An enriched approach to combining high-dimensional genomic and low-dimensional phenotypic data.

We describe an approach for combining and analyzing high-dimensional genomic and low-dimensional phenotypic data. The approach leverages a scheme of weights applied to the variables instead of observations and, hence, permits incorporation of the information provided by the low dimensional data source. It can also be incorporated into commonly used downstream techniques, such as random forest or penalized regression. Finally, the simulated lupus studies involving genetic and clinical data are used to illustrate the overall idea and show that the proposed enriched penalized method can select significant genetic variables while keeping several important clinical variables in the final model.

Improved automated spot counting and modeling with bias correction.

A complete workflow was presented for estimating the concentration of microorganisms in biological samples by automatically counting spots that represent viral plaque forming units (PFU) bacterial colony forming units (CFU), or spot forming units (SFU) in images, and modeling the counts. The workflow was designed for processing images from dilution series but can also be applied to stand-alone images. The accuracy of the methods was greatly improved by adding a newly developed bias correction method. When the spots in images are densely populated, the probability of spot overlapping increases, leading to systematic undercounting. In this paper, this undercount issue was addressed in an empirical way. The proposed empirical bias correction method utilized synthetic images with known spot sizes and counts as a training set, enabling the development of an effective bias correction function using a thin-plate spline model. Its application focused on the bias correction for the automated spot counting algorithm LoST proposed by Lin et al. Simulation results demonstrated that the empirical bias correction significantly improved spot counts, reducing bias for both fixed and random spot sizes and counts.

Production, purification and characterization of a novel antithrombotic and anticoagulant serine protease from food grade microorganism Neurospora crassa.

A novel thrombolytic enzyme was produced by food grade microorganism Neurospora crassa using agro-industrial by-products as substrates. Process parameters were optimized using Plackett-Berman and Box-Benhken design. Under the optimized fermentation conditions, high fibrinolytic activity of 403.59 U/mL was obtained. It was purified with a specific activity of 3572.4 U/mg by ammonium sulfate precipitation and SP Sepharose chromatography. The molecular weight of the enzyme was approximately 32 kDa. It exhibited maximum activity at 40 °C and pH 7.4. Its activity was enhanced by Cu2+, Na+, Zn2+, and completely inhibited by phenylmethanesulfonyl fluoride, soybean trypsin inhibitor, aprotinin, which indicates it could be a serine protease. The enzyme could degrade fibrin clot directly without the need of plasminogen activator, and effectively cleaved Aα, Bß, γ chains of fibrinogen. It could inhibit the formation of blood clots in vitro and acts as an anticoagulant. Compared to heparin the purified enzyme showed extended anticoagulant activity. Blood clots were dissolved effectively and dissolution rate was increased with time. Based on these results, this novel enzyme has the potential to be developed as a thrombolytic agent.

Fermentation optimization and disease suppression ability of a Streptomyces ma. FS-4 from banana rhizosphere soil.

BACKGROUND: Fusarium wilt of banana is one of the most destructive diseases in banana-growing regions worldwide. Soil-borne diseases and soil microbial communities are closely related. The screening of antagonistic bacteria from soil microorganisms in areas with Fusarium wilt of banana is of great practical significance for controlling this disease. RESULTS: A strain designated FS-4 was isolated from healthy banana rhizosphere soil in an area affected by Fusarium wilt. This strain exhibited a significant antagonistic effect on the pathogen. Pot experiments revealed that the fermentation broth of strain FS-4 not only decreased the incidence of banana Fusarium wilt, but also promoted the growth of banana seedlings. The strain was identified as Streptomyces ma. by its morphological, physiological, and biochemical characteristics and 16S rRNA gene sequence analysis. The culture and fermentation conditions for this strain were optimized by single-factor and response surface experiments. The optimum culture conditions for Streptomyces ma. FS-4 were as follows: peptone 0.5%, saccharose 2.4, 0.05% K2HPO4, 0.05% MgCl2, and 0.05% NaCl at an initial pH of 7.0; 180 g at 28 °C; and inoculation size of 6% for 62 h. The diameter of bacteriostasis circle for Bacillus subtilis reached 26.7 mm. CONCLUSION: Streptomyces ma. FS-4 is an important microbial resource as a biological agent for the control of plant pathogenic fungi and can be used to promote banana growth.

Transcriptome analysis of atemoya pericarp elucidates the role of polysaccharide metabolism in fruit ripening and cracking after harvest.

