bluuebunny/crossref_metadata_2025_split huggingface dataset:
The outcomes and prognostic factors of patients requiring prolonged mechanical ventilation
Authors: Lai Chih-Cheng , Shieh Jiunn-Min , Chiang Shyh-Ren , Chiang Kuo-Hwa , Weng Shih-Feng , Ho Chung-Han , Tseng Kuei-Ling , Cheng Kuo-Chen 
Published: June 2016

AbstractThe aims of this study were to investigate the outcomes of patients requiring prolonged mechanical ventilation (PMV) and to identify risk factors associated with its mortality rate. All patients admitted to the respiratory care centre (RCC) who required PMV (the use of MV ≥21 days) between January 2006 and December 2014 were enrolled. A total of 1,821 patients were identified; their mean age was 69.8 ± 14.2 years and 521 patients (28.6%) were aged >80 years. Upon RCC admission, the APACHE II scores were 16.5 ± 6.3 and 1,311 (72.0%) patients had at least one comorbidity. Pulmonary infection was the most common diagnosis (n = 770, 42.3%). A total of 320 patients died during hospitalization and the in-hospital mortality rate was 17.6%. A multivariate stepwise logistic regression analysis indicated that patients were more likely to die if they who were >80 years of age, had lower albumin levels (<2 g/dl) and higher APACHE II scores (≥15), required haemodialysis, or had a comorbidity. In conclusion, the in-hospital mortality for patients requiring PMV in our study was 17% and mortality was associated with disease severity, hypoalbuminaemia, haemodialysis and an older age.
nanoSQUID operation using kinetic rather than magnetic induction
Authors: McCaughan Adam N. , Zhao Qingyuan , Berggren Karl K. 
Published: June 2016

AbstractWe report on a method of nanoSQUID modulation which uses kinetic inductance rather than magnetic inductance to manip-ulate the internal fluxoid state. We produced modulation using injected current rather than an applied magnetic field. Using this injected current, we were able to observe the triangle-wave shaped modulation of the device critical current which was periodic according to the London fluxoid quantization condition. The measurement results also confirmed that the fluxoid state inside a superconducting loop can be manipulated using primarily kinetic inductance. By using primarily kinetic inductance rather than magnetic inductance, the size of the coupling inductor was reduced by a factor of 10. As a result, this approach may provide a means to reduce the size of SQUID-based superconducting electronics. Additionally, this method provides a convenient way to perform kinetic inductance characterizations of superconducting thin films.
Epigenetic differences in monozygotic twins discordant for major depressive disorder
Authors: Malki K , Koritskaya E , Harris F , Bryson K , Herbster M , Tosto M G 
Published: June 2016

AbstractAlthough monozygotic (MZ) twins share the majority of their genetic makeup, they can be phenotypically discordant on several traits and diseases. DNA methylation is an epigenetic mechanism that can be influenced by genetic, environmental and stochastic events and may have an important impact on individual variability. In this study we explored epigenetic differences in peripheral blood samples in three MZ twin studies on major depressive disorder (MDD). Epigenetic data for twin pairs were collected as part of a previous study using 8.1-K-CpG microarrays tagging DNA modification in white blood cells from MZ twins discordant for MDD. Data originated from three geographical regions: UK, Australia and the Netherlands. Ninety-seven MZ pairs (194 individuals) discordant for MDD were included. Different methods to address non independently-and-identically distributed (non-i.i.d.) data were evaluated. Machine-learning methods with feature selection centered on support vector machine and random forest were used to build a classifier to predict cases and controls based on epivariations. The most informative variants were mapped to genes and carried forward for network analysis. A mixture approach using principal component analysis (PCA) and Bayes methods allowed to combine the three studies and to leverage the increased predictive power provided by the larger sample. A machine-learning algorithm with feature reduction classified affected from non-affected twins above chance levels in an independent training-testing design. Network analysis revealed gene networks centered on the PPAR−γ (NR1C3) and C-MYC gene hubs interacting through the AP-1 (c-Jun) transcription factor. PPAR−γ (NR1C3) is a drug target for pioglitazone, which has been shown to reduce depression symptoms in patients with MDD. Using a data-driven approach we were able to overcome challenges of non-i.i.d. data when combining epigenetic studies from MZ twins discordant for MDD. Individually, the studies yielded negative results but when combined classification of the disease state from blood epigenome alone was possible. Network analysis revealed genes and gene networks that support the inflammation hypothesis of MDD.
Elevated paternal glucocorticoid exposure alters the small noncoding RNA profile in sperm and modifies anxiety and depressive phenotypes in the offspring
Authors: Short A K , Fennell K A , Perreau V M , Fox A , O’Bryan M K , Kim J H , Bredy T W , Pang T Y , Hannan A J 
Published: June 2016

