bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insect phylogenomics: new insights on the relationships of lower neopteran orders (Polyneoptera)
Authors: LETSCH HARALD , SIMON SABRINA 
Published: August 2013

AbstractThe branching pattern of the diverse lower neopteran insect lineages (Polyneoptera: cockroaches, mantids, earwigs, grasshoppers, phasmids etc.) is the least resolved problem in insect systematics. Despite the accumulation of various morphological and molecular datasets, the proposed phylogenetic relationships within Polyneoptera remain unstable. In this study we investigate these relationships based on a new transcriptome data matrix covering almost all polyneopteran orders, except for Mantophasmatodea, Grylloblattodea and Mantodea. The data conclusively support a monophyletic Polyneoptera, thus corroborating previous findings from (i) recent large gene studies with smaller taxon sampling and (ii) comprehensive protein coding gene analyses across all insect lineages, and, consequently, rejecting the paraphyletic lower neopteran group suggested by various morphological characters and rRNA gene analyses. The inclusion of several phylogenetically ambiguous polyneopteran orders (Zoraptera, Dermaptera, Plecoptera, Phasmatodea and Embioptera) allows us to further test alternative phylogenetic relationships within Polyneoptera. Previously suggested clades are significantly rejected: Parametabola (= Zoraptera + Paraneoptera), Mystroptera (= Embioptera + Zoraptera) and Orthopterida (= Orthoptera + Phasmatodea). Although the lower neopteran orders are so far only supported as a monophyletic group by autapomorphies in wing base characters, phylogenomic analyses consistently provide further strong support. However, despite the use of this large dataset, several polyneopteran orders still show unstable positions within a monophyletic Polyneoptera.
Clinical, cytologic, and histologic features of a mammary micropapillary carcinoma in a dog
Authors: Salgado Breno S. , Monteiro Lidianne N. , Colodel Márcia M. , Figueiroa Fernanda C. , Soares Luisa M. , Nonogaki Suely , Rocha Rafael M. , Rocha Noeme S. 
Published: August 2013

AbstractMammary invasive micropapillary carcinoma is a rare variant of mammary carcinoma that was recently recognized in dogs. The cytologic features and biologic behavior of such neoplasms in dogs have not yet been widely discussed in the veterinary literature. We report the clinical, cytologic, and histologic features of a canine micropapillary carcinoma in a 13‐year‐old female mongrel dog. The mammary region presented with extreme local pain, severe edema and erythema, and multifocal epidermal ulceration, which is typical for an inflammatory mammary carcinoma. Fine‐needle aspirates were highly cellular and consisted of individual cells and papillary cell clusters with characteristics of malignant epithelial cells. Histologic examination revealed neoplastic cells arranged in small papillae without fibrovascular cores, sometimes inside clear lymphatic spaces, indicating lymphovascular invasion. Regional lymph node evaluation revealed metastatic cells. Due to deteriorating clinical condition the dog was euthanatized 5 months after mastectomy. At necropsy, metastatic neoplastic mammary cells were found in popliteal and mediastinal lymph nodes, the right femoral biceps muscle, liver, heart, lungs, and urinary bladder.
Brill–Noether loci in codimension two
Authors: Tarasca Nicola 
Published: August 2013

AbstractLet us consider the locus in the moduli space of curves of genus$2k$defined by curves with a pencil of degree$k$. Since the Brill–Noether number is equal to$- 2$, such a locus has codimension two. Using the method of test surfaces, we compute the class of its closure in the moduli space of stable curves.
Automorphisms of surfaces of general type with acting trivially in cohomology
Authors: Cai Jin-Xing , Liu Wenfei , Zhang Lei 
Published: August 2013

AbstractIn this paper we prove that surfaces of general type with irregularity $q\geq 3$ are rationally cohomologically rigidified, and so are minimal surfaces $S$ with $q(S)= 2$ unless ${ K}_{S}^{2} = 8\chi ({ \mathcal{O} }_{S} )$. Here a surface $S$ is said to be rationally cohomologically rigidified if its automorphism group $\mathrm{Aut} (S)$ acts faithfully on the cohomology ring ${H}^{\ast } (S, \mathbb{Q} )$. As examples we give a complete classification of surfaces isogenous to a product with $q(S)= 2$ that are not rationally cohomologically rigidified.
Eigenvalues of Hermitian matrices and equivariant cohomology of Grassmannians
Authors: Anderson David , Richmond Edward , Yong Alexander 
Published: August 2013

