bluuebunny/crossref_metadata_2025 huggingface dataset:
Fluorinated Boron‐Dipyrromethene (BODIPY) Dyes: Bright and Versatile Probes for Surface Analysis
Authors: Hecht Mandy , Fischer Tobias , Dietrich Paul , Kraus Werner , Descalzo Ana B. , Unger Wolfgang E. S. , Rurack Knut
Published: January 2013

A family of bright boron‐dipyrromethene‐type fluorophores with a high number of fluorine atoms (F‐BODIPYs) has been developed and characterized by X‐ray crystallography and optical spectroscopy. The introduction of 3,5‐bis(trifluoromethyl)phenyl and pentafluorophenyl moieties significantly enhances the photostability of such dyes, yielding for instance photostable near‐infrared (NIR) fluorophores that show emission maxima>750 nm, when the BODIPY’s π system is extended with two (dimethylamino)styryl and (dimethylamino)naphthastyryl moieties, or green‐emitting BODIPYs with fluorescence quantum yields of unity. When equipped with a suitable group that selectively reacts for instance with amines, F‐BODIPYs can be used as potent dual labels for the quantification of primary amino groups on surfaces by X‐ray photoelectron spectroscopy (XPS) and fluorescence, two powerful yet complementary tools for the analysis of organic surface functional groups. The advantage of reactive F‐BODIPYs is that they allow a fast and non‐destructive mapping of the labelled supports with conventional fluorescence scanners and a subsequent quantification of selected areas of the same sample by the potentially traceable XPS technique. The performance is exemplarily shown here for the assessment of the amino group density on SiO2 supports, one of the most common reactive silica supports, in particular, for standard microarray applications.
Of mice and men: the riddle of tubular regeneration
Authors: Romagnani Paola
Published: January 2013

Regeneration can occur through multiple distinct mechanisms, such as pluripotent stem cells, lineage‐committed progenitors or dedifferentiation. The respective contribution of each of these regenerative strategies in every organ or tissue may be different. Recent results indicate that dedifferentiation contributes less than previously thought, and that stem or progenitor cells seem to be the main drivers of regenerative processes. Our views of regeneration in the kidney are undergoing the same process of revision. Indeed, studies in humans have established the existence of a scattered population of tubular progenitors in the adult kidney. Renal progenitors have been discovered also in other animal classes such as fish and insects. In contrast, in rodents a tubular progenitor phenotype seems to be induced only after tubular injury, suggesting some differences may exist. Is this difference really related to a distinct regenerative strategy or is it simply a matter of the type and modality of cellular markers expressed? It may also be possible that progenitor cells, as well as tubular cell dedifferentiation, act in concert to allow regeneration of a complex organ like the adult mammalian kidney, as recently proposed also for the liver. Further studies are needed to resolve the riddle of tubular regeneration. However, beyond the controversial results obtained from humans and rodents, identification of tubular progenitors in humans can move the field forward and provide a novel perspective for understanding tubular regeneration. Copyright © 2013 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Lymphoproliferative disorder that resembles heptosplenic lymphoma during maintenance treatment for T‐cell acute lymphoblastic leukemia
Authors: Hu YouJun , Ahmed Tahmeena , Zaslav Ann‐Leslie , Golightly Marc , Spitzer Silvia G. , Raetz Elizabeth , Chan Edward L.
Published: January 2013

A 6‐year‐old male presented with a testicular mass, hepatosplenomegaly, and a pleural effusion while undergoing maintenance chemotherapy for treatment of T‐cell acute lymphoblastic leukemia (T‐ALL). He was subsequently diagnosed with a lymphoproliferative disorder that resembled hepatosplenic lymphoma (HSL). While the extranodal presentation and the protracted yet aggressive clinical course are consistent with HSL, the findings of monosomy 8 and polymorphic cell populations are unique and have not been previously described in this type of lymphoma. Pediatr Blood Cancer 2013; 60: E10–E12. © 2013 Wiley Periodicals, Inc.
Molecular characteristics of a pancreatic adenocarcinoma associated with Shwachman‐Diamond syndrome
Authors: Dhanraj Santhosh , Manji Arif , Pinto Dalila , Scherer Stephen W. , Favre Helen , Loh Mignon L. , Chetty Runjan , Wei Alice C. , Dror Yigal
Published: January 2013

Background

Shwachman‐Diamond syndrome (SDS) is characterized by hypoplasia of the bone marrow and exocrine pancreas and a high risk of leukemia. It is unknown whether solid tumors are part of the disease phenotype.

Procedure

We performed copy number alterations using Affymetrix human SNP 6.0 array. Furthermore, we did direct sequencing of pancreatic cancer‐related genes and immunohistochemical expression of selective proteins.

Results

Among 41 patients with SDS who enrolled on the registry, we identified one male patient with a solid tumor: moderately differentiated pancreatic ductal adenocarcinoma. The tumor harbored 41 copy number alterations (CNAs) and had no regions of loss of heterozygosity (LOH). None of these CNAs were exclusive to the tumor. One copy of the tumor suppressor genes CTNNA3 and LGALS9C was lost in both the peripheral blood and tumor. Direct sequencing of TP53, KRAS, and NRAS revealed no mutations. Immunohistochemical staining for cyclin D1, E‐cadherin, p53 MLH1 and MSH2 and β‐catenin, was similar to that seen in non‐hereditary pancreatic cancer.

