bluuebunny/crossref_metadata_2025 huggingface dataset:
Geomorphic and sedimentary responses of the Bull Creek Valley (Southern High Plains, USA) to Pleistocene and Holocene environmental change
Authors: Arauza Hanna M. , Simms Alexander R. , Bement Leland C. , Carter Brian J. , Conley Travis , Woldergauy Ammanuel , Johnson William C. , Jaiswal Priyank
Published: December 2015

Fluvial geomorphology and stratigraphy often reflect past environmental and climate conditions. This study examines the response of Bull Creek, a small ephemeral creek in the Oklahoma panhandle, to environmental conditions through the late Pleistocene and Holocene. Fluvial terraces were mapped and their stratigraphy and sedimentology documented throughout the course of the main valley. Based on their elevations, terraces were broadly grouped into a late-Pleistocene fill terrace (T3) and two Holocene fill-cut terrace sets (T2 and T1). Terrace systems are marked by similar stratigraphies recording the general environmental conditions of the time. Sedimentary sequences preserved in terrace fills record the transition from a perennial fluvial system during the late glacial period and the Younger Dryas to a semiarid environment dominated by loess accumulation and punctuated by flood events during the middle to late Holocene. The highest rates of aeolian accumulation within the valley occurred during the early to middle Holocene. Our data provide significant new information regarding the late-Pleistocene and Holocene environmental history for this region, located between the well-studied Southern and Central High Plains of North America.
White Workers in the Late Apartheid Period: A Report on the Wiehahn Commission and Mineworkers’ Union Archival Collections
Authors: van Zyl-Hermann Danelle
Published: December 2015

This paper offers a critique of the existing historiography on the late apartheid period, arguing that white workers’ role in and experience of the unraveling of racial privilege in the labor arena has been obscured by a focus on the high politics of reform and on anti-apartheid resistance emanating from African labor and the broader black population. Reporting from the archive, it discusses two under-utilized archival collections – that of the Commission of Inquiry into Labour Legislation and of the Mineworkers’ Union – as sources for starting to write white working-class organization, politics, identity, and experience into the history of reform and resistance, thereby adding a new dimension to South Africa’s broadly conceived struggle history.
Hospital Readmissions in Patients With Carbapenem-ResistantKlebsiella pneumoniae
Authors: Messina Julia A. , Cober Eric , Richter Sandra S. , Perez Federico , Salata Robert A. , Kalayjian Robert C. , Watkins Richard R. , Scalera Nikole M. , Doi Yohei , Kaye Keith S. , Evans Scott , Bonomo Robert A. , Fowler Vance G. , van Duin David
Published: December 2015

BACKGROUND

Various transmission routes contribute to spread of carbapenem-resistantKlebsiella pneumoniae(CRKP) in hospitalized patients. Patients with readmissions during which CRKP is again isolated (“CRKP readmission”) potentially contribute to transmission of CRKP.

OBJECTIVE

To evaluate CRKP readmissions in the Consortium on Resistance against Carbapenems inK. pneumoniae(CRaCKLe).

DESIGN

Cohort study from December 24, 2011, through July 1, 2013.

SETTING

Multicenter consortium of acute care hospitals in the Great Lakes region.

PATIENTS

All patients who were discharged alive during the study period were included. Each patient was included only once at the time of the first CRKP-positive culture.

METHODS

All readmissions within 90 days of discharge from the index hospitalization during which CRKP was again found were analyzed. Risk factors for CRKP readmission were evaluated in multivariable models.

RESULTS

Fifty-six (20%) of 287 patients who were discharged alive had a CRKP readmission. History of malignancy was associated with CRKP readmission (adjusted odds ratio [adjusted OR], 3.00 [95% CI, 1.32–6.65],P<.01). During the index hospitalization, 160 patients (56%) received antibiotic treatment against CRKP; the choice of regimen was associated with CRKP readmission (P=.02). Receipt of tigecycline-based therapy (adjusted OR, 5.13 [95% CI, 1.72–17.44], using aminoglycoside-based therapy as a reference in those treated with anti-CRKP antibiotics) was associated with CRKP readmission.

CONCLUSION

Hospitalized patients with CRKP—specifically those with a history of malignancy—are at high risk of readmission with recurrent CRKP infection or colonization. Treatment during the index hospitalization with a tigecycline-based regimen increases this risk.

Infect. Control Hosp. Epidemiol.2016;37(3):281–288
Direct numerical simulation of turbulent channel flow with spanwise rotation
Authors: Xia Zhenhua , Shi Yipeng , Chen Shiyi
Published: December 2015