AbstractThe saturation theorem of Knutson and Tao concerns the nonvanishing of Littlewood–Richardson coefficients. In combination with work of Klyachko, it implies Horn’s conjecture about eigenvalues of sums of Hermitian matrices. This eigenvalue problem has a generalization to majorized sums of Hermitian matrices, due to S. Friedland. We further illustrate the common features between these two eigenvalue problems and their connection to Schubert calculus of Grassmannians. Our main result gives a Schubert calculus interpretation of Friedland’s problem, via equivariant cohomology of Grassmannians. In particular, we prove a saturation theorem for this setting. Our arguments employ the aforementioned work together with recent work of H. Thomas and A. Yong.
Completing the Brauer Trees for the Sporadic Simple Lyons Group
Authors: Müller Jürgen , Neunhöffer Max , Röhr Frank , Wilson Robert 
Published: August 2013

AbstractIn this paper, the Brauer trees are completed for the sporadic simple Lyons group Ly in characteristics 37 and 67. The results are obtained using tools from computational representation theory—in particular, a new condensation technique—and with the assistance of the computer algebra systems MeatAxe and GAP.
Nice Efficient Presentions for all Small Simple Groups and their Covers
Authors: Campbell Colin M. , Havas George , Ramsay Colin , Robertson Edmund F. 
Published: August 2013

AbstractPrior to this paper, all small simple groups were known to be efficient, but the status of four of their covering groups was unknown. Nice, efficient presentations are provided in this paper for all of these groups, resolving the previously unknown cases. The authors‘presentations are better than those that were previously available, in terms of both length and computational properties. In many cases, these presentations have minimal possible length. The results presented here are based on major amounts of computation. Substantial use is made of systems for computational group theory and, in partic-ular, of computer implementations of coset enumeration. To assist in reducing the number of relators, theorems are provided to enable the amalgamation of power relations in certain presentations. The paper concludes with a selection of unsolved problems about efficient presentations for simple groups and their covers.
Optimally Coupling the Kolmogorov Diffusion, and Related Optimal Control Problems
Authors: Jansons Kalvis M. , Metcalfe Paul D. 
Published: August 2013

AbstractWe discuss the optimal Markovian coupling before an exponential time of the Kolmogorov diffusion, and a class of related stochastic control problems in which the aim is to hit the origin before an exponential time. We provide a scaling argument for the optimal control in the near field and use rational WKB approximation to obtain the optimal control in the far field, and compare these analytical results with numerical experiments. In some of these optimal control problems, in which the advection velocity field is bounded, we show that the probability of success agrees exactly with its leading-order asymptotic approximation in some areas of the plane, up to an undetermined multiplicative constant. We conjecture a necessary and sufficient condition for this behaviour, which is strongly supported by numerical experiments.
Point Counting in Families of Hyperelliptic Curves in Characteristic 2
Authors: Hubrechts Hendrik 
Published: August 2013

AbstractLet EΓ be a family of hyperelliptic curves over F2alg cl with general Weierstrass equation given over a very small field F. The author of this paper describes an algorithm for computing the zeta function of Eγ, with γ in a degree n extension field of F, which has time complexity O(n3 + ε) bit operations and memory requirements O(n2) bits. Using a slightly different algorithm, one can get time O(n2.667) and memory O(n2.5), and the computation for n curves of the family can be done in time O(n3.376). All of these algorithms are polynomial-time in the genus.
On Conjugacy Classes of Congruence Subgroups of PSL(2, R)
Authors: Cummins C. J. 
Published: August 2013

AbstractLet G be a subgroup of PSL(2, R) which is commensurable with PSL(2, Z). We say that G is a congruence subgroup of PSL(2, R) if G contains a principal congruence subgroup /overline Γ(N) for some N. An algorithm is given for determining whether two congruence subgroups are conjugate in PSL(2, R). This algorithm is used to determine the PSL(2, R) conjugacy classes of congruence subgroups of genus-zero and genus-one. The results are given in a table.
R-Thanatin Inhibits Growth and Biofilm Formation of Methicillin-Resistant Staphylococcus epidermidis
In Vivo
and
In Vitro
Authors: Hou Zheng , Da Fei , Liu Baohui , Xue Xiaoyan , Xu Xiuli , Zhou Ying , Li Mingkai , Li Zhi , Ma Xue , Meng Jingru , Jia Min , Wang Yukun , Luo Xiaoxing 
Published: August 2013

