bluuebunny/crossref_metadata_2025 huggingface dataset:
The Competitive Advantage of a Dual-Transporter System
Authors: Levy Sagi , Kafri Moshe , Carmi Miri , Barkai Naama
Published: December 2011

Low-affinity nutrient transporters sense depletion earlier than high-affinity transporters, thus preparing cells for starvation.
Robert-Jan Smits: On Tearing Down Silos, Horizon 2020's Chances, and Solving His 'Headache'
Authors: Clery Daniel
Published: December 2011

Last week,
Science
talked with one of the architects of the Horizon 2020 research program: the European Union's director-general for research, Robert-Jan Smits.
First Solid Signs of the Higgs Boson Could Be Announced Next Week
Authors: Cho Adrian
Published: December 2011

Given the amount of data the Large Hadron Collider has produced in 2 years of running, some physicists say that—if it's there—the Higgs boson should begin to emerge from "background" particle collisions.
HALTING HIV/AIDS Epidemics
Authors: Cohen Jon
Published: December 2011

A slew of successes in clinical trials has elated the HIV prevention field, and models now suggest that combining them might virtually stop HIV's spread. But caveats abound.
Development of a Fluorescent Microsphere Immunoassay for Detection of Antibodies against Porcine Reproductive and Respiratory Syndrome Virus Using Oral Fluid Samples as an Alternative to Serum-Based Assays
Authors: Langenhorst Robert J. , Lawson Steven , Kittawornrat Apisit , Zimmerman Jeffrey J. , Sun Zhi , Li Yanhua , Christopher-Hennings Jane , Nelson Eric A. , Fang Ying
Published: December 2011

For effective disease surveillance, rapid and sensitive assays are needed to detect antibodies developed in response to porcine reproductive and respiratory syndrome virus (PRRSV) infection. In this study, we developed a multiplexed fluorescent microsphere immunoassay (FMIA) for detection of PRRSV-specific antibodies in oral fluid and serum samples. Recombinant nucleocapsid protein (N) and nonstructural protein 7 (nsp7) from both PRRSV genotypes (type I and type II) were used as antigens and covalently coupled to Luminex fluorescent microspheres. Based on an evaluation of 488 oral fluid samples with known serostatus, the oral fluid-based FMIAs achieved >92% sensitivity and 91% specificity. For serum samples (
n
= 1,639), the FMIAs reached >98% sensitivity and 95% specificity. The assay was further employed to investigate the kinetics of the antibody response in infected pigs. In oral fluid, the N protein was more sensitive for the detection of early infection (7 and 14 days postinfection), but nsp7 detected a higher level and longer duration of antibody response (28 days postinfection). In serum, the antibodies specific to nsp7 and N proteins were detected as early as 7 days postinfection, and the responses lasted more than 202 days. This study provides a framework from which a more robust assay could be developed to profile the immune response to multiple PRRSV antigens in a single test. The development of oral fluid-based diagnostic tests will change the way we survey diseases in swine herds and improve our ability to cheaply and efficiently track PRRSV infections in both populations and individual animals.
Aerosolized Vaccine as an Unexpected Source of False-Positive Bordetella pertussis PCR Results
Authors: Salimnia Hossein , Lephart Paul R. , Asmar Basim I. , Prebelich Dawn , Paulson Erin , Fairfax Marilynn R.
Published: December 2011

When 13 of 13 nasal wash specimens from a single pediatrician's office tested positive for low quantities of
Bordetella pertussis
DNA, we suspected prelaboratory contamination. Investigation revealed that Pentacel and Adacel vaccines contain high copy numbers of
B. pertussis
DNA, which can be aerosolized, causing false-positive
B. pertussis
PCR results.
Direct Drug Susceptibility Testing of Mycobacterium tuberculosis for Rapid Detection of Multidrug Resistance Using the Bactec MGIT 960 System: a Multicenter Study
Authors: Siddiqi Salman , Ahmed Altaf , Asif Sunil , Behera Digamber , Javaid Mona , Jani Jasmine , Jyoti Arora , Mahatre Radhika , Mahto Dewanand , Richter Elvira , Rodrigues Camilla , Visalakshi Potharaju , Rüsch-Gerdes Sabine
Published: December 2011

Conventional indirect drug susceptibility testing of
Mycobacterium tuberculosis
with liquid medium is well established and offers time-saving and reliable results. This multicenter study was carried out to evaluate if drug susceptibility testing (DST) can be successfully carried out directly from processed smear-positive specimens (direct DST) and if this approach could offer substantial time savings. Sputum specimens were digested, decontaminated, and concentrated by the laboratory routine procedure and were inoculated in Bactec MGIT 960 as well as Lowenstein-Jensen (LJ) medium for primary isolation. All the processed specimens which were acid-fast bacterium (AFB) smear positive were used for setting up direct DST for isoniazid (INH) and rifampin (RIF). After the antimicrobial mixture of polymyxin B, amphotericin B, nalidixic acid, trimethoprim, and azlocillin (PANTA) was added, the tubes were entered in the MGIT 960 instrument using the 21-day protocol (Bactec 960 pyrazinamide [PZA] protocol). Results obtained by direct DST were compared with those obtained by indirect DST to establish accuracy and time savings by this approach. Of a total of 360 AFB smear-positive sputum specimens set up for direct DST at four sites in three different countries, 307 (85%) specimens yielded reportable results. Average reporting time for direct DST was 11 days (range, 10 to 12 days). The average time savings by direct DST compared to indirect DST, which included time to isolate a culture and perform DST, was 8 days (range, 6 to 9 days). When results of direct DST were compared with those of indirect DST, there was 95.1% concordance with INH and 96.1% with rifampin. These findings indicate that direct DST with the Bactec MGIT 960 system offers further time savings and is a quick method to reliably detect multidrug resistance (MDR) cases.
Evolution of Poliovirus Defective Interfering Particles Expressing Gaussia Luciferase
Authors: Song Yutong , Paul Aniko V. , Wimmer Eckard
Published: December 2011