BACKGROUND: Mature fruit cracking during the normal season in African Pride (AP) atemoya is a major problem in postharvest storage. Our current understanding of the molecular mechanism underlying fruit cracking is limited. The aim of this study was to unravel the role starch degradation and cell wall polysaccharide metabolism in fruit ripening and cracking after harvest through transcriptome analysis. RESULTS: Transcriptome analysis of AP atemoya pericarp from cracking fruits of ethylene treatments and controls was performed. KEGG pathway analysis revealed that the starch and sucrose metabolism pathway was significantly enriched, and approximately 39 DEGs could be functionally annotated, which included starch, cellulose, pectin, and other sugar metabolism-related genes. Starch, protopectin, and soluble pectin contents among the different cracking stages after ethylene treatment and the controls were monitored. The results revealed that ethylene accelerated starch degradation, inhibited protopectin synthesis, and enhanced the soluble pectin content, compared to the control, which coincides with the phenotype of ethylene-induced fruit cracking. Key genes implicated in the starch, pectin, and cellulose degradation were further investigated using RT-qPCR analysis. The results revealed that alpha-amylase 1 (AMY1), alpha-amylase 3 (AMY3), beta-amylase 1 (BAM1), beta-amylase 3 (BAM3), beta-amylase 9 (BAM9), pullulanase (PUL), and glycogen debranching enzyme (glgX), were the major genes involved in starch degradation. AMY1, BAM3, BAM9, PUL, and glgX all were upregulated and had higher expression levels with ethylene treatment compared to the controls, suggesting that ethylene treatment may be responsible for accelerating starch degradation. The expression profile of alpha-1,4-galacturonosyltransferase (GAUT) and granule-bound starch synthase (GBSS) coincided with protopectin content changes and could involve protopectin synthesis. Pectinesterase (PE), polygalacturonase (PG), and pectate lyase (PEL) all involved in pectin degradation; PE was significantly upregulated by ethylene and was the key enzyme implicated pectin degradation. CONCLUSION: Both KEGG pathway enrichment analysis of DEGs and material content analysis confirmed that starch decomposition into soluble sugars and cell wall polysaccharides metabolism are closely related to the ripening and cracking of AP atemoya. A link between gene up- or downregulation during different cracking stages of atemoya fruits and how their expression affects starch and pectin contents were established by RT-qPCR analysis.

Genome-Wide Identification of Cyclophilin Gene Family in Cotton and Expression Analysis of the Fibre Development in Gossypium barbadense.

Cyclophilins (CYPs) are a member of the immunophilin superfamily (in addition to FKBPs and parvulins) and play a significant role in peptidyl-prolyl cis-trans isomerase (PPIase) activity. Previous studies have shown that CYPs have important functions in plants, but no genome-wide analysis of the cotton CYP gene family has been reported, and the specific biological function of this gene is still elusive. Based on the release of the cotton genome sequence, we identified 75, 78, 40 and 38 CYP gene sequences from G. barbadense, G. hirsutum, G. arboreum, and G. raimondii, respectively; 221 CYP genes were unequally located on chromosomes. Phylogenetic analysis showed that 231 CYP genes clustered into three major groups and eight subgroups. Collinearity analysis showed that segmental duplications played a significant role in the expansion of CYP members in cotton. There were light-responsiveness, abiotic-stress and hormone-response elements upstream of most of the CYPs. In addition, the motif composition analysis revealed that 49 cyclophilin proteins had extra domains, including TPR (tetratricopeptide repeat), coiled coil, U-box, RRM (RNA recognition motif), WD40 (RNA recognition motif) and zinc finger domains, along with the cyclophilin-like domain (CLD). The expression patterns based on qRT-PCR showed that six CYP expression levels showed greater differences between Xinhai21 (long fibres, G. barbadense) and Ashmon (short fibres, G. barbadense) at 10 and 20 days postanthesis (DPA). These results signified that CYP genes are involved in the elongation stage of cotton fibre development. This study provides a valuable resource for further investigations of CYP gene functions and molecular mechanisms in cotton.

Genome-wide identification and expression profiling reveal tissue-specific expression and differentially-regulated genes involved in gibberellin metabolism between Williams banana and its dwarf mutant.