ABSTRACT

Staphylococcus epidermidis
is one of the most frequent causes of device-associated infections, because it is known to cause biofilms that grow on catheters or other surgical implants. The persistent increasing resistance of
S. epidermidis
and other coagulase-negative staphylococci (CoNS) has driven the need for newer antibacterial agents with innovative therapeutic strategies. Thanatin is reported to display potent antibiotic activities, especially against extended-spectrum-beta-lactamase-producing
Escherichia coli
. The present study aimed to investigate whether a shorter derivative peptide (R-thanatin) could be used as a novel antibacterial agent. We found that R-thanatin was highly potent
in vitro
against coagulase-negative staphylococci, such as
S. epidermidis
,
S. haemolyticus
, and
S. hominis
, and inhibited biofilm formation at subinhibitory concentrations. Properties of little toxicity to human red blood cells (hRBCs) and human umbilical vein endothelial cells, a low incidence of resistance, and relatively high stability in plasma were confirmed. Excellent
in vivo
protective effects were also observed using a methicillin-resistant
S. epidermidis
(MRSE)-induced urinary tract infection rat model. Electron microscopy and confocal laser-scanning microscopy analyses suggested that R-thanatin disturbed cell division of MRSE severely, which might be the reason for inhibition of MRSE growth. These findings indicate that R-thanatin is active against the growth and biofilm formation of MRSE
in vitro
and
in vivo
. R-thanatin might be considered as a specific drug candidate for treating CoNS infections.
N
-Cinnamoylated Aminoquinolines as Promising Antileishmanial Agents
Authors: Vale-Costa S. , Costa-Gouveia J. , Pérez B. , Silva T. , Teixeira C. , Gomes P. , Gomes M. S. 
Published: August 2013

ABSTRACT

A series of cinnamic acid conjugates of primaquine and chloroquine were evaluated for their
in vitro
antileishmanial activities. Although primaquine derivatives had modest activity, chloroquine conjugates exhibited potent activity against both promastigotes (50% inhibitory concentration [IC
50
] = 2.6 to 21.8 μM) and intramacrophagic amastigotes (IC
50
= 1.2 to 9.3 μM) of
Leishmania infantum
. Both the high activity of these chloroquine analogues and their mild-to-low toxicity toward host cells make them promising leads for the discovery of new antileishmanial agents.
Unique Features of a Pseudomonas aeruginosa α2-Macroglobulin Homolog
Authors: Robert-Genthon Mylène , Casabona Maria Guillermina , Neves David , Couté Yohann , Cicéron Félix , Elsen Sylvie , Dessen Andréa , Attrée Ina 
Published: August 2013

ABSTRACT

Human pathogens frequently use protein mimicry to manipulate host cells in order to promote their survival. Here we show that the opportunistic pathogen
Pseudomonas aeruginosa
synthesizes a structural homolog of the human α2-macroglobulin, a large-spectrum protease inhibitor and important player of innate immunity. Small-angle X-ray scattering analysis demonstrated that the fold of
P. aeruginosa
MagD (PA4489) is similar to that of the human macroglobulin and undergoes a conformational modification upon binding of human neutrophil elastase. MagD synthesis is under the control of a general virulence regulatory pathway including the inner membrane sensor RetS and the RNA-binding protein RsmA, and MagD undergoes cleavage from a 165-kDa to a 100-kDa form in all clinical isolates tested. Fractionation and immunoprecipitation experiments showed that MagD is translocated to the bacterial periplasm and resides within the inner membrane in a complex with three other molecular partners, MagA, MagB, and MagF, all of them encoded by the same six-gene genetic element. Inactivation of the whole 10-kb operon on the PAO1 genome resulted in mislocalization of uncleaved, in
trans
-provided MagD as well as its rapid degradation. Thus, pathogenic bacteria have acquired a homolog of human macroglobulin that plays roles in host-pathogen interactions potentially through recognition of host proteases and/or antimicrobial peptides; it is thus essential for bacterial defense.

