bluuebunny/crossref_metadata_2025 huggingface dataset:
Severe thymic hyperplasia in a newborn calf associated with impaired T-cell differentiation
Authors: Fantinato Eleonora , Pravettoni Davide , Forlani Annalisa , Riccaboni Pietro , Binanti Diana
Published: July 2013

A 1-day-old female Holstein–Friesian calf was presented for severe dyspnea. Physical examination revealed respiratory distress, moderate edema of the ventral neck, and swollen jugular veins. The calf died and was submitted for necropsy. A severely enlarged thymus (40 cm × 20 cm × 10 cm) weighing 1.37 kg was detected on gross examination. Histomorphology was normal but no tingible body macrophages were observed in the medullary areas. Immunohistochemistry was characterized by the lack of thymic cluster of differentiation 3 and major histocompatibility complex class II expression compared to age-matched controls. The findings were consistent with severe thymic hyperplasia, a rare congenital condition that is also described in children. Immunohistochemical findings were suggestive of impaired T-cell development and selection associated with lack of apoptosis of thymic cells (lack of tingible body macrophages). Thymic hyperplasia in juvenile animals should be considered among the differential diagnoses of mediastinal masses as a rare cause of respiratory distress in newborn calves.
Individualizing Standardized Tests
Authors: Krohne Kariann , Torres Sandra , Slettebø Åshild , Bergland Astrid
Published: July 2013

In assessing geriatric patients’ functional status, health care professionals use a number of standardized tests. These tests have defined administration procedures that restrict communication and interaction with patients. In this article, we explore the experiences of occupational therapists and physiotherapists acting as standardized test administrators. Drawing on fieldwork, interviews with physiotherapists and occupational therapists, and observations of test situations on acute geriatric wards, we suggest that the test situation generates a tension between what standardization demands and what individualization requires. Our findings illustrate how physiotherapists and occupational therapists navigate between adherence to the test standard and meeting what they consider to be the individual patient’s needs in the test situation. We problematize this navigation, and argue that the health care professional’s use of relational competence is the means to reach and maintain individualization.
The Nature of Life-Transforming Changes Among Cancer Survivors
Authors: Skeath Perry , Norris Shanti , Katheria Vani , White Jonathan , Baker Karen , Handel Dan , Sternberg Esther , Pollack John , Groninger Hunter , Phillips Jayne , Berger Ann
Published: July 2013

Some cancer survivors report positive subjective changes they describe as “life transforming.” We used a grounded theory approach to identify the content, underlying process, and identifying characteristics of self-defined “life-transforming” changes (LTCs) reported by 9 cancer survivors. To actualize their hopes for improvement, participants used a self-guided process centered on pragmatic action: researching options, gaining experience, and frankly evaluating results. Many participants discovered unanticipated personal abilities and resources, and those became highly useful in coping with other challenges apart from cancer. This made the increased personal abilities and resources “life transforming” rather than being substantially limited to reducing cancer-related problems. The action-oriented features and processes of LTCs seemed to be more fully described by experiential learning theory than by posttraumatic growth and coping. Supportive intervention to facilitate positive change processes could decrease suffering and enhance positive psychosocial and spiritual outcomes for cancer survivors.
Dreaming of electric sheep? Exploring the functions of dream-like mechanisms in the development of mental imagery simulations
Authors: Svensson Henrik , Thill Serge , Ziemke Tom
Published: July 2013

According to the simulation hypothesis, mental imagery can be explained in terms of predictive chains of simulated perceptions and actions, i.e., perceptions and actions are reactivated internally by our nervous system to be used in mental imagery and other cognitive phenomena. Our previous research shows that it is possible but not trivial to develop simulations in robots based on the simulation hypothesis. While there are several previous approaches to modelling mental imagery and related cognitive abilities, the origin of such internal simulations has hardly been addressed. The inception of simulation (InSim) hypothesis suggests that dreaming has a function in the development of simulations by forming associations between experienced, non-experienced but realistic, and even unrealistic perceptions. Here, we therefore develop an experimental set-up based on a simple simulated robot to test whether such dream-like mechanisms can be used to instruct research into the development of simulations and mental imagery-like abilities. Specifically, the hypothesis is that ‘dreams’ informing the construction of simulations lead to faster development of good simulations during waking behaviour. The paper presents initial results in favour of the hypothesis.
Natural Disaster and Democratic Legitimacy
Authors: Carlin Ryan E. , Love Gregory J. , Zechmeister Elizabeth J.
Published: July 2013

Can natural disasters undermine democratic legitimacy? This article maps a causal pathway from natural disaster damage to shifts in opinion and behavioral tendencies in less established democracies. It theorizes citizens who suffer damage in such contexts will tend toward lower evaluations of democratic institutions, lower support for democratic values and practices, and stronger dispositions toward action. These expectations are tested with national survey data collected following Chile’s 2010 earthquake and tsunami by analyzing intracountry differences in damage with matching techniques and regression analyses. Results are consistent with expectations, with important implications for Chile and other less established democracies.
The Political Glass Cliff
Authors: Kulich Clara , Ryan Michelle K. , Haslam S. Alexander
Published: July 2013

