bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical factors affecting semen improvement after microsurgical subinguinal varicocelectomy: which subfertile patients benefit from surgery?
Authors: Palmisano Franco , Moreno-Mendoza Daniel , Ievoli Riccardo , Veber-Moisés-Da Silva Gabriel , Gasanz-Serrano Carlos , Villegas-Osorio Juan Fernando , Peraza-Godoy Maria Fernanda , Vives Álvaro , Bassas Lluís , Montanari Emanuele , Ruiz-Castañé Eduard , Sarquella-Geli Joaquim , Sánchez-Curbelo Josvany 
Published: November 2019

Background: The exact mechanism of varicocele-related infertility is still elusive, therefore, the current challenges for its management lie in determining which patients stand to benefit most from surgical correction. The authors aimed to assess the clinical factors affecting semen improvement after left microsurgical subinguinal varicocelectomy (MSV) in relation to patient age, ultrasound varicocele grading (USVG), and presence of a right subclinical varicocele (RSV). Methods: From 2010 to 2017 a total of 228 infertile patients underwent left MSV for clinical varicocele. Descriptive statistics were used to describe the cohort and verify the surgical benefit in terms of semen improvement, in addition, subsets of patients were selected according to clinical covariates. Logistic regression modeling was applied to evaluate the presence of RSV, operative time, age, and USVG as explanatory variables. Results: Sperm concentration (SC), progressive sperm motility (PSM), and normal sperm morphology (NSM) increased significantly after surgery ( p = 0.002; p = 0.011; p = 0.024; respectively). Mean SC improved after MSV in ⩾35 year-old patients and the grade 3 USVG group ( p = 0.01; p = 0.02; respectively). Logistic regression modeling showed a that the probability of SC improvement was 76% lower in subjects presenting RSV ( p = 0.011). In addition, patients with a grade 3 USVG presented a three-times greater probability of SC improvement compared with patients with a lower USVG ( p = 0.035). In addition, older patients showed a greater probability of SC improvement after MSV ( p = 0.041). Conclusions: MSV is an effective varicocele-related infertility treatment that should also be offered to older patients. In addition, patients with a higher USVG benefit from surgery. In infertile men with an RSV in association with a left clinical disease, a bilateral varicocele repair should be considered.
Intermediate Outcomes of Staged Tetralogy of Fallot Repair
Authors: Mahajan Poonam , Ebenroth Eric S. , Borsheim Kirsten , Husain Sabena , Bo Na , Herrmann Jeremy L. , Rodefeld Mark D. , Turrentine Mark W. , Brown John W. , Patel Jyoti K. 
Published: November 2019

Background: The optimal surgical strategy for tetralogy of Fallot (TOF) repair in neonates and young infants requiring early surgical intervention remains controversial. Our surgical center follows the uniform strategy of a staged approach with initial systemic-to-pulmonary artery shunt the majority of time when early surgical intervention is required. We characterized a contemporary cohort of patients with TOF with pulmonary stenosis (PS) undergoing staged repair in order to determine the rate of pulmonary valve-sparing repair (PVSR), growth of the pulmonary valve annulus and pulmonary arteries, postoperative morbidity and mortality, and need for reintervention. Methods: We retrospectively studied patients with TOF/PS who underwent staged repair from 2000 to 2017. Surgical details, postoperative course, and reinterventions were noted. Echocardiographic measurements and Z-score values of pulmonary valve annulus, main pulmonary artery (MPA), right pulmonary artery (RPA), and left pulmonary artery (LPA) diameters were evaluated. Results: Of the 59 patients with staged TOF/PS, PVSR was performed in 25 (42%). There was a 5% incidence of postoperative arrhythmia. The Z-scores of MPA, RPA, and LPA were significantly higher before complete repair when compared to before palliative shunt. The 5 and 10-year survival rates were both 93%, and the probability of freedom from reoperation at 5 and 10 years was 87% and 82%, respectively. Conclusions: Staged repair of TOF in young symptomatic infants results in 42% receiving PVSR, pulmonary artery growth, low incidence of postoperative arrhythmia, and relatively low rate of reoperations.
Functional Capacity Is Affected by Younger Age of Repair in Tetralogy of Fallot Patients But Not by Era of Repair
Authors: Powell Adam W. , Mays Wayne A. , Chin Clifford 
Published: November 2019

