bluuebunny/crossref_metadata_2025 huggingface dataset:
Many closed symplectic manifolds have infinite Hofer–Zehnder capacity
Authors: Usher Michael
Published: May 2012

We exhibit many examples of closed symplectic manifolds on which there is an autonomous Hamiltonian whose associated flow has no nonconstant periodic orbits (the only previous explicit example in the literature was the torus

T

2
n

T^{2n}

(

n
≥
2

n\geq 2

) with an irrational symplectic structure). The underlying smooth manifolds of our examples include, for instance: the

K
3

K3

surface and also infinitely many smooth manifolds homeomorphic but not diffeomorphic to it; infinitely many minimal four-manifolds having any given finitely-presented group as their fundamental group; and simply connected minimal four-manifolds realizing all but finitely many points in the first quadrant of the geography plane below the line corresponding to signature

3
3

. The examples are constructed by performing symplectic sums along suitable tori and then perturbing the symplectic form in such a way that hypersurfaces near the “neck” in the symplectic sum have no closed characteristics. We conjecture that any closed symplectic four-manifold with

b
+

>
1

b^+>1

admits symplectic forms with a similar property.
Incompressibility criteria for spun-normal surfaces
Authors: Dunfield Nathan , Garoufalidis Stavros
Published: May 2012

We give a simple sufficient condition for a spun-normal surface in an ideal triangulation to be incompressible, namely that it is a vertex surface with nonempty boundary which has a quadrilateral in each tetrahedron. While this condition is far from being necessary, it is powerful enough to give two new results: the existence of alternating knots with noninteger boundary slopes, and a proof of the Slope Conjecture for a large class of 2-fusion knots.

While the condition and conclusion are purely topological, the proof uses the Culler-Shalen theory of essential surfaces arising from ideal points of the character variety, as reinterpreted by Thurston and Yoshida. The criterion itself comes from the work of Kabaya, which we place into the language of normal surface theory. This allows the criterion to be easily applied, and gives the framework for proving that the surface is incompressible.

We also explore which spun-normal surfaces arise from ideal points of the deformation variety. In particular, we give an example where no vertex or fundamental surface arises in this way.
R/EBcoexpress: an empirical Bayesian framework for discovering differential co-expression
Authors: Dawson John A. , Ye Shuyun , Kendziorski Christina
Published: May 2012

Summary: R/EBcoexpress implements the approach of Dawson and Kendziorski using R, a freely available, open source statistical programming language. The approach identifies differential co-expression (DC) by examining the correlations among gene pairs using an empirical Bayesian approach, producing a false discovery rate controlled list of DC pairs. This interrogation of DC gene pairs complements but is distinct from differential expression analyses, under the general goal of understanding differential regulation across biological conditions.

Availability and implementation: R/EBcoexpress is freely available and hosted on Bioconductor; a source file and vignette may be found at http://www.bioconductor.org/packages/release/bioc/html/EBcoexpress.html

Contact:  DrJADawson@hotmail.com or kendzior@wisc.edu
CodonLogo: a sequence logo-based viewer for codon patterns
Authors: Sharma Virag , Murphy David P. , Provan Gregory , Baranov Pavel V.
Published: May 2012

Motivation: Conserved patterns across a multiple sequence alignment can be visualized by generating sequence logos. Sequence logos show each column in the alignment as stacks of symbol(s) where the height of a stack is proportional to its informational content, whereas the height of each symbol within the stack is proportional to its frequency in the column. Sequence logos use symbols of either nucleotide or amino acid alphabets. However, certain regulatory signals in messenger RNA (mRNA) act as combinations of codons. Yet no tool is available for visualization of conserved codon patterns.

Results: We present the first application which allows visualization of conserved regions in a multiple sequence alignment in the context of codons. CodonLogo is based on WebLogo3 and uses the same heuristics but treats codons as inseparable units of a 64-letter alphabet. CodonLogo can discriminate patterns of codon conservation from patterns of nucleotide conservation that appear indistinguishable in standard sequence logos.

Availability: The CodonLogo source code and its implementation (in a local version of the Galaxy Browser) are available at http://recode.ucc.ie/CodonLogo and through the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/.

Contact:  p.baranov@ucc.ie or brave.oval.pan@gmail.com
flowPeaks: a fast unsupervised clustering for flow cytometry data via K-means and density peak finding
Authors: Ge Yongchao , Sealfon Stuart C.
Published: May 2012

Motivation: For flow cytometry data, there are two common approaches to the unsupervised clustering problem: one is based on the finite mixture model and the other on spatial exploration of the histograms. The former is computationally slow and has difficulty to identify clusters of irregular shapes. The latter approach cannot be applied directly to high-dimensional data as the computational time and memory become unmanageable and the estimated histogram is unreliable. An algorithm without these two problems would be very useful.

Results: In this article, we combine ideas from the finite mixture model and histogram spatial exploration. This new algorithm, which we call flowPeaks, can be applied directly to high-dimensional data and identify irregular shape clusters. The algorithm first uses K-means algorithm with a large K to partition the cell population into many small clusters. These partitioned data allow the generation of a smoothed density function using the finite mixture model. All local peaks are exhaustively searched by exploring the density function and the cells are clustered by the associated local peak. The algorithm flowPeaks is automatic, fast and reliable and robust to cluster shape and outliers. This algorithm has been applied to flow cytometry data and it has been compared with state of the art algorithms, including Misty Mountain, FLOCK, flowMeans, flowMerge and FLAME.

Availability: The R package flowPeaks is available at https://github.com/yongchao/flowPeaks.

