bluuebunny/crossref_metadata_2025 huggingface dataset:
CRISPR/Cas9 delivery with one single adenoviral vector devoid of all viral genes
Authors: Ehrke-Schulz Eric , Schiwon Maren , Leitner Theo , Dávid Stephan , Bergmann Thorsten , Liu Jing , Ehrhardt Anja
Published: December 2017

The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 system revolutionized the field of gene editing but viral delivery of the CRISPR/Cas9 system has not been fully explored. Here we adapted clinically relevant high-capacity adenoviral vectors (HCAdV) devoid of all viral genes for the delivery of the CRISPR/Cas9 machinery using a single viral vector. We present a platform enabling fast transfer of the Cas9 gene and gRNA expression units into the HCAdV genome including the option to choose between constitutive or inducible Cas9 expression and gRNA multiplexing. Efficacy and versatility of this pipeline was exemplified by producing different CRISPR/Cas9-HCAdV targeting the human papillomavirus (HPV) 18 oncogene E6, the dystrophin gene causing Duchenne muscular dystrophy (DMD) and the HIV co-receptor C-C chemokine receptor type 5 (CCR5). All CRISPR/Cas9-HCAdV proved to be efficient to deliver the respective CRISPR/Cas9 expression units and to introduce the desired DNA double strand breaks at their intended target sites in immortalized and primary cells.
Integrated DNA methylome and transcriptome analysis reveals the ethylene-induced flowering pathway genes in pineapple
Authors: Wang Jiabin , Li Zhiying , Lei Ming , Fu Yunliu , Zhao Jiaju , Ao Mengfei , Xu Li
Published: December 2017

Ethylene has long been used to promote flowering in pineapple production. Ethylene-induced flowering is dose dependent, with a critical threshold level of ethylene response factors needed to trigger flowering. The mechanism of ethylene-induced flowering is still unclear. Here, we integrated isoform sequencing (iso-seq), Illumina short-reads sequencing and whole-genome bisulfite sequencing (WGBS) to explore the early changes of transcriptomic and DNA methylation in pineapple following high-concentration ethylene (HE) and low-concentration ethylene (LE) treatment. Iso-seq produced 122,338 transcripts, including 26,893 alternative splicing isoforms, 8,090 novel transcripts and 12,536 candidate long non-coding RNAs. The WGBS results suggested a decrease in CG methylation and increase in CHH methylation following HE treatment. The LE and HE treatments induced drastic changes in transcriptome and DNA methylome, with LE inducing the initial response to flower induction and HE inducing the subsequent response. The dose-dependent induction of FLOWERING LOCUS T-like genes (FTLs) may have contributed to dose-dependent flowering induction in pineapple by ethylene. Alterations in DNA methylation, lncRNAs and multiple genes may be involved in the regulation of FTLs. Our data provided a landscape of the transcriptome and DNA methylome and revealed a candidate network that regulates flowering time in pineapple, which may promote further studies.
Opportunities to advance sustainable design of nano-enabled agriculture identified through a literature review
Authors: Yin Jiaoyang , Wang Yan , Gilbertson Leanne M.
Published: December 2017

Opportunities to advance agriculture sustainability through innovative nano-enabled design are identified from review of current agriculture and food system applications.
Practical synthesis of enantiopure benzylamines by catalytic hydrogenation or transfer hydrogenation reactions in isopropanol using a Ru-pybox catalyst
Authors: de Julián E. , Menéndez-Pedregal E. , Claros M. , Vaquero M. , Díez J. , Lastra E. , Gamasa P. , Pizzano A.
Published: December 2017

A Ru/Ph-pybox catalyst provides a very high enantioselectivity in the hydrogenation and transfer hydrogenation of N-aryl imines.
4H‐SiC trench MOSFET with integrated fast recovery MPS diode
Authors: Dai Tianxiang , Chan Chun Wa , Deng Xc , Jiang Huaping , Gammon Peter M. , Jennings Mike R. , Mawby Phil A.
Published: December 2017

A 4H‐SiC trench metal–oxide–semiconductor field‐effect‐transistor (MOSFET) design with an integrated merged PiN Schottky (MPS) diode is proposed. The Schottky contact is embedded on the bottom of the trench structure for the first time. The low electric field in the oxide and Schottky contact surface can be achieved simultaneously using the proposed integration design which enhances the oxide reliability and reduces leakage from the Schottky diode. The integration of the MPS diode reduces the total chip area and the required number of dies compared with the conventional method of using an external Schottky diode.
Design of plasmonic rectangular ribbon antenna based on graphene for terahertz band communication
Authors: Naghdehforushha Seyed Arash , Moradi Gholamreza
Published: December 2017

This study proposes a new idea for designing antenna based on graphene for THz application in detailed analysis. Here, design of a novel graphene‐based ribbon antenna is presented based on surface plasmon polariton (SPP) behavioural in graphene. Noble metals support and confine EM waves in infrared region. However, SPP wave propagation is supported by graphene in much lower frequencies of infrared region, in THz region. The conductivity of graphene and SPP waves behavioural in graphene sheet is analysed and studied for designing antenna based on new idea of ribbon antenna. The numerical simulations with COMSOL and CST are presented in proposed new idea structure of antenna. In order to achieve the desired tunable THz band communication, the parametric study method is used for the proposed graphene‐based ribbon antenna to achieve higher efficiency.
Locally Advanced Disease and Pelvic Exenterations
Authors: Kontovounisios Christos , Tekkis Paris
Published: December 2017

