bluuebunny/crossref_metadata_2025 huggingface dataset:
A New Strain of Bean Common Mosaic Virus From Lima Bean (Phaseolus lunatus): Biological and Molecular Characterization
Authors: Feng Xue , Orellana Gardenia E. , Green James C. , Melzer Michael J. , Hu John S. , Karasev Alexander V.
Published: January 2019

Lima bean (Phaseolus lunatus) is a popular cultivated legume vegetable grown in the United States for dry bean or canned bean production. In 2017, two symptomatic P. lunatus plants exhibiting mosaic, vein banding, and growth retardation were collected in a public garden in Honolulu, HI. Both samples contained bean common mosaic virus (BCMV), and the two BCMV isolates were subjected to biological characterization on a panel of 11 differential cultivars of common bean (P. vulgaris), and to molecular characterization through whole genome sequencing. Both samples contained nearly identical BCMV sequences, named BCMV-A1, which, in turn, were 93% identical to the peanut stripe virus strain of BCMV. BCMV-A1 induced an unusually severe systemic necrosis in cultivar ‘Dubbele Witte’, and pronounced necrotic or chlorotic reaction in inoculated leaves of five other bean differentials. BCMV-A1 was able to partially overcome resistance alleles bc-1 and bc-2 expressed singly in common bean, inducing no systemic symptoms. Phylogenetic analysis of the BCMV-A1 sequence, and distinct biological reactions in common bean differentials suggested that BCMV-A1 represented a new lima bean strain of BCMV. In 2017, two BCMV isolates were collected in Idaho from common bean, and based on partial genome sequences were found 99% identical to the BCMV-A1 sequence. The data suggest that the lima bean strain of BCMV may have a wider circulation, including common bean as a host. This new strain of BCMV may thus pose a significant threat to common bean production.
Granulomatous Reaction to Intralesional Kenalog (Triamcinolone) Injection in Acne: A Case Report
Authors: Song Yali , Guo Ying
Published: January 2019

Intralesional Kenalog (triamcinolone) injection is a useful treatment for several skin conditions. Although dermal deposition of triamcinolone has been described in the literature, histopathologic findings of foreign body reactions to it have seldom been reported. Here, we describe a case of a granulomatous reaction to the intralesional injection of triamcinolone acetonide in the treatment of nodulocystic acne.
Tumors of the Ischiorectal Fossa: A Single-Institution Experience
Authors: Zhu Katherine J. , Lee Peter J. , Austin Kirk K. S. , Solomon Michael J.
Published: January 2019

BACKGROUND:

Ischiorectal fossa tumors are rare.

OBJECTIVE:

This study reviews a single institution’s series of ischiorectal tumors with comparison against presacral tumors and assesses the utility of preoperative biopsy and angioembolization.

DESIGN:

This is a retrospective study.

SETTINGS:

This study was conducted at a quaternary referral center.

PATIENTS:

All patients with ischiorectal tumor treated between February 1995 and April 2017 were retrospectively reviewed. Tumors extending secondarily into the ischiorectal fossa and inflammatory pathologies were excluded.

INTERVENTIONS:

Preoperative biopsy, neoadjuvant therapy, angioembolization, and surgical excision of these tumors were reviewed.

MAIN OUTCOME MEASURES:

Demographic, perioperative, pathological, and oncologic outcomes were evaluated.

RESULTS:

Twenty-four patients (15 female; median age 54) were identified. Two-thirds were symptomatic. Forty-six percent had a palpable mass. All patients had CT and/or MRI. Fifty percent had a preoperative biopsy, of which 83% were diagnostic, and management was altered in 50%. All patients underwent surgical excision. Fifty-five percent had local excision, 38% had radical pelvic excision, and 8% had total mesorectal excision. Two patients had preoperative angioembolization. Both had successful R0 local excision. Morbidity occurred in 25%, with 1 major complication. There was no 30-day mortality. Histopathology demonstrated 17 soft tissue tumors (3 malignant), 2 GI stromal tumors, 1 neuroendocrine tumor, 1 Merkel cell carcinoma, 1 basaloid carcinoma, 1 epidermal cyst, and 1 lipoma. R0 resection was achieved in 75%. All patients were alive after a median follow-up of 33 months. Four patients developed recurrence at a median 10 months postoperatively. All recurrences were malignant, and 75% had had a R1 resection.

LIMITATIONS:

This study is limited by its small numbers. The quaternary institution source may introduce bias.

CONCLUSIONS:

Ischiorectal fossa tumors are heterogeneous and more likely to be malignant than presacral tumors. Biopsy can be useful if a malignant diagnosis is suspected and changes management in 50% of cases. Preoperative embolization may be useful for large vascular tumors. R0 resection is important to minimize recurrence. See Video Abstract at http://links.lww.com/DCR/A779.
Sufficient Cause Interaction for Time-to-event Outcomes
Authors: Stensrud Mats Julius , Ryalen Pål Christie , Røysland Kjetil
Published: January 2019

Methods to assess sufficient cause interactions are well developed for binary outcomes. We extend these methods to handle time-to-event outcomes, which occur frequently in medicine and epidemiology. Based on theory for marginal structural models in continuous time, we show how to assess sufficient cause interaction nonparametrically, allowing for censoring and competing risks. We apply the method to study interaction between intensive blood pressure therapy and statin treatment on all-cause mortality.
Autologous Partial-thickness Scleral Flap and Donor Corneal Graft in Management of Tube Erosion of Glaucoma Drainage Device
Authors: Liu Xiongfei , Law Simon K.
Published: January 2019

Purpose:

To evaluate the outcomes of autologous limbus-hinged partial-thickness scleral flap and half-moon-shaped split-thickness donor corneal allograft in management of tube erosion of glaucoma drainage device.

