bluuebunny/crossref_metadata_2025 huggingface dataset:
SMARCB1/INI1 Involvement in Pediatric Chordoma
Authors: Antonelli Manila , Raso Alessandro , Mascelli Samantha , Gessi Marco , Nozza Paolo , Coli Antonella , Gardiman Marina P. , Arcella Antonietta , Massimino Maura , Buttarelli Francesca R. , Giangaspero Felice
Published: September 2016

Chordomas arise in the skull base and spine and usually occur in adults and are rare in the pediatric population. Cases of chordoma in pediatric age are often poorly differentiated, showing cytologic atypia, increased cellularity, and mitosis, and their aggressive behavior is associated with a high incidence of metastatic spread and a short patient survival. Recent studies have described loss of SMARCB1/INI1 protein in poorly differentiated chordomas associated not with point mutations but with SMARCB1/INI1 gene deletions instead. In this study, we considered immunohistochemistry and SMARCB1/INI1 mutational status to examine SMARCB1 status in a series of pediatric chordomas (7 classic and 1 poorly differentiated). We performed immunohistochemical tests for INI1, brachyury, S100, and cytokeratins and conducted a genetic analysis on the SMARCB1 coding sequence (NM_003073) using the Sanger method and multiplex ligation-dependent probe amplification to detect abnormal copy numbers of the gene locus. All 8 cases were positive for brachyury, whereas there was no nuclear SMARCB1/INI1 expression in 4 of the 8 cases, including the poorly differentiated chordoma. Genetic analysis identified a missense mutation in 2 cases and a nonsense mutation associated with loss of SMARCB1/INI1 protein and features of poorly differentiated tumor in 1. These mutations were novel variants occurring in heterozygosity, and they were judged to be pathogenic by 3 different bioinformatic tools. In 7 of 8 cases we performed multiplex ligation-dependent probe amplification, and 3 cases showed deletions at the SMARCB1 locus. Our results confirm the pathogenic involvement of SMARCB1/INI1 in childhood chordoma. We also describe 3 novel pathogenic mutations.
Mature and Immature Solid Teratomas Involving Uterine Corpus, Cervix, and Ovary
Authors: Stolnicu Simona , Szekely Emoke , Molnar Calin , Molnar Claudiu V. , Barsan Iulia , D’Alfonso Valeria , Moldovan Cosmin , Zheng Gang , Ronnett Brigitte M. , Soslow Robert A.
Published: September 2016

Extragonadal teratomas are rare, and localization in the endometrium and cervix is exceptional, with fewer than 10 case reports documented so far in the English literature. We report here the case of a 46-year-old patient who presented with simultaneous immature teratoma in the endometrium and mature teratomas in the ovary in association with gliomatosis peritonei but with no evidence of gestational origin; she subsequently developed multiple solid mature teratomas in the cervix and parauterine tissue. No other similar cases have been previously reported to our knowledge. There are many similarities between the patient’s pattern of recurrence and “growing teratoma syndrome (GTS)”. Although the patient was not treated with chemotherapy after her first presentation and this case does not meet formal criteria for GTS, we believe that the pattern and histology of recurrences in this case represent a variant of GTS. Considering that the initial presentation in this case was endometrial and ovarian makes the occurrence of GTS-like syndrome even more unique.
DNA Genotyping of Suspected Partial Hydatidiform Moles Detects Clinically Significant Aneuploidy
Authors: Colgan Terence J. , Chang Martin C. , Nanji Shabin , Kolomietz Elena
Published: September 2016

The diagnosis of partial hydatidiform mole (PM) is especially difficult early in gestation as the morphology of nonmolar abortus (NMA) may mimic PM. Molecular genotyping analysis can definitively identify diandric triploidy, the genetic basis for PM, whereas NMA cases show a biparental inheritance. This 4-year retrospective study sought to determine what proportion of NMA cases which were initially suspected as being PM was aneuploid, and whether this knowledge of aneuploidy status is clinically useful. Cases with atypical villous morphology on histopathology suggestive of PM were subjected to molecular genotyping. The genotyping testing panel contained 19 highly polymorphic short-tandem repeat markers on chromosomes 13, 18, 21, X, and Y and 2 nonpolymorphic markers for sex determination. Informative molecular genotyping analysis was available in 127 cases (56 PMs and 71 NMAs). Aneuploidy was detected in 15/71 of NMAs (21.1%): 7 cases of trisomy 18, 3 of trisomy 13, 1 of trisomy 21, and 4 of monosomy X. It is concluded that most cases of aneuploid NMAs (11/15) detected by molecular genotyping analysis of atypical villous morphology cases are sporadic in type with a low or age-related recurrence risk. Nevertheless, this information may be useful in subsequent counseling and in women undergoing in vitro fertilization by directing preimplantation genetic diagnosis in subsequent cycles. In about a quarter of aneuploid NMAs (4/15) specific aneuploidy types which may be caused by unbalanced familial chromosome rearrangement are identified and are clinically important to patient management. Detection of clinically relevant aneuploidy in NMAs represents an important secondary benefit to the adoption of molecular genotyping analysis in suspected PM.
Comparison of the Prophylactic Antiemetic Efficacy of Aprepitant Plus Palonosetron Versus Aprepitant Plus Ramosetron in Patients at High Risk for Postoperative Nausea and Vomiting After Laparoscopic Cholecystectomy: A Prospective Randomized-controlled Trial
Authors: Choi Eun Kyung , Kim Dong Gyeong , Jeon Younghoon
Published: September 2016

