bluuebunny/crossref_metadata_2025 huggingface dataset:
pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires
Authors: Vander Heiden Jason A. , Yaari Gur , Uduman Mohamed , Stern Joel N.H. , O’Connor Kevin C. , Hafler David A. , Vigneault Francois , Kleinstein Steven H.
Published: March 2014

Summary: Driven by dramatic technological improvements, large-scale characterization of lymphocyte receptor repertoires via high-throughput sequencing is now feasible. Although promising, the high germline and somatic diversity, especially of B-cell immunoglobulin repertoires, presents challenges for analysis requiring the development of specialized computational pipelines. We developed the REpertoire Sequencing TOolkit (pRESTO) for processing reads from high-throughput lymphocyte receptor studies. pRESTO processes raw sequences to produce error-corrected, sorted and annotated sequence sets, along with a wealth of metrics at each step. The toolkit supports multiplexed primer pools, single- or paired-end reads and emerging technologies that use single-molecule identifiers. pRESTO has been tested on data generated from Roche and Illumina platforms. It has a built-in capacity to parallelize the work between available processors and is able to efficiently process millions of sequences generated by typical high-throughput projects.

Availability and implementation: pRESTO is freely available for academic use. The software package and detailed tutorials may be downloaded from http://clip.med.yale.edu/presto .

Contact:  steven.kleinstein@yale.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
An adaptive workflow coupled with Random Forest algorithm to identify intact N-glycopeptides detected from mass spectrometry
Authors: Liang Suh-Yuen , Wu Sz-Wei , Pu Tsung-Hsien , Chang Fang-Yu , Khoo Kay-Hooi
Published: March 2014

Motivation: Despite many attempts for algorithm development in recent years, automated identification of intact glycopeptides from LC-MS 2 spectral data is still a challenge in both sensitivity and precision.

Results: We implemented a supervised machine learning algorithm, Random Forest, in an automated workflow to identify N-glycopeptides using spectral features derived from ion trap-based LC-MS 2 data. The workflow streamlined high-confident N-glycopeptide spectral data and enabled adaptive model optimization with respect to different sampling strategies, training sample size and feature set. A critical evaluation of the features important for glycopeptide identification further facilitated effective feature selection for model improvement. Using split sample testing method from 577 high-confident N-glycopeptide spectral data, we demonstrated that an optimal true-positive rate, precision and false-positive rate of 73, 88 and 10%, respectively, can be attained for overall N-glycopeptide identification

Availability and implementation: The workflow developed in this work and the application suite, Sweet-Heart, that the workflow supports for N-glycopeptide identification are available for download at http://sweet-heart.glycoproteomics.proteome.bc.sinica.edu.tw/ .

Contact:  syliang@gate.sinica.edu.tw or kkhoo@gate.sinica.edu.tw

Supplementary information:  Supplementary data are available at Bioinformatics online.
Genome-wide quantitative analysis of DNA methylation from bisulfite sequencing data
Authors: Akman Kemal , Haaf Thomas , Gravina Silvia , Vijg Jan , Tresch Achim
Published: March 2014

Summary: Here we present the open-source R/ Bioconductor software package BEAT (BS-Seq Epimutation Analysis Toolkit). It implements all bioinformatics steps required for the quantitative high-resolution analysis of DNA methylation patterns from bisulfite sequencing data, including the detection of regional epimutation events, i.e. loss or gain of DNA methylation at CG positions relative to a reference. Using a binomial mixture model, the BEAT package aggregates methylation counts per genomic position, thereby compensating for low coverage, incomplete conversion and sequencing errors.

Availability and implementation:  BEAT is freely available as part of Bioconductor at www.bioconductor.org/packages/devel/bioc/html/BEAT.html . The package is distributed under the GNU Lesser General Public License 3.0.

Contact:  akman@mpipz.mpg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Bilateral Hypersensitivity to Capsaicin, Thermal, and Mechanical Stimuli in Unilateral Complex Regional Pain Syndrome
Authors: Terkelsen Astrid J. , Gierthmühlen Janne , Finnerup Nanna B. , Højlund Anders P. , Jensen Troels S.
Published: March 2014

Background:

Complex regional pain syndrome is multifactorial. Exaggerated inflammatory responses to limb injury may be involved. The authors hypothesized that capsaicin-induced pain and neurogenic inflammation (skin perfusion and flare area) are increased in patients with complex regional pain syndrome compared with that in controls.

Methods:

Twenty patients with unilateral upper-limb complex regional pain syndrome and 20 age-, sex-, and body mass index–matched controls participated. Topical capsaicin 5% was applied to the back of both hands for 30 min, and pain intensity was assessed on a visual analogue scale. A laser Doppler perfusion imager scanner estimated capsaicin-induced skin perfusion and flare area. Autonomic and small-fiber function was assessed by sensory testing, quantitative sudomotor axon reflex test, and vasoconstrictor responses.

Results:

The authors found bilateral hypersensitivity to capsaicin (P ≤ 0.02), skin fold (P = 0.001), joint pressure (P < 0.0001), cold (P ≤ 0.01), and heat pain (P ≤ 0.04) in patients compared with that in controls and thermal and mechanical hyperalgesia in the complex regional pain syndrome–affected hand compared with that in the unaffected hand (P ≤ 0.001). The patients had normal capsaicin-induced flare areas, thermal detection thresholds, quantitative sudomotor axon reflex test, and vasoconstrictor responses.

