Comparative Analysis of the Efficacies of the GeneXpert and Solid Culture Media Techniques in the Diagnosis of Mycobacterium Tuberculosis

Tuberculosis is one of the predominant infectious diseases causing significant deaths worldwide. Detection of Mycobacterium tuberculosis bacilli (MTB) using culture media was officially recognized by World Health Organization. However, there is a significant limitation in the authenticity of evaluation for its effectiveness on clinically important attributes. GeneXpert detects the presence of Mycobacterium tuberculosis (M. tuberculosis) based on the detection of nucleic acid and is able to identify the resistance of both isoniazid (INH) and Rifampicin (RIF) drugs. In this technique, DNA amplification is done using the GeneXpert instrument in the suspected sample with a specific reagent cartridge. Although GeneXpert is a rapid technique compared to other diagnostic tools for MTB identification due to false-negative results, the culture media technique is still considered the gold standard in detecting M. tuberculosis. The current study was designed to evaluate the comparative efficacies of GeneXpert and the solid culture media technique in identifying MTB. Sputum samples of 250 (n=250) suspected tuberculosis (TB) patients were investigated using both diagnostic techniques. The results revealed that out of the 250 suspected patients, 30 (12%) samples were positive with the culture media technique, while only 17 (6.8%) samples showed positive results with GeneXpert. Culture tests and GeneXpert are not equally efficient in detecting M. tuberculosis. The current study's findings showed that the culture-based detection method for M. tuberculosis is more efficient and reliable than GeneXpert.

Drought stress enhances the efficiency of floral dip method of Agrobacterium-mediated transformation in Arabidopsis thaliana

The Agrobacterium-mediated floral dip protocol is the most extensively used transformation method for a model plant Arabidopsis thaliana. Several useful methods for Agrobacterium tumefaciens-mediated transformations of Arabidopsis are existing, but they are time consuming and with low transformation efficiency. Here, we developed a transgenic Arabidopsis lines TET12p::TET12-RFP in a short period of time and enhanced transformation efficiency by using a modified transformation method by applying drought stress after floral dip. In this protocol, Agrobacterium cells carrying TET12p::TET12-RFP recombinant vectors were resuspended in a solution of 5% sucrose, 0.05% (v/v) silwet L-77 to transform female gametes of developing Arabidopsis inflorescences. Treated Arabidopsis were then applied with different levels of drought stresses to stimulate plants for the utilization of maximum plant energy in seed maturation process. The applied stresses achieved the fast maturation of already treated inflorescences while stopped the growing of newly arising untreated inflorescence, thus decreased the chances of wrong collection of untransformed seeds. Consequently, the collected seeds were mostly transgenic with a transformation frequency of at least 10%, thus the screening for positive transformants selection was more advantageous on a selective medium as compared to a classical floral dip method. Within 2-3 months, two hundred of individual transgenic plants were produced from just 10 infiltrated plants. This study concludes that application of drought stresses in a specific stage of plant is a beneficial strategy for achieving the transgenic Arabidopsis in a short period of time with high transformation efficiency.

Molecular docking, dynamics, and quantum chemical study of vanillylacetone and beta-hydroxy ketone derivatives against Mpro of SARS-CoV-2

This study is carried out to find novel active drug candidates which can effectively bind to key residues of main protease (Mpro) of SARS-CoV-2. We performed molecular docking of fifty-seven (57) ligands from two classes: vanillylacetone and its derivatives and beta-hydroxy ketone derivatives against Mpro of SARS-CoV-2. We also docked three antiviral drugs as reference/benchmark drugs including remdesivir (RDV), chloroquine (CQ), and hydroxychloroquine (HCQ) against Mpro for comparison of inhibition tendencies of selected ligands. Binding energies of our reference drugs are as: CQ = -5.1 kcal mol-1 (with predicted inhibition constant (Ki pred) = 177 μmol), HCQ = -5.7 kcal mol-1 (Ki pred = 64.07 μmol) and RDV -6.3 kcal mol-1 (Ki pred = 13.95 μmol). We got remarkable results for our docked ligands as 79% of total ligands indicated binding energies better than CQ, 39 % better than both HCQ and CQ, and 19 % better than all reference drugs. More interestingly interaction analysis of eight best-docked ligands showed that they interacted with desired key residues of Mpro. We further selected the four best-docked ligands L1 = -6.6 kcal mol-1 (Ki pred =13.95 μmol), L6 = -7.0 kcal mol-1 (Ki pred = 7.08 μmol), L34 = -6.0 kcal mol-1 (Ki pred = 38.54 μmol), and L50 = -6.6 kcal mol-1 (Ki pred =13.95 umol) for further analysis by quantum chemical study, molecular dynamic (MD) simulations and ADMET analysis. We have also carried out MD-simulations of six more docked ligand L2, L14, L20, L36, L46 and L48 some of which were showing weak binding affinities and some average binding affinities to check their simulation behavior. Their RMSD, RMSF and binding free energy results were also quite satisfying. We believe the current investigation will evoke the scientific community and highlights the potential of selected compounds for potential use as antiviral compounds against Mpro of SARS-CoV-2.