Conclusions

Our case raises the possibility that solid tumors are associated with SDS, thereby broadening the clinical phenotype of the disease. The relatively young age at cancer diagnosis and the specific involvement of the pancreas make the possibility of an association with SDS likely. Similar to leukemia in SDS, the pancreatic cancer developed in hypoplastic tissues. This observation and the relative genomic stability of the tumor strengthen the hypothesis of improved adaptation of malignant clones among a population of disadvantaged cells as a mechanism for tumor expansion in SDS. Pediatr Blood Cancer 2013; 60: 754–760. © 2013 Wiley Periodicals, Inc.
Donor–acceptor alternating π‐conjugated polymers containing Di(thiophen‐2‐yl)pyrene and 2,5‐Bis(2‐octyldodecyl)pyrrolo[3,4‐c]pyrrole‐1,4(2H,5H)‐dione for organic thin‐film transistors
Authors: Yang Da Seul , Kim Kyung Hwan , Cho Min Ju , Jin Jung‐Il , Choi Dong Hoon
Published: January 2013

New diketopyrrolopyrrole (DPP)‐containing conjugated polymers such as poly(2,5‐bis(2‐octyldodecyl)‐3‐(5‐(pyren‐1‐yl)thiophen‐2‐yl)‐6‐(thiophen‐2‐yl)pyrrolo[3,4‐c]pyrrole‐1,4(2H,5H)‐dione) (P(DTDPP‐alt‐(1,6)PY)) and poly(2,5‐bis(2‐octyldodecyl)‐3‐(5‐(pyren‐2‐yl)thiophen‐2‐yl)‐6‐(thiophen‐2‐yl)pyrrolo[3,4‐c]pyrrole‐1,4(2H,5H)‐dione) (P(DTDPP‐alt‐(2,7)PY)) were successfully synthesized via Suzuki coupling reactions under Pd(0)‐catalyzed conditions. P(DTDPP‐alt‐(2,7)PY), incorporating 2,5‐bis(2‐octyldodecyl)‐3,6‐di(thiophen‐2‐yl)pyrrolo[3,4‐c]pyrrole‐1,4(2H,5H)‐dione (DTDPP) at the 2,7‐position of a pyrene ring showed a lower band‐gap energy (E. = 1.65 eV) than the 1,6‐substituted analog, P(DTDPP‐alt‐(1,6)PY) (E = 1.71 eV). The energies of the molecular frontier orbitals of the substituted polymers were successfully tuned by changing the anchoring position of DTDPP from the 1,6‐ to the 2,7‐position of the pyrene ring. An organic thin‐film transistor fabricated using the newly synthesized P(DTDPP‐alt‐(2,7)PY), as a semiconductor material exhibited a maximum mobility of up to 0.23 cm2 V−1 s−1 (Ion/off ∼ 106), which was much larger than that obtained using P(DTDPP‐alt‐(1,6)PY). This distinction is attributed to morphological differences in the solid state arising from differences between the geometrical configurations of DTDPP and the pyrene ring. In addition, the organic phototransistor devices made of P(DTDPP‐alt‐(2,7)PY) showed interesting photoinduced enhancement of drain current when irradiating the excitation light whose intensity is very small. Based on the photoinduced effect on IDS, photocontrolled memory could be realized under the variation of gate voltages. © 2013 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2013
Diblock copolymer–azobenzene complexes through hydrogen bonding: Self‐assembly and stable photoinduced optical anisotropy
Authors: del Barrio Jesús , Blasco Eva , Oriol Luis , Alcalá Rafael , Sánchez‐Somolinos Carlos
Published: January 2013

We have demonstrated the preparation of a series of photoaddressable supramolecular block copolymers by mixing a carboxy‐terminated azobenzene derivative, 6‐[4‐(4′‐cyanophenylazo)phenyloxy]hexanoic acid (AZO), and two polystyrene‐b‐poly(4‐vinylpiridine) (PS‐b‐P4VP) block copolymers. AZO can be selectively attached to the P4VP block of PS‐b‐P4VP through hydrogen bonding interactions. The assembly of AZO with vinylpyridine group‐containing polymers was initially investigated on a model system composed of P4VP homopolymer and AZO. Homogeneous liquid crystalline materials were obtained for ratios of AZO to vinylpyridine repeating unit, x, lower or equal to 0.50. Mixtures with higher x resulted in heterogeneous materials showing clear macrophase separation. Accordingly, a series of hydrogen‐bonded complexes of PS‐b‐P4VP and AZO, PS‐b‐P4VP(AZO)x, with x = 0.25 and x = 0.50 were prepared. Lamellar and spherical morphologies were observed for the complexes based on PS24‐b‐P4VP9.5 (Mn,PS = 24,000, Mn,P4VP = 9500) and PS24‐b‐P4VP1.9 (Mn,PS = 24,000, Mn,P4VP = 1900), respectively. Photoinduced orientation of the azobenzene units was obtained in films of P4VP(AZO)x and PS‐b‐P4VP(AZO)x with x = 0.25 and 0.50 by using 488 nm linearly polarized light and characterized through birefringence and dichroism measurements. This investigation shows a versatile and less laborious approach to azobenzene‐containing polymer materials with low chromophore content, of interest in optical application. © 2013 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2013
Donor–acceptor (donor) polymers with differently conjugated side groups at the acceptor units for photovoltaics
Authors: Qin Hongmei , Li Lisheng , Liang Tianxiang , Peng Xiaobin , Peng Junbiao , Cao Yong
Published: January 2013