Background: Cardiopulmonary exercise testing is widely used to assess functional capacity in patients with tetralogy of Fallot after surgical repair. Little is known regarding the impact of age at the time of primary complete repair and surgical era effect on exercise capacity. Methods: A retrospective, single-center chart review was done from 1976 to 2016 on pediatric patients with tetralogy of Fallot who underwent cardiopulmonary exercise testing with cycle ergometry utilizing the James protocol and were then sorted by repair before/after 1990 and by age of complete repair before/after one year. Exclusion criteria included submaximal tests, incomplete data, previous pulmonary valve replacement, and surgery prior to complete repair (ie, Blalock-Taussig shunt placement). Results: When comparing the groups who underwent primary complete repair before (N = 39) and after (N = 26) one year of age, the younger group demonstrated a higher percentage of predicted peak oxygen consumption ([Formula: see text] o 2peak; 83.1% ± 11.8% vs 73.1% ± 16.1%; P = .005) despite having worse pulmonary insufficiency at the time of exercise testing. There were no differences in heart rate and blood pressure response. Age of repair was independently associated with [Formula: see text] o 2peak. Data were statistically similar to the study eras (repair before 1990, N = 23; repair after 1990, N = 65): percentage of predicted [Formula: see text] o2peak (81.4% ± 13.6% vs 79.1% ± 14.4%, P = .5), maximal systolic blood pressure (155.1 ± 22.4 mm Hg vs 153.9 ± 17 mm Hg, P = .8), and percentage of predicted maximal heart rate (89.8% ± 9% vs 92% ± 7.1%, P = .3). Conclusions: Older age at primary repair appears to negatively impact [Formula: see text] o2peak; however, era effect does not appear to influence cardiopulmonary exercise testing outcomes.
The Ozaki Procedure With CardioCel Patch for Children and Young Adults With Aortic Valve Disease: Preliminary Experience – a Word of Caution
Authors: Chivers Sian C. , Pavy Carine , Vaja Ricky , Quarto Cesare , Ghez Olivier , Daubeney Piers E. F. 
Published: November 2019

Background: The Ozaki procedure is a surgical technique for patients with significant aortic stenosis or regurgitation or both where valve repair cannot be performed. Individual cusps are cut from glutaraldehyde-treated autologous pericardium or bovine pericardium and implanted into the aortic valve position. Encouraging results have been reported within the adult population. There are limited published data on success of this procedure in younger patients. Methods: We present a series of five children and young adults who underwent the Ozaki procedure with neoaortic valve cusps made from CardioCel, a decellularized bovine pericardial patch treated with a monomeric glutaraldehyde. Results: There were no complications in the initial postoperative period and short inpatient stay. At a mean follow-up of 29.6 months (range: 22-36 months), 4 patients had no evidence of stenosis and 3 patients had trivial or no regurgitation from the neoaortic valve. Overall, two patients had complications related to the valve and underwent reintervention during the follow-up period with a Ross procedure. One of these patients who was not taking long-term anticoagulation experienced a transient ischemic attack. Conclusions: Our experience demonstrates that the Ozaki procedure with CardioCel in pediatric and young adult patients should be approached with caution. Further research with larger groups of pediatric patients, comparison of different graft materials, and longer follow-up is required to ascertain long-term success in children.
The vascular effect of glibenclamide: A systematic review
Authors: Al-Karagholi Mohammad Al-Mahdi , Sode Michael , Gozalov Aydin , Ashina Messoud 
Published: November 2019

Objective: To systematically review the vascular effects of glibenclamide. Background: Infusion of adenosine triphosphate (ATP)-sensitive potassium (KATP) channel opener (KCO) levcromakalim dilates cranial arteries and induces headache and migraine attacks. Recent data show that levcromakalim-induced vasodilation is associated with headache. Glibenclamide is a KATP channel blocker that may alter the vascular tone and thus has an impact on headache or migraine prevention. Methods: A search through PubMed was undertaken for studies investigating the vascular effects of glibenclamide in vitro as well as in vivo published until July 2019. Results: We identified 58 articles; 31 in vitro studies, 24 in vivo studies and 3 studies with both. The main findings were that glibenclamide inhibited levcromakalim-induced and other KCOs-induced vasodilation, while the basal vascular tone remained unchanged. Conclusion: Glibenclamide could inhibit vasodilation by KCOs, and further studies are needed to clarify the vascular effect of glibenclamide on human cranial arteries.
Wood identification of Japanese Shinto deity statues in Matsunoo-taisha Shrine in Kyoto by synchrotron X-ray microtomography and conventional microscopy methods
Authors: Tazuru Suyako , Sugiyama Junji 
Published: November 2019

