bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emergency Repair of Severe Limb Injuries With Free Flow-Through Chimeric Anterolateral Thigh Perforator Flap
Authors: Zheng Xiaoju , Zhan Yi , Li Haijun , Zhang Zhong , Xue Xuewen , Wang Baoshan , Qi Jian 
Published: June 2019

Background
Complex limb trauma often involves both soft tissue and vascular defects, and is challenging for surgeons. The traditional musculocutaneous flap cannot achieve a 3-dimensional wound repair. Here we report our experience with a single-stage reconstruction and revascularization performed on complex extremity injuries using a free flow-through chimeric anterolateral thigh perforator (ALTP) flap.

Patients and Methods
Seventeen patients (16 men; aged 19–55 years) with complex soft tissue defects attended our hospital from January 2010 to November 2017. All patients underwent reconstruction based on free flow-through chimeric ALTP flap for complex injuries in their extremities. The wound size ranged from 16 × 8 to 45 × 30 cm. The injured artery was flow-through anastomosed with the descending branch of the lateral femoral circumflex artery to regain blood flow. The muscle flap was used to fill the deep dead space on the injury site. The skin and fascial flaps were used for superficial cover. The donor site defects were sutured directly in 6 patients; simultaneous skin grafts were applied in the remaining 11 patients.

Results
The ALTP flaps survived in 15 patients. Failure necessitated limb amputation in 2 patients. Six patients received both skin and fasciae flaps; 11 received flaps comprising the skin, fasciae, and vastus lateralis muscle. Partial necrosis after skin grafting was observed in 11 patients, and the wounds healed either by dressing change (1 patient) or second skin graft (10 patients). All donor sites healed without complications. All patients were followed up for 5 to 60 months (mean, 21.8 months).

Conclusions
The flow-through chimeric ALTP flap can be used for 1-stage reconstruction of 3-dimensional soft tissue defects and vascular gap. It is feasible for managing complex injuries of both the upper and lower extremities in emergency settings.
Posterior Perichondrioadipodermal flap
Authors: Ersen Burak 
Published: June 2019

Introduction
Complications after otoplasty procedure can be divided into early- and late-period complications, with the former occurring up to 14 days postoperatively and the latter occurring after the initial 14-day period. Indications for revision surgery of ear deformations after primary otoplasty are generally related to late complications. The majority of patients demand secondary treatment because of unsatisfactory cosmetic results.

Methods
A total of 32 patients (18 male and 14 female patients) underwent revision otoplasty with the same surgeon between May 2015 and May 2018. Patient ages ranged from 24 to 70 years. In total, 21 patients underwent bilateral revision otoplasty, whereas 11 patients underwent unilateral revision otoplasty. Patients were also evaluated for complaint and deformity type such as suture extrusion, recurrence, asymmetry, and postauricular area sensitivity or pain. Patients were also evaluated for previously performed primary otoplasty technique.

Results
There were mainly 4 long-term complications for revision otoplasty: suture extrusion, asymmetry, recurrence, and long-term pain and sensitivity in the posterior auricular area. In 12 cases, the complaint was suture extrusion; in 8 cases, patients complained about both suture extrusion and asymmetry. Bilateral recurrence was present in 10 cases, and in 2 cases, revision otoplasty was performed because of long-term pain and sensitivity.

Discussion
In this study, it was aimed to demonstrate that posterior perichondrioadipodermal flap is a safe and simple method for revision otoplasty. The technique is highly advantageous if the primary otoplasty technique is a cartilage-sparing method. However, if the primary otoplasty technique is a cartilage-sculpting method, the efficiency of this technique remains unknown because no patient in this study had cartilage-sculpting otoplasty as primary otoplasty, which is possibly the main drawback of this study.
Comparative Analysis of the Healing Effects of the Transplanted Cell Sheets to the Experimentally Injured Maxillary Sinuses
Authors: Topdag Murat , Karaoz Erdal , Kara Ahmet , Subasi Cansu , Duman Busra Oncel , Demir Necdet , Konuk Esma , Ozturk Murat , Iseri Mete 
Published: June 2019

Background:
In our study, the authors aimed to obtain a live and functional sinus epithelium with mesenchymal stem cells and nasal mucosa epithelial cells from rabbits which are cultured in temperature-responsive culture plates to get a single-layer.