We compared the antiemetic efficacy of aprepitant plus palonosetron versus aprepitant plus ramosetron in patients after laparoscopic cholecystectomy. A total of 88, nonsmoking, female patients undergoing laparoscopic cholecystectomy were randomly allocated to 2 groups of 44 each who received palonosetron 0.075 mg (aprepitant plus palonosetron group) and ramosetron 0.3 mg (aprepitant plus ramosetron group) after induction of anesthesia. All patients received aprepitant 80 mg 2 hours before surgery. The incidence of postoperative nausea and vomiting (PONV), use of rescue antiemetic, pain severity, and any side effects were assessed for 24 hours after surgery. The incidence of PONV and use of rescue antiemetic were less in aprepitant plus palonosetron group than in aprepitant plus ramosetron group for 24 hours after surgery (P<0.05, respectively). There was no difference in pain severity and side effects including headache and drowsiness. Aprepitant plus palonosetron significantly prevents PONV, compared with aprepitant plus ramosetron in patients at high risk for PONV after laparoscopic cholecystectomy.
Is da Vinci Xi Better than da Vinci Si in Robotic Rectal Cancer Surgery? Comparison of the 2 Generations of da Vinci Systems
Authors: Ozben Volkan , Cengiz Turgut B. , Atasoy Deniz , Bayraktar Onur , Aghayeva Afag , Erguner Ilknur , Baca Bilgi , Hamzaoglu Ismail , Karahasanoglu Tayfun
Published: September 2016

Background:

We aimed to compare perioperative outcomes for procedures using the latest generation of da Vinci robot versus its previous version in rectal cancer surgery.

Patients and Methods:

Fifty-three patients undergoing robotic rectal cancer surgery between January 2010 and March 2015 were included. Patients were classified into 2 groups (Xi, n=28 vs. Si, n=25) and perioperative outcomes were analyzed.

Results:

The groups had significant differences including operative procedure, hybrid technique and redocking (P>0.05). In univariate analysis, the Xi group had shorter console times (265.7 vs. 317.1 min, P=0.006) and total operative times (321.6 vs. 360.4 min, P=0.04) and higher number of lymph nodes harvested (27.5 vs. 17.0, P=0.008). In multivariate analysis, Xi robot was associated with a shorter console time (odds ratio: 0.09, P=0.004) with no significant differences regarding other outcomes.

Conclusions:

Both generations of da Vinci robot led to similar short-term outcomes in rectal cancer surgery, but the Xi robot allowed shorter console times.
The impact of early palliative care on the quality of care during the last days of life: what does the evidence say?
Authors: Zambrano Sofia C. , Fliedner Monica C. , Eychmüller Steffen
Published: September 2016

Purpose of review

The aim of this review is to critically appraise the existing evidence on ‘early palliative care’ (EPC), discuss its relationship with advance care planning, and to reflect on the impact of EPC on the quality of care provided during the last days of life.

Recent findings

There are indicators that EPC may help to avoid aggressive treatment, shorten hospital stay, improve overall quality of life, and to see more frequently dying and death at the preferred place of care.

The evidence from randomized controlled trials supports the integration of palliative care early in the disease trajectory. However, in terms of outcomes and quality indicators for care in the last days of life, evidence is still lacking. Predominantly, when it comes to the outcomes which may be more difficult to assess, such as spiritual aspects, or the social network, for which more comprehensive information is needed. These outcomes should not be neglected in palliative care studies, particularly when they can provide meaningful information about patient and family adjustment, and focus on psychosocial aspects rather than physical symptom control.
Practical multimodal care for cancer cachexia
Authors: Maddocks Matthew , Hopkinson Jane , Conibear John , Reeves Annie , Shaw Clare , Fearon Ken C.H.
Published: September 2016

Purpose of review

Cancer cachexia is common and reduces function, treatment tolerability and quality of life. Given its multifaceted pathophysiology a multimodal approach to cachexia management is advocated for, but can be difficult to realise in practice. We use a case-based approach to highlight practical approaches to the multimodal management of cachexia for patients across the cancer trajectory.

Recent findings

Four cases with lung cancer spanning surgical resection, radical chemoradiotherapy, palliative chemotherapy and no anticancer treatment are presented. We propose multimodal care approaches that incorporate nutritional support, exercise, and anti-inflammatory agents, on a background of personalized oncology care and family-centred education. Collectively, the cases reveal that multimodal care is part of everyone's remit, often focuses on supported self-management, and demands buy-in from the patient and their family. Once operationalized, multimodal care approaches can be tested pragmatically, including alongside emerging pharmacological cachexia treatments.

We demonstrate that multimodal care for cancer cachexia can be achieved using simple treatments and without a dedicated team of specialists. The sharing of advice between health professionals can help build collective confidence and expertise, moving towards a position in which every team member feels they can contribute towards multimodal care.
Analysis of Surgical Outcomes and Determinants of Litigation Among Women With Transvaginal Mesh Complications
Authors: Zoorob Dani , Karram Mickey , Stecher Anna , Maxwell Rose , Whiteside James
Published: September 2016

Objectives

To identify litigation predictors among women with complications of transvaginal mesh.

