bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rescue of endemic states in interconnected networks with adaptive coupling
Authors: Vazquez F. , Serrano M. Ángeles , Miguel M. San 
Published: July 2016

AbstractWe study the Susceptible-Infected-Susceptible model of epidemic spreading on two layers of networks interconnected by adaptive links, which are rewired at random to avoid contacts between infected and susceptible nodes at the interlayer. We find that the rewiring reduces the effective connectivity for the transmission of the disease between layers, and may even totally decouple the networks. Weak endemic states, in which the epidemics spreads when the two layers are interconnected but not in each layer separately, show a transition from the endemic to the healthy phase when the rewiring overcomes a threshold value that depends on the infection rate, the strength of the coupling and the mean connectivity of the networks. In the strong endemic scenario, in which the epidemics is able to spread on each separate network –and therefore on the interconnected system– the prevalence in each layer decreases when increasing the rewiring, arriving to single network values only in the limit of infinitely fast rewiring. We also find that rewiring amplifies finite-size effects, preventing the disease transmission between finite networks, as there is a non zero probability that the epidemics stays confined in only one network during its lifetime.
Rev-erbα in the brain is essential for circadian food entrainment
Authors: Delezie Julien , Dumont Stéphanie , Sandu Cristina , Reibel Sophie , Pevet Paul , Challet Etienne 
Published: July 2016

AbstractForaging is costly in terms of time and energy. An endogenous food-entrainable system allows anticipation of predictable changes of food resources in nature. Yet the molecular mechanism that controls food anticipation in mammals remains elusive. Here we report that deletion of the clock componentRev-erbαimpairs food entrainment in mice.Rev-erbαglobal knockout (GKO) mice subjected to restricted feeding showed reduced elevations of locomotor activity and body temperature prior to mealtime, regardless of the lighting conditions. The failure to properly anticipate food arrival was accompanied by a lack of phase-adjustment to mealtime of the clock protein PERIOD2 in the cerebellum, and by diminished expression of phosphorylated ERK 1/2 (p-ERK) during mealtime in the mediobasal hypothalamus and cerebellum. Furthermore, brain-specific knockout (BKO) mice forRev-erbαdisplay a defective suprachiasmatic clock, as evidenced by blunted daily activity under a light-dark cycle, altered free-running rhythm in constant darkness and impaired clock gene expression. Notably, brain deletion ofRev-erbαtotally prevented food-anticipatory behaviour and thermogenesis. In response to restricted feeding, brain deletion ofRev-erbαimpaired changes in clock gene expression in the hippocampus and cerebellum, but not in the liver. Our findings indicate thatRev-erbαis required for neural network-based prediction of food availability.
The genome and transcriptome of Trichormus sp. NMC-1: insights into adaptation to extreme environments on the Qinghai-Tibet Plateau
Authors: Qiao Qin , Huang Yanyan , Qi Ji , Qu Mingzhi , Jiang Chen , Lin Pengcheng , Li Renhui , Song Lirong , Yonezawa Takahiro , Hasegawa Masami , Crabbe M. James C. , Chen Fan , Zhang Ticao , Zhong Yang 
Published: July 2016

AbstractThe Qinghai-Tibet Plateau (QTP) has the highest biodiversity for an extreme environment worldwide, and provides an ideal natural laboratory to study adaptive evolution. In this study, we generated a draft genome sequence of cyanobacteria Trichormus sp. NMC-1 in the QTP and performed whole transcriptome sequencing under low temperature to investigate the genetic mechanism by which T. sp. NMC-1 adapted to the specific environment. Its genome sequence was 5.9 Mb with a G+C content of 39.2% and encompassed a total of 5362 CDS. A phylogenomic tree indicated that this strain belongs to the Trichormus and Anabaena cluster. Genome comparison between T. sp. NMC-1 and six relatives showed that functionally unknown genes occupied a much higher proportion (28.12%) of the T. sp. NMC-1 genome. In addition, functions of specific, significant positively selected, expanded orthogroups, and differentially expressed genes involved in signal transduction, cell wall/membrane biogenesis, secondary metabolite biosynthesis, and energy production and conversion were analyzed to elucidate specific adaptation traits. Further analyses showed that the CheY-like genes, extracellular polysaccharide and mycosporine-like amino acids might play major roles in adaptation to harsh environments. Our findings indicate that sophisticated genetic mechanisms are involved in cyanobacterial adaptation to the extreme environment of the QTP.
Dexter energy transfer pathways
Authors: Skourtis Spiros S. , Liu Chaoren , Antoniou Panayiotis , Virshup Aaron M. , Beratan David N. 
Published: July 2016

