bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic Data Quality Impacts Automated Detection of Lateral Gene Transfer in Fungi
Authors: Dupont Pierre-Yves , Cox Murray P 
Published: February 2017

Abstract
Lateral gene transfer (LGT, also known as horizontal gene transfer), an atypical mechanism of transferring genes between species, has almost become the default explanation for genes that display an unexpected composition or phylogeny. Numerous methods of detecting LGT events all rely on two fundamental strategies: primary structure composition or gene tree/species tree comparisons. Discouragingly, the results of these different approaches rarely coincide. With the wealth of genome data now available, detection of laterally transferred genes is increasingly being attempted in large uncurated eukaryotic datasets. However, detection methods depend greatly on the quality of the underlying genomic data, which are typically complex for eukaryotes. Furthermore, given the automated nature of genomic data collection, it is typically impractical to manually verify all protein or gene models, orthology predictions, and multiple sequence alignments, requiring researchers to accept a substantial margin of error in their datasets. Using a test case comprising plant-associated genomes across the fungal kingdom, this study reveals that composition- and phylogeny-based methods have little statistical power to detect laterally transferred genes. In particular, phylogenetic methods reveal extreme levels of topological variation in fungal gene trees, the vast majority of which show departures from the canonical species tree. Therefore, it is inherently challenging to detect LGT events in typical eukaryotic genomes. This finding is in striking contrast to the large number of claims for laterally transferred genes in eukaryotic species that routinely appear in the literature, and questions how many of these proposed examples are statistically well supported.
A Dense Brown Trout (Salmo trutta) Linkage Map Reveals Recent Chromosomal Rearrangements in theSalmoGenus and the Impact of Selection on Linked Neutral Diversity
Authors: Leitwein Maeva , Guinand Bruno , Pouzadoux Juliette , Desmarais Erick , Berrebi Patrick , Gagnaire Pierre-Alexandre 
Published: February 2017

AbstractHigh-density linkage maps are valuable tools for conservation and eco-evolutionary issues. In salmonids, a complex rediploidization process consecutive to an ancient whole genome duplication event makes linkage maps of prime importance for investigating the evolutionary history of chromosome rearrangements. Here, we developed a high-density consensus linkage map for the brown trout (Salmo trutta), a socioeconomically important species heavily impacted by human activities. A total of 3977 ddRAD markers were mapped and ordered in 40 linkage groups using sex- and lineage-averaged recombination distances obtained from two family crosses. Performing map comparison between S. trutta and its sister species, S. salar, revealed extensive chromosomal rearrangements. Strikingly, all of the fusion and fission events that occurred after the S. salar/S. trutta speciation happened in the Atlantic salmon branch, whereas the brown trout remained closer to the ancestral chromosome structure. Using the strongly conserved synteny within chromosome arms, we aligned the brown trout linkage map to the Atlantic salmon genome sequence to estimate the local recombination rate in S. trutta at 3721 loci. A significant positive correlation between recombination rate and within-population nucleotide diversity (π) was found, indicating that selection constrains variation at linked neutral sites in brown trout. This new high-density linkage map provides a useful genomic resource for future aquaculture, conservation, and eco-evolutionary studies in brown trout.
An Induced Chromosomal Translocation in Soybean Disrupts a KASI Ortholog and Is Associated with a High-Sucrose and Low-Oil Seed Phenotype
Authors: Dobbels Austin A , Michno Jean-Michel , Campbell Benjamin W , Virdi Kamaldeep S , Stec Adrian O , Muehlbauer Gary J , Naeve Seth L , Stupar Robert M 
Published: February 2017