Methodology/Principal:
Twenty-two female New Zealand rabbits were included in the study. Two of them were used to obtain mesenchymal stem cells. A total of 40 maxillary sinuses were randomly divided into 5 groups: 1) control group which is used to investigate normal rabbit maxillary mucosa, 2) secondary healing group, 3) mesenchymal stem cell graft group, 4) differentiated mesenchymal stem cell group, and 5) nasal mucosal graft group. The animals were sacrificed at the 28th day after the surgery.
Scanning electron microscopy, transmission electron microscopy, and immunohistochemical investigations were performed.

Results:
With these investigations, it was shown that; all graft groups were histologically better than secondary healing group and when the authors compared the graft groups, differentiated mesenchymal stem cell group were the best.

Conclusion:
Our study results showed that endoscopic sinus surgery and treatment with cell sheets, which were generated in temperature-responsive culture dishes, had more functional respiratory epithelium.
Extended Central Artery Perforator Propeller Flap for Large Nasal Defects
Authors: Baltu Yahya , Dölen Utku C. , Aydin Orhan 
Published: June 2019

Abstract
Various local flaps have been defined for small skin defects of the nose. However, the repair of large nasal defects is only possible with flaps allowing a large tissue transfer, such as a free flap, forehead flap, and nasolabial flap. In this study, large nasal defects were reconstructed with extended central artery perforator propeller (CAPP) flaps in an attempt to describe a single-stage procedure as an alternative technique to the median forehead flap. Thirteen large nasal skin defects, including dorsum and nasal sidewall and/or dome, were repaired with a CAPP flap between January 2015 and March 2018. A total of 13 patients aged 19 to 92 years were included. The mean follow-up period was 14.9 months. Pathological diagnoses were basal cell carcinoma in 5 patients, squamous cell carcinoma in 6 patients, and trauma in 2 patients. Defect size ranged between 3 × 3 and 4 × 5 cm. Flap size ranged between 3 × 7 and 5 × 10 cm. No major complications including total flap failure, hematoma, or infection were observed. However, a partial flap necrosis occurred in 1 patient. In 3 patients, scar revision surgery was performed at the postoperative period. In conclusion, CAPP flap use is a safe and reliable option to repair large nasal defects. This flap is able to cover large nasal defects including dorsal, dome, and nasal sidewall defects in a single-stage procedure. Requiring no pedicle separation, this flap is an alternative option to the conventional median forehead flap.
A Descriptive Study of Data Collection Systems Used in Electroconvulsive Therapy Units in the Province of Quebec, Canada
Authors: Haesebaert Julie , Moreno Alexander , Lesage Alain , Patry Simon , Lemasson Morgane 
Published: June 2019

Objectives
This study aimed to describe the data collection systems routinely used by electroconvulsive therapy (ECT) units across the province of Quebec, Canada.

Methods
We conducted a descriptive, cross-sectional study. Using an online survey, 31 ECT units delivering inpatient or outpatient ECT treatments in the province of Quebec provided information on the data collection systems used, data recorded, data collection strategies, indicators of satisfaction, limitations of the current data collection systems, and expectations toward the improvement of ECT data collection.

Results
Most units routinely collected information on individuals receiving ECT treatments, mainly on the medical chart (80%) and in paper format (71%). Most units (88.9%) collected ECT data manually. Electroconvulsive therapy parameters are collected by 66% to 80% of units, but only 16% of them have computerized records. The main limitations of the current systems are as follows: (a) the low frequency of computerization, (b) the underutilization of data, and (c) difficulties in the integration of information from different ECT units. Although 83.3% were satisfied with the current data collection strategies, 80% had a very positive opinion about the development and implementation of an innovative ECT provincial data collection registry.

Conclusions
An integrated ECT provincial data collection system could overcome the variability documented in existing strategies and respond to the current provincial needs and expectations. Also, an integrated ECT provincial data collection system could support both clinical research and quality assurance necessary to inform standards of ECT practice in Quebec.
Repetitive Transcranial Magnetic Stimulation in the Treatment of Skin Picking Disorder
Authors: Aydin Efruz Pirdoğan , Kenar Jülide Güler , Altunay İlknur Kivanc , Kaymak Derya , Özer Ömer Akil , Karamustafalioğlu Kayihan Oğuz 
Published: June 2019

Objectives
Skin picking disorder (SPD) falls into the category of “obsessive-compulsive disorder and related disorders” in the Diagnostic and Statistical Manual of Mental Disorders (Fifth Edition). Repetitive transcranial magnetic stimulation (rTMS) treatment has been reported to be a promising therapy in obsessive-compulsive disorder–related disorders. The purpose of this study was to demonstrate the efficacy of rTMS treatment in patients with SPD.