Four new donor–acceptor (donor) [D–A(D)], PBDT‐PTQ, PBDT‐PTTQ, PBDT‐TQ, and PBDT‐TTQ, bearing the same backbone of alternative benzodithiophene (BDT) and quinoxaline units but with phenylene thienyl, phenylene di‐thienyl, thienyl and di‐thienyl groups (other donors), respectively, at the acceptor quinoxaline units, were designed and synthesized to investigate the impacts of the conjugated side chains at the acceptor units on the photovoltaic properties of polymers. The power conversion efficiencies (PCEs) of the polymer solar cells (PSCs) based on PBDT‐TQ:[6,6]‐phenyl‐C‐70‐butyric acid methyl ester (PC70BM) and PBDT‐PTQ:PC70BM reach to 4.39 and 3.58%, respectively, which are 43 and 17% higher, respectively, than that of a reported alkylphenyl substituted polymer with the same main chain. However, the PCEs based on PBDT‐TTQ and PBDT‐PTTQ, in which an additional thiophene is added at a side chain of PBDT‐TQ and PBDT‐PTQ, respectively, decline. The mechanism how the conjugated side chains affect the performance of the PSCs is also discussed. © 2013 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2013
Attractive Nitramines and Related PBXs
Authors: Elbeih Ahmed , Zeman Svatopluk , Jungová Marcela , Vávra Pavel
Published: January 2013

At present, cis‐1,3,4,6‐tetranitro‐octahydroimidazo‐[4,5‐d]imidazole (bicyclo‐HMX, BCHMX) and ε‐2,4,6,8,10,12‐hexanitro‐2,4,6,8,10,12‐hexaazaisowurtzitane (ε‐HNIW, CL‐20) are a topic of interest from the attractive and the potentially attainable nitramines. They were chosen to be studied in comparison with 1,3,5‐trinitro‐1,3,5‐triazinane (RDX) and β‐1,3,5,7‐tetranitro‐1,3,5‐tetrazocane (β‐HMX). Marginal attention is devoted also to 4,8,10,12‐tetranitro‐2,6‐dioxa‐tetraazawurtzitane (Aurora 5). BCHMX, ε‐HNIW, RDX, and HMX were studied as plastic bonded explosives (PBXs) with elastic properties based on Composition C4 and Semtex 10 matrices. Also they were studied as a highly pressed PBXs based on the Viton A binder. The detonation parameters and sensitivity aspects of these nitramines and their corresponding PBXs were determined. Relative explosive strengths (RS) of these compositions are mentioned with mutual relationships between the measured RS values and some detonation parameters. These relationships indicate a possibility of changes in detonation chemistry of these mixtures filled mainly by HNIW. A sensitivity of RS‐CL20 (HNIW with reduced sensitivity) is reported and the new findings in the friction sensitivity are discussed.
First‐principles study of hydrogenated CdS nanowires
Authors: Li Ping , Zhang Chang‐wen , Zheng Fu‐bao , Lian Jie , Ren Miao‐Juan , Li Feng , Yuan Min
Published: January 2013

Based on first‐principles simulations, the electronic and magnetic properties of bare and hydrogenated CdS nanowires (NWs) are investigated. We find that surface relaxation plays an important role for the hydrogenated CdS NWs and therefore leads to drastic changes of electronic properties. The magnetic properties can be tuned by controlling passivation on surface sites with hydrogen. While hydrogenated NWs on surface S atoms are nonmagnetic, hydrogenation on surface Cd atoms, and especially a monolayer of H on the surface, results in half‐metallic properties, due to the redistributions of surface electrons in the sulfur p orbital.
EPR spectra of Cr3+ ion in the Van Vleck paramagnet EuAl3(BO3)4
Authors: Prokhorov A.D. , Zubov E.E. , Prokhorov A.A. , Chernush L.F. , Minyakaev R. , Dyakonov V.P. , Szymczak H.
Published: January 2013

We have presented new results on the EPR spectra and the ground state of the Cr3+ ion replacing Y3+ in YAl3(BO3)4 and Eu3+ in EuAl3(BO3)4 single crystals. The EPR studies performed at frequencies of about 9.4 and 37 GHz in a temperature range of 300–4.2 K have revealed the peculiarities and differences of EPR spectra of Cr3+ ion as well as determined the spin‐Hamiltonian parameters (g‐factors, D, and E fine‐structure parameters and their signs) in both crystals. The value and sign of the D parameter in both crystals are determined by both the nearest ligands around the Cr3+ ion and the spin–orbit interaction. The interaction between Cr3+ ion and rare‐earth ion weakly influences on the ground‐state splitting, while the changes of g‐factors are mainly caused by the Cr3+ and Eu3+ ions interactions. The EPR spectra and contributions determining the value of spin‐Hamiltonian parameters were analyzed on the basis of the superposition model of the crystal field.
Gaps in Exposure to Essential Competencies in Hand Surgery Fellowship Training: A National Survey of Program Directors
Authors: Sears Erika Davis , Larson Bradley P. , Chung Kevin C.
Published: January 2013

Background

Graduate medical education has moved towards competency-based training. The aim of this study was to assess hand surgery program directors' opinions of exposure gaps in core competencies rated as essential for hand surgery training.

Methods

We surveyed the 74 ACGME hand surgery fellowship program directors. Respondents rated their opinion of 9 general areas of practice, 97 knowledge topics, and 172 procedures into one of three categories: essential, exposure needed, or unnecessary. Program directors also rated trainee exposure of each component at their respective program. Moderate and large exposure gaps were respectively defined as presence of at least 25 and 50 % of programs rating trainees as not having proficiency in the component at the end of training.

Results

Sixty-two of 74 program directors (84 %) responded to the survey. For the 76 knowledge topics and 98 procedures rated as essential, a majority of the knowledge topics (61 %; n=46) and procedures (72 %; n=71) had at least a moderate exposure gap. In addition, 22 % ( n=17) of the essential knowledge topics and 26 % ( n=25) of the essential procedures had a large exposure gap.