Methods:

Consecutive patients who had undergone a limbus-hinged partial-thickness scleral flap and half-moon-shaped split-thickness corneal graft were reviewed. Primary outcome was surgical success of coverage of the exposed tube without complications or additional surgeries. Secondary outcomes were visual acuity (VA), intraocular pressure, number of glaucoma medications, surgical complications, and additional surgeries.

Results:

From March 1, 2016 to August 30, 2017 (18 mo), 8 consecutive cases (7 patients) of tube erosions were included for analysis. Mean follow-up and age were 16.6±5.4 months and 74.4±15.2 years, respectively. Mean number of intraocular surgeries was 4.8±1.6 (range: 3 to 6 surgeries) and intraocular glaucoma surgeries was 2.9±1.7 (range: 1 to 6 surgeries) before tube erosion. There were no intraoperative or postoperative complications or recurrence of tube erosion in any patient. Differences between the preoperative and postoperative number of medications (2.6±1.8, 2.9±1.8, respectively; P=0.171) and intraocular pressure (12.9±6.9, 10.8±3.5 mm Hg, respectively; P=0.209) were not statistically significant. Preoperative and 3-month postoperative VA were identical in all eyes except in 1 eye that the VA improved from 20/300 to 20/70 after repair.

Conclusions:

Combination of limbus-hinged partial-thickness scleral flap and half-moon-shaped split-thickness corneal allograft is a viable surgical option to repair tube erosion.
Use of a Collagen Matrix Implant as an Adjuvant in Combined Surgery Involving Phacoemulsification and Nonpenetrating Deep Sclerectomy
Authors: Paletta Guedes Ricardo A. , Gravina Daniela M. , Paletta Guedes Vanessa M. , Chaoubah Alfredo
Published: January 2019

Aim:

To assess the efficacy and safety of the Ologen collagen matrix as an adjuvant for combined phacoemulsification and nonpenetrating deep sclerectomy (Phaco-NPDS), in addition to mitomycin C (MMC).

Materials and Methods:

This was a longitudinal retrospective comparative study of eyes treated with Phaco-NPDS, with (group 1) or without (group 2) an Ologen collagen matrix implant, in addition to MMC. The main outcome measures were operative success [absolute success: intraocular pressure (IOP) <18 mm Hg and an at least 20% reduction from baseline without medication; relative success: IOP<18 mm Hg and at least 20% reduction from baseline IOP with or without medication], mean reductions (%) in IOP and medication use; number of postoperative reinterventions (goniopuncture, needling, reoperation), and number of complications.

Results:

The mean age of the study population (N=100) was 72.0±9.7 years. Groups 1 (n=51) and 2 (n=49) achieved absolute success rates of 72.5% and 55.1%, respectively (P=0.054), and relative success rates of 90.2% and 83.7%, respectively (P=0.251). From a similar baseline IOP (19.8 and 20.7 mm Hg in groups 1 and 2, respectively, P=0.527), eyes in group 1 achieved a significant lower 12-month IOP (11.7 vs. 14.5 mm Hg, respectively, P=0.002) and a lower rate of medication use (0.2 vs. 0.9, respectively, P<0.001). Eyes in group 2 presented with a higher rate of bleb failure (12.2% vs. 2.0%, P=0.028), leading to a higher rate of needling procedures (38.8% vs. 2.0%, P<0.001) during the postoperative period.

Conclusions:

The adjunctive use of Ologen collagen matrix in addition to MMC during Phaco-NPDS was associated with a higher rate of absolute success, a lower mean IOP at 12 months, a lower rate of bleb failure, and a lower rate of postoperative bleb needling.
Ziprasidone Augmentation of SSRI Antidepressants in Posttraumatic Stress Disorder
Authors: Hamner Mark B. , Hernandez-Tejada Melba A. , Zuschlag Zachary D. , Agbor-Tabi Deborah , Huber Michael , Wang Zhewu
Published: January 2019

Background

Posttraumatic stress disorder (PTSD) is often a chronic, disabling illness for which antidepressant medications (ie, SSRI) are considered the primary psychopharmacological treatment. However, many patients remain refractory to antidepressants alone or in combination with psychotherapy. Safe and effective treatments for individuals with refractory PTSD are needed. This study aimed to examine ziprasidone augmentation of SSRI treatment of PTSD.

Methods

This was a 2-phase study. In phase 1, subjects were treated with paroxetine or sertraline for 8 weeks. Individuals refractory to the SSRI treatment then entered into phase II of the study and were randomized, in a double-blind fashion, to 8 weeks of treatment with either ziprasidone or placebo. The primary outcome measure was change in Clinician Administered PTSD Scale total scores with the intent-to-treat sample. Secondary outcome measures included Positive and Negative Syndrome Scale scores, measures of depression and anxiety, and safety measures.

Results

No significant differences were observed on the Clinician Administered PTSD Scale, Positive and Negative Syndrome Scale, or other outcome measures between ziprasidone and placebo groups. No significant differences were observed for safety measures including metabolic profiles, extrapyramidal symptoms/movement disorder rating scales, nor study dropout.