Methods
Fifteen patients with SPD were assigned to receive 3 weeks' treatment with either active (n = 8) or sham rTMS targeting the pre–supplementary motor area. Patients were evaluated using the Beck Depression Inventory, Beck Anxiety Inventory, Skin Picking Impact Scale, and the Yale-Brown Obsessive Compulsive Scale Modified for Neurotic Excoriation. Response to treatment was defined as a ≥35% decrease on Yale-Brown Obsessive Compulsive Scale modified for Neurotic Excoriation.

Results
Treatment response was achieved in 62.5% of patients (5/8) in the active group and 33.3% of patients (2/6) in the sham group. However, there were no significant differences between the groups in terms of primary and secondary outcomes.

Conclusions
In this exploratory study, active rTMS could not be demonstrated to be superior over sham in treatment of SPD. The results of this study indicate the need for further rTMS studies to be conducted with larger sample sizes and subtypes of SPD.
Landscape of the Dark Transcriptome Revealed through Re-mining Massive RNA-Seq Data
Authors: Li Jing , Singh Urminder , Arendsee Zebulun , Wurtele Eve Syrkin 
Published: June 2019

AbstractThe “dark transcriptome” can be considered the multitude of sequences that are transcribed but not annotated as genes. We evaluated expression of 6,692 annotated genes and 29,354 unannotated ORFs in theSaccharomyces cerevisiaegenome across diverse environmental, genetic and developmental conditions (3,457 RNA-Seq samples). Over 48% of the transcribed ORFs have translation evidence. Phylostratigraphic analysis infers most of these transcribed ORFs would encode species-specific proteins (“orphan-ORFs”); hundreds have mean expression comparable to annotated genes. These data reveal unannotated ORFs most likely to be protein-coding genes. We partitioned a co-expression matrix by Markov Chain Clustering; the resultant clusters contain 2,468 orphan-ORFs. We provide the aggregated RNA-Seq yeast data with extensive metadata as a project in MetaOmGraph, a tool designed for interactive analysis and visualization. This approach enables reuse of public RNA-Seq data for exploratory discovery, providing a rich context for experimentalists to make novel, experimentally-testable hypotheses about candidate genes.
Accurate, ultra-low coverage genome reconstruction and association studies in Hybrid Swarm mapping populations
Authors: Weller Cory A. , Tilk Susanne , Rajpurohit Subhash , Bergland Alan O. 
Published: June 2019

AbstractGenetic association studies seek to uncover the link between genotype and phenotype, and often utilize inbred reference panels as a replicable source of genetic variation. However, inbred reference panels can differ substantially from wild populations in their genotypic distribution, patterns of linkage-disequilibrium, and nucleotide diversity. As a result, associations discovered using inbred reference panels may not reflect the genetic basis of phenotypic variation in natural populations. To address this problem, we evaluated a mapping population design where dozens to hundreds of inbred lines are outbred for few generations, which we call the Hybrid Swarm. The Hybrid Swarm approach has likely remained underutilized relative to pre-sequenced inbred lines due to the costs of genome-wide genotyping. To reduce sequencing costs and make the Hybrid Swarm approach feasible, we developed a computational pipeline that reconstructs accurate whole genomes from ultra-low-coverage (0.05X) sequence data in Hybrid Swarm populations derived from ancestors with phased haplotypes. We evaluate reconstructions using genetic variation from the Drosophila Genetic Reference Panel as well as variation from neutral simulations. We compared the power and precision of GWAS using the Hybrid Swarm, inbred lines, recombinant inbred lines, and highly outbred populations across a range of allele frequencies, effect sizes, and genetic architectures. Our simulations show that these different mapping panels vary in their power and precision, largely depending on the architecture of the trait. The Hybrid Swam and RILs outperform inbred lines for quantitative traits, but not for monogenic ones. Taken together, our results demonstrate the feasibility of the Hybrid Swarm as a cost-effective method of fine-scale genetic mapping.
One step towards bioremediating a heavily polluted river: Metagenomic insights on the function of microbial community
Authors: Breton-Deval Luz , Sanchez-Reyes Ayixon , Sánchez-Flores Alejandro , Juárez Katy , Mussali-Galante Patricia 
Published: June 2019