An archival study of U.K. General Election results from 2001, 2005, and 2010 revealed that Conservative black and minority ethnic (BME) candidates were less successful than their white counterparts. However, mediation analyses demonstrate that this lack of success can be explained by the lower winnability of BME candidates’ seats, such that the opposition candidate held a seat with a significantly larger majority compared with white candidates’ opponents. Results and implications are discussed in the framework of the “glass cliff,” previously demonstrated for women, in the sense that the seats minority groups contested were harder to win compared with majority groups.
Dynamic linear models-based time series decomposition and its application on bearing fault diagnosis
Authors: Tang Haifeng , Chen Jin , Dong Guangming
Published: July 2013

Although various methods have been presented in the literature for rotating machine fault detection, it still remains a huge challenge to accurately extract features from non-stationary vibration signals with a high noise level, typically in the case of rolling element bearings faults diagnosis. Due to its random and non-stationary nature, fault related features are difficult to extract by common techniques and are usually overwhelmed by noise and macro-structural vibrations. In this paper, a new time series decomposition method based on a dynamic linear model is proposed, which provides time domain decomposition of a non-stationary signal into collections of latent components. The signal of a damaged bearing consists of exponentially decaying ringing that occurs periodically at the bearing characteristic defect frequency. Dynamic linear models with time-varying cyclical components provide a more generalized and adaptive description on rolling element bearings’ vibration signal with time-varying cyclical behavior. This allows the precise isolation of latent, quasi-cyclical bearing fault components via inferences on the time-varying parameters which characterize these components. An accelerated whole lifetime test of bearing has been performed to collect vibration data, which is utilized to validate the effectiveness of the proposed method.
The nonlinear analysis of a pure rolling low-noise excavating system with one-pair clearance
Authors: Su-xia Zhang , Long-xu Xu , Xi-jun Liu , Shu-jun Hou
Published: July 2013

In this paper, the nonlinear dynamics equations of a pure rolling low-noise excavating system with one clearance are derived, and the characters and the factors affecting the response, such as rotating angular velocity, mass center of crank, elastic coefficient in the normal direction and the size of clearance, are discussed. The results show that, the larger the elastic coefficient is, the more stable the system is; the value of the elastic coefficient at clearance has almost no affect on the load torque, whether from the magnitude or fluctuation. When the size of clearance and rotational velocity are increased, the interactive forces will increase, and the maximum value of impact force is increased also. The results provide preference for the design of low-noise system in actual engineering.
Active suppression of imbalance vibration in the magnetically suspended control moment gyro
Authors: Xu Xiangbo , Fang Jiancheng , Li Haitao , Cui Peiling
Published: July 2013

The magnetically suspended control moment gyro (MSCMG) system is an actuator for attitude control of spacecrafts. It consists of a gimbal and a high-speed rotor suspended by magnetic bearings (MBs). The imbalance vibration due to the high-speed rotor can cause a velocity ripple to the gimbal and be transmitted to the spacecraft to decrease its attitude control precision. To suppress the imbalance vibration, this paper introduces an active control method in both the MBs and gimbal systems. Firstly, the structure and dynamics of the MSCMG system with the MBs and gimbal are described, and the transmission of the imbalance vibration is discussed. Then a notch filter with a phase shift and a feedforward controller are designed to prevent the MB system from generating the imbalance vibration by making the rotor rotate around its inertial axis. To correct the feedforward control errors resulting from power amplifiers, phase and gain compensations are made. Finally, another notch filter with a phase shift is employed to suppress the velocity ripple caused by the residual vibration from the MB system, and a constant-gain Kalman filter is adopted to obtain the best real-time estimate value of the gimbal velocity. Stabilities of the vibration control method and the Kalman filter are analyzed. Simulations and experiments have been performed to validate the proposed control method, which has a short computation time and can be used in many practical applications.
Managing Information
Authors: Galasiński Dariusz , Ziółkowska Justyna
Published: July 2013

Doctors are required to document their examinations of the patient. This task is particularly important in psychiatry, where what the patient says is practically the only source of information available to the clinician. In our article we shall focus on the process of information management in psychiatry and trace the information which was recorded in the patients’ notes back to its origin in the interview. Our data consists of eight recordings of psychiatric interviews along with the patients’ notes.

Our main argument is that the notes are not merely written from the point of view of the psychiatrist, but might have little or nothing to do with the interview. We demonstrate, first, that accurate notes are a record of how the doctor conducted the interview. Second, the notes doctors made also misrepresent the interview with the patient: doctors record false information, distort it, take out of its context.
“I Was Born . . .” (No You Were Not!)
Authors: kumar hari stephen
Published: July 2013