Conclusions

Although no significant differences were noted in efficacy or safety measures between ziprasidone and placebo in this pilot study, the small sample size prevents definitive conclusions.
Correlation Between Clinical Signs and High‐resolution Manometry Data in Children
Authors: Juzaud Marine , Lamblin Marie‐Dominique , Fabre Alexandre , Alessandrini Marine , Baumstarck Karine , Bazin Camille , Esteve Clothilde , Laborde Nolwenn , Osei Lindsay , Michaud Laurent , Gottrand Frederic , Vitton Veronique
Published: January 2019

Objectives:

High‐resolution manometry (HRM) is the gold standard for diagnosis of esophageal motility disorders. However, clinical signs associated with these disorders are nonspecific, and it is difficult to correlate clinical signs with HRM data. The main objective of our study was to assess the positive predictive value (PPV) and negative predictive value (NPV) of each clinical sign, as well as their sensitivity and specificity in the diagnosis of esophageal motility disorders.

Methods:

This is a bicentric retrospective cohort study based on HRM data collected between May 2012 and May 2016. The studied symptoms were weight loss, feeding difficulties, swallowing disorders, dysphagia, food blockages, vomiting, gastroesophageal reflux disease (GERD), belching, and respiratory symptoms. HRM data were analyzed according to the Chicago Classification (3.0).

Results:

In total, 271 HRM data were analyzed, of which 90.4% showed abnormal results. HRM was well tolerated in 91% of the cases. The most common esophageal motility disorder was ineffective esophageal motility (38%). Weight loss was significantly associated (P = 0.003) with an abnormal HRM with a 96% PPV.

Conclusions:

With nonspecific clinical signs suggesting an esophageal motility disorder, weight loss was a predictive sign of abnormal HRM results. HRM was well tolerated in pediatric patients, and ineffective esophageal motility appears to be the most frequent motility disorder in our cohort, as already observed in adult patient studies.
Preterm Birth Has Effects on Gut Colonization in Piglets Within the First 4 Weeks of Life
Authors: Kamal Shamrulazhar Shamzir , Andersen Anders Daniel , Krych Lukasz , Lauridsen Charlotte , Sangild Per Torp , Thymann Thomas , Nielsen Dennis Sandris
Published: January 2019

Objectives:

Preterm neonates have an immature gastrointestinal tract and show an altered bacterial colonization of the gut. However, it is not clear if such immature gut microbiota (GM) colonization is induced by specific delivery, diet, environment, and/or host factors related to preterm birth. Using piglets as models for infants, we hypothesized that both shortened gestational age (GA) and start of enteral feeding affect GM composition after caesarean delivery and rearing in identical environments.

Methods:

Caesarean‐delivered preterm and term pigs were reared in incubators and fed total parenteral nutrition (TPN) or gradually increasing early enteral feeding (EEF) for 5 days, followed by full enteral feeding with bovine milk until day 26. GM composition was determined by 16S rRNA gene‐amplicon sequencing and luminal short‐chain fatty acids (SCFAs) by GC‐MS.

Results:

Both GA and EEF feeding affected GM composition on day 5, but only the GA effect persisted until day 26. On day 5, Enterobacteriaceae were dominant, with Lachnospiraceae members also being abundant. Enterobacteriaceae still dominated the GM at day 26 but with higher Akkermansia relative abundance in term pigs. Colonic concentrations of acetate and propionate were higher, and formate lower in term pigs, relative to preterm pigs on day 26.

Conclusions:

Preterm and term piglets, born and reared in similar ways, show differences in GM colonization during the first 4 weeks of life, which may play a role for early and later gut dysfunction resulting from preterm birth.
Long‐term Outcomes of an Interdisciplinary Tube Weaning Program
Authors: Marinschek Sabine , Pahsini Karoline , Scheer Peter Jaron , Dunitz‐Scheer Marguerite
Published: January 2019

Background and Objectives:

Children who become tube‐dependent need specialized treatment in order to make the transition to oral feeding. Little is known about long‐term effects of tube weaning programs. This study analyzes long‐term effects (outcome, growth, and nutrition data) in a large sample of formerly tube‐dependent children 1 to 6 years after participation in tube weaning programs, based on the “Graz model of tube weaning.”

Methods:

Parents of children who completed a tube weaning program between 2009 and 2014 (N = 564) were asked to complete a questionnaire on their child's growth and nutrition. Data was analyzed using SPSS V22.0 for Windows (SPSS, Chicago, IL).

Results:

Response rate was 47.16% (N = 266). Seven children had died between completion of the program and the long‐term follow‐up. Two hundred and thirty‐nine children (92.3%) were still exclusively orally fed 1 to 6 years after completion of the weaning program, 17 children (6.6%) were partially tube‐fed. Three children were completely tube‐fed (1.1%). Growth data showed no significant changes in zBMI (World Health Organization standards z values for body mass index) between completion of weaning and long‐term follow‐up. Provided data on nutrition of fully orally fed patients showed that most children (N = 162, 68%) were eating an age‐appropriate diet, whereas a small percentage (N = 10, 4%) were fed with a high‐caloric formula, a selective diet (N = 12, 5%), or a liquid/pureed diet (N = 55, 23%).

