bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete Genome Sequence of a Novel Picobirnavirus, Otarine Picobirnavirus, Discovered in California Sea Lions
Authors: Woo Patrick C. Y. , Lau Susanna K. P. , Bai Ru , Teng Jade L. L. , Lee Paul , Martelli Paolo , Hui Suk-Wai , Yuen Kwok-Yung 
Published: May 2012

ABSTRACT
We discovered a novel otarine picobirnavirus in fecal samples of California sea lions. Its genome contains a large segment with two open reading frames (ORFs), ORF1 encoding a putative protein of 163 amino acids with unknown function and ORF2 encoding capsid protein, and a small segment with one ORF encoding RNA-dependent RNA polymerase.
Complete Genome Sequence of Bacillus cereus Bacteriophage PBC1
Authors: Kong Minsuk , Kim Minsik , Ryu Sangryeol 
Published: May 2012

ABSTRACT

Bacillus cereus
is a ubiquitous, spore-forming bacterium associated with food poisoning cases. To develop an efficient biocontrol agent against
B. cereus
, we isolated lytic phage PBC1 and sequenced its genome. PBC1 showed a very low degree of homology to previously reported phages, implying that it is novel. Here we report the complete genome sequence of PBC1 and describe major findings from our analysis.
Combination use of Beck Depression Inventory and two-question case-finding instrument as a screening tool for depression in the workplace
Authors: Adachi Yasunori , Aleksic Branko , Nobata Ryoko , Suzuki Tatsuyo , Yoshida Keizo , Ono Yuichiro , Ozaki Norio 
Published: May 2012

ObjectivesThe present study aimed to validate screening tools that could be used to identify depression among workers.DesignDiagnostic test study.SettingsWorkers from three Japanese companies agreed to participate.ParticipantsRecruitment for the group 1 occurred between January 2001 and February 2004, and 89 participants (81 men and 8 women with a mean age of 38.4±6.6 years) (98.8%) took part in the study. Recruitment for the group 2 occurred between July 2000 and February 2004, and 1500 participants (1408 men and 92 women with a mean age of 40.9±7.2 years) (94.2%) took part in the study. Demographic data are shown in supplementary table 1.InterventionsPrimary and secondary outcome measures: the Beck Depression Inventory (BDI) and a two-question case-finding instrument (TQI) were administered to 89 workers and Mini-International Neuropsychiatric Interview was conducted to verify the diagnosis of depression. A second group of 1500 workers completed the BDI and TQI to detect possible sample bias for the distribution of depression. Specificity, sensitivity and positive predictive value were calculated in order to obtain the optimal cut-off scores for BDI and TQI and receiver operating characteristic curves, and Youden Index were applied to further refine the optimal cut-off scores.ResultsWhen paired together, BDI score ≥10 and TQI score of 2 adequately identified workers who had major depressive disorder and those who had other psychiatric disorders that are frequently comorbid with major depressive disorder.ConclusionsThe combination of BDI score ≥10 and TQI score of 2 can adequately screen for current and potential cases of depression among workers. Furthermore, BDI and TQI offer the advantage of being relatively easy to administer to a large number of workers. Early detection of depression could improve treatment outcomes and decrease economic burden.Trail registration
Exercise Training Attenuates MuRF-1 Expression in the Skeletal Muscle of Patients With Chronic Heart Failure Independent of Age
Authors: Gielen Stephan , Sandri Marcus , Kozarez Irina , Kratzsch Jürgen , Teupser Daniel , Thiery Joachim , Erbs Sandra , Mangner Norman , Lenk Karsten , Hambrecht Rainer , Schuler Gerhard , Adams Volker 
Published: May 2012

Background—
Muscle wasting occurs in both chronic heart failure (CHF) and normal aging and contributes to exercise intolerance and increased morbidity/mortality. However, the molecular mechanisms of muscle atrophy in CHF and their interaction with aging are still largely unknown. We therefore measured the activation of the ubiquitin-proteasome system and the lysosomal pathway of intracellular proteolysis in muscle biopsies of CHF patients and healthy controls in two age strata and assessed the age-dependent effects of a 4-week endurance training program on the catabolic-anabolic balance.

