bluuebunny/crossref_metadata_2025 huggingface dataset:
Pathological Confirmation of Para‐Aortic Lymph Node Status as a Potential Criterion for the Selection of Intrahepatic Cholangiocarcinoma Patients for Radical Resection with Regional Lymph Node Dissection
Authors: Nakayama Tomohide , Tsuchikawa Takahiro , Shichinohe Toshiaki , Nakamura Toru , Ebihara Yuma , Hirano Satoshi
Published: December 2013

Background

Para‐aortic lymph node (PAN) metastasis traditionally has been defined as distant metastasis. Many studies suggest that lymph node metastasis in intrahepatic cholangiocarcinoma (ICC) is one of the strongest prognostic factors for patient survival; however, the status of the PAN was not examined separately from regional lymph node metastasis in these reports. Here, we investigated whether regional lymph node metastasis without PAN metastasis in ICC can be classified as resectable disease and whether curative resection can have a prognostic impact.

Methods

Between 1998 and 2010, a total of 47 ICC patients underwent hepatic resection and systematic lymphadenectomy with curative intent. We routinely dissected the PANs and had frozen‐section pathological examinations performed intraoperatively. If PAN metastases were identified, curative resection was abandoned. We retrospectively investigated the prognostic factors for patient survival after curative resection for ICC without PAN metastases, with particular attention paid to the prognostic impact of lymphadenectomy.

Results

Univariate analysis identified concomitant portal vein resection, concomitant hepatic artery resection, intraoperative blood loss, intraoperative transfusion, and residual tumor as significant negative prognostic factors. However, lymph node status was not identified as a significant prognostic factor. The 14 patients with node‐positive cancer had a survival rate of 20 % at 5 years. Based on multivariate analysis, intraoperative transfusion was an independent prognostic factor associated with a poor prognosis (risk ratio = 4.161; P = 0.0056).

Conclusions

Regional lymph node metastasis in ICC should be classified as resectable disease, because the survival rate after surgical intervention was acceptable when PAN metastasis was pathologically negative.
Massive Hemobilia: A Diagnostic and Therapeutic Challenge
Authors: Devakumar Murugesan Satish , Sathyanesan Jeswanth , Lakshmanan Anand , Ramaswami Sukumar , Perumal Senthilkumar , Ulagendra Perumal Srinivasan , Ramasamy Ravi , Palaniappan Ravichandran
Published: December 2013

Background

Massive hemobilia is a rare but potentially life‐threatening cause of upper gastrointestinal hemorrhage. In this retrospective analysis, we have evaluated the challenges involved in the diagnosis and management of massive hemobilia.

Methods

Between 2001 and 2011, a total of 20 consecutive patients (14 males) who were treated in our department for massive hemobilia were included in the study and their records were retrospectively analyzed.

Results

Causes of hemobilia were blunt liver trauma (n = 9), hepatobiliary intervention (n = 4), post‐laparoscopic cholecystectomy hepatic artery pseudoaneurysm (n = 3), hepatobiliary tumors (n = 3), and vascular malformation (n = 1). Melena, abdominal pain, hematemesis, and jaundice were the leading symptoms. All patients had undergone upper GI endoscopy, abdominal ultrasound, and computerized tomography of the abdomen. An angiogram and therapeutic embolization were done in 12 patients and was successful in nine but failed in three, requiring surgery. Surgical procedures performed were right hepatectomy (n = 4), extended right hepatectomy (n = 1), segmentectomy (n = 1), extended cholecystectomy (n = 1), repair of the pseudoaneurysm (n = 3), and right hepatic artery ligation (n = 1).

Conclusion

The successful diagnosis of hemobilia depends on a high index of suspicion for patients with upper GI bleeding and biliary symptoms. Although transarterial embolization is the therapeutic option of choice for massive hemobilia, surgery has a definitive role in patients with hemodynamic instability, after failed embolization, and in patients requiring laparotomy for other reasons.
Short‐Term and Long‐Term Outcomes After Gastrectomy for Gastric Cancer in Patients With Chronic Kidney Disease
Authors: Matsumoto Sohei , Takayama Tomoyoshi , Wakatsuki Kohei , Tanaka Tetsuya , Migita Kazuhiro , Nakajima Yoshiyuki
Published: December 2013

Background

The incidence of chronic kidney disease (CKD) is increasing, which might be an obstacle to various aspects of gastric cancer treatment, such as perisurgical management and postsurgical follow‐up. The present study aimed to evaluate the short‐ and long‐term surgical outcomes following gastrectomy in patients with CKD.

Methods

We retrospectively analyzed surgical complications and prognosis of patients with gastric cancer. These patients were divided into three groups according to the glomerular filtration rate (GFR): 49 patients with severe CKD (GFR < 29 ml/min/1.73 m2), 128 with mild CKD (GFR 30–59), and 798 in the controls (GFR ≥ 60).

Results

The incidences of anastomotic leakage and intraabdominal abscess in the mild and severe CKD groups were higher than that in the control group. The incidences of wound infection, cardiovascular and pulmonary events, and in‐hospital mortality in the severe CKD group were higher than those in the other two groups. Severe surgical complications were associated with co‐morbidities other than CKD, serum albumin level, estimated blood loss, surgery duration in the mild and severe CKD group. The 3‐year overall survival rates for the severe CKD, mild CKD, and control groups were 48.6, 80.9, and 85.0 %, respectively, indicating significant differences between the severe CKD group and other two groups.