915 An Unusual Case of Breast Tuberculosis: A Case Report

Background

Breast Tuberculosis (TB) is a rare form of extra-pulmonary tuberculosis. It can mimic the presentation of many breast diseases including malignancy. We present a case of breast tuberculosis that had negative cultures from breast tissue while positive on lymph node biopsy.

Case presentation

A 36-year-old Libyan British lady presented to the symptomatic breast clinic with a large left breast mass during the first trimester of her fifth pregnancy. She has received antibiotics to treat mastitis but with no improvement. On Examination she had large left upper quadrant mass with skin tethering as well as palpable left axillary lymph nodes. Ultrasound imaging suggested features suspicious for malignancy and hence core biopsies were obtained which showed chronic inflammatory changes only. Ziehl Neelson stain was negative at this stage. A week later she developed low grade fever as well as signs of infection at biopsy site, this was treated with flucloxacillin, pus aspirated from underlying mass and sent for culture and sensitivity. Unfortunately, this lady travelled to Tunisia after her review and was subsequently diagnosed with breast tuberculosis on cultures from lymph node biopsies. On her return to our clinic, she was on appropriate treatment for TB, she had good response to treatment and follow up ultrasound showed stable residual collection.

Conclusions

This case illustrates the challenges in the diagnosis of breast tuberculosis as it is a rare entity of a disease that remains less prevalent in European countries. In most cases full recovery can be expected with anti- tuberculous treatment.

A comparative study on the virulence of entomopathogenic fungi against Trogoderma granarium (Everts) (Coleoptera: Dermestidae) in stored grains rice

Entomopathogenic fungi (EPF) now a possible safer microbial control measure that could be considered as a substitute for chemical control of insect pests. Three EPF viz., Metarihizium anisopliae, Isaria furnosoroseus and Beauveria bassiana were evaluated for their virulence against the grubs of Khapra beetle, Trogoderma granarium (Everts) under laboratory conditions. The isolates were applied by two methods viz., diet incorporation and an immersion method with 3rd instar 20 grubs of T. granarium for each. The virulence of EPF was determined using percent mortality. Significantly higher mortality was observed in M. anisopliae applied through immersion (98.33%) and diet incorporation (93.33%) methods followed by B. bassiana (90.83 and 85.83%, respectively). The mortality caused by I. furnosoroseus was statistically lower in immersion and diet incorporation methods i.e. 81.67 and 73.33%, respectively. Based on the immersion method, all EPF were studied for multiple conidial concentration i.e., 1×104, 1×105, 1×106, 1×107 and 1×108 under the same in-vitro conditions. All the isolates were pathogenic to grub of T. granarium at the highest conidial concentration. M. anisopliae was proved the most effective virulent resulting in 98.33% mortality of the pest with LT50 4.61 days at 1 × 108 conidial concentration followed by 90.83 and 81.67 percent mortality with 5.07 and 8.01 days LT50, in the application of B. bassiana and I. furnosoroseus, respectively. M. anisopliae showed higher efficacy and could be considered as promising EPF for the development of myco-insecticides against effective biocontrol of T. granarium.