Methods

Chart review and patient survey were conducted among women who had undergone a complication-related explant of a transvaginal prolapse or incontinence sling mesh. Trained study personnel administered a 57-question survey addressing subjective complaints related to bowel, bladder, sexual dysfunction, and development of pain or recurrent prolapse. These data were analyzed with respect to the subject's reported pursuit of litigation related to the mesh complication. Categorical and continuous variables were analyzed using the χ2 test and the t test as indicated.

Results

Ninety-five (68%) of 139 women completed the surveys with 60% of the patients pursuing litigation at the time of the survey. Individual risk factors for pursuing litigation included development of vaginal pain after mesh placement (P = 0.01); dyspareunia after mesh placement (P = 0.01); persistence of dyspareunia, suprapubic pain, and groin pain after mesh excision (P = 0.04, P = 0.02, and P = 0.001, respectively); unsuccessful attempts at conservative management of pelvic pain using pelvic floor rehabilitation (P = 0.002).

Conclusion

There is an association between a higher likelihood of pursuing litigation and new-onset or persistent pain symptoms attributable to transvaginal mesh.
Female Urethral Diverticulum: Presentation, Diagnosis, and Predictors of Outcomes After Surgery
Authors: El-Nashar Sherif A. , Singh Ruchira , Bacon Melissa M. , Kim-Fine Shunaha , Occhino John A. , Gebhart John B. , Klingele Christopher J.
Published: September 2016

Introduction and Hypothesis

To report on clinical presentation, diagnosis, and outcomes after treatment of female urethral diverticulum (UD).

Methods

Using a record linkage system, women with a new diagnosis of UD at Mayo Clinic from January 1, 1980, through December 31, 2011, were identified. The presenting symptoms, clinical characteristics, diagnosis, and management of women presenting with UD were recorded. Outcomes after surgery were assessed using survival analysis. All statistical analyses were 2-sided and P values less than 0.05 were considered significant. Statistical analysis was done using SAS version 9.2 and JMP version 9.0 (SAS Institute Inc.).

Results

A total of 164 cases were identified. Median age at diagnosis was 46 years (range, 21–83). The most common presenting symptom was recurrent urinary tract infection (98, 59.8%), followed by urinary incontinence (81, 49.4%), dysuria (62, 37.8%), dyspareunia (37, 22.6%), and hematuria (15, 9.1%). Examination revealed vaginal mass in 55 (33.5%) of the women. A significant trend was noted toward an increase in use of both magnetic resonance imaging and computed tomography (P < 0.001) along with a progressive decrease in use of urethrogram (P < 0.001) for diagnosis of UD over the years. Among 114 women who underwent surgical treatment for UD, 14(12.3%) women presented with recurrent UD and the 5-year recurrence rate after surgery for UD was 23.4% (95% confidence interval, 13.9–37.0) and a reoperation rate of 17.0% (95% confidence interval, 8.8–30.2) at 5 years.

Conclusions

Female UD is a rare and unique condition. Clinical presentation is usually nonspecific, and magnetic resonance imaging is commonly used for confirming the diagnosis. Recurrence is not uncommon, and repeat surgical intervention might be needed.
Long-Term Effectiveness of Uterosacral Colpopexy and Minimally Invasive Sacral Colpopexy for Treatment of Pelvic Organ Prolapse
Authors: Unger Cecile A. , Barber Matthew D. , Walters Mark D. , Paraiso Marie Fidela R. , Ridgeway Beri , Jelovsek J. Eric
Published: September 2016

Objectives

The objective of this study was to estimate rates of recurrent pelvic organ prolapse (POP) 6 years after patients underwent transvaginal uterosacral colpopexy, or laparoscopic or robotic sacral colpopexy at a large tertiary care center. We hypothesized that recurrence rates would be higher than those previously reported.

Methods

This is a retrospective study of women who underwent uterosacral colpopexy, laparoscopic, and robotic sacral colpopexy for treatment of POP between 2006 and 2012. A composite outcome for recurrent POP was defined as subjective failure (vaginal bulge symptoms), objective failure (prolapse to or beyond the hymen), or any retreatment for POP (reoperation or use of a pessary). Kaplan-Meier survival curves were generated from each patient's date of follow-up, and parametric survival modeling was used to estimate recurrent POP over 6 years. Annual estimated recurrence rates by type of colpopexy are reported using the composite and individual definitions for recurrent POP.

Results

One thousand three hundred eighty-one subjects met inclusion criteria: 983 (71.1 %) uterosacral, 256 (18.5%) laparoscopic, and 142 (11.2%) robotic colpopexies. Median (range) months to failure using composite recurrence were as follows: uterosacral, 17.1 (7.6–41); laparoscopic, 10.1 (4.7–25.1); robotic, 9.7 (1.6–17.2). By year 6 in the model, the estimated composite recurrence rates for the uterosacral colpopexy, robotic, and laparoscopic sacral colpopexy groups were 43%, 49%, and 57%, respectively.

Conclusions

Estimated recurrence rates for uterosacral ligament colpopexy, laparoscopic, and robotic sacral colpopexy may be as high as 40% to 60% 6 years after surgery.
A Prospective Observational Study of the Classification of the Perineum and Evaluation of Perineal Repair at the Time of Posterior Colporrhaphy
Authors: Christmann-Schmid Corina , Wierenga Annemijn Philine Annette , Frischknecht Eveline , Maher Christopher
Published: September 2016

Objective

The aim of this prospective observational study was to obtain a better understanding of the anatomy and to classify the observed different perineal presentations at the time of posterior colporrhaphy and to describe specific surgical techniques used.