Conclusions

Patients with severe CKD show an increased risk of morbidity and mortality following gastrectomy, and their prognosis is usually poor. Studies with a large cohort are essential to refine the risk stratification for gastrectomy in this high‐risk population.
Development, Implementation, and Evaluation of a Hybrid Electronic Medical Record System Specifically Designed for a Developing World Surgical Service
Authors: Laing G. L. , Bruce J. L. , Skinner D. L. , Allorto N. L. , Clarke D. L. , Aldous C.
Published: December 2013

Background

The Pietermaritzburg Metropolitan Trauma Service previously successfully constructed and implemented an electronic surgical registry (ESR). This study reports on our attempts to expand and develop this concept into a multi‐functional hybrid electronic medical record (HEMR) system for use in a tertiary level surgical service. This HEMR system was designed to incorporate the function and benefits of an ESR, an electronic medical record (EMR) system, and a clinical decision support system (CDSS).

Methods

Formal ethical approval to maintain the HEMR system was obtained. Appropriate software was sourced to develop the project. The data model was designed as a relational database. Following the design and construction process, the HEMR file was launched on a secure server. This provided the benefits of access security and automated backups. A systematic training program was implemented for client training. The exercise of data capture was integrated into the process of clinical workflow, taking place at multiple points in time. Data were captured at the times of admission, operative intervention, endoscopic intervention, adverse events (morbidity), and the end of patient care (discharge, transfer, or death).

Results

A quarterly audit was performed 3 months after implementation of the HEMR system. The data were extracted and audited to assess their quality. A total of 1,114 patient entries were captured in the system. Compliance rates were in the order of 87–100 %, and client satisfaction rates were high.

Conclusions

It is possible to construct and implement a unique, simple, cost‐effective HEMR system in a developing world surgical service. This information system is unique in that it combines the discrete functions of an EMR system with an ESR and a CDSS. We identified a number of potential limitations and developed interventions to ameliorate them. This HEMR system provides the necessary platform for ongoing quality improvement programs and clinical research.
Changes in expression levels of oxidative stress‐related genes in mouse epididymides by neonatal exposure to low‐dose decabromodiphenyl ether
Authors: Nakamoto Makoto , Miyaso Hidenobu , Komiyama Masatoshi , Matsuno Yoshiharu , Mori Chisato
Published: December 2013

Decabromodiphenyl ether (decaBDE), one of the polybrominated diphenyl ethers (PBDEs), is the most well‐known flame retardant and is used worldwide. In a previous study, we identified adverse effects of neonatal decaBDE exposure on mouse epididymides, such as decreased epididymal weight. On the other hand, neonatal exposure to diethylstilbestrol (DES), an artificial estrogenic compound, also causes several adverse effects on epididymides. DES exposure results in decreased epididymal weight, morphological abnormalities, and permanent alterations in the expression levels of several genes. The molecular mechanisms underlying the harmful effects of decaBDE exposure remain unclear. Many studies have reported that PBDEs have estrogenic activity, which may contribute to the induction of the adverse effects of decaBDE exposure. We aimed to examine the effects of neonatal decaBDE exposure on epididymides. Our data showed that (1) no histological change was observed on epididymal tissues from neonatal decaBDE exposure, unlike the effect of DES, (2) decaBDE exposure did not induce the alterations in gene expression observed with DES exposure; instead alterations in gene expression of certain oxidative stress‐related genes were observed, and (3) the expression of ubiquitin C increased in decaBDE‐exposed mouse epididymides. Our present data suggest the possibility that increased oxidative stress plays a role in the harmful effects observed in mouse epididymides after decaBDE‐exposure.
Evaluating an Animal Model of Compulsive Hoarding in Humans
Authors: Andrews-McClymont Jennifer G. , Lilienfeld Scott O. , Duke Marshall P.
Published: December 2013

Recently, researchers have begun to advocate use of an animal model for understanding compulsive hoarding in humans. Nevertheless, a comprehensive review of the literature for this argument is lacking. We compare data for compulsive hoarding behavior in humans with hoarding in several vertebrates (rat, bird, and primate) to examine the potential validity of an animal model of hoarding. Although the strength of each animal model varies, there is provisional evidence in support of an analogue between hoarding in nonhuman animals (especially rodents) and humans, most notably on neurobiological grounds. Nevertheless, substantially more evidence is needed before this relationship can be confirmed with confidence. We identify gaps in the literature and offer suggestions for further investigation of the validity of animal models of human hoarding.
Cognitive Traits as Sexually Selected Fitness Indicators
Authors: Klasios John
Published: December 2013

The evolutionary psychologist Geoffrey Miller has argued that various features of human psychology have been sculpted, at least in part, by the evolutionary process of sexual selection via mate choice. This paper specifically examines the central claim of Miller's account, namely that certain cognitive traits have evolved to function as good genes fitness indicators. First, I expound on and clarify key foundational concepts comprising the focal hypothesis, especially condition-dependence, mutation target size, and mutation-selection balance. Second, I proceed to highlight some subtle distinctions with respect to the concepts of exaptation and adaptation, as well as Fisherian runaway selection and good genes sexual selection, all of which in turn bear importantly on the overall framework of cognitive traits as fitness indicators. Third and finally, I close out the paper by examining various conceptual and methodological criteria which are integral to identifying sexually selected adaptations, then briefly examine some empirical work that has aimed to test the hypothesis that traits such as humor and creativity function as sexually attractive fitness indicators.
Making Sense of Relational Processes and Other Psychological Phenomena: The Participatory Perspective as a Post-Cartesian Alternative to Gergen's Relational Approach
Authors: Westerman Michael A.
Published: December 2013