Contact:  yongchao.ge@mssm.edu

Supplementary information:  Supplementary data are available at Bioinformatics online
Pancreatic Insufficiency Is Not a Prevalent Problem in Alagille Syndrome
Authors: Kamath Binita M. , Piccoli David A. , Magee John C. , Sokol Ronald J. ,   Childhood Liver Disease Research and Education Network (ChiLDREN)
Published: May 2012

Alagille syndrome (ALGS) is an inherited multisystem disorder in which pancreatic insufficiency (PI) has been regarded a minor but important clinical manifestation. As part of a multicenter prospective study, 42 patients with ALGS underwent fecal elastase (FE) measurement to screen for exocrine PI. FE measurements were normal (>200 μg/g) in 40 (95%) and indeterminate (100–200 μg/g) in 2 (5%). As FE is the most reliable screen for PI, these data suggest that PI is not a prevalent problem in ALGS.
Serial Evaluation of Children With ALF With Advanced MRI, Serum Proinflammatory Cytokines, Thiamine, and Cognition Assessment
Authors: Srivastava Anshu , Yadav Santosh K. , Borkar Vibhor V. , Yadav Abhishek , Yachha Surender K. , Thomas Michael A. , Rathore Ram K.S. , Pandey Chandra M. , Gupta Rakesh K.
Published: May 2012

Objectives:

This prospective, sequential study was done to understand changes in cerebral edema (CE) on magnetic resonance imaging and magnetic resonance spectroscopy, liver functions, and neurocognitive testing (NCT) in children with acute liver failure (ALF).

Methods:

A total of 11 ALF and 8 healthy controls were evaluated with advanced magnetic resonance (MR) imaging, blood proinflammatory cytokines (PCs), thiamine levels, liver functions, and NCT. Reevaluation was done at 43.5 ± 26.9 days (first follow‐up, n = 8) and 157.3 ± 52.3 days (second follow‐up, n = 6) after discharge.

Results:

At diagnosis, patients with ALF had vasogenic and cytotoxic CE, raised brain glutamine (23.2 ± 3.4 vs 15.3 ± 2.7), and serum PCs (tumor necrosis factor [TNF]‐α 40.1 ± 8.9 vs 7.2 ± 2.7 pg/mL, interleukin [IL]‐6 29.2 ± 14.4 vs 4.7 ± 1.2 pg/mL). The mammillary bodies (MBs) were smaller, and brain choline (1.9 ± 0.36 vs 2.6 ± 0.6) and blood thiamine (55.2 ± 6.7 vs 81.8 ± 10.2 nmol/L) were lower than controls. At first follow‐up, the brain glutamine and CE recovered. Brain choline and MBs volume showed improvement and thiamine levels normalized. Significant reduction in TNF‐α and IL‐6 was seen. The patients performed poorly on NCT, which normalized at second follow‐up. Liver biochemistry and thiamine levels were normal and TNF‐α and IL‐6 showed further reduction at second follow‐up.

Conclusions:

Patients with ALF have CE contributed by raised brain glutamine and PCs. MBs are small because of thiamine deficiency and show recovery in follow‐up. CE and brain glutamine recover earlier than normalization of NCT and liver functions. Persistence of raised cytokines up to 6 months after insult suggests possible contribution from liver regeneration.
Effect of Bowel Cleansing for Colonoscopy on Fecal Calprotectin Levels in Pediatric Patients
Authors: Kolho Kaija‐Leena , Alfthan Henrik , Hämäläinen Esa
Published: May 2012

The recent development of easily applicable fecal surrogate markers of intestinal inflammation, such as fecal calprotectin (FC), has provided a new means for objectively assessing disease activity in patients with chronic inflammatory bowel disease. Because the use of these markers is about to emerge, it is important to be aware of the possible limitations of measurements. We assessed levels of FC during bowel cleansing. In patients with high FC levels at baseline, the values measured during bowel cleansing varied considerably, remaining high or even returning to normal. Thus, stool sampling for FC assessment is not recommended during bowel preparation for colonoscopy.
Endoscopic Surveillance and Primary Prophylaxis Sclerotherapy of Esophageal Varices in Biliary Atresia
Authors: Lampela Hanna , Kosola Silja , Koivusalo Antti , Lauronen Jouni , Jalanko Hannu , Rintala Risto , Pakarinen Mikko P.
Published: May 2012

Objectives:

Evidence‐based recommendations on endoscopic screening and prophylactic treatment of esophageal varices in patients with biliary atresia (BA) are scarce. We assessed the efficiency of endoscopic surveillance and risk factors of esophageal varices and associated upper gastrointestinal bleeding.

Methods:

A total of 47 consecutive children with BA and portoenterostomy underwent yearly endoscopies and prophylactic injection sclerotherapy of esophageal varices between 1987 and 2009. The median follow‐up was 1.7 years (range 0.5–18.9) and overall 2‐year survival 71%. Disease characteristics, clearance of jaundice, laboratory tests reflecting liver function and hypersplenism, as well as sonographic signs of portal hypertension were related to endoscopic findings and bleeding episodes.

Results:

Grade 2 to 3 varices developed with similar frequency after failed (18/28, 64%) and successful portoenterostomy (10/19, 53%) in 28 patients. Following failed portoenterostomy, esophageal varices were encountered significantly earlier (8 [4–23] vs 19 [4–165] months, P = 0.004), and they reappeared after eradication more often (16/16 vs 4/10, P = 0.001). Varices bled only after failed portoenterostomy (13/28 vs 0/19, P < 0.001). Increased serum bilirubin concentration >40 μmol/L at 3 months after portoenterostomy was a risk factor of upper gastrointestinal bleeding (odds ratio [OR] 17, 95% confidence interval [CI] 1.7–175, P = 0.017).

Conclusions:

In future studies as well as clinical surveillance of BA patients' varices, successful and failed portoenterostomy patients should be approached as separate groups with divergent prognoses. After failed portoenterostomy, surveillance should start early, for example, at 6 months.
1-{(1Z)-1-[3-(2,4-Dichlorophenoxy)propoxy]-1-(2,4-difluorophenyl)prop-1-en-2-yl}-1H-1,2,4-triazole
Authors: Luan Yuan-yuan , Hu Yong-hong , Guo Song , Zhu Jing , Yang Wen-ge
Published: May 2012

In the title compound, C20H17Cl2F2N3O2, the triazole ring makes dihedral angles of 28.0 (3) and 72.5 (2)° with the 2,4-dichloropheny and 2,4-difluorophenyl rings, respectively, and the molecule adopts a Z-conformation about the C=C double bond. In the crystal, C—H...O and C—H...N hydrogen bonds link the molecules.
5-Methoxy-2-[(5-methoxy-1H-indol-1-yl)carbonyl]-1H-indole
Authors: Attia Mohamed I. , El-Brollosy Nasser R. , El-Emam Ali A. , Ng Seik Weng , Tiekink Edward R. T.
Published: May 2012