Methods

To classify the observed perineal findings, the Pelvic Organ Prolapse Quantification System with a newly introduced additional measurement of the perineal ridge (PR) was taken intraoperatively and postoperatively in 121 consecutive women undergoing posterior colporrhaphy. Dependent on the preoperative classification of the perineum as being normal (type 1), deficient (type 2), or with a PR (type 3), a specific surgical repair was performed for each type of perineal presentation.

Results

The perineal presentations were categorized into 3 defined groups. Type 1 (normal perineum) was seen in 40%, type 2 (deficient perineum) in 13%, and type 3 (PR) in 47%. A type 1 correlates with prior cesarean section (P = 0.29), a type 2 correlates with prior vaginal delivery (P = 0.05), and type 3 perineum with prior pelvic floor surgery (P < 0.0001). When perineal type–specific surgical techniques were performed, the perineal body length increased postoperatively in type 2 (P < 0.05), decreased in type 3 (P < 0.05), and remained unchanged in those with type 1 defects.

Conclusions

This study demonstrates that the perineal region can be clearly defined into 3 categories. The distinct perineal presentation correlates with the previous gynecological history. With a specific perineal repair at the time of posterior colporrhaphy, the perineal anatomy can be restored in the short term.
Characterizing the Bladder's Response to Onabotulinum Toxin Type A Using a Rat Model
Authors: Dieter Alexis A. , Wu Jennifer M. , Siddiqui Nazema Y. , Degoski Danielle J. , Brooks Jillene M. , Dolber Paul C. , Fraser Matthew O.
Published: September 2016

Objectives

The aim of this study was to characterize the response of the rat bladder neuromuscular system to intramural injection of onabotulinum toxin type A (BoNT/A) over 9 weeks using in vivo cystometry (CMG) and in vitro contractility (IVC).

Methods

Chronic bladder catheters were implanted in female Sprague-Dawley rats, and either (1) BoNT/A (10 units in 20 μL saline) or (2) saline (20 μL) was injected in 5 × 4 μL doses throughout the bladder wall. At 1, 3, 6, and 9 weeks after injection, conscious restrained CMG was performed. At each time point, 25% of each group (8 BoNT/A and 4 controls) was euthanized and bladders harvested for IVC. We measured IVC in response to electric field stimulation, carbachol, and potassium chloride.

Results

In total, 47 animals were included; 31 underwent BoNT/A injection, and 16 received sham (saline). Bladder capacities did not differ significantly between groups for each time point. One week after injection BoNT/A animals exhibited significantly longer bladder contraction durations and lower voiding efficiencies compared with controls. By 3 weeks these values returned to control levels. For BoNT/A animals, contractile response to carbachol stimulation was enhanced at 3 weeks. Otherwise, there were no differences in IVC responses.

Conclusions

One week after BoNT/A injection, prolonged bladder contractions are noted in rats. This may reflect supraspinal compensation for denervation by increasing the duration of efferent drive during voiding. After 3 weeks postinjection, we observed no differences in either CMG or IVC responses suggesting either compensatory efferent sprouting, increased gap junction formation, or loss of BoNT/A effect.
National Assessment of Advancing Age on Perioperative Morbidity and Length of Stay Associated With Minimally Invasive Sacrocolpopexy
Authors: Chaudhry Zaid , Cohen Seth Ashley , Tarnay Christopher
Published: September 2016

Objective

The aim of the study was to assess the impact of age on 30-day perioperative complications and length of stay (LOS) for minimally invasive sacrocolpopexy (MISC) using a national database.

Methods

We performed an institutional review board–exempt retrospective analysis of prospectively collected data, using the National Surgical Quality Improvement Program database to analyze MISC performed at participating hospitals from 2010 to 2013. Age was stratified into the following 5 categories: younger than 60, 60 to 64, 65 to 69, 70 to 74, and 75 years or older. Complications were tabulated on the basis of available categories and were assessed using logistic multivariate regression. Length of stay was deemed abnormal if 3 days or more.

Results

A total of 1201 patients were identified as having undergone MISC. Mean (SD) patients age was 61.3 (11.1) years. Most patients had an American Society of Anesthesiologists (ASA) class of 2 (68.3%) or an ASA class of 3 (23.6%). Older patients had a significantly higher ASA class and lower body mass index. The most common complications were urinary tract infection (3.4%), readmission (2.7%), and return to the operating room (1.5%). Urinary tract infection (P = 0.93), readmission (P = 0.38), and return to the operating room (P = 0.17) were not significantly different between age groups. Older patients did not have greater odds of having an LOS of 3 days or more versus 1 day or 0 to 2 days.

Conclusions

Returns to the operating room, readmission, and urinary tract infection were the most common adverse events and did not differ between age groups. Older patients did not have greater odds of having an increased LOS. Minimally invasive sacrocolpopexy seems to be safe among appropriately selected elderly patients.
Identifying Gaps and Inconsistencies in Urogynecologic Surgical Training of Obstetrics and Gynecology Residents
Authors: Weber LeBrun Emily E. , Asumu Hazel , Richardson Anne M. , Cooper LouAnn A. , Davis John D.
Published: September 2016

Objective

This study aims to determine the expectations of Obstetrics and Gynecology (ObGyn) residency and Female Pelvic Medicine & Reconstructive Surgery (FPMRS) fellowship program directors (FPDs) for the independent performance of urogynecologic procedures during residency and to compare these expectations with the Council on Resident Education in Obstetrics and Gynecology (CREOG) educational objectives.