Gergen's (2009 , 2011a , 2011b ) relational approach and the participatory perspective ( Westerman, 2005 , 2006 , 2014 ; Westerman & Steen, 2007 ) both subscribe to the view that we need to depart from treating the individual as the bounded, separate agent of the Cartesian framework. However, whereas Gergen's position moves away from individualistic accounts by holding that all psychological processes originate in relational processes in the dyad, the participatory perspective accomplishes this shift by viewing the person from the outset as a participant in the world of practical activities. In this article, I discuss implications that follow from this difference in starting points, including a number of ways in which the participatory perspective avoids problematic features of Gergen's approach. I argue that the participatory perspective offers a more sound framework for studying psychological phenomena, including interpersonal, or relational, processes themselves, the founding term of Gergen's relational approach. Regarding relational processes, it enables us to address questions about (a) continuity in interpersonal behavior across relationship contexts, and (b) how relational processes within a dyad change. I maintain that the limitations of Gergen's relational approach reflect the fact that it actually represents a variant of the Cartesian framework, even though Gergen's goal was to depart from that framework. In addition, I maintain that the participatory perspective provides a more adequate basis for work in the field because it successfully goes beyond Cartesianism.
Moral Ambivalence: Modeling and Measuring Bivariate Evaluative Processes in Moral Judgment
Authors: Navarick Douglas J.
Published: December 2013

Moral judgments often appear to arise from quick affectively toned intuitions rather than from conscious application of moral principles. Sometimes people feel that an action they observe or contemplate could be judged as either right or wrong. Models of moral intuition need to specify mechanisms that could account for such moral ambivalence. The basic implication of moral ambivalence is that right and wrong are regions of a bivariate scale rather than a bipolar scale. The former allows for equally strong positive and negative evaluations of a stimulus, but the latter requires one evaluation to get weaker as the other one gets stronger ( Cacioppo & Berntson, 1994 ). Covariation of evaluative activations is supported by classic animal research on approach–avoidance conflict showing that when rats are both rewarded and punished in the goal region of a runway, their approach and avoidance tendencies both increase as they get closer to the goal. The relevance of this research to moral judgment is underscored by recent studies indicating that judgments of right and wrong are fundamentally expressions of approach and avoidance motivation. Experimental and historical analyses illustrate 2 potential effects of ambivalence on moral judgment, vacillation and suppression, and a proposed model shows how the bivariate scale can be applied to existing formulations, including Haidt's moral foundations theory. Studies of moral judgment that use rating scales, questionnaires, or interviews should give participants the option to express ambivalence (e.g., “can't decide,” “don't know”) instead of requiring definitive judgments, which is the current practice.
Assessing Psychosocial Functioning Among Youth With Newly Diagnosed Inflammatory Bowel Disease (IBD): An Interdisciplinary Clinic Approach
Authors: Maddux Michele Herzer , Bass Julie A. , Geraghty-Sirridge Christy , Carpenter Ellen , Christenson Kathy
Published: December 2013

An integrated approach to healthcare brings together professionals from various disciplines and establishes comprehensive treatment plans that address the biological, psychological, and social needs of a patient. Youth with inflammatory bowel disease (IBD) are at risk of psychosocial difficulties and often need psychosocial support near the time of diagnosis in addition to traditional medical support. The need for a biopsychosocial approach to healthcare that emphasizes health promotion among youth with IBD is thus quite great. The purpose of this article is to describe the New Patient IBD Clinic, a clinic that applies a biopsychosocial model of care to the treatment of youth newly diagnosed with IBD. Psychosocial data obtained from 108 youth ages 8–18, as part of standard clinical care during their visit to the IBD clinic, are described and discussed in the context of a patient’s overall functioning, adjustment, and quality of life. Implications for clinical care and treatment planning and recommendations for developing an integrated care model are also discussed.
Magnetically driven middle ear ossicles for optical measurement of vibrations in an ear with opened tympanic membrane
Authors: Peacock J. , von Unge M. , Dirckx J.
Published: December 2013

Vibrations of the middle ear ossicles are easily measured by means of laser vibrometry. However, laser vibrometry requires free visual access to the object under investigation, and acquiring free visual access to the ossicles through the ear canal requires the removal of the tympanic membrane (TM), with the result that the ossicles can no longer be stimulated acoustically. To overcome this, we devised a new setup in which the ossicles can be driven magnetically. After measuring the response of the TM to an acoustic signal, we then remove it and attach a small magnet to the exposed manubrium (a part of the most lateral auditory ossicle, the malleus, which is normally attached to the TM). An electromagnetic excitation coil is then used to drive the magnet, and the output to the coil adjusted until the vibration of the manubrium, as measured by the vibrometer, matches that measured in response to the acoustic signal. Such a setup may have uses in research on middle ear mechanics, such as the measurement of nonlinearities in their response, as well as applications in the diagnosis of middle ear conditions such as the fixation of the ossicles by otosclerosis or in chronic otitis media. We describe our setup and discuss the viability of our method and its future clinical potential by presenting some measurements on an artificially fixated ear.
Effect of frequency tuning on bremsstrahlung spectra, beam intensity, and shape in the 10 GHz NANOGAN electron cyclotron resonance ion source
Authors: Rodrigues G. , Mal Kedar , Kumar Narender , Baskaran R. , Lakshmy P. S. , Mathur Y. , Kumar P. , Kanjilal D. , Roy A.
Published: December 2013