The asymmetric unit of the title compound, C19H16N2O3, comprises three independent molecules (A, B and C). The inversion-related molecule of A is virtually superimposable upon the other two molecules. In each molecule, there is a twist in the link between the approximately syn carbonyl and amine groups [the N—C—C—O torsion angles range from 19.73 (19) to −21.2 (2)°]. Each molecule has a bent shape quantified in terms of the dihedral angle between the indole and indole fused-ring systems [range = 45.69 (5)–47.91 (5)°]. In the crystal, the A and B molecules form dimeric aggregates via ten-membered {...HNC2O}2 synthons, while the C molecules self-associate similarly but about a centre of inversion.
6-Chloro-1-({[(2E)-2-methyl-3-phenylprop-2-en-1-yl]oxy}methyl)-1,2,3,4-tetrahydroquinazoline-2,4-dione
Authors: El-Brollosy Nasser R. , Attia Mohamed I. , El-Emam Ali A. , Ng Seik Weng , Tiekink Edward R. T.
Published: May 2012

In the title compound, C19H17ClN2O3, the conformation about the ethylene bond [1.333 (2) Å] is E. The ten atoms comprising the quinazoline ring are essentially planar (r.m.s. deviation = 0.032 Å) and their mean plane forms a dihedral angle of 13.89 (7)° with the terminal phenyl ring; the molecule has an open conformation as these substituents are directed away from each other. In the crystal, centrosymmetrically related molecules are connected via N—H...O hydrogen bonds between the amide groups, leading to eight-membered {...HNCO}2 synthons. These are consolidated into a three-dimensional architecture by C—H...O, C—H...π and π–π interactions [ring centroid(N2C4)...centroid(C6) distance = 3.5820 (11) Å].
4,5-Dibromo-2,7-di-tert-butyl-9,9-dimethyl-9H-thioxanthene
Authors: Rubio Omayra H. , Fuentes de Arriba Angel L. , Sanz Francisca , Muniz Francisco M. , Morán Joaquín R.
Published: May 2012

In the title compound, C23H28Br2S, the thioxanthene unit is twisted, showing a dihedral angle of 29.3 (5)° between the benzene rings. When projected along [001], the packing shows two types of channels. The crystal studied was a racemic twin.
5-[1-(4-Methoxyphenyl)-2-nitrobutyl]-4-phenyl-1,2,3-selenadiazole
Authors: Sugumar P. , Sankari S. , Manisankar P. , Ponnuswamy M. N.
Published: May 2012

In the title compound, C19H19N3O3Se, the selenadiazole ring is essentially planar (r.m.s. deviation = 0.001 Å). The heterocyclic ring makes dihedral angles of 50.2 (2) and 76.3 (9)°, respectively, with the methoxyphenyl and phenyl rings.
2,2-Dibromo-N-(4-fluorophenyl)acetamide
Authors: Qian Xiangjun , Fang Zheng , Bao Shuxin , Guo Kai , Wei Ping
Published: May 2012

In the crystal structure of the title compound, C8H6Br2FNO, C—H...O and N—H...O hydrogen bonding results in six-membered rings and links the molecules into chains running parallel to the c axis. The dihedral angle between the fluorophenyl ring and the acetamide group is 29.5 (5)°.
3-(Adamantan-1-yl)-1-[(4-benzylpiperazin-1-yl)methyl]-4-[(E)-(2-hydroxybenzylidene)amino]-1H-1,2,4-triazole-5(4H)-thione
Authors: El-Emam Ali A. , Al-Omar Mohamed A. , Al-Tamimi Abdul-Malek S. , Ng Seik Weng , Tiekink Edward R. T.
Published: May 2012

In the title compound, C31H38N6OS, the conformation about the N=C [1.285 (2) Å] imine bond is E. The piperazine ring has a chair conformation and occupies a position almost perpendicular to the plane through the triazole ring; the benzene ring forms a dihedral angle of 31.95 (10)° with the triazole ring. Overall, the molecule has the shape of a flattened bowl. The hydroxy group is disordered over two positions. The major component has a site-occupancy factor of 0.762 (3) and forms an intramolecular O—H...N(imine) bond to close an S(6) loop. The minor component of the disordered hydroxy group forms an O—H...N(piperazine) hydrogen bond. These, along with C—H...S and C—H...N interactions, link molecules into a three-dimensional architecture.
3-Nitro-N-[(pyrrolidin-1-yl)carbothioyl]benzamide
Authors: Zulkifli Nursakinah , Yusoff Siti Fairus M. , Yamin Bohari M.
Published: May 2012

In the molecule of the title compound, C12H13N3O3S, the pyrrolidine ring adopts a half-chair conformation and the dihedral angle formed by the nitro group with the benzene ring is 15.18 (18)°. In the crystal, molecules are linked by N—H...S and C—H...O intermolecular hydrogen bonds into chains parallel to the c axis.
3-(Adamantan-1-yl)-4-methyl-1-[(4-phenylpiperazin-1-yl)methyl]-1H-1,2,4-triazole-5(4H)-thione dichloromethane hemisolvate
Authors: El-Emam Ali A. , Al-Omar Mohamed A. , Al-Tamimi Abdul-Malek S. , Ng Seik Weng , Tiekink Edward R. T.
Published: May 2012

The asymmetric unit of the title dichloromethane hemisolvate, C24H33N5S·0.5CH2Cl2, comprises an adamantanyl/triazole derivative and half a CH2Cl2 molecule of crystallization; the latter is disordered about a twofold axis of symmetry. The piperazine ring has a chair conformation and the two N-bound substituents occupy equatorial positions. The piperazine residue is almost normal to the triazole ring [N—N—C—N torsion angle = −79.9 (3)°] so that to a first approximation, the molecule has an L-shape. Linear supramolecular chains parallel to [001] are formed via C—H...S interactions. Two such chains are linked into a double chain via C—H...Cl interactions involving the disordered CH2Cl2 molecules of solvation.
O-Propyl N-phenylthiocarbamate
Authors: Sudkaow Panyapon , Yeo Chien Ing , Ng Seik Weng , Tiekink Edward R. T.
Published: May 2012