Methods and Results—

Sixty CHF patients (30 patients aged ≤55 years, mean age 46±5 years; 30 patients aged ≥65 years, mean age 72±5 years) and 60 healthy controls (30 subjects aged ≤55 years, mean age 50±5 years; 30 subjects aged ≥65 years, mean age 72±4 years) were randomized to 4 weeks of supervised endurance training or to a control group. Before and after the intervention, vastus lateralis muscle biopsies were obtained. The expressions of cathepsin-L and the muscle-specific E3 ligases MuRF-1 and MAFbx were measured by real-time polymerase chain reaction and confirmed by Western blot. At baseline, MuRF-1 expression was significantly higher in CHF patients versus healthy controls (mRNA: 624±59 versus 401±25 relative units;
P
=0.007). After 4 weeks of exercise training, MuRF-1 mRNA expression was reduced by −32.8% (
P
=0.02) in CHF patients aged ≤55 years and by −37.0% (
P
<0.05) in CHF patients aged ≥65 years.

Conclusions—
MuRF-1, a component of the ubiquitin-proteasome system involved in muscle proteolysis, is increased in the skeletal muscle of patients with heart failure. Exercise training results in reduced MuRF-1 levels, suggesting that it blocks ubiquitin-proteasome system activation and does so in both younger and older CHF patients.

Clinical Trial Registration—

URL:
http://www.clinicaltrials.gov
. Unique identifier: NCT00176319.
Investigating Interannual Variability of Precipitation at the Global Scale: Is There a Connection with Seasonality?
Authors: Fatichi S. , Ivanov V. Yu. , Caporali E. 
Published: May 2012

Abstract
Interannual variability of precipitation can directly or indirectly affect many hydrological, ecological, and biogeochemical processes that, in turn, influence climate. Despite the significant importance of the phenomenon, few studies have attempted to elucidate spatial patterns of this variability at the global scale. This study uses land gauge precipitation records of the Global Historical Climatology Network, version 2, as well as reanalysis data to provide an assessment of the spatial organization of characteristics of precipitation interannual variability. The coefficient of variation, skewness, and short- and long-range dependence of the precipitation variability are analyzed. Among the major inferences is that the coefficient of variation of annual precipitation shows a significant correlation with intra-annual seasonality. Specifically, subyearly precipitation anomalies occurring in locations with pronounced seasonality affect the total yearly amount, imposing a higher variability in the annual precipitation fluctuations. Furthermore, the study illustrates that a positive skewness of the distribution of annual precipitation is a robust property worldwide and its magnitude is related to the coefficient of variation. Additionally, annual precipitation exhibits very weak small-lag autocorrelation. Conversely, the intensity of long-memory–long-range dependence is significantly larger than zero, hinting that organized long-term variations are an important feature of the interannual variability of precipitation.
Assessing the Influence of the MJO on Strong Precipitation Events in Subtropical, Semi-Arid North-Central Chile (30°S)
Authors: Juliá Cristóbal , Rahn David A. , Rutllant José A. 
Published: May 2012

Abstract
Annual precipitation in subtropical, semiarid north-central Chile (30°S) during rainy years comprises a few (3–5) strong events in the fall and winter, which are presumably modulated by the Madden–Julian oscillation (MJO). Precipitation from 1979–2009 was recorded daily at three stations along the Elqui Valley. The relationship between the MJO and precipitation is investigated from two perspectives: 1) examining a MJO index (MJOI) based on the actual precipitation events and 2) examining the likelihood of precipitation based on a favorable MJOI. About 80% of the strong precipitation events at the coast in La Serena are related to an active MJO near the central equatorial Pacific. These events are often typified by broad, slow moving synoptic systems in phase with the MJO propagation. Blocking in the far southeast Pacific is associated with precipitation 75% of the time, while deep troughs make up the rest.
A relationship between a MJOI and strong rainfall suggests that, though it could be used as a potential diagnostic, the number of cases where there is a favorable MJOI but no precipitation (i.e., false alarms) limits its utility. Additional criteria such as the Southern Oscillation (SO) and Antarctic Oscillation (AAO) phases were used to reject false alarms. Rejecting cases with positive values of the SO index reduced the number of false alarms from 70% to 58%, leaving about two false alarms for every correctly diagnosed event. The AAO index could not discriminate between false alarms and real cases. While a favorable MJOI increases the likelihood of precipitation in the Elqui Valley, false alarms remain problematic.
Forecast Advisory for the Late Fall Heavy Rainfall/Flood Event in Central Vietnam Developed from Diagnostic Analysis
Authors: Chen Tsing-Chang , Yen Ming-Cheng , Tsay Jenq-Dar , Alpert Jordan , Tan Thanh Nguyen Thi 
Published: May 2012