Studies on the effect of the frequency tuning on the bremsstrahlung spectra, beam intensities, and beam shape of various ions have been carried out in the 10 GHz NANOGAN ECR ion source. The warm and cold components of the electrons were found to be directly correlated with beam intensity enhancement in case of Ar9+ but not so for O5+. The warm electron component was, however, much smaller compared to the cold component. The effect of the fine tuning of the frequency on the bremsstrahlung spectrum, beam intensities and beam shape is presented.
Synthesis of endohedral iron-fullerenes by ion implantation
Authors: Minezaki H. , Ishihara S. , Uchida T. , Muramatsu M. , Rácz R. , Asaji T. , Kitagawa A. , Kato Y. , Biri S. , Yoshida Y.
Published: December 2013

In this paper, we discuss the results of our study of the synthesis of endohedral iron-fullerenes. A low energy Fe+ ion beam was irradiated to C60 thin film by using a deceleration system. Fe+-irradiated C60 thin film was analyzed by high performance liquid chromatography and laser desorption/ ionization time-of-flight mass spectrometry. We investigated the performance of the deceleration system for using a Fe+ beam with low energy. In addition, we attempted to isolate the synthesized material from a Fe+-irradiated C60 thin film by high performance liquid chromatography.
Dual passivation of GaAs (110) surfaces using O2/H2O and trimethylaluminum
Authors: Kent Tyler J. , Edmonds Mary , Chagarov Evgueni , Droopad Ravi , Kummel Andrew C.
Published: December 2013

The nucleation and passivation of oxide deposition was studied on defect-free GaAs (110) surfaces to understand passivation of surfaces containing only III-V heterobonds. The passivation process on GaAs (110) was studied at the atomic level using scanning tunneling microscopy while the electronic structure was determined by scanning tunneling spectroscopy (STS). The bonding of the oxidant and reductant were modeled with density functional theory. To avoid Fermi level pinning during gate oxide atomic layer deposition, a dual passivation procedure was required using both a reductant, trimethylaluminum (TMA), and an oxidant, O2 or H2O. Dosing GaAs (110) with TMA resulted in the formation of an ordered complete monolayer of dimethylaluminum which passivates the group V dangling bonds but also forms metal-metal bonds with conduction band edge states. These edge states were suppressed by dosing the surface with oxidants O2 or H2O which selectively react with group III-aluminum bonds. The presence of an ordered Al monolayer with a high nucleation density was indirectly confirmed by XPS and STS.
Local changes of work function near rough features on Cu surfaces operated under high external electric field
Authors: Djurabekova Flyura , Ruzibaev Avaz , Holmström Eero , Parviainen Stefan , Hakala Mikko
Published: December 2013

Metal surfaces operated under high electric fields produce sparks even if they are held in ultra high vacuum. In spite of extensive research on the topic of vacuum arcs, the mystery of vacuum arc origin still remains unresolved. The indications that the sparking rates depend on the material motivate the research on surface response to extremely high external electric fields. In this work by means of density-functional theory calculations we analyze the redistribution of electron density on {100} Cu surfaces due to self-adatoms and in presence of high electric fields from −1 V/nm up to −2 V/nm (−1 to −2 GV/m, respectively). We also calculate the partial charge induced by the external field on a single adatom and a cluster of two adatoms in order to obtain reliable information on charge redistribution on surface atoms, which can serve as a benchmarking quantity for the assessment of the electric field effects on metal surfaces by means of molecular dynamics simulations. Furthermore, we investigate the modifications of work function around rough surface features, such as step edges and self-adatoms.
Transport properties of paired Majorana bound states in a parallel junction
Authors: Jiang Cui , Gong W. J. , Zheng Yi-Song
Published: December 2013

The transport properties of a paired Majorana bound states (MBSs) in a parallel junction are theoretically investigated, by considering the influence of different MBS-lead coupling manners, i.e., left-right asymmetric coupling, upper-down asymmetric coupling, and left-right upper-down asymmetric coupling. The calculation results show that the MBS-lead coupling manners affect the transport properties in a substantial way. For the former two configurations, the shot noise Fano factor in the zero-bias limit is related to the value of the conductance maximum with F0=1+12Tmax (conductance G=e2hT). When both the left-right and upper-down symmetries are broken, such a relation is modified into F0=1−12T0. These results will be helpful for describing the transport characteristics of the junction with MBSs.
Schottky barrier height reduction for metal/n-InP by inserting ultra-thin atomic layer deposited high-k dielectrics
Authors: Zheng Shan , Yang Wen , Sun Qing-Qing , Chen Lin , Zhou Peng , Wang Peng-Fei , Wei Zhang David , Xiao Fei
Published: December 2013

