bluuebunny/crossref_metadata_2025_split huggingface dataset:
Circadian variations in the liver metabolites of medaka (Oryzias latipes)
Authors: Fujisawa Koichi , Takami Taro , Kimoto Yoshitaka , Matsumoto Toshihiko , Yamamoto Naoki , Terai Shuji , Sakaida Isao 
Published: February 2016

AbstractCircadian rhythms are biological rhythms with a period of around 24 hours. In this study, we compared the metabolome of the liver of medaka during the day and night. To comprehensively analyze the circadian variations in the levels of metabolites in the liver, livers were isolated from Zeitgeber time (ZT)4 and ZT16 and the variations in metabolite levels were evaluated. Inosinemonophosphate (IMP) and uridinemonophosphate (UMP) were found to be increased at night, indicating that nucleotide synthesis is most active during the night. Furthermore, the levels of metabolites of the tricarboxylic acid cycle were also reduced at night. In addition, the levels of many amino acids were reduced during the night, suggesting that the amino acids had been degraded. Moreover, the citrulline/ornithine ratio, which is related to arginine consumption, was lower during the day than at night. This pattern suggests that the urea cycle is activated during the day, whereas large amounts of nitric oxide and citrulline may be produced from arginine via nitric oxide synthase during the night. The results of this metabolomic analysis may be useful in future fundamental research to provide insight into chronobiology as well as applied research on drug evaluations using medaka as a model species.
Human Campylobacteriosis in Luxembourg, 2010–2013: A Case-Control Study Combined with Multilocus Sequence Typing for Source Attribution and Risk Factor Analysis
Authors: Mossong Joël , Mughini-Gras Lapo , Penny Christian , Devaux Anthony , Olinger Christophe , Losch Serge , Cauchie Henry-Michel , van Pelt Wilfrid , Ragimbeau Catherine 
Published: February 2016

AbstractCampylobacteriosis has increased markedly in Luxembourg during recent years. We sought to determine which Campylobacter genotypes infect humans, where they may originate from and how they may infect humans. Multilocus sequence typing was performed on 1153 Campylobacter jejuni and 136 C. coli human strains to be attributed to three putative animal reservoirs (poultry, ruminants, pigs) and to environmental water using the asymmetric island model. A nationwide case-control study (2010–2013) for domestic campylobacteriosis was also conducted, including 367 C. jejuni and 48 C. coli cases and 624 controls. Risk factors were investigated by Campylobacter species and for strains attributed to different sources using a combined case-control and source attribution analysis. 282 sequence types (STs) were identified: ST-21, ST-48, ST-572, ST-50 and ST-257 were prevailing. Most cases were attributed to poultry (61.2%) and ruminants (33.3%). Consuming chicken outside the home was the dominant risk factor for both Campylobacter species. Newly identified risk factors included contact with garden soil for either species and consuming beef specifically for C. coli. Poultry-associated campylobacteriosis was linked to poultry consumption in wintertime and ruminant-associated campylobacteriosis to tap-water provider type. Besides confirming chicken as campylobacteriosis primary source, additional evidence was found for other reservoirs and transmission routes.
Anomalously strong two-electron one-photon X-ray decay transitions in CO caused by avoided crossing
Authors: Couto Rafael C. , Guarise Marco , Nicolaou Alessandro , Jaouen Nicolas , Chiuzbăian Gheorghe S. , Lüning Jan , Ekholm Victor , Rubensson Jan-Erik , Såthe Conny , Hennies Franz , Kimberg Victor , Guimarães Freddy F. , Agren Hans , Gel’mukhanov Faris , Journel Loïc , Simon Marc 
Published: February 2016