Two independent molecules comprise the asymmetric unit in the title thiocarbamide derivative, C10H13NOS. These differ in the relative orientations of terminal ethyl groups [C—C—C—O torsion angles = −66.95 (13) and 55.92 (13)°, respectively]. The phenyl ring is twisted out of the plane of the central residue [Cq—N—Cph—Cph = −146.20 (12) and −144.15 (12)°, respectively; q = quaternary and ph = phenyl]. The independent molecules are linked into a dimeric aggregate by N—H...S hydrogen bonds and an eight-membered thioamide {...H—N—C=S}2 synthon.
Bis(2,S-dimethyldithiocarbazate-κ2
N
3,S)(nitrato-κO)copper(II) nitrate
Authors: Hazari Saroj K. S. , Dey B. K. , Ganguly B. , Ng Seik Weng , Tiekink Edward R. T.
Published: May 2012

The title complex, [Cu(NO3)(C3H8N2S2)2]NO3, represents a low-symmetry polymorph (P-1, Z = 4) of a previously reported form [P-1, Z = 2; Ali et al. (2011). Polyhedron, 30, 542–548]. The CuII atom in each independent cation is found within a distorted square-pyramidal N2S2O coordination geometry defined by two N,S-bidentate ligands and an O atom derived from a monodentate nitrate. The primary difference between the cations is found in the relative orientations of the coordinated nitrate groups, which are directed to opposite sides of the molecule. Supramolecular layers along [110] and sustained by N—H...O interactions feature in the crystal packing. These are connected along the c axis by C—H...O interactions.
Aqua[6-carboxylato-N′-(pyridin-2-ylmethylidene)pyridine-2-carbohydrazidato]copper(II) trihydrate
Authors: Huang Yu-Min , Wu Wen-Shi , Wang Xin-Yu
Published: May 2012

In the title compound, [Cu(C13H8N4O3)(H2O)]·3H2O, the complex molecule, except for the aqua ligand, is essentially planar [r.m.s. deviation = 0.034 (2) Å]. The coordination polyhedron of the Cu2+ cation is a square-pyramid, with the aqua ligand at the apex. The compound exhibits a three-dimensional structure, which is is stabilized by O—H...O and O—-H...N hydrogen bonds and π–π interactions [centroid–centroid distance = 2.987 (3) Å].
Dibromidobis[1-(2-bromobenzyl)-3-(pyrimidin-2-yl)-1H-imidazol-2(3H)-one]copper(II)
Authors: Lu Chun-Xin
Published: May 2012

In the title complex, [CuBr2(C14H11BrN4O)2], the CuII ion is located on an inversion centre and is coordinated by two ketonic O atoms, two N atoms and two Br atoms, forming a distorted octahedral coordination environment. The two carbonyl groups are trans positioned with C=O bond lengths of 1.256 (5) Å, in agreement with a classical carbonyl bond. The Cu—O bond length is 2.011 (3) Å. The two bromobenzyl rings are approximately parallel to one another, forming a dihedral angle of 70.1 (4)° with the coordination plane.
K2[FeII
3(P2O7)2(H2O)2]
Authors: Yang Juan , Zhang Xin , Liu Biao , Sun Wei , Huang Ya-Xi
Published: May 2012

The title compound, dipotassium diaquabis(diphosphato)triferrate(II), K2[FeII
3(P2O7)2(H2O)2], was synthesized under solvothermal conditions. The crystal structure is isotypic with its Co analogue. In the structure, there are two crystallographically distinct Fe positions; one lies on an inversion center, the other on a general position. The first Fe2+ cation adopts a regular octahedral coordination with six O atoms, whereas the other is coordinated by five O atoms and a water molecule. The [FeO6] octahedron shares its trans-edges with an adjacent [FeO5(H2O)] octahedron; in turn, the [FeO5(H2O)] octahedron shares skew-edges with a neighbouring [FeO6] octahedron and an [FeO5(H2O)] octahedron, resulting in a zigzag octahedral chain running along [001]. The zigzag chains are linked to each other by the P2O7 diphosphate groups, leading to a corrugated iron diphosphate layer, [Fe3(P2O7)2(H2O)2]2−, parallel to (100). The interlayer space is occupied by K+ cations, which adopt an eight-coordination to seven O atoms and one water molecule from a neighbouring iron diphosphate layer. Thus, the K+ ions not only compensate the negative charge of the layer but also link the layers into a network structure.
3-Ethenyl-1-(4-methylphenylsulfonyl)-1H-indole
Authors: Zukerman-Schpector Julio , Wulf Glaudeston D. , Stefani Hélio A. , Vasconcelos Stanley N. S. , Ng Seik Weng , Tiekink Edward R. T.
Published: May 2012

Two independent but very similar molecules comprise the asymmetric unit of the title compound, C17H15NO2S. The molecules have L-shapes with the dihedral angles between the fused-ring system (r.m.s. deviations = 0.036 and 0.019 Å, respectively) and the benzene ring being almost the same, i.e. 82.98 (12) and 84.46 (13)°, respectively. The terminal ethenyl group is almost coplanar with the ring to which it is connected [C—C—C—C torsion angles = −173.7 (4) and −171.7 (4)°, respectively]. Supramolecular arrays parallel to (-124) stabilized by C—H...O and C—H...π interactions feature in the crystal packing.
N,N′-Bis(4-methylphenyl)-N′′-(2,2,2-trichloroacetyl)phosphoric triamide
Authors: Raissi Shabari Akbar , Pourayoubi Mehrdad , Fadaei Hassan , Nečas Marek , Babiak Michal
Published: May 2012

The P atom in the title compound, C16H17Cl3N3O2P, is bonded in a distorted tetrahedral geometry with the phosphoryl and carbonyl groups anti with respect to one another. In the crystal, molecules are linked through (N—H)2...O(=P) and N—H...O(=C) hydrogen bonds into chains along [001]. The phosphoryl O atom acts as a double hydrogen-bond acceptor.
2-Benzyl-3-hydroxy-3-methyl-2,3-dihydro-1H-isoindol-1-one
Authors: Wang Hong-Yao , Yang Jing-Kui
Published: May 2012