Fermi level pinning at metal/n-InP interface and effective Schottky barrier height (ФB,eff) were optimized by inserting ultrathin dielectrics in this work. Comparing the inserted monolayer and bilayer high-k dielectrics, we demonstrated that the introduction of bilayer dielectrics can further reduce ФB,eff (from 0.49 eV to 0.22 eV) than the monolayer dielectric (from 0.49 eV to 0.32 eV) even though the overall dielectric thickness was thicker. The additional dipole formed at high-k/high-k interfaces could be used to expound the mechanism. This work proposed an effective solution to reduce resistance contacts for InP based transistors and Schottky barrier transistors.
Transport properties in AlInSb/InAsSb heterostructures
Authors: Zhang Yuwei , Zhang Yang , Wang Chengyan , Zeng Yiping
Published: December 2013

Based on theoretical studies of transport properties in InAsSb-based quantum well heterostructures, we propose a material design for InAsSb quantum well with AlInSb barrier. Variation of electron mobility and two-dimensional electron gas concentration in AlyIn1−ySb/InAs1−xSbx heterostructures over the compositional range of which InAsSb is fully strained to AlInSb are investigated, where impact from dislocation scattering could be minimized. In comparison with InAs and InSb based quantum well heterostructures, InAsSb is advantageous in achieving the highest electron mobility despite of alloy disorder scattering. The maximum mobility of 37 000 cm2/V s is attainable in 15 nm InAs0.2Sb0.8 quantum well with Al0.24In0.76Sb barrier and there is great potential for further improvement. Our InAsSb based quantum well heterostructure is proved to be a robust structure for high-speed applications.
The effect of nanoparticles on thin film elasto-hydrodynamic lubrication
Authors: Ghaednia Hamed , Babaei Hasan , Jackson Robert L. , Bozack Michael J. , Khodadadi J. M.
Published: December 2013

Carefully conducted friction tests of a nano-lubricant in the thin film elasto-hydrodynamic lubrication regime showed that the presence of nanoparticles reduces friction. By using surface analyses techniques and molecular dynamics simulations, we explored the effectiveness of different interactions in the system, namely the interactions between nanoparticles with the lubricant or surfaces. Based on the results, the friction reduction mechanism was found to be that the nanoparticles induce an obstructed flow (plug flow) in the thin film between lubricated surfaces. This reduces friction by forcing only a few layers of lubricant molecules to slide on each other.
Mechanical behavior of water filled C60
Authors: Min K. , Barati Farimani A. , Aluru N. R.
Published: December 2013

We present the mechanical properties of H2O(n)@C60 under hydrostatic strain and a point load using Density Functional Theory. In each case, we performed mechanical tests under both tension and compression. The bulk modulus and elastic modulus increase as the number of water molecules increases. For fracture behavior, two mechanisms are observed: First, under compression, due to the interaction and bond formation between water and C60, structures with more water molecules begin to exhibit fracture at a lower strain. Second, under tension, fracture is initiated from the bond dissociation of C-C bonds on the C60 surface.
Phase behavior of oscillating double droplets
Authors: Tilger Christopher F. , Olles Joseph D. , Hirsa Amir H.
Published: December 2013

Double droplet systems are comprised of two coupled spherical interfaces. These systems are effective harmonic oscillators, due to their low dissipation and fast response; features enabled by their pinned contact lines. Here, millimeter scale coupled droplets of water are actuated with a sinusoidal driving pressure. The phase and transient behavior of the driven double droplet system is characterized. With the exact position of the double droplets determined, implementation of devices such as tunable lenses, thermal switches, and liquid adhesion mechanisms can be realized.
A novel improved particle swarm optimization maximum power point tracking control method for photovoltaic array by using current calculated predicted arithmetic under partially shaded conditions
Authors: Liu Liqun , Liu Chunxia , Gao Huimin
Published: December 2013

First, a novel current calculated (CC) principle is discussed in the study of the characteristics of the photovoltaic (PV) array under partial shading irradiation conditions. In this paper, the particle swarm optimization maximum power point tracking (MPPT) control method integrates with the proposed current calculated method to realize the rapid and accurate tracking efficiency for PV power under partial shading conditions. The proposed CC method is used as a tool to study the effects of partial shading and distribution of multiple peaks. In addition, the combined MPPT method is easy to gain the global peak of multiple PV arrays at complex partial shading. The experimental and simulation results prove the availability as compared with the traditional Perturbation and Observation method.
Improving chemical vapor deposition graphene conductivity using molybdenum trioxide: An in-situ field effect transistor study
Authors: Han Cheng , Lin Jiadan , Xiang Du , Wang Chaocheng , Wang Li , Chen Wei
Published: December 2013

By using in situ field effect transistor characterization integrated with molecular beam epitaxy technique, we demonstrate the strong surface transfer p-type doping effect of single layer chemical vapor deposition (CVD) graphene, through the surface functionalization of molybdenum trioxide (MoO3) layer. After doping, both the hole and electron mobility of CVD graphene are nearly retained, resulting in significant enhancement of graphene conductivity. With coating of 10 nm MoO3, the conductivity of CVD graphene can be increased by about 7 times, showing promising application for graphene based electronics and transparent, conducting, and flexible electrodes.
Low loss hollow optical-waveguide connection from atmospheric pressure to ultra-high vacuum
Authors: Ermolov A. , Mak K. F. , Tani F. , Hölzer P. , Travers J. C. , Russell P. St. J.
Published: December 2013