AbstractRecent studies have suggested that physiological and behavioral traits may be transgenerationally inherited through the paternal lineage, possibly via non-genomic signals derived from the sperm. To investigate how paternal stress might influence offspring behavioral phenotypes, a model of hypothalamic–pituitary–adrenal (HPA) axis dysregulation was used. Male breeders were administered water supplemented with corticosterone (CORT) for 4 weeks before mating with untreated female mice. Female, but not male, F1 offspring of CORT-treated fathers displayed altered fear extinction at 2 weeks of age. Only male F1 offspring exhibited altered patterns of ultrasonic vocalization at postnatal day 3 and, as adults, showed decreased time in open on the elevated-plus maze and time in light on the light–dark apparatus, suggesting a hyperanxiety-like behavioral phenotype due to paternal CORT treatment. Interestingly, expression of the paternally imprinted gene Igf2 was increased in the hippocampus of F1 male offspring but downregulated in female offspring. Male and female F2 offspring displayed increased time spent in the open arm of the elevated-plus maze, suggesting lower levels of anxiety compared with control animals. Only male F2 offspring showed increased immobility time on the forced-swim test and increased latency to feed on the novelty-supressed feeding test, suggesting a depression-like phenotype in these animals. Collectively, these data provide evidence that paternal CORT treatment alters anxiety and depression-related behaviors across multiple generations. Analysis of the small RNA profile in sperm from CORT-treated males revealed marked effects on the expression of small noncoding RNAs. Sperm from CORT-treated males contained elevated levels of three microRNAs, miR-98, miR-144 and miR-190b, which are predicted to interact with multiple growth factors, including Igf2 and Bdnf. Sustained elevation of glucocorticoids is therefore involved in the transmission of paternal stress-induced traits across generations in a process involving small noncoding RNA signals transmitted by the male germline.
Plastische Rekonstruktion nach Sternumosteomyelitis mittels gefäßgestielter Latissimus-dorsi-Lappenplastik
Authors: Spindler N. , Langer S. 
Published: June 2016

Zusammenfassung
Zielsetzung: Durchführung eines sternalen Knochen- und Weichteil-Débridements nach abgelaufener Sternumosteomyelitis mit simultaner Defektdeckung mittels gefäßgestielten Latissimus-dorsi-Lappens.
Indikation: Tiefe sternale Wundheilungsstörungen können mittels verschiedener Lappenplastiken gedeckt werden. Der Latissimus-dorsi-Lappen bildet eine schnelle, suffiziente und zuverlässige Deckungsoption für sternale Defekte. Des Weiteren kann bei ausgeprägter Radikalität des Weichteil- und Knochen-Débridements eine einzeitige Deckung erfolgen.
Methode: Aufzeigen einzelner OP-Schritte zur Durchführung eines sternalen Débridements mit simultaner Defektdeckung mittels gefäßgestielter Latissimus-dorsi-Lappenplastik.
Schlussfolgerung: Die Radikalität des Débridements ist entscheidend für den weiteren Therapieerfolg und erlaubt es, Débridement sowie simultan die lappenplastische Deckung durchzuführen. Das gleichzeitige Arbeiten von 2 Operateuren verkürzt dabei die Operationszeit für den Patienten deutlich.
A field experiment shows that subtle linguistic cues might not affect voter behavior
Authors: Gerber Alan S. , Huber Gregory A. , Biggers Daniel R. , Hendry David J. 
Published: June 2016

Significance
An important development in social psychology is the discovery of minor interventions that have large behavioral effects. A leading example is a recent PNAS paper showing that a modest intervention inspired by psychological theory—wording survey items to encourage subjects to think of themselves as voters (noun treatment) rather than as voting (verb treatment)—has a large positive effect on political participation (voter turnout). We replicate and extend these experiments. In a large-scale field experiment, we find that encouraging subjects to think of themselves as voters rather than as voting has no effect on turnout and we estimate that both are less effective than a standard get out the vote mobilization message.
δ-COP contains a helix C-terminal to its longin domain key to COPI dynamics and function
Authors: Arakel Eric C. , Richter Kora P. , Clancy Anne , Schwappach Blanche 
Published: June 2016