Exogenous application of bio-stimulant and growth retardant improved the productivity of cotton cultivars under different planting arrangement

Optimum planting arrangement is an important attribute for efficient utilization of available resources and to obtain high yield of cotton. Application of plant growth promoter and retardant on cotton in improved planting density are the innovative techniques in the establishment of more productive cotton crop. Therefore, we planned a field study to assess the role of bio-stimulant and growth retardant in the resource utilization efficiency of cotton cultivars planted under variable row spacing at Agronomic Research Area Bahauddin Zakariya University and Usmania Agricultural Farm Shujabad during Kharif 2012. Experimental treatments consisted of cotton genotypes viz. CIM-573 and CIM-598, cultivated under conventional (75 cm), medium (50 cm) and ultra-narrow row spacing (25 cm) with foliar spray of bio-stimulant (moringa leaf extract) and growth retardant (mepiquate chloride), either sole or in combination, keeping distilled water as a control. Exogenously applied MLE alone and MLE + MC significantly enhanced the number of squares, flowers and green bolls per plant leading to higher cotton seed and lint yield of CIM 598 cultivar cultivated under conventional row spacing. While application of MC alone and MLE + MC produced maximum micronaire value, fiber strength and fiber uniformity ratio of CIM 573 cultivar cultivated under conventional row spacing. The results suggested that application of MLE is a possible approach to enhance the cotton productivity and the use of MC to enhance the fiber quality attributes under conventional row spacing.

Biological screening and docking studies of unique hybrids synthesized by conventional versus microwave assisted techniques

Purpose: To carry out the synthesis of various hybrids of 1,2,4-triazole in search of potential therapeutic enzyme inhibitory agents, and carry out docking and bovine serum albumin (BSA) binding studies on docking and bovine serum albumin (BSA) binding studies on the hybrids. Methods: The target compounds were synthesized by following a multistep protocol. Compound 1 was synthesized from 4-methoxybenzenesulfonyl chloride (a) and ethyl isonipecotate (b). Compound 1 was refluxed with hydrazine to synthesize compound 2, which was converted to compound 3 through two consecutive steps. Compound 4 and different amines (5a-5i), were utilized to synthesize an array of electrophiles (6a-6i). A series of 1,2,4-triazole hybrids (7a-7i) were synthesized at room temperature by stirring together 3 and 6a-6i. The final structures of 7a-7i were elucidated through 1H-NMR, 13C-NMR and EI-MS spectroscopy. The BSA binding studies were performed by fluorometric titration. Furthermore, antioxidant and enzyme inhibition activities were determined colorimetrically. Results: Compound 7d was the most active antioxidant agent, compared to butylated hydroxyanisole (BHA), while compounds 7d, 7e, 7f, 7g and 7i proved to be potent urease inhibitors with half-maximal inhibitory concentration (IC50) values of 19.5 ± 0.12, 21.1 ± 0.68, 18.2 ± 0.78, 19.9 ± 0.77 and 17.9 ± 0.10 µM, respectively, compared to thiourea with an IC50 of 24.3 ± 0.24 µM. Compounds 7a, 7b, 7d, and 7e exhibited high butyrylcholinesterase inhibition potential, compared to eserine. Conclusion: The synthesized compounds require studies further as potential therapeutic enzyme inhibitory agents in view of their urease inhibition as well as antioxidant activity.

Resource use efficiency of cotton in improved vs conventional planting geometry with exogenous application of bio-stimulant and synthetic growth retardant

Plant growth regulators and improved planting density are the innovative techniques in the establishment of more productive cotton crop. A field study was planned to assess the role of growth regulators in the resource utilization efficiency of cotton cultivars under different row spacing at Agronomic Research Area, Bahauddin Zakariya University Multan and Usmania Agricultural Farm, Shujaabad during Kharif 2012. The study was comprised of cotton cultivars viz. CIM-573 and CIM-598, cultivated under conventional (75 cm), medium (50 cm) and improved ultra-narrow row spacing (25 cm) and foliar spray of growth regulators viz. moringa leaf extract (MLE) and mepiquat chloride (MC), either alone or in combination, distilled water as a control. The application of MLE alone and in combination (MLE + MC) showed the promoting effect on crop growth rate, net assimilation rate, leaf area index, leaf area duration, sympodial branches and number of bolls leading to higher seed cotton yield of both cotton cultivars grown under conventional row spacing. While application of MC averts the plant growth without considerably improving the productivity. MLE being rich source of growth promoting hormone and nutrients showed its potential to a far greater extent under conventional row spacing in efficient utilization of available resources compared to MC and distilled water.