Abstract
The formations of heavy rainfall/flood (HRF) events in Vietnam are studied from diagnostic analyses of 31 events during the period 1979–2009. HRF events develop from the cold surge vortices formed around the Philippines. These vortices’ speed, size, and rainfall, which evolve into HRF events, are enhanced distinguishably from non-HRF vortices, as they reach Vietnam. The HRF cyclone, the North Pacific anticyclone, and the northwestern Pacific explosive cyclone simultaneously reach their maximum intensities when the HRF event occurs. An HRF cyclone attains its maximum intensity by the in-phase constructive interference of three monsoon (30–60, 12–24, and 5 days) modes identified by the spectral analysis of zonal winds. The rainfall center of an HRF event is formed and maintained by the in-phase constructive interference of rainfall and convergence of water vapor flux anomalies, respectively, from three monsoon modes. Forecast times of regional models are dependent and constrained on the scale of the limited domain. For 5-day forecasts, a global or at least a hemispheric model is necessary. Using the salient features described above, a 5-day forecast advisory is introduced to supplement forecasts of HRF events made by the global model. Non-HRF vortices are filtered by threshold values for the deepening rate of explosive cyclones and basic characteristics of the HRF events predicted by the global model. A necessary condition for an HRF event is the in-phase superposition of the three monsoon modes. One-week forecasts for 12 HRF events issued by the NCEP Global Forecast System are tested. Results demonstrate the feasibility of the forecast advisory to predict the occurrence dates of HRF events.
Snail Controls the Mesenchymal Phenotype and Drives Erlotinib Resistance in Oral Epithelial and Head and Neck Squamous Cell Carcinoma Cells
Authors: Dennis Miranda , Wang Guanyu , Luo Jie , Lin Yuan , Dohadwala Mariam , Abemayor Elliot , Elashoff David A. , Sharma Sherven , Dubinett Steven M. , St. John Maie A. 
Published: May 2012

ObjectiveThe presence of regional metastases in patients with head and neck squamous cell carcinoma (HNSCC) is a common and adverse event associated with poor prognosis. The authors’ recent work on human HNSCC tissues underlies Snail’s role as a molecular prognostic marker for HNSCC. Snail positivity is significantly predictive of poorly differentiated, lymphovascular invasive, and regionally metastatic tumors. Here, the authors investigate the capacity of Snail to drive epithelial‐mesenchymal transition (EMT) in human oral epithelial cell lines and its ability to confer drug resistance.Study DesignSnail was overexpressed in HNSCC and oral epithelial cell lines. Anchorage independent growth assays, wound healing assays, invasion and migration assays, spheroid modeling, and cell survival assays were performed.SettingAcademic tertiary medical center.Subjects and MethodsSnail overexpressing HNSCC (OSC, Tu212, Tu686) and oral epithelial cell lines (HOK 16‐B, OKF‐6) were evaluated using assays for wound healing, invasion and migration, 3‐dimensional growth, Western blot, and immunofluorescence.ResultsThe overexpression of Snail in human HNSCC and oral epithelial cell lines drives EMT. The transfection of Snail confers the expression of a mesenchymal molecular signature, including downregulation of the epithelial adherens, such as E‐cadherin and β‐catenin, and induction of mesenchymal markers. Snail‐overexpressing cell lines demonstrate rapid growth in Anchorage‐independent growth assays, a decreased capacity to form tight spheroids, an increased resistance to erlotinib, and an increased capacity for invasion.ConclusionSnail controls the mesenchymal phenotype and drives erlotinib resistance in HNSCC cells. Snail may prove to be a useful marker in predicting epidermal growth factor receptor inhibitor responsiveness.
Management Outcomes of Facial Nerve Tumors
Authors: Channer Guyan A. , Herman Björn , Telischi Fred F. , Zeitler Daniel , Angeli Simon I. 
Published: May 2012