Conclusions:

Many children who undergo a tube weaning program based on the “Graz model of tube weaning” are able to stay on full oral feeds in the years after completion of the wean without deterioration of growth.
Hepatic Lesions Associated With McCune Albright Syndrome
Authors: Johansen Lauren , Haller Wolfram , Thyagarajan Manigandan , Kelly Deirdre , McKiernan Patrick
Published: January 2019

McCune‐Albright syndrome (MAS) results from a GNAS gene mutation. It is associated with café au lait macules, fibrous dysplasia, and several endocrinopathies to include gonadotropin‐independent precocious puberty, growth hormone excess, Cushing syndrome, thyroid disease, and renal phosphate wasting. It is recognized to be a rare cause of neonatal cholestasis. We describe the hepatic outcome of 3 children with MAS referred to a single national liver unit. All presented with high gamma‐glutamyl transpeptidase cholestasis and hepatitis. Cholestasis resolved by 1 year; but hepatic inflammation persisted, and 2 children developed progressive atypical focal nodular hyperplasia and 1 developed hepatoblastoma. This the first reported malignant hepatic lesion associated with MAS. MAS should be considered part of the differential diagnosis of neonatal cholestasis and affected children should be closely monitored for the development of hepatic lesions with regular liver ultrasound and alpha fetoprotein level.
Successful Management of Hepatosplenic Infection Due to Saccharomyces cerevisiae in a Child With Acute Lymphoblastic Leukemia
Authors: Davies Emma , Shipp Adam , Hawkes Rob , Wynn Robert F.
Published: January 2019

Saccharomyces cerevisiae is an emerging pathogen within the immunocompromised. We present a 4-year-old boy with acute lymphoblastic leukemia presenting with polymerase chain reaction-confirmed hepatosplenic S. cerevisiae infection and significant immune reconstitution symptoms. We explore the challenges of monitoring treatment efficacy using C-Reactive protein, β-D-glucan, and imaging and the administration of chemotherapy alongside antifungals and steroids for control of immune reconstitution syndrome.
Immunohistochemistry Use by Diagnostic Category and Pathologist in 4477 Prostate Core Biopsy Sets Assessed at Two Hospitals
Authors: Bonert Michael , El-Shinnawy Ihab , Rahman Mozibur , Major Pierre , Salama Samih , Shayegan Bobby , Cutz Jean-Claude , Kapoor Anil
Published: January 2019

Background:

Immunohistochemistry (IHC) use in prostate cores is not routinely determined and its value assessed.

Methods:

Pathology reports for cases accessioned 2011 to 2017 at two hospitals were retrieved. IHC orders by pathologist and hospital were extracted with a custom program and tabulated. The diagnostic category (and highest grade cancer if applicable) was obtained by a hierarchical (free text) string matching algorithm.

Results:

The study period contained 4477 biopsy sets. Categorized by worst pathology (% stained), the cohort was: benign: 1184 cases (42%); prostatic intraepithelial neoplasia: 168 (68%); suspicious: 323 (93%); grade group 1 cancer (WHO1): 900 (78%); grade group two (WHO2): 840 (60%); WHO3 cancer: 451 (54%); WHO4 cancer: 363 (46%); WHO5 cancer: 215 (56%); cancer grade not specified: 33 (52%). The hospital was a predictor; site A(2716 biopsies) and site B(1761) accounted for 10,183 and 14,852 IHC, respectively. The cases with IHC decreased in the last 4 years (site A: 57->45%, site B: 79->73%). Thirty-five pathologists read >20 cases each and together interpreted 4418 (range, 21 to 415; median, 88). In total 24,766 IHCs were done on the 4,418 cases (5.6/case). The mean/median/SD/max/min IHCs/case for the 35 pathologists was 5.6/4.1/3.9/15.2/0.9. High IHC users (1st and 2nd quintile pathologists) called more suspicious for malignancy but not significantly more WHO1 than low IHC users.

Conclusions:

IHC use is most frequent at the benign/malignant interface, and dependent on the pathologist and hospital; however, it is independent of WHO1 cancer rate. Diagnostic rate information can inform and define appropriate and rational IHC use. We plan to follow IHC utilization retrospectively in relation to the diagnostic category going forward.
A Systematic Review and Meta-Analysis of Anterior Versus Lateral Approach for Laparoscopic Splenectomy
Authors: Rehman Sheik , Hajibandeh Shahin , Hajibandeh Shahab
Published: January 2019

Background:

As the experience grew with laparoscopic splenectomy (LS) more surgeons appreciate the advantages of lateral approach compared with conventional anterior approach. In view of this we aimed to compare anterior approach and lateral approach in LS.

Methods:

We conducted a search of electronic information sources to identify all randomized controlled trials (RCTs) and observational studies comparing anterior and lateral approach in patients undergoing LS. Primary outcomes included need for blood transfusion, intraoperative blood loss, and conversion to open surgery. The secondary outcomes included postoperative morbidity, operative time, time to oral intake, length of hospital stay, need for reoperation, and mortality. Random or fixed-effects modeling were applied to calculate pooled outcome data.