A series of direct numerical simulations of turbulent channel flow with spanwise rotation at fixed global friction Reynolds number is performed to investigate the rotation effects on the mean velocity, streamwise velocity fluctuations, Reynolds shear stress and turbulent kinetic energy. The global friction Reynolds number is chosen to be $Re_{{\it\tau}}=u_{{\it\tau}}^{\ast }h^{\ast }/{\it\nu}^{\ast }=180$ ($u_{{\it\tau}}^{\ast }$ is the global friction velocity, $h^{\ast }$ is the channel half-width and ${\it\nu}^{\ast }$ is the kinematic viscosity), while the global-friction-velocity-based rotation number $Ro_{{\it\tau}}=2{\it\Omega}^{\ast }h^{\ast }/u_{{\it\tau}}^{\ast }$ (${\it\Omega}^{\ast }$ is the dimensional angular velocity) varies from 0 to 130. In the previously reported $2{\it\Omega}^{\ast }$-slope region for the mean velocity, a linear behaviour for the streamwise velocity fluctuations, a unit-slope linear profile for the Reynolds shear stress and a $-2Ro_{{\it\tau}}$-slope linear profile for the production term of $\langle u^{\prime }u^{\prime }\rangle$ have been identified for the first time. The critical rotation number, which corresponds to the laminar limit, is predicted to be equal to $Re_{{\it\tau}}$ according to the unit-slope linear profile of the Reynolds shear stress. Our results also show that a parabolic profile of the mean velocity can be identified around the ‘second plateau’ region of the Reynolds shear stress for $Ro_{{\it\tau}}\geqslant 22$. The parabolas at different rotation numbers have the same shape of $1/Re_{{\it\tau}}$, the radius of curvature at the vertex. Furthermore, the system rotation increases the volume-averaged turbulent kinetic energy at lower rotation rates, and then decreases it when $Ro_{{\it\tau}}\gtrsim 16$.
Do tissue spears used to clear ear canal pus improve hearing? A case series study of hearing in remote Australian Aboriginal children with chronic suppurative otitis media before and after dry mopping with tissue spears
Authors: Sparrow K , Sanchez L , Turner D , MacFarlane P , Carney A S
Published: December 2015

Objective:

To determine whether the use of tissue spears to remove otorrhoea from Aboriginal children's ear canals improves hearing in the affected ear.

Design:

Case series study with controls.

Methods:

The study comprised 61 Aboriginal children from communities in the remote arid zone of South Australia who had otorrhoea obscuring the tympanic membrane in 1 or both ears. Eighty ears were treated with tissue spears, and hearing was assessed before and after treatment.

Results:

Forty-two children had unilateral and 19 had bilateral active disease. An additional 13 ears without otorrhoea served as controls. Improvement by 5 dB HL or greater in a four-frequency pure tone average occurred in 41.3 per cent of treated ears. Subsequently, blinded audiologists made qualitative judgements that a functional improvement in hearing had occurred after tissue spear use in 28.4 per cent of ears.

Conclusion:

Tissue spears can improve hearing thresholds in a significant proportion of children with otorrhoea. However, the duration of the effect is unknown.
‘All newcomers now’: Narrating social and material aspects of post-war resettlement in northwest Cambodia
Authors: Arensen Lisa
Published: December 2015

This article examines one Cambodian village's efforts to resettle a war-altered landscape and reconstruct a sense of belonging in the aftermath of war. The resettlement of Reaksmei Songha village entailed physically settling over the sediments and traces of a fractured and violent past, as settlers cleared a landscape of foliage and the explosive remnants of war. Settlers living side by side had often fought on different sides of the war, yet divisive former allegiances were rarely discussed. Instead, a post-war sense of communal belonging was constructed through references to accounts of the resettlement period, focusing upon common elements of struggle and hardship.
From brooding to hatching: new insights from a female Octopus vulgaris in the wild
Authors: Garci Manuel E. , Hernández-Urcera Jorge , Gilcoto Miguel , Fernández-Gago Raquel , González Ángel F. , Guerra Ángel
Published: December 2015

A brooding Octopus vulgaris female was monitored for 128 days in her natural habitat. The main reproductive events and embryonic development in relation to the temperature inside the spawning den, which was recorded by long-battery-life mini-data loggers, are described in the wild. The den temperature ranged from 12.9 to 19.3°C. The total number of egg strings was 160, and the total number of eggs spawned ranged between 139,040 and 241,760 (mean 190,400). The brooding period, the egg laying interval and the duration of the hatching course lasted 128, 35 and 43 days, respectively. Both egg laying and hatching were intermittent processes. The time taken for embryonic development was variable (85–128 d) and depended on the laying date, temperature and position of the string in the egg cluster and the position of the egg in the egg string. The first hatching observed occurred after a progressive and gradual increase of the temperature from 14.9 to 19.3°C. The 280 min of video recordings taken by scuba divers showed that several times, this female opened and closed a small window in the obstructions of the den entrance to facilitate a way out for the hatchling batches.
A new species of Gourretia (Decapoda: Axiidea: Gourretiidae) from the Persian Gulf, Iran
Authors: Sepahvand Vahid , Pouyani Nasrollah Rastegar , Momtazi Farzaneh
Published: December 2015

Sampling in subtidal waters of the Persian Gulf revealed a new species of ghost shrimp from the family Gourretiidae. Gourretia qeshmensis sp. nov. resembles G. sinica from the South China Sea and G. manihinae from Tanzania. Gourretia qeshmensis sp. nov. differs from these two species by characters of the ischium of the large cheliped, pereopod 3, exopod of the uropod and maxilliped 3.
Seroconversion for cytomegalovirus infection in a cohort of pregnant women in Québec, 2010–2013
Authors: LAMARRE V. , GILBERT N. L. , ROUSSEAU C. , GYORKOS T. W. , FRASER W. D.
Published: December 2015