Significance
We systematically dissect the structural elements of the δ subunit of the coat protein I (COPI) vesicle coat. We demonstrate that the µ-homology domain is dispensable for essential COPI functions. We map a key helix, positionally analogous to a helix observed in clathrin adaptor (AP) structures but without assigned function in AP, let alone COPI. This helix shows all features of an amphipathic helix that can enable interactions of a protein with the membrane. Indeed, the residues on its hydrophobic surface were specifically required for its function. Both findings substantially refine current models of coat formation and restrict the mechanisms of how the coat polymer is constructed or how HDEL cargo is recognized by COPI.
Brain white matter structure and
COMT
gene are linked to second-language learning in adults
Authors: Mamiya Ping C. , Richards Todd L. , Coe Bradley P. , Eichler Evan E. , Kuhl Patricia K. 
Published: June 2016

Significance
Second-language learning in adulthood is a topic of wide interest given globalization, and levels of proficiency are highly variable among individuals. Here we demonstrate a significant correlation between individuals’ white matter fiber-tract properties in language areas and participation in an English language immersion program. Moreover, we found that this relationship was influenced by genetic variation (catechol-O-methyltransferase gene). Individuals with the Methionine (Met)/Valine (Val) or Val/Val genotype, but not the Met/Met genotype, showed higher fractional anisotropy and lower radial diffusivity during immersion. Values of brain measurements reversed after the immersion ended. These results suggest that second-language learning is influenced by an interaction between brain white matter structure and genetic factors.
Phosphorylation of CMG helicase and Tof1 is required for programmed fork arrest
Authors: Bastia Deepak , Srivastava Pankaj , Zaman Shamsu , Choudhury Malay , Mohanty Bidyut K. , Bacal Julien , Langston Lance D. , Pasero Philippe , O’Donnell Michael E. 
Published: June 2016

Significance
Programmed replication fork arrest (PFA) at specific terminator sites and the proteins that bind to these sites functionally interconnect replication, transcription, and recombination. PFA prevents collision between replication and transcription that can cause genome instability, promotes intrachromatid recombination at ribosomal (r)DNA that controls replicative life span, and maintains rDNA homeostasis. This work reveals the mechanism of PFA by showing that the Tof1 protein of budding yeast remains associated with the replication fork only when it is phosphorylated, and uses the CMG helicase that drives the replication fork as a landing pad. Tof1–Csm3 promotes PFA by preventing the terminator protein Fob1 from getting displaced by other factors such as the Rrm3 helicase by counteracting the latter. This important mechanism appears to be evolutionarily conserved.
A time-varying group sparse additive model for genome-wide association studies of dynamic complex traits
Authors: Marchetti-Bowick Micol , Yin Junming , Howrylak Judie A. , Xing Eric P. 
Published: June 2016

Abstract
Motivation: Despite the widespread popularity of genome-wide association studies (GWAS) for genetic mapping of complex traits, most existing GWAS methodologies are still limited to the use of static phenotypes measured at a single time point. In this work, we propose a new method for association mapping that considers dynamic phenotypes measured at a sequence of time points. Our approach relies on the use of Time-Varying Group Sparse Additive Models (TV-GroupSpAM) for high-dimensional, functional regression.
Results: This new model detects a sparse set of genomic loci that are associated with trait dynamics, and demonstrates increased statistical power over existing methods. We evaluate our method via experiments on synthetic data and perform a proof-of-concept analysis for detecting single nucleotide polymorphisms associated with two phenotypes used to assess asthma severity: forced vital capacity, a sensitive measure of airway obstruction and bronchodilator response, which measures lung response to bronchodilator drugs.
Availability and Implementation: Source code for TV-GroupSpAM freely available for download at http://www.cs.cmu.edu/~mmarchet/projects/tv_group_spam, implemented in MATLAB.
Contact: epxing@cs.cmu.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
GSA-Lightning: ultra-fast permutation-based gene set analysis
Authors: Chang Billy Heung Wing , Tian Weidong 
Published: June 2016

Abstract
Summary: The computational speed of many gene set analysis methods can be slow due to the computationally demanding permutation step. This article introduces GSA-Lightning, a fast implementation of permutation-based gene set analysis. GSA-Lightning achieves significant speedup compared with existing methods, particularly when the number of gene sets and permutations are large.
Availability and implementation: The GSA-Lightning R package is available on Github at https://github.com/billyhw/GSALightning and on R Bioconductor. The package also contains a comprehensive user's guide with a step-by-step tutorial vignette.
Contact: weidong.tian@fudan.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Gender Differences in Alzheimer Disease: Brain Atrophy, Histopathology Burden, and Cognition
Authors: Filon Jessica R. , Intorcia Anthony J. , Sue Lucia I. , Vazquez Arreola Elsa , Wilson Jeffrey , Davis Kathryn J. , Sabbagh Marwan N. , Belden Christine M. , Caselli Richard J. , Adler Charles H. , Woodruff Bryan K. , Rapscak Steven Z. , Ahern Geoffrey L. , Burke Anna D. , Jacobson Sandra , Shill Holly A. , Driver-Dunckley Erika , Chen Kewei , Reiman Eric M. , Beach Thomas G. , Serrano Geidy E. 
Published: June 2016