Abstract
Research on the wood species of Japanese Buddhist statues has an over 60 years’ history and recently many Buddhist “Ichiboku” statues carved out of a single bole made from the Nara to Heian periods were scientifically revealed to be made of Torreya nucifera. Shinto deity statues in Japan, however, have not yet been investigated scientifically. Because many Shinto deity statues are enshrined behind closed doors, there are fewer opportunities to investigate them. To examine the differences and similarities in wood selection between Buddhist and Shinto deity statues, wood identification was conducted on the 11 Shinto deity statues of Matsunoo-taisha Shrine, Kyoto, Japan, using synchrotron X-ray microtomography and conventional microscopy methods. The results indicated two female deity statues with the ink inscriptions indicating the production year of 1143 were of Torreya nucifera, one female deity statue of Zelkova serrata, and the other eight statues, i.e., two female deity statues, four male deity statues and two priestly attire deity statues of Prunus s.l. spp.
Cancer Cell Membrane Decorated Silica Nanoparticle Loaded with miR495 and Doxorubicin to Overcome Drug Resistance for Effective Lung Cancer Therapy
Authors: He Jinyuan , Gong Chulian , Qin Jie , Li Mingan , Huang Shaohong 
Published: November 2019

Abstract
Current cancer therapy usually succumbs to many extracellular and intracellular barriers, among which untargeted distribution and multidrug resistance (MDR) are two important difficulties responsible for poor outcome of many drug delivery systems (DDS). Here, in our study, the dilemma was addressed by developing a cancer cell membrane (CCM)-coated silica (SLI) nanoparticles to co-deliver miR495 with doxorubicin (DOX) for effective therapy of lung cancer (CCM/SLI/R-D). The homologous CCM from MDR lung cancer cells (A549/DOX) was supposed to increase the tumor-homing property of the DDS to bypass the extracellular barriers. Moreover, the MDR of cancer cells were conquered through downregulation of P-glycoprotein (P-gp) expression using miR495. It was proved that miR495 could significantly decrease the expression of P-gp which elevated intracellular drug accumulation in A549/DOX. The in vitro and in vivo results exhibited that CCM/SLI/R-D showed a greatly enhanced therapeutic effect on A549/DOX, which was superior than applying miR495 or DOX alone. The preferable effect of CCM/SLI/R-D on conquering the MDR in lung cancer provides a novel alternative for effective chemotherapy of MDR cancers.
Dorsal penile frenulum a rare congenital abnormality
Authors: Mukendi A. M. , Doherty S. W. 
Published: November 2019

AbstractBackgroundDorsal penile frenulum is noted to be an extremely rare congenital penile abnormality. Only two cases have been reported in the literature.Case presentationA 31-year-old male was involved in a motor vehicle accident and sustained a pelvic fracture and a scrotal laceration which was the main reason for urology consult. Genital examination revealed a circumcised penis, the presence of two frenula and a right scrotal laceration. Scrotal laceration was cleaned and closed. Orthopaedic surgeon took over the patient for the pelvic fracture.ConclusionThis is the third reported case of a dorsal penile frenulum incidentally found in a circumcised male and completely asymptomatic. A brief review of relevant embryology and anatomy is herein discussed.
Recommendations for performance optimizations when using GATK3.8 and GATK4
Authors: Heldenbrand Jacob R , Baheti Saurabh , Bockol Matthew A , Drucker Travis M , Hart Steven N , Hudson Matthew E , Iyer Ravishankar K , Kalmbach Michael T , Kendig Katherine I , Klee Eric W , Mattson Nathan R , Wieben Eric D , Wiepert Mathieu , Wildman Derek E , Mainzer Liudmila S 
Published: November 2019

Abstract

Background
Use of the Genome Analysis Toolkit (GATK) continues to be the standard practice in genomic variant calling in both research and the clinic. Recently the toolkit has been rapidly evolving. Significant computational performance improvements have been introduced in GATK3.8 through collaboration with Intel in 2017. The first release of GATK4 in early 2018 revealed rewrites in the code base, as the stepping stone toward a Spark implementation. As the software continues to be a moving target for optimal deployment in highly productive environments, we present a detailed analysis of these improvements, to help the community stay abreast with changes in performance.