Cytomegalovirus (CMV) is the leading cause of congenital infection and non-genetic sensorineural hearing loss in children. There are no recent data on the incidence of CMV infection during pregnancy in Canada. This present study was undertaken to determine the seroprevalence of CMV IgG antibodies and the rate of seroconversion in a cohort of pregnant women in the province of Québec, Canada. We used serum samples and questionnaire data collected as part of the 3D Pregnancy and Birth Cohort Study (2010–2013) conducted in Québec, Canada. CMV IgG antibodies were determined in serum samples collected at the first and third trimesters. Associations between independent variables and seroprevalence were assessed using logistic regression, and associations with seroconversions, by Poisson regression. Of 1938 pregnant women tested, 40·4% were seropositive for CMV at baseline. Previous CMV infection was associated with: working as a daycare educator, lower education, lower income, having had children, first language other than French or English, and being born outside Canada or the United States. Of the 1122 initially seronegative women, 24 (2·1%) seroconverted between their first and third trimesters. The seroconversion rate was 1·4 [95% confidence interval (CI) 0·9–2·1]/10 000 person-days at risk or 3·9 (95% CI 2·5–5·9)/100 pregnancies (assuming a 280-day gestation). The high proportion of pregnant women susceptible to CMV infection (nearly 60%) and the subsequent rate of seroconversion are of concern.
Development of a reliable GC-MS method for fatty acid profiling using direct transesterification of minimal quantities of microscopic orchid seeds
Authors: Colville Louise , Marks Tim R. , Pritchard Hugh W. , Custódio Ceci C. , Machado-Neto Nelson B.
Published: December 2015

Orchid seeds are among the smallest seeds in nature and they are naturally rich in fatty acids. However, the fatty acid composition of orchid seeds has not been investigated because the sample masses utilized for widely used methods for fatty acid profiling would generally require prohibitively large numbers (i.e. 10,000s) of seeds. The present work aimed to develop a method for fatty acid analysis using gas chromatography–mass spectrometry on small quantities (mg) of seeds. The method was developed using the seeds of two species,Dactylorhiza fuchsii, a temperate terrestrial, andGrammatophyllum speciosum, a tropical epiphyte. A range of sample masses was tested to determine the minimum mass required to achieve reliable fatty acid composition data. A direct transesterification method was used, which did not require extraction of fatty acids from seeds prior to analysis, and the effects of seed processing (crushed versus intact seeds) and incubation time in toluene on fatty acid yield were tested. Stable fatty acid profiles were obtained using as little as 10 mg of seeds. Neither crushing the seeds nor extending the toluene incubation step had much effect on the fatty acid yield. The simple direct transesterification method presented will enable the fatty acid composition of orchid seeds, and possibly other small seeds, to be determined reliably for studies into seed development, storage and germination.
Manipulative Waiters with Probabilistic Intuition
Authors: BEDNARSKA-BZDȨGA MAŁGORZATA , HEFETZ DAN , KRIVELEVICH MICHAEL , ŁUCZAK TOMASZ
Published: December 2015

For positive integersnandqand a monotone graph property$\mathcal{A}$, we consider the two-player, perfect information game WC(n,q,$\mathcal{A}$), which is defined as follows. The game proceeds in rounds. In each round, the first player, called Waiter, offers the second player, called Client,q+ 1 edges of the complete graphKnwhich have not been offered previously. Client then chooses one of these edges which he keeps and the remainingqedges go back to Waiter. If, at the end of the game, the graph which consists of the edges chosen by Client satisfies the property$\mathcal{A}$, then Waiter is declared the winner; otherwise Client wins the game. In this paper we study such games (also known as Picker–Chooser games) for a variety of natural graph-theoretic parameters, such as the size of a largest component or the length of a longest cycle. In particular, we describe a phase transition type phenomenon which occurs when the parameterqis close tonand is reminiscent of phase transition phenomena in random graphs. Namely, we prove that ifq⩾ (1 + ϵ)n, then Client can avoid components of ordercϵ−2lnnfor some absolute constantc> 0, whereas forq⩽ (1 − ϵ)n, Waiter can force a giant, linearly sized component in Client's graph. In the second part of the paper, we prove that Waiter can force Client's graph to be pancyclic for everyq⩽cn, wherec> 0 is an appropriate constant. Note that this behaviour is in stark contrast to the threshold for pancyclicity and Hamiltonicity of random graphs.
Local Maxima of Quadratic Boolean Functions
Authors: SPINK HUNTER
Published: December 2015

How many strict local maxima can a real quadratic function on {0, 1}n have? Holzman conjectured a maximum of $\binom{n }{ \lfloor n/2 \rfloor}$. The aim of this paper is to prove this conjecture. Our approach is via a generalization of Sperner's theorem that may be of independent interest.
Intracellular Biosynthesis of Fluorescent CdSe Quantum Dots in Bacillus subtilis: A Strategy to Construct Signaling Bacterial Probes for Visually Detecting Interaction Between Bacillus subtilis and Staphylococcus aureus
Authors: Yan Zheng-Yu , Ai Xiao-Xia , Su Yi-Long , Liu Xin-Ying , Shan Xiao-Hui , Wu Sheng-Mei
Published: December 2015

In this work, fluorescent Bacillus subtilis (B. subtilis) cells were developed as probes for imaging applications and to explore behaviorial interaction between B. subtilis and Staphylococcus aureus (S. aureus). A novel biological strategy of coupling intracellular biochemical reactions for controllable biosynthesis of CdSe quantum dots by living B. subtilis cells was demonstrated, through which highly luminant and photostable fluorescent B. subtilis cells were achieved with good uniformity. With the help of the obtained fluorescent B. subtilis cells probes, S. aureus cells responded to co-cultured B. subtilis and to aggregate. The degree of aggregation was calculated and nonlinearly fitted to a polynomial model. Systematic investigations of their interactions implied that B. subtilis cells inhibit the growth of neighboring S. aureus cells, and this inhibition was affected by both the growth stage and the amount of surrounding B. subtilis cells. Compared to traditional methods of studying bacterial interaction between two species, such as solid culture medium colony observation and imaging mass spectrometry detection, the procedures were more simple, vivid, and photostable due to the efficient fluorescence intralabeling with less influence on the cells’ surface, which might provide a new paradigm for future visualization of microbial behavior.
Assessment of nitrogen and phosphorus loads present in environments impacted by alternative poultry processing operations utilized in pasture-raised poultry production
Authors: O'Bryan Corliss A. , Crandall Philip , Jaroni Divya , Ricke Steven C. , Gibson Kristen E.
Published: December 2015