While literary critics applaud Barack Obama’s memoir Dreams from My Father for its polyvocal self-authorizations, the book’s broader cultural context shows how politics and public performances constrain possibilities for multicultural identities. The fluid personal identity authorized by the book faces political pressures that require public reaffirmation of dominant narratives of both Whiteness and monocultural American supremacy. I trace specific counterattacks on Obama’s identity during the 2008 U.S. presidential election cycle, including “controversies” around his birth narratives. I evoke my own narratives as a Brown-and-bearded American immigrant to complicate my audiencing of Obama’s performative responses to “Birtherism” even after he was elected president. I focus especially on his interaction with Donald Trump prior to the raid that killed Osama bin Laden in May 2011. In such moments, I argue that Obama navigates away from self-authorizing his multicultural American identities and toward authorizing American power in ways that reinscribe a monocultural nationalism.
Hospitality Industry Web-Based Self-Service Technology Adoption Model
Authors: Lee Louisa Yee-Sum
Published: July 2013

Technology advancement induces information technology infusion in business processes and service encounter. The airline industry employs web-based self-service technology (SST), namely, airline online check-in system, to provide more choice, control, and convenience to passengers. Customer adoption intention of web-based SST is particularly momentous, since customer adoption highly drives the service development. Technology acceptance model (TAM), a robust framework measuring factors affecting technology acceptance intention, has been broadly examined in numerous settings. However, inconsistent results are noted in Western and non-Western countries, and the model is challenged from limited cultural orientation. In response to this criticism, this research aims to identify culturally unique dimensions for TAM and construct a framework for hospitality web-based SST adoption from Westerns’ and Asians’ perspectives. Etic–emic approach, incorporating literature search and focus group interviews with Asian respondents, was employed to provide a thoughtful review of examined factors and generate new factors from an Asian perspective.
Self-esteem and quality of life of people living with HIV/AIDS
Authors: Manhas Coral
Published: July 2013

In India in 2009, it was estimated that 2.4 million people were living with HIV, which equates to a prevalence of 0.3 percent. While this seems low, because India’s population is so large, this rate is third in the world in terms of the absolute number of people living with HIV/AIDS. This study evaluated the self-esteem and quality of life of people living with HIV/AIDS in the Indian population using a correlational design. A significant positive correlation between self esteem and the different dimensions of quality of life was established. Interventions designed for people with HIV/AIDS could well include self esteem as a moderator of quality of life.
Perceptions of cancer as a death sentence: Prevalence and consequences
Authors: Moser Richard P , Arndt Jamie , Han Paul K , Waters Erika A , Amsellem Marni , Hesse Bradford W
Published: July 2013

Research suggests that perceiving cancer as a death sentence is a critical determinant of health care–seeking behaviors. However, there is limited information regarding the prevalence of this perception in the US population. Cross-sectional analysis of data (n = 7674 adults) from the 2007-2008 administration of the nationally representative Health Information National Trends Survey (HINTS 3) was performed. A majority (61.6%) of respondents perceived cancer as death sentence, and more than one-third (36%) of respondents reported that they avoid seeing their physicians. In the adult US population, perceiving cancer as a death sentence is common and is associated with education level and avoidance of physicians.
From knowledge to action in public health management: Experiences from a Norwegian context
Authors: Lillefjell M. , Knudtsen M. S. , Wist G. , Ihlebæk C.
Published: July 2013

Aims: A pro-active approach that incorporates the effective use of scientific evidence and data is a major goal in public health work. This study aimed to identify local and regional strengths and barriers to identify, translate, and use relevant evidence of “what works” in public health management. Methods: Focus group discussions were performed among 22 researchers, public health leaders and/or leaders with organisational and policy responsibilities in two municipalities, one county, and a university research centre. Results: Access to the population’s health data is insufficient for taking action. The focus group discussions clarified a need for a skills programme that specifically focuses on analysis and process expertise. Moreover, communication and collaboration among key stakeholders involved in evidence-based practices like research, policy, and practice should be enhanced in order to facilitate evidence-based policy making. Conclusions: The complex relationship between context and behaviour and the necessity of influencing systems and structures as well as individuals to promote change underlines the need for a clear national initiative to facilitate knowledge exchanges among practitioners, policy makers, and researchers.
Perceived gender inequality in the couple relationship and musculoskeletal pain in middle-aged women and men
Authors: Bohlin Anna , Ahlgren Christina , Hammarstrom Anne , Gustafsson Per E.
Published: July 2013

Aims: Musculoskeletal pain is a major health problem, especially in women, and is partially determined by psychosocial factors. The aim of the present study was to investigate whether gender inequality in the couple relationship was related to musculoskeletal pain. Methods: Participants ( n=721; 364 women and 357 men) were all individuals living in a couple relationship in the Northern Swedish Cohort, a 26-year Swedish cohort study. Self-administered questionnaire data at age 42 years comprised perceived gender inequality in the couple relationship and musculoskeletal pain (in three locations, summarised into one score and median-split), concurrent demographic factors, psychological distress, and previous musculoskeletal pain at age 30 years. Associations were examined using logistic regression. Results: Gender inequality was positively associated with symptoms of musculoskeletal pain in the total sample, remaining significant after addition of possible confounders and of previous musculoskeletal pain. Separate adjustment for concurrent psychological distress attenuated the association but not below significance. The association was present and of comparable strength in both women and men. Conclusions: Gender inequality in the couple relationship might contribute to the experience of musculoskeletal pain in both women and men. The results highlight the potential adverse bodily consequences of living in unequal relationships.
Carotid Cavernous Fistulae Occurring After the Use of the Fogarty Catheter in Carotid Surgery
Authors: Orozco Ludwig D. , Stacy Jason D. , Luqman Ali W. , Buciuc Razvan F. , Luzardo Gustavo D.
Published: July 2013