Conclusions:

The main finding is bilaterally increased capsaicin-induced pain in patients compared with controls. The flare response to capsaicin was normal, suggesting that the increased pain response was not due to increased neurogenic inflammation. The bilateral hypersensitivity to painful chemical, thermal, and mechanical stimuli not confined to the innervation area of a peripheral nerve or root cannot be explained by a regional change and may partly be due to central sensitization.
Amphiphilic drug interactions with model cellular membranes are influenced by lipid chain-melting temperature
Authors: Casey Duncan , Charalambous Kalypso , Gee Antony , Law Robert V. , Ces Oscar
Published: March 2014

Small-molecule amphiphilic species such as many drug molecules frequently exhibit low-to-negligible aqueous solubility, and generally have no identified transport proteins assisting their distribution, yet are able to rapidly penetrate significant distances into patient tissue and even cross the blood–brain barrier. Previous work has identified a mechanism of translocation driven by acid-catalysed lipid hydrolysis of biological membranes, a process which is catalysed by the presence of cationic amphiphilic drug molecules. In this study, the interactions of raclopride, a model amphiphilic drug, were investigated with mixtures of biologically relevant lipids across a range of compositions, revealing the influence of the chain-melting temperature of the lipids upon the rate of acyl hydrolysis.
Modification of mean wake flow behind a very slender axisymmetric body of revolution by imposed nonlinear unstable helical modes
Authors: Lee Kiseok , Liu Joseph T. C.
Published: March 2014

For a sufficiently slender axially symmetric body placed in a uniform stream, only convectively unstable modes are found in previous experiments. This work imposes theoretically and computationally a pair of most unstable helical modes, symmetrically and asymmetrically. The Reynolds stress modification of the developing laminar mean wake flow is modified into an elliptic-like cross section for symmetrical forcing; the consequences of unequal upstream amplitudes are also explored. Energy-transfer mechanisms between the mean flow and the relevant dominant modes and between the modes through ‘triad interactions’ are studied. The results from dynamical considerations provide the physical understanding of the generation of a standing wave mode at twice the azimuthal wavenumber; it is necessary that the wave envelopes of participating modes, including that of the mean flow, overlap in their spatial development, which is a necessary supplement to kinematical conditions for such interactions to take place effectively. Standing wave motions, which are otherwise only found naturally in wakes behind blunt-trailing-edge axisymmetric bodies, can be rendered present through appropriate forcing and nonlinear interactions behind very slender axisymmetric bodies.
Micropolar continuum modelling of bi-dimensional tetrachiral lattices
Authors: Chen Y. , Liu X. N. , Hu G. K. , Sun Q. P. , Zheng Q. S.
Published: March 2014

The in-plane behaviour of tetrachiral lattices should be characterized by bi-dimensional orthotropic material owing to the existence of two orthogonal axes of rotational symmetry. Moreover, the constitutive model must also represent the chirality inherent in the lattices. To this end, a bi-dimensional orthotropic chiral micropolar model is developed based on the theory of irreducible orthogonal tensor decomposition. The obtained constitutive tensors display a hierarchy structure depending on the symmetry of the underlying microstructure. Eight additional material constants, in addition to five for the hemitropic case, are introduced to characterize the anisotropy under
Z
2
invariance. The developed continuum model is then applied to a tetrachiral lattice, and the material constants of the continuum model are analytically derived by a homogenization process. By comparing with numerical simulations for the discrete lattice, it is found that the proposed continuum model can correctly characterize the static and wave properties of the tetrachiral lattice.
Characterization of an in-vacuum PILATUS 1M detector
Authors: Wernecke Jan , Gollwitzer Christian , Müller Peter , Krumrey Michael
Published: March 2014

A dedicated in-vacuum X-ray detector based on the hybrid pixel PILATUS 1M detector has been installed at the four-crystal monochromator beamline of the PTB at the electron storage ring BESSY II in Berlin, Germany. Owing to its windowless operation, the detector can be used in the entire photon energy range of the beamline from 10 keV down to 1.75 keV for small-angle X-ray scattering (SAXS) experiments and anomalous SAXS at absorption edges of light elements. The radiometric and geometric properties of the detector such as quantum efficiency, pixel pitch and module alignment have been determined with low uncertainties. The first grazing-incidence SAXS results demonstrate the superior resolution in momentum transfer achievable at low photon energies.
Case of vemurafenib‐induced Sweet's syndrome
Authors: Yorio Jeffrey T. , Mays Steven R. , Ciurea Ana M. , Cohen Philip R. , Wang Wei‐Lien , Hwu Wen‐Jen , Gonzalez Nydia , Richard Jessica L. , Kim Kevin B.
Published: March 2014

Vemurafenib is a targeted therapy that has become standard treatment for patients with advanced melanoma with a V600E BRAF mutation. It has been associated with frequent skin toxicity, including photosensitivity, rash and squamous cell carcinomas. We present an 83‐year‐old woman with an advanced V600E BRAF‐mutant melanoma who developed a severe skin rash and fatigue after taking vemurafenib. The dose was reduced from 960 to 720 to 480 mg twice a day; however, she was subsequently admitted to the hospital with fever, chills, fatigue, confusion and a diffuse skin eruption. She then developed hypoxia and acute renal failure that required hemodialysis. A biopsy of her skin lesions revealed a neutrophilic dermatitis with papillary dermal edema, consistent with Sweet's syndrome. Her symptoms resolved upon discontinuation of vemurafenib and treatment with prednisone. This constellation of symptoms and clinical course are consistent with drug‐induced Sweet's syndrome caused by vemurafenib.
Variants in melanogenesis‐related genes associate with skin cancer risk among Japanese populations
Authors: Yoshizawa Junko , Abe Yuko , Oiso Naoki , Fukai Kazuyoshi , Hozumi Yutaka , Nakamura Tomohiro , Narita Tomohiko , Motokawa Tomonori , Wakamatsu Kazumasa , Ito Shosuke , Kawada Akira , Tamiya Gen , Suzuki Tamio
Published: March 2014