Advanced primary and recurrent colorectal cancer can be successfully treated by experienced, dedicated centers delivering good outcomes with low mortality and morbidity. Development and implementation of a comprehensive referral pathway is to be encouraged. Multidisciplinary team management is essential in the management of this complex group of patients and is associated with significantly more complete preoperative evaluation and more accurate provision of patient information, as well as improved access to the most appropriate individualized management plan. A structured selection process can improve outcomes through standardized approaches to service delivery to provide the highest quality of care.
Coronary Artery Disease in Young Females: Current Scenario
Authors: Kher Monica , Sathyanarayan Bysani
Published: December 2017

Background Despite coronary artery disease (CAD) being the leading cause of morbidity and mortality in females, women still have been underrepresented in clinical trials. We have abundant data for young males with obstructive CAD, but there is scarcity of data for young females.

Objectives To observe the presentation, disease pattern, risk factors, ventricular function, and percutaneous coronary intervention (PCI) efficiency in young females in comparison with young males with obstructive CAD who required PCI.

Material and Methods We conducted a hospital-based retrospective study and analyzed the data of young patients (< 45 years of age) who had undergone PCI over the past 2 years. We observed the demographic profile, clinical findings, and investigative and treatment modalities in these patients.

Results Total 200 young patients underwent PCI for obstructive CAD over a span of 2 years. Among these patients, 42 patients were females. In comparison to males, hypertension (43.7% vs. 69.1%, p = 0.008) was more among females, which was statistically significant. Smoking was predominant in young males than young females. Also, males presented as acute ST-elevation MI, whereas females presented with unstable angina or non–ST-elevation MI (NSTEMI). Multivessel involvement, LV dysfunction, success of PCI, and complication rates were similar in both the groups. Anemia was more predominant in females (< 11 g/dL) than in males (< 13 g/dL). Also, complexity of lesion on angiography (B2 or C type of lesions) was greater in females than males, which was statistically significant (p = 0.02).

Conclusion Diabetes, hypertension, and other metabolic factors play a very important role in the onset of CAD in young women. NSTEMI and complex lesions showed greater predominance in females than in males in our study. However, the success and complication rate of PCI remained the same.
Management of Malocclusion after Maxillofacial Trauma
Authors: Sharma Ashish , Hondorp Brian , Gaiduchik Andrey , Baba Nadim , Thakker Jayini , Inman Jared
Published: December 2017

Efficacious management of malocclusion following maxillofacial trauma requires understanding of the interaction between teeth and alveolar bone, facial skeleton, temporomandibular joints, and facial neuromusculature. Success is best achieved with a multidisciplinary approach. This article describes the management of malocclusion after primary repair by highlighting important clinical features and offering guidelines for secondary repair through revision surgical reduction, prosthodontic rehabilitation, orthodontic therapy, restorative dentistry, and orthognathic surgery.
HLA-haploidentische Stammzelltransplantation: Posttransplantations-Cyclophosphamid
Authors: Fraccaroli Alessia , Tischer Johanna
Published: December 2017

In der allogenen Blutstammzelltransplantation bezeichnet „haploidentisch“ einen Spender aus der Familie, der genetisch in den HLA-Merkmalen nur zu 50% mit seinem Empfänger übereinstimmt. Diese „Disparität“ stellt eine große immunologische Barriere für die Transplantation dar, die schwere Komplikationen wie Transplantatabstoßung, GvHD und Infektionen zur Folge haben kann. Dieses im Vergleich zur HLA-gematchten Transplantation erhöhte Risiko sowie aufwendige Herstellungsverfahren (In-vitro-Manipulation des Blutstammzellpräparats zur T-Zell-Depletion) zur Reduktion der aggressiven Immunogenität des Transplantats limitierten die Anwendung der HLA-haploidentischen Stammzelltransplantation bisher. Die unmanipulierte Haplo-HSZT mit Einsatz von Posttransplantations-Cyclophosphamid zur GvHD-Prophylaxe stellt ein neueres, simples und sicheres haploidentisches Transplantationsverfahren mit geringer Abstoßungsrate, guter hämatopoetischer Rekonstitution, wenig GvHD sowie günstiger Immunrekonstitution und wenig Infektionen dar. Somit ist bei niedriger TRM eine sichere Überwindung der HLA-Barriere mit guter Kontrolle der bidirektionalen Alloreaktivität möglich. Behandlungsergebnisse ähnlich wie bei einer HLA-kompatiblen Transplantation können erreicht werden. Andere alternative Transplantationsverfahren, wie die der MMUD-T, manipulierten Haplo-HSZT und CBT, treten aufgrund schlechterer Spenderverfügbarkeit und Verträglichkeit sowie aufwendiger Herstellungsverfahren in den Hintergrund. Die Verwendung eines sequenziellen Therapiekonzepts, das eine intensive Chemotherapie vor Start der Konditionierung zur Haplo-HSZT zur Reduktion der Leukämielast vorsieht, führt auch in der unmanipulierten Haplo-HSZT mit PTCY zu einer verbesserten Erkrankungskontrolle bei Patienten mit rezidivierter und refraktärer hämatologischer Erkrankung ohne Erhöhung der TRM..
Die durchflusszytometrische Verträglichkeitsprobe – sensitivere Diagnostik zur Prädiktion von Transplantatabstoßungen
Authors: Lindemann Monika , Heinold Andreas , Lenz Veronika , Horn Peter , Heinemann Falko
Published: December 2017

