SMARTp: A SMART design for nonsurgical treatments of chronic periodontitis with spatially referenced and nonrandomly missing skewed outcomes

This paper proposes dynamic treatment regimes (DTRs) as effective individualized treatment strategies for managing chronic periodontitis. The proposed DTRs are studied via SMARTp —a two-stage sequential multiple assignment randomized trial (SMART) design. For this design, we propose a statistical analysis plan and a novel cluster-level sample size calculation method that factors in typical features of periodontal responses such as non-Gaussianity, spatial clustering, and nonrandom missingness. Here, each patient is viewed as a cluster, and a tooth within a patient's mouth is viewed as an individual unit inside the cluster, with the tooth-level covariance structure described by a conditionally autoregressive structure. To accommodate possible skewness and tail behavior, the tooth-level clinical attachment level (CAL) response is assumed to be skew-t, with the nonrandomly missing structure captured via a shared parameter model corresponding to the missingness indicator. The proposed method considers mean comparison for the regimes with or without sharing an initial treatment, where the expected values and corresponding variances or covariance for the sample means of a pair of DTRs are derived by the inverse probability weighting and method of moments. Simulation studies are conducted to investigate the finite-sample performance of the proposed sample size formulas under a variety of outcome-generating scenarios. An R package SMARTp implementing our sample size formula is available at the Comprehensive R Archive Network for free download.     

Catch composition of drift gillnets in a multi-species fishery with an emphasis on kingfish (Scomberomorus commerson) in Northern Persian Gulf

Gillnets are the primary fishing gear used in tropical multi-species fisheries along the Iranian southern coastal waters. Therefore, it is necessary to investigate the catch composition and performance of fishing gear for the possible negative effects on the stocks. Catch data and length frequency distribution (just for Kingfish, S. commerson) were examined for three kinds of drift gillnets: 1) small-meshed nets, 2) medium-meshed nets, and 3) nets with a single mesh size of 165 mm. This study was conducted in the northern part of the Persian Gulf from 2014 to 2015. Overall, 60 species of 32 families from four fish groups (i.e., Pelagic, Demersal, Benthopelagic, and Reef-associated) were recorded. Each net-type was used to target more than one species, with most species being considered as bycatch. Commercial fish species were caught the most, accounting for around 83% of the total catches. S. commerson is targeted by all kinds of nets, with medium-meshed nets being most efficient. The majority of S. commerson caught by the nets were immature. Overall, the total ban of gillnets with small mesh sizes is recommended to protect young S. commerson and prevent the possible risk of growth overfishing. Studies on gillnet selectivity are needed to set minimum mesh regulations for S. commerson and other commercial species if the potential impacts of gillnet are known.     

Acute phase response in lame cattle with interdigital dermatitis

This study was undertaken to evaluate acute phase response via assessing the concentration of serum sialic acids (total, lipid-bound and protein-bound), inflammatory mediators (IFN-γ and TNF-α) and acute phase proteins [haptoglobin (Hp) and serum amyloid A (SAA)] in lame cattle with interdigital dermatitis. Fifteen hoof scrapings from lame cows were collected from eight commercial dairy farms. As a consequence of the difficulty in culturing and isolation, a PCR technique was used to detect the organism. None of the colonies on enriched blood agar was identified as Fusobacterium necrophorum. Four (26.6%) out of the 15 hoof scrapings examined tested positive for the presence of the lktA gene (402 bp) of F. necrophorum. It seems that culture cannot be considered as the gold standard method for F. necrophorum isolation. Molecular detection is suggested as an alternative method. In the blood serum of different groups of animals (control, lameness and F. necrophorum-positive lameness) Hp, SAA, total sialic acid, lipid-bound sialic acid, and protein-bound sialic acid, and IFN-γ and TNF-α were measured using validated standard procedures. All parameters were significantly higher in the lameness group and the F. necrophorum-positive lameness group compared with the healthy group (P < 0.01 in all cases). Mean SAA concentrations in the lameness group and the F. necrophorum-positive lameness group was relatively 4.6 and 8.0 times higher than the control group. Corresponding measures for Hp indicate a 3.3 times increase in the lameness group compared to the control. In the lameness group, significant associations were observed for Hp with PBSA, SAA with TSA, TSA with PBSA, TSA with LBSA, PBSA with LBSA, and SAA with IFN-γ.     