Significance
Controlling the dynamics of excitons—including their transport, fission, fusion, and free carrier generation—presents a central challenge in energy science, optoelectronics, and photobiology. We develop a coupling-pathway theory for triplet energy transfer, a process controlled by the structure of the medium between donor and acceptor sites, and find two competing coupling pathway mechanisms. At shorter distances or high tunneling gaps, the electron and hole move sequentially from donor to acceptor, accessing donor–acceptor charge-transfer exciton virtual states; at longer distances or lower tunneling gaps, virtual exciton states of the bridge mediate the transport. Molecular design strategies can leverage these competing mechanisms and their distinctive dependences on molecular structure.
Temperate phages both mediate and drive adaptive evolution in pathogen biofilms
Authors: Davies Emily V. , James Chloe E. , Williams David , O’Brien Siobhan , Fothergill Joanne L. , Haldenby Sam , Paterson Steve , Winstanley Craig , Brockhurst Michael A. 
Published: July 2016

SignificanceDuring chronic infection, bacterial pathogens undergo rapid evolutionary adaptation and extensive genetic diversification affecting patient symptoms and treatment outcomes. Temperate phages are common in pathogen genomes, and phage particles can reach high abundance in human infections, but their role in pathogen evolution is unclear. Using experimental evolution and population genomics, we show that temperate phages found in human infections accelerated pathogen evolution by increasing the supply of beneficial mutations and imposing strong selection on bacterial populations. Notably, phages accelerated the loss of clinically important virulence-related bacterial traits, including motility and quorum sensing. Temperate phages are likely therefore to facilitate rapid evolution of bacterial pathogens and contribute to their adaptation to the host environment and clinical treatments.
Ascorbate attenuates pulmonary emphysema by inhibiting tobacco smoke and Rtp801-triggered lung protein modification and proteolysis
Authors: Gupta Indranil , Ganguly Souradipta , Rozanas Christine R. , Stuehr Dennis J. , Panda Koustubh 
Published: July 2016

SignificanceTobacco smoking causes emphysema, a fatal disease involving extensive structural damage of the lung. Besides directly oxidizing lung proteins, tobacco smoke activates Rtp801, a proinflammatory cellular factor that induces overproduction of NO by inducible NOS and consequent lung protein nitration and damage. Such oxidized or nitrated lung proteins become susceptible to breakdown by lung proteases causing emphysema. On interacting with the antioxidant vitamin C, tobacco smoke loses its ability to cause lung protein oxidation or damage, indicating that its oxidant(s) are primarily responsible for triggering lung injury. Vitamin C provides comprehensive protection against tobacco smoke-induced emphysema by attenuating direct damage of the lung by its oxidant(s) and their ability to activate cellular damage machineries including Rtp801 and lung proteases.
In situ characterization of the mTORC1 during adipogenesis of human adult stem cells on chip
Authors: Wu Xuanye , Schneider Nils , Platen Alina , Mitra Indranil , Blazek Matthias , Zengerle Roland , Schüle Roland , Meier Matthias 
Published: July 2016

Significance
Adipogenesis is vital for animals to maintain energy balance by storing lipid. As a crucial integrator of nutrient, energy, and metabolite signals, mammalian target of rapamycin (mTOR) reportedly regulates adipogenesis. However, conventional cell cultures are limited to mimicking in vivo conditions, and previous reports do not provide the localization information of mTOR during adipogenesis. Here, we developed an automated microfluidic large-scale integration platform for differentiating human adult stem cells into mature adipocytes with standardized nutrient availability over weeks. With an integrated multiplexed immunoassay, we detected interaction, phosphorylation, and abundance changes of mTOR under the defined conditions. High-content analysis of single-cell data revealed that mTOR complex 1 changes its subcellular position in a temporally synchronized process with lysosomes during adipogenesis.
Large scale, synchronous variability of marine fish populations driven by commercial exploitation
Authors: Frank Kenneth T. , Petrie Brian , Leggett William C. , Boyce Daniel G. 
Published: July 2016