Results
We re-evaluated multiple options, such as threading, parallel garbage collection, I/O options and data-level parallelization. Additionally, we considered the trade-offs of using GATK3.8 and GATK4. We found optimized parameter values that reduce the time of executing the best practices variant calling procedure by 29.3% for GATK3.8 and 16.9% for GATK4. Further speedups can be accomplished by splitting data for parallel analysis, resulting in run time of only a few hours on whole human genome sequenced to the depth of 20X, for both versions of GATK. Nonetheless, GATK4 is already much more cost-effective than GATK3.8. Thanks to significant rewrites of the algorithms, the same analysis can be run largely in a single-threaded fashion, allowing users to process multiple samples on the same CPU.

Conclusions
In time-sensitive situations, when a patient has a critical or rapidly developing condition, it is useful to minimize the time to process a single sample. In such cases we recommend using GATK3.8 by splitting the sample into chunks and computing across multiple nodes. The resultant walltime will be nnn.4 hours at the cost of $41.60 on 4 c5.18xlarge instances of Amazon Cloud. For cost-effectiveness of routine analyses or for large population studies, it is useful to maximize the number of samples processed per unit time. Thus we recommend GATK4, running multiple samples on one node. The total walltime will be ∼34.1 hours on 40 samples, with 1.18 samples processed per hour at the cost of $2.60 per sample on c5.18xlarge instance of Amazon Cloud.
Template-switching artifacts resemble alternative polyadenylation
Authors: Balázs Zsolt , Tombácz Dóra , Csabai Zsolt , Moldován Norbert , Snyder Michael , Boldogkői Zsolt 
Published: November 2019

Abstract

Background
Alternative polyadenylation is commonly examined using cDNA sequencing, which is known to be affected by template-switching artifacts. However, the effects of such template-switching artifacts on alternative polyadenylation are generally disregarded, while alternative polyadenylation artifacts are attributed to internal priming.

Results
Here, we analyzed both long-read cDNA sequencing and direct RNA sequencing data of two organisms, generated by different sequencing platforms. We developed a filtering algorithm which takes into consideration that template-switching can be a source of artifactual polyadenylation when filtering out spurious polyadenylation sites. The algorithm outperformed the conventional internal priming filters based on comparison to direct RNA sequencing data. We also showed that the polyadenylation artifacts arise in cDNA sequencing at consecutive stretches of as few as three adenines. There was no substantial difference between the lengths of poly(A) tails at the artifactual and the true transcriptional end sites even though it is expected that internal priming artifacts have shorter poly(A) tails than genuine polyadenylated reads.

Conclusions
Our findings suggest that template switching plays an important role in the generation of spurious polyadenylation and support the need for more rigorous filtering of artifactual polyadenylation sites in cDNA data, or that alternative polyadenylation should be annotated using native RNA sequencing.
Cloning and functional analysis of the FAD2 gene family from desert shrub Artemisia sphaerocephala
Authors: Miao Xiumei , Zhang Lijing , Hu Xiaowei , Nan Shuzhen , Chen Xiaolong , Fu Hua 
Published: November 2019

Abstract

Background
Linoleic acid is an important polyunsaturated fatty acid, required for all eukaryotes. Microsomal delta-12 (Δ12) oleate desaturase (FAD2) is a key enzyme for linoleic acid biosynthesis. Desert shrub Artemisia sphaerocephala is rich in linoleic acid, it has a large FAD2 gene family with twenty-six members. The aim of this work is to unveil the difference and potentially functionality of AsFAD2 family members.

Results
Full-length cDNAs of twenty-one AsFAD2 genes were obtained from A. sphaerocephala. The putative polypeptides encoded by AsFAD2 family genes showed a high level of sequence similarity and were relatively conserved during evolution. The motif composition was also relatively conservative. Quantitative real-time PCR analysis revealed that the AsFAD2–1 gene was strongly expressed in developing seeds, which may be closely associated with the high accumulating ability of linoleic acid in A. sphaerocephala seeds. Although different AsFAD2 family members showed diverse response to salt stress, the overall mRNA levels of the AsFAD2 family genes was stable. Transient expression of AsFAD2 genes in the Nicotiana benthamiana leaves revealed that the encoded proteins were all located in the endoplasmic reticulum. Heterologous expression in Saccharomyces cerevisiae suggested that only three AsFAD2 enzymes, AsFAD2–1, − 10, and − 23, were Δ12 oleate desaturases, which could convert oleic acid to linoleic acid, whereas AsFAD2–1 and AsFAD2–10 could also produce palmitolinoleic acid.