Results:

We identified 1 RCT and 4 retrospective observational studies, enrolling 728 patients. The baseline characteristics included populations in both groups were comparable. Anterior approach was associated with higher need for blood transfusion [odds ratio (OR), 4.83, 95% confidence interval (CI), 2.31-10.97; P=0.0001]; higher risks of intraoperative blood loss [mean difference (MD), 101.06, 95% CI, 52.05-150.06; P=0.0001], conversion to open surgery (OR, 3.33, 95% CI, −1.32 to 8.43; P=0.01), postoperative morbidity (OR, 3.86, 95% CI, −2.23 to 6.67; P=0.00001) and need for reoperation (OR, 6.91, 95% CI, −1.07 to 44.6; P=0.04); longer operative time (MD, 2.51, 95% CI, −1.43 to 3.59; P=0.00001), time to oral intake (MD, 0.60, 95% CI, −0.14 to −1.07; P=0.01), and length of stay (MD, 2.52, 95% CI, −1.43 to 3.59; P=0.00001) compared with lateral approach. There was no difference in the risk of mortality between the 2 groups (risk difference, 0.00, 95% CI, −0.01 to 0.02; P=0.61).

Conclusions:

The best available evidence suggests that the lateral approach is superior to anterior approach in LS as indicated by better access, more secure hemostasis, less conversion to open surgery, less morbidity, earlier recovery, and shorter length of hospital stay. The quality of the available evidence is moderate; high-quality RCTs are required to provide more robust basis for definite conclusions.
Chromatin modifiers alter recombination between divergent DNA sequences
Authors: Chakraborty Ujani , Mackenroth Beata , Shalloway David , Alani Eric
Published: January 2019

Recombination between divergent DNA sequences is actively prevented by heteroduplex rejection mechanisms. In baker’s yeast such anti-recombination mechanisms can be initiated by the recognition of DNA mismatches in heteroduplex DNA by MSH proteins, followed by recruitment of the Sgs1-Top3-Rmi1 helicase-topoisomerase complex to unwind the recombination intermediate. We previously showed that the repair/rejection decision during single-strand annealing recombination is temporally regulated by MSH protein levels and by factors that excise non-homologous single-stranded tails. These observations, coupled with recent studies indicating that mismatch repair factors interact with components of the histone chaperone machinery, encouraged us to explore roles for epigenetic factors and chromatin conformation in regulating the decision to reject vs. repair recombination between divergent DNA substrates. This work involved the use of an inverted repeat recombination assay thought to measure sister chromatid repair during DNA replication. Our observations are consistent with the histone chaperones CAF-1 and Rtt106 and the histone deacetylase Sir2 acting to suppress heteroduplex rejection and the Rpd3, Hst3 and Hst4 deacetylases acting to promote heteroduplex rejection. These observations and double mutant analysis have led to a model in which nucleosomes located at DNA lesions stabilize recombination intermediates and compete with mismatch repair factors that mediate heteroduplex rejection.

Recombination between divergent DNA sequences is actively prevented by heteroduplex rejection mechanisms. In this study we explored roles for epigenetic factors and chromatin conformation in regulating the decision to reject vs. repair recombination between divergent DNA substrates. Our observations are consistent with the histone chaperones CAF-1 and Rtt106 and the histone deacetylase Sir2 acting to suppress heteroduplex rejection and the Rpd3, Hst3 and Hst4 deacetylases acting to promote heteroduplex rejection. These observations have led to a model in which nucleosomes located at DNA lesions stabilize recombination intermediates and compete with mismatch repair factors that mediate heteroduplex rejection.
Comparative Population Genomics of Bread Wheat(Triticum aestivum)Reveals Its Cultivation and Breeding History in China
Authors: Chen Haofeng , Jiao Chengzhi , Wang Ying , Wang Yuange , Tian Caihuan , Yu Haopeng , Wang Jing , Wang Xiangfeng , Lu Fei , Fu Xiangdong , Xue Yongbiao , Jiang Wenkai , Ling Hongqing , Lu Hongfeng , Jiao Yuling
Published: January 2019

The evolution of bread wheat(Triticum aestivum)is distinctive in that domestication, natural hybridization, and allopolyploid speciation have all had significant effects on the diversification of its genome. Wheat was spread around the world by humans and has been cultivated in China for ~4,600 years. Here, we report a comprehensive assessment of the evolution of wheat based on the genome-wide resequencing of 120 representative landraces and elite wheat accessions from China and other representative regions. We found substantially higher genetic diversity in the A and B subgenomes than in the D subgenome. Notably, the A and B subgenomes of the modern Chinese elite cultivars were mainly derived from European landraces, while Chinese landraces had a greater contribution to their D subgenomes. The duplicated copies of homoeologous genes from the A, B, and D subgenomes were commonly found to be under different levels of selection. Our genome-wide assessment of the genetic changes associated with wheat breeding in China provides new strategies and practical targets for future breeding.
Dowsing for salinity tolerance related genes in chickpea through genome wide association and in silico PCR analysis
Authors: Ahmed Shaimaa M. , Alsamman A.M. , Mubarak M.H. , Badawy M.A. , Kord M.A. , Momtaz O.A. , Hamwieh A.
Published: January 2019