The Fogarty catheter represents a major advancement for the effective removal of distal thrombi during vascular surgery, including carotid endarterectomy (CEA). One complication related to its use is injury to the cavernous carotid artery with development of a carotid cavernous fistula (CCF). Including a recent case at our institution, 21 patients with a Fogarty-related CCF have been reported since 1967. We performed a detailed review of all Fogarty-related CCFs during the treatment of carotid occlusive disease. We suggest a management algorithm for post-CEA acute carotid occlusion.
Systemic light-chain amyloidosis presenting with rapid progressive heart failure
Authors: Sunbul Murat , Durmus Erdal , Kivrak Tarik , Besiroglu Fatih , Gerin Fatma , Sari Ibrahim , Mutlu Bulent
Published: July 2013

Systemic amyloid light-chain (AL) amyloidosis is caused by deposition of immunoglobulin light-chain proteins. AL amyloidosis is a rapidly progressive disease that affects multiple organs. Cardiac involvement is frequent (50%) and the median survival is 5 months following diagnosis. Although transthoracic echocardiography can show characteristics findings, further diagnostic modalities are required for diagnosis. The gold standard of the diagnosis is presence of the amyloid in a tissue biopsy specimen. We present here a case of AL amyloidosis with presenting rapid progressive heart failure. Despite improvements in diagnostic and therapeutic modalities, diagnosis is difficult and prognosis is still poor in patients with cardiac involvement as in the present case.
Anxiety in Parkinson’s disease: identification and management
Authors: Chen Jack J. , Marsh Laura
Published: July 2013

Anxiety disturbances are recognized as common psychiatric comorbidities in Parkinson’s disease (PD) and contribute to significant impairments in areas of cognitive, functional, motor and social performance. Anxiety in PD results in reduced quality of life, higher levels of care dependency and increased caregiver burden. Surprisingly, there is a paucity of treatment data. In one randomized, controlled study, bromazepam was found to be effective for anxiety in PD. However, usage of benzodiazepines in the PD population is limited by potential risk of confusion and falls. There are no controlled studies of selective serotonin reuptake inhibitors (SSRIs) for anxiety in PD. However, results from uncontrolled studies suggest that SSRIs are effective for anxiety in PD, although in these studies anxiety outcomes were secondary. This review underscores that, given the high prevalence of anxiety disturbances in PD, there is a significant paucity of treatment data for this population. Additional studies are warranted. In the meantime, clinicians should rely on empiric assessments of known risks and putative benefits to guide treatment decisions. Cognitive and behavioral therapies (with or without pharmacotherapy) have demonstrated efficacy and warrant consideration. When feasible, a targeted and individualized multimodal approach utilizing psychotherapeutic interventions along with pharmacologic therapies should be considered.
Magnetic Resonance Imaging Findings of Snowboarding Osteochondral Injuries to the Middle Talocalcaneal Articulation
Authors: Clanton Thomas O. , Chacko Anna K. , Matheny Lauren M. , Hartline Braden E. , Ho Charles P.
Published: July 2013

This report presents 2 cases of subtle injuries to the subtalar joint, specifically, osteochondral defects of the middle facet of the talus and concomitant involvement of the middle talocalcaneal articulation sustained while snowboarding. The 3T magnetic resonance image revealed fracture of the lateral talar process with osteochondral lesions of the middle talocalcaneal articulation. This injury can lead to severe and chronic disability if undetected and could ultimately end athletic participation prematurely.
Inherited susceptibility to chronic lymphocytic leukemia: evidence and prospects for the future
Authors: Brown Jennifer R.
Published: July 2013

Chronic lymphocytic leukemia (CLL) is the most common leukemia in the United States and one of the most heritable cancers. A family history of the disease is perhaps the best defined risk factor, and approximately 15–20% of CLL patients have a family member with CLL or a related lymphoproliferative disorder. Much effort has been devoted to trying to elucidate the mechanisms underlying this genetic risk. Familial CLL appears to be clinically and biologically similar to sporadic CLL, and most if not all CLL appears to be preceded by monoclonal B-cell lymphocytosis (MBL), which does appear to occur at higher frequency in relatives in families with CLL. Neither linkage studies nor candidate gene association studies have proven particularly informative in CLL, but genomewide association studies have identified multiple low-risk variants that together explain about 16% of the familial risk of CLL. Studies of individual families have identified higher-risk single nucleotide polymorphisms or copy number variants associated with disease risk in those families. Current efforts to identify additional risk loci are focused on applying next-generation sequencing to the germline of informative CLL families as well as individuals with sporadic CLL.
Early life factors initiate a ‘vicious circle’ of affective and gastrointestinal symptoms: A longitudinal study
Authors: Jones Michael P , Van Oudenhove Lukas , Koloski Natasha , Tack Jan , Talley Nicholas J
Published: July 2013

Objective

Functional gastrointestinal disorders (FGID) have been shown to be associated with both comorbid mood disorders and traumatic events such as abuse earlier in life. In a longitudinal study, we tested a model that hypothesized: (i) childhood abuse was associated with subsequent mood disorder and pain or interference in life by bowel symptoms both directly and indirectly via neurotic personality; and (ii) an ongoing cycle of mood disorder impacts on bowel symptoms.