Polioviruses (PVs) carrying a reporter gene are useful tools for studies of virus replication, particularly if the viral chimeras contain the polyprotein that provides all of the proteins necessary for a complete replication cycle. Replication in HeLa cells of a previously constructed poliovirus expressing the gene for
Renilla
luciferase (RLuc) fused to the N terminus of the polyprotein H
2
N-RLuc-P1-P2-P3-COOH (P1, structural domain; P2 and P3, nonstructural domains) led to the deletion of RLuc after only one passage. Here we describe a novel poliovirus chimera that expresses
Gaussia
luciferase (GLuc) inserted into the polyprotein between P1 and P2 (N
2
H-P1-GLuc-P2-P3-COOH). This chimera, termed PV-GLuc, replicated to 10% of wild-type yield. The reporter signal was fully retained for three passages and then gradually lost. After six passages the signal was barely detectable. On further passages, however, the GLuc signal reappeared, and after eight passages it had reached the same levels observed with the original PV-GLuc at the first passage. We demonstrated that this surprising observation was due to coevolution of defective interfering (DI) particles that had lost part or all of the capsid coding sequence (ΔP1-GLuc-P2-P3) and wild-type-like viruses that had lost the GLuc sequence (P1-P2-P3). When used at low passage, PV-GLuc is an excellent tool for studying aspects of genome replication and morphogenesis. The GLuc protein was secreted from mammalian cells but, in agreement with published data, was not secreted from PV-GLuc-infected cells due to poliovirus-induced inhibition of cellular protein secretion. Published evidence indicates that individual expression of enterovirus polypeptide 3A, 2B, or 2BC in COS-1 cells strongly inhibits host protein secretion. In HeLa cells, however, expression of none of the poliovirus polypeptides, either singly or in pairs, inhibited GLuc secretion. Thus, inhibition of GLuc secretion in PV-infected HeLa cells is likely a result of the interaction between several viral and cellular proteins that are different from those in COS-1 cells.
Low-Dose Penile SIVmac251 Exposure of Rhesus Macaques Infected with Adenovirus Type 5 (Ad5) and Then Immunized with a Replication-Defective Ad5-Based SIV
gag/pol/nef
Vaccine Recapitulates the Results of the Phase IIb Step Trial of a Similar HIV-1 Vaccine
Authors: Qureshi Huma , Ma Zhong-Min , Huang Ying , Hodge Gregory , Thomas Michael A. , DiPasquale Janet , DeSilva Veronique , Fritts Linda , Bett Andrew J. , Casimiro Danilo R. , Shiver John W. , Robert-Guroff Marjorie , Robertson Michael N. , McChesney Michael B. , Gilbert Peter B. , Miller Christopher J.
Published: December 2011

The Step Trial showed that the MRKAd5 HIV-1 subtype B Gag/Pol/Nef vaccine did not protect men from HIV infection or reduce setpoint plasma viral RNA (vRNA) levels but, unexpectedly, it did modestly enhance susceptibility to HIV infection in adenovirus type 5 (Ad5)-seropositive, uncircumcised men. As part of the process to understand the results of the Step Trial, we designed a study to determine whether rhesus macaques chronically infected with a host-range mutant Ad5 (Ad5hr) and then immunized with a replication defective Ad5 SIVmac239 Gag/Pol/Nef vaccine were more resistant or susceptible to SIV infection than unimmunized rhesus macaques challenged with a series of escalating dose penile exposures to SIVmac 251. The Ad5 SIV vaccine induced CD8
+
T cell responses in 70% of the monkeys, which is similar to the proportion of humans that responded to the vaccine in the Step Trial. However, the vaccine did not protect vaccinated animals from penile SIV challenge. At the lowest SIV exposure dose (10
3
50% tissue culture infective doses), 2 of 9 Ad5-seropositive animals immunized with the Ad5 SIV vaccine became infected compared to 0 of 34 animals infected in the other animal groups (naive animals, Ad5-seropositive animals immunized with the empty Ad5 vector, Ad5-seronegative animals immunized with the Ad5 SIV vaccine, and Ad5-seronegative animals immunized with the empty Ad5 vector). Penile exposure to more concentrated virus inocula produced similar rates of infection in all animal groups. Although setpoint viral loads were unaffected in Step vaccinees, the Ad5 SIV-immunized animals had significantly lower acute-phase plasma vRNA levels compared to unimmunized animals. Thus, the results of the nonhuman primate (NHP) study described here recapitulate the lack of protection against HIV acquisition seen in the Step Trial and suggest a greater risk of infection in the Ad5-seropositive animals immunized with the Ad5 SIV vaccine. Further studies are necessary to confirm the enhancement of virus acquisition and to discern associated mechanisms.
Molecular community analysis of magnesium-rich bittern brine recovered from a Tunisian solar saltern
Authors: Baati Houda , Jarboui Raja , Gharsallah Néji , Sghir Abdelghani , Ammar Emna
Published: December 2011