Soil salinity is a major abiotic stress severely limits agricultural crop production throughout the world, and the stress is increasing particularly in the irrigated agricultural areas. Chickpea (Cicer arietinum L.) is an important grain legume that plays a significant role in the nutrition of the developing world. In this study, we used a chickpea subset collected from the genebank of the International Center for Agricultural Research in the Dry Area (ICARDA). This collection was selected by using the focused identification of germplasm strategy (FIGS). The subset included 138 genotypes which have been screened in the open field (Arish, Sinai, Egypt) and in the greenhouse (Giza, Egypt) by using the hydroponic system at 100 mM NaCl concentration. The experiment was laid out in randomized alpha lattice design in two replications. The molecular characterization was done by using sixteen SSR markers (collected from QTL conferred salinity tolerance in chickpea), 2,500 SNP and 3,031 DArT markers which have been developed and used for association study. The results indicated significant differences between the chickpea genotypes. Based on the average of the two hydroponic and field experiments, seven tolerant genotypes IGs (70782, 70430, 70764, 117703, 6057, 8447 and 70249) have been identified. The data analysis indicated one SSR (TAA170), three DArT (DART2393, DART769 and DART2009) and eleven SNP markers (SNP2021, SNP1268, SNP1451, SNP1487, SNP1667, SNP2095, SNP190, SNP2247 SNP1947, SNP2331 and SNP948) were associated with salinity tolerance. The flanking regions of these markers revealed genes with a known role in the salinity tolerance, which could be candidates for marker-assisted selection in chickpea breeding programs.
Changing environments and genetic variation: inbreeding does not compromise short-term physiological responses
Authors: Buckley James , Daly Rónán , Cobbold Christina , Burgess Karl , Mable Barbara K.
Published: January 2019

Selfing plant lineages are surprisingly widespread and successful in a broad range of environments, despite showing reduced genetic diversity, which is predicted to reduce long-term evolutionary potential. However, short-term capacity to respond appropriately to new conditions might not require high levels of standing genetic variation. The purpose of this study was to directly test whether mating system variation and its associated changes in genetic variability in natural populations affected responses to short-term environmental challenges.

We compared relative fitness and metabolome profiles of naturally outbreeding (genetically diverse) and inbreeding (genetically depauperate) populations of a long-lived perennial plant, Arabidopsis lyrata, under constant growth chamber conditions and an outdoor common garden environment outside its native range.

We found no effect of mating system on survival or reproductive output, although several phenological traits showed different associations with latitude for outcrossing and inbreeding populations. Natural inbreeding had no effect on the plasticity of physiological responses, using either multivariate approaches or analysis of variation in individual metabolites. Moreover, while both growing environment and time significantly affected the relative abundance of individual metabolites, inbreeding populations responded similarly to outbreeding populations, suggesting adaptation to the outdoor environment, regardless of mating system.

We conclude that low genetic diversity in naturally inbred populations may not compromise fitness or short-term capacity for appropriate physiological responses to environmental change. The absence of natural costs of inbreeding could help to explain the global success of clonal or asexual mating strategies for adapting to a wide range of environments.
N-terminal mutants of human apolipoprotein A-I: structural perturbations associated to protein misfolding
Authors: Gaddi Gisela M. , Gisonno Romina , Rosú Silvana A. , Curto Lucrecia M. , Elías Esteban E. , Prieto Eduardo D. , Schinella Guillermo R. , Finarelli Gabriela S. , Cortez M. Fernanda , Ramella Nahuel A. , Tricerri M. Alejandra
Published: January 2019

Since the early description of different human apolipoprotein A-I variants associated to amyloidosis, the reason that determines its deposition inducing organ failure has been under research. To shed light into the events associated to protein aggregation, we studied the effect of the structural perturbations induced by the replacement of a Leucine in position 60 by an Arginine as it occurs in the natural amyloidogenic variant (L60R). Circular dichroism, intrinsic fluorescence measurements and assays of binding to ligands indicate that L60R is more unstable, more sensitive to proteolysis and interacts with sodium dodecyl sulfate (a model of negative lipids) more than the protein with the native sequence and other natural variant tested, involving a replacement of a Trytophan by and Arginine in the amino acid 50 (W50R). In addition, the small structural rearrangement observed under physiological pH leads to the release of tumor necrosis factor α and interleukin-lβ from a model of macrophages. Our results strongly suggest that the chronic disease may be a consequence of the loss in the native conformation which alters the equilibrium among native and cytotoxic proteins conformation.
Training load and body composition in adults practicing cyclical exercises
Authors: da Silva Raquel Suelen Brito , de Souza Marizângela Ferreira , Silveira Costa Matheus da , Maciel Franca Gisele Augusta , Cardoso Glêbia Alexa , Batista Joane Raquel Estrela , Arruda Lopes Carolina Farias , Barbosa Francisca Karinny Lemos , Silva Alexandre Sérgio
Published: January 2019

Although meta-analyzes point to a weight loss of no more than 3 kg to exercise, body fat of the athletes are below of the population. Then training load may be a determining factor in body composition. This study verified if dose of physical training adopted by exercise practitioners is determinant in body composition. Was a cross-sectional retrospective study carried out with 122 individuals (45.8 ± 13.0 years, 50 men) who practiced cyclic exercises (running, walking or cycling) randomly recruited in six regions which the city was geographically divided. Caloric expenditure was estimated in the trainings based on the frequency, intensity and duration of the exercises and the body composition was assessed by electrical bioimpedance. The subjects practiced 4.3 ± 1.5 weekly sessions, with mean duration of 56.7 ± 28.2 minutes/session and caloric expenditure/day of 410.2 ± 384.1 kcal/day. Linear regression test revealed a negative correlation (p=0.000) between the mean daily expenditure and all measures of adiposity tested (absolute and relative body fat and visceral fat), and evidenced that the training load explains 56% of the proposed model. When adjusted for sex, the correlation remained in men and disappeared in women. Men’s with energy expenditure higher than 785 kcal/day presented lower fat stores than congeners with minor diary training load. Conclude that training load adopted by physical exercise practitioners is an influencing factor in the body composition of men, but not of women. Load adopted in conventional programs training seems insufficient to produce adequate body composition.
Corrosion resistance and mechanism of micro-nano structure super-hydrophobic surface prepared by laser etching combined with coating process
Authors: Zhang Qianqian , Zhang Huichen
Published: January 2019

Purpose

The purpose of this paper is to evaluate the effect of micro-nano mixed super-hydrophobic structure on corrosion resistance and mechanism of magnesium alloys.