Design

Subjects from the general population classified as irritable bowel syndrome and/or functional dyspepsia (IBS/FD, n  = 207) or free of FGID (n  = 100) were prospectively studied every 6 months over 18 months. In addition to bowel symptom interference and abdominal pain, measures of personality (neuroticism), childhood abuse history, depression, and anxiety were obtained. The hypothesized model was tested via Path Modelling.

Results

Childhood abuse was found to be directly associated with neuroticism but only indirectly associated with baseline interference and mood disorders (via neuroticism). The data further supported an ongoing cycle of elevations in mood disorders and pain/interference by bowel symptoms. The data supported direct effects of interference at one time point on interference at the subsequent time point in addition to indirect effects of prior anxiety and depression. Repeating the model with pain frequency as the outcome yielded almost identical findings which suggests the findings are generalized across domains of symptoms and quality‐of‐life.

Conclusion

Our data provide support for a model characterized by a ‘vicious circle’ between mood disorders and FGID symptoms in adulthood, with initial input from early life factors.
Endosonography For Right‐sided and Acute Upper Intestinal Misery: the EFRAIM study
Authors: Jung Andreas , Schlag Christoph , Becker Valentin , von Delius Stefan , Lersch Christian , Jeliazkova Petia , Herner Alexander , Bajbouj Monther , Schuster Tibor , Meining Alexander
Published: July 2013

Background

Acute upper abdominal pain is a frequent symptom leading to hospital admission.

Objective

To determine whether a primary intra‐ and extraluminal diagnostic approach enabled by endoscopic ultrasound is as effective as a conventional diagnostic algorithm of transabdominal ultrasound followed by oesophagogastroduodenoscopy.

Methods

A total of 240 patients who presented with acute right‐sided and/or upper abdominal pain were prospectively recruited. Exclusion criteria were chronic pain, malignancy, prior abdominal surgery, bleeding, peritonitis, and elevated liver enzymes or lipase as defined 3‐times higher than upper reference value. All patients underwent first transabdominal ultrasound and were then randomized (1 : 1) to either endoscopy followed by endoscopic ultrasound or vice versa. Patients and respective examiners were blinded to prior findings.

Results

A total of 223 patients were included. Endoscopic ultrasound provided a higher diagnostic yield than the combination of transabdominal ultrasound and endoscopy (62.3 vs. 50.7%; p  = 0.001). For mucosal/intraluminal lesions, we observed a very good agreement between both endoscopic modalities (kappa 0.89). The agreement for pancreatic and biliary causes was good between both ultrasound modalities (kappa 0.66).

Conclusions

Due to its high diagnostic yield, endoscopic ultrasound as a primary diagnostic modality appears to be a valuable option in patients with acute upper abdominal pain.
The value of allogeneic and autologous hematopoietic stem cell transplantation in prognostically favorable acute myeloid leukemia with double mutant CEBPA
Authors: Schlenk Richard F. , Taskesen Erdogan , van Norden Yvette , Krauter Jürgen , Ganser Arnold , Bullinger Lars , Gaidzik Verena I. , Paschka Peter , Corbacioglu Andrea , Göhring Gudrun , Kündgen Andrea , Held Gerhard , Götze Katharina , Vellenga Edo , Kuball Juergen , Schanz Urs , Passweg Jakob , Pabst Thomas , Maertens Johan , Ossenkoppele Gert J. , Delwel Ruud , Döhner Hartmut , Cornelissen Jan J. , Döhner Konstanze , Löwenberg Bob
Published: July 2013

Key Points

In AML with bialleleic CEBPA-mut relapse-free survival was improved by allogeneic and autologous hematopoietic stem cell transplantation. In relapsed patients second complete remission rate was high and survival was favorable after an allogeneic transplantation.
Design and validation of a supragenome array for determination of the genomic content of Haemophilus influenzae isolates
Authors: Eutsey Rory A , Hiller N Luisa , Earl Joshua P , Janto Benjamin A , Dahlgren Margaret E , Ahmed Azad , Powell Evan , Schultz Matthew P , Gilsdorf Janet R , Zhang Lixin , Smith Arnold , Murphy Timothy F , Sethi Sanjay , Shen Kai , Post J Christopher , Hu Fen Z , Ehrlich Garth D
Published: July 2013

Background

Haemophilus influenzae colonizes the human nasopharynx as a commensal, and is etiologically associated with numerous opportunistic infections of the airway; it is also less commonly associated with invasive disease. Clinical isolates of H. influenzae display extensive genomic diversity and plasticity. The development of strategies to successfully prevent, diagnose and treat H. influenzae infections depends on tools to ascertain the gene content of individual isolates.