Abstract
Mutagenesis is a useful tool in many crop species to induce heritable genetic variability for trait improvement and gene discovery. In this study, forward screening of a soybean fast neutron (FN) mutant population identified an individual that produced seed with nearly twice the amount of sucrose (8.1% on dry matter basis) and less than half the amount of oil (8.5% on dry matter basis) as compared to wild type. Bulked segregant analysis (BSA), comparative genomic hybridization, and genome resequencing were used to associate the seed composition phenotype with a reciprocal translocation between chromosomes 8 and 13. In a backcross population, the translocation perfectly cosegregated with the seed composition phenotype and exhibited non-Mendelian segregation patterns. We hypothesize that the translocation is responsible for the altered seed composition by disrupting a β-ketoacyl-[acyl carrier protein] synthase 1 (KASI) ortholog. KASI is a core fatty acid synthesis enzyme that is involved in the conversion of sucrose into oil in developing seeds. This finding may lead to new research directions for developing soybean cultivars with modified carbohydrate and oil seed composition.
A New Reference Genome Assembly for the Microcrustacean Daphnia pulex
Authors: Ye Zhiqiang , Xu Sen , Spitze Ken , Asselman Jana , Jiang Xiaoqian , Ackerman Matthew S , Lopez Jacqueline , Harker Brent , Raborn R Taylor , Thomas W Kelley , Ramsdell Jordan , Pfrender Michael E , Lynch Michael 
Published: February 2017

Abstract
Comparing genomes of closely related genotypes from populations with distinct demographic histories can help reveal the impact of effective population size on genome evolution. For this purpose, we present a high quality genome assembly of Daphnia pulex (PA42), and compare this with the first sequenced genome of this species (TCO), which was derived from an isolate from a population with &gt;90% reduction in nucleotide diversity. PA42 has numerous similarities to TCO at the gene level, with an average amino acid sequence identity of 98.8 and &gt;60% of orthologous proteins identical. Nonetheless, there is a highly elevated number of genes in the TCO genome annotation, with ∼7000 excess genes appearing to be false positives. This view is supported by the high GC content, lack of introns, and short length of these suspicious gene annotations. Consistent with the view that reduced effective population size can facilitate the accumulation of slightly deleterious genomic features, we observe more proliferation of transposable elements (TEs) and a higher frequency of gained introns in the TCO genome.
A Nonsense Variant in the ST14 Gene in Akhal-Teke Horses with Naked Foal Syndrome
Authors: Bauer Anina , Hiemesch Theresa , Jagannathan Vidhya , Neuditschko Markus , Bachmann Iris , Rieder Stefan , Mikko Sofia , Penedo M Cecilia , Tarasova Nadja , Vitková Martina , Sirtori Nicolò , Roccabianca Paola , Leeb Tosso , Welle Monika M 
Published: February 2017

Abstract
Naked foal syndrome (NFS) is a genodermatosis in the Akhal-Teke horse breed. We provide the first scientific description of this phenotype. Affected horses have almost no hair and show a mild ichthyosis. So far, all known NFS affected horses died between a few weeks and 3 yr of age. It is not clear whether a specific pathology caused the premature deaths. NFS is inherited as a monogenic autosomal recessive trait. We mapped the disease causing genetic variant to two segments on chromosomes 7 and 27 in the equine genome. Whole genome sequencing of two affected horses, two obligate carriers, and 75 control horses from other breeds revealed a single nonsynonymous genetic variant on the chromosome 7 segment that was perfectly associated with NFS. The affected horses were homozygous for ST14:c.388G&gt;T, a nonsense variant that truncates &gt;80% of the open reading frame of the ST14 gene (p.Glu130*). The variant leads to partial nonsense-mediated decay of the mutant transcript. Genetic variants in the ST14 gene are responsible for autosomal recessive congenital ichthyosis 11 in humans. Thus, the identified equine ST14:c.388G&gt;T variant is an excellent candidate causative variant for NFS, and the affected horses represent a large animal model for a known human genodermatosis. Our findings will enable genetic testing to avoid the nonintentional breeding of NFS-affected foals.
Independent Maternal and Fetal Genetic Effects on Midgestational Circulating Levels of Environmental Pollutants
Authors: Traglia Michela , Croen Lisa A , Lyall Kristen , Windham Gayle C , Kharrazi Marty , DeLorenze Gerald N , Torres Anthony R , Weiss Lauren A 
Published: February 2017