Design/methodology/approach

A super-hydrophobic surface was fabricated on AZ91 and WE43 magnesium alloys by laser etching and micro-arc oxidation (MAO) with SiO2 nanoparticles coating and low surface energy material modification. The corrosion resistance properties of the prepared super-hydrophobic surfaces were studied based on polarization curves and immersion tests.

Findings

Compared with bare substrates, the corrosion resistance of super-hydrophobic surfaces was improved significantly. The corrosion resistance of super-hydrophobic surface is related to micro-nano composite structure, static contact angle and pretreatment method. The more uniform the microstructure and the larger the static contact angle, the better the corrosion resistance of the super-hydrophobic surface. The corrosion resistance of super-hydrophobic by MAO is better than that of laser machining. Corrosion of super-hydrophobic surface can be divided into air valley action, physical shielding, pretreatment layer action and substrate corrosion.

Originality/value

The super-hydrophobic coatings can reduce the contact of matrix with water so that a super-hydrophobic coating would be an effective way for magnesium alloy anti-corrosion. Therefore, the corrosion resistance properties and mechanism of the prepared super-hydrophobic magnesium alloys were investigated in detail.
Acceptance and adoption of open access publishing by researchers in India
Authors: Nazim Mohammad , Zia Sana
Published: January 2019

Purpose

This paper aims to examine the level of open access (OA) adoption by researchers in Indian Institutes of Technology (IITs), identify predictors of OA status (OA vs non-OA) and explore the availability of OA versions of the articles and venues used by the researches for hosting of their articles.

Design/methodology/approach

Articles contributed by the researchers in IITs were searched using an advance search option in the Web of Science Core collection database. The search was restricted to journal articles published in English language in the year 2015. Of the 10,049 articles retrieved, 1,023 (10 per cent of the total) were chosen randomly. Articles selected after randomizations were exported to MS Excel for further analyses. Title of each article was searched in Google Scholar to assess its OA availability and venues used by the author for self-archiving. Details of ten articles could not be traced in Google Scholar, and they were excluded from the analysis. Based on the analysis of URLs, all OA articles were classified into three categories: gold OA, green OA and both gold and green OA. The OA articles available through green route were further classified into six categories based on the analysis of the websites and the self-archiving venues used by the authors: institutional repository, subject repository, researcher or scholar’s website, organizational website, ResearchGate and other websites.

Findings

Of 1,013 articles examined, OA versions were found for 68.70 per cent of articles. Of the total OA articles, 10.26 per cent articles were available through gold OA and 58.44 per cent were available through green OA, while remaining 6.21 per cent were available via both gold and green OA routes. Although researchers use different venues for self-archiving their articles, ResearchGate and institutional repositories are the most preferred choices by the researchers in IITs. Researchers in IITs are seemed to be unaware of the self-archiving policies of publishers, as more than 85 per cent self-archived articles were found as final PDF versions that are normally not allowed by the publishers.

Research limitations/implications

This study is limited to IITs, but it offers theoretical implications for extending its scope to different subjects and institutes. The findings of the study may be useful for the publishers and institutions for formulating OA policies. The findings of the study might be used for raising awareness of OA among researchers and encouraging them to contribute their research outcome in OA outlets.

Originality/value

This is the first study in India focusing on the availability of OA research.
The emergence of Chinese entrepreneurs: social connections and innovation
Authors: Dai Shuanping , Wang Yuanyuan , Liu Yang
Published: January 2019

Purpose

This paper aims to explore empirically the emergence of entrepreneurs in China’s transition context since the 1980s.

Design/methodology/approach

This paper applies the China Private Enterprises Survey Database and historical evidence and Chi-Square test to identify the emergence patterns of China’s entrepreneurs in different historical stages.

Findings

This longitudinal study finds that factors such as working experience, education background and social connection had strong influences on entrepreneurship, but the impact of these have varied significantly along with institutional changes over the past three decades. It also identifies that the majority of emergent entrepreneurs were formerly low-level public servants and high-qualified managers in state-owned enterprises. Additionally, significant trends including an increasing number of female entrepreneurs, a decreasing impact from political networks, improving investment in innovation and diversifying financial sources are also found.

Originality/value

This paper is the first to apply the Chinese Private Enterprises Survey database to investigate the emergence patterns of China’s entrepreneurs in different historical stages after the 1978 reform.
Fuzzy overall equipment effectiveness and line performance measurement using artificial neural network
Authors: Fekri Sari Mahsa , Avakh Darestani Soroush
Published: January 2019

Purpose

The overall equipment effectiveness (OEE) is a powerful metric in production as well as one of the methods in evaluating function for measuring productivity in the production process. In the existing method, measuring OEE is based on three main elements consisting availability, performance and quality. The purpose of this paper is to evaluate the recognized metrics of production: OEE and overall line effectiveness (OLE) by using smart systems techniques.