AbstractMultiple studies suggest that females are affected by Alzheimer disease (AD) more severely and more frequently than males. Other studies have failed to confirm this and the issue remains controversial. Difficulties include differences in study methods and male versus female life expectancy. Another element of uncertainty is that the majority of studies have lacked neuropathological confirmation of the AD diagnosis. We compared clinical and pathological AD severity in 1028 deceased subjects with full neuropathological examinations. The age of dementia onset did not differ by gender but females were more likely to proceed to very severe clinical and pathological disease, with significantly higher proportions having a Mini-Mental State Examination score of 5 or less and Braak stage VI neurofibrillary degeneration. Median neuritic plaque densities were similar in females and males with AD but females had significantly greater tangle density scores. In addition, we found that AD-control brain weight differences were significantly greater for females, even after adjustment for age, disease duration, and comorbid conditions. These findings suggest that when they are affected by AD, females progress more often to severe cognitive dysfunction, due to more severe neurofibrillary degeneration, and greater loss of brain parenchyma.
Impact of pretreatment whole-tumor perfusion computed tomography and 18F-fluorodeoxyglucose positron emission tomography/computed tomography measurements on local control of non–small cell lung cancer treated with stereotactic body radiotherapy
Authors: Aoki Masahiko , Akimoto Hiroyoshi , Sato Mariko , Hirose Katsumi , Kawaguchi Hideo , Hatayama Yoshiomi , Seino Hiroko , Kakehata Shinya , Tsushima Fumiyasu , Fujita Hiromasa , Fujita Tamaki , Fujioka Ichitaro , Tanaka Mitsuki , Miura Hiroyuki , Ono Shuichi , Takai Yoshihiro 
Published: June 2016

Abstract
This study aimed to investigate the correlation between the average iodine density (AID) detected by dual-energy computed tomography (DE-CT) and the maximum standardized uptake value (SUVmax) yielded by [18F] fluorodeoxyglucose positron emission tomography (18F-FDG PET) for non–small cell lung cancer (NSCLC) treated with stereotactic body radiotherapy (SBRT). Seventy-four patients with medically inoperable NSCLC who underwent both DE-CT and 18F-FDG PET/CT before SBRT (50‒60 Gy in 5‒6 fractions) were followed up after a median interval of 24.5 months. Kaplan–Meier analysis was used to determine associations between local control (LC) and variables, including AID, SUVmax, tumor size, histology, and prescribed dose. The median AID and SUVmax were 18.64 (range, 1.18–45.31) (100 µg/cm3) and 3.2 (range, 0.7–17.6), respectively. No correlation was observed between AID and SUVmax. Two-year LC rates were 96.2% vs 75.0% (P = 0.039) and 72.0% vs 96.2% (P = 0.002) for patients classified according to high vs low AID or SUVmax, respectively. Two-year LC rates for patients with adenocarcinoma vs squamous cell carcinoma vs unknown cancer were 96.4% vs 67.1% vs 92.9% (P = 0.008), respectively. Multivariate analysis identified SUVmax as a significant predictor of LC. The 2-year LC rate was only 48.5% in the subgroup of lower AID and higher SUVmax vs &gt;90% (range, 94.4–100%) in other subgroups (P = 0.000). Despite the short follow-up period, a reduction in AID and subsequent increase in SUVmax correlated significantly with local failure in SBRT-treated NSCLC patients. Further studies involving larger populations and longer follow-up periods are needed to confirm these results.
Statin Effects to Reduce Hepatosteatosis as Measured by Computed Tomography in Patients With Human Immunodeficiency Virus
Authors: Lo Janet , Lu Michael T. , Kim Elli A. , Nou Eric , Hallett Travis R. , Park Jakob , Hoffmann Udo , Grinspoon Steven K. 
Published: June 2016