Human skin color is known to be associated with the risk of cutaneous cancer. Some reports indicated that pigmentation‐related gene variants were associated with cutaneous cancer risk in Caucasian populations, but there are no similar reports in East Asian populations. This study aimed to evaluate the association between pigmentation‐related genes and the risk of skin cancer in Japanese populations. We studied the associations between 12 variants of four pigmentation‐related genes and melanin index variations in 198 Japanese patients with skin cancer and compared these findings to those of 500 Japanese controls by using multiple logistic regression analysis. Furthermore, we analyzed an independent sample of 107 Japanese patients with skin cancer. A non‐synonymous variant, H615R in the oculocutaneous albinism 2 gene (OCA2), was associated with the risk of malignant melanoma in the Yamagata group (odds ratio [OR], 0.38; 95% confidence interval [CI], 0.17–0.86; P = 0.020). Another non‐synonymous variant, A481T in OCA2, was associated with the risk of squamous cell carcinoma and actinic keratosis in the Osaka group (OR, 3.16; 95% CI, 1.41–7.04; P = 0.005). In malignant melanoma cases, the minor allele in OCA2 H615R might have induced the development of lesions in sun‐exposed skin (OR, 26.32; 95% CI, 1.96–333; P = 0.014). Our results suggest that some OCA2 variants are definite risk factors for the onset of cutaneous cancer in Japanese populations.
Tritrophic interactions between parasitoids and cereal aphids are mediated by nitrogen fertilizer
Authors: Aqueel Muhammad A. , Raza Abu‐bakar M. , Balal Rashad M. , Shahid Muhammad A. , Mustafa Irfan , Javaid Muhammad M. , Leather Simon R.
Published: March 2014

Host plant nutritional quality can directly and indirectly affect the third trophic levels. The aphid–parasitoid relationship provides an ideal system to investigate tritrophic interactions (as the parasitoids are completely dependent for their development upon their hosts) and assess the bottom up forces operating at different concentrations of nitrogen applications. The effects of varying nitrogen fertilizer on the performance of Aphidius colemani (V.) reared on Sitobion avenae (F.) and Aphidius rhopalosiphi (D.) reared on Rhopalosiphum padi (L.) were measured. Parasitism and percent emergence of parasitoids were positively affected by nitrogen fertilizer treatments while developmental duration (egg, larval, and pupal stages) was not affected by increasing nitrogen inputs. In males and females of both parasitoid species, adult longevity increased with the increasing nitrogen fertilizer. Hind tibia length and mummy weight of both parasitoid species increased with nitrogen fertilizer concentrations, as a result of larger aphids. This study showed that nitrogen application to the soil can have important consequences for aboveground multitrophic interactions.
Preparation of Chitosan–TPP Microspheres as Resveratrol Carriers
Authors: Cho Ah Ra , Chun Yong Gi , Kim Bum Keun , Park Dong June
Published: March 2014

Resveratrol (3,4′,5‐trihydroxy‐trans‐stilbene)‐loaded chitosan–sodium tripolyphosphate (TPP) microspheres using high (310 to 375 kDa) and medium (190 to 310 kDa) molecular weight chitosan and TPP in varying concentrations were produced to improve resveratrol bioavailability. A 450 μm nozzle encapsulator was used to produce the microspheres. The mean microsphere particle size was between 160 and 206 μm, and exhibited a narrower size distribution as the TPP solution concentration increased. The encapsulation efficiency increased from 94% to 99% with a decrease in chitosan concentration from 1% to 0.5% and a decrease in crystallinity of the microspheres. FTIR data showed a polyelectrolyte interaction between chitosan and TPP. X‐ray diffraction patterns were matched up with DSC and FTIR, which shows decrease of crystallinity and enhancement of hydrogen bonding with TPP concentration. An increase in the concentration of TPP solution from 1% to 3% led to a lower initial burst of resveratrol release. These results suggest that chitosan–TPP microspheres could be used as a potential delivery system to control the release of resveratrol.
Diet Effects in Gut Microbiome and Obesity
Authors: Chen Jia , He Xianzhi , Huang Jinhai
Published: March 2014

The 100 trillion microbes in human gut coevolve with the host and exert significant influences on human health. The gut microbial composition presents dynamic changes correlated with various factors including host genotypes, age, and external environment. Effective manipulation of the gut microbiota through diets (both long‐term and short‐term diet patterns), probiotics and/or prebiotics, and antibiotics has been proved being potential to prevent from metabolic disorders such as obesity in many studies. The dietary regulation exerts influences on microbial metabolism and host immune functions through several pathways, of which may include selectively bacterial fermentation of nutrients, lower intestinal barrier function, overexpression of genes associated with disorders, and disruptions to both innate and adaptive immunity. Discoveries in the interrelationship between diet, intestinal microbiome, and body immune system provide us novel perceptions to the specific action mechanisms and will promote the development of therapeutic approaches for obesity.
Ham Particle Size Influences Saltiness Perception in Flans
Authors: Emorine M. , Septier C. , Thomas‐Danguin T. , Salles C.
Published: March 2014