ABSTRACTThe objective of this study is to understand the functional potential of the microbial community related to bioremediation activity and its relationship with the pollution of each site to enhance the future design of more accurate bioremediation processes. Water samples were collected at four sampling sites along the Apatlaco River (S1-S4), and a whole metagenome shotgun sequencing was performed to know and understand the microbial community involved in bioremediation. Additionally, HMMER was used for searching sequence homologs related to PET and polystyrene biodegradation and metal transformation in Apatlaco River metagenomes. The Apatlaco River is characterized by the presence of a broad spectrum of microorganisms with the metabolic potential to carry out bioremediation activities. Every site along the Apatlaco River has a particular community to perform bioremediation activities. The first site S1 has Thiomonas, Polaromonas, Pedobacter, and Myroides, S2 has Pedobacter, Myroides, Pseudomonas and Acinetobacter, S3, Thiomonas, Myroides, Pseudomonas, Acinetobacter and Aeromonas; S4, Thiomonas, Myroides and Pseudomonas, Thauera.Furthermore, every site is rich in specific enzymes such as S1 has dioxygenase and dehydrogenase, which can degrade Catechol, Biphenyl, Naphthalene, and Phthalate. While, S2 and S3 are rich in dioxygenase and decarboxylating dehydrogenases to degrade Toluene, Fluorobenzoate, Xylene, Phenylpropanoate, and Phenol. S3 also has monooxygenases which degrade Benzene, and all the earlier mentioned enzymes were also found at S4.
Perturbing proteomes at single residue resolution using base editing
Authors: Després Philippe C , Dubé Alexandre K , Seki Motoaki , Yachie Nozomu , Landry Christian R 
Published: June 2019

AbstractBase editors derived from CRISPR-Cas9 systems and DNA editing enzymes offer an unprecedented opportunity for the precise modification of genes, but have yet to be used at a genome-scale throughput. Here, we test the ability of an editor based on a cytidine deaminase, the Target-AID base editor, to systematically modify genes genome-wide using the set of yeast essential genes. We tested the effect of mutating around 17,000 individual sites in parallel across more than 1,500 genes in a single experiment. We identified over 1,100 sites at which mutations have a significant impact on fitness. Using previously determined and preferred Target-AID mutational outcomes, we predicted the protein variants caused by each of these gRNAs. We found that gRNAs with significant effects on fitness are enriched in variants predicted to be deleterious by independent methods based on site conservation and predicted protein destabilization. Finally, we identify key features to design effective gRNAs in the context of base editing. Our results show that base editing is a powerful tool to identify key amino acid residues at the scale of proteomes.
Functional Analysis of FRIGIDA Using Naturally Occurring Variation inArabidopsis thaliana
Authors: Zhang Lei , Jiménez-Gómez José M 
Published: June 2019

AbstractTheFRIGIDAlocus (FRI, AT4G00650) has been extensively studied inArabidopsis thalianabecause of its role creating flowering time diversity. The FRI protein regulates flowering induction by binding partner proteins on its N- and C-terminus domains and creating a supercomplex that promotes transcription of the floral repressor FLC. Despite the knowledge accumulated on FRI, the function of the highly conserved central domain of the protein is still unknown. Functional characterization of naturally occurring DNA polymorphisms can provide useful information about the role of a protein and the localization of its operative domains. In the case of FRI, deleterious mutations are positively selected and widespread in nature, making them a powerful tool to study the function of the different domains of the protein. Here we explore natural sequence variation in the FRI locus in more than 1000 Arabidopsis accessions. We identify new mutations predicted to compromise the function of the protein and confirm our predictions by cloning 22 different alleles of FRI and expressing them in a common null genetic background. Our analysis allows us to pinpoint two single amino acid changes in the central domain that render the protein non-functional. We show that these two mutations determine the stability and cellular localization of the FRI protein. In summary, our work makes use of natural variants at the FRI locus to help understanding the function of the central domain of the FRI protein.
MicrographCleaner: a python package for cryo-EM micrograph cleaning using deep learning
Authors: Sanchez-Garcia Ruben , Segura Joan , Maluenda David , Sorzano C.O.S. , Carazo J.M. 
Published: June 2019