Materials and Methods

Two parallel, anonymous surveys were distributed simultaneously to all directors of accredited ObGyn residency and FPMRS fellowship programs in the United States. Respondents provided their own professional and program demographic information and indicated whether they expected their residents to independently perform 27 selected urogynecologic procedures.

Results

Among residency program directors (RPDs) and FPDs, the online survey response rate was 24.8% (n = 59) and 51.9% (n = 27), respectively. More RPDs expected residents to perform prolapse procedures with mesh, including laparoscopic sacrocolpopexy, all apical suspensions, mesh excisions, and cystotomy repairs, than FPDs. In addition, RPDs expected mastery of most urogynecologic procedures by the Post Graduate Year 3 level, whereas most FPDs did not expect independent performance of these procedures during residency at all. There were notable differences between RPDs' expectations and CREOG objectives regarding several surgical procedures. Whereas CREOG recommends independent performance of anterior and posterior repair, vaginal suspension, vaginal hysterectomy, and transobturator slings, a significant number of RPDs did not report expecting mastery of these procedures during residency. Approximately 30% of RPDs expected residents to perform open sacrocolpopexy and vesicovaginal fistula repair, whereas CREOG recommends only the understanding of these, without procedural mastery.

Conclusions

Although community needs vary by region and setting, CREOG objectives serve as the standard for resident surgical education. This study highlights the discordance between these objectives and ObGyn RDPs' reported expectations for resident performance as well as those held by FPMRS FPDs, the outcome of which reflects a misalignment in graduate medical education between RPDs and FPDs, thus hindering a clear standard for resident surgical competencies.
The Real-time fMRI Neurofeedback Based Stratification of Default Network Regulation Neuroimaging Data Repository
Authors: McDonald Amalia R , Muraskin Jordan , Van Dam Nicholas T , Froehlich Caroline , Puccio Benjamin , Pellman John , Bauer Clemens CC , Akeyson Alexis , Breland Melissa M , Calhoun Vince D , Carter Steven , Chang Tiffany P , Gessner Chelsea , Gianonne Alyssa , Giavasis Steven , Glass Jamie , Homan Steven , King Margaret , Kramer Melissa , Landis Drew , Lieval Alexis , Lisinski Jonathan , Mackay-Brandt Anna , Miller Brittny , Panek Laura , Reed Hayley , Santiago Christine , Schoell Eszter , Sinnig Richard , Sital Melissa , Taverna Elise , Tobe Russell , Trautman Kristin , Varghese Betty , Walden Lauren , Wang Runtang , Waters Abigail B , Wood Dylan , Castellanos F Xavier , Leventhal Bennett , Colcombe Stanley J , LaConte Stephen , Milham Michael P , Craddoc R Cameron
Published: September 2016

This data descriptor describes a repository of openly shared data from an experiment to assess inter-individual differences in default mode network (DMN) activity. This repository includes cross-sectional functional magnetic resonance imaging (fMRI) data from the Multi Source Interference Task, to assess DMN deactivation, the Moral Dilemma Task, to assess DMN activation, a resting state fMRI scan, and a DMN neurofeedback paradigm, to assess DMN modulation, along with accompanying behavioral and cognitive measures. We report technical validation from n=125 participants of the final targeted sample of 180 participants. Each session includes acquisition of one whole-brain anatomical scan and whole-brain echo-planar imaging (EPI) scans, acquired during the aforementioned tasks and resting state. The data includes several self-report measures related to perseverative thinking, emotion regulation, and imaginative processes, along with a behavioral measure of rapid visual information processing.

Technical validation of the data confirms that the tasks deactivate and activate the DMN as expected. Group level analysis of the neurofeedback data indicates that the participants are able to modulate their DMN with considerable inter-subject variability. Preliminary analysis of behavioral responses and specifically self-reported sleep indicate that as many as 73 participants may need to be excluded from an analysis depending on the hypothesis being tested.
Biosynthesis of the Antibiotic Nonribosomal Peptide Penicillin in Baker’s Yeast
Authors: Awan Ali R. , Blount Benjamin A. , Bell David J. , Ho Jack C. H. , McKiernan Robert M. , Ellis Tom
Published: September 2016

Fungi are a valuable source of enzymatic diversity and therapeutic natural products including antibiotics. By taking genes from a filamentous fungus and directing their efficient expression and subcellular localisation, we here engineer the baker’s yeastSaccharomyces cerevisiaeto produce and secrete the antibiotic penicillin, a beta-lactam nonribosomal peptide. Using synthetic biology tools combined with long-read DNA sequencing, we optimise productivity by 50-fold to produce bioactive yields that allow spentS. cerevisiaegrowth media to have antibacterial action againstStreptococcusbacteria. This work demonstrates thatS. cerevisiaecan be engineered to perform the complex biosynthesis of multicellular fungi, opening up the possibility of using yeast to accelerate rational engineering of nonribosomal peptide antibiotics.
Homeostasis of columnar synchronization during cortical map formation
Authors: Colonnese Matthew T. , Shen Jing
Published: September 2016