Significance
Large-scale synchronous variation in the abundance of marine fish populations has generally been viewed as a response to coupled atmosphere–ocean forcing. The possibility that commercial exploitation could contribute significantly to these variations has been largely dismissed. We demonstrate, using data from 22 Atlantic cod stocks distributed across the North Atlantic, that fishing pressure can cause synchronous changes in stock abundance at spatial and temporal scales comparable to those attributed to climate forcing. We conclude that an understanding of the underlying causes of the large-scale, often synchronous variability of exploited marine fish populations and their underlying food chains will require greater acceptance of the potential importance of exploitation than has been evident to date.
Cardiolipin binds selectively but transiently to conserved lysine residues in the rotor of metazoan ATP synthases
Authors: Duncan Anna L. , Robinson Alan J. , Walker John E. 
Published: July 2016

Significance
ATP, the fuel of life, is produced by a molecular machine consisting of two motors linked by a rotor. One motor generates rotation by consuming energy derived from oxidative metabolism or photosynthesis; the other uses energy transmitted by the rotor to put ATP molecules together from their building blocks ADP and phosphate. The anionic lipid cardiolipin, a component of bacterial membranes and the inner membranes of mitochondria where the machine is found, is an essential component of the enzyme. It interacts specifically, transiently, and repeatedly with the rotor of the machine, possibly lubricating its rotation or participating directly in the generation of rotation from the transmembrane proton motive force.
Dependence and independence of survival parameters on linear energy transfer in cells and tissues
Authors: Ando Koichi , Goodhead Dudley T. 
Published: July 2016

AbstractCarbon-ion radiotherapy has been used to treat more than 9000 cancer patients in the world since 1994. Spreading of the Bragg peak is necessary for carbon-ion radiotherapy, and is designed based on the linear–quadratic model that is commonly used for photon therapy. Our recent analysis using in vitro cell kills and in vivo mouse tissue reaction indicates that radiation quality affects mainly the alpha terms, but much less the beta terms, which raises the question of whether this is true in other biological systems. Survival parameters alpha and beta for 45 in vitro mammalian cell lines were obtained by colony formation after irradiation with carbon ions, fast neutrons and X-rays. Relationships between survival parameters and linear energy transfer (LET) below 100 keV/μm were obtained for 4 mammalian cell lines. Mouse skin reaction and tumor growth delay were measured after fractionated irradiation. The Fe-plot provided survival parameters of the tissue reactions. A clear separation between X-rays and high-LET radiation was observed for alpha values, but not for beta values. Alpha values/terms increased with increasing LET in any cells and tissues studied, while beta did not show a systematic change. We have found a puzzle or contradiction in common interpretations of the linear-quadratic model that causes us to question whether the model is appropriate for interpreting biological effectiveness of high-LET radiation up to 500 keV/μm, probably because of inconsistency in the concept of damage interaction. A repair saturation model proposed here was good enough to fit cell kill efficiency by radiation of wide-ranged LET. A model incorporating damage complexity and repair saturation would be suitable for heavy-ion radiotherapy.
Does Stenting as a Bridge to Surgery in Left-Sided Colorectal Cancer Obstruction Really Worsen Oncological Outcomes?
Authors: Kwak Min Seob , Kim Wan Soo , Lee Jeong-Mi , Yang Dong-Hoon , Yoon Yong Sik , Yu Chang Sik , Kim Jin Cheon , Byeon Jeong-Sik 
Published: July 2016

BACKGROUND:
Although self-expandable metal stents are used as a bridge to surgery in patients with colorectal cancer obstruction, their long-term oncological outcomes are unclear.

OBJECTIVE:
The aim of this study was to investigate long-term oncological outcomes of self-expandable metal stents as a bridge to surgery (stent group) compared with direct surgery (direct operation group) in patients with left-sided colorectal cancer obstruction.

DESIGN:
This was a retrospective chart review.

SETTINGS:
This study was conducted at a single tertiary academic center.

PATIENTS:
Of 113 patients who underwent curative surgery for left-sided colorectal cancer obstruction at Asan Medical Center between 2005 and 2011, 42 underwent direct surgery and 71 underwent self-expandable metal stent insertion followed by elective surgery. After 1:1 propensity-score matching, 42 patients were enrolled in both groups, and their postsurgical outcomes were compared.

MAIN OUTCOME MEASURES:
The primary outcomes of this study were long-term oncological outcomes, including overall survival and recurrence-free survival of patients in both groups.