One major issue of the food industry is reducing sodium content while maintaining food acceptability and liking. Despite extensive research in this field, little has been published on real complex food products. The aim of this study was to investigate whether the size of particles, a parameter easily adjusted in food processing, could influence the salty taste of low‐salt food product. We thus evaluated the effect of ham particle sizes (4 levels, including a zero level) on salt perception and the consumer liking of flans varying in their overall salt concentrations (low‐ and high‐salt content). Two consumer panels, composed of 107 and 77 subjects, rated, respectively, the saltiness of and liking for the developed flans (8 samples). The outcomes of this study indicated first, that the addition of ham to flans increased the salty taste perception and second, that a decrease in ham particle size (ground ham) increased the perceived saltiness. Moreover, low‐ and high‐salt flans were equally liked, demonstrating that food manufacturers could reduce the salt contents (here, by over 15%) while maintaining consumer acceptability through the manipulation of the size of the salt‐providing particles.
Detection of C. Botulinum Types in Honey by mPCR
Authors: Gücükoğlu Ali , Terzi Göknur , Çadirci Özgür , Alişarli Mustafa , Kevenk Onur , Uyanik Tolga
Published: March 2014

The aim of this study was to determine the prevalence of Clostridium botulinum in honey samples using conventional methods and multiplex PCR (mPCR). A total number of 150 honey samples were randomly collected from apiaries, retail shops, weekly open bazaars, and supermarkets in Samsun, Turkey. Of 150 honey samples, 4 (2.6%) were positive for the botulinum neurotoxin gene by mPCR analysis. A total of 4 C. botulinum isolates were obtained from the mPCR positive samples, of which 3 were type A and 1 was type B. No samples were positive regarding the type E and type F neurotoxin genes. This is the first report of type A and type B spores of C. botulinum being detected and isolated in Turkey. This study revealed that some honey samples may present a potential hazard for food borne and infant botulism.
Phenolic Compounds and Antioxidant Capacities of 10 Common Edible Flowers from China
Authors: Xiong Lina , Yang Jiajia , Jiang Yirong , Lu Baiyi , Hu Yinzhou , Zhou Fei , Mao Shuqin , Shen Canxi
Published: March 2014

The free and bound phenolic compounds in 10 common Chinese edible flowers were investigated using reversed phase high‐performance liquid chromatography. Their antioxidant capacities were evaluated using 2,2‐diphenyl‐1‐picrylhydrazyl (DPPH) radical‐scavenging activity, 2,2'‐azino‐bis(3‐ethylbenzothiazoline‐6‐sulphonic acid) (ABTS) radical‐scavenging activity, oxygen radical absorption capacity (ORAC), ferric reducing antioxidant power (FRAP), and cellular antioxidant activity (CAA). Free factions were more prominent in phenolic content and antioxidant capacity than bound fractions. Paeonia suffruticosa and Flos lonicerae showed the highest total phenolic content (TPC) 235.5 mg chlorogenic acid equivalents/g of dry weight and total flavonoid content 89.38 mg rutin equivalents/g of dry weight. The major phenolic compounds identified were gallic acid, chlorogenic acid, and rutin. P. suffruticosa had the highest antioxidant capacity in the DPPH, ABTS, and ORAC assays, which were 1028, 2065, 990 μmol Trolox equivalents/g of dry weight, respectively, whereas Rosa chinensis had the highest FRAP value (2645 μmol Fe2+ equivalents /g of dry weight). The P. suffruticosa soluble phenolics had the highest CAA, with the median effective dose (EC50) 26.7 and 153 μmol quercetin equivalents/100 g of dry weight in the phosphate buffered saline (PBS) and no PBS wash protocol, respectively. TPC was strongly correlated with antioxidant capacity (R = 0.8443 to 0.9978, P < 0.01), which indicated that phenolics were the major contributors to the antioxidant activity of the selected edible flowers.
A Fast and Validated Method for the Determination of Malondialdehyde in Fish Liver Using High‐Performance Liquid Chromatography with a Photodiode Array Detector
Authors: Faizan Mohammad , Esatbeyoglu Tuba , Bayram Banu , Rimbach Gerald
Published: March 2014

Malondialdehyde (MDA) is a biomarker of lipid peroxidation and is present in foods and biological samples such as plasma. A high‐performance liquid chromatography (HPLC) method was applied to determine MDA in fish liver samples after derivatization with 2,4‐dinitrophenylhydrazine (DNPH) using a ODS2 column (10 cm × 4.6 mm, 3 μm) and a photodiode array detector. The mobile phase consisted of 0.2% acetic acid (v/v) in distilled water and acetonitrile (42:58, v/v). The present method was validated in terms of linearity, lower limit of quantification, lower limit of detection, precision, accuracy, recovery, and stability of MDA according to U.S. Food and Drug Administration (FDA) guidelines. The limit of quantification of MDA was 0.39 μmol/L, which is comparable to other methods. The recovery of the spiked MDA liver samples was in the range of 92.4% to 104.2%. This newly modified HPLC method is specific, sensitive, and accurate and allows the analysis of MDA within 4 min in fish liver but also in other tissues and plasma.
Molecular Identification of Microbial Community in Surface and Undersurface Douchi During Postfermentation
Authors: Chen Tingtao , Wang Mengjuan , Li Shengjie , Wu Qinglong , Wei Hua
Published: March 2014