BACKGROUND: Dwarfism is one of the most valuable traits in banana breeding because semi-dwarf cultivars show good resistance to damage by wind and rain. Moreover, these cultivars present advantages of convenient cultivation, management, and so on. We obtained a dwarf mutant '8818-1' through EMS (ethyl methane sulphonate) mutagenesis of Williams banana 8818 (Musa spp. AAA group). Our research have shown that gibberellins (GAs) content in 8818-1 false stems was significantly lower than that in its parent 8818 and the dwarf type of 8818-1 could be restored by application of exogenous GA3. Although GA exerts important impacts on the 8818-1 dwarf type, our understanding of the regulation of GA metabolism during banana dwarf mutant development remains limited. RESULTS: Genome-wide screening revealed 36 candidate GA metabolism genes were systematically identified for the first time; these genes included 3 MaCPS, 2 MaKS, 1 MaKO, 2 MaKAO, 10 MaGA20ox, 4 MaGA3ox, and 14 MaGA2ox genes. Phylogenetic tree and conserved protein domain analyses showed sequence conservation and divergence. GA metabolism genes exhibited tissue-specific expression patterns. Early GA biosynthesis genes were constitutively expressed but presented differential regulation in different tissues in Williams banana. GA oxidase family genes were mainly transcribed in young fruits, thus suggesting that young fruits were the most active tissue involved in GA metabolism, followed by leaves, bracts, and finally approximately mature fruits. Expression patterns between 8818 and 8818-1 revealed that MaGA20ox4, MaGA20ox5, and MaGA20ox7 of the MaGA20ox gene family and MaGA2ox7, MaGA2ox12, and MaGA2ox14 of the MaGA2ox gene family exhibited significant differential expression and high-expression levels in false stems. These genes are likely to be responsible for the regulation of GAs content in 8818-1 false stems. CONCLUSION: Overall, phylogenetic evolution, tissue specificity and differential expression analyses of GA metabolism genes can provide a better understanding of GA-regulated development in banana. The present results revealed that MaGA20ox4, MaGA20ox5, MaGA20ox7, MaGA2ox7, MaGA2ox12, and MaGA2ox14 were the main genes regulating GA content difference between 8818 and 8818-1. All of these genes may perform important functions in the developmental processes of banana, but each gene may perform different functions in different tissues or during different developmental stages.

Forearm and elbow secondary surgical procedures in neonatal brachial plexus palsy: a systematic scoping review.

Background: Neonatal Brachial plexus palsy is an injury during delivery that can lead to loss of motor function and limited range of motion in patients due to damage of nerves in the brachial plexus. This scoping review aims to explore types of procedures performed and assess outcomes of forearm and elbow secondary surgery in pediatric patients. Methods: Searches of PubMed, Cochrane, Cumulative Index to Nursing and Allied Health Literature, Web of Sciences, and Scopus were completed to obtain studies describing surgical treatment of elbow and forearm in pediatric patients with neonatal Brachial plexus palsy. 865 abstracts and titles were screened by two independent reviewers resulting in 295 full text papers; after applying of inclusion and exclusion criteria 18 articles were included. The level of evidence of this study is level IV. Results: Ten main procedures were performed to regain function of the forearm and elbow in neonatal brachial plexus birth palsy patients. Procedures had different aims, with supination contracture (6) and elbow flexion restoration (5) being the most prevalent. The variance between preoperative and postoperative soft tissue and bony procedures outcomes decreased and showed improvement with respect to the aim of each procedure category. For soft tissue procedures, a statistically significant increase was found between preoperative and postoperative values for active elbow flexion, passive supination, and active supination. For bony procedures, there was a statistically significant decrease between preoperative and postoperative values of passive and active supination. Conclusion: Overall, all procedures completed in the assessed articles of this study were successful in their aim. Bony procedures, specifically osteotomies, were found to have a wider range of results, whereas soft tissue procedures were found to be more consistent and reproducible with respect to their outcomes. Bony and soft tissue procedures were found vary in their aims and outcomes. This study indicates the need for further research to augment knowledge about indications and long-term benefits to each procedure.

Screening and Analysis of Antifungal Strains Bacillus subtilis JF-4 and B. amylum JF-5 for the Biological Control of Fusarium Wilt of Banana.