IMPORTANCE
The pathogenesis of
Pseudomonas aeruginosa
is multifactorial and relies on surface-associated and secreted proteins with different toxic activities. Here we show that the bacterium synthesizes a 160-kDa structural homolog of the human large-spectrum protease inhibitor α2-macroglobulin. The bacterial protein is localized in the periplasm and is associated with the inner membrane through the formation of a multimolecular complex. Its synthesis is coregulated at the posttranscriptional level with other virulence determinants, suggesting that it has a role in bacterial pathogenicity and/or in defense against the host immune system. Thus, this new
P. aeruginosa
macromolecular complex may represent a future target for antibacterial developments.
Small-Molecule Inhibitors of
toxT
Expression in Vibrio cholerae
Authors: Anthouard Rebecca , DiRita Victor J. 
Published: August 2013

ABSTRACT

Vibrio cholerae
, a Gram-negative bacterium, infects humans and causes cholera, a severe disease characterized by vomiting and diarrhea. These symptoms are primarily caused by cholera toxin (CT), whose production by
V. cholerae
is tightly regulated by the virulence cascade. In this study, we designed and carried out a high-throughput chemical genetic screen to identify inhibitors of the virulence cascade. We identified three compounds, which we named toxtazin A and toxtazin B and Bʹ, representing two novel classes of
toxT
transcription inhibitors. All three compounds reduce production of both CT and the toxin-coregulated pilus (TCP), an important colonization factor. We present evidence that toxtazin A works at the level of the
toxT
promoter and that toxtazins B and Bʹ work at the level of the
tcpP
promoter. Treatment with toxtazin B results in a 100-fold reduction in colonization in an infant mouse model of infection, though toxtazin A did not reduce colonization at the concentrations tested. These results add to the growing body of literature indicating that small-molecule inhibitors of virulence genes could be developed to treat infections, as alternatives to antibiotics become increasingly needed.

IMPORTANCE
V. cholerae
caused more than 580,000 infections worldwide in 2011 alone (WHO, Wkly. Epidemiol. Rec. 87:289-304, 2012). Cholera is treated with an oral rehydration therapy consisting of water, glucose, and electrolytes. However, as
V. cholerae
is transmitted via contaminated water, treatment can be difficult for communities whose water source is contaminated. In this study, we address the need for new therapeutic approaches by targeting the production of the main virulence factor, cholera toxin (CT). The high-throughput screen presented here led to the identification of two novel classes of inhibitors of the virulence cascade in
V. cholerae
, toxtazin A and toxtazins B and Bʹ. We demonstrate that (i) small-molecule inhibitors of virulence gene production can be identified in a high-throughput screen, (ii) targeting virulence gene production is an effective therapeutic strategy, and (iii) small-molecule inhibitors can uncover unknown layers of gene regulation, even in well-studied regulatory cascades.
Structure-Informed Design of an Enzymatically Inactive Vaccine Component for Group A
Streptococcus
Authors: Henningham Anna , Ericsson Daniel J. , Langer Karla , Casey Lachlan W. , Jovcevski Blagojce , Chhatwal G. Singh , Aquilina J. Andrew , Batzloff Michael R. , Kobe Bostjan , Walker Mark J. 
Published: August 2013

ABSTRACT

Streptococcus pyogenes
(group A
Streptococcus
[GAS]) causes ~700 million human infections/year, resulting in >500,000 deaths. There is no commercial GAS vaccine available. The GAS surface protein arginine deiminase (ADI) protects mice against a lethal challenge. ADI is an enzyme that converts arginine to citrulline and ammonia. Administration of a GAS vaccine preparation containing wild-type ADI, a protein with inherent enzymatic activity, may present a safety risk. In an approach intended to maximize the vaccine safety of GAS ADI, X-ray crystallography and structural immunogenic epitope mapping were used to inform vaccine design. This study aimed to knock out ADI enzyme activity without disrupting the three-dimensional structure or the recognition of immunogenic epitopes. We determined the crystal structure of ADI at 2.5 Å resolution and used it to select a number of amino acid residues for mutagenesis to alanine (D166, E220, H275, D277, and C401). Each mutant protein displayed abrogated activity, and three of the mutant proteins (those with the D166A, H275A, and D277A mutations) possessed a secondary structure and oligomerization state equivalent to those of the wild type, produced high-titer antisera, and avoided disruption of B-cell epitopes of ADI. In addition, antisera raised against the D166A and D277A mutant proteins bound to the GAS cell surface. The inactivated D166A and D277A mutant ADIs are ideal for inclusion in a GAS vaccine preparation. There is no human ortholog of ADI, and we confirm that despite limited structural similarity in the active-site region to human peptidyl ADI 4 (PAD4), ADI does not functionally mimic PAD4 and antiserum raised against GAS ADI does not recognize human PAD4.