ObjectivesPrimary facial nerve tumors (FNTs) present in varying ways. In this study, the authors present their institutional experience with the management of facial nerve tumors, including their recommendations for available therapies such as observation, microsurgical decompression or removal, and stereotactic radiation. They emphasize the auditory and facial nerve function outcomes.Study DesignRetrospective case review.SettingTertiary referral center.Subjects and MethodsRetrospective review of all cases of FNT seen at the authors’ tertiary care academic medical center over a 10‐year period (2002‐2011). The clinical presentation, treatment modality, and outcome parameters of cochlear and facial nerve function were assessed.ResultsTwelve patients were identified. House‐Brackmann grades on presentation were 4 grade I, 2 grade II, 2 grade III, 1 grade IV, and 3 grade V, with 2 grade V patients declining to grade VI shortly after presentation. Seven patients presented with serviceable hearing and 4 with nonserviceable hearing. Treatment options/arms included observation with serial clinicoradiological review (2 cases), stereotactic radiation with the CyberKnife (3 cases), wide fallopian canal decompression (3 cases), microsurgical excision and repair (3 cases), and biopsy followed by observation (1 case). At the end of the review period, facial nerve function was stable in 8 patients, improved in 3, and declined in 1, and none had documented worsening of hearing based on American Academy of Otolaryngology—Head and Neck Surgery Foundation classification.ConclusionsManagement of FNT is largely based on the clinicoradiological picture. Each treatment arm is different, but overall auditory and facial function can be maintained.
Characteristics of Patients With the “Malignant Obesity Hypoventilation Syndrome” Admitted to an ICU
Authors: Marik Paul E. , Desai Himanshu 
Published: May 2012

Background: The incidence of obesity in westernized nations is increasing at an alarming rate. We have noted an increasing number of patients admitted to our intensive care unit (ICU) with hypercapnic respiratory failure and multisystem organ dysfunction related to obesity. We have coined the term the malignant obesity hypoventilation syndrome (MOHS) to describe this entity. Methods: We reviewed the hospital records of all patients who were admitted to our ICU over an 8-month period, with a body mass index (BMI) greater than 40 kg/m2 and a PaCO2 greater than 45 mm Hg. We excluded patients with musculoskeletal disease, intrinsic lung disease, and those with >20 pack-year smoking history. Results: Sixty-one patients (8% of all admissions) met the inclusion criteria for our study. The patients’ mean BMI was 48.9 ± 8.6 kg/m2. The patients’ mean age was 59 ± 11; 47 (77%) were female and 56 (92%) were black. All patients were admitted to the ICU with hypercapnic respiratory failure. The patients had been admitted to our hospital on average 6 times over the previous 2 years; 75% had been erroneously diagnosed and treated for chronic obstructive pulmonary disease (COPD)/asthma and 86% had been treated with diuretics for congestive cardiac failure. All patients had type 2 diabetes and the metabolic syndrome. Three patients had a tracheotomy in place at admission and required mechanical ventilation. All of the remaining patients were treated with noninvasive bilevel positive airway pressure (BiPAP), with 23 patients failing BiPAP and requiring mechanical ventilation. Seven patients had a tracheotomy performed. On the basis of unexplained abnormalities of liver function tests, 39 patients (64%) were presumptively diagnosed with nonalcoholic steatohepatitis (NASH). Pulmonary function tests were suggestive of a restrictive pattern in all patients tested. By echocardiography 43 (71%) patients had left ventricular hypertrophy and 37 (61%) patients had features of left ventricular diastolic dysfunction. Forty-seven (77%) patients had pulmonary hypertension, which was moderate to severe (pulmonary systolic pressure >45 mm Hg) in 25 cases. All patients had an elevated C-reactive protein (9.4 ± 6.9 mg/dL), and all but 1 were vitamin D deficient (13.5 ± 8.5 ng/mL). Eleven patients (18%) died during the index hospitalization. Conclusions: MOHS is a serious multisystem disorder with a high mortality that appears to be relatively common, frequently misdiagnosed, and inadequately treated.
Platelets support a protective immune response to LCMV by preventing splenic necrosis
Authors: Loria Gilbert David , Romagnoli Pablo A. , Moseley Nelson B. , Rucavado Alexandra , Altman John D. 
Published: May 2012