The microbial community of a magnesium-rich bittern brine saturated with NaCl (380–400 g/L) from a Tunisian solar saltern was investigated using a molecular approach based on 16S rRNA gene analysis and viability tests. The results revealed the existence of microbial flora. Viability test assessment showed that 46.4% of this flora was viable but not detectable by culturability tests. 16S rRNA genes from 49 bacterial clones and 38 archaeal clones were sequenced and phylogenetically analyzed. Eleven operational taxonomic units (OTUs) determined by the DOTUR program with 97% sequence similarity were generated for Bacteria. These OTUs were affiliated with Bacteroidetes and Gammaproteobacteria. The archaeal community composition exhibited more diversity with 38 clones, resulting in 13 OTUs affiliated with the Euryarchaeota phylum. Diversity measurement showed a more diverse archaeal than bacterial community at the saturated pond.
Identification of virulence factors in Vibrio cholerae isolated from Iraq during the 2007–2009 outbreak
Authors: Saleh Tahreer Hadi , Sabbah Majeed Arsheed , Jasem Kifah A. , Hammad Zuhair N.
Published: December 2011

Thousands of people were infected with Vibrio cholerae during the outbreak in Iraq in 2007–2009. Vibrio cholerae was shown to be variable in its content of virulence determinants and in its antibiotic sensitivity. This study was designed to isolate and characterize clinical and environmental V. cholerae isolates and to determine antibiotic sensitivity, enzyme and toxin production, and the presence of virulence genes. Eighty clinical and five environmental bacterial isolates were collected and diagnosed by subjecting them to microscopic, biochemical, serological, and molecular analysis. The results revealed that 55% of clinical isolates belonged to the Inaba serotype, 32.5% to the Ogawa serotypes, and 12.5% to the Non-O1 serotype. All environmental V. cholerae isolates belonged to the Non-O1 serotype. All environmental isolates were sensitive to all examined antimicrobial agents, while all clinical isolates showed a high sensitivity (100%) to ampicillin, gentamicin, cephalothin, tetracycline, erythromycin, and ciprofloxacin, and a high resistance (97.5%) to co-trimoxazole, nalidixic acid, and chloramphenicol. It was found that all V. cholerae (O1) isolates were resistant to the Vibrio static O129 and all Non-O1 V. cholerae isolates were sensitive to the Vibrio static O129. All clinical and environmental isolates produced hemolysin (100%) and lecithinase (100%), while they showed various production rates of protease (90% of clinical and 60% of environmental) and lipase (50% of clinical and 20% of environmental). The ompW gene was amplified in all the clinical and environmental V. cholerae isolates, but not in other related and nonrelated bacteria. Multiplex PCR analysis showed that the toxR gene was amplified in all clinical and environmental isolates, while ctxA, ctxB, tcpA genes were amplified only in clinical (O1) isolates. This study indicates the differences in the production of some enzymes and toxins and in the content of virulence genes between clinical and environmental isolates in Iraq during the outbreak (2007–2009).
Computational prediction of microRNAs and their targets from three unicellular algae species with complete genome sequences
Authors: Huang Aiyou , Wu Xiaojie , Wang Guangce , Jia Zhaojun , He Linwen
Published: December 2011

The genome sequences of Phaeodactylum tricornutum , Thalassiosira pseudonana , and Cyanidioschyzon merolae have provided significant evidence for the secondary endosymbiosis of diatoms in regard to the genome. Yet little about their relationships in regard to gene regulation pattern, such as microRNA (miRNA), has been reported. Using a homology search based on genomic sequences, 13, 3, and 7 predicted miRNA genes were found in genomes from P. tricornutum, T. pseudonana, and C. merolae, respectively. Of the 23 miRNA genes, 18 had homology with animal miRNAs, implying that they are ancestral miRNAs. A phylogenetic tree based on common miRNA families shared by these three unicellular algae, higher plants, and animals showed that P. tricornutum shared most miRNAs with animals. The phylogenetic tree also showed that C. merolae shared more miRNAs with plants than did the two diatoms, and the majority of its miRNAs were shared with the two diatoms. Our results were consistent with diatoms originating from a secondary endosymbiosis.
Role of ω-hydroxylase in adenosine-mediated aortic response through MAP kinase using A2A-receptor knockout mice
Authors: Ponnoth Dovenia S. , Nayeem Mohammed A. , Kunduri Swati S. , Tilley Stephen L. , Zeldin Darryl C. , Ledent Catherine , Mustafa S. Jamal
Published: December 2011