IMPORTANCE
We present an example of structural biology informing human vaccine design. We previously showed that the administration of the enzyme arginine deiminase (ADI) to mice protected the mice against infection with multiple GAS serotypes. In this study, we determined the structure of GAS ADI and used this information to improve the vaccine safety of GAS ADI. Catalytically inactive mutant forms of ADI retained structure, recognition by antisera, and immunogenic epitopes, rendering them ideal for inclusion in GAS vaccine preparations. This example of structural biology informing vaccine design may underpin the formulation of a safe and efficacious GAS vaccine.
A systematic review of shockwave therapies in soft tissue conditions: focusing on the evidence
Authors: Speed Cathy 
Published: August 2013

Background‘Shock wave’ therapies are now extensively used in the treatment of musculoskeletal injuries. This systematic review summarises the evidence base for the use of these modalities.MethodsA thorough search of the literature was performed to identify studies of adequate quality to assess the evidence base for shockwave therapies on pain in specific soft tissue injuries. Both focused extracorporeal shockwave therapy (F-ESWT) and radial pulse therapy (RPT) were examined.Results23 appropriate studies were identified. There is evidence for the benefit of F-ESWT and of RPT in a number of soft tissue musculoskeletal conditions, and evidence that both treatment modalities are safe. There is evidence that F-ESWT is effective in the treatment of plantar fasciitis, calcific tendinitis, and that RPT is effective in plantar fasciitis. Where benefit is seen in F-ESWT, it appears to be dose dependent, with greater success seen with higher dose regimes. There is low level evidence for lack of benefit of low-dose F-ESWT and RPT in non-calcific rotator cuff disease and mixed evidence in lateral epicondylitis.
The predictive validity of a single leg bridge test for hamstring injuries in Australian Rules Football Players
Authors: Freckleton Grant , Cook Jill , Pizzari Tania 
Published: August 2013

BackgroundHamstring muscle strain injuries (HMSI) are the greatest injury problem in kicking sports such as Australian Rules Football. Reduced hamstring muscle strength is commonly perceived to be a risk factor for hamstring injury; however, evidence is inconclusive. Testing hamstring strength with the hip and knee at functional angles and assessing endurance parameters may be more relevant for examining the risk of hamstring injury.ObjectiveThe primary aim of this prospective study was to examine if reduced hamstring muscle strength assessed with the single leg hamstring bridge (SLHB) was a risk factor for hamstring injury.MethodsHamstring muscle strength of 482 amateur and semielite players from 16 football clubs, mean age 20.7 (range 16–34 years), was tested during the 2011 preseason. Players were then monitored throughout the 2011 playing season for HMSI.ResultsA total of 28 hamstring injuries, 16 right and 12 left, were recorded. Players who sustained a right HMSI during the season had a significantly lower mean right SLHB score (p=0.029), were older (p=0.002) and were more likely to have sustained a past right hamstring injury (p=0.02) or right knee injury (p=0.035). For left-sided hamstring injury, the injured group was more likely to be left leg dominant (p=0.001), older athletes (p=0.002) and there was a trend towards a history of left hamstring injury (p=0.07).ConclusionsThis study demonstrated a significant deficit in preseason SLHB scores on the right leg of players that subsequently sustained a right-sided hamstring injury. Age, previous knee injury and a history of hamstring injury were other risk factors supported in this study. Low hamstring strength appears to be a risk factor for hamstring injury; however, due to the confounding variables and low injury rate in this study, further studies are required.