To find the reason for fermentation failure of surface Douchi during postfermentation, the microbial communities in undersurface and surface samples were investigated using cell counting method and denaturing gradient gel electrophoresis (DGGE). The results showed that the microbial biomass in surface Douchi was obviously different from that in undersurface Douchi even sampled from the same fermentation tanks, and a 10‐ to 100‐fold reduction of microbial cell counts in undersurface had been observed. The bacterial DGGE profile and principal component analysis (PCA) results indicated that only Lactococcus lacts subsp. lactis and Bacillus thermoamylovorans were detected from surface Douchi, while Lactococcus lacts subsp. lactis, Staphylococcus lentus and 2 uncultured strains occupied the dominant positions in undersurface Douchi; when amplified using Bacillus‐specific primers, Bacillus thermoamylovorans, Bacillus subtilis, and Enterobacter sp. were found in undersurface Douchi, while only Bacillus thermoamylovorans were detected from surface Douchi; compared to the bacteria and Bacillus, the DGGE profiles and PCA plot of fungi indicated that the fungal community between surface and undersurface Douchi was similar and mainly composed by yeasts. In this study, we detected the microbial biomass and species in postfermentation stage of Douchi, and the various microbial diversity in undersurface and surface samples might be the cause of the fermentation failure in surface fermentation tanks.
Modeling and Forecasting Realized Volatilities of Korean Financial Assets Featuring Long Memory and Asymmetry
Authors: Park Soyoung , Shin Dong W.
Published: March 2014

Long memory, asymmetry, volatility spillover aspects of the realized volatilities (RVs) of the log returns of the Korean KOSPI, the Korean won/US dollar exchange rate, Korean treasury bond futures, and the US S&P 500 index are investigated in this paper. For all RVs, significant long memories and asymmetries are identified, which can improve forecasts if suitably used. A new long memory asymmetric threshold HAR‐RV (heteroskedastic autoregressive realized volatility) model is proposed. The new model shows explicit differences between the coefficients of daily, weekly, and monthly RVs for days of positive returns and those for days of negative returns. By analyzing the RVs, we find that pseudo out‐of‐sample forecast performance of the proposed model is better than a widely used existing asymmetric long memory model in about half of cases considered. The new model as well as another existing asymmetric model show that forecast improvements due to implied volatilities for the S&P 500 index decrease when asymmetries in RVs are accounted for. The two asymmetric models find significant decompositions of the spillover effects from the influential market S&P 500 index to the influenced market KOSPI (or from the KOSPI to the Korean won/US dollar exchange rate) into three oscillating components: substantial positive short‐term daily spillovers, moderate negative weekly spillovers, and somewhat positive long‐term monthly spillovers.
Individuals’ Return Predictability in Market and Limit Trades
Authors: Lee Hyo‐Jeong , Choe Hyuk
Published: March 2014

This paper studies individuals’ return predictability and its economic sources for each trade type using a long‐period database containing detailed information of every transaction on the Korea Stock Exchange. Both market and limit trades of individual investors have short‐horizon return predictability. Return predictability in limit trades is related to compensation for liquidity provision, but that in market trades seems to be given for private information and be amplified by the serially correlated trading of individual investor groups. The return predictability of individuals’ total trades is economically insignificant, implying that individuals’ return predictability is not a special anomaly refuting market efficiency.
Influence of Common Mucosal Co‐Factors on HIV Infection in the Female Genital Tract
Authors: Ferreira Victor H. , Kafka Jessica K. , Kaushic Charu
Published: March 2014

Women constitute almost half of HIV‐infected population globally, and the female genital tract (FGT) accounts for approximately 40% of all new HIV infections worldwide. The FGT is composed of upper and lower parts, distinct in their morphological and functional characteristics. Co‐factors in the genital microenvironment, such as presence of hormones, semen, and other sexually transmitted infections, can facilitate or deter HIV infection and play a critical role in determining susceptibility to HIV. In this review, we examine some of these co‐factors and their potential influence. Presence of physical and chemical barriers such as epithelial tight junctions, mucus, and anti‐microbial peptides can actively block and inhibit viral replication, presenting a significant deterrent to HIV. Upon exposure, HIV and other pathogens first encounter the genital epithelium: cells that express a wide repertoire of pattern recognition receptors that can recognize and directly initiate innate immune responses. These and other interactions in the genital tract can lead to direct and indirect inflammation and enhance the number of local target cells, immune activation, and microbial translocation, all of which promote HIV infection and replication. Better understanding of the dynamics of HIV transmission in the female genital tract would be invaluable for improving the design of prophylactic strategies against HIV.
Ochre fingerprints: Distinguishing among Malawian mineral pigment sources with Homogenized Ochre Chip LA–ICPMS
Authors: Zipkin A. M. , Hanchar J. M. , Brooks A. S. , Grabowski M. W. , Thompson J. C. , Gomani‐Chindebvu E.
Published: March 2014