Pasture-raised poultry (PP) production systems allow chickens, turkeys or other poultry types to be raised entirely on pasture or in small, open-air moveable pens with access to fresh pasture daily. With an increase in consumer demand for poultry products produced using more humane and potentially environmentally sustainable practices, PP production systems are regaining popularity among farmers across the USA. The majority of research on PP is related to meat quality and forage conditions while the environmental effects have remained largely unstudied. The rotation of poultry on pasture is one of the primary best management practices (BMP) used to avoid over grazing and buildup of excess nutrients and pathogens; however, BMPs for handling and processing of the associated wastes (i.e., wastewater, feathers, offal) related to on-farm processing and mobile poultry processing units (MPPU) are not as well established. Therefore, a study with PP growers in the southern USA was initiated to provide important baseline information on the potential environmental impacts of processing methods used by PP production systems. Here, three farms utilizing on-farm processing were sampled over a 9-month period and two farms utilizing a MPPU pilot plant were sampled over a 3-month period. Soil, compost and wastewater samples were collected during each sampling date for on-farm processing while only wastewater was collected at the MPPU pilot plant. Soil samples (24-cm cores) were analyzed for total nitrogen (TN), Mehlich-3 extractable phosphorus (M3-P) and moisture content. Compost derived from processing wastes was analyzed for TN, total phosphorus (TP), water extractable P and moisture content. Wastewaters were analyzed for total Kjeldahl nitrogen (TKN) and TP. Soil TN levels (0.075–0.30%) reported here are comparable with TN levels reported for various soils in the Southeastern USA while M3-P was generally below levels found in agricultural soils subject to conventional poultry litter application based on previously published data. Conversely, TN and TP levels—0.3 to 1.3 and <0.4%, respectively—in compost were well below recommended values (i.e., approximately 2% each of N and P) for compost highlighting an opportunity for PP growers to create a more useful compost for land application. Last, wastewater collected from both, on-farm processing and the MPPU measure TKN and TP levels were much less than conventional processing. Overall, the present study provided baseline data on soil and compost nutrients related to on-farm poultry processing as well as wastewater composition for on-farm processing and MPPUs.
Cultural legacies and political preferences: the failure of separatism in the Swiss Jura
Authors: Siroky David S. , Mueller Sean , Hechter Michael
Published: December 2015

The study of secession generally stresses the causal influence of cultural identities, political preferences, or ecological factors. Whereas these different views are often considered to be mutually exclusive, this paper proposes a two-stage model in which they are complementary. We posit that cultural identities matter for explaining secessionism, but not because of primordial attachments. Rather, religious and linguistic groups matter because their members are imbued with cultural legacies that lead to distinct political preferences – in this case preferences over welfare statism. Further, ecological constraints such as geography and topography affect social interaction with like-minded individuals. On the basis of both these political preferences and ecological constraints, individuals then make rational choices about the desirability of secession. Instrumental considerations are therefore crucial in explaining the decision to secede, but not in a conventional pocketbook manner. To examine this theory, we analyze the 2013 referendum on the secession of the Jura Bernois region from the Canton of Berne in Switzerland, using municipal level census and referendum data. The results lend support to the theory and suggest one way in which the politics of identity, based on factors like language and religion, can be fused with the politics of interest (preferences for more or less state intervention into the polity and economy) to better understand group behavior.
Special agreements as a means of enhancing compliance with IHL in non-international armed conflicts: An inquiry into the governing legal regime
Authors: Heffes Ezequiel , Kotlik Marcos D.
Published: December 2015

Common Article 3 to the four Geneva Conventions encourages the parties to a non-international armed conflict to bring into force international humanitarian law provisions through the conclusion of special agreements. Since armed groups are ever more frequent participants in contemporary armed conflicts, the relevance of those agreements as means to enhance compliance with IHL has grown as well. The decision-making process of special agreements recognizes that all the parties to the conflict participate in the clarification and expansion of the applicable rights and obligations in a way that is consistent with the principle of equality of belligerents. This provides incentives for armed groups to respect the IHL rules they have themselves negotiated. However, even upon the conclusion of such agreements, it remains unclear which legal regime governs them. This paper will argue that special agreements are governed by international law instead of domestic law or asui generislegal regime.
Infant gut immunity: a preliminary study of IgA associations with breastfeeding
Authors: Bridgman S. L. , Konya T. , Azad M. B. , Sears M. R. , Becker A. B. , Turvey S. E. , Mandhane P. J. , Subbarao P. ,   CHILD Study Investigators, Scott J. A. , Field C. J. , Kozyrskyj A. L.
Published: December 2015

