bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Insertion Green Monster (iGM) Method for Expression of Multiple Exogenous Genes in Yeast
Authors: Labunskyy Vyacheslav M , Suzuki Yo , Hanly Timothy J , Murao Ayako , Roth Frederick P , Gladyshev Vadim N 
Published: April 2014

Abstract
Being a simple eukaryotic organism, Saccharomyces cerevisiae provides numerous advantages for expression and functional characterization of proteins from higher eukaryotes, including humans. However, studies of complex exogenous pathways using yeast as a host have been hampered by the lack of tools to engineer strains expressing a large number of genetic components. In addition to inserting multiple genes, it is often desirable to knock out or replace multiple endogenous genes that might interfere with the processes studied. Here, we describe the “insertion Green Monster” (iGM) set of expression vectors that enable precise insertion of many heterologous genes into the yeast genome in a rapid and reproducible manner and permit simultaneous replacement of selected yeast genes. As a proof of principle, we have used the iGM method to replace components of the yeast pathway for methionine sulfoxide reduction with genes encoding the human selenoprotein biosynthesis machinery and generated a single yeast strain carrying 11 exogenous components of the selenoprotein biosynthetic pathway in precisely engineered loci.
Mapping Small Effect Mutations inSaccharomyces cerevisiae: Impacts of Experimental Design and Mutational Properties
Authors: Duveau Fabien , Metzger Brian P H , Gruber Jonathan D , Mack Katya , Sood Natasha , Brooks Tiffany E , Wittkopp Patricia J 
Published: April 2014

AbstractGenetic variants identified by mapping are biased toward large phenotypic effects because of methodologic challenges for detecting genetic variants with small phenotypic effects. Recently, bulk segregant analysis combined with next-generation sequencing (BSA-seq) was shown to be a powerful and cost-effective way to map small effect variants in natural populations. Here, we examine the power of BSA-seq for efficiently mapping small effect mutations isolated from a mutagenesis screen. Specifically, we determined the impact of segregant population size, intensity of phenotypic selection to collect segregants, number of mitotic generations between meiosis and sequencing, and average sequencing depth on power for mapping mutations with a range of effects on the phenotypic mean and standard deviation as well as relative fitness. We then used BSA-seq to map the mutations responsible for three ethyl methanesulfonate−induced mutant phenotypes in Saccharomyces cerevisiae. These mutants display small quantitative variation in the mean expression of a fluorescent reporter gene (−3%, +7%, and +10%). Using a genetic background with increased meiosis rate, a reliable mating type marker, and fluorescence-activated cell sorting to efficiently score large segregating populations and isolate cells with extreme phenotypes, we successfully mapped and functionally confirmed a single point mutation responsible for the mutant phenotype in all three cases. Our simulations and experimental data show that the effects of a causative site not only on the mean phenotype, but also on its standard deviation and relative fitness should be considered when mapping genetic variants in microorganisms such as yeast that require population growth steps for BSA-seq.
Oviposition Preferences ofAgrilus planipennis(Coleoptera: Buprestidae) for Different Ash Species Support the Mother Knows Best Hypothesis
Authors: Rigsby Chad M , Muilenburg Vanessa , Tarpey Thaddeus , Herms Daniel A , Cipollini Don 
Published: April 2014

AbstractThe “mother knows best” hypothesis states that adults should choose hosts for oviposition on which their offspring will best perform, maximizing their own fitness. It has been hypothesized that this preference—performance relationship for wood-boring insects is especially important because larvae are not able to switch hosts, although no study has examined oviposition choices for these insects. We examined oviposition preferences of the emerald ash borer, Agrilus planipennis Fairmaire (Coleoptera: Buprestidae), in two common gardens, one on the campus of Wright State University in Dayton, OH, and the other at the Michigan State University Tollgate Research Farm in Novi, MI, by wrapping cheesecloth around ash trunks to assess passive oviposition patterns.Wefound that in both gardens, ash species native to North America, which are highly susceptible to the emerald ash borer, consistently received more ova than Manchurian ash, which is indigenous to Asia and more resistant to the emerald ash borer. Susceptible trees in the Novi garden received 93 times the number of ova and susceptible trees at the Wright State garden received up to 25 times the number of ova that were received by Manchurian ash in each of their respective gardens. Neither tree size nor vigor affected oviposition choice. There were also higher numbers of adult exit holes on North American than Manchurian ash in both common gardens. The observed oviposition preferences in this study align with patterns of adult feeding preference, ash host mortality, and exit hole numbers from other studies. These observations also suggest that oviposition preferences may contribute to interspecific patterns of host resistance and mortality. Collectively, our results demonstrate that the emerald ash borer prefers to oviposit on species on which its offspring will best perform, suggesting that there is strong selection for the ability to recognize host cues that predict better larval survival and performance.
Characterization of Circulating and Endothelial Progenitor Cells in Patients With Extreme-Duration Type 1 Diabetes
Authors: Hernandez Sonia L. , Gong Jennifer H. , Chen Liming , Wu I-Hsien , Sun Jennifer K. , Keenan Hillary A. , King George L. 
Published: April 2014