Bei der Lebendnierenspende hat man die Chance, das immunologische Risiko vor Transplantation sehr detailliert zu testen. Neben der Bestimmung der humanen Leukozytenantigene (HLA) ist die Suche nach HLA-Antikörpern und die Verträglichkeitsprobe (Crossmatch) zwingend erforderlich, wobei in Deutschland derzeit als Standard die komplementvermittelte Zytotoxizität gemessen wird (CDC-Crossmatch). Es geht darum, herauszufinden, ob der Empfänger präformierte spenderspezifische Antikörper hat, die eine Transplantatabstoßung auslösen können. Im Ausland, beispielsweise in Großbritannien, ist dagegen das durchflusszytometrische Crossmatch inzwischen als Standardverfahren etabliert. Dieses wurde bereits 1983 beschrieben und ist sensitiver als das CDC-Crossmatch. Es gibt inzwischen umfangreiche Studien, die zeigen, dass ein positives durchflusszytometrisches Crossmatch ein erhöhtes Risiko für antikörpervermittelte Abstoßungen anzeigt. Dies konnte in unserer Kohorte bestätigt werden, in der ein positives durchflusszytometrisches Crossmatch für die T-Zellen ein 10,1-fach und für die B-Zellen ein 3,2-fach erhöhtes Risiko anzeigt.
Laryngektomie: Prognosefaktoren für Liegedauer, Reoperation und Readmission
Authors: Jadeed Rawad
Published: December 2017

Helman SN et al. Predictors of Stay, Reoperation, and Readmission Following Total Laryngektomie. Laryngoscope 2017; 127: 1339–1344

Nach totaler Laryngektomie kommt es in bis zu 34 % der Fälle zu Komplikationen. Die Rehospitalisierungsrate ist hoch und beträgt mehr als
26 %. Verlängerte stationäre Aufenthaltsdauer, ungeplante Rückkehr in der Operationssaal und stationäre Wiederaufnahme sind 3 Faktoren, die
hohe Kosten verursachen und wichtige Indikatoren der Versorgungsqualität darstellen. US-Forscher suchten diesbezüglich nach unabhängigen
perioperativen Risikofaktoren.
Switching probability of all-perpendicular spin valve nanopillars
Authors: Tzoufras M.
Published: December 2017

In all-perpendicular spin valve nanopillars the probability density of the free-layer magnetization is independent of the azimuthal angle and its evolution equation simplifies considerably compared to the general, nonaxisymmetric geometry. Expansion of the time-dependent probability density to Legendre polynomials enables analytical integration of the evolution equation and yields a compact expression for the practically relevant switching probability. This approach is valid when the free layer behaves as a single-domain magnetic particle and it can be readily applied to fitting experimental data.
Evaluation of the performance of a new solar ventilated window: Modeling and experimental verification
Authors: Pang Zhihong , Xu Peng , Lu Xing , Qiu Shunian , Chen Lu , Hou Jin
Published: December 2017

Two long-existing problems of conventional windows are that: first, they cause serious energy losses in a building; and second, they deteriorate indoor ventilating conditions. To solve this problem, a new design of a Solar Ventilated Window (SVW) is presented in this paper in order to reduce building energy consumption and ameliorate indoor ventilation. This paper first reviews the progress of current fenestration researches and explains novelty and working principles of this SVW. Then, both simulating and experimental studies are conducted to evaluate the performance of this device. Last, some further simulations are conducted to optimize the configuration of the SVW and examine the feasibility of the SVW in different climate zones. The simulating and experimental results confirm that the SVW can sustainably improve the indoor ventilating condition, reduce building heating and cooling load, and cut energy consumption for heating, ventilation, and air conditioning, but its performance and energy saving effect vary with weather and climate.
Rigorous numerical modeling of scattering-type scanning near-field optical microscopy and spectroscopy
Authors: Chen Xinzhong , Lo Chiu Fan Bowen , Zheng William , Hu Hai , Dai Qing , Liu Mengkun
Published: December 2017

Over the last decade, scattering-type scanning near-field optical microscopy and spectroscopy have been widely used in nano-photonics and material research due to their fine spatial resolution and broad spectral range. A number of simplified analytical models have been proposed to quantitatively understand the tip-scattered near-field signal. However, a rigorous interpretation of the experimental results is still lacking at this stage. Numerical modelings, on the other hand, are mostly done by simulating the local electric field slightly above the sample surface, which only qualitatively represents the near-field signal rendered by the tip-sample interaction. In this work, we performed a more comprehensive numerical simulation which is based on realistic experimental parameters and signal extraction procedures. By directly comparing to the experiments as well as other simulation efforts, our methods offer a more accurate quantitative description of the near-field signal, paving the way for future studies of complex systems at the nanoscale.
Electron transport properties of degenerate n-type GaN prepared by pulsed sputtering
Authors: Ueno Kohei , Fudetani Taiga , Arakawa Yasuaki , Kobayashi Atsushi , Ohta Jitsuo , Fujioka Hiroshi
Published: December 2017