Results

We describe and validate a Haemophilus influenzae supragenome hybridization (SGH) array that can be used to characterize the full genic complement of any strain within the species, as well as strains from several highly related species. The array contains 31,307 probes that collectively cover essentially all alleles of the 2890 gene clusters identified from the whole genome sequencing of 24 clinical H. influenzae strains. The finite supragenome model predicts that these data include greater than 85% of all non-rare genes (where rare genes are defined as those present in less than 10% of sequenced strains). The veracity of the array was tested by comparing the whole genome sequences of eight strains with their hybridization data obtained using the supragenome array. The array predictions were correct and reproducible for ~ 98% of the gene content of all of the sequenced strains. This technology was then applied to an investigation of the gene content of 193 geographically and clinically diverse H. influenzae clinical strains. These strains came from multiple locations from five different continents and Papua New Guinea and include isolates from: the middle ears of persons with otitis media and otorrhea; lung aspirates and sputum samples from pneumonia and COPD patients, blood specimens from patients with sepsis; cerebrospinal fluid from patients with meningitis, as well as from pharyngeal specimens from healthy persons.

Conclusions

These analyses provided the most comprehensive and detailed genomic/phylogenetic look at this species to date, and identified a subset of highly divergent strains that form a separate lineage within the species. This array provides a cost-effective and high-throughput tool to determine the gene content of any H. influenzae isolate or lineage. Furthermore, the method for probe selection can be applied to any species, given a group of available whole genome sequences.
Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea
Authors: Yelton Alexis P , Comolli Luis R , Justice Nicholas B , Castelle Cindy , Denef Vincent J , Thomas Brian C , Banfield Jillian F
Published: July 2013

Background

Metal sulfide mineral dissolution during bioleaching and acid mine drainage (AMD) formation creates an environment that is inhospitable to most life. Despite dominance by a small number of bacteria, AMD microbial biofilm communities contain a notable variety of coexisting and closely related Euryarchaea, most of which have defied cultivation efforts. For this reason, we used metagenomics to analyze variation in gene content that may contribute to niche differentiation among co-occurring AMD archaea. Our analyses targeted members of the Thermoplasmatales and related archaea. These results greatly expand genomic information available for this archaeal order.

Results

We reconstructed near-complete genomes for uncultivated, relatively low abundance organisms A-, E-, and Gplasma, members of Thermoplasmatales order, and for a novel organism, Iplasma. Genomic analyses of these organisms, as well as Ferroplasma type I and II, reveal that all are facultative aerobic heterotrophs with the ability to use many of the same carbon substrates, including methanol. Most of the genomes share genes for toxic metal resistance and surface-layer production. Only Aplasma and Eplasma have a full suite of flagellar genes whereas all but the Ferroplasma spp. have genes for pili production. Cryogenic-electron microscopy (cryo-EM) and tomography (cryo-ET) strengthen these metagenomics-based ultrastructural predictions. Notably, only Aplasma, Gplasma and the Ferroplasma spp. have predicted iron oxidation genes and Eplasma and Iplasma lack most genes for cobalamin, valine, (iso)leucine and histidine synthesis.

Conclusion

The Thermoplasmatales AMD archaea share a large number of metabolic capabilities. All of the uncultivated organisms studied here (A-, E-, G-, and Iplasma) are metabolically very similar to characterized Ferroplasma spp., differentiating themselves mainly in their genetic capabilities for biosynthesis, motility, and possibly iron oxidation. These results indicate that subtle, but important genomic differences, coupled with unknown differences in gene expression, distinguish these organisms enough to allow for co-existence. Overall this study reveals shared features of organisms from the Thermoplasmatales lineage and provides new insights into the functioning of AMD communities.
Transcriptome analyses of the human retina identify unprecedented transcript diversity and 3.5 Mb of novel transcribed sequence via significant alternative splicing and novel genes
Authors: Farkas Michael H , Grant Gregory R , White Joseph A , Sousa Maria E , Consugar Mark B , Pierce Eric A
Published: July 2013

Background

The retina is a complex tissue comprised of multiple cell types that is affected by a diverse set of diseases that are important causes of vision loss. Characterizing the transcripts, both annotated and novel, that are expressed in a given tissue has become vital for understanding the mechanisms underlying the pathology of disease.

Results

We sequenced RNA prepared from three normal human retinas and characterized the retinal transcriptome at an unprecedented level due to the increased depth of sampling provided by the RNA-seq approach. We used a non-redundant reference transcriptome from all of the empirically-determined human reference tracks to identify annotated and novel sequences expressed in the retina. We detected 79,915 novel alternative splicing events, including 29,887 novel exons, 21,757 3′ and 5′ alternate splice sites, and 28,271 exon skipping events. We also identified 116 potential novel genes. These data represent a significant addition to the annotated human transcriptome. For example, the novel exons detected increase the number of identified exons by 3%. Using a high-throughput RNA capture approach to validate 14,696 of these novel transcriptome features we found that 99% of the putative novel events can be reproducibly detected. Further, 15-36% of the novel splicing events maintain an open reading frame, suggesting they produce novel protein products.