OBJECTIVE
We characterized and correlated endothelial progenitor cells (EPCs) and circulating progenitor cells (CPCs) with lack of vascular complications in the Joslin Medalist Study in patients with type 1 diabetes for 50 years or longer.

RESEARCH DESIGN AND METHODS
EPC and CPC levels were ascertained by flow cytometry and compared among Medalists (n = 172) with or without diabetic retinopathy (DR; n = 84 of 162), neuropathy (n = 94 of 165), diabetic nephropathy (DN; n = 18 of 172), cardiovascular disease (CVD; n = 63 of 168), age-matched controls (n = 83), type 2 diabetic patients (n = 36), and younger type 1 diabetic patients (n = 31). Mitogens, inflammatory cytokines, and oxidative markers were measured in blood or urine. Migration of cultured peripheral blood mononuclear cells (PBMCs) from Medalists and age-matched controls were compared.

RESULTS
Medalists’ EPC and CPC levels equaled those of their nondiabetic age-matched controls, were 10% higher than those in younger type 1 diabetic patients, and were 20% higher than those in age-matched type 2 diabetic patients. CPC levels were 15% higher in Medalists without CVD and nephropathy than in those affected, whereas EPC levels were significantly higher in those without peripheral vascular disease (PVD) than those with PVD. Stromal-derived factor 1 (SDF-1) levels were higher in Medalists with CVD, DN, and DR than in those not affected and their controls. IGF-I levels were lower in Medalists and correlated inversely with CPC levels. Additionally, cultured PBMCs from Medalists migrated more than those from nondiabetic controls.

CONCLUSIONS
Normal levels of EPC and CPC in the Medalists, unlike other groups with diabetes, especially those without CVD, support the idea that endogenous factors exist to neutralize the adverse effects of metabolic abnormalities of diabetes on vascular tissues.
Effects of Whole-Body Vibration Therapy on Body Functions and Structures, Activity, and Participation Poststroke: A Systematic Review
Authors: Liao Lin-Rong , Huang Meizhen , Lam Freddy M.H. , Pang Marco Y.C. 
Published: May 2014

BackgroundWhole-body vibration (WBV) has gained increasing popularity in rehabilitation. Recent studies have investigated the application of WBV in individuals with chronic illnesses, including stroke.PurposeThe purpose of this study was to compare WBV exercise with the same exercise condition without WBV and with other types of physical exercise in enhancing body functions and structures, activity, and participation in individuals with stroke and examine its safety.Data SourceElectronic searches were conducted on MEDLINE, CINAHL, PEDro, PubMed, PsycINFO, and Science Citation Index.Study SelectionRandomized controlled trials (RCTs) that investigated the effects of WBV among individuals with stroke were identified by 2 independent researchers. Ten articles (9 studies, totaling 333 study participants) satisfied the selection criteria and were included in this review.Data ExtractionThe methodological quality was rated using the PEDro scale. The results were extracted by 2 independent researchers and confirmed with the principal investigator.Data SynthesisOnly 2 RCTs were considered as demonstrating level 1 evidence (PEDro score ≥6 and sample size &gt;50). Two RCTs examined the effects of a single WBV session, and 7 RCTs examined the effects of WBV programs spanning 3 to 12 weeks. No consistent benefits on bone turnover, leg motor function, balance, mobility, sensation, fall rate, activities of daily living, or societal participation were found, regardless of the nature of the comparison group. Adverse events were minor.LimitationsA broad approach was used, with stroke as an inclusion criterion for review. No solid evidence was found concerning the effects of WBV on subgroups of people with specific stroke-related deficits due to the heterogeneity of patient groups.ConclusionsBased on the review, there is insufficient evidence to support clinical use of WBV in enhancing body functions and structures, activity, and participation after stroke.
Correlation of bone marrow aspiration and biopsy findings in diagnosing hematological disorders - a study of 89 cases
Authors: Parajuli S , Tuladhar A 
Published: April 2014