Noncanonical effector functions of the T-memory-like T-PLL cell are shaped by cooperative TCL1A and TCR signaling

T-cell prolymphocytic leukemia (T-PLL) is a poor-prognostic neoplasm. Differentiation stage and immune-effector functions of the underlying tumor cell are insufficiently characterized. Constitutive activation of the T-cell leukemia 1A (TCL1A) oncogene distinguishes the (pre)leukemic cell from regular postthymic T cells. We assessed activation-response patterns of the T-PLL lymphocyte and interrogated the modulatory impact by TCL1A. Immunophenotypic and gene expression profiles revealed a unique spectrum of memory-type differentiation of T-PLL with predominant central-memory stages and frequent noncanonical patterns. Virtually all T-PLL expressed a T-cell receptor (TCR) and/or CD28-coreceptor without overrepresentation of specific TCR clonotypes. The highly activated leukemic cells also revealed losses of negative-regulatory TCR coreceptors (eg, CTLA4). TCR stimulation of T-PLL cells evoked higher-than-normal cell-cycle transition and profiles of cytokine release that resembled those of normal memory T cells. More activated phenotypes and higher TCL1A correlated with inferior clinical outcomes. TCL1A was linked to the marked resistance of T-PLL to activation- and FAS-induced cell death. Enforced TCL1A enhanced phospho-activation of TCR kinases, second-messenger generation, and JAK/STAT or NFAT transcriptional responses. This reduced the input thresholds for IL-2 secretion in a sensitizer-like fashion. Mice of TCL1A-initiated protracted T-PLL development resembled such features. When equipped with epitope-defined TCRs or chimeric antigen receptors, these Lckpr-hTCL1Atg T cells gained a leukemogenic growth advantage in scenarios of receptor stimulation. Overall, we propose a model of T-PLL pathogenesis in which TCL1A enhances TCR signals and drives the accumulation of death-resistant memory-type cells that use amplified low-level stimulatory input, and whose loss of negative coregulators additionally maintains their activated state. Treatment rationales are provided by combined interception in TCR and survival signaling.

Elemental analysis of sage (herb) using calibration-free laser-induced breakdown spectroscopy

In this work, laser-induced breakdown spectroscopy (LIBS) has been used for the quantitative and qualitative analysis of the sage sample using the calibration-free LIBS (CF-LIBS) technique. The sage plasma is generated by focusing the second harmonics (532 nm) of a Q-switched Nd:YAG laser with a repetition rate of 10 Hz and pulse duration of 5 ns. The emission spectra are recorded using a LIBS 2000 detection system spectrometer consisting of five high-resolution spectrometers covering a wavelength range from 200 to 720 nm. The optical emission spectra of the sage sample reveal the spectral lines of Fe, Ca, Ti, Co, Mn, Ni, and Cr. The plasma temperature and electron number density of the neutral spectral lines of the pertinent elements have been deduced using the Boltzmann plot and Stark-broadening line profile method, with average values 8855±885K and 3.89×10¹⁶cm^-3, respectively. The average values of the plasma parameters were used for the quantification of the detected elements in the sample. Based on the calibration-free method, the measured results demonstrate that Fe is the major constituent in the sample, having a percentage concentration of 48.1%, while the remaining elements are Ca, Ti, Co, Mn, Ni, and Cr, with percentage concentrations 0.7%, 5.3%, 8%, 11%, 12.3%, and 14.6%, respectively. This study demonstrates the feasibility of LIBS for the compositional analysis of major and trace elements present in the plant samples and its further applications in medicine.