AbstractThe unique opportunity to study and control electron-nuclear quantum dynamics in coupled potentials offered by the resonant inelastic X-ray scattering (RIXS) technique is utilized to unravel an anomalously strong two-electron one-photon transition from core-excited to Rydberg final states in the CO molecule. High-resolution RIXS measurements of CO in the energy region of 12–14 eV are presented and analyzed by means of quantum simulations using the wave packet propagation formalism and ab initio calculations of potential energy curves and transition dipole moments. The very good overall agreement between the experimental results and the theoretical predictions allows an in-depth interpretation of the salient spectral features in terms of Coulomb mixing of “dark” with “bright” final states leading to an effective two-electron one-photon transition. The present work illustrates that the improved spectral resolution of RIXS spectra achievable today may call for more advanced theories than what has been used in the past.
Experimental demonstration on the deterministic quantum key distribution based on entangled photons
Authors: Chen Hua , Zhou Zhi-Yuan , Zangana Alaa Jabbar Jumaah , Yin Zhen-Qiang , Wu Juan , Han Yun-Guang , Wang Shuang , Li Hong-Wei , He De-Yong , Tawfeeq Shelan Khasro , Shi Bao-Sen , Guo Guang-Can , Chen Wei , Han Zheng-Fu 
Published: February 2016

AbstractAs an important resource, entanglement light source has been used in developing quantum information technologies, such as quantum key distribution(QKD). There are few experiments implementing entanglement-based deterministic QKD protocols since the security of existing protocols may be compromised in lossy channels. In this work, we report on a loss-tolerant deterministic QKD experiment which follows a modified “Ping-Pong”(PP) protocol. The experiment results demonstrate for the first time that a secure deterministic QKD session can be fulfilled in a channel with an optical loss of 9 dB, based on a telecom-band entangled photon source. This exhibits a conceivable prospect of ultilizing entanglement light source in real-life fiber-based quantum communications.
Reproduction, abundance and survivorship of two Alveopora spp. in the mesophotic reefs of Eilat, Red Sea
Authors: Eyal-Shaham Lee , Eyal Gal , Tamir Raz , Loya Yossi 
Published: February 2016

AbstractAlthough the study of coral reproduction has advanced tremendously over the last few decades, a particular gap exists in our knowledge of the reproductive modes of corals from ‘mesophotic coral ecosystems’ (MCEs) found at 30–150 m depth. Here, we report for the first time on the reproductive patterns, living cover and survivorship under different light treatments of two scleractinian species from the MCEs of Eilat, Red-Sea: Alveopora allingi and A. ocellata. Both species are found exclusively within MCEs and are high in both abundance and relative cover. These species display a synchronous gametogenic cycles with consecutive oocyte growth and development. Peak of reproductive activity occurs in late summer (September-October), typified by accelerated oocyte growth, coinciding with the rise in seawater temperature. Estimates of fecundity show mean monthly maxima of 48.5 ± 26.3 and 23.5 ± 11.8 (Mean ± SE) oocytes per cm2 for A. allingi and A. ocellata respectively, prior to spawning. A comparison of light and temperature regimes in the shallow vs. MCE environments is presented and the response of these species to changes in these parameters is discussed. A call encouraging the much-needed studies on the sexuality and reproductive modes of MCE coral species is expressed.
Multiple functions of Na/K-ATPase in dopamine-induced salivation of the Blacklegged tick, Ixodes scapularis
Authors: Kim Donghun , Urban Joshua , Boyle Daniel L. , Park Yoonseong 
Published: February 2016

AbstractControl of salivary secretion in ticks involves autocrine dopamine activating two dopamine receptors: D1 and Invertebrate-specific D1-like dopamine receptors. In this study, we investigated Na/K-ATPase as an important component of the secretory process. Immunoreactivity for Na/K-ATPase revealed basal infolding of lamellate cells in type-I, abluminal interstitial (epithelial) cells in type-II and labyrinth-like infolding structures opening towards the lumen in type-III acini. Ouabain (10 μmol l−1), a specific inhibitor of Na/K-ATPase, abolished dopamine-induced salivary secretion by suppressing fluid transport in type III acini. At 1 μmol l−1, ouabain, the secreted saliva was hyperosmotic. This suggests that ouabain also inhibits an ion resorptive function of Na/K-ATPase in the type I acini. Dopamine/ouabain were not involved in activation of protein secretion, while dopamine-induced saliva contained constitutively basal level of protein. We hypothesize that the dopamine-dependent primary saliva formation, mediated by Na/K-ATPase in type III and type II acini, is followed by a dopamine-independent resorptive function of Na/K-ATPase in type I acini located in the proximal end of the salivary duct.
SpyRing interrogation: analyzing how enzyme resilience can be achieved with phytase and distinct cyclization chemistries
Authors: Schoene Christopher , Bennett S. Paul , Howarth Mark 
Published: February 2016