Conclusions
This research reported the cloning, expression studies, subcellular localization and functional identification of the large AsFAD2 gene family. These results should be helpful in understanding fatty acid biosynthesis in A. sphaerocephala, and has the potential to be applied in the study of plant fatty acids traits.
Structural development and physicochemical properties of starch in caryopsis of super rice with different types of panicle
Authors: Chen Xinyu , Chen Mingxin , Lin Guoqiang , Yang Yang , Yu Xurun , Wu Yunfei , Xiong Fei 
Published: November 2019

Abstract

Background
Starch is the main storage substance in rice caryopsis and its properties will determine the quality of rice. Super rice has been extensively studied due to its high-yield characteristics, but the knowledge of amyloplast development and starch quality in caryopsis of super rice especially with large panicle is limited.

Results
To address this, large panicle typed and normal panicle typed super rice cultivar Yongyou2640 (YY2640) and Nangeng9108 (NG9108) were investigated in this study. The development of amyloplast in YY2640 caryopsis was better than NG9108, showing faster degradation rate of pericarp amyloplast and better filling degree of endosperm amyloplast. Meanwhile, the starch granule of YY2640 presented as polyhedral shape with smooth surface and the granule size was slightly larger than NG9108. The starch of YY2640 exhibited the lower amylose content, ratio of amylose to amylopectin and the higher level of amylopectin short and long branch-chains compared with NG9108, but there was no significant difference in amylopectin branching degree between them. Two rice starches both showed the characteristics of A-type crystal, and the relative crystallinity and external ordered degree of YY2640 starch were higher than those of NG9108. Furthermore, YY2640 starch showed better pasting properties with lower pasting temperature, shorter pasting time, higher peak viscosity, trough viscosity, breakdown value and lower setback value because of lower apparent amylose content.

Conclusions
Overall, the development and filling of amyloplast in YY2640 caryopsis were better than those of NG9108, thus leading to better starch quality of YY2640.
Rapid identification and characterization of genetic loci for defective kernel in bread wheat
Authors: Fu Chao , Du Jiuyuan , Tian Xiuling , He Zhonghu , Fu Luping , Wang Yue , Xu Dengan , Xu Xiaoting , Xia Xianchun , Zhang Yan , Cao Shuanghe 
Published: November 2019

AbstractBackgroundWheat is a momentous crop and feeds billions of people in the world. The improvement of wheat yield is very important to ensure world food security. Normal development of grain is the essential guarantee for wheat yield formation. The genetic study of grain phenotype and identification of key genes for grain filling are of great significance upon dissecting the molecular mechanism of wheat grain morphogenesis and yield potential.ResultsHere we identified a pair of defective kernel (Dek) isogenic lines, BL31 and BL33, with plump and shrunken mature grains, respectively, and constructed a genetic population from the BL31/BL33 cross. Ten chromosomes had higher frequency of polymorphic single nucleotide polymorphism (SNP) markers between BL31 and BL33 using Wheat660K chip. Totally 783 simple sequence repeat (SSR) markers were chosen from the above chromosomes and 15 of these were integrated into two linkage groups using the genetic population. Genetic mapping identified three QTL,QDek.caas-3BS.1,QDek.caas-3BS.2andQDek.caas-4AL, explaining 14.78–18.17%, 16.61–21.83% and 19.08–28.19% of phenotypic variances, respectively. Additionally, five polymorphic SNPs from Wheat660K were successfully converted into cleaved amplified polymorphic sequence (CAPS) markers and enriched the target regions of the above QTL. Biochemical analyses revealed that BL33 has significantly higher grain sucrose contents at filling stages and lower mature grain starch contents than BL31, indicating that the Dek QTL may be involved in carbohydrate metabolism. As such, the candidate genes for each QTL were predicated according to International Wheat Genome Sequence Consortium (IWGSC) RefSeq v1.0.ConclusionsThree major QTL for Dek were identified and their causal genes were predicted, laying a foundation to conduct fine mapping and dissect the regulatory mechanism underlying Dek trait in wheat.