Secretory immunoglobulin A (IgA) plays a critical role in gut mucosal immune defense. Initially provided by breastmilk, IgA production by the infant gut is gradually stimulated by developing gut microbiota. This study reports associations between infant fecal IgA concentrations 4 months after birth, breastfeeding status and other pre/postnatal exposures in 47 infants in the Canadian Healthy Infant Longitudinal Development cohort. Breastfed infants and first-born infants had higher median fecal IgA concentrations (23.11 v. 9.34 µg/g protein, P<0.01 and 22.19 v. 8.23 µg/g protein, P=0.04). IgA levels increased successively with exclusivity of breastfeeding (β-coefficient, 0.37, P<0.05). This statistical association was independent of maternal parity and household pets. In the absence of breastfeeding, female sex and pet exposure elevated fecal IgA to levels found in breastfed infants. In addition to breastfeeding, infant fecal IgA associations with pre/postnatal exposures may affect gut immunity and risk of allergic disease.
Speeded Probed Recall Is Affected by Grouping
Authors: Morra Sergio , Epidendio Valentina
Published: December 2015

Abstract. Most of the evidence from previous studies on speeded probed recall supported primacy-gradient models of serial order representation. Two experiments investigated the effect of grouping on speeded probed recall. Six-word lists, followed by a number between 1 and 6, were presented for speeded recall of the word in the position indicated by the number. Grouping was manipulated through interstimulus intervals. In both experiments, a significant Position × Grouping interaction was found in RT. It is concluded that the results are not consistent with models of order representation only based on a primacy gradient. Possible alternative representations of serial order are also discussed; a case is made for a holistic order representation.
The Uncanny Valley: Existence and Explanations
Authors: Wang Shensheng , Lilienfeld Scott O. , Rochat Philippe
Published: December 2015

More than 40 years ago, Japanese roboticist Masahiro Mori (1970/2005) proposed the “uncanny valley” hypothesis, which predicted a nonlinear relation between robots’ perceived human likeness and their likability. Although some studies have corroborated this hypothesis and proposed explanations for its existence, the evidence on both fronts has been mixed and open to debate. We first review the literature to ascertain whether the uncanny valley exists. We then try to explain the uncanny phenomenon by reviewing hypotheses derived from diverse theoretical and methodological perspectives within psychology and allied fields, including evolutionary, social, cognitive, and psychodynamic approaches. Next, we provide an evaluation and critique of these studies by focusing on their methodological limitations, leading us to question the accepted definition of the uncanny valley. We examine the definitions of human likeness and likability, and propose a statistical test to preliminarily quantify their nonlinear relation. We argue that the uncanny valley hypothesis is ultimately an engineering problem that bears on the possibility of building androids that may some day become indistinguishable from humans. In closing, we propose a dehumanization hypothesis to explain the uncanny phenomenon.
Layer-by-layer functionalized nanotube arrays: A versatile microfluidic platform for biodetection
Authors: Yost Allison L. , Shahsavari Setareh , Bradwell Grinia M. , Polak Roberta , Fachin Fabio , Cohen Robert E. , McKinley Gareth H. , Toner Mehmet , Rubner Michael F. , Wardle Brian L.
Published: December 2015

We demonstrate the layer-by-layer (LbL) assembly of polyelectrolyte multilayers (PEM) on three-dimensional nanofiber scaffolds. High porosity (99%) aligned carbon nanotube (CNT) arrays are photolithographically patterned into elements that act as textured scaffolds for the creation of functionally coated (nano)porous materials. Nanometer-scale bilayers of poly(allylamine hydrochloride)/poly(styrene sulfonate) (PAH/SPS) are formed conformally on the individual nanotubes by repeated deposition from aqueous solution in microfluidic channels. Computational and experimental results show that the LbL deposition is dominated by the diffusive transport of the polymeric constituents, and we use this understanding to demonstrate spatial tailoring on the patterned nanoporous elements. A proof-of-principle application, microfluidic bioparticle capture using N-hydroxysuccinimide-biotin binding for the isolation of prostate-specific antigen (PSA), is demonstrated.
Chip-scale gas chromatography: From injection through detection
Authors: Akbar Muhammad , Restaino Michael , Agah Masoud
Published: December 2015

Miniaturized gas chromatography (µGC) systems hold potential for the rapid analysis of volatile organic compounds (VOCs) in an extremely compact and low-power enabled platform. Here, we utilize microfabrication technology to demonstrate the single chip integration of the key components of a µGC system in a two-step planar fabrication process. The 1.5 × 3 cm microfluidic platform includes a sample injection unit, a micromachined semi-packed separation column (µSC) and a micro-helium discharge photoionization detector (µDPID). The sample injection unit consists of a T-shaped channel operated with an equally simple setup involving a single three-way fluidic valve, a micropump for sample loading and a carrier gas supply for subsequent analysis of the VOCs. The innovative sample injection technique described herein requires a loading time of only a few seconds and produces sharp and repeatable sample pulses (full width at half maximum of approximately 200 ms) at a carrier gas flow rate that is compatible with efficient chromatographic separation. Furthermore, our comprehensive characterization of the chip reveals that a wide variety of VOCs with boiling points in the range of 110–216 °C can be analyzed in less than 1 min by optimizing the flow and temperature programming conditions. Moreover, the analysis of four VOCs at the concentration level of one part per million in an aqueous sample (which corresponds to a headspace concentration in the lower parts-per-billion regime) was performed with a sampling time of only 6 s. The µDPID has demonstrated a linear dynamic range over three orders of magnitude. The system presented here could potentially be used to monitor hazardous VOCs in real time in industrial workplaces and residential settings.
A genome-wide association study identifies four novel susceptibility loci underlying inguinal hernia
Authors: Jorgenson Eric , Makki Nadja , Shen Ling , Chen David C. , Tian Chao , Eckalbar Walter L. , Hinds David , Ahituv Nadav , Avins Andrew
Published: December 2015