AbstractEnzymes catalyze reactions with exceptional selectivity and rate acceleration but are often limited by instability. Towards a generic route to thermo-resilience, we established the SpyRing approach, cyclizing enzymes by sandwiching between SpyTag and SpyCatcher (peptide and protein partners which lock together via a spontaneous isopeptide bond). Here we first investigated the basis for this resilience, comparing alternative reactive peptide/protein pairs we engineered from Gram-positive bacteria. Both SnoopRing and PilinRing cyclization gave dramatic enzyme resilience, but SpyRing cyclization was the best. Differential scanning calorimetry for each ring showed that cyclization did not inhibit unfolding of the inserted β-lactamase. Cyclization conferred resilience even at 100 °C, where the cyclizing domains themselves were unfolded. Phytases hydrolyze phytic acid and improve dietary absorption of phosphate and essential metal ions, important for agriculture and with potential against human malnutrition. SpyRing phytase (PhyC) resisted aggregation and retained catalytic activity even following heating at 100 °C. In addition, SpyRing cyclization made it possible to purify phytase simply by heating the cell lysate, to drive aggregation of non-cyclized proteins. Cyclization via domains forming spontaneous isopeptide bonds is a general strategy to generate resilient enzymes and may extend the range of conditions for isolation and application of enzymes.
Highly efficient optogenetic cell ablation in C. elegans using membrane-targeted miniSOG
Authors: Xu Suhong , Chisholm Andrew D. 
Published: February 2016

AbstractThe genetically encoded photosensitizer miniSOG (mini Singlet Oxygen Generator) can be used to kill cells in C. elegans. miniSOG generates the reactive oxygen species (ROS) singlet oxygen after illumination with blue light. Illumination of neurons expressing miniSOG targeted to the outer mitochondrial membrane (mito-miniSOG) causes neuronal death. To enhance miniSOG’s efficiency as an ablation tool in multiple cell types we tested alternative targeting signals. We find that membrane targeted miniSOG allows highly efficient cell killing. When combined with a point mutation that increases miniSOG’s ROS generation, membrane targeted miniSOG can ablate neurons in less than one tenth the time of mito-miniSOG. We extend the miniSOG ablation technique to non-neuronal tissues, revealing an essential role for the epidermis in locomotion. These improvements expand the utility and throughput of optogenetic cell ablation in C. elegans.
Absence of N-terminal acetyltransferase diversification during evolution of eukaryotic organisms
Authors: Rathore Om Singh , Faustino Alexandra , Prudêncio Pedro , Van Damme Petra , Cox Cymon J. , Martinho Rui Gonçalo 
Published: February 2016

AbstractProtein N-terminal acetylation is an ancient and ubiquitous co-translational modification catalyzed by a highly conserved family of N-terminal acetyltransferases (NATs). Prokaryotes have at least 3 NATs, whereas humans have six distinct but highly conserved NATs, suggesting an increase in regulatory complexity of this modification during eukaryotic evolution. Despite this and against our initial expectations, we determined that NAT diversification did not occur in the eukaryotes, as all six major human NATs were most likely present in the Last Eukaryotic Common Ancestor (LECA). Furthermore, we also observed that some NATs were actually secondarily lost during evolution of major eukaryotic lineages; therefore, the increased complexity of the higher eukaryotic proteome occurred without a concomitant diversification of NAT complexes.
Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data
Authors: Kumar Shailesh , Vo Angie Duy , Qin Fujun , Li Hui 
Published: February 2016