We report a systematic investigation of the transport properties of highly degenerate electrons in Ge-doped and Si-doped GaN epilayers prepared using the pulsed sputtering deposition (PSD) technique. Secondary-ion mass spectrometry and Hall-effect measurements revealed that the doping efficiency of PSD n-type GaN is close to unity at electron concentrations as high as 5.1 × 1020 cm−3. A record low resistivity for n-type GaN of 0.16 mΩ cm was achieved with an electron mobility of 100 cm2 V−1 s−1 at a carrier concentration of 3.9 × 1020 cm−3. We explain this unusually high electron mobility of PSD n-type GaN within the framework of conventional scattering theory by modifying a parameter related to nonparabolicity of the conduction band. The Ge-doped GaN films show a slightly lower electron mobility compared with Si-doped films with the same carrier concentrations, which is likely a consequence of the formation of a small number of compensation centers. The excellent electrical properties presented in this letter clearly demonstrate the striking advantages of the low-temperature PSD technique for growing high-quality and highly conductive n-type GaN.
Key gravity wave suspension system proves to be minimizing noise
Authors: Liebendorfer Adam
Published: December 2017

Researchers report that the system controlling for vibrational noise in the test masses at the Laser Interferometer Gravitational-Wave Observatory is dampening noise with great effectiveness.
Cryoelectron microscopy pioneers win chemistry Nobel
Authors: Miller Johanna L.
Published: December 2017

Proteins frozen in vitreous ice are now being imaged with atomic resolution.
Effects of immunocastration on the performance and meat quality traits of feedlot-finished Bos indicus (Nellore) cattle
Authors: Gómez J. F. M. , Netto A. Saran , Antonelo D. S. , Silva J. , Sene G. A. , Silva H. B. , Dias N. P. , Leme P. R. , Silva S. L.
Published: December 2017

This study aimed to evaluate the effects of immunocastration on the performance, testosterone concentration, carcass traits and meat quality of feedlot-finished Nellore cattle. Fifty-eight males (430 ± 36 kg bodyweight; 24 months old) were separated into three groups in a randomised complete design: surgically castration (n = 15), immunocastrated (anti-gonadotropin-releasing hormone (Bopriva®) vaccine, n = 21) and non-castrated (n = 22). The animals were housed in individual pens and fed ad libitum for 90 days with a common diet comprising 70% concentrate and 30% roughage (corn silage). The non-castrated animals had a greater average daily gain, feed efficiency, hot carcass weight and carcass yield than the surgically castrated and immunocastrated animals (P < 0.05). Surgically castrated cattle grew faster and more efficiently than those castrated immunologically (P < 0.05). The surgically castrated and immunocastrated animals had higher colour values L*, a* and b* and cooking loss than non-castrated animals (P < 0.05). In conclusion, immunocastration decreased cattle performance compared with surgically castrated or non-castrated animals. However, immunocastration resulted in better meat quality compared with non-castrated, making it an alternative to surgical castration with no negative effects on animal welfare.
Protein kinase C and calcineurin cooperatively mediate cell survival under compressive mechanical stress
Authors: Mishra Ranjan , van Drogen Frank , Dechant Reinhard , Oh Soojung , Jeon Noo Li , Lee Sung Sik , Peter Matthias
Published: December 2017

Significance

Cells are constantly exposed to a variety of mechanical cues, and respond by activating conserved signaling pathways that modulate their profiliation and intracellular organization. For instance, cells in solid tumors experience sustained compression from the microenvironment, and compressive stress is known to trigger an invasive phenotype in some cancer cells. However, despite its importance for health and disease, the specific mechanosensors and the downstream signaling network mediating these physiological responses remain largely unknown, in part due to the lack of appropriate experimental systems. Here, we develop a microfluidic platform that allows triggering compressive mechanical stress in a reversible and controllable manner, and we identify cell surface receptors that specifically sense compressive mechanical stress and generate synergistic cellular responses.
Microstructure of Al/Al bimetallic composites by lost foam casting with Zn interlayer
Authors: Jiang Wenming , Jiang Zailiang , Li Guangyu , Wu Yao , Fan Zitian
Published: December 2017

A novel method named the lost foam casting (LFC) liquid–liquid compound process with a Zn interlayer was proposed to prepare the Al/Al bimetallic composites, and the microstructure of the Al/Al bimetallic composites was investigated in the present work. The results showed that the Al/Al bimetallic composites were successfully produced using the novel process. The Zn interlayer prevented different liquid metals from directly mixing. A uniform and compact metallurgical interface was obtained between the Al and the A356 aluminium alloy, which consisted of the η-Zn, α-Al rich, α +  η eutectoid, and primary silicon phases. The microhardness of the interface layer was significantly higher in comparison with those of the Al and A356 matrixes.
Carbon Monoxide Off-Gassing From Bags of Wood Pellets
Authors: Rahman Mohammad Arifur , Rossner Alan , Hopke Philip K
Published: December 2017