Effect of Sub-lethal Doses of Imidacloprid on Learning and Memory Formation of Indigenous Arabian Bee (Apis mellifera jemenitica Ruttner) Adult Foragers

The indigenous bee race Apis mellifera jemenitica Ruttner of Saudi Arabia can learn and retain memories established by the classical conditioning of proboscis extension response (PER). The insecticide imidacloprid has shown a drastic effect on the olfactory behavior of A. m. jemenitica in the harsh arid climatic conditions of central Saudi Arabia. The oral feeding of single imidacloprid sub-lethal doses (1.0 ng, 0.5 ng, or 0.1 ng) under laboratory conditions significantly impaired associative learning during the 2nd and 3rd conditioning trials compared to control bees (0 ng). The memory tests also revealed significant impairment in memory formation at 1 h, 2 h, and 24 h after conditioning compared to control bees. Even the lowest dose (0.1 ng/bee) can significantly impair the bees' ability to learn and memorize. This impairment effect was dose dependent and increased with increasing doses. The higher dose (1.0 ng) completely impaired the learning but still showed a little memory and reflected the potential recovery of bees from insecticide-induced impairment with the passage of time. To our knowledge, this is the first study in A. m. jemenitica that demonstrated the drastic effect of neonicotinoids on associative learning in indigenous bees. This study further expresses the possible severity of insecticidal exposure to bees in actual field conditions and its effect on the neural functions used in important behavior involved in the foraging of bees.

Pharmacological activities of a novel phthalic acid ester and iridoid glycoside isolated from the root bark of Anthocleista vogelii Planch

In this study, a novel phthalic acid ester (1) and a known iridoid glycoside (2) were isolated from the root bark of Anthocleista vogelii. The structures of the novel compound and iridoid glycoside were elucidated on the basis of their chemical and spectral data (UV, FT-IR, EI-MS, 1D and 2D NMR) and found to be phthalic acid ester, 4-ethyl-6-propyl-4,5,6,7-tetrahydro3H-2,8-benzodioxacycloundecine-1,9-dione (1) and sweroside (2). The compounds were evaluated for their in vitro inhibitory activities against pancreatic lipase, α-amylase and αglucosidase, and in vivo laxative activity in rats. The metabolite phthalic acid ester (1) exhibited moderate inhibitory activity against pancreatic lipase (IC₅₀ = 24.43 ± 0.096 µg/mL) and relatively good activity against α-glucosidase (IC₅₀ = 10.28 ± 0.015 µg/mL). Sweroside (2) displayed weak activity against α-glucosidase (IC₅₀ = 40.28 ± 0.063 µg/mL) but significantly (p<0.05) increased the feacal output of the treated animals compared to the normal and sodium picosulfate controls.

H-D Analysis Employing Energy Transfer from Metastable Excited-State He in Double-Pulse LIBS with Low-Pressure He Gas

A laser-induced-breakdown-spectroscopy (LIBS) experiment with a unique double-pulse setup and operated in low-pressure (3 kPa) He ambient gas is performed to study the detection of light elements, such as hydrogen (H) and deuterium (D), as well as elements of high excitation energies, such as fluorine (F) and chlorine (Cl), which are usually difficult to detect using ordinary LIBS techniques. A nanosecond Nd:YAG laser operated in its fundamental wavelength with energy of 54 mJ is focused onto the Al target to generate the He plasma. Another picosecond Nd:YAG laser operated in its fundamental wavelength with energy of 2 mJ is focused onto the sample surface and activated 2 μs before the operation of the nanosecond laser. The application to polyvinyl chloride (PVC) and polytetrafluoroethylene (PTFE) samples produces sharp and high-intensity Cl- and F-emission lines. Meanwhile, the sharp and well-resolved H-D-emission lines with merely 0.18 nm wavelength separation are also clearly detected from a zircaloy sample. Further measurement of a set of zircaloy samples containing different concentrations of D yields a linear calibration curve with a zero intercept. The detection limit of D is found to be about 10 ppm.

NiO-nanoflakes grafted graphene: an excellent photocatalyst and a novel nanomaterial for achieving complete pathogen control

The increased levels of industrial pollutants in water and of drug-resistant pathogens more generally are a serious threat to human and aquatic life. Herein, we present the solar-light-induced dye removal and bactericidal properties of nickel oxide (NiO) and graphene nanoplatelet (GNP) nanocomposites. The conducting nature of GNPs is the key factor that accounts for the enhanced photocatalytic and antibacterial activity. Remarkably, the graphene/NiO nanocomposite shows outstanding photocatalytic activity (99% degradation) as compared to NiO (34%) alone, which makes it a potential candidate for the depollution of dye-contaminated water. In addition, the optimized amount of GNPs in the graphene/NiO nanocomposite renders it an exceptional antibacterial material, producing 100% growth inhibition of pathogenic microorganisms (both Gram-positive and Gram-negative bacteria). Therefore, the graphene/NiO nanocomposite can be an innovative material to achieve complete pathogen control, alongside being an economic solution for water treatment.