AbstractRNA-Seq made possible the global identification of fusion transcripts, i.e. “chimeric RNAs”. Even though various software packages have been developed to serve this purpose, they behave differently in different datasets provided by different developers. It is important for both users and developers to have an unbiased assessment of the performance of existing fusion detection tools. Toward this goal, we compared the performance of 12 well-known fusion detection software packages. We evaluated the sensitivity, false discovery rate, computing time and memory usage of these tools in four different datasets (positive, negative, mixed and test). We conclude that some tools are better than others in terms of sensitivity, positive prediction value, time consumption and memory usage. We also observed small overlaps of the fusions detected by different tools in the real dataset (test dataset). This could be due to false discoveries by various tools, but could also be due to the reason that none of the tools are inclusive. We have found that the performance of the tools depends on the quality, read length and number of reads of the RNA-Seq data. We recommend that users choose the proper tools for their purpose based on the properties of their RNA-Seq data.
Automatic graphene transfer system for improved material quality and efficiency
Authors: Boscá Alberto , Pedrós Jorge , Martínez Javier , Palacios Tomás , Calle Fernando 
Published: February 2016

AbstractIn most applications based on chemical vapor deposition (CVD) graphene, the transfer from the growth to the target substrate is a critical step for the final device performance. Manual procedures are time consuming and depend on handling skills, whereas existing automatic roll-to-roll methods work well for flexible substrates but tend to induce mechanical damage in rigid ones. A new system that automatically transfers CVD graphene to an arbitrary target substrate has been developed. The process is based on the all-fluidic manipulation of the graphene to avoid mechanical damage, strain and contamination and on the combination of capillary action and electrostatic repulsion between the graphene and its container to ensure a centered sample on top of the target substrate. The improved carrier mobility and yield of the automatically transferred graphene, as compared to that manually transferred, is demonstrated by the optical and electrical characterization of field-effect transistors fabricated on both materials. In particular, 70% higher mobility values, with a 30% decrease in the unintentional doping and a 10% strain reduction are achieved. The system has been developed for lab-scale transfer and proved to be scalable for industrial applications.
Cell–cell communication enhances the capacity of cell ensembles to sense shallow gradients during morphogenesis
Authors: Ellison David , Mugler Andrew , Brennan Matthew D. , Lee Sung Hoon , Huebner Robert J. , Shamir Eliah R. , Woo Laura A. , Kim Joseph , Amar Patrick , Nemenman Ilya , Ewald Andrew J. , Levchenko Andre 
Published: February 2016

Significance
What new properties may result from collective cell behavior, and how may these emerging capabilities influence shaping and function of tissues, in health and disease? Here, we explored these questions in the context of epithelial branching morphogenesis. We show experimentally that, whereas individual mammary epithelial cells are incapable of sensing extremely weak gradients of a growth factor, cellular collectives in organotypic cultures exhibit reliable, gradient-driven, directional growth. This underscores a critical importance of collective cell–cell communication and computation in gradient sensing. We develop and verify a biophysical theory of such communication and identify the mechanisms by which it is implemented in the mammary epithelium, quantitatively analyzing both advantages and limitations of biochemical cellular communication in collective decision making.
Community Correctional Agents’ Views of Medication-Assisted Treatment: Examining Their Influence on Treatment Referrals and Community Supervision Practices
Authors: Mitchell Shannon Gwin , Willet Jennifer , Monico Laura B. , James Amy , Rudes Danielle S. , Viglioni Jill , Schwartz Robert P. , Gordon Michael S. , Friedmann Peter D. 
Published: February 2016

Background Alcohol and opioid use disorders are common among adults under community supervision. Although several medications (medication-assisted treatment or MAT) are Food and Drug Administration (FDA)-approved to treat such disorders, they are underutilized with this population despite established effectiveness at decreasing substance use. This paper examines how community correctional agents’ understanding of addiction and views of MAT influence their professional actions regarding addiction medications. Methods A total of 118 semistructured qualitative interviews were conducted with community correctional agents taking part in the CJ-DATS MATICCE implementation study across 20 parole/probation offices in 9 US states. Using grounded theory methodology and an iterative analytic approach, issues of role perception, views of MAT, current treatment referral, and community supervision practices were explored. Results Agents often had limited autonomy to make direct treatment referrals, regardless of their views of MAT, as they were required to follow court orders and their organization's policies and procedures. Within some organizations, community correctional agents held sufficient autonomy to make direct treatment referrals, with agents struggling to reconcile their desire to support their clients who needed MAT with concerns about the abuse potential of opioid agonist medications. Viewing MAT as a “treatment of last resort” was counterbalanced by the view that it was an effective evidence-based practice. Agents described how MAT impacted their ability to supervise clients and how their knowledge and understanding of MAT was directly influenced by watching their clients who were successful or unsuccessful on MAT. Even those agents who were more accepting of MAT were largely unsupportive of it long-term use. Conclusions Community correctional agents’ views of MAT were influenced by their understanding of addiction as well as their experiences supervising clients receiving treatment with medications, but whether or not MAT referrals were made was not always within their control.
High Frequency of Clinically Significant Bacteremia in Adults Hospitalized With Falciparum Malaria
Authors: Nyein Phyo Pyae , Aung Ne Myo , Kyi Tint Tint , Htet Zaw Win , Anstey Nicholas M. , Kyi Mar Mar , Hanson Josh 
Published: February 2016