Background: Bone marrow examination is an important diagnostic tool to evaluate various disorders which includes both neoplastic and non- neoplastic hematological diseases. Few studies have compared the relative value of aspirate with trephine biopsy. The present study was conducted to compare the role of bone marrow aspirate and trephine biopsy to formulate an effective and rapid method for diagnosing wide spectrum of hematological diseases. Materials and Methods: This is a three year retrospective study done from July 2010 to June 2013. A total of 95 cases presented with clinical haematological disorders; of which only 89 were biopsied and the correlation done. All the smears and sections were reviewed for morphological details and findings on aspirate and biopsy and compared to each other. Results: Out of the 89 cases selected for study; bone marrow aspiration revealed diagnostic materials in 75 cases and 14 cases were inconclusive for a definite diagnosis. The diagnostic accuracy of the bone marrow aspiration cytology was 84.26%. Eighty eight cases were diagnosed on trephine biopsy of bone marrow with diagnostic accuracy of 98.87%. Conclusion: Both the aspiration cytology and trephine biopsy complement each other for evaluating any haematological disorder. Though cellular morphology is better understood in marrow aspirates and is equally effective to biopsy in diagnosing various anemias and leukemias; however it is the histopathological study of trephine biopsy that gives well preserved marrow architecture with its all cellular and stromal components. modalities including radiological, microbiological and serological tests. DOI: http://dx.doi.org/10.3126/jpn.v4i7.10294 Journal of Pathology of Nepal (2014) Vol. 4, 534-538
Smear technique for intraoperative diagnosis of central nervous system neoplasms
Authors: Shrestha S , Thapa BK , Bhattarai B 
Published: April 2014

Background: Smear cytology has become increasily popular as an alternative to frozen section for the rapid diagnosis of most of central nervous system lesions. The aim of this study was to assess the utility of smear technique for the rapid diagnosis in the neurosurgical biopsies and to compare the smear cytological features with the final histopathological examination. Materials and Methods: This was a prospective study conducted in the Department of Pathology of BP Koirala Memorial cancer Hospital for a period of one year. Sixty cases of clinically suspected CNS tumors were sent for intraoperative smear cytological examination and histological examination. Both techniques were then compared for their ability to diagnose as well as grade the tumors. Results: Gliomas (51.6%) were the most frequently occurring tumors in the total cases. Diagnostic accuracy of squash/smear technique achieved was 88 %( 53/60) when compared with histopathological diagnoses. In two cases, smears comprised of blood clots and no opinion was possible in cytology. Complete discrepancy was seen in five cases that included two cases of atypical meningioma, a one case each of germinoma, glioblastoma and metastatic tumor. Conclusion: Smear technique is a fairly accurate, rapid, easily reproducible and cost effective tool to diagnose brain tumours. Smear cytology is of great value in Intraoperative consultation of central nervous system lesions. DOI: http://dx.doi.org/10.3126/jpn.v4i7.10296 Journal of Pathology of Nepal (2014) Vol. 4, 544-547
Antibiotic susceptibility pattern of staphylococcus aureus and methicillin-resistant staphylococcus aureus in a tertiary care hospital
Authors: Bhatt CP , Karki BMS , Baral B , Gautam S , Shah A , Chaudhary A 
Published: April 2014