In this study, we compared the effectiveness of instrumental neutron activation analysis (INAA) of bulk ochre to laser ablation‐inductively coupled plasma mass spectrometry of homogenized ochre chips (HOC LA–ICPMS) at distinguishing among three ochre sources in northern Malawi. Both techniques upheld the Provenance Postulate; however, HOC LA–ICPMS required less sample material than INAA and facilitated fast, inexpensive replicate observations that allowed for more robust statistical analysis. Our results indicated that HOC LA–ICPMS is a maturing technique that will be a valuable option for analysing artefacts that require minimally destructive sampling but are too large to fit into the laser cell for direct ablation. With regard to the statistical procedures used, stepwise canonical discriminant analysis was demonstrated to be a highly effective method for distinguishing among ochre sources, even in the presence of significant intra‐source and intra‐sample heterogeneity. Continued development of the HOC sample preparation technique will expand the range of archaeological ochre artefacts that can be included in provenance studies and prevent bias towards artefacts of convenient‐to‐analyse dimensions.
A multicentre phase II study of vorinostat in patients with relapsed or refractory indolent B‐cell non‐Hodgkin lymphoma and mantle cell lymphoma
Authors: Ogura Michinori , Ando Kiyoshi , Suzuki Tatsuya , Ishizawa Kenichi , Oh Sung Yong , Itoh Kuniaki , Yamamoto Kazuhito , Au Wing Yan , Tien Hwei‐Fang , Matsuno Yoshihiro , Terauchi Takashi , Yamamoto Keiko , Mori Masahiko , Tanaka Yoshinobu , Shimamoto Takashi , Tobinai Kensei , Kim Won Seog
Published: March 2014

Although initial rituximab‐containing chemotherapies achieve high response rates, indolent B‐cell non‐Hodgkin lymphoma (B‐NHL), such as follicular lymphoma (FL), is still incurable. Therefore, new effective agents with novel mechanisms are anticipated. In this multicentre phase II study, patients with relapsed/refractory indolent B‐NHL and mantle cell lymphoma (MCL) received vorinostat 200 mg twice daily for 14 consecutive days in a 21‐d cycle until disease progression or unacceptable toxicity occurred. The primary endpoint was overall response rate (ORR) in FL patients and safety and tolerability in all patients. Secondary endpoints included progression‐free survival (PFS). Fifty‐six eligible patients were enrolled; 50 patients (39 with FL, seven with other B‐NHL, and four with MCL) were evaluable for ORR, and 40 patients had received rituximab‐containing prior chemotherapeutic regimens. For the 39 patients with FL, the ORR was 49% [95% confidence interval (CI): 32·4, 65·2] and the median PFS was 20 months (95% CI: 11·2, 29·7). Major toxicities were manageable grade 3/4 thrombocytopenia and neutropenia. Vorinostat offers sustained antitumour activity in patients with relapsed or refractory FL with an acceptable safety profile. Further investigation of vorinostat for clinical efficacy is warranted.
Developing outcome measures for a Family Intensive Support Service for Children presenting with challenging behaviours
Authors: Mulligan Bethany , John Mary , Coombes Rachel , Singh Rosemary
Published: March 2014

Accessible summary

Services should give support to the whole family who live with a child with a learning disability.

The aim of this study was to understand how helpful a family support service is in reducing challenging behaviour in children with learning disabilities.

We did this by looking at the outcome measures they already use.

We wanted to find out how good they are at measuring change.

We found that

The Family Intensive Support Service (FISS) reduced challenging behaviour in children and increased parent's ability to cope with and manage challenging behaviour.

Outcome measures used by the FISS team were good at showing change.

Seven per cent of individuals with learning disabilities also display challenging behaviour (Challenging behaviour: analysis and intervention in people with severe intellectual disabilities, 2001, Cambridge, Cambridge University Press), which has an effect on the whole family. Services need to be developed to support and reflect this need (Better health, better lives: children and young people with intellectual disabilities and their families, 2010, Romania, Bucherest). This is a retrospective pre‐ and postevaluation study examining the utility of specific outcome measures assessing the effectiveness of interventions addressing behavioural problems within a Family Intensive Support Service (FISS). After one year, FISS successfully reduced problematic behaviours and increased a sense of coping and ability to manage the behaviour for parents. The outcome measures used were sensitive enough to show change on specific subscales of the measure. Further research is needed to look at whether there is a need to create a new measure encapsulating the best elements of these measures.
Toward a standard stratigraphical classification practice for the Baltic Sea sediments: the CUAL approach
Authors: Virtasalo Joonas J. , Hämäläinen Jyrki , Kotilainen Aarno T.
Published: March 2014

The Late Pleistocene and Holocene glacial and postglacial sediments of the Baltic Sea basin are conventionally classified into units according to the so‐called Baltic Sea stages: Baltic Ice Lake, Yoldia Sea, Ancylus Lake and Litorina Sea. The Baltic Sea stages have been identified in offshore sediment cores by fundamentally different criteria, precluding detailed comparisons of the sediment units amongst different sea areas and studies. Here, long sediment cores and reflection seismic and pinger sub‐bottom profiles were studied from an offshore area in the Gulf of Finland, northern Baltic Sea. The strata are divided on the basis of sedimentological criteria into three allostratigraphical formations with subordinate allostratigraphical members and lithostratigraphical formations, following the combined allostratigraphical and lithostratigraphical (CUAL) approach. Sedimentological features are recommended as the primary stratigraphical classification criteria because they do not require the palaeoenvironmental inferences of salinity and water level that are inherent in the conventional classification practice. The presented stratigraphical division is proposed as a flexible template for future stratigraphical work on the Baltic Sea basin, whereby lower‐rank allounits and lithounits can be included and removed locally, while the alloformations will remain at the highest hierarchical level and guarantee regional correlatability. The stratigraphical division is compatible with international guidelines, facilitating communication to the wider scientific community and comparison with other similar basins.
The ecophysiology of seed persistence: a mechanistic view of the journey to germination or demise
Authors: Long Rowena L. , Gorecki Marta J. , Renton Michael , Scott John K. , Colville Louise , Goggin Danica E. , Commander Lucy E. , Westcott David A. , Cherry Hillary , Finch‐Savage William E.
Published: March 2014