Conclusion

This study illuminates the discrepancies between what is believed to be important for practicing hand surgeons and graduates' proficiency as perceived by program directors. The field of hand surgery must work to determine if program directors have unrealistic expectations for what is essential for practicing hand surgeons or if reforms are needed to improve exposure to essential skills in hand surgery training.
Safety of phosphatidylserine containing omega3 fatty acids in ADHD children: A double-blind placebo-controlled trial followed by an open-label extension
Authors: Manor I. , Magen A. , Keidar D. , Rosen S. , Tasker H. , Cohen T. , Richter Y. , Zaaroor-Regev D. , Manor Y. , Weizman A.
Published: January 2013

Objective:

To evaluate the safety of phosphatidylserine (PS) enriched with omega3 fatty acids, mainly eicosapentaenoic (PS-Omega3) in children with attention-deficit hyperactivity disorder (ADHD).

Methods:

Two hundred children diagnosed with ADHD were randomised to receive either PS-Omega3 (300 mg PS-Omega3/day) or placebo for 15 weeks. One hundred and fifty children continued into an open-label extension for an additional 15 weeks in which they all consumed PS-Omega3 (150 mg PS-Omega3/day). Standard blood biochemical and haematological safety parameters, blood pressure, heart rate, weight and height were evaluated. Adverse events and the Side Effect Rating Scale were also assessed.

Results:

One hundred and sixty-two participants completed the double-blind phase. No significant differences were noted between the two study groups in any of the safety parameters evaluated. One hundred and forty participants completed the open-label phase. At the end of this phase, no significant changes from baseline were observed in any of the studied parameters among participants who consumed PS-Omega3 for 30 weeks.

Conclusions:

Study results demonstrate that consumption of PS-Omega3 by children with ADHD, as indicated in a 30-week evaluation period, is safe and well tolerated, without any negative effect on body weight or growth.
Clinical features and short‐term outcomes of triplet pregnancies in Japan
Authors: Morikawa Mamoru , Cho Kazutoshi , Yamada Takashi , Yamada Takahiro , Sato Shoji , Minakami Hisanori
Published: January 2013

Objective

To review clinical features and short‐term outcomes of triplet pregnancies among Japanese women.

Methods

A retrospective analysis was carried out among 320 Japanese women with triplet pregnancies (8 monochorionic, 75 dichorionic, and 150 trichorionic triplets; 87 with unknown placental chorionicity) who delivered at 22 gestational weeks or more between January 2005 and December 2008.

Results

Delivery was by cesarean for 315 (98%) women. Gestational age at delivery was 32.3 ± 2.8 weeks (mean ± SD) and 33.2 weeks (median), and 97%, 61%, and 14% of women delivered at less than 37, less than 34, and less than 30 gestational weeks, respectively. For live‐born infants, mean birth weight was 1762 ± 437 g, 1608 ± 396 g, and 1406 ± 380 g for the heaviest, middle, and lightest triplet, respectively. Eighteen (5.6%) women experienced perinatal mortality (3 triplets for 1 woman, 2 triplets for 4 women, and 1 triplet for 13 women). Perinatal mortality was 25 deaths per 1000 deliveries, and decreased with increasing number of chorionic membranes (125, 44, and 20 per 1000 mono‐, di‐, and trichorionic triplet deliveries, respectively).

Conclusion

Short‐term outcomes were good among triplet pregnancies in Japan. The data may be useful for counseling Japanese women with triplet pregnancies.
The Kotuikan ring structure as possible evidence for a large impact event in the northern Siberian craton
Authors: Glukhovskii M.Z. , Kuz’min M.I.
Published: January 2013

Remote-sensing, cosmogeological, tectonic, geophysical, structural, compositional, isotopic, and geochronological criteria permit identifying the Kotuikan ring structure in the northern Siberian Platform as a Paleoproterozoic large astrobleme, close in age to the Vredefort and Sudbury impact structures. Also, indirect evidence for two more large impact structures was obtained here. This confirms widely hypothesized massive bombardment of the early Earth by asteroids and a possible effect of large impact events on the Earth’s mantle dynamics and rotation regime, that is, the tectonic evolution of our planet, including plate tectonics.
A heuristic method for the analytical solution of Maxwell’s equations for direct current
Authors: Gubatenko V.P.
Published: January 2013

We propose a heuristic method for the analytical solution of electrical-prospecting problems for direct currents and 3D isotropic media. The corresponding parameters of the medium (conductivity, magnetic permeability) are determined from Maxwell’s equations by the assignment of electric- or magnetic-field intensity in the analytical form. The application of this method is illustrated with examples.
Pressure gradient effects on the large-scale structure of turbulent boundary layers
Authors: Harun Zambri , Monty Jason P. , Mathis Romain , Marusic Ivan
Published: January 2013