A technique for optically accessing ultra-high vacuum environments, via a photonic-crystal fiber with a long small hollow core, is described. The small core and the long bore enable a pressure ratio of over 108 to be maintained between two environments, while permitting efficient and unimpeded delivery of light, including ultrashort optical pulses. This delivery can be either passive or can encompass nonlinear optical processes such as optical pulse compression, deep UV generation, supercontinuum generation, or other useful phenomena.
Coherence of magnetic resonators in a metamaterial
Authors: Hou Yumin
Published: December 2013

The coherence of periodic magnetic resonators (MRs) under oblique incidence is studied using simulations. The correlated phase of interaction including both the retardation effect and relative phase difference between two MRs is defined, and it plays a key role in the MR interaction. The correlated phase is anisotropic, as is the coherence condition. The coherence condition is the same as the Wood's anomaly and verified by the Fano resonance. This study shows that the applications of the Fano resonance of periodic MRs will become widespread owing to achieving the Fano resonance simply by tuning the incident angle.
Neutral genomic regions refine models of recent rapid human population growth
Authors: Gazave Elodie , Ma Li , Chang Diana , Coventry Alex , Gao Feng , Muzny Donna , Boerwinkle Eric , Gibbs Richard A. , Sing Charles F. , Clark Andrew G. , Keinan Alon
Published: December 2013

Significance

Recent rapid growth of human populations predicts that a large number of genetic variants in populations today are very rare, i.e., appear in a small number of individuals. This effect is similar to that of purifying selection, which drives deleterious alleles to become rarer. Recent studies of the genetic signature left by rapid growth were confounded by purifying selection since they focused on genes. Here, to study recent human history with minimal confounding by selection, we sequenced and examined genetic variants far from genes. These data point to the human population size growing by about 3.4% per generation over the last 3,000–4,000 y, resulting in a greater than 100-fold increase in population size over that epoch.
Oncogenic KIT-containing exosomes increase gastrointestinal stromal tumor cell invasion
Authors: Atay Safinur , Banskota Samagya , Crow Jennifer , Sethi Geetika , Rink Lori , Godwin Andrew K.
Published: December 2013

Significance

Elevated expression of matrix metalloproteinase 1 (MMP1) is associated with a poor prognosis in a wide variety of advancing tumors, and thus MMPs have emerged as attractive targets for therapeutic strategies of metastatic tumors. However, clinical trials using MMP inhibitors in cancer therapy have proved to be disappointing. These studies support the contention that the use of broad-spectrum inhibitors of MMPs is insufficient for clinical benefit, as new compensatory pathways such as continuous production of exosomes derived from the tumor will be unaffected and will enhance the MMP produced by stromal cells. Therefore, a better understanding of the mechanisms used by tumor-derived exosomes in the induction of MMPs would permit the development of successful clinical strategies for novel MMP inhibitors.
Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation in
Escherichia coli
Authors: Quandt Erik M. , Deatherage Daniel E. , Ellington Andrew D. , Georgiou George , Barrick Jeffrey E.
Published: December 2013

Significance

Unexpected evolutionary innovations that lead to qualitatively new traits may result from complex genetic and ecological interactions that develop over long timescales. In a 25-y evolution experiment with
Escherichia coli
, a rare metabolic innovation arose that allowed a previously untapped resource to be exploited. By dissecting the genetics of this trait using a recursive genomewide recombination and sequencing method (REGRES), we identified a key mutation that converts a rudimentary form of the innovation into a refined trait that confers a decisive competitive advantage. The effects of this mutation demonstrate how improvement of an emergent trait can be as important to its eventual success as earlier mutations or environmental conditions that may have been necessary for it to evolve in the first place.
ParP prevents dissociation of CheA from chemotactic signaling arrays and tethers them to a polar anchor
Authors: Ringgaard Simon , Zepeda-Rivera Martha , Wu Xiaoji , Schirner Kathrin , Davis Brigid M. , Waldor Matthew K.
Published: December 2013

Significance

Targeting of cellular components to a particular site in a cell is often a highly regulated process, even in cells as small as bacteria. Robust chemotactic signaling, which is used by motile bacteria to survey their environments and navigate in response to them, requires appropriate cellular distribution of a large chemosensory apparatus. Here, we report how polarly flagellated vibrios ensure polar localization of their chemotactic machinery by capturing signaling proteins at the pole. Polar localization is mediated by a tripartite protein interaction network in which one protein prevents disassociation of a key signaling component from chemotactic complexes and tethers the complexes to a polar anchor. Polar tethering and localization are prerequisites for proper chemotaxis.
Hemozoin-generated vapor nanobubbles for transdermal reagent- and needle-free detection of malaria
Authors: Lukianova-Hleb Ekaterina Y. , Campbell Kelly M. , Constantinou Pamela E. , Braam Janet , Olson John S. , Ware Russell E. , Sullivan David J. , Lapotko Dmitri O.
Published: December 2013

Significance

We report a noninvasive rapid transdermal detection of malaria infection without drawing blood or using any reagents. Our method uses harmless laser pulses to generate and detect through the skin tiny vapor nanobubbles specifically in malaria parasites in a patient’s body. This method is distinct from all previous diagnostic approaches, which all rely upon using a needle to obtain blood, require reagents to detect the infection, and are time- and labor-consuming. This nanobubble transdermal detection adds a new dimension to malaria diagnostics and can in the future support the rapid, high-throughput, and high-sensitive diagnosis and screening by nonmedical personnel under field conditions, including the detection of early and asymptomatic disease.
Water access points and hydration pathways in CLC H
+
/Cl
−
transporters
Authors: Han Wei , Cheng Ricky C. , Maduke Merritt C. , Tajkhorshid Emad
Published: December 2013