Key PointsLevels of circulating platelets determine the degree of pathology observed during arenavirus infections. While moderate platelet drops result in deficient immune control of an LCMV infection, severe platelet-drops result in systemic hemorrhages.
How I treat pediatric acute myeloid leukemia
Authors: Rubnitz Jeffrey E. 
Published: May 2012

AbstractAcute myeloid leukemia is a heterogeneous disease that accounts for approximately 20% of acute leukemias in children and adolescents. Despite the lack of targeted therapy for most subtypes and a dearth of new agents, survival rates have reached approximately 60% for children treated on clinical trials in developed countries. Most of the advances have been accomplished by better risk classification, the implementation of excellent supportive care measures, adaptation of therapy on the basis of each patient's response to therapy, and improvements in allogeneic hematopoietic stem cell transplantation. However, it is unlikely that further gains can be made through these measures alone. In this regard, high-resolution, genome-wide analyses have led to greater understanding of the pathogenesis of this disease and the identification of molecular abnormalities that are potential targets of new therapies. The development of molecularly targeted agents, some of which are already in clinical trials, holds great promise for the future.
The footprint of metabolism in the organization of mammalian genomes
Authors: Berná Luisa , Chaurasia Ankita , Angelini Claudia , Federico Concetta , Saccone Salvatore , D'Onofrio Giuseppe 
Published: May 2012

Abstract

Background
At present five evolutionary hypotheses have been proposed to explain the great variability of the genomic GC content among and within genomes: the mutational bias, the biased gene conversion, the DNA breakpoints distribution, the thermal stability and the metabolic rate. Several studies carried out on bacteria and teleostean fish pointed towards the critical role played by the environment on the metabolic rate in shaping the base composition of genomes. In mammals the debate is still open, and evidences have been produced in favor of each evolutionary hypothesis. Human genes were assigned to three large functional categories (as well as to the corresponding functional classes) according to the KOG database: (i) information storage and processing, (ii) cellular processes and signaling, and (iii) metabolism. The classification was extended to the organisms so far analyzed performing a reciprocal Blastp and selecting the best reciprocal hit. The base composition was calculated for each sequence of the whole CDS dataset.

Results
The GC3 level of the above functional categories was increasing from (i) to (iii). This specific compositional pattern was found, as footprint, in all mammalian genomes, but not in frog and lizard ones. Comparative analysis of human versus both frog and lizard functional categories showed that genes involved in the metabolic processes underwent the highest GC3 increment. Analyzing the KOG functional classes of genes, again a well defined intra-genomic pattern was found in all mammals. Not only genes of metabolic pathways, but also genes involved in chromatin structure and dynamics, transcription, signal transduction mechanisms and cytoskeleton, showed an average GC3 level higher than that of the whole genome. In the case of the human genome, the genes of the aforementioned functional categories showed a high probability to be associated with the chromosomal bands.

Conclusions
In the light of different evolutionary hypotheses proposed so far, and contributing with different potential to the genome compositional heterogeneity of mammalian genomes, the one based on the metabolic rate seems to play not a minor role. Keeping in mind similar results reported in bacteria and in teleosts, the specific compositional patterns observed in mammals highlight metabolic rate as unifying factor that fits over a wide range of living organisms.