Design/methodology/approach

In this paper, to improve the calculative methods and productivity with three methods: measuring OEE using Mamdani fuzzy inference systems (FIS), measuring OEE using Sugeno FIS, and measuring OLE using FIS and artificial neural networks (ANNs) are proposed.

Findings

The proposed methodologies aim to decrease some weaknesses of OEE and OLE methods by exploiting intelligent system techniques, such as FIS and ANNs. In particular, this research will solve the following issues that occur in manual and automatic data gathering. This technique is an effective way of measuring OEE and OLE with regard to different weights of losses as well as difference in the weight of the machines. In addition, it allows the operator’s knowledge to take a part in the measurement using uncertain input and output with implementation of linguistic terms. The presented method is the details and capabilities of those methods in various tested scenarios, and the results have been fully analyzed.

Originality/value

In relation to other methodologies, it allows the operator’s knowledge to take part in the measurement using uncertain input and output with implementation of linguistic terms. The presented method is the details and capabilities of those methods in various tested scenarios, and the results have been fully analyzed.
A must for agencies or a candidate for deletion
Authors: Xie Sherry Li
Published: January 2019

Purpose

This paper aims to report on a study that aimed at analyzing the relationships between information security and records management (RM), both as programs/functions established in organizations. Similar studies were not found in relevant literature.

Design/methodology/approach

The study used the classic grounded theory methodology. Pursuing the general curiosity about the information security-RM relationship in organizations, the study selected the United States (US) Federal Government as its field of entrance and followed the process of the classic grounded theory methodology that starts from the letting of the emergence of the research question to the formulation of a substantive theory that answered the question.

Findings

On the emergent question that why, despite the legislative establishment of agency RM programs and the use of the term records in their work, the US Federal Government information security community considered RM a candidate for deletion (CFD), the study coded the truncated application of the encompassing definition of records as the underlying reason. By this code, along with its three properties, i.e. limitations by the seemingly more encompassing coverage of information, insufficient legislative/regulatory support and the use of the terms of evidence and preservation in the records definition, the CFD consideration and the associated phenomena of unsound legislative/regulatory conceptualization, information shadow, information ignorance and archival shadow were explained.

Research limitations/implications

The study results suggested the data for subsequent theoretical sampling to be the operational situations of individual agency RM programs.

Practical implications

The rationale presented in the study regarding the encompassing nature of records and the comprehensive scope of RM program can be used for building strong RM business cases.

Originality/value

The study appears to be the first of its kind, which examined the RM–information security relationship in a very detailed setting.
Histogenesis of cutaneous malignant melanoma: The vast majority do not develop from melanocytic nevus but arise de novo as melanoma in situ
Authors: Saida Toshiaki
Published: January 2019

It has been considered that most cutaneous malignant melanomas arise from pre‐existing melanocytic nevus. Many clinical and histopathological studies seem to support this concept. Dysplastic nevus originally proposed by Clark's group is a key entity of the intermediate lesion between benign nevus and melanoma. The latest edition of the WHO Classification of Skin Tumours (2018) has excluded Clark nevus (dysplastic nevus of mild atypia) from dysplastic nevus, the latter being now classified into the low‐ and high‐grade by the degrees of nuclear atypia. The World Health Organization classification regards dysplastic nevus of both grades as the intermediate lesion between common acquired nevus and the radial growth‐phase melanoma. An extensive genetic study recently performed by Bastian's group indicated the existence of intermediate lesions between nevus and melanoma. In spite of these findings, some investigators doubt the concept of the intermediate lesions including dysplastic nevus and insist that the majority of melanomas arise de novo as melanoma in situ, not in association with a preceding nevus. The concept of de novo genesis of melanoma may be supported by a recent meta‐analysis study revealing that 71% of melanomas likely arose de novo and 29% from pre‐existing nevus. In this review article, from the viewpoint of de novo genesis of melanoma, the author critically discusses the relevant findings of melanoma genesis and proposes a new framework to interpret the morphological and genetic data alternatively. Clarification of the oncogenic process of melanoma has great impact not only on clinical dermatology but also on basic oncology.
Endophytes from wild cereals protect wheat plants from drought by alteration of physiological responses of the plants to water stress
Authors: Llorens Eugenio , Sharon Or , Camañes Gemma , García‐Agustín Pilar , Sharon Amir
Published: January 2019

Endophytes contribute to plant performance, especially under harsh conditions. We therefore hypothesized that wild plants have retained beneficial endophytes that are less abundant or not present in related crop plants. To test this hypothesis, we selected two endophytes that were found in Sharon goatgrass, an ancestor of wheat, and tested their effect on bread wheat. Both endophytes infected wheat and improved sustainability and performance under water‐limited conditions. To determine how the endophytes modify plant development, we measured parameters of plant growth and physiological status and performed a comparative metabolomics analysis. Endophyte‐treated wheat plants had reduced levels of stress damage markers and reduced accumulation of stress‐adaptation metabolites. Metabolomics profiling revealed significant differences in the response to water stress of endophyte‐treated plants compared with untreated plants. Our results demonstrate the potential of endophytes from wild plants for improvement of related crops and show that the beneficial effects of two endophytes are associated with alteration of physiological responses to water‐limited conditions.