Previously, we have shown that A2A adenosine receptor (A2AAR) knockout mice (KO) have increased contraction to adenosine. The signaling mechanism(s) for A2AAR is still not fully understood. In this study, we hypothesize that, in the absence of A2AAR, ω-hydroxylase (Cyp4a) induces vasoconstriction through mitogen-activated protein kinase (MAPK) via upregulation of adenosine A1 receptor (A1AR) and protein kinase C (PKC). Organ bath and Western blot experiments were done using isolated aorta from A2AKO and corresponding wild-type (WT) mice. Isolated aortic rings from WT and A2AKO mice were precontracted with submaximal dose of phenylephrine (10−6 M), and concentration responses for selective A1AR, A2AAR agonists, angiotensin II and cytochrome P-450-epoxygenase, 20-hydroxyeicosatrienoic acid (20-HETE) PKC, PKC-α, and ERK1/2 inhibitors were obtained. 2- p-(2-Carboxyethyl)-phenethylamino-5′- N-ethylcarboxamidoadenosine hydrochloride (CGS-21680, A2AAR agonist) induced concentration-dependent relaxation in WT, which was blocked by methylsulfonyl-propargyloxyphenylhexanamide (cytochrome P-450-epoxygenase inhibitor; 10−5 M) and also with removal of endothelium. A1 agonist, 2-chloro- N6-cyclopentyladenosine (CCPA) produced higher contraction in A2AKO aorta than WT (49.2 ± 8.5 vs. 27 ± 5.9% at 10−6 M, P < 0.05). 20-HETE produced higher contraction in A2AKO than WT (50.6 ± 8.8 vs. 21.1 ± 3.3% at 10−7 M, P < 0.05). Contraction to CCPA in WT and A2AKO aorta was inhibited by PD-98059 (p42/p44 MAPK inhibitor; 10−6 M), chelerythrine chloride (nonselective PKC blocker; 10−6 M), Gö-6976 (selective PKC-α inhibitor; 10−7 M), and HET0016 (20-HETE inhibitor; 10−5 M). Also, contraction to 20-HETE in WT and A2AKO aorta was inhibited by PD-98059 and Gö-6976. Western blot analysis indicated the upregulation of A1AR, Cyp4a, PKC-α, and phosphorylated-ERK1/2 in A2AKO compared with WT ( P < 0.05), while expression of Cyp2c29 was significantly higher in WT. CCPA (10−6 M) increased the protein expression of PKC-α and phosphorylated-ERK1/2, while HET0016 significantly reduced the CCPA-induced increase in expression of these proteins. These data suggest that, in the absence of A2AAR, Cyp4a induces vasoconstriction through MAPK via upregulation of A1AR and PKC-α.
Foot anatomy specialization for postural sensation and control
Authors: Wright W. G. , Ivanenko Y. P. , Gurfinkel V. S.
Published: December 2011

Anthropological and biomechanical research suggests that the human foot evolved a unique design for propulsion and support. In theory, the arch and toes must play an important role, however, many postural studies tend to focus on the simple hinge action of the ankle joint. To investigate further the role of foot anatomy and sensorimotor control of posture, we quantified the deformation of the foot arch and studied the effects of local perturbations applied to the toes (TOE) or 1st/2nd metatarsals (MT) while standing. In sitting position, loading and lifting a 10-kg weight on the knee respectively lowered and raised the foot arch between 1 and 1.5 mm. Less than 50% of this change could be accounted for by plantar surface skin compression. During quiet standing, the foot arch probe and shin sway revealed a significant correlation, which shows that as the tibia tilts forward, the foot arch flattens and vice versa. During TOE and MT perturbations (a 2- to 6-mm upward shift of an appropriate part of the foot at 2.5 mm/s), electromyogram (EMG) measures of the tibialis anterior and gastrocnemius revealed notable changes, and the root-mean-square (RMS) variability of shin sway increased significantly, these increments being greater in the MT condition. The slow return of RMS to baseline level (>30 s) suggested that a very small perturbation changes the surface reference frame, which then takes time to reestablish. These findings show that rather than serving as a rigid base of support, the foot is compliant, in an active state, and sensitive to minute deformations. In conclusion, the architecture and physiology of the foot appear to contribute to the task of bipedal postural control with great sensitivity.
Decoding 3D reach and grasp from hybrid signals in motor and premotor cortices: spikes, multiunit activity, and local field potentials
Authors: Bansal Arjun K. , Truccolo Wilson , Vargas-Irwin Carlos E. , Donoghue John P.
Published: December 2011

Neural activity in motor cortex during reach and grasp movements shows modulations in a broad range of signals from single-neuron spiking activity (SA) to various frequency bands in broadband local field potentials (LFPs). In particular, spatiotemporal patterns in multiband LFPs are thought to reflect dendritic integration of local and interareal synaptic inputs, attentional and preparatory processes, and multiunit activity (MUA) related to movement representation in the local motor area. Nevertheless, the relationship between multiband LFPs and SA, and their relationship to movement parameters and their relative value as brain-computer interface (BCI) control signals, remain poorly understood. Also, although this broad range of signals may provide complementary information channels in primary (MI) and ventral premotor (PMv) areas, areal differences in information have not been systematically examined. Here, for the first time, the amount of information in SA and multiband LFPs was compared for MI and PMv by recording from dual 96-multielectrode arrays while monkeys made naturalistic reach and grasp actions. Information was assessed as decoding accuracy for 3D arm end point and grip aperture kinematics based on SA or LFPs in MI and PMv, or combinations of signal types across areas. In contrast with previous studies with ≤16 simultaneous electrodes, here ensembles of >16 units (on average) carried more information than multiband, multichannel LFPs. Furthermore, reach and grasp information added by various LFP frequency bands was not independent from that in SA ensembles but rather typically less than and primarily contained within the latter. Notably, MI and PMv did not show a particular bias toward reach or grasp for this task or for a broad range of signal types. For BCIs, our results indicate that neuronal ensemble spiking is the preferred signal for decoding, while LFPs and combined signals from PMv and MI can add robustness to BCI control.
From Tumor Immunosuppression to Eradication: Targeting Homing and Activity of Immune Effector Cells to Tumors
Authors: Draghiciu Oana , Nijman Hans W. , Daemen Toos
Published: December 2011

Unraveling the mechanisms used by the immune system to fight cancer development is one of the most ambitious undertakings in immunology. Detailed knowledge regarding the mechanisms of induction of tolerance and immunosuppression within the tumor microenvironment will contribute to the development of highly effective tumor eradication strategies. Research within the last few decades has shed more light on the matter. This paper aims to give an overview on the current knowledge of the main tolerance and immunosuppression mechanisms elicited within the tumor microenvironment, with the focus on development of effective immunotherapeutic strategies to improve homing and activity of immune effector cells to tumors.
Acute Abdomen and Perforated Bowel with a Rare Pathology: Nonfamilial Visceral Myopathy
Authors: Burcharth Jakob , Olsen Caroline , Rosenberg Jacob
Published: December 2011