Type III effector VopC mediates invasion for Vibrio species

Vibrio spp. are associated with infections caused by contaminated food and water. A type III secretion system (T3SS2) is a shared feature of all clinical isolates of V. parahaemolyticus and some V. cholerae strains. Despite its being responsible for enterotoxicity, no molecular mechanism has been determined for the T3SS2-dependent pathogenicity. Here, we show that although Vibrio spp. are typically thought of as extracellular pathogens, the T3SS2 of Vibrio mediates host cell invasion, vacuole formation, and replication of intracellular bacteria. The catalytically active effector VopC is critical for Vibrio T3SS2-mediated invasion. There are other marine bacteria encoding VopC homologs associated with a T3SS; therefore, we predict that these bacteria are also likely to use T3SS-mediated invasion as part of their pathogenesis mechanisms. These findings suggest a new molecular paradigm for Vibrio pathogenicity and modify our view of the roles of T3SS effectors that are translocated during infection.     

Sgs1 truncations induce genome rearrangements but suppress detrimental effects of BLM overexpression in Saccharomyces cerevisiae

RecQ-like DNA helicases are conserved from bacteria to humans. They perform functions in the maintenance of genome stability, and their mutation is associated with cancer predisposition and premature aging syndromes in humans. Here, a series of C-terminal deletions and point mutations of Sgs1, the only RecQ-like helicase in yeast, show that the Helicase/RNase D C-terminal domain and the Rad51 interaction domain are dispensable for Sgs1's role in suppressing genome instability, whereas the zinc-binding domain and the helicase domain are required. BLM expression from the native SGS1 promoter had no adverse effects on cell growth and was unable to complement any sgs1Δ defects. BLM overexpression, however, significantly increased the rate of accumulating gross-chromosomal rearrangements in a dosage-dependent manner and greatly exacerbated sensitivity to DNA-damaging agents. Co-expressing sgs1 truncations of up to 900 residues, lacking all known functional domains of Sgs1, suppressed the hydroxyurea sensitivity of BLM-overexpressing cells, suggesting a functional relationship between Sgs1 and BLM. Protein disorder prediction analysis of Sgs1 and BLM was used to produce a functional Sgs1-BLM chimera by replacing the N-terminus of BLM with the disordered N-terminus of Sgs1. The functionality of this chimera suggests that it is the disordered N-terminus, a site of protein binding and posttranslational modification, that confers species specificity to these two RecQ-like proteins.     

Abundance and biological parameters of psyllophagous coccinellids in pistachio orchards

The abundance of coccinellids on pistachio trees was monitored at both a cultivated pistachio plantation and a wild pistachio growing area in Rafsanjan, Iran. Eleven ladybird species were identified from planted pistachio trees with Adalia bipunctata (Linnaeus) and Oenopia conglobata contaminata (Menetries) the most abundant ladybirds. At the wild pistachio plantation site, 17 coccinellid species were collected, with Brumus undulatus Weise the most abundant ladybird, followed by A. bipunctata and O. conglobata contaminata. Three species of Coccinellidae were evaluated for their potential for biological control of the common pistachio psylla (CPP), Agonoscena pistaciae Burckhardt and Lauterer. Coccinella undecimpunctata aegyptica (Reiche), Exochomus nigripennis (Erichson) and Hippodamia variegata (Goeze) developed successfully on A. pistaciae nymphs and reproduced successfully. Development and reproduction of these ladybirds were also examined on an alternative prey, the cotton aphid Aphis gossypii Glover, the most abundant aphid species on herbal weeds in pistachio orchards. The highest intrinsic rate of natural increase (r_m value) was observed in C. undecimpunctata aegyptica, 0.22 and 0.23 when it was fed on A. pistaciae and A. gossypii Glover, respectively. In comparison, the lowest r_m values (0.12 and 0.13) were found in E. nigripennis on the CPP and cotton aphid diets, respectively. Exochomus nigripennis consumed the largest number of psyllid nymphs during larval period, while the adults consumed the lowest number of psyllid nymphs daily. Although eight psyllophagous coccinellid species were collected in colonies of the CPP on pistachio trees, they did not regulate psyllid numbers below damaging levels. At present, conservation should assume a central role in biological control strategies for this pest.     

