kong SAR

Abstract The H5N1 virus (H5N1/97) that caused the bird flu incident in Hong Kong in 1997 has not been isolated since the poultry slaughter in late 1997. But the donor of its H5 hemagglutinin gene, Goose/Guangdong/1/96-like (Gs/Gd/96-like) virus, established a distinct lineage and continued to circulate in geese in the area. In 2000, a virus from the Goose/Guangdong/1/96 lineage was isolated for the first time from domestic ducks. Subsequently, it has undergone reassortment, and these novel reassortants now appear to have replaced Gs/Gd/96-like viruses from its reservoir in geese and from ducks. The internal gene constellation is also different from H5N1/97, but these variants have the potential for further reassortment events that may allow the interspecies transmission of the virus.
Additional Psychometric Evidence and Construct Validity for a Revised Preferences Scale of Morningness

The Preferences Scale of morningness was originally conceived as a two‐factor, 11‐item model. More recently, a two‐factor, six‐item model has been developed and supported in two independent samples. These competing models were examined using structural equation modeling in a mixed student and working sample (n=120). The results supported the two factor, six‐item model (χ2(8, N=120)=10.84, p>0.05) as best fitting the sample data. The two factors explained 59% of the variance and Cronbach's alpha was 0.71. Significant differences (p<0.01) in self‐reported driving ability between morning and evening types were obtained by time‐of‐day, providing some evidence of construct validity. Morning types rated their performance as better in the morning hours and evening types rated their performance as better at night. We then examined whether self‐rated performance is subject to some degree of bias. For both morning and evening types, there was a tendency for those scoring high on self‐deception to rate their driving ability as better, but these differences were not significant. Overall, these findings suggest that self‐ratings are suitable for use in determining construct validity. Recommendations for future studies are made.
Loss minimization of electric drive systems using a DC/DC converter and an optimized battery voltage in automotive applications

Voltage source inverters generally feed the traction motor from a battery in automotive applications. By implementing a DC/DC converter between battery and inverter, the DC-link voltage is adjustable. This paper discusses the benefits of the variable DC-link voltage as an additional degree of freedom for a loss minimized control of electric drives in battery supplied vehicles. Inverter systems with and without DC/DC converter are compared and operating areas of improved efficiency are identified. Energy saving potentials resulting from an optimized battery voltage are discussed for different driving cycles.
Effect of plasma lipoprotein concentration on endocrine and meat quality characteristics, fatness and fat composition of hybrid entire boars.

Hybrid entire boars from Lithuanian indigenous wattle x wild boar intercross were used to establish low and high lipoprotein groups of hybrid animals in which low-density and high-density lipoprotein concentrations differed statistically significantly. The average age of the hybrids with a significantly lower level of plasma lipoproteins was higher and the testosterone concentration was lower compared to the animals with higher concentrations. The backfat thickness and loin area of the boars with a lower concentration of high-density lipoproteins (HDL) and total lipoproteins was higher than of the boars with higher concentrations of these lipoproteins. There were no significant differences in the longissimus dorsi muscle fatty acid composition between the boars with low and high concentration of low-density lipoproteins (LDL). However, the increase of plasma HDL was monitored to relate to possible decrease of C17:0 and C17:1, and increase of C16:1 in longissimus dorsi muscle, and decrease of C18:3n-3 in subcutaneous tissue. The hybrids with lower plasma total lipoproteins had lower content of C17:0 and C18:3n-3 and tended to have lower content of C20:0, C17:1 but have higher content of C16:1 and C20:1 in the longissimus dorsi muscle, and also lower content of C17:0 and C18:3n-3 and higher content of C16:1 and C20:1 in the subcutaneous tissue.
Allergic Reactions to Propofol in Egg-Allergic Children