Seed persistence is the survival of seeds in the environment once they have reached maturity. Seed persistence allows a species, population or genotype to survive long after the death of parent plants, thus distributing genetic diversity through time. The ability to predict seed persistence accurately is critical to inform long‐term weed management and flora rehabilitation programs, as well as to allow a greater understanding of plant community dynamics. Indeed, each of the 420000 seed‐bearing plant species has a unique set of seed characteristics that determine its propensity to develop a persistent soil seed bank. The duration of seed persistence varies among species and populations, and depends on the physical and physiological characteristics of seeds and how they are affected by the biotic and abiotic environment. An integrated understanding of the ecophysiological mechanisms of seed persistence is essential if we are to improve our ability to predict how long seeds can survive in soils, both now and under future climatic conditions. In this review we present an holistic overview of the seed, species, climate, soil, and other site factors that contribute mechanistically to seed persistence, incorporating physiological, biochemical and ecological perspectives. We focus on current knowledge of the seed and species traits that influence seed longevity under ex situ controlled storage conditions, and explore how this inherent longevity is moderated by changeable biotic and abiotic conditions in situ, both before and after seeds are dispersed. We argue that the persistence of a given seed population in any environment depends on its resistance to exiting the seed bank via germination or death, and on its exposure to environmental conditions that are conducive to those fates. By synthesising knowledge of how the environment affects seeds to determine when and how they leave the soil seed bank into a resistance–exposure model, we provide a new framework for developing experimental and modelling approaches to predict how long seeds will persist in a range of environments.
Nucleocytoplasmic protein translocation during mitosis in the social amoebozoan Dictyostelium discoideum
Authors: O'Day Danton H. , Budniak Aldona
Published: March 2014

Mitosis is a fundamental and essential life process. It underlies the duplication and survival of all cells and, as a result, all eukaryotic organisms. Since uncontrolled mitosis is a dreaded component of many cancers, a full understanding of the process is critical. Evolution has led to the existence of three types of mitosis: closed, open, and semi‐open. The significance of these different mitotic species, how they can lead to a full understanding of the critical events that underlie the asexual duplication of all cells, and how they may generate new insights into controlling unregulated cell division remains to be determined. The eukaryotic microbe Dictyostelium discoideum has proved to be a valuable biomedical model organism. While it appears to utilize closed mitosis, a review of the literature suggests that it possesses a form of mitosis that lies in the middle between truly open and fully closed mitosis—it utilizes a form of semi‐open mitosis. Here, the nucleocytoplasmic translocation patterns of the proteins that have been studied during mitosis in the social amoebozoan D. discoideum are detailed followed by a discussion of how some of them provide support for the hypothesis of semi‐open mitosis.
LABOR MARKET IMPACTS OF SMOKING REGULATIONS ON THE RESTAURANT INDUSTRY
Authors: GURLEY‐CALVEZ TAMI , HAMMOND GEORGE W. , CHILDS RANDALL A.
Published: March 2014

This paper examines the impact of smoking regulations on restaurant employment in West Virginia, a state with a high rate of smoking prevalence. Using a confidential establishment‐level dataset, our results suggest that smoking bans reduced restaurant employment by between 0.7 and 1.5 workers, depending on model specification. We find that smoking restrictions have heterogeneous impacts across establishments, with the largest impacts on mid‐sized establishments, defined as those with 10–29 employees. Our results also suggest that the impact of smoking restrictions was larger in counties with higher rates of smoking prevalence. (JELL51, D78, H0)
Pigmented extramammary Paget disease of the thigh mimicking a melanocytic tumor: report of a case and review of the literature
Authors: De la Garza Bravo Maria M. , Curry Jonathan L. , Torres‐Cabala Carlos A. , Ivan Doina S. , Drucker Carol , Prieto Victor G. , Tetzlaff Michael T.
Published: March 2014

Importance

Extramammary Paget disease (EMPD) is an uncommon tumor that presents in apocrine‐rich skin as an irregular, pruritic plaque. Histopathologically, EMPD consists of an intraepidermal proliferation of atypical epithelioid cells. Rarely, the tumor cells contain intracytoplasmic melanin pigment, and the lesion clinically and histopathologically can mimic a melanocytic proliferation.

Observations

A 51‐year‐old female with a history of breast carcinoma presented with a pigmented patch on her right thigh of 6 months duration. The clinical impression was an atypical melanocytic nevus. Histopathologic examination revealed an intraepidermal proliferation of epithelioid cells along the dermal–epidermal junction with pagetoid migration. The tumor cells exhibited increased cytoplasm containing conspicuous melanin pigment and enlarged oval‐irregular nuclei. Immunohistochemical studies showed the tumor cells to be strongly and diffusely positive for cytokeratin 8/18, cytokeratin 7 and p63; focally and weakly positive for epithelial membrane antigen (EMA), but negative for cytokeratin 5/6, Cam5.2, carcinoembryonic antigen (CEA), human melanoma black 45 (HMB‐45), tyrosinase and Sox‐10, supporting the diagnosis of pigmented EMPD. The lesion was subsequently excised, and the patient is free of disease after 24 months.