Cerebrospinal fluid procalcitonin as a biomarker of bacterial meningitis in neonates

OBJECTIVE

The objective of the study was to study the performance of cerebrospinal fluid (CSF) procalcitonin as a marker for bacterial meningitis in neonates, and to determine its optimal 'cutoff' in CSF that can be called significant for the diagnosis.

STUDY DESIGN

Neonates qualifying for lumbar puncture were prospectively studied. Procalcitonin and established CSF parameters were recorded.

RESULTS

At a cut-off value of 0.33 ng ml^-1, CSF procalcitonin had a sensitivity of 0.92, specificity of 0.87, with positive and negative likelihood ratios of 7.13 and 0.092, respectively. The area under the curve for different CSF parameters was: 0.926 (0.887 to 0.964) (P<0.001) for procalcitonin, 0.965 (0.956 to 0.974) for total leukocyte count, 0.961 (0.94 to 0.983) for neutrophil count, 0.874 (0.825 to 0.923) for protein, 0.946 (0.914 to 0.978) for sugar and 0.92 (0.955 to 0.992) for CSF:serum sugar ratio. The lumbar puncture was traumatic in 36 (21.4%) patients; out of these 15 (41.7%) had bacterial meningitis and 21 (58.3%) had no meningitis. In traumatic lumbar tap group, the median (IQR) CSF procalcitonin in patients with and without meningitis was 1.41 (0.32-3.42) ng/ml and 0.21(0.20-0.31) ng/ml respectively (p<0.05).

CONCLUSIONS

Procalcitonin measurement has diagnostic efficiency similar to the established CSF markers. Routine assessment of procalcitonin in clean non-contaminated CSF may not yield additional information, but it may have clinical utility in situations where diagnosis of meningitis is in dilemma, as in the case of blood contamination of CSF in traumatic lumbar punctures.

Recurrent activating mutations of CD28 in peripheral T-cell lymphomas

Peripheral T-cell lymphomas (PTCLs) comprise a heterogeneous group of mature T-cell neoplasms with a poor prognosis. Recently, mutations in TET2 and other epigenetic modifiers as well as RHOA have been identified in these diseases, particularly in angioimmunoblastic T-cell lymphoma (AITL). CD28 is the major co-stimulatory receptor in T cells which, upon binding ligand, induces sustained T-cell proliferation and cytokine production when combined with T-cell receptor stimulation. We have identified recurrent mutations in CD28 in PTCLs. Two residues-D124 and T195-were recurrently mutated in 11.3% of cases of AITL and in one case of PTCL, not otherwise specified (PTCL-NOS). Surface plasmon resonance analysis of mutations at these residues with predicted differential partner interactions showed increased affinity for ligand CD86 (residue D124) and increased affinity for intracellular adaptor proteins GRB2 and GADS/GRAP2 (residue T195). Molecular modeling studies on each of these mutations suggested how these mutants result in increased affinities. We found increased transcription of the CD28-responsive genes CD226 and TNFA in cells expressing the T195P mutant in response to CD3 and CD86 co-stimulation and increased downstream activation of NF-κB by both D124V and T195P mutants, suggesting a potential therapeutic target in CD28-mutated PTCLs.

Groundwater vulnerability to pollution mapping of Ranchi district using GIS

Groundwater pollution due to anthropogenic activities is one of the major environmental problems in urban and industrial areas. The present study demonstrates the integrated approach with GIS and DRASTIC model to derive a groundwater vulnerability to pollution map. The model considers the seven hydrogeological factors [Depth to water table (D), net recharge (R), aquifer media (A), soil media (S), topography or slope (T), impact of vadose zone (I) and hydraulic Conductivity(C)] for generating the groundwater vulnerability to pollution map. The model was applied for assessing the groundwater vulnerability to pollution in Ranchi district, Jharkhand, India. The model was validated by comparing the model output (vulnerability indices) with the observed nitrate concentrations in groundwater in the study area. The reason behind the selection of nitrate is that the major sources of nitrate in groundwater are anthropogenic in nature. Groundwater samples were collected from 30 wells/tube wells distributed in the study area. The samples were analyzed in the laboratory for measuring the nitrate concentrations in groundwater. A sensitivity analysis of the integrated model was performed to evaluate the influence of single parameters on groundwater vulnerability index. New weights were computed for each input parameters to understand the influence of individual hydrogeological factors in vulnerability indices in the study area. Aquifer vulnerability maps generated in this study can be used for environmental planning and groundwater management.