Visceral myopathy is a rare chronic disease affecting the peristalsis of the bowel causing intermittent pseudoobstruction. We report an atypical case of an eighty-nine-year-old woman with no prior history of abdominal illness who was admitted to our hospital with 2 days of increasing nausea, abdominal distension, and abdominal pain. On arrival at the hospital, she was critically ill. Abdominal X-ray showed distended loops of the colon and liquid levels resembling colonic obstruction. A subsequent abdominal CT scan confirmed the colonic obstruction. A suspicion of sigmoid volvulus was raised, that is why a barium enema was performed but no lower colonic obstruction could be confirmed. Acute laparotomy showed perforated cecum without intestinal obstruction. Postoperatively, the patient became septic which was fatal for the patient. Pathology gave the diagnosis visceral myopathy. It is very difficult to make the diagnosis clinically and radiologically since visceral myopathy mimics other more common gastrointestinal diseases. It is important to consider visceral myopathy as a possible diagnosis in cases with recurrent episodes of abdominal pain, vomiting, and abdominal distension, but without actual intestinal obstruction.
The Effect of Variability in the Powder/Liquid Ratio on the Strength of Zinc Phosphate Cement
Authors: McKenna Jill E. , Ray Noel J. , McKenna Gerald , Burke Francis M.
Published: December 2011

Aim. To investigate (a) variability in powder/liquid proportioning and (b) effect of variability on diametral tensile strength (DTS), in a zinc phosphate cement. Statistical analyses () were by Student’st-test in the case of powder/liquid ratio and one-way ANOVA and Tukey HSD for pair-wise comparisons of mean DTS. The Null hypotheses were that (a) the powder-liquid mixing ratios would not differ from the manufacturer’s recommended ratio (b) DTS of the set cement samples using the extreme powder/liquid ratios would not differ from those made using the recommended ratio.Methodology. 34 dental students dispensed the components according to the manufacturer’s instructions. The maximum and minimum powder/liquid ratios, together with the manufacturer’s recommended ratio, were used to prepare samples for DTS testing.Results. Powder/liquid ratios ranged from 2.386 to 1.018. The mean ratio (1.644) was not significantly different from the recommended value of 1.718 (). DTS values for the maximum and minimum ratios were both significantly different from each other () and from the mean value obtained from the recommended ratio ().Conclusions. Variability exists in powder/liquid ratio for hand dispensed zinc phosphate cement. This variability can affect the DTS of the set material.
A Case of an Unusually Aggressive Cutaneous Anaplastic Large T-Cell Lymphoma in an HIV Patient Treated with CHOP
Authors: Hurtado-Cordovi Jorge , Hanna Louay , Gotlieb Vladimir , Multz Alan S. , Pigal Anastasia
Published: December 2011

Anaplastic large cell lymphoma (ALCL) is the second most common malignancy of T-cell phenotype. This case report describes an unusual rapidly progressing cutaneous anaplastic large T-cell lymphoma in an HIV patient. Our patient is a twenty-year-old African American male with perinatally acquired HIV who presented with a2×2centimeter necrotic lesion in the right 1st toe; however, 2-3 weeks later multiple smaller lesions appeared on the anterior aspect of the right foot, ankle, and thigh. Biopsy showed cells strongly positive for CD3 and CD30 and negative for CD56 and the ALK gene product. CT of the chest, abdomen, and pelvis was negative for extracutaneous involvement favoring cutaneous ALCL. Patient was treated with 6 cycles of CHOP (cyclophosphamide, hydroxydaunorubicin, vincristine, and prednisone) chemotherapy and went into complete remission. Due to the aggressive course that this malignancy follows in HIV patients we suggest prompt treatment with systemic therapy.
A Case of Orthostatic Tachycardia Syndrome Presenting with Panic Attack during Tilt Table Testing
Authors: Kataoka H.
Published: December 2011

A 26-year-old woman experienced syncope on standing 2–3 times a year for more than 15 years. The attack was typically associated with palpitations and frequently accompanied by a feeling of intense fear. The patient underwent head-up tilt table testing at 70°for 40 min to determine the cause of the syncope. The tilt test results suggested that the etiology of the syncope was orthostatic tachycardia syndrome complicated by panic attack-associated hypocapnic hyperventilation, which presumably caused a greater degree of deep cerebral hypoperfusion than would be expected with orthostatic tachycardia syndrome alone, ultimately leading to the patient’s symptoms, including syncope. In conclusion, monitoring the ventilation and/or arterial CO2 level during head-up tilt table testing is occasionally required when evaluating patients with postural syncope.
Obstructive Parotitis Secondary to an Acute Masseteric Bend
Authors: Reddy Ryan , White David R. , Gillespie M. Boyd
Published: December 2011