Background: Methicillin resistant Staphylococcus aureushas emerged as one of the most important nosocomial pathogens. It invokes a tremendous financial burden and enhanced morbidity and mortality due to difficult to treat systemic infections.Aim of this study was to determine antibiotic susceptibility pattern of Staphylococcus aureus and Methicillin resistant Staphylococcus aureus. Materials and Methods: Different clinical specimens were collected and processed for routine culture and antibiotic sensitivity test by standard microbiology techniques. Results: Out of 1173 samples received for microbiological examination, 100 were found to be S. aureus with 19% cases were Methicillin resistant Staphylococcus aureus (MRSA). Fourteen MRSA were found from inpatient and 5 were from outpatient. MRSA was found higher in female than male and maximum number (31.5%) was found in age group 0-10 years. Staphylococcus aureus was 100% sensitive to Vancomycin followed by Amikacin (90%), Gentamycin (83%), and tetracycline (81%). On urine isolates Nitrofurantoin(91.6%) was drug of choice. All the isolates were resistant to Penicillin G. In case of Methicillin resistant Staphylococcus aureus showed 100% sensitive to Vancomycin followed by Amikacin (84.2%), Tetracycline (63.1%), Ciprofloxacin (42%) and Gentamycin (36.8%). Among urine isolates Nitrofutantoin showed 87.5% sensitive followed by Norfloxacin (75%). Conclusion: Methicillin resistant Staphylococcus aureus was found 19% of Staphylococcus aureus isolates. It was most common in females, hospitalized patients and young age group. Vancomycin seems to be drug of choice followed by Amikacin. It would be helpful to formulating and monitoring the antibiotic policy and ensure proper empiric treatment. DOI: http://dx.doi.org/10.3126/jpn.v4i7.10297 Journal of Pathology of Nepal (2014) Vol. 4, 548-551
Utility of prospective step sections in diagnostic skin histopathology for small biopsies
Authors: Kattel G , Sinha AK , Agrawal S 
Published: April 2014

Background: Small skin biopsies have a cosmetic advantage and prospective step sections could potentially improve turnaround time without compromising diagnostic information. The study aimed to examine the use of prospective step sections of small skin biopsies and its effect on histopathological diagnosis and turnaround time. Materials and Methods: This was a hospital based cross-sectional study at Department of Pathology and Department of Dermatology, BPKIHS from June 2011- June 2012. Diagnoses /comment on three levels of prospectively taken 3mm biopsies were compared with those of 5mm biopsies taken from the same/similar lesion from 100 patients. Additional sections from 5mm biopsies were taken retrospectively. Percentage, proportion, mean, standard deviation, diagnostic sensitivity, kappa statistics and paired sample t- test were used as statistical tools. Results: Of 100 cases, 80 were diagnosed using 5mm biopsies while 73 were diagnosed using 3mm biopsies. On additional step sections of 3mm biopsies, 3 more cases were diagnosed. When compared with 5mm biopsies, the sensitivity of the 3mm biopsy rose from 90% to 93.8% after additional sections while the measure of agreement rose from 0.751 to 0.826.Mean turnaround time for prospectively sectioned 3mm biopsies was 2.56 days and that of retrospectively sectioned 5 mm biopsies was 4.64 days with their difference being statistically significant. Conclusion: A statistically significant decrease in turnaround time and an increase in sensitivity and agreement after step sections elucidates the utility of prospective step sectioned 3 mm biopsies in diagnostic skin histopathology. DOI: http://dx.doi.org/10.3126/jpn.v4i7.10298 Journal of Pathology of Nepal (2014) Vol. 4, 552-559
A study on microvascular density in breast carcinoma
Authors: Pyakurel D , Karki S , Agrawal CS 
Published: April 2014

Background: Breast Cancer is the most frequent neoplasm causing death in women between 35-55 years of age. Of the Prognostic indicators existing for breast cancer, axillary lymph node status has been regarded as the most important one. Twenty to thirty percent of all lymph node negative patients will still develop a recurrence of the disease within 10 years of initial treatment. Therefore, a new prognostic marker that could identify patients at high risk of tumor recurrence more accurately than existing indicators would be of great value, one potential indicator is tumor-induced angiogenesis. Materials and Methods: This is a six months prospective (January 2010-June 2010) and 1 year retrospective (Jan2009-Dec2009) study which included thirty five breast cancer cases visiting the Surgical OPD. Angiogenesis was estimated by determining micro vessel counting after immune staining the paraffin embedded tissue sections using anti-CD34 antibody. Results: Age of the patients ranged from 25 to 80 years with a mean age of 45.48 years. Most of the cases were infiltrating ductal carcinoma comprising of 33 cases (94.28%). Three cases (9.10%) showed vascular invasion by the tumor. Majority showed (63.64%) vessel count of less than 200 per 10 high power fields. Conclusion: Micro vascular density positively correlated with size of the tumor, lymph nodes involved by the tumor and Nottingham prognostic index. In the future, Antibodies specific to proliferating endothelium, together with the development of automated image analysis, may improve the accuracy and value of measuring angiogenesis-induced microvessel density. DOI: http://dx.doi.org/10.3126/jpn.v4i7.10315 Journal of Pathology of Nepal (2014) Vol. 4, 570-575
Lymph node infarction and lymphoma
Authors: Pai R , Ghartimagar D , Khadilkar U , Pai M , Kini A 
Published: April 2014