Wood pellets are increasingly used for space heating in the United States and globally. Prior work has shown that stored bulk wood pellets produce sufficient carbon monoxide (CO) to represent a health concern and exceed regulatory standards for occupational exposures. However, most of the pellets used for residential heating are sold in 40-pound (18.1 kg) plastic bags. This study measured CO emission factors from fresh, bagged-wood pellets as a function of temperature and relative humidity. CO concentrations increased with increasing temperature and moisture in the container. CO measurements in a pellet mill warehouse with stored pallets of bagged pellets had 8-h average CO concentrations up to 100 ppm exceeding occupational standards for worker exposure. Thus, manufacturers, distributors, and home owners should be aware of the potential for CO in storage areas and design facilities with appropriate ventilation and CO sensors.
Model-based design of bistable cell factories for metabolic engineering
Authors: Srinivasan Shyam , Cluett William R , Mahadevan Radhakrishnan
Published: December 2017

Motivation

Metabolism can exhibit dynamic phenomena like bistability due to the presence of regulatory motifs like the positive feedback loop. As cell factories, microorganisms with bistable metabolism can have a high and a low product flux at the two stable steady states, respectively. The exclusion of metabolic regulation and network dynamics limits the ability of pseudo-steady state stoichiometric models to detect the presence of bistability, and reliably assess the outcomes of design perturbations to metabolic networks.

Results

Using kinetic models of metabolism, we assess the change in the bistable characteristics of the network, and suggest designs based on perturbations to the positive feedback loop to enable the network to produce at its theoretical maximum rate. We show that the most optimal production design in parameter space, for a small bistable metabolic network, may exist at the boundary of the bistable region separating it from the monostable region of low product fluxes. The results of our analysis can be broadly applied to other bistable metabolic networks with similar positive feedback network topologies. This can complement existing model-based design strategies by providing a smaller number of feasible designs that need to be tested in vivo.

Availability and implementation

http://lmse.biozone.utoronto.ca/downloads/

Supplementary information

Supplementary data are available at Bioinformatics online.
Patient portal use and hospital outcomes
Authors: Dumitrascu Adrian G , Burton M Caroline , Dawson Nancy L , Thomas Colleen S , Nordan Lisa M , Greig Hope E , Aljabri Duaa I , Naessens James M
Published: December 2017

Objectives

To determine whether use of a patient portal during hospitalization is associated with improvement in hospital outcomes, 30-day readmissions, inpatient mortality, and 30-day mortality.

Materials and Methods

We performed a retrospective propensity score–matched study that included all adult patients admitted to Mayo Clinic Hospital in Jacksonville, Florida, from August 1, 2012, to July 31, 2014, who had signed up for a patient portal account prior to hospitalization (N = 7538).

Results

Out of the admitted patients with a portal account, 1566 (20.8%) accessed the portal while in the hospital. Compared to patients who did not access the portal, patients who accessed the portal were younger (58.8 years vs 62.3 years), had fewer elective admissions (54.2% vs 64.1%), were more frequently admitted to medical services (45.8% vs 35.2%), and were more likely to have liver disease (21.9% vs 12.9%) and higher disease severity scores (0.653 vs 0.456). After propensity score matching, there was no statistically significant difference between the 2 cohorts with respect to 30-day readmission (P = .13), inpatient mortality (P = .82), or 30-day mortality (P = .082).

Conclusion

Use of the patient portal in the inpatient setting may not improve hospital outcomes. Future research should examine the association of portal use with more immediate inpatient health outcomes such as patient experience, patient engagement, medication reconciliation, and prevention of adverse events.
Thoracic Epidural Analgesia and Mortality in Acute Pancreatitis: A Multicenter Propensity Analysis
Authors: Jabaudon Matthieu , Belhadj-Tahar Nouria , Rimmelé Thomas , Joannes-Boyau Olivier , Bulyez Stéphanie , Lefrant Jean-Yves , Malledant Yannick , Leone Marc , Abback Paer-Selim , Tamion Fabienne , Dupont Hervé , Lortat-Jacob Brice , Guerci Philippe , Kerforne Thomas , Cinotti Raphael , Jacob Laurent , Verdier Philippe , Dugernier Thierry , Pereira Bruno , Constantin Jean-Michel
Published: December 2017

Objective:

Recent preclinical and clinical data suggest that thoracic epidural analgesia, a technique primarily aimed at decreasing pain, might exert anti-inflammatory effects, enhance splanchnic and pancreatic blood flow during acute pancreatitis; however, the influence of epidural analgesia on mortality remains under investigated in this setting. This study was therefore designed to assess the impact of epidural analgesia on mortality in ICU patients with acute pancreatitis.

Design:

Multicenter retrospective, observational, cohort study.

Setting:

Seventeen French and Belgian ICUs.

Patients:

All patients admitted to with acute pancreatitis between June 2009 and March 2014.

Interventions:

The primary exposure was thoracic epidural analgesia versus standard care without epidural analgesia. The primary outcome was 30-day mortality. Propensity analyses were used to control for bias in treatment assignment and prognostic imbalances.

Measurements and Main Results:

One thousand three ICU patients with acute pancreatitis were enrolled, of whom 212 died within 30 days. Epidural analgesia was used in 46 patients and was associated with reduced mortality in unadjusted analyses (4% vs. 22%; p = 0.003). After adjustment for baseline variables associated with mortality, epidural analgesia was still an independent predictor of 30-day mortality (adjusted odds ratio, 0.10; [95% CI, 0.02–0.49]; p = 0.004). Using propensity score analysis, the risk of all-cause 30-day mortality in patients with acute pancreatitis receiving epidural analgesia was significantly lower than that in matched patients who did not receive epidural analgesia (2% vs. 17%; p = 0.01).