Significance

CLC transporters are biologically essential proteins that catalyze the transmembrane exchange of chloride for protons. The permeation pathway for chloride through the transporters has been well characterized. Here, we study the more elusive permeation pathway for protons. Through computational modeling, we show that water molecules can permeate deep inside the protein and form continuous wires. To test the hypothesis that these water wires mediate proton transport, we mutated residues predicted to impede water wire formation and experimentally evaluated the effects of the mutations. The results from our concerted computational and experimental approach strongly support the role of water in proton transport by CLCs and provide a valuable framework for investigating their overall transport mechanism.
Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet superresolution microscopy
Authors: Zhao Ziqing W. , Roy Rahul , Gebhardt J. Christof M. , Suter David M. , Chapman Alec R. , Xie X. Sunney
Published: December 2013

Significance

We developed an optical imaging technique that combines reflected light-sheet illumination with superresolution microscopy, allowing us to image inside mammalian nuclei at subdiffraction-limit resolution and to count biomolecules with single-copy accuracy. Applying this technique to probe the spatial organization of RNA polymerase II-mediated transcription, we found that the majority of the transcription foci consist of only one RNAP II molecule, contrary to previous proposals. By quantifying the global extent of clustering across RNAP II molecules in the nucleus, we provide clear and convincing answers to the controversy surrounding the prevalent existence of “transcription factories.” Moreover, our work presents imaging and analysis tools for the quantitative characterization of nuclear structures, which could be generally applied to probe many other mammalian systems.
Catfish Sampling Techniques: Where We Are Now and Where We Should Go
Authors: Bodine Kristopher A , Shoup Daniel E , Olive Jason , Ford Zachary L , Krogman Rebecca , Stubbs Tyler J
Published: December 2013

We review the peer-reviewed literature regarding sampling of the three most commonly managed ictalurids: Channel Catfish, Blue Catfish, and Flathead Catfish. For each species, we summarize what is known about data quality (accuracy and precision) and sampling efficiency of the most commonly used gears for surveying these species. We identify research needs and provide information to guide gear selection based on different sampling objectives. To rank gear-specific sampling efficiency (catch/h and catch/person-h), we report median catch rates and the interpolated 25th and 75th percentiles of published means. We also describe the accuracy of relative abundance and size-related metrics for each gear. For Channel Catfish, tandem baited hoop nets provide the most efficient (11–24 fish/net/tandem set, 20–60 fish/person-h) and accurate samples. Low-frequency electrofishing provides the most efficient samples of Blue Catfish (23–373 fish/h, 2.1–11.3 fish/person-h) and Flathead Catfish (19–62 fish/h, 2.1–2.5 fish/person-h) and the most accurate samples of Blue Catfish. No accuracy studies exist for Flathead Catfish. Other gears examined for each species may also be useful for some sampling objectives; however, most are inefficient or lack accuracy.

RESUMEN

en este trabajo se hace una revisión de la literatura sobre el muestreo de los tres ictalúridos más comunmente explotados: el bagre de canal, el bagre azul y el bagre piltontle. Para cada especie, se resume lo que se sabe sobre la calidad de los datos (exactitud y precisión) y la eficiencia de muestreo de las artes (equipo) más frecuentemente utilizadas para muestrear estas especies. Se identifican necesidades de investigación y se brinda información que puede servir de guía para la selección de artes de pesca de acuerdo a los objetivos de muestreo. Con la finalidad de calificar la eficiencia específica del equipo de muestreo (captura-h y captura/persona-h) se reporta tanto la mediana de las tasas de captura como una extrapolación de los percentiles 25 y 75 de las medias reportadas en la literatura. También se describe la exactitud de las medidas de abundancia relativa y las relacionadas a la talla para cada arte. Para el bagre de canal, el tándem de redes de aros con carnada produjo las muestras más eficientes (11–24 peces/red/tándem, 20–60 peces/persona-h) y exactas. La electro-pesca de baja frecuencia fue el arte más eficiente para el bagre azul (23–373 peces-h, 2.1–11.3 peces/persona-h) y el bagre piltontle (19–62 peces-h, 2.1–2.5 peces/persona-h) y produjo las muestras más exactas en el caso del bagre azul. No existen estudios de exactitud para el bagre piltontle. Para cada especie se examinaron otras artes que pudieran ser útiles para ciertos objetivos de pesca; no obstante, la mayoría son ineficientes o carecen de exactitud.
New histone supply regulates replication fork speed and PCNA unloading
Authors: Mejlvang Jakob , Feng Yunpeng , Alabert Constance , Neelsen Kai J. , Jasencakova Zuzana , Zhao Xiaobei , Lees Michael , Sandelin Albin , Pasero Philippe , Lopes Massimo , Groth Anja
Published: December 2013