Research into high-Reynolds-number turbulent boundary layers in recent years has brought about a renewed interest in the larger-scale structures. It is now known that these structures emerge more prominently in the outer region not only due to increased Reynolds number (Metzger & Klewicki, Phys. Fluids, vol. 13(3), 2001, pp. 692–701; Hutchins & Marusic, J. Fluid Mech., vol. 579, 2007, pp. 1–28), but also when a boundary layer is exposed to an adverse pressure gradient (Bradshaw, J. Fluid Mech., vol. 29, 1967, pp. 625–645; Lee & Sung, J. Fluid Mech., vol. 639, 2009, pp. 101–131). The latter case has not received as much attention in the literature. As such, this work investigates the modification of the large-scale features of boundary layers subjected to zero, adverse and favourable pressure gradients. It is first shown that the mean velocities, turbulence intensities and turbulence production are significantly different in the outer region across the three cases. Spectral and scale decomposition analyses confirm that the large scales are more energized throughout the entire adverse pressure gradient boundary layer, especially in the outer region. Although more energetic, there is a similar spectral distribution of energy in the wake region, implying the geometrical structure of the outer layer remains universal in all cases. Comparisons are also made of the amplitude modulation of small scales by the large-scale motions for the three pressure gradient cases. The wall-normal location of the zero-crossing of small-scale amplitude modulation is found to increase with increasing pressure gradient, yet this location continues to coincide with the large-scale energetic peak wall-normal location (as has been observed in zero pressure gradient boundary layers). The amplitude modulation effect is found to increase as pressure gradient is increased from favourable to adverse.
Obtaining accurate mean velocity measurements in high Reynolds number turbulent boundary layers using Pitot tubes
Authors: Bailey S. C. C. , Hultmark M. , Monty J. P. , Alfredsson P. H. , Chong M. S. , Duncan R. D. , Fransson J. H. M. , Hutchins N. , Marusic I. , McKeon B. J. , Nagib H. M. , Örlü R. , Segalini A. , Smits A. J. , Vinuesa R.
Published: January 2013

This article reports on one component of a larger study on measurement of the zero-pressure-gradient turbulent flat plate boundary layer, in which a detailed investigation was conducted of the suite of corrections required for mean velocity measurements performed using Pitot tubes. In particular, the corrections for velocity shear across the tube and for blockage effects which occur when the tube is in close proximity to the wall were investigated using measurements from Pitot tubes of five different diameters, in two different facilities, and at five different Reynolds numbers ranging from ${\mathit{Re}}_{\theta } = 11\hspace{0.167em} 100$ to 67 000. Only small differences were found amongst commonly used corrections for velocity shear, but improvements were found for existing near-wall proximity corrections. Corrections for the nonlinear averaging of the velocity fluctuations were also investigated, and the results compared to hot-wire data taken as part of the same measurement campaign. The streamwise turbulence-intensity correction was found to be of comparable magnitude to that of the shear correction, and found to bring the hot-wire and Pitot results into closer agreement when applied to the data, along with the other corrections discussed and refined here.
Healing through ICT: Enhancing wellbeing in an Aboriginal community
Authors: Madden Dianna , Cadet-James Yvonne , Watkin-Lui Felecia , Atkinson Ian
Published: January 2013

Many Aboriginal Australians report a diminished sense of wellbeing in their everyday activities due to racism and separation from their traditional lands and culture. Our research sought to discover whether access and use of culturally appropriate Information and Communication Technology's (ICTs), could have an ameliorative benefit, enhancing participants’ sense of support and engagement with their culture. While multiple studies have shown that access and use of ICTs can provide real benefits in regards to empowerment, few studies have focused specifically on the well-being aspects. The research in this project was a Participatory Action Research (PAR) study with women and girls of the Gugu Badhun (an Aboriginal Australian language group) to explore ways to better support their familial and cultural activities associated with identity and group sustainability. The research was divided into three action-research cycles: group interviews and focus groups, use of a technology probe, and feedback from the participants. The technology probe was a web-based application with access limited to the women in the study. Use of the probe enabled the participants to mentally revisit scenes that had been highly significant to them and to reframe these incidents in ways that enhanced their feelings of wellbeing. The probe site allowed the women a platform to discuss concepts intrinsic to their lives, and how these ideas interlink and enmesh with each other, such as the importance of connection to country, and offline activities surrounding identity and sustainability as a group thereby enhancing their wellbeing.
Modelling of genetic interactions improves prediction of hybrid patterns – a case study in domestic fowl
Authors: ÁLVAREZ-CASTRO JOSÉ M. , LE ROUZIC ARNAUD , ANDERSSON LEIF , SIEGEL PAUL B. , CARLBORG ÖRJAN
Published: January 2013

A major challenge in complex trait genetics is to unravel how multiple loci and environmental factors together cause phenotypic diversity. Both first (F1) and second (F2) generation hybrids often display phenotypes that deviate from what is expected under intermediate inheritance. We have here studied two chicken F2populations generated by crossing divergent chicken lines to assess how epistatic loci, identified in earlier quantitative trait locus (QTL) studies, contribute to hybrid deviations from the mid-parent phenotype. Empirical evidence suggests that the average phenotypes of the intercross birds tend to be lower than the midpoint between the parental means in both crosses. Our results confirm that epistatic interactions, despite a relatively small contribution to the phenotypic variance, play an important role in the deviation of hybrid phenotypes from the mid-parent values (i.e. multi-locus hybrid genotypes lead to lower rather than higher body weights). To a lesser extent, dominance also appears to contribute to the mid-parent deviation, at least in one of the crosses. This observation coincides with the hypothesis that hybridization tends to break up co-adapted gene complexes, i.e. generate Bateson–Dobzhansky–Muller incompatibilities.
Degree of fetal growth restriction associated with schizophrenia risk in a national cohort
Authors: Eide M. G. , Moster D. , Irgens L. M. , Reichborn-Kjennerud T. , Stoltenberg C. , Skjærven R. , Susser E. , Abel K.
Published: January 2013

Background

Accumulating evidence suggests that fetal growth restriction may increase risk of later schizophrenia but this issue has not been addressed directly in previous studies. We examined whether the degree of fetal growth restriction was linearly related to risk of schizophrenia, and also whether maternal pre-eclampsia, associated with both placental dysfunction and poor fetal growth, was related to risk of schizophrenia.