Conclusions:

Among critically ill patients with acute pancreatitis, mortality at 30 days was lower in patients who received epidural analgesia than in comparable patients who did not. These findings support ongoing research on the use of epidural analgesia as a therapeutic intervention in acute pancreatitis.
Cosmetic Adolescent Filler: An Innovative Treatment of the “Selfie” Complex
Authors: Berros Philipe , Armstrong Blair K. , Foti Pauline , Mancini Ronald
Published: December 2017

Purpose:

“Selfie” photography is increasing among teenagers, accentuates congenital anomalies, and impacts self-confidence. Tear trough deformity is most commonly due to aging, but also occurs as a congenital anomaly and can be a major source of insecurity and embarrassment.

Objective:

The purpose of this study is to show the efficacy and safety of hyaluronic acid gel filler in a teenage patient with congenital tear trough deformity.

Material and Method:

We describe the case of a teenager who underwent hyaluronic acid gel filling to the tear trough deformity at age 14 years. Prospective follow up was assessed for 5 years.

Results:

The patient improved clinical appearance and self confidence. Her satisfaction level was high, and no complication occurred during entire follow up.

Conclusion:

In this case, hyaluronic gel acid filler was safe and effective for augmentation of congenital tear trough. The patient was satisfied and experienced increased self-esteem.
Procedural pain and oral glucose in preterm neonates: brain development and sex-specific effects
Authors: Schneider Juliane , Duerden Emma G. , Guo Ting , Ng Karin , Hagmann Patric , Bickle Graz Myriam , Grunau Ruth E. , Chakravarty M. Mallar , Hüppi Petra S. , Truttmann Anita C. , Miller Steven P.
Published: December 2017

Our objectives were to determine whether procedural pain and glucose exposure are associated with altered structural and functional brain development differently in preterm males and females, and neurodevelopment at 18-month corrected age. Fifty-one very preterm neonates (22 males; median [interquartile range] gestational age 27.6 [2.0] weeks) underwent 3 serial scans including T1-weighted and resting-state functional magnetic resonance imaging (MRI) at median postmenstrual weeks: 29.4, 31.9, and 41.1. Thalamus, basal ganglia, and total brain volumes were segmented. Functional resting-state MRI data were extracted from the independent-components maps. Pain was operationalized as the total number of neonatal intensive care unit–administered invasive procedures. Neurodevelopmental outcomes at 18-month corrected age were assessed with the Bayley Scales of Infant Development, second edition. Generalized estimating equations assessed the association of pain and glucose exposure with brain structural and functional development. More invasive procedures were independently associated with slower growth of thalamic (P < 0.001), basal ganglia (P = 0.028), and total brain volumes (P = 0.001), particularly in females. Similar relationships were observed between glucose exposure and brain volumes. Functional connectivity between thalamus and sensorimotor cortices was negatively associated with number of invasive procedures. Greater procedural pain and higher glucose exposure were related to poorer neurodevelopmental outcomes. These findings suggest that structural and functional brain development is vulnerable to procedural pain. Glucose used for analgesia does not appear to mitigate the adverse impact of pain on brain development. The vulnerability of brain development in females towards early pain is distinct from other neonatal morbidities. The link between pain and glucose with neurodevelopment suggests that these factors have long-lasting impact.
Self-Reported Mild Traumatic Brain Injuries in Relation to Rumination and Depressive Symptoms: Moderating Role of Sex Differences and a Brain-Derived Neurotrophic Factor Gene Polymorphism
Authors: Gabrys Robert L. , Dixon Kaylyn , Holahan Matthew R. , Anisman Hymie
Published: December 2017

Objective:

Mild traumatic brain injuries (mTBIs) have frequently been associated with the emergence and persistence of depressive symptoms. However, the factors which contribute to the increased risk for depression after these head injuries remain unclear. Accordingly, we examined the relationship between frequency of self-reported mTBIs and current symptoms of depression and the mediating role of rumination and cognitive flexibility. We also examined whether these relations were moderated by sex differences and the presence of the Val66Met polymorphism in a gene coding for brain-derived neurotrophic factor (BDNF).

Design:

Retrospective, cross-sectional.

Setting:

Carleton University.

Participants:

Two hundred nineteen Carleton University undergraduate students.

Main Outcome Measures:

Cognitive flexibility as assessed by the Wisconsin Card Sorting Task (WCST); subtypes of rumination (Ruminative Response Scale; Treynor, Gonzalez, and Nolen-Hoeksema, 2003); depressive symptoms (Beck Depression Inventory; Beck, Ward, and Mendelson, 1961).

Results:

Greater frequency of self-reported mTBIs was associated with more frequent depressive rumination among women, but not men, which was accompanied by elevated current depressive symptoms. In addition, among Met allele carriers of the BDNF polymorphism, but not those who were Val homozygotes, greater frequency of mTBIs was related to higher levels of brooding, which was accompanied by heightened depressive symptoms. Brain-derived neurotrophic factor genotype also moderated the relationship between self-reported mTBIs and cognitive flexibility in that more frequent mTBIs were associated with more perseverative errors on the WCST among Met carriers, but not Val homozygotes.