Abstract
Maternal exposure to environmental pollutants could affect fetal brain development and increase autism spectrum disorder (ASD) risk in conjunction with differential genetic susceptibility. Organohalogen congeners measured in maternal midpregnancy blood samples have recently shown significant, but negative associations with offspring ASD outcome. We report the first large-scale maternal and fetal genetic study of the midpregnancy serum levels of a set of 21 organohalogens in a subset of 790 genotyped women and 764 children collected in California by the Early Markers for Autism (EMA) Project. Levels of PCB (polychlorinated biphenyl) and PBDE (polybrominated diphenyl ether) congeners showed high maternal and fetal estimated SNP-based heritability (h2g) accounting for 39–99% of the total variance. Genome-wide association analyses identified significant maternal loci for p,p′-DDE (P = 7.8 × 10−11) in the CYP2B6 gene and for BDE-28 (P = 3.2 × 10−8) near the SH3GL2 gene, both involved in xenobiotic and lipid metabolism. Fetal genetic loci contributed to the levels of BDE-100 (P = 4.6 × 10−8) and PCB187 (P = 2.8 × 10−8), near the potential metabolic genes LOXHD1 and PTPRD, previously implicated in neurodevelopment. Negative associations were observed for BDE-100, BDE153, and the sum of PBDEs with ASD, partly explained by genome-wide additive genetic effects that predicted PBDE levels. Our results support genetic control of midgestational biomarkers for environmental exposures by nonoverlapping maternal and fetal genetic determinants, suggesting that future studies of environmental risk factors should take genetic variation into consideration. The independent influence of fetal genetics supports previous hypotheses that fetal genotypes expressed in placenta can influence maternal physiology and the transplacental transfer of organohalogens.
Adaptation of Candida albicans to Reactive Sulfur Species
Authors: Chebaro Yasmin , Lorenz Michael , Fa Alice , Zheng Rui , Gustin Michael 
Published: February 2017

Abstract
Candida albicans is an opportunistic fungal pathogen that is highly resistant to different oxidative stresses. How reactive sulfur species (RSS) such as sulfite regulate gene expression and the role of the transcription factor Zcf2 and the sulfite exporter Ssu1 in such responses are not known. Here, we show that C. albicans specifically adapts to sulfite stress and that Zcf2 is required for that response as well as induction of genes predicted to remove sulfite from cells and to increase the intracellular amount of a subset of nitrogen metabolites. Analysis of mutants in the sulfate assimilation pathway show that sulfite conversion to sulfide accounts for part of sulfite toxicity and that Zcf2-dependent expression of the SSU1 sulfite exporter is induced by both sulfite and sulfide. Mutations in the SSU1 promoter that selectively inhibit induction by the reactive nitrogen species (RNS) nitrite, a previously reported activator of SSU1, support a model for C. albicans in which Cta4-dependent RNS induction and Zcf2-dependent RSS induction are mediated by parallel pathways, different from S. cerevisiae in which the transcription factor Fzf1 mediates responses to both RNS and RSS. Lastly, we found that endogenous sulfite production leads to an increase in resistance to exogenously added sulfite. These results demonstrate that C. albicans has a unique response to sulfite that differs from the general oxidative stress response, and that adaptation to internal and external sulfite is largely mediated by one transcription factor and one effector gene.
A study on clinical profile and management of lump in breast at tertiary rural hospital, Wardha, Maharashtra, India
Authors: Chandak S. R. , Tabrez Md. Omar 
Published: February 2017

Background: Breast lumps diseases are one of the most common diseases in India which include congenital, traumatic, inflammatory, hormonal mastopathy, benign and malignant neoplastic conditions. Around 200,000 cases of breast diseases are diagnosed annually. In India, as there is no study of breast disease conducted separately in rural India hence studies are required to evaluate the incidence and prevalence of breast lump diseases so that interventions can be done to educate and guide people about the risk factors, importance of screening and management strategies.Methods: We have conducted our study on 50 cases of lump in breast with the objective to know their incidence, clinical, pathological and radiological features of various breast swellings and different investigative approach different treatment modalities and their outcome presenting in rural India.Results: The present study of lump in the breast was based on 50 cases admitted in AVBRH, Wardha, Maharashtra, India. During this period maximum patient were of benign breast lump as compared to malignant. All patients were females with age variation from 15 years to 55 years. Majority of patients had lumps varying from 2 months to more than 12 months.Conclusions: Most of the patients from benign lump were managed with excision of lump and all patient of malignant lump underwent mastectomy.
Clinical profile in cases of intestinal perforation
Authors: Utaal Maneshwar Singh , Bali Sharadendu , Batra Pooja , Garg Navdeep 
Published: February 2017