BACKGROUND: Egg and/or soy allergy are often cited as contraindications to propofol administration. Our aim was to determine whether children with an immunoglobulin (Ig)E-mediated egg and/or soy allergy had an allergic reaction after propofol use. METHODS: We performed a retrospective case review over an 11-year period (1999–2010) of children with IgE-mediated egg and/or soy allergy who had propofol administered to them at the Children's Hospital Westmead, Sydney. RESULTS: Twenty-eight egg-allergic patients with 43 propofol administrations were identified. No child with a soy allergy who had propofol was identified. Twenty-one children (75%) were male, the median age at anesthesia was 2.4 years (range, 1–15 years), and the presence of other atopic disease was common (eczema 61%, asthma 32%, peanut allergy 43%). Most children (n = 19, 68%) had a history of an IgE-mediated clinical reaction to egg with evidence of a significantly positive egg white skin prick test (SPT) reaction (≥7 mm). Two of these had a history of egg anaphylaxis. The remaining children (n = 9, 32%) had never ingested egg because of significantly positive SPT (≥7 mm). All SPTs to egg were performed within 12 months of propofol administration. There was one nonanaphylactic immediate allergic reaction (n = 1 of 43, 2%) that occurred 15 minutes after propofol administration in a 7-year-old boy with a history of egg anaphylaxis and multiple other IgE-mediated food allergies (cow's milk, nut, and sesame). SPT to propofol was positive at 3 mm. No other egg-allergic child reacted to propofol. CONCLUSIONS: Despite current Australian labeling warnings, propofol was frequently administered to egg-allergic children. Propofol is likely to be safe in the majority of egg-allergic children who do not have a history of egg anaphylaxis.
The implementation of dynamic assignment of rights, responsibilities and sanctions to external agents in normative multiagent systems

The Implementation of Dynamic Assignment of Rights, Responsibilities and Sanctions to External Agents in Normative Multiagent Systems Farnaz Derakhshan Recently, the design and development o f multiagent systems (MASs) has become increasingly concerned with the recognition that they will be used in a dynamic and open environment. In such environments, it is a very difficult and complicated task to anticipate all possible runtime situations at design time. Therefore, in order to respond to changes in this environment it is necessary to allow the system to provide dynamic responses at runtime. This thesis is concerned with one particular aspect o f such responses. Our novel contribution is that we explicitly identify, clarify and address the problem o f dynamic assignment o f rights, responsibilities (R&Rs) and sanctions to external agents in normative M ASs. The background setting o f this work deals with the topic o f dynamism in normative M ASs and attempts to address and combine some issues regarding dynamic resources in M ASs and different types of norms in legal systems consisting of various types o f legal modalities, including obligation, prohibition, permission and right; enforcement modalities, including punishment, reward and compensation; and all key elements o f norms such as addressee, beneficiary, temporal notions, and preconditions. Following this introduction, we propose two alternative methods for dynamic assignment o f R&Rs and sanctions to external agents, and propose a formalism to represent a comm onsense understanding of our solution. The first m ethod is based on role hierarchies in M ASs and the second method is based on conditional norms. Both m ethods have common features including reliance on the concept o f role, using a normative Knowledge Base (KB) and sensitivity to runtime occurrences affecting the MAS. The significant differences o f these two mechanisms lie in the definition o f roles and normative KBs. Furthermore, we consider aspects o f implementation based on common features of the proposed methods, which we follow with a general implementation architecture for dynamic assignment of R&Rs and sanctions to external agents. Using this general architecture and guidelines, we present an agent-based auction application to dem onstrate the practical feasibility of our approach and o f our architecture. The implementation o f an agent auction that we present allows us to examine and compare the functionality of our two methods under various scenarios, including different runtim e occurrences and various types o f legal notions.
The art of compromise

Policy is modeled as the outcome of negotiations between two three-party parliamentary states. An election in jurisdiction A determines the composition of the legislature that selects a representative to negotiate an intergovernmental policy agreement with the representative from the legislature of jurisdiction B. Negotiations are modeled using Nash’s (1950) bargaining framework, modified to account for a simultaneous legislative ratification vote. Though agreements favor the legislative representative least willing to compromise, agreements between the bargainers may not follow the ordering of the parties’ ideal policies. An electoral outcome where support for the center party comes from extreme voters may emerge.
Treatment Factors Associated With Survival in Early-Stage Oral Cavity Cancer: Analysis of 6830 Cases From the National Cancer Data Base.