Conclusion

We present this unusual case of pigmented EMPD arising on the thigh to draw attention to the entity and to underscore the potentially misleading clinical, histopathologic and immunophenotypic features that mimic other cutaneous intraepidermal lesions.
Extramedullary acute leukemia developing in a pre‐existing osteoma cutis
Authors: Wang Jian‐Feng , O'Malley Dennis P.
Published: March 2014

Primary osteoma cutis (cutaneous ossification) is an uncommon disease in which there is bone formation within the skin in the absence of a demonstrable pre‐existing condition. Osteoma cutis is a chronic and benign condition. We report a case of a 45‐year‐old man who developed extramedullary acute leukemia with a myeloid immunophenotype (myeloid sarcoma) with its initial presentation within an isolated pre‐existing osteoma cutis in the post‐auricular scalp without evidence of systemic acute leukemia or chronic myeloid stem cell disorders. The tumor was surgically excised without complications. Four months later, acute leukemia recurred in the contralateral posterior mandible and showed an immunophenotype consistent with acute lymphoblastic leukemia/lymphoma. The patient now has been treated by standard protocols for acute leukemia. The diagnosis of an extramedullary acute leukemia is challenging because of its inconsistent clinical and histopathologic presentations. Extramedullary acute leukemia developing in a pre‐existing osteoma cutis is very unusual and has not been previously reported in the literature.
Metamorphic labral axis patterning in the beetle Tribolium castaneum requires multiple upstream, but few downstream, genes in the appendage patterning network
Authors: Smith Frank W. , Angelini David R. , Gaudio Matthew S. , Jockusch Elizabeth L.
Published: March 2014

The arthropod labrum is an anterior appendage‐like structure that forms the dorsal side of the preoral cavity. Conflicting interpretations of fossil, nervous system, and developmental data have led to a proliferation of scenarios for labral evolution. The best supported hypothesis is that the labrum is a novel structure that shares development with appendages as a result of co‐option. Here, we use RNA interference in the red flour beetle Tribolium castaneum to compare metamorphic patterning of the labrum to previously published data on ventral appendage patterning. As expected under the co‐option hypothesis, depletion of several genes resulted in similar defects in the labrum and ventral appendages. These include proximal deletions and proximal‐to‐distal transformations resulting from depletion of the leg gap genes homothorax and extradenticle, large‐scale deletions resulting from depletion of the leg gap gene Distal‐less, and smaller distal deletions resulting from knockdown of the EGF ligand Keren. However, depletion of dachshund and many of the genes that function downstream of the leg gap genes in the ventral appendages had either subtle or no effects on labral axis patterning. This pattern of partial similarity suggests that upstream genes act through different downstream targets in the labrum. We also discovered that many appendage axis patterning genes have roles in patterning the epipharyngeal sensillum array, suggesting that they have become integrated into a novel regulatory network. These genes include Notch, Delta, and decapentaplegic, and the transcription factors abrupt, bric à brac, homothorax, extradenticle and the paralogs apterous a and apterous b.
Ontogenetic allometry in the thoracolumbar spine of mammal species with differing gait use
Authors: Jones Katrina E. , German Rebecca Z.
Published: March 2014

Vertebrae are serially homologous structures with tight integration through their evolution and development. However, in mammals, the thoracic and lumbar regions are morphologically and functionally differentiated. We test the hypothesis that locomotor specialization is associated with altered post‐natal growth patterns in vertebrae from different vertebral regions. We use longitudinal data to examine thoracolumbar growth in two specialized half‐bounding (Oryctolagus cuniculusandChinchilla lanigera) and two non‐specialized (Cavia porcellusandMonodelphis domestica) species with similar body sizes. Lateral X‐rays of 38 individuals were the source of centrum length, centrum height and intervertebral space length measures for 19–20 thoracolumbar vertebrae. The repeated measurements design included the same individuals soon after birth and again at adult size. Data from columns with different vertebral counts were compared by either summing (length) or averaging (height) within regions, and individual vertebrae were directly compared at the first and last five vertebral positions. Specialized half‐bounders had longer lumbar regions than generalists, which was attributable to positively allometric growth of the lumbar centra. Lumbar centrum length was more variable both ontogenetically and interspecifically than the other variables, suggesting heterochrony may be generating lumbar variation. Craniocaudal patterns of centrum growth correlate with expression of regionalizing genes (i.e.,Hox).
Temporary preservation of avulsed tooth in oral submucosal tissue: an experimental study in cat
Authors: Jamalpour Mohammad Reza , Soltanian Ali Reza , Tootunchi Amir Sasan , Roshanipaian Milad
Published: March 2014

Objective

The purpose of this study was to determine the ability of oral submucosal tissue to serve as a temporary storage medium for the maintenance of periodontal ligament (PDL) cell viability of avulsed teeth.

Materials and methods

Thirty cats were divided into five groups. After extraction of three teeth in each cat, one tooth was put in the depth of cat's oral submucosal tissue and the other two teeth were put in Hanks’ balanced salt solution (HBSS) and tap water. The teeth were removed after 8, 24, 48, 72, and 168 h from their mediums and sent for laboratory processing and counting of vital periodontal cells.

Results

Statistical analysis demonstrated that submucosal tissue kept PDL cells viable as good as HBSS.

Conclusion

This animal study showed that the efficacy of oral submucosal tissue in maintaining the viability of human PDL cells is similar to that of HBSS.