Conclusions:

The present findings raise the possibility that the evolution of depression after mTBIs may be dependant on a BDNF polymorphism and sex differences.
Childhood and Adolescent Cancer in the State of Pernambuco, Brazil: Incidence, Geographical Distribution, and Association With Environmental Health Indicators
Authors: Bastos Lídia N.V. , Silveira José C. , Luna Carlos F. , Lucena-Silva Norma
Published: December 2017

Cases of childhood and adolescent cancer diagnosed from 2009 to 2012 in the state of Pernambuco, Brazil, were analyzed considering the patients’ sex and age, the type of cancer and the municipality of living to determine the incidence, geographical distribution, and association with environmental health indicators. The spatial distribution pattern of the cancer incidence was estimated using the Global Moran’s index. The association between environmental health indicators and cancer incidence was evaluated by multiple regression. From 2009 to 2012, 1261 new cases of cancer were diagnosed in patients younger than 20 years old in the state of Pernambuco. Leukemia/lymphoma were the most common type of cancer contemplating 45.28% of the cases. The average age-adjusted incidence rate was 113 cases per million with no spatial distribution pattern. The municipalities were clustered according to their degree of inequality (P=0.017), human development index (P=0.001), population growth rate (P=0.008), urbanization level (P=0.001), number of agricultural crops per capita (P=0.001), and number of industries per capita (P=0.030). However, only urbanization level was positive correlated with incidence of pediatric cancer (P=0.009) likely because in more developed cities, people are more exposed to potential oncogenic factors, such as air and water pollution and processed and ultraprocessed food. The better access to specialized health services, which increases the chances of early diagnosis, may also contributes for a higher number of cases in more developed cities.
A Severe Case of Murine Typhus Presenting With Anemia and Severe Thrombocytopenia
Authors: Wulff Jade , Margolin Judith , Coleman Nana E. , Demmler-Harrison Gail , Lam Fong , Shah Mona D.
Published: December 2017

We discuss a child with severe thrombocytopenia and mild anemia admitted to the Hematology service who quickly deteriorated to a life-threatening state. However, once rickettsial disease was considered in the differential diagnosis and empiric doxycycline begun, she quickly and fully recovered. A diagnostic panel, including Rickettsia typhi serology, confirmed the diagnosis of murine typhus but this occurred weeks after she had recovered. Given the potential severity of rickettsial diseases and the ease of modern travel across geographic borders, hematology-oncology providers everywhere must consider rickettsial diseases in their differential diagnosis of critically ill children and begin empiric therapy with doxycycline promptly.
Statistical methods for large ensemble of super-resolution stochastic single particle trajectories
Authors: Hoze N. , Holcman D.
Published: December 2017

Following recent progresses in super-resolution microscopy obtained in the last decade, massive amount of redundant single stochastic trajectories are now available for statistical analysis. Flows of trajectories of molecules or proteins are sampling the cell membrane or its interior at a very high time and space resolution. Several statistical analysis were developed to extract information contained in these data, such as the biophysical parameters of the underlying stochastic motion to reveal the cellular organization. These trajectories can further reveal hidden subcellular organization. We present here the statistical analysis of these trajectories based on the classical Langevin equation, which serves as a model of trajectories. Parametric and non-parametric estimators are constructed by discretizing the stochastic equations and they allow recovering tethering forces, diffusion tensor or membrane organization from measured trajectories, that differ from physical ones by a localization noise. Modeling, data analysis and automatic detection algorithms serve extracting novel biophysical features such as potential wells and other sub-structures, such as rings at an unprecedented spatiotem-poral resolution. It is also possible to reconstruct the surface membrane of a biological cell from the statistics of projected random trajectories.
Peripatric speciation associated with genome expansion and female-biased sex ratios in the moss genus Ceratodon
Authors: Nieto-Lugilde Marta , Werner Olaf , McDaniel Stuart F. , Koutecký Petr , Kučera Jan , Rizk Samah Mohamed , Ros Rosa M.
Published: December 2017

PREMISE OF THE STUDY

A period of allopatry is widely believed to be essential for the evolution of reproductive isolation. However, strict allopatry may be difficult to achieve in some cosmopolitan, spore-dispersed groups, like mosses. Here we examine the genetic and genome size diversity in Mediterranean populations of the moss Ceratodon purpureus s.l. to evaluate the role of allopatry and ploidy change in population divergence.

METHODS

We sampled populations of the genus Ceratodon from mountainous areas and lowlands of the Mediterranean region, and from western and central Europe. We performed phylogenetic and coalescent analyses on sequences from five nuclear introns and a chloroplast locus to reconstruct their evolutionary history. We also estimated the genome size using flow cytometry, employing propidium iodide, and determined their sex using a sex-linked PCR marker.

KEY RESULTS

Two well differentiated clades were resolved, discriminating two homogeneous groups: the widespread C. purpureus and a local group mostly restricted to the mountains in southern Spain. The latter also possessed a genome size 25% larger than the widespread C. purpureus, and the samples of this group consist entirely of females. We also found hybrids, and some of them had a genome size equivalent to the sum of the C. purpureus and Spanish genome, suggesting that they arose by allopolyploidy.