In the title compound, C16H15NO2, the isoindoline ring system is approximately planar (mean deviation = 0.0186 Å) and makes a dihedral angle of 61.91 (4)° with the phenyl ring. In the crystal, molecules form inversion dimers via pairs of O—H...O hydrogen bonds.
3-(1,2-Di-p-tolylvinyl)-2-methyl-1H-indole
Authors: Senthamizhselvi R. , Bhaskar G. , Seshadri P. R. , Perumal P. T. , Illangovan K.
Published: May 2012

In the title compound, C25H23N, the indole unit makes a dihedral angles of 79.03 (5) and 61.82 (4)° with the benzene rings. No classical hydrogen bonds are found in the crystal structure.
5,5-Dimethyl-2,2-bis(pyridin-2-yl)-1,3-diazinane
Authors: Warad Ismail , Alruwaili Afaf , Al-Resayes Saud I. , Choudhary M. Iqbal , Yousuf Sammer
Published: May 2012

In the molecule of the title compound, C16H20N4, the 1,3-diazinane ring adopts a chair conformation and the dihedral angle formed by the pyridine rings is 78.64 (8)°. The molecular conformation is stabilized by an intramolecular C—H...N hydrogen bond, forming an S(6) ring motif. In the crystal, centrosymmetrically related molecules are linked into dimers by pairs of N—H...N hydrogen bonds, generating rings of R
2
2(10) graph-set motif.
(5Z)-5-(2-Hydroxybenzylidene)-3-(4-methylphenyl)-2-sulfanylidene-1,3-thiazolidin-4-one
Authors: Shahwar Durre , Tahir M. Nawaz , Kashif Misbah , Saeed Afifa , Bukhari Sana
Published: May 2012

In the title compound, C17H13NO2S2, the dihedral angles between the 2-sulfanylidene-1,3-thiazolidin-4-one group and the pendant toluene and 2-hydroxybenzene rings are 74.62 (6) and 8.73 (12)°, respectively. An intramolecular C—H...S interaction occurs. In the crystal, inversion dimers linked by pairs of O—H...O hydrogen bonds generate R
2
2(16) loops. This link is reinforced by a pair of C—H...O hydrogen bonds. The dimers are connected by weak C—H...S interactions.
1-(4-Chlorobutanoyl)-3-(2-nitrophenyl)thiourea
Authors: Ngah Nurziana , Kadir Maisara , Yamin Bohari M. , Yusof M. Sukeri M.
Published: May 2012

The asymmetric unit of the title compound, C11H12ClN3O3S, contains two independent molecules with different conformations in which the benzene ring and the thiourea fragment form dihedral angles of 87.28 (12) and 66.44 (10)°. The O atom of the thioamide group is involved in bifurcated N—H...O intra- and intermolecular hydrogen bonding; the latter interaction links the independent molecules into a dimer. In the crystal, N—H...S interactions link the molecules into chains propagating along the c axis.
4-Hydroxy-2-methyl-1,1-dioxo-N-phenyl-2H-1λ6,2-benzothiazine-3-carboxamide
Authors: Aman Farhana , Siddiqui Waseeq Ahmad , Ashraf Adnan , Siddiqui Hamid Latif , Parvez Masood
Published: May 2012

In the title molecule, C16H14N2O4S, the thiazine ring adopts a twist chair conformation with the N and adjacent C atom displaced by 0.966 (3) and 0.386 (4) Å, respectively, on the same side of the mean plane formed by the remaining ring atoms. The dihedral angle between the mean planes of the benzene rings is 37.65 (10)°. The molecular structure features an intramolecular O—H...O hydrogen bond, which generates an S(6) ring. In the crystal, molecules are linked by N—H...O and C—H...O hydrogen bonds.
3,5-Bis(4-fluorophenyl)isoxazole
Authors: Fun Hoong-Kun , Arshad Suhana , Samshuddin S. , Narayana B. , Sarojini B. K.
Published: May 2012

In the crystal structure of the title compound, C15H9F2NO, the complete molecule is generated by a crystallographic twofold rotation axis and the O and N atoms of the central isoxazole ring are statistically disordered with equal site occupancies. The terminal benzene rings form a dihedral angle of 24.23 (3)° with the isoxazole ring. The dihedral angle between the benzene rings is 47.39 (2)°. No significant intermolecular interactions are observed.
2-Methylsulfanyl-1,2,4-triazolo[1,5-a]quinazolin-5(4H)-one
Authors: Al-Salahi Rashad , Al-Omar Mohamed , Abbas Mohammed , Ng Seik Weng
Published: May 2012

The non-H atoms of the title compound, C10H8N4OS, lie approximately in a common plane (r.m.s. deviation = 0.058 Å). In the crystal, two molecules are linked across a center of inversion by a pair of N—H...N hydrogen bonds, forming a a dimer.
2-Methylsulfonyl-1,2,4-triazolo[1,5-a]quinazolin-5(4H)-one
Authors: Al-Salahi Rashad , Marzouk Mohamed , Abbas Mohammed , Ng Seik Weng
Published: May 2012

The triazoloquinazoline fused-ring system of the title compound, C10H8N4O3S, is essentially planar (r.m.s. deviation = 0.027 Å). In the crystal, adjacent molecules are linked by N—H...Osulfonyl hydrogen bonds, generating a helical chain running along the b axis.
2-Phenoxy-1,2,4-triazolo[1,5-a]quinazolin-5(4H)-one
Authors: Al-Salahi Rashad , Nabih Lolak , Al-Omar Mohamed , Ng Seik Weng
Published: May 2012

The triazoloquinazole ring system in the title compound, C15H10N4O2 is approximately planar (r.m.s. deviation = 0.035 Å). The phenyl ring of the phenoxy substitutent is aligned at 59.3 (1)° with respect to this ring system. In the crystal, two molecules are linked about a center of inversion by a pair of N—H...O hydrogen bonds, generating a dimer.
3-Benzyl-8-methoxy-2-sulfanylidene-1,2,3,4-tetrahydroquinazolin-4-one
Authors: Al-Salahi Rashad , Al-Omar Mohamed , Marzouk Mohamed , Ng Seik Weng
Published: May 2012