Method

A population-based cohort of single live births in the Medical Birth Registry of Norway (MBRN) between 1967 and 1982 was followed to adulthood (n = 873 612). The outcome was schizophrenia (n=2207) registered in the National Insurance Scheme (NIS). The degree of growth restriction was assessed by computing sex-specific z scores (standard deviation units) of ‘birth weight for gestational age’ and ‘birth length for gestational age’. Analyses were adjusted for potential confounders. Maternal pre-eclampsia was recorded in the Medical Birth Registry by midwives or obstetricians using strictly defined criteria.

Results

The odds ratio (OR) for schizophrenia increased linearly with decreasing birth weight for gestational age z scores (p value for trend = 0.005). Compared with the reference group (z scores 0.01–1.00), the adjusted OR [95% confidence interval (CI)] for the lowest z-score category (< − 3.00) was 2.0 (95% CI 1.2–3.5). A similar pattern was observed for birth length for gestational age z scores. Forty-nine individuals with schizophrenia were identified among 15 622 births with pre-eclampsia. The adjusted OR for schizophrenia following maternal pre-eclampsia was 1.3 (95% CI 1.0–1.8).

Conclusions

Associations of schizophrenia risk with degree of fetal growth restriction and pre-eclampsia suggest future research into schizophrenia etiology focusing on mechanisms that influence fetal growth, including placental function.
Differential patterns of activity and functional connectivity in emotion processing neural circuitry to angry and happy faces in adolescents with and without suicide attempt
Authors: Pan L. A. , Hassel S. , Segreti A. M. , Nau S. A. , Brent D. A. , Phillips M. L.
Published: January 2013

Background

Neural substrates of emotion dysregulation in adolescent suicide attempters remain unexamined.

Method

We used functional magnetic resonance imaging to measure neural activity to neutral, mild or intense (i.e. 0%, 50% or 100% intensity) emotion face morphs in two separate emotion-processing runs (angry and happy) in three adolescent groups: (1) history of suicide attempt and depression (ATT, n = 14); (2) history of depression alone (NAT, n = 15); and (3) healthy controls (HC, n = 15). Post-hoc analyses were conducted on interactions from 3 group × 3 condition (intensities) whole-brain analyses (p < 0.05, corrected) for each emotion run.

Results

To 50% intensity angry faces, ATT showed significantly greater activity than NAT in anterior cingulate gyral–dorsolateral prefrontal cortical attentional control circuitry, primary sensory and temporal cortices; and significantly greater activity than HC in the primary sensory cortex, while NAT had significantly lower activity than HC in the anterior cingulate gyrus and ventromedial prefrontal cortex. To neutral faces during the angry emotion-processing run, ATT had significantly lower activity than NAT in the fusiform gyrus. ATT also showed significantly lower activity than HC to 100% intensity happy faces in the primary sensory cortex, and to neutral faces in the happy run in the anterior cingulate and left medial frontal gyri (all p < 0.006,corrected). Psychophysiological interaction analyses revealed significantly reduced anterior cingulate gyral–insula functional connectivity to 50% intensity angry faces in ATT v. NAT or HC.

Conclusions

Elevated activity in attention control circuitry, and reduced anterior cingulate gyral–insula functional connectivity, to 50% intensity angry faces in ATT than other groups suggest that ATT may show inefficient recruitment of attentional control neural circuitry when regulating attention to mild intensity angry faces, which may represent a potential biological marker for suicide risk.
Modulation of extracellular d-serine content by calcium permeable AMPA receptors in rat medial prefrontal cortex as revealed by in vivo microdialysis
Authors: Ishiwata Sayuri , Umino Asami , Umino Masakazu , Yorita Kazuko , Fukui Kiyoshi , Nishikawa Toru
Published: January 2013

In mammalian brains, d-serine has been shown to be required for the regulation of glutamate neurotransmission as an endogenous co-agonist for the N-methyl-d-aspartate type glutamate receptor that is essential for the expression of higher-order brain functions. The exact control mechanisms for the extracellular d-serine dynamics, however, await further elucidation. To obtain an insight into this issue, we have characterized the effects of agents acting at the α-amino-3-hydroxy-5-methyl-4-isoxazolepropioinic acid (AMPA) type glutamate receptor on the extracellular d-serine contents in the medial prefrontal cortex of freely moving rats by an in vivo microdialysis technique in combination with high-performance liquid chromatography with fluorometric detection. In vivo experiments are needed in terms of a crucial role of d-serine in the neuron-glia communications despite the previous in vitro studies on AMPA receptor-d-serine interactions using the separated preparations of neurons or glial cells. Here, we show that the intra-cortical infusion of (S)-AMPA, an active enantiomer at the AMPA receptor, causes a significant and concentration-dependent reduction in the prefrontal extracellular contents of d-serine, which is reversed by an AMPA/kainate receptor antagonist, 2,3-dioxo-6-nitro-1,2,3,4-tetrahydrobenzo[f]quinoxaline-7-sulfonamide disodium salt, and a calcium permeable AMPA receptor antagonist, 1-naphthyl acetyl spermine. The d-serine reducing effects of (S)-AMPA are augmented by co-infusion of cyclothiazide that prevents AMPA receptor desensitization. Our data support the view that a calcium permeable AMPA receptor subtype may exert a phasic inhibitory control on the extracellular d-serine release in the mammalian prefrontal cortex in vivo.
To Free or Not to Free? State Obligations and the Rescue and Release of Marine Mammals: A Case Study of ‘Morgan the Orca’
Authors: Trouwborst Arie , Caddell Richard , Couzens Ed
Published: January 2013