Synchronous spontaneous activity is critical for circuit development. A key open question is to what degree is this synchronization models adult activity or is specifically tuned for circuit development. To address this we used multi-electrode array recordings of spontaneous activity in non-anesthetized neonatal mice to quantify firing rates, synchronization, binary spike-vectors and population-coupling of single-units throughout the period of map formation. Consistent with the first hypothesis, adult-like network interactions are established during the period of retinal waves, before the onset of vision and normal inhibition, and are largely conserved throughout juvenile ages. Significant differences from mature properties were limited to initial topographic map formation, when synchronization was lower than expected by chance, suggesting active decoupling in early networks. These findings suggest that developmental activity models adult synchronization, and that there is remarkable homeostasis of network properties throughout development, despite massive changes in the drive and circuit basis of cortical activity.
TheDrosophilaGene Expression Tool (DGET) for expression analyses
Authors: Hu Yanhui , Comjean Aram , Perrimon Norbert , Mohr Stephanie
Published: September 2016

Background

Next-generation sequencing technologies have greatly increased our ability to identify gene expression levels, including at specific developmental stages and in specific tissues. Gene expression data can help researchers understand the diverse functions of genes and gene networks, as well as help in the design of specific and efficient functional studies, such as by helping researchers choose the most appropriate tissue for a study of a group of genes, or conversely, by limiting a long list of gene candidates to the subset that are normally expressed at a given stage or in a given tissue.

Results

We report aDrosophilaGene Expression Tool (DGET,www.flyrnai.org/tools/dget/web/), which stores and facilitates search of RNA-Seq based expression profiles available from the modENCODE consortium and other public data sets. Using DGET, researchers are able to look up gene expression profiles, filter results based on threshold expression values, and compare expression data across different developmental stages, tissues and treatments. In addition, at DGET a researcher can analyze tissue or stage-specific enrichment for an inputted list of genes (e.g. ‘hits’ from a screen) and search for additional genes with similar expression patterns. We performed a number of analyses to demonstrate the quality and robustness of the resource. In particular, we show that evolutionary conserved genes expressed at high or moderate levels in both fly and human tend to be expressed in similar tissues. Using DGET, we compared whole tissue profile and sub-region/cell-type specific datasets and estimated the potential cause of false positives in one dataset. We also demonstrated the usefulness of DGET for synexpression studies by querying genes with similar expression profile to the mesodermal master regulator Twist.

Conclusion

Altogether, DGET provides a flexible tool for expression data retrieval and analysis with short or long lists ofDrosophilagenes, which can help scientists to design stage- or tissue-specificin vivostudies and do other subsequent analyses.
MCbiclust: a novel algorithm to discover large-scale functionally related gene sets from massive transcriptomics data collections
Authors: Bentham Robert B. , Bryson Kevin , Szabadkai Gyorgy
Published: September 2016

The potential to understand fundamental biological processes from gene expression data has grown parallel with the recent explosion of the size of data collections. However, to exploit this potential, novel analytical methods are required, capable of handling massive data matrices. We found current methods limited in the size of correlated gene sets they could discover within biologically heterogeneous data collections, hampering the identification of multi-gene controlled fundamental cellular processes such as energy metabolism, organelle biogenesis and stress responses. Here we describe a novel biclustering algorithm called Massively Correlated Biclustering (MCbiclust) that selects samples and genes from large datasets with maximal correlated gene expression, allowing regulation of complex pathway to be examined. The method has been evaluated using synthetic data and applied to large bacterial and cancer cell datasets. We show that the large biclusters discovered, so far elusive to identification by existing techniques, are biologically relevant and thus MCbiclust has great potential use in the analysis of transcriptomics data to identify large scale unknown effects hidden within the data. The identified massive biclusters can be used to develop improved transcriptomics based diagnosis tools for diseases caused by altered gene expression, or used for further network analysis to understand genotype-phenotype correlations.
A machine learning classifier trained on cancer transcriptomes detects NF1 inactivation signal in glioblastoma
Authors: Way Gregory P. , Allaway Robert J. , Bouley Stephanie J. , Fadul Camilo E. , Sanchez Yolanda , Greene Casey S.
Published: September 2016

Background:We have identified molecules that exhibit synthetic lethality in cells with loss of the neurofibromin 1 (NF1) tumor suppressor gene. However, recognizing tumors that have inactivation of theNF1tumor suppressor function is challenging because the loss may occur via mechanisms that do not involve mutation of the genomic locus. Degradation of the NF1 protein, independent ofNF1mutation status, photocopies inactivating mutations to drive tumors in human glioma cell lines. NF1 inactivation may alter the transcriptional landscape of a tumor and allow a machine learning classifier to detect which tumors will benefit from synthetic lethal molecules.

Results:We developed a strategy to predict tumors with low NF1 activity and hence tumors that may respond to treatments that target cells lacking NF1. Using RNAseq data from The Cancer Genome Atlas (TCGA), we trained an ensemble of 500 logistic regression classifiers that integrates mutation status with whole transcriptomes to predict NF1 inactivation in glioblastoma (GBM). On TCGA data, the classifier detectedNF1mutated tumors (test set area under the receiver operating characteristic curve (AUROC) mean = 0.77, 95% quantile = 0.53 – 0.95) over 50 random initializations. On RNA-Seq data transformed into the space of gene expression microarrays, this method produced a classifier with similar performance (test set AUROC mean = 0.77, 95% quantile = 0.53 – 0.96). We applied our ensemble classifier trained on the transformed TCGA data to a microarray validation set of 12 samples with matched RNA and NF1 protein-level measurements. The classifier’s NF1 score was associated with NF1 protein concentration in these samples.