The tetrahydroquinazole fused-ring system of the title compound, C16H14N2O2S, is roughly planar (r.m.s. deviation = 0.039 Å); the phenyl ring of the benzyl substituent is aligned at 78.1 (1)° with respect to the mean plane of the fused-ring system. In the crystal, two molecules are linked by a pair of N—H...S hydrogen bonds about a center of inversion, generating a dimer.
3-(Prop-2-en-1-yl)-2-sulfanylidene-1,2,3,4-tetrahydroquinazolin-4-one
Authors: Al-Salahi Rashad , Al-Omar Mohamed , Marzouk Mohamed , Ng Seik Weng
Published: May 2012

The tetrahydroquinazoline fused-ring system of the title compound, C11H10N2OS, is approximately planar (r.m.s. deviation = 0.019 Å). In the crystal, adjacent molecules are linked by N—H...O hydrogen bonds, forming a chain running along the b axis.
N-[2,4-Dioxo-3-azatricyclo[7.3.1.05,13]trideca-1(13),5,7,9,11-pentaen-3-yl]thiourea
Authors: Al-Salahi Rashad , Al-Omar Mohamed , Marzouk Mohamed , Ng Seik Weng
Published: May 2012

In the two independent molecules in the asymmetric unit of the title compound, C13H9N3O2S, the azatricyclotridecapentaene ring system is approximately planar with r.m.s. deviations of 0.022 and 0.033 Å. The urea unit connected to the fused rings is approximately perpendicular [dihedral angles = 82.4 (1) and 82.7 (1)°]. In the crystal, the molecules associate by N—H...O hydrogen bonds, forming a chain running along the a axis. The crystal studied was a non-merohedral twin with a fractional contribution of 49.6 (1)% for the minor domain.
Tris(2-acetylcyclopentan-1-onato-κ2
O,O′)aluminium
Authors: Perdih Franc
Published: May 2012

In the title compound, [Al(C7H9O2)3], the AlIII cation is coordinated by six O atoms from three 2-acetylcyclopentanonate ligands in a slightly distorted octahedral environment, with Al—O bond lengths in the range 1.882 (2)–1.896 (2) Å. In the crystal, molecules are linked together via C—H...O interactions. One of the C atoms in one ring has a large thermal motion compared to the other atoms, indicating some possible disorder. However, the treatment of this C atom as disordered over two positions did not give a significant improvement.
N′-(3-Hydroxybenzylidene)-4-methylbenzohydrazide
Authors: Liu Ji-Lai , Sun Ming-Hui , Ma Jing-Jun
Published: May 2012

The title compound, C15H14N2O2, was obtained from the reaction of 3-hydroxybenzaldhyde and 4-methylbenzohydrazide in methanol. In the molecule, the benzene rings form a dihedral angle of 2.9 (3)°. In the crystal, N—H...O and O—H...O hydrogen bonds link the molecules into layers parallel to (101). The crystal packing also exhibits π–π interactions between the aromatic rings [centroid–centroid distance = 3.686 (4) Å].
2,6-Bis(1H-benzimidazol-2-yl)pyridine butyric acid monosolvate dihydrate
Authors: Lin Songzhu , Jia Ruokun , He Aimin
Published: May 2012

In the title compound, C19H13N5·C4H8O2·2H2O, the molecular skeleton of the 2,6-bis(benzimidazol-2-yl)pyridine (bbip) molecule is essentially planar (r.m.s. deviation = 0.023 Å). An extensive three-dimensional network of intermolecular N—H...O, O—H...O and O—H...N hydrogen bonds consolidates the crystal packing, which also exhibits π–π interactions between the five- and six-membered rings from neighbouring bbip molecules.
3-Ethyl-1H-1,2,4-triazole-5(4H)-thione
Authors: Jing Bi , Du Yuao-Chao , Zhu Ai-Xin
Published: May 2012

The molecule of the title compound, C4H7N3S, exists as the thione tautomer in the solid state. The asymmetric unit consits of one molecule in which all atoms are located on a crystallographic mirror plane. In the crystal, adjacent molecules are linked by N—H...N and N—H...S hydrogen bonds into chains running along the a axis. π–π stacking interactions between the triazole rings [centroid–centroid distance = 3.740 (1) Å and interplanar distance = 3.376 Å] may further stabilize the structure.
9-Phenyl-4,5-diaza-9H-fluoren-9-ol monohydrate
Authors: Yin Guo-Jie , Yang Gang-Bin , Wang Shi-Min
Published: May 2012

The title compound, C17H12N2O·H2O, was synthesized by the reaction of 4,5-diazafluoren-9-one with a Grignard reagent in ether (the reaction mixture being hydrolysed with saturated NH4Cl solution), and crystallizes with two organic molecules and two water molecules in the asymmetric unit. The 4,5-diazafluorene fragment is approximately planar, with r.m.s. deviations of 0.0448 and 0.0198 Å in the two molecules. The dihedral angles between the 4,5-diazafluorene planes and the phenyl ring are 80.49 (6) and 76.57 (7)°. The crystal packing features O—H...N and O—H...O hydrogen bonds involving the bridging solvent water molecules, which link the molecules into a three-dimensional network.
N-(Anthracen-9-ylmethyl)adamantan-1-amine
Authors: Fan Wei-Qiang , Chen Fu-Xiao
Published: May 2012

In the crystal stucture of the of the title compound, C25H27N, stong π–π interactions are found between adjacent anthracene fragments, with a shortest centroid–centroid distance of 3.5750 (9) Å.
(Z)-3-(4-Chlorophenyl)-1-(2,4-difluorophenyl)-2-(1H-1,2,4-triazol-1-yl)prop-2-en-1-one
Authors: Peng Xin-Mei , Yin Ben-Tao , Zhou Cheng-He
Published: May 2012