Inguinal hernia repair is one of the most commonly performed operations in the world, yet little is known about the genetic mechanisms that predispose individuals to develop inguinal hernias. We perform a genome-wide association analysis of surgically confirmed inguinal hernias in 72,805 subjects (5,295 cases and 67,510 controls) and confirm top associations in an independent cohort of 92,444 subjects with self-reported hernia repair surgeries (9,701 cases and 82,743 controls). We identify four novel inguinal hernia susceptibility loci in the regions of EFEMP1, WT1, EBF2 and ADAMTS6. Moreover, we observe expression of all four genes in mouse connective tissue and network analyses show an important role for two of these genes (EFEMP1 and WT1) in connective tissue maintenance/homoeostasis. Our findings provide insight into the aetiology of hernia development and highlight genetic pathways for studies of hernia development and its treatment.
RSV-specific airway resident memory CD8+ T cells and differential disease severity after experimental human infection
Authors: Jozwik Agnieszka , Habibi Maximillian S. , Paras Allan , Zhu Jie , Guvenel Aleks , Dhariwal Jaideep , Almond Mark , Wong Ernie H. C. , Sykes Annemarie , Maybeno Matthew , Del Rosario Jerico , Trujillo-Torralbo Maria-Belen , Mallia Patrick , Sidney John , Peters Bjoern , Kon Onn Min , Sette Alessandro , Johnston Sebastian L. , Openshaw Peter J. , Chiu Christopher
Published: December 2015

In animal models, resident memory CD8+ T (Trm) cells assist in respiratory virus elimination but their importance in man has not been determined. Here, using experimental human respiratory syncytial virus (RSV) infection, we investigate systemic and local virus-specific CD8+ T-cell responses in adult volunteers. Having defined the immunodominance hierarchy, we analyse phenotype and function longitudinally in blood and by serial bronchoscopy. Despite rapid clinical recovery, we note surprisingly extensive lower airway inflammation with persistent viral antigen and cellular infiltrates. Pulmonary virus-specific CD8+ T cells display a CD69+CD103+ Trm phenotype and accumulate to strikingly high frequencies into convalescence without continued proliferation. While these have a more highly differentiated phenotype, they express fewer cytotoxicity markers than in blood. Nevertheless, their abundance before infection correlates with reduced symptoms and viral load, implying that CD8+ Trm cells in the human lung can confer protection against severe respiratory viral disease when humoral immunity is overcome.
Chloroquine alleviates etoposide-induced centrosome amplification by inhibiting CDK2 in adrenocortical tumor cells
Authors: Chen T-Y , Syu J-S , Lin T-C , Cheng H-l , Lu F-l , Wang C-Y
Published: December 2015

The antitumor drug etoposide (ETO) is widely used in treating several cancers, including adrenocortical tumor (ACT). However, when used at sublethal doses, tumor cells still survive and are more susceptible to the recurring tumor due to centrosome amplification. Here, we checked the effect of sublethal dose of ETO in ACT cells. Sublethal dose of ETO treatment did not induce cell death but arrested the ACT cells in G2/M phase. This resulted in centrosome amplification and aberrant mitotic spindle formation leading to genomic instability and cellular senescence. Under such conditions, Chk2, cyclin A/CDK2 and ERK1/2 were aberrantly activated. Pharmacological inactivation of Chk2, CDK2 or ERK1/2 or depletion of CDK2 or Chk2 inhibited the centrosome amplification in ETO-treated ACT cells. In addition, autophagy was activated by ETO and was required for ACT cell survival. Chloroquine, the autophagy inhibitor, reduced ACT cell growth and inhibited ETO-induced centrosome amplification. Chloroquine alleviated CDK2 and ERK, but not Chk2, activation and thus inhibited centrosome amplification in either ETO- or hydroxyurea-treated ACT cells. In addition, chloroquine also inhibited centrosome amplification in osteosarcoma U2OS cell lines when treated with ETO or hydroxyurea. In summary, we have demonstrated that chloroquine inhibited ACT cell growth and alleviated DNA damage-induced centrosome amplification by inhibiting CDK2 and ERK activity, thus preventing genomic instability and recurrence of ACT.
CancerNet: a database for decoding multilevel molecular interactions across diverse cancer types
Authors: Meng X , Wang J , Yuan C , Li X , Zhou Y , Hofestädt R , Chen M
Published: December 2015