RESULTS:
Three- and 5-year overall survival rates were similar in the stent (87.0% and 71.0%) and direct operation (76.4% and 76.4%) groups (p = 0.931). Three- and 5-year recurrence-free survival rates were also similar in the stent (91.9% and 66.4%) and direct operation (81.2% and 71.2%) groups (p = 0.581), as were postsurgical complication rates (9.5% and 16.7%; p = 0.344). No patient in either group experienced a permanent stoma.

LIMITATIONS:
This study was limited by its small patient numbers and retrospective nature.

CONCLUSIONS:
The long-term oncological outcomes of self-expandable metal stents as a bridge to surgery may not be inferior to those of direct surgery for left-sided colorectal cancer obstruction.
Characteristics of Antibiotic Prophylaxis and Risk of Surgical Site Infections in Open Colectomies
Authors: Poeran Jashvant , Wasserman Isaac , Zubizarreta Nicole , Mazumdar Madhu 
Published: July 2016

BACKGROUND:
Despite numerous trials assessing optimal antibiotic prophylaxis strategies for colorectal surgery, few studies have assessed real-world practice on a national scale with respect to risk of surgical site infections.

OBJECTIVE:
Using a large national claims database we aimed to describe current use of prophylactic antibiotics (type and duration) and associations with surgical site infection after open colectomies.

DESIGN:
This was a retrospective study using the Premier Perspective database.

SETTINGS:
Included were patient hospitalizations nationwide from January 2006 to December 2013.

PATIENTS:
A total of 90,725 patients who underwent an open colectomy in 445 different hospitals were included in the study.

MAIN OUTCOME MEASURES:
Multilevel, multivariable logistic regressions measured associations between surgical site infection and type of antibiotic used and duration (day of surgery only, day of surgery and the day after, and >1 day after surgery).

RESULTS:
Overall surgical site infection prevalence was 5.2% (n = 4750). Most patients (41.8%) received cefoxitin for prophylaxis; other choices were ertapenem (18.2%), cefotetan (10.3%), metronidazole with cefazolin (9.9%), and ampicillin with sulbactam (7.6%), whereas 12.2% received other antibiotics. Distribution of prophylaxis duration was 51.6%, 28.5%, and 19.9% for day of surgery only, day of surgery and the day after, and >1 day after surgery, respectively. Compared with cefoxitin, lower odds for surgical site infection were observed for ampicillin with sulbactam (OR = 0.71 (95% CI, 0.63–0.82)), ertapenem (OR = 0.65 (95% CI, 0.58–0.71)), metronidazole with cefazolin (OR = 0.56 (95% CI, 0.49–0.64)), and “other” (OR = 0.81 (95% CI, 0.73–0.90)); duration was not significantly associated with altered odds for surgical site infection. Sensitivity analyses supported the main findings.

LIMITATIONS:
The study was limited by its lack of detailed clinical information in the billing data set used.

CONCLUSIONS:
In this national study assessing real-world use of prophylactic antibiotics in open colectomies, the type of antibiotic used appeared to be associated with up to 44% decreased odds for surgical site infections. Although there are numerous trials on optimal prophylactic strategies, studies that particularly focus on factors that influence the choice of prophylactic antibiotic might provide insights into ways of reducing the burden of surgical site infections in colorectal surgeries.
Psychological Symptom Amplification: Are Psychological Symptoms Subject to “Somatization”-Like Processes?
Authors: Kontos Nicholas , Querques John , Freudenreich Oliver 
Published: July 2016

Abstract
Many patients demonstrate amplified somatic symptom experiences that are felt by providers to cause excessive distress and functional impairment, and that can be diagnostically misleading. Terms attached to these presentations include somatization, medically unexplained symptoms, and, most recently, somatic symptom disorder. The analogous amplification of psychological symptoms has not been considered. Accordingly, this column makes a case for discussion and investigation of psychological symptom amplification (PSA), a process made possible by the medical legitimization of certain types of human suffering. As various forms of psychological suffering gain greater medical legitimacy, PSA becomes increasingly relevant. Circumstantial evidence suggests that unrecognized PSA may distort research findings and clinical efficacy in psychiatry. The largely symptom-based nature of psychiatric diagnosis makes PSA a challenging, but necessary, object of further scientific and clinical scrutiny.
Posttraumatic Stress Disorder, Overweight, and Obesity: A Systematic Review and Meta-analysis
Authors: Suliman Sharain , Anthonissen Lise , Carr Jonathan , du Plessis Stefan , Emsley Robin , Hemmings Sian M. J. , Lochner Christine , McGregor Nathaniel , van den Heuvel Leigh , Seedat Soraya 
Published: July 2016