Background: Intestinal perforation is a surgical emergency with a wide variety of clinical features and causes. Regional variations are common with regards to the cause of intestinal perforation, and need to be evaluated in local settings. The study was conducted to determine the clinical profile of patients with intestinal perforation, with regard to clinical presentation, investigative results, pathological features, surgical findings, complications and outcome.Methods: Detailed information was recorded on 40 cases of intestinal perforation with regard to clinical features, investigative results, surgical findings, post-operative course and outcome. The data was analysed with appropriate statistical methods.Results: The site of perforation was gastric 27.5%, duodenum 20%, jejunum 5%, ileum 35%, appendix 10% and colon 2.5%. Main causes included peptic ulcer 42.5%, typhoid 25% and few cases of trauma, tuberculosis, appendicitis and malignancy. Peritonitis was universal. Primary repair, resection with anastomosis, appendectomy and stoma were the operative procedures. Morbidity rate was 60.0% and mortality rate was 12.5%.Conclusions: Commonest site of perforation was gastro-duodenal while commonest cause was peptic ulcer disease. Morbidity and mortality was comparable with other studies.
Prognostic predictors in polytraumatized children and their impact on outcome
Authors: Essa Ahmed Abdelhady , El-Shaboury Islam M. , Ibrahim Mohammed A. , Abdelgwad Emadeldien A. , Gadelrab Mohammed A. 
Published: February 2017

Background: Trauma is the leading cause of death and disability in children ≥ 1 year of age. More than 80% of injuries are caused by blunt trauma. Most seriously injured children have multiple injuries. Injury scoring systems are designed to accurately assess injury severity, appropriately triage the injured, and develop and refine trauma patient care. The pediatric trauma scoring (PTS) was devised specifically for the triage of pediatric trauma patients. The pediatric trauma scoring (PTS) was devised specifically for the triage of pediatric trauma patients. The PTS is calculated as the sum of individual scores from six clinical variables. The variables include weight, airway, systolic blood pressure (SBP), central nervous system (CNS) status (level of consciousness), presence of an open wound, and skeletal injuries. Other predicting factors for morbidity and mortality in polytraumatised children include age and gender of the patients, trauma type, arrival interval time, Glasgow Coma Scale (GCS), respiratory rate, heart rate, hematocrit value at admission. These factors can further help to prevent mortality. The objectives of this study were to assess the prognosis of polytraumatised pediatric patients by evaluation of pediatric trauma scoring system and clinical predictors of morbidity and mortality as prognostic predictors of trauma in pediatric patients.Methods: This was adescriptive study, included 60 polytraumatised pediatric patients who were attended emergency department in Suez Canal University Hospital, Ismailia, Egypt.Results: This study showed that the mean of the pediatric trauma scoring system was 10±2. According to the nature of the most severe injury, this study showed that 43 % of injuries among patients were of extremities and pelvis nature. According to length of resuscitation time among patients, this study showed that the mean time of resuscitation was 35.5±8.23 minutes. According to the type of treatment done for the patients, this study showed that 72% of the patients didn't need surgical intervention. This study showed that regarding the final outcome of the patients, 68% of the patients were admitted to inpatient.Conclusions: This study showed that both heart rate and respiratory rate had good sensitivity while both of them had lower specificity. This study showed that GCS good specificity and fair sensitivity. Regarding the PTS, this study showed that PTS had the highest specificity and the highest sensitivity among all the predictors.
Bacteriological profile of burn patients and antimicrobial susceptibility pattern of burn wound isolates
Authors: Sharma Latika , Srivastava Harshit , Pipal Dharmendra Kumar , Dhawan Rohit , Purohit Poojan M. , Bhargava Anupam 
Published: February 2017