Protein–protein interactions (PPIs) and microRNA (miRNA)–target interactions are important for deciphering the mechanisms of tumorigenesis. However, current PPI databases do not support cancer-specific analysis. Also, no available databases can be used to retrieve cancer-associated miRNA–target interactions. As the pathogenesis of human cancers is affected by several miRNAs rather than a single miRNA, it is needed to uncover miRNA synergism in a systems level. Here for each cancer type, we constructed a miRNA–miRNA functionally synergistic network based on the functions of miRNA targets and their topological features in that cancer PPI network. And for the first time, we report the cancer-specific database CancerNet (http://bis.zju.edu.cn/CancerNet), which contains information about PPIs, miRNA–target interactions and functionally synergistic miRNA–miRNA pairs across 33 human cancer types. In addition, PPI information across 33 main normal tissues and cell types are included. Flexible query methods are allowed to retrieve cancer molecular interactions. Network viewer can be used to visualize interactions that users are interested in. Enrichment analysis tool was designed to detect significantly overrepresented Gene Ontology categories of miRNA targets. Thus, CancerNet serves as a comprehensive platform for assessing the roles of proteins and miRNAs, as well as their interactions across human cancers.
The Roles of MicroRNA-122 Overexpression in Inhibiting Proliferation and Invasion and Stimulating Apoptosis of Human Cholangiocarcinoma Cells
Authors: Liu Ning , Jiang Fan , He Tian-Lin , Zhang Jun-Kuan , Zhao Juan , Wang Chun , Jiang Gui-Xing , Cao Li-Ping , Kang Peng-Cheng , Zhong Xiang-Yu , Lin Tian-Yu , Cui Yun-Fu
Published: December 2015

Our study investigated whether microRNA-122 (miR-122) played important roles in the proliferation, invasion and apoptosis of human cholangiocarcinoma (CC) cells. QBC939 and RBE cells lines were chosen and divided into five groups: miR-122 mimic group, anti-miR-122 group, negative control (NC) group, mock group and blank group. MiR-122 expression was measured by qRT-PCR. Roles of miR-122 in cell proliferation, apoptosis and invasion were investigated using MTT assay, flow cytometer and Transwell invasion assay, respectively. MiR-122 expression was lower in CC tissues and QBC939 cell than that in normal bile duct tissues, HCCC-9810 and RBE cells. In both QBC939 and RBE cells lines, miR-122 expression was higher in miR-122 mimic group than that in NC group, mock group and blank group; opposite results were found in anti-miR-122 group. Cell proliferation and invasion were remarkably inhibited in miR-122 mimic group after 48 h/72 h transfection, while apoptotic cells numbers were much greater in miR-122 mimic group; the opposite results were obtained from anti-miR-122 group (all P < 0.05). MiR-122 expression was significantly weaker in CC tissues and miR-122 overexpression might play pivotal roles in inhibiting proliferation, stimulating apoptosis and suppressing invasion of CC cells, suggesting a new target for CC diagnosis and treatment.
Fast non-Abelian geometric gates via transitionless quantum driving
Authors: Zhang J. , Kyaw Thi Ha , Tong D. M. , Sjöqvist Erik , Kwek Leong-Chuan
Published: December 2015

A practical quantum computer must be capable of performing high fidelity quantum gates on a set of quantum bits (qubits). In the presence of noise, the realization of such gates poses daunting challenges. Geometric phases, which possess intrinsic noise-tolerant features, hold the promise for performing robust quantum computation. In particular, quantum holonomies, i.e., non-Abelian geometric phases, naturally lead to universal quantum computation due to their non-commutativity. Although quantum gates based on adiabatic holonomies have already been proposed, the slow evolution eventually compromises qubit coherence and computational power. Here, we propose a general approach to speed up an implementation of adiabatic holonomic gates by using transitionless driving techniques and show how such a universal set of fast geometric quantum gates in a superconducting circuit architecture can be obtained in an all-geometric approach. Compared with standard non-adiabatic holonomic quantum computation, the holonomies obtained in our approach tends asymptotically to those of the adiabatic approach in the long run-time limit and thus might open up a new horizon for realizing a practical quantum computer.
PI3K/Akt signaling pathway triggers P2X7 receptor expression as a pro-survival factor of neuroblastoma cells under limiting growth conditions
Authors: Gómez-Villafuertes Rosa , García-Huerta Paula , Díaz-Hernández Juan Ignacio , Miras-Portugal Mª Teresa
Published: December 2015

The expression of purinergic P2X7 receptor (P2X7R) in neuroblastoma cells is associated to accelerated growth rate, angiogenesis, metastasis and poor prognosis. Noticeably, P2X7R allows the survival of neuroblastoma cells under restrictive conditions, including serum and glucose deprivation. Previously we identified specificity protein 1 (Sp1) as the main factor involved in the transcriptional regulation of P2rx7 gene, reporting that serum withdrawal triggers the expression of P2X7R in Neuro-2a (N2a) neuroblastoma cell line. Here we demonstrate that PI3K/Akt pathway is crucial for the upregulation of P2X7R expression in serum-deprived neuroblastoma cells, circumstance that facilitates cell proliferation in the absence of trophic support. The effect exerted by PI3K/Akt is independent of both mTOR and GSK3, but requires the activation of EGF receptor (EGFR). Nuclear levels of Sp1 are strongly reduced by inhibition of PI3K/Akt pathway and blockade of Sp1-dependent transcription with mithramycin A prevents upregulation of P2rx7 gene expression following serum withdrawal. Furthermore, atypical PKCζ plays a key role in the regulation of P2X7R expression by preventing phosphorylation and, consequently, activation of Akt. Altogether, these data indicate that activation of EGFR enhanced the expression of P2X7R in neuroblastoma cells lacking trophic support, being PI3K/Akt/PKCζ signaling pathway and Sp1 mediating this pro-survival outcome.
Non-Faradaic Electrochemical Detection of Exocytosis from Mast and Chromaffin Cells Using Floating-Gate MOS Transistors
Authors: Jayant Krishna , Singhai Amit , Cao Yingqiu , Phelps Joshua B. , Lindau Manfred , Holowka David A. , Baird Barbara A. , Kan Edwin C.
Published: December 2015