Conclusions

To our knowledge, this is the first application of RNA capture to perform large-scale validation of novel transcriptome features. In total, these analyses provide extensive detail about a previously uncharacterized level of transcript diversity in the human retina.
Analysis of copy number variants by three detection algorithms and their association with body size in horses
Authors: Metzger Julia , Philipp Ute , Lopes Maria Susana , da Camara Machado Artur , Felicetti Michela , Silvestrelli Maurizio , Distl Ottmar
Published: July 2013

Background

Copy number variants (CNVs) have been shown to play an important role in genetic diversity of mammals and in the development of many complex phenotypic traits. The aim of this study was to perform a standard comparative evaluation of CNVs in horses using three different CNV detection programs and to identify genomic regions associated with body size in horses.

Results

Analysis was performed using the Illumina Equine SNP50 genotyping beadchip for 854 horses. CNVs were detected by three different algorithms, CNVPartition, PennCNV and QuantiSNP. Comparative analysis revealed 50 CNVs that affected 153 different genes mainly involved in sensory perception, signal transduction and cellular components. Genome-wide association analysis for body size showed highly significant deleted regions on ECA1, ECA8 and ECA9. Homologous regions to the detected CNVs on ECA1 and ECA9 have also been shown to be correlated with human height.

Conclusions

Comparative analysis of CNV detection algorithms was useful to increase the specificity of CNV detection but had certain limitations dependent on the detection tool. GWAS revealed genome-wide associated CNVs for body size in horses.
Defining natural species of bacteria: clear-cut genomic boundaries revealed by a turning point in nucleotide sequence divergence
Authors: Tang Le , Li Yang , Deng Xia , Johnston Randal N , Liu Gui-Rong , Liu Shu-Lin
Published: July 2013

Background

Bacteria are currently classified into arbitrary species, but whether they actually exist as discrete natural species was unclear. To reveal genomic features that may unambiguously group bacteria into discrete genetic clusters, we carried out systematic genomic comparisons among representative bacteria.

Results

We found that bacteria of Salmonella formed tight phylogenetic clusters separated by various genetic distances: whereas over 90% of the approximately four thousand shared genes had completely identical sequences among strains of the same lineage, the percentages dropped sharply to below 50% across the lineages, demonstrating the existence of clear-cut genetic boundaries by a steep turning point in nucleotide sequence divergence. Recombination assays supported the genetic boundary hypothesis, suggesting that genetic barriers had been formed between bacteria of even very closely related lineages. We found similar situations in bacteria of Yersinia and Staphylococcus.

Conclusions

Bacteria are genetically isolated into discrete clusters equivalent to natural species.
Novel polymerase gamma (POLG1) gene mutation in the linker domain associated with parkinsonism
Authors: Dolhun Rachel , Presant Erin M , Hedera Peter
Published: July 2013

Background

Mutations in the POLG1 gene have variable phenotypic presentations and a high degree of clinical suspicion is necessary for their recognition. Parkinsonism and ataxia are the most common movement disorders associated with POLG1 mutations but no phenotype-genotype correlation has been established.

Case presentation

We identified a male patient with progressive external ophthalmoplegia who also developed a progressive bradykinesia, rigidity and camptocormia in the third decade. Parkinsonism was partially responsive to dopaminegic replacement. His father and brother had reportedly similar clinical problems. Genetic analysis identified a novel mutation p.K512M in the POLG1 gene.

Conclusion

This report further expands the spectrum of POLG1-associated neurologic problems with the report of a novel mutation in the linker region of the gene, which are rarely associated with parkinsonism.
Successful reduction of hospital-acquired methicillin-resistant Staphylococcus aureus in a urology ward: a 10-year study
Authors: Tatokoro Manabu , Kihara Kazunori , Masuda Hitoshi , Ito Masaya , Yoshida Soichiro , Kijima Toshiki , Yokoyama Minato , Saito Kazutaka , Koga Fumitaka , Kawakami Satoru , Fujii Yasuhisa
Published: July 2013

Background

To eradicate hospital-acquired methicillin-resistantStaphylococcus aureus(MRSA) using a stepwise infection control strategy that includes an avoidance of antimicrobial prophylaxis (AMP) based on surgical wound classification and an improvement in operative procedures in gasless single-port urologic surgery.

Methods

The study was conducted at an 801-bed university hospital. Since 2001, in the urology ward, we have introduced the stepwise infection control strategy. In 2007, surveillance cultures for MRSA in all urological patients were commenced. The annual incidence of MRSA was calculated as a total number of newly identified MRSA cases per 1,000 patient days. Trend analysis was performed using a Poisson regression.

Results

Over the study period, 139,866 patients, including 10,201 urology patients, were admitted to our hospital. Of these patients, 3,719 patients, including 134 ones in the urology ward, were diagnosed with MRSA throughout the entire hospital. Although the incidence of MRSA increased throughout the entire hospital (p= 0.002), it decreased significantly in the urology ward (p< 0.0001). Of the 134 cases, 45 (33.6%) were classified as “imported,” and 89 (66.4%) as “acquired.” In the urology ward, the incidence of acquired MRSA decreased significantly over time (p< 0.0001), whereas the incidence of imported MRSA did not change over time (p= 0.66). A significant decrease (p< 0.0001) in the incidence of clinically significant MRSA infection over time was found.