Modeling of crossbred cattle growth, comparison between cubic and piecewise random regression models

Two analyses, cubic and piecewise random regression, were conducted to model growth of crossbred cattle from birth to about two years of age, investigating the ability of a piecewise procedure to fit growth traits without the complications of the cubic model. During a four-year period (1994-1997) of the Australian "Southern Crossbreeding Project", mature Hereford cows (N = 581) were mated to 97 sires of Angus, Belgian Blue, Hereford, Jersey, Limousin, South Devon, and Wagyu breeds, resulting in 1141 steers and heifers born over four years. Data included 13 (for steers) and eight (for heifers) live body weight measurements, made approximately every 50 days from birth until slaughter. The mixed model included fixed effects of sex, sire breed, age (linear, quadratic and cubic), and their interactions between sex and sire breed with age. Random effects were sire, dam, management (birth location, year, post-weaning groups), and permanent environmental effects and for each of these when possible, their interactions with linear, quadratic and cubic growth. In both models, body weights of all breeds increased over pre-weaning period, held fairly steady (slightly flattening) over the dry season then increased again towards the end of the feedlot period. The number of estimated parameters for the cubic model was 22 while for the piecewise model it was 32. It was concluded that the piecewise model was very similar to the cubic model in the fit to the data; with the piecewise model being marginally better. The piecewise model seems to fit the data better at the end of the growth period.     

Differential regulation of aquaporins, small GTPases and V-ATPases proteins in rice leaves subjected to drought stress and recovery

Mechanisms of drought tolerance are complex, interacting, and polygenic. This paper describes patterns of gene expression at precise physiological stages of drought in 35-day-old seedlings of Oryza sativa cv. Nipponbare. Drought was imposed gradually for up to 15 days, causing abscisic acid levels to rise and growth to cease, and plants were then re-watered. Proteins were identified from leaf samples after moderate drought, extreme drought, and 3 and 6 days of re-watering. Label-free quantitative shotgun proteomics resulted in identification of 1548 non-redundant proteins. More proteins were down-regulated in early stages of drought but more were up-regulated as severe drought developed. After re-watering, there was notable down regulation, suggesting that stress-related proteins were being degraded. Proteins involved in signalling and transport became dominant as severe drought took hold but decreased again on re-watering. Most of the nine aquaporins identified were responsive to drought, with six decreasing rapidly in abundance as plants were re-watered. Nine G-proteins appeared in large amounts during severe drought and dramatically degraded once plants were re-watered. We speculate that water transport and drought signalling are critical elements of the overall response to drought in rice and might be the key to biotechnological approaches to drought tolerance.     

Type VI Secretion System Toxins Horizontally Shared between Marine Bacteria

The type VI secretion system (T6SS) is a widespread protein secretion apparatus used by Gram-negative bacteria to deliver toxic effector proteins into adjacent bacterial or host cells. Here, we uncovered a role in interbacterial competition for the two T6SSs encoded by the marine pathogen Vibrio alginolyticus. Using comparative proteomics and genetics, we identified their effector repertoires. In addition to the previously described effector V12G01_02265, we identified three new effectors secreted by T6SS1, indicating that the T6SS1 secretes at least four antibacterial effectors, of which three are members of the MIX-effector class. We also showed that the T6SS2 secretes at least three antibacterial effectors. Our findings revealed that many MIX-effectors belonging to clan V are “orphan” effectors that neighbor mobile elements and are shared between marine bacteria via horizontal gene transfer. We demonstrated that a MIX V-effector from V. alginolyticus is a functional T6SS effector when ectopically expressed in another Vibrio species. We propose that mobile MIX V-effectors serve as an environmental reservoir of T6SS effectors that are shared and used to diversify antibacterial toxin repertoires in marine bacteria, resulting in enhanced competitive fitness.     

Significant Efficiency Enhancement in Ultrathin CZTS Solar Cells by Combining Al Plasmonic Nanostructures Array and Antireflective Coatings

In the few past years, the economic and eco-friendly Cu₂ZnSnS₄ (CZTS) solar cells have caught lots of attentions. However, due to rather poor efficiency, identifying deficiencies and making improvements is necessary. In the present study, the performance improvement of ultrathin CZTS solar cells was achieved through (1) incorporation of anti-reflective coating (ARC) on the surface of cell and (2) embedding Al plasmonic nanostructures with different radius, periods, and vertical positions in the absorber layer. Various thicknesses of CZTS absorber layer were simulated optically and electrically using FDTD and DEVICE solver of Lumerical software. The reference solar cell consists of a 1.5-nm-thick CZTS absorber and exhibit an efficiency of up to 5.67%, short-circuit current density (Jsc) of 18.48 mA cm⁻² and open circuit voltage of 0.58 V. Result showed a remarkable performance enhancement of the solar cell in spite of a very thin absorber layer. For a 500-μm-thick CZTS solar cell with the assistance of ARC and embedding Al plasmonic nanostructures, the efficiency is increased to 7.45% due to an increase in Jsc to 22.62 mA cm⁻² with an open circuit voltage of 0.62 V.