Aims: To investigate 3 cases of chronic parotitis secondary to an acute bend in Stensen’s duct caused by an enlargement of the masseteric space. Results: Three female patients presented with symptoms consistent with obstructive parotitis including glandular swelling and tenderness during meals. A 10-year-old patient had unilateral facial swelling with enlargement of the masseter muscle and mandible later diagnosed as fibrous dysplasia. Salivary endoscopy showed an acute bend in Stensen’s duct secondary to a mass effect. The patient’s parotid swelling resolved following debulking of the mandibular mass and sialendoscopy with irrigation. Two adult patients with bilateral parotid involvement presented with bilateral masseteric hypertrophy and dental wear facets consistent with bruxism. Salivary endoscopy revealed bilateral kinking of Stensen’s duct with jaw closure. Both patients improved symptomatically following nightly bite guard use and ultrasound-guided Botox injections of the masseter muscle and parotid. Conclusion: Obstructive parotitis is rarely caused by an acute masseteric bend. Diagnosis of a kinking Stensen’s duct is aided with salivary endoscopy and imaging to determine the precipitating pathology. In the case of masseteric hypertrophy, symptomatic improvement can be achieved with Botox-induced atrophy of masseteric hypertrophy or with surgical reduction for associated fibrous dysplasia.
Multimodality Treatment with Conventional Transcatheter Arterial Chemoembolization and Radiofrequency Ablation for Unresectable Hepatocellular Carcinoma
Authors: Ashoori N. , Paprottka P. , Trumm C. , Bamberg F. , Kolligs F.T. , Rentsch M. , Reiser M.F. , Jakobs T.F.
Published: December 2011

Background/Aims: To evaluate the efficacy of multimodality treatment consisting of conventional transcatheter arterial chemoembolization (TACE) and radiofrequency ablation (RFA) in patients with non-resectable and non-ablatable hepatocellular carcinoma (HCC). Methods: In this retrospective study, 85 consecutive patients with HCC (59 solitary, 29 multifocal HCC) received TACE followed by RFA between 2001 and 2010. The mean number of tumors per patient was 1.6 ± 0.7 with a mean size of 3.0 ± 0.9 cm. Both local efficacy and patient survival were evaluated. Results: Of 120 treated HCCs, 99 (82.5%) showed a complete response (CR), while in 21 HCCs (17.5%) a partial response was depicted. Patients with solitary HCC revealed CR in 91% (51/56); in patients with multifocal HCC (n = 29) CR was achieved in 75% (48 of 64 HCCs). The median survival for all patients was 25.5 months. The 1-, 2-, 3- and 5-year survival rates were 84.6, 58.7, 37.6 and 14.6%, respectively. Statistical analysis revealed a significant difference in survival between Barcelona Clinic Liver Cancer (BCLC) A (73.4 months) and B (50.3 months) patients, while analyses failed to show a difference for Child-Pugh score, Cancer of Liver Italian Program (CLIP) score and tumor distribution pattern. Conclusion: TACE combined with RFA provides an effective treatment approach with high local tumor control rates and promising survival data, especially for BCLC A patients. Randomized trials are needed to compare this multimodality approach with a single modality approach for early-stage HCC.
openBIS: a flexible framework for managing and analyzing complex data in biology research
Authors: Bauch Angela , Adamczyk Izabela , Buczek Piotr , Elmer Franz-Josef , Enimanev Kaloyan , Glyzewski Pawel , Kohler Manuel , Pylak Tomasz , Quandt Andreas , Ramakrishnan Chandrasekhar , Beisel Christian , Malmström Lars , Aebersold Ruedi , Rinn Bernd
Published: December 2011

Background

Modern data generation techniques used in distributed systems biology research projects often create datasets of enormous size and diversity. We argue that in order to overcome the challenge of managing those large quantitative datasets and maximise the biological information extracted from them, a sound information system is required. Ease of integration with data analysis pipelines and other computational tools is a key requirement for it.

Results

We have developed openBIS, an open source software framework for constructing user-friendly, scalable and powerful information systems for data and metadata acquired in biological experiments. openBIS enables users to collect, integrate, share, publish data and to connect to data processing pipelines. This framework can be extended and has been customized for different data types acquired by a range of technologies.

Conclusions

openBIS is currently being used by several SystemsX.ch and EU projects applying mass spectrometric measurements of metabolites and proteins, High Content Screening, or Next Generation Sequencing technologies. The attributes that make it interesting to a large research community involved in systems biology projects include versatility, simplicity in deployment, scalability to very large data, flexibility to handle any biological data type and extensibility to the needs of any research domain.
qDTY
1.1
, a major QTL for rice grain yield under reproductive-stage drought stress with a consistent effect in multiple elite genetic backgrounds
Authors: Vikram Prashant , Swamy BP Mallikarjuna , Dixit Shalabh , Ahmed Helal Uddin , Teresa Sta Cruz Ma , Singh Alok Kumar , Kumar Arvind
Published: December 2011

Background

Drought is one of the most important abiotic stresses causing drastic reductions in yield in rainfed rice environments. The suitability of grain yield (GY) under drought as a selection criterion has been reported in the past few years. Most of the quantitative trait loci (QTLs) for GY under drought in rice reported so far has been in the background of low-yielding susceptible varieties. Such QTLs have not shown a similar effect in multiple high- yielding drought-susceptible varieties, thus limiting their use in marker-assisted selection. Genetic control of GY under reproductive-stage drought stress (RS) in elite genetic backgrounds was studied in three F3:4 mapping populations derived from crosses of N22, a drought-tolerant aus cultivar, with Swarna, IR64, and MTU1010, three high-yielding popular mega-varieties, with the aim to identify QTLs for GY under RS that show a consistent effect in multiple elite genetic backgrounds. Three populations were phenotyped under RS in the dry seasons (DS) of 2009 and 2010 at IRRI. For genotyping, whole-genome scans for N22/MTU1010 and bulked segregant analysis for N22/Swarna and N22/IR64 were employed using SSR markers.

Results

A major QTL for GY under RS, qDTY

1.1
, was identified on rice chromosome 1 flanked by RM11943 and RM431 in all three populations. In combined analysis over two years, qDTY

1.1
showed an additive effect of 29.3%, 24.3%, and 16.1% of mean yield in N22/Swarna, N22/IR64, and N22/MTU1010, respectively, under RS. qDTY

1.1
also showed a positive effect on GY in non-stress (NS) situations in N22/Swarna, N22/IR64 over both years, and N22/MTU1010 in DS2009.