Abstract
Background.  African children with severe falciparum malaria commonly have concomitant Gram-negative bacteremia, but co-infection has been thought to be relatively rare in adult malaria.
Methods.  Adults with a diagnosis of falciparum malaria hospitalized at 4 tertiary referral hospitals in Myanmar had blood cultures collected at admission. The frequency of concomitant bacteremia and the clinical characteristics of the patients, with and without bacteremia, were explored.
Results.  Of 67 adults hospitalized with falciparum malaria, 9 (13% [95% confidence interval, 5.3%–21.6%]) were also bacteremic on admission, 7 (78%) with Gram-negative enteric organisms (Escherichia coli [n = 3], typhoidal Salmonella species [n = 3], nontyphoidal Salmonella [n = 1]). Bacteremic adults had more severe disease (median Respiratory Coma Acidosis Malaria [RCAM] score 3; interquartile range [IQR], 1–4) than those without bacteremia (median RCAM score 1; IQR, 1–2) and had a higher frequency of acute kidney injury (50% vs 16%, P = .03). Although 35 (52%) were at high risk of death (RCAM score ≥2), all 67 patients in the study survived, 51 (76%) of whom received empirical antibiotics on admission.
Conclusions.  Bacteremia was relatively frequent in adults hospitalized with falciparum malaria in Myanmar. Like children in high transmission settings, bacteremic adults in this low transmission setting were sicker than nonbacteremic adults, and were often difficult to identify at presentation. Empirical antibiotics may also be appropriate in adults hospitalized with falciparum malaria in low transmission settings, until bacterial infection is excluded.
A Comparison of Sequential Glaucoma Drainage Device Implantation Versus Cyclophotocoagulation Following Failure of a Primary Drainage Device
Authors: Levinson Joshua D. , Giangiacomo Annette L. , Beck Allen D. , Pruett Paul B. , Superak Hillary M. , Lynn Michael J. , Costarides Anastasios P. 
Published: February 2016

Purpose:
To compare sequential glaucoma drainage device (GDD) implantation with transscleral diode cyclophotocoagulation (CPC) following failure of a primary GDD.

Materials and Methods:
A retrospective review of all patients who underwent GDD implantation at a single institution over 10 years. Patients who required an additional GDD and/or CPC were analyzed. Success was defined as absence of loss of light perception, reoperation for glaucoma, and intraocular pressure (IOP) >21 or <6 at 2 consecutive visits after an initial 3-month period.

Results:
Thirty-two patients received sequential GDD. Twenty-one underwent CPC. Cohorts were statistically similar in regards to age, sex, race, and number of previous surgeries. Preoperatively, the GDD cohort had a lower IOP and better visual acuity. The mean length of follow-up was 37.9 months for the GDD group and 46.3 months for CPC. Both procedures significantly reduced IOP; however, CPC led to a greater reduction (P=0.0172). Survival analysis found the 5-year probability of surgical success to be 65.3% for sequential GDD and 58.0% for CPC (P=0.8678). No cases of phthisis occurred in either group. There were 2 cases of endophthalmitis (6.3%) in the GDD group, and none in the CPC group. In eyes without preexisting corneal edema, estimated corneal decompensation probability at 3 years was 31.6% for GDD and 6.7% for CPC (P=0.0828).

Conclusions:
Sequential GDD and CPC are both effective at reducing IOP following the failure of a primary GDD. CPC after GDD failure warrants further investigation as it led to a greater reduction in IOP with fewer serious adverse events.