The asymmetric unit of the title compound, C17H10ClF2N3O, contains three independent molecules. In each molecule, the C=C bond has a cis conformation with respect to the triazole and chlorophenyl groups. The dihedral angles formed by the triazole ring with the diflurophenyl and chlorophenyl benzene rings, respectively, are 20.10 (14) and 73.22 (15), 25.31 (15) and 84.44 (15), and 16.44 (13) and 61.72 (14)° in the three molecules while the dihedral angles between the benzene rings are 66.54 (13), 85.82 (12) and 58.37 (12)°.
3-Amino-N-benzyl-6-(4-fluorophenyl)thieno[2,3-b]pyridine-2-carboxamide
Authors: Zhao Jin-Ni , Yang Sheng-Yong , Yang Li
Published: May 2012

In the title compound, C21H16FN3OS, the thieno[2,3-b]pyridine system forms dihedral angles of 10.57 (12) and 83.87 (5)° with the fluorophenyl ring at the 6-position and the phenyl ring of the benzyl group, respectively. In the crystal, molecules are linked by weak N—H...N anf N—H...O hydrogen bonds and π–π stacking interactions involving fluorophenyl rings of adjacent molecules, with a centroid–centroid distance of 3.648 (10) Å. In addition, intramolecular N—H...S and N—H...O hydrogen bonds contribute to the stability of the molecular conformation.
[4-(2-tert-Butoxy-2-oxoethoxy)naphthalen-1-yl]diphenylsulfonium trifluoromethanesulfonate
Authors: Kang Sung Kwon , Jang Siyoung
Published: May 2012

In the cation of the title salt, C28H27O3S+·CF3O3S−, the dihedral angle between the naphthalene ring system and the –C(=O)—O– plane is 80.39 (9)°. The three methyl groups of the tert-butyl group are each disordered over two orientations with an occupancy ratio of 0.712 (18):0.288 (18).
Prescribing without evidence – pregnancy
Authors: Thomas Simon H. L. , Yates Laura M.
Published: May 2012

Prescribing of medicines during pregnancy is common, and for some groups of women is essential for maintaining maternal and therefore fetal health. Pregnant women and prescribers are rightly concerned, however, about the potential adverse fetal effects of medicines. These may include fetal death or stillbirth, congenital malformations, developmental impairment, neonatal effects or late carcinogenesis. It is therefore essential that the risks and benefits for mother and fetus are considered carefully before prescribing in pregnancy. This is often challenging because of the paucity of information available. To complicate the issue further, drug pharmacokinetics are commonly altered in pregnancy, potentially affecting optimal dosing as well as interpretation of plasma concentration measurements, with specific information on individual drugs seldom available. Most drugs cross the placenta, especially lipophilic drugs and those with low plasma protein binding. Active membrane transporters also have an important role in enhancing or preventing drug transfer, although this is not yet clearly understood. Animal studies have limited applicability to humans because of species‐specific effects, and clinical trials in pregnancy are only undertaken in special circumstances. Prescribers therefore need to rely on observational studies of fetal outcomes following drug exposure in human pregnancy. These often involve limited numbers, and data are also subject to confounding and bias, making interpretation difficult. It therefore remains essential that appropriate mechanisms for systematic data collection, including congenital malformation registries, teratology information services, pregnancy registers and linked population registries, are maintained and enhanced to increase the amount and quality of information available.
The prognostic impact of clinical and molecular features in hairy cell leukaemia variant and splenic marginal zone lymphoma
Authors: Hockley Sarah L. , Else Monica , Morilla Alison , Wotherspoon Andrew , Dearden Claire , Catovsky Daniel , Gonzalez David , Matutes Estella
Published: May 2012

Hairy cell leukaemia variant (HCL‐variant) and splenic marginal zone lymphoma (SMZL) are disorders with overlapping features. We investigated the prognostic impact in these disorders of clinical and molecular features including
IGH
VDJ
rearrangements,
IGHV
gene usage and
TP

53 mutations. Clinical and laboratory data were collected before therapy from 35 HCL‐variant and 68 SMZL cases. End‐points were the need for treatment and overall survival. 97% of HCL‐variant and 77% of SMZL cases required treatment (P = 0·009). Survival at 5 years was significantly worse in HCL‐variant [57% (95% confidence interval 38–73%)] compared with SMZL [84% (71–91%); Hazard Ratio 2·25 (1·20–4·25), P = 0·01]. In HCL‐variant, adverse prognostic factors for survival were older age (P = 0·04), anaemia (P = 0·01) and
TP

53 mutations (P = 0·02). In SMZL, splenomegaly, anaemia and
IGHV
genes with >98% homology to the germline predicted the need for treatment; older age, anaemia and
IGHV
unmutated genes (100% homology) predicted shorter survival.
IGHV
gene usage had no impact on clinical outcome in either disease. The combination of unfavourable factors allowed patients to be stratified into risk groups with significant differences in survival. Although HCL‐variant and SMZL share some features, they have different outcomes, influenced by clinical and biological factors.
Malignancy through cooperation: an evolutionary game theory approach
Authors: Liu Q. , Liu Z.
Published: May 2012

Objective

Traditional cancer initiation theory propounds evolution of a monoclonal population of fully transformed tumour cells to form a malignant tumour. Cooperation between surrounding stroma and the tumour also often leads to malignancy. This cooperation may exist as a result of sharing of growth signals or growth factors secreted by stromal cells, which can cause those with proliferative phenotypes to switch to motile phenotypes. Mathematical models of sharing of growth factors between cancer stem cells and stromal cells can allow for deeper understanding of tumourigenesis through cooperation. The study presented here describes a novel evolutionary game theoretical approach to investigate emergence of malignancy through interactions among cells of three different phenotypes, one of which produces growth factors.

Materials and methods

Three different scenarios have been considered, and types of behaviour of the three phenotypes during interactions, have been modelled in terms of cost and benefit variables. Phenotypic compositions of such a tumour at equilibrium have been analysed, and evolution of the population, with respect to time, has been investigated.

Results

Results suggest the role of cooperation in forming a malignant tumour and show, in all three cases, that emergence of triple polymorphism, two‐strategy polymorphism, and fixation of one phenotype, were possible at equilibrium. The models also suggest that under certain conditions, one phenotype may be completely eliminated from the population, thus leading to new possibilities for potential treatments.