Background: Infection is a common cause of morbidity and mortality in burn patients. Clinical diagnosis of bacteremia and/or sepsis in burn patients is difficult for a number of reasons. It could be symptomatic and/or asymptomatic as a result of immune deficiency secondary to thermal injury.Methods: A retrospective study was conducted at Mahatma Gandhi Hospital Burn Unit Associated with Dr. S. N. Medical College, Jodhpur, Rajasthan. Fifty burn patients were investigated for bacterial profile of burn wound infections. Specimens were collected on 3rd and 7th day of burns in the form of wound swabs. The organisms were isolated and identified by standard microbiological methods. Antimicrobial susceptibility test was done by Kirby -Bauer disc diffusion method.Results: Gram negative organisms were found to be more prevalent. The most common isolate was Pseudomonas aeruginosa (P. aeruginosa) -38%, followed by Staphylococcus aureus (S. aureus) -35%, Klebsiella spp.-8%, Acinetobacter spp -5%, Staphylococcus epidermidis - 5%, Proteus spp. -3% and Escherichia coli -1%.Conclusions: Pseudomonas was the commonest cause of infection in fire burn patients in our setting followed by S. aureus. About 82% of the isolates showed multiple resistances. In light of our findings, regular antibiotic resistance test has to be done for each patient in order to select an appropriate antimicrobial agent.
Conservative management of early uncomplicated appendicitis in children
Authors: Maini Sunil Kumar , Jain Neeraj Kumar , Jain Manjari Goel , Khobragade Vicky 
Published: February 2017

Background: Right lower abdominal pain management in children is a challenging task for the surgeon. Most of the time right lower abdominal pain ends up in acute appendicitis. For long time appendicetomy was the treatment of choice. However surgical intervention has its own disadvantages such as pain, scarring, adhesions, hernia development and venous thrombosis disease. Anxiety and fear of surgery were also two difficulties in obtaining consent for surgery. Parents often request and insist for medical management. Their unwillingness for surgical intervention was the most important reason for medical management of uncomplicated acute appendicitis.Methods: Our prospective observational study was conducted in the Department of General Surgery, R.K.D.F. Medical College and Research Centre, Bhopal, Madhya Pradesh, India during period of January 2014 to January 2016 and follow up was done till December 2016. Our target group was children under 16 years. A total of 92 children with complaint of right lower abdominal pain attended the hospital for treatment. Routine investigations including ultrasonography of abdomen were performed for all the patients. Out of 92 patients diagnosis of acute appendicitis was made in 74 patients, Surgery was performed in 32 patients, while remaining 42 patients were treated conservatively and the results were analyzed.Results: In this study of 92 patients of pain in right iliac fossa below 16 years, 74 (80.43%) were diagnosed as acute appendicitis. 32 (43.24%) Patients were operated earlier. 42 (56.75%) Patient were treated conservatively. Out of 42 patients, 12 (16.21%) patients were operated within 1 year, 30 (40.54%) Patients didn’t require any surgical intervention during 1 year follow up. In present study, significant role of antibiotic was found in conservative management of acute appendicitis in children. So it can be concluded that conservative management of acute appendicitis in children can be attempted under observation.Conclusions: Antibiotics are both effective and safe as primary treatment for patients with uncomplicated acute appendicitis. Initial antibiotic treatment merits consideration as a primary treatment option for early uncomplicated appendicitis. Appendicectomy should be done but conservative management of acute appendicitis in children can be attempted under observation.
Access loop Roux-en-Y hepaticojejunostomy: revisited a study of twenty two cases over 15 years (2001-2015)
Authors: Ray M. S. , Deepak B. S. 
Published: February 2017

Background: Access-loop Roux-en-Y hepaticojejunostomy (HJ), an interesting and an unique surgical technique described in the past seems to have resurfaced amidst commendation and condemnation.Methods: The technique involves the incorporation of a cutaneous access stoma in the Roux-en-Y loop of jejunum used for the anastomosis. This stoma provides permanent access to the bilio-enteric anastomosis and thus to the hepatobiliary tree for non-operative management of chronic and recurrent biliary tract problems. Here we are presenting our experience in 22 cases managed by us with “access-loop Roux-en-Y hepaticojejunostomy (HJ)” over a period of 15 years (2001 to 2016).Results: 22 cases were managed successfully. The maximum follow-up was for 05 years with no recurrence or stricture only 01 patient had a small Incisional hernia.Conclusions: The objective of this work is to, describe an optional technique (although less known and practiced) during the accomplishment of a "roux-en-Y" hepaticojejunostomy that, allows future endoscopic and interventional radiology access to the bilio-enteric anastomosis.