Cobalt chromium-based biodegradable polymer sirolimus-eluting stent: rationale, evidence and clinical experience

Metallic drug-eluting stents (DES) are the first choice for percutaneous coronary interventional treatment of coronary artery disease at present. Although they have overcome some disadvantages and limitations of plain balloon angioplasty and bare-metal stents, chronic local inflammatory reactions related to permanent polymer existence and poor vascular healing after first generation DES implantation may translate into the increased risk of late and very late stent thrombosis. There have been technological developments in stent design, materials and coatings, including more conformable platform designs, biocompatible or biodegradable polymers and improved kinetics of drug release. The newer generation DES have proven superior to previous DES technology in terms of both safety and efficacy. Accumulating evidence has suggested that DES with cobalt chromium stent platform, modified biodegradable polymer coatings, and rapamycin derivative drugs are associated with improved clinical outcomes. Currently, several new cobalt chromium biodegradable polymer sirolimus-eluting stents have been introduced to clinical practice. This review will describe basic concept and rationale behind the newer cobalt chromium biodegradable polymer sirolimus-eluting stents, systematically present the new clinical experiences with several representative devices.

Novel bioresorbable scaffolds technologies: current status and future directions

Over the past century, coronary artery disease (CAD) has remained a leading cause of death worldwide, managed with enormous progress by medicine, from the development of advanced drugs to highly sophisticated revascularization modalities. Among them, as confirmed by recent studies, bioresorbable scaffolds (BRSs) have shown to have the potential to overtake conventional stents. This review presents their material composition and properties, those currently used in clinical evaluation, and their current limitations and potential improvements.

Revascularization strategies for patients with stable coronary artery disease

Patients with coronary artery disease who have prognostically significant lesions or symptoms despite optimum medical therapy require mechanical revascularization with coronary artery bypass grafting (CABG), percutaneous coronary intervention (PCI) or both. In this review, we will evaluate the evidence-based use of the two revascularization approaches in treating patients with coronary artery disease. CABG has been the predominant mode of revascularization for more than half a century and is the preferred strategy for patients with multivessel disease, especially those with diabetes mellitus, left ventricular systolic dysfunction or complex lesions. There have been significant technical and technological advances in PCI over recent years, and this is now the preferred revascularization modality in patients with single-vessel or low-risk multivessel disease. Percutaneous coronary intervention can also be considered to treat complex multivessel disease in patients with increased risk of adverse surgical outcomes including frail patients and those with chronic obstructive pulmonary disease. Improvements in both CABG (including total arterial revascularization, off-pump CABG and 'no-touch' graft harvesting) and PCI (including newer-generation stents, adjunctive pharmacotherapy and intracoronary imaging) mean that they will continue to challenge each other in the future. A 'heart team' approach is strongly recommended to select an evidence-based, yet individualized, revascularization strategy for all patients with complex coronary artery disease. Finally, optimal medical therapy is important for all patients with coronary artery disease, regardless of the mode of revascularization.

High-resolution chromatin immunoprecipitation (ChIP) sequencing reveals novel binding targets and prognostic role for SOX11 in mantle cell lymphoma

Sex determining region Y-box 11 (SOX11) expression is specific for mantle cell lymphoma (MCL) as compared with other non-Hodgkin's lymphomas. However, the function and direct-binding targets of SOX11 in MCL are largely unknown. We used high-resolution chromatin immunoprecipitation sequencing to identify the direct target genes of SOX11 in a genome-wide, unbiased manner and elucidate its functional significance. Pathway analysis identified WNT, PKA and TGF-beta signaling pathways as significantly enriched by SOX11-target genes. Quantitative chromatin immunoprecipitation sequencing and promoter reporter assays confirmed that SOX11 directly binds to individual genes and modulates their transcription activities in these pathways in MCL. Functional studies using RNA interference demonstrate that SOX11 directly regulates WNT in MCL. We analyzed SOX11 expression in three independent well-annotated tissue microarrays from the University of Wisconsin (UW), Karolinska Institute and British Columbia Cancer Agency. Our findings suggest that high SOX11 expression is associated with improved survival in a subset of MCL patients, particularly those treated with intensive chemotherapy. Transcriptional regulation of WNT and other biological pathways affected by SOX11-target genes may help explain the impact of SOX11 expression on patient outcomes.