Wild animals periodically encounter difficulties or suffer injuries that require human intervention and assistance. The natural assumption is that a surviving animal will, where viable, be released back to the wild. But is there a formal legal obligation for a rescuer to do so? This question arose recently in the context of ‘Morgan’, a female killer whale rescued in poor health in Dutch waters. Morgan was successfully restored to full health, but the Dutch authorities subsequently declined to repatriate her to the wild and, controversially, transferred her to a zoological facility in Spain. This article examines the largely unexplored legal obligations incumbent upon the Netherlands in respect of rehabilitated cetaceans, in the process exposing certain problems of clarity and consistency within the present regulatory framework. By necessary implication, this article identifies emerging issues of interpretation posed by the Morgan saga, illustrating the tensions between animal welfare and nature conservation – especially in the transboundary context – and concluding firmly that the Dutch authorities erred legally in making their final decision.
Neurovascular Protection by Targeting Early Blood–Brain Barrier Disruption with Neurotrophic Factors after Ischemia–Reperfusion in Rats
Authors: Pillai Deepu R , Shanbhag Nagesh C , Dittmar Michael S , Bogdahn Ulrich , Schlachetzki Felix
Published: January 2013

The ‘new penumbra’ concept imbues the transition between injury and repair at the neurovascular unit with profound implications for selecting the appropriate type and timing of neuroprotective interventions. In this conceptual study, we investigated the protective effects of pigment epithelium-derived factor (PEDF) and compared them with the properties of epidermal growth factor (EGF) in a rat model of ischemia–reperfusion injury. We initiated a delayed intervention 3 hours after reperfusion using equimolar amounts of PEDF and EGF. These agents were then administered intravenously for 4 hours following reperfusion after 1 hour of focal ischemia. Magnetic resonance imaging indices were characterized, and imaging was performed at multiple time points post reperfusion. PEDF and EGF reduced lesion volumes at all time points as observed on T2-weighted images (T2-LVs). In addition PEDF selectively attenuated lesion volume expansion at 48 hours after reperfusion and persistently modulated blood–brain barrier (BBB) permeability at all time points. Intervention with peptides is suspected to cause edema formation at distant regions. The observed T2-LV reduction and BBB modulation by these trophic factors is probably mediated through a number of diverse mechanisms. A thorough evaluation of neurotrophins is still necessary to determine their time-dependent contributions against injury and their modulatory effects on repair after stroke.
Generation and Reactions of Pyridyllithiums via Br/Li Exchange Reactions Using Continuous Flow Microreactor Systems
Authors: Nagaki Aiichiro , Yamada Daisuke , Yamada Shigeyuki , Doi Masatomo , Ichinari Daisuke , Tomida Yutaka , Takabayashi Naofumi , Yoshida Jun-ichi
Published: January 2013

A continuous flow microreactor method for generating and carrying out reactions on pyridyllithiums has been developed based on Br/Li exchange reactions of bromopyridines and dibromopyridines. The reactions can be carried out without using cryogenic conditions by virtue of short residence times and efficient heat transfer, while very low temperatures such as –78 or –110°C are required for conventional batch macro methods. Moreover, sequential introduction of two different electrophiles has been successfully achieved using dibromopyridines in an integrated flow microreactor system composed of four micromixers and four microtube reactors.
Pathway of actin filament branch formation by Arp2/3 complex revealed by single-molecule imaging
Authors: Smith Benjamin A. , Daugherty-Clarke Karen , Goode Bruce L. , Gelles Jeff
Published: January 2013

Actin filament nucleation by actin-related protein (Arp) 2/3 complex is a critical process in cell motility and endocytosis, yet key aspects of its mechanism are unknown due to a lack of real-time observations of Arp2/3 complex through the nucleation process. Triggered by the verprolin homology, central, and acidic (VCA) region of proteins in the Wiskott-Aldrich syndrome protein (WASp) family, Arp2/3 complex produces new (daughter) filaments as branches from the sides of preexisting (mother) filaments. We visualized individual fluorescently labeled Arp2/3 complexes dynamically interacting with and producing branches on growing actin filaments in vitro. Branch formation was strikingly inefficient, even in the presence of VCA: only ∼1% of filament-bound Arp2/3 complexes yielded a daughter filament. VCA acted at multiple steps, increasing both the association rate of Arp2/3 complexes with mother filament and the fraction of filament-bound complexes that nucleated a daughter. The results lead to a quantitative kinetic mechanism for branched actin assembly, revealing the steps that can be stimulated by additional cellular factors.
Sampling Efficiency of the Moore Egg Collector
Authors: Worthington Thomas A. , Brewer Shannon K. , Grabowski Timothy B. , Mueller Julia
Published: January 2013

Quantitative studies focusing on the collection of semibuoyant fish eggs, which are associated with a pelagic broadcast-spawning reproductive strategy, are often conducted to evaluate reproductive success. Many of the fishes in this reproductive guild have suffered significant reductions in range and abundance. However, the efficiency of the sampling gear used to evaluate reproduction is often unknown and renders interpretation of the data from these studies difficult. Our objective was to assess the efficiency of a modified Moore egg collector (MEC) using field and laboratory trials. Gear efficiency was assessed by releasing a known quantity of gellan beads with a specific gravity similar to that of eggs from representatives of this reproductive guild (e.g., the Arkansas River Shiner Notropis girardi) into an outdoor flume and recording recaptures. We also used field trials to determine how discharge and release location influenced gear efficiency given current methodological approaches. The flume trials indicated that gear efficiency ranged between 0.0% and 9.5% (n = 57) in a simple 1.83-m-wide channel and was positively related to discharge. Efficiency in the field trials was lower, ranging between 0.0% and 3.6%, and was negatively related to bead release distance from the MEC and discharge. The flume trials indicated that the gellan beads were not distributed uniformly across the channel, although aggregation was reduced at higher discharges. This clustering of passively drifting particles should be considered when selecting placement sites for an MEC; further, the use of multiple devices may be warranted in channels with multiple areas of concentrated flow.