Abstract
Previous reports have suggested a high prevalence of overweight and obesity among individuals with posttraumatic stress disorder (PTSD). Few studies, however, systematically analyze the relationship between PTSD and body mass index (BMI). We conducted a systematic review and meta-analysis aimed at estimating the association between PTSD and BMI. Fifty-four articles were reviewed, 30 of which (with 191,948 individuals with PTSD and 418,690 trauma-exposed individuals or healthy controls) were eligible for inclusion in the meta-analysis. The pooled standard mean difference, based on a random-effects model, was 0.41 (95% confidence interval, 0.28–0.54; z = 6.26; p < .001). Statistical heterogeneity between the included studies was high (p < .001; I2 = 99%). Despite limitations, the findings of this systematic review and meta-analysis suggest an association between PTSD and BMI. Furthermore, longitudinal studies tentatively indicate that PTSD may lead to an increase in BMI and, as such, to the development of overweight/obesity, particularly in women. Further prospective studies and research elaborating the nature and etiology of the association are required.
Effects of topical combinations of clonidine and pentoxifylline on capsaicin-induced allodynia and postcapsaicin tourniquet-induced pain in healthy volunteers: a double-blind, randomized, controlled study
Authors: Ragavendran J. Vaigunda , Laferrière André , Bennett Gary J. , Ware Mark A. , Gandhi Wiebke , Bley Keith , Schweinhardt Petra , Coderre Terence J. 
Published: July 2016

Abstract
This double-blind randomized controlled study was designed to evaluate the analgesic effects of topical treatments with clonidine (CLON) and pentoxifylline (PTX) tested alone or as low- and high-dose combinations in a human experimental model of pain. Of 69 healthy subjects aged 18 to 60 years, 23 each were randomly allocated to low-dose (0.04% + 2%) and high-dose (0.1% + 5%) CLON + PTX groups. Both of these groups also received their corresponding placebos in one of 2 treatment periods separated by at least 48 hours. Twenty-three additional subjects received either CLON (0.1%) or PTX (5%) as single drug treatments, in each of 2 treatment periods. Assessment of analgesic efficacy was based on allodynic effects of previous intraepidermal capsaicin injection, as well as postcapsaicin tourniquet-induced pain 50 minutes following capsaicin injection. Visual Analogue Scale (VAS) ratings of pain intensity and the area of dynamic mechanical allodynia were the primary outcome measures, whereas area of punctate mechanical allodynia (PMA) served as a secondary outcome measure. Topical treatments with high- or low-dose combinations significantly reduced VAS ratings compared with corresponding placebo treatments throughout the period of postcapsaicin tourniquet-induced pain. Importantly, the high-dose combination produced lower VAS ratings than CLON alone, which were lower than PTX alone. Results also revealed significant inhibition of postcapsaicin dynamic mechanical allodynia and PMA for the high-dose combination compared with placebo, and of PMA for CLON compared with the low-dose combination. Hence, the present data are supportive of further clinical investigation of the high-dose topical combination of CLON + PTX in complex regional pain syndrome and neuropathic pain patients, for which our preclinical data predict efficacy.
Work out by Walking
Authors: Browne Julia , Penn David L. , Battaglini Claudio L. , Ludwig Kelsey 
Published: July 2016

Abstract
The health benefits of exercise are well documented, yet annual health care costs related to physical inactivity are well within the billions. Furthermore, individuals with schizophrenia spectrum disorders (SSDs) are more likely to lead sedentary lives, exercise less than the general population, and die prematurely from preventable causes. Previous research examining the effects of exercise on individuals with SSDs has been encouraging yet limited in creating accessible and sustainable interventions. The current pilot study developed and evaluated the impact of Work out by Walking (WOW), a multicomponent group walking intervention on the health of 16 individuals with SSDs. Results indicated improvements in indicators of physical health, activity level, social support, and mental health and a high level of program satisfaction. Future research should examine multicomponent group walking programs for individuals with SSDs in larger samples and with the inclusion of a comparison condition.