Conclusions:We demonstrate that TCGA can be used to train accurate predictors of NF1 inactivation in GBM. The ensemble classifier performed well for samples with very high or very low NF1 protein concentrations but had mixed performance in samples with intermediate NF1 concentrations. Nevertheless, high-performing and validated predictors have the potential to be paired with targeted therapies and personalized medicine.
Identification of misclassified ClinVar variants using disease population prevalence
Authors: Shah Naisha , Claire Hou Ying-Chen , Yu Hung-Chun , Sainger Rachana , Dec Eric , Perkins Brad , Caskey C. Thomas , Venter J. Craig , Telenti Amalio
Published: September 2016

There is a significant interest in the standardized classification of human genetic variants. The availability of new large datasets generated through genome sequencing initiatives provides a ground for the computational evaluation of the supporting evidence. We used whole genome sequence data from 8,102 unrelated individuals to analyze the adequacy of estimated rates of disease on the basis of genetic risk and the expected population prevalence of the disease. Analyses included the ACMG recommended 56 gene-condition sets for incidental findings and 631 genes associated with 348 OrphaNet conditions. A total of 21,004 variants were used to identify patterns of inflation (i.e. excess genetic risk). Inflation, i.e., misclassification, increases as the level of evidence in ClinVar supporting the pathogenic nature of the variant decreases. The burden of rare variants was a main contributing factor of the observed inflation indicating misclassified benign private mutations. We also analyzed the dynamics of re-classification of variant pathogenicity in ClinVar over time. The study strongly suggests that ClinVar includes a significant proportion of wrongly ascertained variants, and underscores the critical role of ClinVar to contrast claims, and foster validation across submitters.
Temperature regulates splicing efficiency of the cold-inducible RNA-binding protein gene Cirbp
Authors: Gotic Ivana , Omidi Saeed , Fleury-Olela Fabienne , Molina Nacho , Naef Felix , Schibler Ueli
Published: September 2016

In mammals, body temperature fluctuates diurnally around a mean value of 36°C–37°C. Despite the small differences between minimal and maximal values, body temperature rhythms can drive robust cycles in gene expression in cultured cells and, likely, animals. Here we studied the mechanisms responsible for the temperature-dependent expression of cold-inducible RNA-binding protein (CIRBP). In NIH3T3 fibroblasts exposed to simulated mouse body temperature cycles, Cirbp mRNA oscillates about threefold in abundance, as it does in mouse livers. This daily mRNA accumulation cycle is directly controlled by temperature oscillations and does not depend on the cells’ circadian clocks. Here we show that the temperature-dependent accumulation of Cirbp mRNA is controlled primarily by the regulation of splicing efficiency, defined as the fraction of Cirbp pre-mRNA processed into mature mRNA. As revealed by genome-wide “approach to steady-state” kinetics, this post-transcriptional mechanism is widespread in the temperature-dependent control of gene expression.
The potential of epigenetics in stress-enhanced fear learning models of PTSD
Authors: Blouin Ashley M. , Sillivan Stephanie E. , Joseph Nadine F. , Miller Courtney A.
Published: September 2016

Prolonged distress and dysregulated memory processes are the core features of post-traumatic stress disorder (PTSD) and represent the debilitating, persistent nature of the illness. However, the neurobiological mechanisms underlying the expression of these symptoms are challenging to study in human patients. Stress-enhanced fear learning (SEFL) paradigms, which encompass both stress and memory components in rodents, are emerging as valuable preclinical models of PTSD. Rodent models designed to study the long-term mechanisms of either stress or fear memory alone have identified a critical role for numerous epigenetic modifications to DNA and histone proteins. However, the epigenetic modifications underlying SEFL remain largely unknown. This review will provide a brief overview of the epigenetic modifications implicated in stress and fear memory independently, followed by a description of existing SEFL models and the few epigenetic mechanisms found to date to underlie SEFL. The results of the animal studies discussed here highlight neuroepigenetics as an essential area for future research in the context of PTSD through SEFL studies, because of its potential to identify novel candidates for neurotherapeutics targeting stress-induced pathogenic memories.
Dopamine receptor DOP-4 modulates habituation to repetitive photoactivation of a C. elegans polymodal nociceptor
Authors: Ardiel Evan L. , Giles Andrew C. , Yu Alex J. , Lindsay Theodore H. , Lockery Shawn R. , Rankin Catharine H.
Published: September 2016

Habituation is a highly conserved phenomenon that remains poorly understood at the molecular level. Invertebrate model systems, like Caenorhabditis elegans, can be a powerful tool for investigating this fundamental process. Here we established a high-throughput learning assay that used real-time computer vision software for behavioral tracking and optogenetics for stimulation of the C. elegans polymodal nociceptor, ASH. Photoactivation of ASH with ChR2 elicited backward locomotion and repetitive stimulation altered aspects of the response in a manner consistent with habituation. Recording photocurrents in ASH, we observed no evidence for light adaptation of ChR2. Furthermore, we ruled out fatigue by demonstrating that sensory input from the touch cells could dishabituate the ASH avoidance circuit. Food and dopamine signaling slowed habituation downstream from ASH excitation via D1-like dopamine receptor, DOP-4. This assay allows for large-scale genetic and drug screens investigating mechanisms of nociception modulation.
Effects of drugs of abuse on hippocampal plasticity and hippocampus-dependent learning and memory: contributions to development and maintenance of addiction
Authors: Kutlu Munir Gunes , Gould Thomas J.
Published: September 2016