Non Hodgkin lymphoma with infarction at initial presentation is rare and can be confused with an acute inflammatory process. A 47 year-old-man presented with complaint of swelling in the left parotid region for 2 weeks which increased in size with severe, continuous and throbbing pain in the last 2-3 days. A clinical diagnosis of parotid abscess was made. Incision and drainage did not yield any pus. Fine needle aspiration cytology showed a highly cellular tumor comprising of somewhat uniform round cells with granular nuclear chromatin. Ghost outline of cytoplasm was noted. A diagnosis of infarcted neoplasm of the parotid gland, probably acinic cell carcinoma was suggested. Histopathologically, it was reported as non-Hodgkin lymphoma with infarction which was confirmed by immunohistochemistry. DOI: http://dx.doi.org/10.3126/jpn.v4i7.10319 Journal of Pathology of Nepal (2014) Vol. 4, 591-593
Metaplastic carcinoma of breast
Authors: Dewasi N , Bhattacharya D , Sarker PG , Das M , Ghosh S , Ghosh TK 
Published: April 2014

Metaplastic carcinomas of breast are a heterogeneous group of malignant tumours in which part or all of the carcinomatous epithelium is transformed into a nonglandular (metaplastic) growth process. This rare neoplasm usually runs an aggressive course. DOI: http://dx.doi.org/10.3126/jpn.v4i7.10320 Journal of Pathology of Nepal (2014) Vol. 4, 594-596
The endoscopic endonasal approach for the management of craniopharyngiomas: a series of 103 patients
Authors: Cavallo Luigi Maria , Frank Giorgio , Cappabianca Paolo , Solari Domenico , Mazzatenta Diego , Villa Alessandro , Zoli Matteo , D'Enza Alfonso Iodice , Esposito Felice , Pasquini Ernesto 
Published: May 2014

Object
Despite their benign histological appearance, craniopharyngiomas can be considered a challenge for the neurosurgeon and a possible source of poor prognosis for the patient. With the widespread use of the endoscope in endonasal surgery, this route has been proposed over the past decade as an alternative technique for the removal of craniopharyngiomas.

Methods
The authors retrospectively analyzed data from a series of 103 patients who underwent the endoscopic endonasal approach at two institutions (Division of Neurosurgery of the Università degli Studi di Napoli Federico II, Naples, Italy, and Division of Neurosurgery of the Bellaria Hospital, Bologna, Italy), between January 1997 and December 2012, for the removal of infra- and/or supradiaphragmatic craniopharyngiomas. Twenty-nine patients (28.2%) had previously been surgically treated.

Results
The authors achieved overall gross-total removal in 68.9% of the cases: 78.9% in purely infradiaphragmatic lesions and 66.3% in lesions involving the supradiaphragmatic space. Among lesions previously treated surgically, the gross-total removal rate was 62.1%. The overall improvement rate in visual disturbances was 74.7%, whereas worsening occurred in 2.5%. No new postoperative defect was noted. Worsening of the anterior pituitary function was reported in 46.2% of patients overall, and there were 38 new cases (48.1% of 79) of postoperative diabetes insipidus. The most common complication was postoperative CSF leakage; the overall rate was 14.6%, and it diminished to 4% in the last 25 procedures, thanks to improvement in reconstruction techniques. The mortality rate was 1.9%, with a mean follow-up duration of 48 months (range 3–246 months).

Conclusions
The endoscopic endonasal approach has become a valid surgical technique for the management of craniopharyngiomas. It provides an excellent corridor to infra- and supradiaphragmatic midline craniopharyngiomas, including the management of lesions extending into the third ventricle chamber. Even though indications for this approach are rigorously lesion based, the data in this study confirm its effectiveness in a large patient series.