IMPORTANCE Most patients with oral cavity squamous cell cancer (OCSCC) are initially seen at an early stage (I and II). Although patient and tumor prognostic features have been analyzed extensively, population-level data examining how variations in treatment factors impact survival are lacking to date. OBJECTIVE To analyze associations between treatment variables and survival in stages I and II oral cavity squamous cell carcinoma. DESIGN, SETTING, AND PARTICIPANTS Retrospective study of cases in the National Cancer Data Base. Patients diagnosed as having stage I or II OCSCC between January 1, 2003, and December 31, 2006, and treated with surgery were identified. Univariate and multivariable analyses of overall survival based on patient, disease, and treatment characteristics were conducted. MAIN OUTCOMES AND MEASURES Overall survival and survival at 5 years. RESULTS In total, 6830 patients were included. Survival at 5 years was 69.7% (4760 patients). On univariate analysis, treatment factors associated with improved survival included treatment at academic or research institutions, no radiation therapy, no chemotherapy, and negative margins (P < .001 for all). Neck dissection was associated with improved survival (P = .001), reflecting pathologic restaging and elimination of patients with occult nodal disease. Patients treated at academic or research institutions were more likely to receive neck dissection and less likely to receive radiation therapy or have positive margins. On multivariable analysis, neck dissection (hazard ratio [HR], 0.85; 95% CI, 0.76-0.94; P = .003) and treatment at academic or research institutions (HR, 0.88; 95% CI, 1.01-1.26; P = .03) were associated with improved survival, whereas positive margins (HR, 1.27; 95% CI, 1.08-1.49; P = .005), insurance through Medicare (HR, 1.45; 95% CI, 1.25-1.69; P < .001) or Medicaid (HR, 1.96; 95% CI, 1.60-2.39; P < .001), and adjuvant radiation therapy (HR, 1.31; 95% CI, 1.16-1.49; P < .001) or adjuvant chemotherapy (HR, 1.34; 95% CI, 1.03-1.75; P = .03) were associated with compromised survival. CONCLUSIONS AND RELEVANCE Prognostic impacts of treatment factors in early OCSCC are presented. Overall survival for early OCSCC varies with demographic and tumor characteristics but also varies with treatment and system factors, which may represent targets for improving outcomes in this disease.
Narrative Perspectives on Self-Directed Foreign Language Learning in a Computer- and Mobile-Assisted Language Learning Context

Millions of learners around the world use self-directed computer- and mobile-assisted language learning (CALL, MALL) programs to study foreign languages. One such program, Duolingo, currently attracts over 120 million users and is claimed (by the publisher) to be a highly effective method of language learning. While L2 researchers have shown limited engagement with similar large-scale commercial programs, issues related to learner persistence, motivation, and program efficacy have been reported. This study investigates the experiences and efficacy of learning Turkish on Duolingo for 12 weeks, drawing on a methodological tradition of researcher narratives. Three graduate student researchers kept diaries and completed weekly reflections on their Turkish learning experiences, which served as source material for individual narrative analysis. The resulting narratives were discussed and analyzed collaboratively from an ecological perspective. Strategies used by the researcher-participants were heavily influenced by ecological factors. Persistence in learning was found to be influenced by ecological factors and varied across timescales. Ultimately, the researcher-participants had limited Turkish learning outcomes and felt demotivated to continue studying on Duolingo. Implications for CALL/MALL design include presenting materials in a meaningful context, capitalizing on social affordances, and providing meaningful feedback to learners in order to facilitate learning and goal-setting.