Conclusions

This is the first reported QTL in rice with a major and consistent effect in multiple elite genetic backgrounds under both RS and NS situations. Consistency of the QTL effect across different genetic backgrounds makes it a suitable candidate for use in marker-assisted breeding.
Rationale and study design for a randomised controlled trial to reduce sedentary time in adults at risk of type 2 diabetes mellitus: project stand (Sedentary Time ANd diabetes)
Authors: Wilmot Emma G , Davies Melanie J , Edwardson Charlotte L , Gorely Trish , Khunti Kamlesh , Nimmo Myra , Yates Thomas , Biddle Stuart JH
Published: December 2011

Background

The rising prevalence of Type 2 Diabetes Mellitus (T2DM) is a major public health problem. There is an urgent need for effective lifestyle interventions to prevent the development of T2DM. Sedentary behaviour (sitting time) has recently been identified as a risk factor for diabetes, often independent of the time spent in moderate-to-vigorous physical activity. Project STAND (Sedentary Time ANd Diabetes) is a study which aims to reduce sedentary behaviour in younger adults at high risk of T2DM.

Methods/Design

A reduction in sedentary time is targeted using theory driven group structured education. The STAND programme is subject to piloting and process evaluation in line with the MRC framework for complex interventions. Participants are encouraged to self-monitor and self-regulate their behaviour. The intervention is being assessed in a randomised controlled trial with 12 month follow up. Inclusion criteria are a) aged 18-40 years with a BMI in the obese range; b) 18-40 years with a BMI in the overweight range plus an additional risk factor for T2DM. Participants are randomised to the intervention (n = 89) or control (n = 89) arm. The primary outcome is a reduction in sedentary behaviour at 12 months as measured by an accelerometer (count < 100/min). Secondary outcomes include physical activity, sitting/lying time using the ActivPAL posture monitor, fasting and 2 h oral glucose tolerance test, lipids, inflammatory biomarkers, body weight, waist circumference, blood pressure, illness perceptions, and efficacy beliefs for behaviour change.

Conclusions

This is the first UK trial to address sedentary behaviour change in a population of younger adults at risk of T2DM. The results will provide a platform for the development of a range of future multidisciplinary interventions in this rapidly expanding high-risk population.

Trial registration

Current controlled trials ISRCTN08434554, MRC project 91409.
ATP synthase ecto-α-subunit: a novel therapeutic target for breast cancer
Authors: Pan Jian , Sun Li-Chao , Tao Yan-Fang , Zhou Zhuan , Du Xiao-Li , Peng Liang , Feng Xing , Wang Jian , Li Yi-Ping , Liu Ling , Wu Shui-Yan , Zhang Yan-Lan , Hu Shao-Yan , Zhao Wen-Li , Zhu Xue-Ming , Lou Guo-Liang , Ni Jian
Published: December 2011

Background

Treatment failure for breast cancer is frequently due to lymph node metastasis and invasion to neighboring organs. The aim of the present study was to investigate invasion- and metastasis-related genes in breast cancer cells in vitro and in vivo. Identification of new targets will facilitate the developmental pace of new techniques in screening and early diagnosis. Improved abilities to predict progression and metastasis, therapeutic response and toxicity will help to increase survival of breast cancer patients.

Methods

Differential protein expression in two breast cancer cell lines, one with high and the other with low metastatic potential, was analyzed using two-dimensional liquid phase chromatographic fractionation (Proteome Lab PF 2D system) followed by matrix-assisted laser desorption/time-of-flight mass spectrometry (MALDI-TOF/MS).

Results

Up regulation of α-subunit of ATP synthase was identified in high metastatic cells compared with low metastatic cells. Immunohistochemical analysis of 168 human breast cancer specimens on tissue microarrays revealed a high frequency of ATP synthase α-subunit expression in breast cancer (94.6%) compared to normal (21.2%) and atypical hyperplasia (23%) breast tissues. Levels of ATP synthase expression levels strongly correlated with large tumor size, poor tumor differentiation and advanced tumor stages (P < 0.05). ATP synthase α-subunit over-expression was detected on the surface of a highly invasive breast cancer cell line. An antibody against the ATP synthase α-subunit inhibited proliferation, migration and invasion in these breast cancer cells but not that of a non-tumor derived breast cell line.

Conclusions

Over-expression of ATP synthase α-subunit may be involved in the progression and metastasis of breast cancer, perhaps representing a potential biomarker for diagnosis, prognosis and a therapeutic target for breast cancer. This finding of this study will help us to better understand the molecular mechanism of tumor metastasis and to improve the screening, diagnosis, as well as prognosis and/or prediction of responses to therapy for breast cancer.
An occupancy-based and channel-aware multi-level adaptive scheme for video communications over wireless channels
Authors: Mukhtar Husameldin , Hassan Mohamed , Landolsi Taha
Published: December 2011

Video streaming over wireless channels is challenged with the time-varying nature of the underlying channels and the stringent requirements of video applications. In particular, video streaming has strict requirements on bandwidth, delay, and loss rate while wireless channels are dynamic and error-prone by nature. In this article, we propose a novel multilevel adaptive scheme that is designed to mitigate the challenges facing video streaming over unreliable channels. This is done while preventing potential playback discontinuities and guaranteeing a graceful degradation of the rendered video quality. Scalable video coding, adaptive modulation, and adaptive channel coding are integrated to achieve the objectives of the proposed scheme. If adaptive modulation and channel coding are not enough to guarantee the on-time delivery of decodable video frames, we adopt scalable coding. Simulation results show that the proposed adaptive scheme achieves an improvement of about 2.5 dB in the peak signal-to-noise ratio over a nonadaptive one. In addition, the proposed scheme reduces the number of starvation instances by 50 and 90% in the cases of Stop-and-Wait and Go-Back-N automatic repeat requests, respectively.
Diagnosis and management of an immature teratoma during ovarian stimulation: a case report
Authors: Douay-Hauser Nathalie , Koskas Martin , Walker Francine , Luton Dominique , Yazbeck Chadi
Published: December 2011