Abstract
Hepatosteatosis is highly prevalent among patients living with human immunodeficiency virus. In a 1-year, randomized, double-blind trial of atorvastatin or placebo, atorvastatin increased liver/spleen ratio among patients with nonalcoholic fatty liver disease, indicating a reduction in hepatosteatosis. This reduction in hepatosteatosis is associated with reduction in low-density lipoprotein cholesterol with statin therapy.
Morbidity and Mortality Among Community-Based People Who Inject Drugs With a High Hepatitis C and Human Immunodeficiency Virus Burden in Chennai, India
Authors: Mehta Shruti H. , McFall Allison M. , Srikrishnan Aylur K. , Kumar M. Suresh , Nandagopal Paneerselvam , Cepeda Javier , Thomas David L. , Sulkowski Mark S. , Solomon Sunil S. 
Published: June 2016

Abstract
Background.  There are limited data on clinical outcomes of hepatitis C virus (HCV) infection from low- and middle-income countries. We characterize mortality and liver disease progression in a cohort of people who inject drugs (PWID) with high HCV burden.
Methods.  In a cohort of PWID in Chennai, India, 851 persons were observed semiannually. Information on death was obtained through verbal autopsy and liver disease progression, which was defined as an incident liver stiffness measurement of ≥12.3 kPa if it was &lt;12.3 at baseline. Poisson and Cox regression were used to identify factors associated with mortality and disease progression, respectively.
Results.  At baseline, 36.9% of cases were infected with HCV, 16.7% were infected with human immunodeficiency virus (HIV), 71.6% had no or mild stiffness, 14.9% had moderate stiffness, and 13.5% had severe stiffness or cirrhosis. Mortality was significantly higher among those with moderate (mortality rate ratio [MRR] = 2.31) and severe stiffness (MRR = 4.86) at baseline, those with ongoing substance use, those who were HIV monoinfected and not on antiretroviral therapy (ART) (MRR = 6.59), and those who were HIV/HCV coinfected regardless of ART status (MRR for no ART = 5.34; MRR for ART = 4.51). Of those with no or mild stiffness, 25.9% and 6.4% had evidence of progression to moderate and severe stiffness or cirrhosis, respectively; 38.3% of those with moderate stiffness had evidence of progression to severe stiffness or cirrhosis. Factors associated with progression included age, alcohol use, body mass index, and chronic HCV infection.
Conclusions.  We observed significant morbidity and mortality primarily driven by untreated HIV, HIV/HCV coinfection, and alcohol use. Even with improved access to HIV treatment, in the absence of HCV treatment, outcomes are unlikely to improve for HIV/HCV-coinfected persons.
The Effects of a 4-Layer Compression Bandaging System on Skin Perfusion Pressure in Healthy Adults
Authors: Chimera Nicole J. , Brass Corstiaan , Terryberry Karl , Matthews Lynn , Boggs Ryan G. , Denz William , Brogan Michael 
Published: June 2016

ABSTRACT

OBJECTIVE:
Current practice precludes compression in patients with wounds and reduced arterial flow; however, this treatment may reduce edema and vascular resistance, thus improving distal circulation. The objective of this study was to determine the effects of compression on skin perfusion pressure (SPP), edema, and ankle range of motion.

DESIGN:
This was a quasi-experimental time series.

SETTING:
The study was conducted at The Center for Skin Integrity in Cheektowaga, New York.

PARTICIPANTS:
The study participants were 20 healthy adults, 10 in a younger age bracket (22.10 [SD, 2.77] years, 23.14 [SD, 5.03] kg/m2) and 10 in an older age bracket (55.90 [SD, 4.48] years, 28.84 [SD, 4.83] kg/m2).

INTERVENTIONS:
Sixty minutes of Profore Multi-layer Compression was performed.

MAIN OUTCOME MEASURES:
Precompression and postcompression measurements: SPP, Ankle Brachial Index, calf circumference (15 cm proximal to lateral malleolus), and static and dynamic ankle dorsiflexion range of motion (DF ROM) compared between young and older adults.

MAIN RESULTS:
There was a significant main effect for time for SPP (P = .049) and static (P = .02) and dynamic (P = .03) DF ROM. Skin perfusion pressure significantly increased at 40, 50, and 60 minutes of compression compared with precompression. Static and dynamic DF ROM significantly increased from precompression to postcompression. Although not statistically significant, calf circumference decreased by 6 cm in the older-adult group postcompression.

CONCLUSION:
A 4-layer compression dressing system improved SPP; this may be secondary to the decongestion of a proximal confined space. The 4-layer compression dressing also improves DF ROM postcompression and may reduce lower-extremity edema. Seeing these results in healthy participants suggests the need for future research in a patient population to determine if compression can be used to offload arterial structures and thus promote wound healing in patients.