PURPOSE: This study aimed to identify the antagonistic bacteria from the rhizosphere of healthy bananas that can effectively suppress the Fusarium wilt of banana, and to further investigate the inhibitory mechanism. METHOD: The primary and secondary screening techniques were implemented using the double-plate and fermentation antagonism methods. The strain was identified based on physiological and biochemical tests, 16S rRNA gene sequencing, and specific gene amplification. The effects of crude extract on the protein content, lipid peroxidation, and pectinase activity of mycelia were determined from the identified isolates. RESULTS: Two antagonistic bacteria, JF-4 and JF-5, were screened and initially identified as Bacillus subtilis (GenBank: OR125631) and B. amylum (GenBank: OR125632). The greenhouse experiment showed that the biological control efficiency of the two antagonists against the Fusarium wilt of banana was 48.3% and 40.3%, respectively. The catalase content produced by lipid peroxidation increased significantly after treatment with the crude extracts of JF-4 and JF-5 at concentrations of 0.69 µmol/L and 0.59 µmol/L, respectively. The protein and ergosterol content and pectinase activity decreased significantly. The two antagonistic bacteria might inhibit the growth of pathogens by enhancing lipid peroxidation and decreasing the synthesis of cell metabolites. Twenty compounds were identified by gas chromatography-mass spectrometry (GC-MS). B. subtilis JF-4 was further sequenced and assembled to obtain a complete circular chromosome genome of 681,804,824 bp. The genome consisted of a 4,310,825-bp-long scaffold. CONCLUSION: The findings of this study may help elucidate the mechanism behind this biocontrol isolate.

Outcomes of humeral osteotomies versus soft-tissue procedures in secondary surgical procedures for neonatal brachial plexus palsy: a meta-analysis.

Secondary surgical procedures can be used in brachial plexus birth injury to correct shoulder movement imbalances. This study compares outcomes of the two secondary surgical procedure types: humeral osteotomies and soft tissue procedures. Outcome measures assessed included active and passive internal and external rotation, active and passive abduction and adduction, active and passive flexion and extension, percentage of the humeral head anterior to the middle glenoid fossa, glenoid version, and Mallet Score. Nineteen full-text articles were included in the analysis. Humeral osteotomies resulted in a loss of internal rotation postoperatively (-15.94°). Active internal rotation was not evaluated for soft tissue procedures. All other assessed outcomes were improved postoperatively for bony and soft tissue procedures. Bony procedures exhibited a greater degree of active external rotation postoperatively when compared to soft tissue procedures (+67° vs. +40°). Both bony and soft tissue procedures Improve shoulder function in children with neonatal brachial plexus palsy, however, soft tissue procedures showed greater consistency in outcomes. Level of Evidence: IV.

Automated Spot Counting in Microbiology.

Biological samples are routinely analyzed for microbe concentration. The samples are diluted, loaded onto established host cell cultures, and incubated. If infectious agents are present in the samples, they form circular spots that do not contain the host cells. Each spot is assumed to be originated from a single microbial unit such as a bacterial colony forming unit or viral plaque forming unit. The undiluted sample concentration is estimated by counting the spots and back-calculating. Counting the number of spots by trained technicians is currently the gold standard but it is laborious, subjective, and hard to scale. This paper presents a new automated algorithm for spot counting, Localized and Sequential Thresholding (LoST). Validation studies showed that LoST performance was comparable with manual counting and outperformed several existing tools on images with overlapping spots. The LoST algorithm employs sequential thresholding through a two-stage segmentation and borrows information across all images from the same dilution series to fine-tune the count and identify right censoring. The algorithm increases the efficiency of the spot counting and the quality of the downstream analysis, especially when coupled with an appropriate statistical serial dilution model to enhance the undiluted sample concentration estimation procedure.

Assessment of one-year risk of ischemic stroke versus major bleeding in patients with atrial fibrillation.