Correct duplication of DNA sequence and its organization into chromatin is central to genome function and stability. However, it remains unclear how cells coordinate DNA synthesis with provision of new histones for chromatin assembly to ensure chromosomal stability. In this paper, we show that replication fork speed is dependent on new histone supply and efficient nucleosome assembly. Inhibition of canonical histone biosynthesis impaired replication fork progression and reduced nucleosome occupancy on newly synthesized DNA. Replication forks initially remained stable without activation of conventional checkpoints, although prolonged histone deficiency generated DNA damage. PCNA accumulated on newly synthesized DNA in cells lacking new histones, possibly to maintain opportunity for CAF-1 recruitment and nucleosome assembly. Consistent with this, in vitro and in vivo analysis showed that PCNA unloading is delayed in the absence of nucleosome assembly. We propose that coupling of fork speed and PCNA unloading to nucleosome assembly provides a simple mechanism to adjust DNA replication and maintain chromatin integrity during transient histone shortage.
Cytoplasmic protein methylation is essential for neural crest migration
Authors: Vermillion Katie L. , Lidberg Kevin A. , Gammill Laura S.
Published: December 2013

As they initiate migration in vertebrate embryos, neural crest cells are enriched for methylation cycle enzymes, including S-adenosylhomocysteine hydrolase (SAHH), the only known enzyme to hydrolyze the feedback inhibitor of trans-methylation reactions. The importance of methylation in neural crest migration is unknown. Here, we show that SAHH is required for emigration of polarized neural crest cells, indicating that methylation is essential for neural crest migration. Although nuclear histone methylation regulates neural crest gene expression, SAHH and lysine-methylated proteins are abundant in the cytoplasm of migratory neural crest cells. Proteomic profiling of cytoplasmic, lysine-methylated proteins from migratory neural crest cells identified 182 proteins, several of which are cytoskeleton related. A methylation-resistant form of one of these proteins, the actin-binding protein elongation factor 1 alpha 1 (EF1α1), blocks neural crest migration. Altogether, these data reveal a novel and essential role for post-translational nonhistone protein methylation during neural crest migration and define a previously unknown requirement for EF1α1 methylation in migration.
TRAF3 regulates the effector function of regulatory T cells and humoral immune responses
Authors: Chang Jae-Hoon , Hu Hongbo , Jin Jin , Puebla-Osorio Nahum , Xiao Yichuan , Gilbert Brian E. , Brink Robert , Ullrich Stephen E. , Sun Shao-Cong
Published: December 2013

Regulatory T cells (Treg cells) control different aspects of immune responses, but how the effector functions of Treg cells are regulated is incompletely understood. Here we identified TNF receptor–associated factor 3 (TRAF3) as a regulator of Treg cell function. Treg cell–specific ablation of TRAF3 impaired CD4 T cell homeostasis, characterized by an increase in the Th1 type of effector/memory T cells. Moreover, the ablation of TRAF3 in Treg cells resulted in increased antigen-stimulated activation of follicular T helper cells (TFH cells), coupled with heightened formation of germinal centers and production of high-affinity IgG antibodies. Although the loss of TRAF3 did not reduce the overall frequency of Treg cells, it attenuated the antigen-stimulated production of follicular Treg cells (TFR cells). TRAF3 signaling in Treg cells was required to maintain high level expression of inducible co-stimulator (ICOS), which in turn was required for TFR cell generation and inhibition of antibody responses. These findings establish TRAF3 as a mediator of Treg cell function in the regulation of antibody responses and suggest a role for TRAF3 in mediating ICOS expression in Treg cells.
CCR7 provides localized access to IL-2 and defines homeostatically distinct regulatory T cell subsets
Authors: Smigiel Kate S. , Richards Elizabeth , Srivastava Shivani , Thomas Kerri R. , Dudda Jan C. , Klonowski Kimberly D. , Campbell Daniel J.
Published: December 2013

Immune tolerance and activation depend on precise control over the number and function of immunosuppressive Foxp3+ regulatory T (T reg) cells, and the importance of IL-2 in maintaining tolerance and preventing autoimmunity is clear. However, the homeostatic requirement for IL-2 among specific populations of peripheral T reg cells remains poorly understood. We show that IL-2 selectively maintains a population of quiescent CD44loCD62Lhi T reg cells that gain access to paracrine IL-2 produced in the T cell zones of secondary lymphoid tissues due to their expression of the chemokine receptor CCR7. In contrast, CD44hiCD62LloCCR7lo T reg cells that populate nonlymphoid tissues do not access IL-2–prevalent regions in vivo and are insensitive to IL-2 blockade; instead, their maintenance depends on continued signaling through the co-stimulatory receptor ICOS (inducible co-stimulator). Thus, we define a fundamental homeostatic subdivision in T reg cell populations based on their localization and provide an integrated framework for understanding how T reg cell abundance and function are controlled by unique signals in different tissue environments.
Nonlinear stability of spherical self-similar flows to the compressible Euler equations
Authors: Ha Seung-Yeal , Huang Hsiu-Chuan , Lien Wen-Ching
Published: December 2013

We present the nonlinear stability of spherical self-similar flows arising from the uniform expansion of a spherical piston toward still gas. If the perturbation of the expansion speed of the piston is sufficiently small compared with the strength of the leading shock, a global weak solution of the isentropic compressible Euler system exists in the region between the spherical piston and the leading shock under the structural condition on the shock Mach number and the nondimensional piston speed. Moreover, we show that the perturbed flow tends to the corresponding self-similar flow time-asymptotically. Our analysis is based on the modified Glimm scheme.