Conclusions

This study explains some current experimental findings from a theoretical viewpoint, and may provide new approaches for future research in oncology.
Eggshell colour is more strongly affected by maternal identity than by dietary antioxidants in a captive poultry system
Authors: Dearborn Donald C. , Hanley Daniel , Ballantine Katherine , Cullum John , Reeder DeeAnn M.
Published: May 2012

1.Biologists have long puzzled over the apparent conspicuousness of blue‐green eggshell coloration in birds. One candidate explanation is the ‘sexual signalling hypothesis’ that the blue‐green colour of eggshells can reveal an intrinsic aspect of females' physiological quality, with only high‐quality females having sufficient antioxidant capacity to pigment their eggs with large amounts of biliverdin. Subsequent work has argued instead that eggshell colour might signal condition‐dependent traits based on diet.

2.Using Araucana chickens that lay blue‐green eggs, we explored (i) whether high levels of dietary antioxidants yield eggshells with greater blue‐green reflectance, (ii) whether females differ from one another in eggshell coloration despite standardized environments, diets and rearing conditions, and (iii) the relative strength with which diet vs. female identity affects eggshell coloration.

3.We reared birds to maturity and then placed them on either a high‐ or low‐antioxidant diet, differing fourfold in Vitamin E acetate and Vitamin A retinol. After 8 weeks, the treatments were reversed, such that females laid eggs on both diets in an order‐balanced design. We measured the reflectance spectra of 545 eggs from 25 females.

4.Diet had a very limited effect on eggshell spectral reflectance, but individual females differed strongly and consistently from one another, despite having been reared under uniform conditions. However, predictions from avian visual modelling suggest that most of the egg colour differences between females, and nearly all of the differences between diets, are unlikely to be visually discriminable.

5.Our data suggest that eggshell reflectance spectra may carry information on intrinsic properties of the female that laid the eggs, but the utility of this coloration as a signal to conspecifics in this species may be limited by the sensitivity of a receiver to detect it.
The consequences of alternative parental care tactics in free‐ranging pythons in tropical Australia
Authors: Stahlschmidt Zachary R. , Shine Richard , DeNardo Dale F.
Published: May 2012

1.Life‐history theory attributes the evolution of parental care to the benefits to offspring viability outweighing any costs to parental viability. However, the consequences of parental care tactics to parent(s) and the developmental environment have seldom been measured under field conditions.

2.Laboratory research on pythons shows that maternal nest‐site selection and egg brooding benefit embryos, but prolonged nest attendance may impose fitness costs to free‐ranging females. A population of water pythons (Liasis fuscus) in tropical Australia provides an excellent opportunity to examine this parent–offspring trade‐off because females exhibit parental care polymorphism wherein some individuals brood their eggs only briefly (<10 days) post‐oviposition (‘short brooders’) while others remain with their eggs throughout the incubation period (>50 days; ‘long brooders’).

3.We used radiotelemetry, temperature and humidity data loggers, ultrasonography, haematological techniques, and habitat analyses to examine the correlates and consequences of maternal nesting decisions in 14 free‐ranging female pythons over the 4‐month reproductive season.

4.Nest‐site selection and maternal attendance enhanced thermal and hydric regimes within the nest. Egg production by reproducing female pythons resulted in high energetic costs (loss of 60% of maternal body mass) and increased parasite load. However, the estimated mass loss because of brooding was (i) low (<5%), (ii) inversely related to fecundity (females that produced relatively large clutches tended to select lower temperatures and thus lost less mass during brooding) and (iii) surprisingly unrelated to brooding duration. Phenotypic traits of short and long brooders were similar, but long brooders had higher haemoparasite burdens prior to oviposition. Clutches of long brooders were laid in more open sites (less canopy cover) and experienced warmer and more humid conditions than did those of short brooders.

5.Together with previous research, we suggest several explanations for the maintenance of maternal care polymorphism within this population, such as a trade‐off between offspring number and quality (long brooders may produce fewer clutches during their lifespan but enhance offspring quality). Our study provides detailed measurements of the correlates and consequences of parental care in a free‐ranging reptile, and it clarifies the trade‐offs mediated by taxonomically widespread maternal decisions (e.g. nest‐ or oviposition‐site selection and nest attendance).
Below‐ground plant species richness: new insights from DNA‐based methods
Authors: Pärtel Meelis , Hiiesalu Inga , Öpik Maarja , Wilson Scott D.
Published: May 2012

1.Ideas about mechanisms controlling plant species richness are founded on empirical studies of above‐ground vegetation. In many ecosystems, however, the majority of vegetation (e.g. 50–90% in temperate grasslands) occurs below‐ground as roots, rhizomes and shoot bases. Whether the richness patterns described for above‐ground vegetation also hold for the large below‐ground component is still unknown.

2.Here, we provide a concise overview how the use of DNA‐based techniques might alter our perception of richness patterns in plant communities. We focus mainly on temperate grasslands, but new patterns should also arise in other community types (except epiphyte‐rich ecosystems).

3.We hypothesise that DNA‐based measurements of below‐ground plant richness will reveal that richness is greater below‐ than above‐ground because many perennial plants persist below‐ground even in the temporary absence of above‐ground shoots, and because the roots and rhizomes of plant individuals occupy larger areas than do shoots. Consequently, the species–area relationship may show steeper slopes for below‐ground than above‐ground richness. Further, above‐ground richness may not be a constant proportion of below‐ground richness, so the ratio of below/above‐ground richness may vary along environmental gradients of productivity, disturbance and heterogeneity.

4.We also hypothesize that the often‐observed decrease in above‐ground richness with increasing productivity may not occur for below‐ground richness, partly for the reasons noted above, and partly because of differences between above‐ and below‐ground resources. Light is supplied largely in one dimension and does not persist in the environment for later uptake, whereas nutrients and water are supplied in three dimensions and can persist in the soil. Together, these differences should allow more niche differentiation and greater species richness below‐ground.

5.Current DNA‐based methods that allow measurement of below‐ground richness in the field are likely to reveal patterns different from those well‐documented for above‐ground richness and may also produce new insights about plant community structure and function.