Background: Patients diagnosed with atrial fibrillation (AF) are at increased risk of stroke. Several guidelines to assess the risk of ischemic stroke and major bleeding in AF patients have been published. The CHA 2 DS 2 -VASc score has been adopted widely for predicting stroke within one year of the index AF diagnosis and is used to guide the prescription of anticoagulants. Anticoagulation therapy increases the risk of bleeding and scoring systems such as HAS-BLED assess the risk of major bleeding in anticoagulated patients. Despite these advances, no study has examined the risks of the two outcomes simultaneously. How patients' fear of particular outcomes affects these risks also remains unknown. Methods: We incorporated the risks of ischemic stroke and major bleeding within one year of the index AF admission as well as the fear of stroke and bleeding of each individual patient. The patients enrolled in this retrospective observational study were identified using hospital admission data from the Myocardial Infarction Data Acquisition System (MIDAS), a statewide database including all hospitalizations for cardiovascular disease in New Jersey. Probabilities of the outcomes (ischemic stroke, major bleeding, both, or neither within one year of the index AF admission) were estimated using multinomial regression with patient demographics and comorbidities (heart failure [HF], hypertension [HTN], diabetes mellitus [DM], anemia, chronic obstructive pulmonary disease [COPD], kidney disease [KD], prior stroke or transient ischemic attack [TIA]) as predictors. These estimates were used in a Deming regression to model the association of ischemic stroke and major bleeding in grouped patients. The assessment of the importance of each outcome was superimposed on the final model to arrive at a recommendation for anticoagulation therapy. Results: The results of the Deming regression indicated a positive relationship between ischemic stroke and major bleeding (slope = 1.67, 95% confidence interval [CI] 1.37 to 1.97). Estimates of the risks of the two outcomes and the lines of best fit from Deming regression were determined. This model for risk assessment of stroke and major bleeding within one year of the index AF hospital admission combined objective data and subjective assessment of the relative fear of stroke versus bleeding by each hypothetical patient on 0-100 scale. Examples with the fears of stroke versus major bleeding being equal (50-50) and a higher fear of stroke (80-20) are presented. Conclusions: The new model for risk assessment of ischemic stroke and major bleeding within one year of the index AF hospital admission proposed in this work used objective, empirically driven measures, and subjective assessment of the outcomes' importance for individual patients. Such models may assist physicians in their decision making regarding anticoagulation therapy.

Analysis of transcriptome data and quantitative trait loci enables the identification of candidate genes responsible for fiber strength in Gossypium barbadense.

Gossypium barbadense possesses a superior fiber quality because of its fiber length and strength. An in-depth analysis of the underlying genetic mechanism could aid in filling the gap in research regarding fiber strength and could provide helpful information for Gossypium barbadense breeding. Three quantitative trait loci related to fiber strength were identified from a Gossypium barbadense recombinant inbred line (PimaS-7 × 5917) for further analysis. RNA sequencing was performed in the fiber tissues of PimaS-7 × 5917 0-35 days postanthesis. Four specific modules closely related to the secondary wall-thickening stage were obtained using the weighted gene coexpression network analysis. In total, 55 genes were identified as differentially expressed from 4 specific modules. Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes were used for enrichment analysis, and Gbar_D11G032910, Gbar_D08G020540, Gbar_D08G013370, Gbar_D11G033670, and Gbar_D11G029020 were found to regulate fiber strength by playing a role in the composition of structural constituents of cytoskeleton and microtubules during fiber development. Quantitative real-time PCR results confirmed the accuracy of the transcriptome data. This study provides a quick strategy for exploring candidate genes and provides new insights for improving fiber strength in cotton.

Controlled Study of Traditional Ultrasound and Ultrasound Elastography on the Diagnosis of Breast Masses.

This study aims to explore the application values of traditional ultrasound (contrast ultrasound [CUS]) and ultrasound elastography (UE) (including gray-scale ultrasound, color Doppler flow imaging, spectral Doppler ultrasound) in the diagnosis of breast masses. Postoperative histopathological diagnosis was used as the gold standard. One hundred seventy benign and malignant breast lesions from our hospital were retrospectively analyzed. The sensitivity, specificity, and diagnostic accuracy differences of breast malignancy diagnosed by UE and CUS were compared. The sensitivity, specificity, and diagnostic accuracy rates of breast malignancy diagnosed by UE were 98.7%, 90.2%, and 97.7%, whereas that by CUS were 93.6%, 76.1%, and 78.9%, respectively. The specificity and diagnosis rate of UE in the differential diagnosis of malignant breast lesions are superior to those of CUS and have an important clinical value.

Microchannel refill: a new method for fabricating 2D nanochannels in polymer substrates.

In this paper, we present a new approach that is capable of fabricating nanochannels in a poly(methyl methacrylate) (PMMA) substrate. This method, which we call microchannel refill (MR), utilizes the refilling of glassy thermoplastics under thermal compression to reduce a microscopic channel to a nanochannel. It only has two main steps. First, a microchannel is fabricated in a PMMA substrate using normal hot embossing. Second, the microchannel is compressed under a certain temperature and pressure to obtain a nanochannel. We show that a nanochannel with a width as small as 132 nm (with a depth of 85 nm) can be easily produced by choosing the appropriate compression temperature, compression pressure, original microchannel width and original microchannel aspect ratio. Compared with most current nanochannel fabrication methods, MR is a quick, simple and cost-effective way to produce nanochannels in polymer substrates.