Are two-centimeter breast cancers large or small?

BACKGROUND

Node-negative breast cancers from 2 cm to 5 cm in size are classified as stage ii, and smaller cancers, as stage i. We sought to determine if the prognosis of women with a breast cancer exactly 2 cm in size more closely resembles that of women with a stage i or a stage ii breast cancer.

METHODS

Using a cohort of 4265 young women with breast cancer, we compared the 10-year breast cancer mortality rates for women who had a tumour 0.1-1.9 cm, exactly 2.0 cm, and 2.1-2.9 cm.

RESULTS

In the first 3 years after diagnosis, the survival pattern of women with a 2.0-cm breast cancer was nearly identical to that of women with a larger cancer (2.1-3.0 cm). From year 3 to year 10, the relative survival of women with a 2.0-cm breast cancer was improved and nearly identical to that of women with a smaller cancer. The 10-year survival rate was 89.3% for women with tumours less than 20 mm, 86.1% for women with tumours equal to 20 mm, and 81.2% for women with 21-mm to 29-mm tumours.

CONCLUSIONS

For young women with small breast cancers, the relative mortality from breast cancer is dynamic with increasing tumour size and varies with time from diagnosis.

Choices for Young Women at Intermediate Risk of Breast Cancer

Women with an inherited mutation in BRCA1 or BRCA2 have a lifetime risk of breast cancer that ap- proaches 80% [...]

Use of simple sequence repeat markers for DNA fingerprinting and diversity analysis of sugarcane (Saccharum spp) cultivars resistant and susceptible to red rot

Red rod is an economically important disease of sugarcane caused by the fungus Colletotrichum falcatum. We used a simple sequence repeat (SSR)-based marker system to identify and analyze genetic relationships of red rot resistant and susceptible sugarcane cultivars grown in Pakistan. Twenty-one highly polymorphic SSR markers were used for DNA fingerprinting and genetic diversity analysis of 20 sugarcane cultivars. These SSR markers were found to be highly robust; we identified 144 alleles, with 3-11 alleles per marker and a mean of 6.8. Three SSR markers were able to identify all 20 cultivars. DNAMAN(®)-generated homology tree was used to analyze genetic diversity among these cultivars; all cultivars shared 58% or more similarity. We correlated polymorphism information content and resolving power values with marker effectiveness in the process of sugarcane cultivar identification. We concluded that a small number of SSR-derived DNA markers will allow breeders to identify red rot resistant and susceptible cultivars.

The miRNA-17∼92 cluster mediates chemoresistance and enhances tumor growth in mantle cell lymphoma via PI3K/AKT pathway activation

The median survival of patients with mantle cell lymphoma (MCL) ranges from 3 to 5 years with current chemotherapeutic regimens. A common secondary genomic alteration detected in MCL is chromosome 13q31-q32 gain/amplification, which targets a microRNA (miRNA) cluster, miR-17∼92. On the basis of gene expression profiling, we found that high level expression of C13orf25, the primary transcript from which these miRNAs are processed, was associated with poorer survival in patients with MCL (P=0.021). We demonstrated that the protein phosphatase PHLPP2, an important negative regulator of the PI3K/AKT pathway, was a direct target of miR-17∼92 miRNAs, in addition to PTEN and BIM. These proteins were down-modulated in MCL cells with overexpression of the miR-17∼92 cluster. Overexpression of miR-17∼92 activated the PI3K/AKT pathway and inhibited chemotherapy-induced apoptosis in MCL cell lines. Conversely, inhibition of miR-17∼92 expression suppressed the PI3K/AKT pathway and inhibited tumor growth in a xenograft MCL mouse model. Targeting the miR-17∼92 cluster may therefore provide a novel therapeutic approach for patients with MCL.