We present non-faradaic electrochemical recordings of exocytosis from populations of mast and chromaffin cells using chemoreceptive neuron MOS (CνMOS) transistors. In comparison to previous cell-FET-biosensors, the CνMOS features control (CG), sensing (SG) and floating gates (FG), allows the quiescent point to be independently controlled, is CMOS compatible and physically isolates the transistor channel from the electrolyte for stable long-term recordings. We measured exocytosis from RBL-2H3 mast cells sensitized by IgE (bound to high-affinity surface receptors FcεRI) and stimulated using the antigen DNP-BSA. Quasi-static I-V measurements reflected a slow shift in surface potential ("Equation missing") which was dependent on extracellular calcium ([Ca]o) and buffer strength, which suggests sensitivity to protons released during exocytosis. Fluorescent imaging of dextran-labeled vesicle release showed evidence of a similar time course, while un-sensitized cells showed no response to stimulation. Transient recordings revealed "Equation missing" fluctuations with a rapid rise and slow decay. Chromaffin cells stimulated with high KCl showed both slow "Equation missing" shifts and extracellular action potentials exhibiting biphasic and inverted capacitive waveforms, indicative of varying ion-channel distributions across the cell-transistor junction. Our approach presents a facile method to simultaneously monitor exocytosis and ion channel activity with high temporal sensitivity without the need for redox chemistry.
Caspase-11 and caspase-1 differentially modulate actin polymerization via RhoA and Slingshot proteins to promote bacterial clearance
Authors: Caution Kyle , Gavrilin Mikhail A. , Tazi Mia , Kanneganti Apurva , Layman Daniel , Hoque Sheshadri , Krause Kathrin , Amer Amal O.
Published: December 2015

Inflammasomes are multiprotein complexes that include members of the NOD-like receptor family and caspase-1. Caspase-1 is required for the fusion of the Legionella vacuole with lysosomes. Caspase-11, independently of the inflammasome, also promotes phagolysosomal fusion. However, it is unclear how these proteases alter intracellular trafficking. Here, we show that caspase-11 and caspase-1 function in opposing manners to phosphorylate and dephosphorylate cofilin, respectively upon infection with Legionella. Caspase-11 targets cofilin via the RhoA GTPase, whereas caspase-1 engages the Slingshot phosphatase. The absence of either caspase-11 or caspase-1 maintains actin in the polymerized or depolymerized form, respectively and averts the fusion of pathogen-containing vacuoles with lysosomes. Therefore, caspase-11 and caspase-1 converge on the actin machinery with opposing effects to promote vesicular trafficking.
A lipasin/Angptl8 monoclonal antibody lowers mouse serum triglycerides involving increased postprandial activity of the cardiac lipoprotein lipase
Authors: Fu Zhiyao , Abou-Samra Abdul B. , Zhang Ren
Published: December 2015

Lipasin/Angptl8 is a feeding-induced hepatokine that regulates triglyceride (TAG) metabolism; its therapeutical potential, mechanism of action and relation to the lipoprotein lipase (LPL), however, remain elusive. We generated five monoclonal lipasin antibodies, among which one lowered the serum TAG level when injected into mice and the epitope was determined to be EIQVEE. Lipasin-deficient mice exhibited elevated postprandial activity of LPL in the heart and skeletal muscle, but not in white adipose tissue (WAT), suggesting that lipasin suppresses the activity of LPL specifically in cardiac and skeletal muscles. Consistently, mice injected with the effective antibody or with lipasin deficiency had increased postprandial cardiac LPL activity and lower TAG levels only in the fed state. These results suggest that lipasin acts, at least in part, in an endocrine manner. We propose the following model: feeding induces lipasin, activating the lipasin-Angptl3 pathway, which inhibits LPL in cardiac and skeletal muscles to direct circulating TAG to WAT for storage; conversely, fasting induces Angptl4, which inhibits LPL in WAT to direct circulating TAG to cardiac and skeletal muscles for oxidation. This model suggests a general mechanism by which TAG trafficking is coordinated by lipasin, Angptl3 and Angptl4 at different nutritional statuses.
Identification of Nα-acetyl-α-lysine as a probable thermolyte and its accumulation mechanism in Salinicoccus halodurans H3B36
Authors: Jiang Kai , Xue Yanfen , Ma Yanhe
Published: December 2015

Salinicoccus halodurans H3B36 is a moderate halophile that was isolated from a 3.2-m-deep sediment sample in Qaidam Basin, China. Our results suggest that Nα-acetyl-α-lysine can accumulate and act as a probable thermolyte in this strain. The accumulation mechanism and biosynthetic pathway for this rare compatible solute were also elucidated. We confirmed that the de novo synthesis pathway of Nα-acetyl-α-lysine in this strain starts from aspartate and passes through lysine. Through RNA sequencing, we also found an 8-gene cluster (orf_1582–1589) and another gene (orf_2472) that might encode the biosynthesis of Nα-acetyl-α-lysine in S. halodurans H3B36. Orf_192, orf_193 and orf_1259 might participate in the transportation of precursors for generating Nα-acetyl-α-lysine under the heat stress. The transcriptome reported here also generated a global view of heat-induced changes and yielded clues for studying the regulation of Nα-acetyl-α-lysine accumulation. Heat stress triggered a global transcriptional disturbance and generated a series of actions to adapt the strain to heat stress. Furthermore, the transcriptomic results showed that the regulon of RpoN (orf_2534) may be critical to conferring heat stress tolerance and survival to S. halodurans.