Conclusions

Stepwise infection control strategy that includes a reduction or avoidance of antimicrobial prophylaxis in minimally invasive surgery can contribute to a reduction in hospital-acquired MRSA.

Trial registration

Current study has approved by the institutional ethical review board (No.1141).
Saturated fatty acid palmitate-induced insulin resistance is accompanied with myotube loss and the impaired expression of health benefit myokine genes in C2C12 myotubes
Authors: Yang Ming , Wei Dandan , Mo Chunfen , Zhang Jie , Wang Xu , Han Xiaojuan , Wang Zhe , Xiao Hengyi
Published: July 2013

Background

Excessive circular fatty acid, particlarly saturated fatty acid, can result in insulin resistance in skeletal muscle, but other adverse effects of fatty acid accumulation in myocytes remain unclear.

Methods

Differentiated C2C12 myotubes were used. The effects of palmitate on cell viability, glucose uptake, gene expression and myotube loss were evaluated by MTT assay, 2NBDG uptake, qRT-PCR, Western Blot and crystal staining-based myotube counting, respectively. In some expreiments, oleate was administrated, or the inhibitors of signaling pathways were applied.

Results

Palmitate-induced cellular insulin resistance was clarified by the reduced Akt phosphorylation, glucose uptake and Glut4 expression. Palmitate-caused myotube loss was clearly observed under microscope and proved by myotube counting and expression analysis of myotube marker genes. Moreover, palmitate-induced transcriptional suppression of three health benefit myokine genes (FNDC5, CTRP15 and FGF21) was found, and the different involvement of p38 and PI3K in the transcription of these genes was noticed.

Conclusions

Palmitate-induced insulin resistance accompanys myotube loss and the impaired expression of FNDC5, CTRP15 and FGF21genes in C2C12 myotubes. These results provide novel evidence indicating the negative role of high concentration of palmitate in myotubes.
Proteomic analysis of the inhibitory effect of epigallocatechin gallate on lipid accumulation in human HepG2 cells
Authors: Liu Zhonghua , Li Qin , Huang Jianan , Liang Qionglin , Yan Yujun , Lin Haiyan , Xiao Wenjun , Lin Yong , Zhang Sheng , Tan Bin , Luo Guoan
Published: July 2013

Background

(−)-Epigallocatechin-3-gallate (EGCG), the most abundant catechin found in green tea, effectively reduces body weight and tissue and blood lipid accumulation. To explore the mechanism by which EGCG inhibits cellular lipid accumulation in free fatty acid (FFA) induced HepG2 cell culture, we investigated the proteome change of FFA-induced HepG2 cells exposed to EGCG using two-dimensional gel electrophoresis and mass spectrometry.

Results

In this study, 36 protein spots showed a significant change in intensity by more than 1.5-fold from the control group to the FFA group and from the FFA group to the FFA + EGCG group. Among them, 24 spots were excised from gels and identified by LC-MS/MS. In total, 18 proteins were successfully identified. All identified proteins were involved in lipid metabolism, glycometabolism, antioxidant defense, respiration, cytoskeleton organization, signal transduction, DNA repair, mRNA processing, iron storage, or were chaperone proteins. This indicated that these physiological processes may play roles in the mechanism of inhibition of lipid accumulation by EGCG in FFA-induced HepG2 cells. Western blotting analysis was used to verify the expression levels of differentially expressed proteins, which agree with the proteomic results.

Conclusions

From the proteomic analysis, we hypothesized that EGCG reduced cellular lipid accumulation in FFA-induced HepG2 cells through the activation of AMP-activated protein kinase (AMPK) resulting from the generation of reactive oxygen species (ROS). The induction of ROS may be a result of EGCG regulation of the antioxidant defense system. Activation of AMPK shifted some FFA toward oxidation, away from lipid and triglyceride storage, and suppressed hepatic gluconeogenesis. The findings of this study improve our understanding of the molecular mechanisms of inhibition of lipid accumulation by EGCG in HepG2 cells.
High sensitivity of middle-wavelength infrared photodetectors based on an individual InSb nanowire
Authors: Kuo Cheng-Hsiang , Wu Jyh-Ming , Lin Su-Jien , Chang Wen-Chih
Published: July 2013

Single-crystal indium antimony (InSb) nanowire was fabricated into middle-infrared photodetectors based on a metal–semiconductor-metal (M-S-M) structure. The InSb nanowires were synthesized using an electrochemical method at room temperature. The characteristics of the FET reveal an electron concentration of 3.6 × 1017 cm−3 and an electron mobility of 215.25 cm2 V−1 s−1. The photodetectors exhibit good photoconductive performance, excellent stability, reproducibility, superior responsivity (8.4 × 104 A W−1), and quantum efficiency (1.96 × 106%). These superior properties are attributed to the high surface-to-volume ratio and single-crystal 1D nanostructure of photodetectors that significantly reduce the scattering, trapping, and the transit time between the electrodes during the transport process. Furthermore, the M-S-M structure can effectively enhance space charge effect by the formation of the Schottky contacts, which significantly assists with the electron injection and photocurrent gain.