Introduction

The discovery of a mature teratoma (dermoid cyst) of the ovary during ovarian stimulation is not a rare event. Conversely, we could not find any reported cases of immature teratoma in such a situation. Clinical and ultrasound arguments for this immature form are scarcely or poorly evaluated.

Case Presentation

We describe the case of a 31-year-old Caucasian woman with primary infertility, who developed an immature teratoma during an in vitro fertilization ovarian stimulation cycle.

Conclusions

Ultrasound signs of an atypical cyst during ovarian stimulation allowed us to adopt a careful medical attitude and to adapt the required surgical oncological treatment.
Regulation of myotube formation by the actin-binding factor drebrin
Authors: Mancini Annalisa , Sirabella Dario , Zhang Weijia , Yamazaki Hiroyuki , Shirao Tomoaki , Krauss Robert S
Published: December 2011

Background

Myogenic differentiation involves cell-cycle arrest, activation of the muscle-specific transcriptome, and elongation, alignment and fusion of myoblasts into multinucleated myotubes. This process is controlled by promyogenic transcription factors and regulated by signaling pathways in response to extracellular cues. The p38 mitogen-activated protein kinase (p38 MAPK) pathway promotes the activity of several such transcription factors, including MyoD and MEF2, thereby controlling the muscle-specific transcription program. However, few p38-regulated genes that play a role in the regulation of myogenesis have been identified.

Methods

RNA interference (RNAi), chemical inhibition and immunofluorescence approaches were used to assess the role of drebrin in differentiation of primary mouse myoblasts and C2C12 cells.

Results

In a search for p38-regulated genes that promote myogenic differentiation, we identified Dbn1, which encodes the actin-binding protein drebrin. Drebrin is an F-actin side-binding protein that remodels actin to facilitate the change of filopodia into dendritic spines during synaptogenesis in developing neurons. Dbn1 mRNA and protein are induced during differentiation of primary mouse and C2C12 myoblasts, and induction is substantially reduced by the p38 MAPK inhibitor SB203580. Primary myoblasts and C2C12 cells depleted of drebrin by RNAi display reduced levels of myogenin and myosin heavy chain and form multinucleated myotubes very inefficiently. Treatment of myoblasts with BTP2, a small-molecule inhibitor of drebrin, produces a phenotype similar to that produced by knockdown of drebrin, and the inhibitory effects of BTP2 are rescued by expression of a mutant form of drebrin that is unable to bind BTP2. Drebrin in myoblasts is enriched in cellular projections and cell cortices and at regions of cell-cell contact, all sites where F-actin, too, was concentrated.

Conclusions

Our findings reveal that Dbn1 expression is a target of p38 MAPK signaling during myogenesis and that drebrin promotes myoblast differentiation.
Risk factors for repetition and suicide following self-harm in
older adults: multicentre cohort study
Authors: Murphy Elizabeth , Kapur Navneet , Webb Roger , Purandare Nitin , Hawton Keith , Bergen Helen , Waters Keith , Cooper Jayne
Published: December 2011

Background

Older adults have elevated suicide rates. Self-harm is the most important
risk factor for suicide. There are few population-based studies of
self-harm in older adults.

Aims

To calculate self-harm rates, risk factors for repetition and rates of
suicide following self-harm in adults aged 60 years and over.

Method

We studied a prospective, population-based self-harm cohort presenting to
six general hospitals in three cities in England during 2000 to 2007.

Results

In total 1177 older adults presented with self-harm and 12.8% repeated
self-harm within 12 months. Independent risk factors for repetition were
previous self-harm, previous psychiatric treatment and age 60–74 years.
Following self-harm, 1.5% died by suicide within 12 months. The risk of
suicide was 67 times that of older adults in the general population. Men
aged 75 years and above had the highest suicide rates.

Conclusions

Older adults presenting to hospital with self-harm are a high-risk group
for subsequent suicide, particularly older men.
Systematic isolation of microbial metabolites for natural products depository (NPDepo)
Authors: Osada Hiroyuki , Nogawa Toshihiko
Published: December 2011

A microbial fraction library has been constructed as a part of RIKEN Natural Products Depository (NPDepo) to discover and isolate novel metabolites with unique biological activity from microbial sources efficiently and rapidly. The fraction library was made by a systematic separation method based on basic chromatographic techniques. Each fraction in the library was analyzed by liquid chromatography/mass spectrometry (LC/MS) to reveal physicochemical properties of each metabolite within the fraction, and the results were applied to construct a database for rapid discovery of novel and structurally unique compounds. We developed a new type of metabolite database called MP (microbial products) plot to visualize each metabolite on a 2D area. The combination of the fraction library and the database led to the discovery and isolation of novel metabolites, verticilactam, which was a 16-membered macrolactam with an unprecedented β-keto-amide moiety, and spirotoamides A and B, which had a highly substituted 6,6-spiroaccetal moiety and a carboxamide moiety. Moreover, based on the utilization of the MP plot, the new capacity of a streptomycete to produce specific metabolites was discovered.