It has long been hypothesized that conditioning mechanisms play major roles in addiction. Specifically, the associations between rewarding properties of drugs of abuse and the drug context can contribute to future use and facilitate the transition from initial drug use into drug dependency. On the other hand, the self-medication hypothesis of drug abuse suggests that negative consequences of drug withdrawal result in relapse to drug use as an attempt to alleviate the negative symptoms. In this review, we explored these hypotheses and the involvement of the hippocampus in the development and maintenance of addiction to widely abused drugs such as cocaine, amphetamine, nicotine, alcohol, opiates, and cannabis. Studies suggest that initial exposure to stimulants (i.e., cocaine, nicotine, and amphetamine) and alcohol may enhance hippocampal function and, therefore, the formation of augmented drug-context associations that contribute to the development of addiction. In line with the self-medication hypothesis, withdrawal from stimulants, ethanol, and cannabis results in hippocampus-dependent learning and memory deficits, which suggest that an attempt to alleviate these deficits may contribute to relapse to drug use and maintenance of addiction. Interestingly, opiate withdrawal leads to enhancement of hippocampus-dependent learning and memory. Given that a conditioned aversion to drug context develops during opiate withdrawal, the cognitive enhancement in this case may result in the formation of an augmented association between withdrawal-induced aversion and withdrawal context. Therefore, individuals with opiate addiction may return to opiate use to avoid aversive symptoms triggered by the withdrawal context. Overall, the systematic examination of the role of the hippocampus in drug addiction may help to formulate a better understanding of addiction and underlying neural substrates.
Ecologically relevant neurobehavioral assessment of the development of threat learning
Authors: Boulanger Bertolus Julie , Mouly Anne-Marie , Sullivan Regina M.
Published: September 2016

As altricial infants gradually transition to adults, their proximate environment changes. In three short weeks, pups transition from a small world with the caregiver and siblings to a complex milieu rich in dangers as their environment expands. Such contrasting environments require different learning abilities and lead to distinct responses throughout development. Here, we will review some of the learned fear conditioned responses to threats in rats during their ontogeny, including behavioral and physiological measures that permit the assessment of learning and its supporting neurobiology from infancy through adulthood. In adulthood, odor–shock conditioning produces robust fear learning to the odor that depends upon the amygdala and related circuitry. Paradoxically, this conditioning in young pups fails to support fear learning and supports approach learning to the odor previously paired with shock. This approach learning is mediated by the infant attachment network that does not include the amygdala. During the age range when pups transition from the infant to the adult circuit (10–15 d old), pups have access to both networks: odor–shock conditioning in maternal presence uses the attachment circuit but the adult amygdala-dependent circuit when alone. However, throughout development (as young as 5 d old) the attachment associated learning can be overridden and amygdala-dependent fear learning supported, if the mother expresses fear in the presence of the pup. This social modulation of the fear permits the expression of defense reactions in life threatening situations informed by the caregiver but prevents the learning of the caregiver itself as a threat.
DNA methylation: a permissive mark in memory formation and maintenance
Authors: Oliveira Ana M.M.
Published: September 2016

DNA methylation was traditionally viewed as a static mechanism required during cell fate determination. This view has been challenged and it is now accepted that DNA methylation is involved in the regulation of genomic responses in mature neurons, particularly in cognitive functions. The evidence for a role of DNA methylation in memory formation and maintenance comes from the increasing number of studies that have assessed the effects of manipulation of DNA methylation modifiers in the ability to form and maintain memories. Moreover, insights from genome-wide analyses of the hippocampal DNA methylation status after neuronal activity show that DNA methylation is dynamically regulated. Despite all the experimental evidence, we are still far from having a clear picture of how DNA methylation regulates long-term adaptations. This review aims on one hand to describe the findings that led to the confirmation of DNA methylation as an important player in memory formation. On the other hand, it tries to integrate these discoveries into the current views of how memories are formed and maintained.
The neural circuits of innate fear: detection, integration, action, and memorization
Authors: Silva Bianca A. , Gross Cornelius T. , Gräff Johannes
Published: September 2016

How fear is represented in the brain has generated a lot of research attention, not only because fear increases the chances for survival when appropriately expressed but also because it can lead to anxiety and stress-related disorders when inadequately processed. In this review, we summarize recent progress in the understanding of the neural circuits processing innate fear in rodents. We propose that these circuits are contained within three main functional units in the brain: a detection unit, responsible for gathering sensory information signaling the presence of a threat; an integration unit, responsible for incorporating the various sensory information and recruiting downstream effectors; and an output unit, in charge of initiating appropriate bodily and behavioral responses to the threatful stimulus. In parallel, the experience of innate fear also instructs a learning process leading to the memorization of the fearful event. Interestingly, while the detection, integration, and output units processing acute fear responses to different threats tend to be harbored in distinct brain circuits, memory encoding of these threats seems to rely on a shared learning system.