CONCLUSIONS

These data suggest that a new species of Ceratodon arose via peripatric speciation, potentially involving a genome size change and a strong female-biased sex ratio. The new species has hybridized in the past with C. purpureus.
Classifying cells with Scasat - a tool to analyse single-cell ATAC-seq
Authors: Baker Syed Murtuza , Rogerson Connor , Hayes Andrew , Sharrocks Andrew D. , Rattray Magnus
Published: December 2017

Motivation

The assay for transposase-accessible chromatin using sequencing (ATAC-seq) reveals the landscape and principles of DNA regulatory mechanisms by identifying the accessible genome of mammalian cells. When done at single-cell resolution, it provides an insight into the cell-to-cell variability that emerges from identical DNA sequences by identifying the variability in the genomic location of open chromatin sites in each of the cells. Processing of single-cell ATAC-seq requires a number of steps and a simple pipeline to processes and analyse single-cell ATAC-seq is not yet available.

Results

This paper presents ScAsAT (single-cell ATAC-seq analysis tool), a complete pipeline to process scATAC-seq data with simple steps. The pipeline is developed in a Jupyter notebook environment that holds the executable code along with the necessary description and results. For the initial sequence processing steps, the pipeline uses a number of well-known tools which it executes from a python environment for each of the fastq files. While functions for the data analysis part are mostly written in R, it is robust, flexible, interactive and easy to extend. The pipeline was applied to a single-cell ATAC-seq dataset in order to identify different cell-types from a complex cell mixture. The results from Scasat showed that open chromatin location corresponding to potential regulatory elements can account for cellular heterogeneity and can identify regulatory regions that separates cells from a complex population.

Availability

The jupyter notebook with the complete pipeline applied to the dataset published with this paper are publicly available on the Github (https://github.com/ManchesterBioinference/Scasat). An additional notebook is also provided for analysis of a publicly available dataset. The fastq files are submitted at ArrayExpress database at EMBL-EBI (www.ebi.ac.uk/arrayexpress) under accession number E-MTAB-6116.

Contact

syed.murtuzabaker@manchester.ac.uk and magnus.rattray@manchester.ac.uk

Supplementary information

Supplementary data are available at bioRxiv online.
Recombination of ecologically and evolutionarily significant loci maintains genetic cohesion in thePseudomonas syringaespecies complex
Authors: Dillon Marcus M. , Thakur Shalabh , Almeida Renan N.D. , Guttman David S.
Published: December 2017

Pseudomonas syringaeis a highly diverse bacterial species complex capable of causing a wide range of serious diseases on numerous agronomically important crop species. Here, we examine the evolutionary relationships of 391 agricultural and environmental strains from theP. syringaespecies complex using whole-genome sequencing and evolutionary genomic analyses. Our collection includes strains from 11 of the 13 previously described phylogroups isolated off of over 90 hosts. We describe the phylogenetic distribution of all orthologous gene families in theP. syringaepan-genome, reconstruct the phylogeny ofP. syringaeusing a core genome alignment and a hierarchical clustering analysis of pan-genome content, predict ecologically and evolutionary relevant loci, and establish the forces of molecular evolution operating on each gene family. We find that the common ancestor of the species complex likely carried a Rhizobium-like type III secretion system (TTSS) and later acquired the canonical TTSS. The phylogenetic analysis also showed that the species complex is subdivided into primary and secondary phylogroups based on genetic diversity and rates of genetic exchange. The primary phylogroups, which largely consist of agricultural isolates, are no more divergent than a number of other bacterial species, while the secondary phylogroups, which largely consists of environmental isolates, have levels of diversity more in line with multiple distinct species within a genus. An analysis of rates of recombination within and between phylogroups revealed a higher rate of recombination within primary phylogroups than between primary and secondary phylogroups. We also found that “ecologically significant” virulence-associated loci and “evolutionary significant” loci under positive selection are over-represented among loci that undergo inter-phylogroup genetic exchange. These results indicate that while inter-phylogroup recombination occurs relatively rarely in the species complex, it is an important force of genetic cohesion, particularly among the strains in the primary phylogroups. This level of genetic cohesion and the shared plant-associated niche argues for considering the primary phylogroups as a true biological species.
Testing Serum Batches for Mouse Embryonic Stem Cell Culture
Authors: Behringer Richard , Gertsenstein Marina , Nagy Kristina Vintersten , Nagy Andras
Published: December 2017

The variability in embryonic stem (ES) cell culture is due primarily to serum. Serum is typically produced in large batches from many animals. However, samples may differ depending on the age and diet of the animals, the country of origin, and other factors creating lot-to-lot variations. Some vendors test FBS lots for compatibility with ES cell culture. Many laboratories prefer to test serum batches themselves to identify the lot giving optimal growth. In this protocol, small quantities of specific serum batches are obtained from different suppliers and tested for their ability to support ES cells in an undifferentiated state. A complete test includes the serum batches’ influence on plating efficiency, cell morphology, toxicity, and, if possible, their ability to support generation of chimeras.
Retaining public value and public law value in outsourcing
Authors: Rush Christine L. , Zingale Nicholas C.
Published: December 2017

We argue that the proliferation of governance in the public sector has raised questions regarding individual constitutional rights. While some proclaim cost savings and entrepreneurial solutions to vexing social ills, others suspect that these benefits donʼt outweigh the risk of diminished accountability and the loss of constitutional protection over public service production. We propose a new model to examine the relationships between direct government, governance, public value, and public law value. We apply this model to analyze two landmark Supreme Court cases and one contemporary federal appellate court case to explore the ongoing tension between the governance model and public service production. Our findings suggest that enforcible contract language and public-private entwinement can be used as tools to protect constitutional rights in the face of increasing pressure of governance approaches.