Received August 8, 2012; accepted October 12, 2012
A comprehensive SNP and indel imputability database
Authors: Duan Qing , Liu Eric Yi , Croteau-Chonka Damien C. , Mohlke Karen L. , Li Yun
Published: January 2013

Motivation: Genotype imputation has become an indispensible step in genome-wide association studies (GWAS). Imputation accuracy, directly influencing downstream analysis, has shown to be improved using re-sequencing-based reference panels; however, this comes at the cost of high computational burden due to the huge number of potentially imputable markers (tens of millions) discovered through sequencing a large number of individuals. Therefore, there is an increasing need for access to imputation quality information without actually conducting imputation. To facilitate this process, we have established a publicly available SNP and indel imputability database, aiming to provide direct access to imputation accuracy information for markers identified by the 1000 Genomes Project across four major populations and covering multiple GWAS genotyping platforms.

Results: SNP and indel imputability information can be retrieved through a user-friendly interface by providing the ID(s) of the desired variant(s) or by specifying the desired genomic region. The query results can be refined by selecting relevant GWAS genotyping platform(s). This is the first database providing variant imputability information specific to each continental group and to each genotyping platform. In Filipino individuals from the Cebu Longitudinal Health and Nutrition Survey, our database can achieve an area under the receiver-operating characteristic curve of 0.97, 0.91, 0.88 and 0.79 for markers with minor allele frequency >5%, 3–5%, 1–3% and 0.5–1%, respectively. Specifically, by filtering out 48.6% of markers (corresponding to a reduction of up to 48.6% in computational costs for actual imputation) based on the imputability information in our database, we can remove 77%, 58%, 51% and 42% of the poorly imputed markers at the cost of only 0.3%, 0.8%, 1.5% and 4.6% of the well-imputed markers with minor allele frequency >5%, 3–5%, 1–3% and 0.5–1%, respectively.

Availability:  http://www.unc.edu/∼yunmli/imputability.html

Supplementary information: Supplementary data are available at Bioinformatics online.

Contact:  yunli@med.unc.edu
GeStoDifferent: a Cytoscape plugin for the generation and the identification of gene regulatory networks describing a stochastic cell differentiation process
Authors: Antoniotti Marco , Bader Gary D. , Caravagna Giulio , Crippa Silvia , Graudenzi Alex , Mauri Giancarlo
Published: January 2013

Summary: The characterization of the complex phenomenon of cell differentiation is a key goal of both systems and computational biology. GeStoDifferent is a Cytoscape plugin aimed at the generation and the identification of gene regulatory networks (GRNs) describing an arbitrary stochastic cell differentiation process. The (dynamical) model adopted to describe general GRNs is that of noisy random Boolean networks (NRBNs), with a specific focus on their emergent dynamical behavior. GeStoDifferent explores the space of GRNs by filtering the NRBN instances inconsistent with a stochastic lineage differentiation tree representing the cell lineages that can be obtained by following the fate of a stem cell descendant. Matched networks can then be analyzed by Cytoscape network analysis algorithms or, for instance, used to define (multiscale) models of cellular dynamics.

Availability: Freely available at http://bimib.disco.unimib.it/index.php/Retronet#GESTODifferent or at the Cytoscape App Store http://apps.cytoscape.org/.

Contact:  marco.antoniotti@unimib.it
KEGGParser: parsing and editing KEGG pathway maps in Matlab
Authors: Arakelyan Arsen , Nersisyan Lilit
Published: January 2013

Summary: KEGG pathway database is a collection of manually drawn pathway maps accompanied with KGML format files intended for use in automatic analysis. KGML files, however, do not contain the required information for complete reproduction of all the events indicated in the static image of a pathway map. Several parsers and editors of KEGG pathways exist for processing KGML files. We introduce KEGGParser—a MATLAB based tool for KEGG pathway parsing, semiautomatic fixing, editing, visualization and analysis in MATLAB environment. It also works with Scilab.

Availability and implementation: The source code is available at http://www.mathworks.com/matlabcentral/fileexchange/37561.

Contact:  aarakelyan@sci.am

Supplementary information:  Supplementary data are available at Bioinformatics online.
Moderate turbidity enhances schooling behaviour in fish larvae in coastal waters
Authors: Ohata Ryosuke , Masuda Reiji , Takahashi Kohji , Yamashita Yoh
Published: January 2013

We evaluated the effects of turbidity on school formation in ayu (Plecoglossus altivelis) [24.5 ± 2.2 mm standard length (Ls)], Japanese anchovy (Engraulis japonicus) (29.1 ± 3.1 mm Ls) larvae, which often live in turbid coastal waters, and yellowtail (Seriola quinqueradiata) juveniles (37.1 ± 2.5 mm Ls), which live in clear offshore waters. Fish were introduced into experimental tanks at one of five turbidity levels obtained by dissolving 0, 5, 20, 50, or 300 mg l−1 of kaolin in seawater. Their behaviour was video recorded, and the nearest neighbour distance (DNN) and separation angle (AS) were compared among turbidity levels. Mean DNN of ayu was significantly smaller at 20 and 50 mg l−1 than any other level of turbidity, as was AS at 20 mg l−1 compared with 0 mg l−1. Mean AS of anchovy was smaller at 50 mg l−1 of turbidity than any others. In contrast, mean DNN of yellowtail was larger at 300 mg l−1 than any others. These results suggest that moderate turbidities enhance schooling behaviour in ayu and Japanese anchovy larvae, whereas turbidity has an inhibitive effect on schooling of yellowtail juveniles, corresponding well to the habitat characteristics of each species.