AbstractCryo-EM Single Particle Analysis workflows require from tens of thousands of high-quality particle projections to unveil the three-dimensional structure of macromolecules. Conventional methods for automatic particle picking tend to suffer from high false-positive rates, hurdling the reconstruction process. One common cause of this problem is the presence of carbon and different types of high-contrast contaminations. In order to overcome this limitation, we have developed MicrographCleaner, a deep learning package designed to discriminate which regions of micrographs are suitable for particle picking and which are not in an automatic fashion. MicrographCleaner implements a U-net-like deep learning model trained on a manually curated dataset compiled from over five hundred micrographs. The benchmarking, carried out on about one hundred independent micrographs, shows that MicrographCleaner is a very efficient approach for micrograph preprocessing. MicrographCleaner (micrograph_cleaner_em) package is available at PyPI and Anaconda Cloud and also as a Scipion/Xmipp protocol. Source code is available at https://github.com/rsanchezgarc/micrograph_cleaner_em.
Anin silicoanalysis of robust but fragile gene regulation links enhancer length to robustness
Authors: Barr Kenneth A , Reinitz John , Radulescu Ovidiu 
Published: June 2019

1AbstractOrganisms must ensure that expression of genes is directed to the appropriate tissues at the correct times, while simultaneously ensuring that these gene regulatory systems are robust to perturbation. This idea is captured by a mathematical concept calledr-robustness, which says that a system is robust to a perturbation in up tor -1 randomly chosen parameters. In this work we use this idea to investigate the robustness of gene regulation using a sequence level model of theDrosophila melanogastergeneeven-skipped. We find that gene regulation can be remarkably sensitive to changes in transcription factor concentrations at the boundaries of expression features, while it is robust to perturbation elsewhere. We also find that the length of sequence used to control an expression feature correlates negatively with the number of nucleotides that are sensitive to mutation in both natural andin silicopredicted enhancers. In all cases, the exact degree of robustness obtained is dependent not only on DNA sequence, but also on the local concentration of regulatory factors. By analyzing both natural and synthetic sequences, we provide strong quantitative evidence that increased sequence length makes gene regulatory systems more robust to genetic perturbation.2Author SummaryRobustness assures that organisms can survive when faced with unpredictable environments or genetic mutations. In this work, we characterize the robustness of gene regulation using an experimentally validated model of the regulation of theDrosophilageneeven-skipped. We use a mathematically precise definition of robustness that allows us to make quantitative comparisons of robustness between different genetic sequences or between different nuclei. From this analysis, we found that genetic sequences that were not previously known to be important for gene regulation reduce sensitivity to genetic perturbation. In contrast, we found that gene regulation can be very sensitive to the levels of regulators. This extreme sensitivity was only observed at the boundaries of expression features, where switch-like behavior is desirable. This highlights the importance of considering context when assessing robustness.
Integrated Approach On Degaradtion Of Azo Dyes Using Laccase Enzyme And Nanoparticle With Its Interaction By In Silco Analysis
Authors: Sridharan Rajalakshmi , Krishnaswamy Veena Gayathri , Murali.K Archana , Rajagopal Revathy , Kumar. D Thirumal , Doss.C George Priya 
Published: June 2019

ABSTRACTAzo dyes, released by the textile industries causes severe damage to the environment and living organisms. The degradation of azo dyes is widely studied using enzymatic methods. Laccase, is a copper containing enzyme that degrades the azo dyes into less toxic compounds. In this work, Laccase enzyme produced by the alkaliphile Pseudomonas mendocina in the degradation of mixed azo dye showed 0.386 U/Ml activity at pH 8.5. Combination of enzymatic and green synthesised nanoparticle were used in the degradation mixed azo dye. Laccase used in the degradation of mixed azo dyes showed 58.46% in 72 hours while the photocatalytic degradation of mixed azo dyes showed 15.98%. The degradation of azo dyes using copper iodide nanoparticle resulted in 15.835% of mixed azo dye degradation. But it was noticed that combined method removed 62.35% of mixed azo dyes in 60 minutes. Interaction of laccase enzyme with azo dyes using in silico analysis predicted the binding energy of RR (−7.19 kcal/mol), RB (−8.57 kcal/mol) and RBL (−9.17 kcal/mol).