bluuebunny/crossref_metadata_2025 huggingface dataset:
Selective nonoperative management of pharyngoesophageal injuries secondary to penetrating neck trauma: A single-center review of 86 cases
Authors: Madsen Andre S. , Oosthuizen George V. , Bruce John L. , Bekker Wanda , Laing Grant L. , Clarke Damian L.
Published: May 2018

BACKGROUND

This article describes our experience with penetrating pharyngoesophageal injuries (PEI) in the light of a selective conservative approach, and has the objective to define criteria for nonoperative management (NOM).

METHODS

This retrospective single-center review of patients with penetrating neck injury treated for confirmed PEI over a 6-year period aimed to test our proposed hypothesis that NOM is safe for hemodynamically stable patients with PEI, who have no competing indications for exploration, have no established sepsis, and who have a water-soluble contrast swallow either showing no- or a contained extravasation.

RESULTS

Eighty-six (9%) patients with PEI (oropharynx, 17; hypopharynx, 40; esophagus, 29) of 948 patients with penetrating neck injury were included. Of the cohort 38 (44%) underwent NOM (oropharynx, 15 [88%]; hypopharynx, 18 [45%]; esophagus, 5 [17%]), and 48 (56%) were managed operatively. The median length of stay was 12 days (interquartile range, 19–8). Fifteen (17%) had a persistent leak and six (7%) mediastinitis. Five (6%) patients died but only one (1%) had isolated PEI. Retrospectively, 27 patients fulfilled our proposed criteria for NOM of which 23 had been treated actively by NOM (oropharynx, 8; hypopharynx, 12; esophagus, 3). For these patients, the length of stay was 10.0 days (interquartile range, 13–6), and none developed deep wound sepsis, mediastinitis, persistent leaks, or died. Of the remaining patients treated by NOM without fulfilling the proposed criteria, two were palliated (esophagus) and 13 were managed actively (oropharynx, 7; hypopharynx, 6). Only four of these patients (oropharynx, 1; hypopharynx, 3) were assessed with water-soluble contrast swallow, which showed noncontained extravasation, and three complicated with persistent leaks.

CONCLUSION

Nonoperative management of PEI is safe for a carefully selected subgroup of patients. However, most injuries to the caudal part of the cervical digestive tract mandate urgent exploration.

LEVEL OF EVIDENCE

Clinical Management Study, Level V evidence.
Do screening and a randomized brief intervention at a Level 1 trauma center impact acute stress reactions to prevent later development of posttraumatic stress disorder?
Authors: Manser Stacey Stevens , Houck Katherine , Kramer Mark D. , Tabas Irene A. , Brown Carlos V.R. , Coopwood Ben
Published: May 2018

BACKGROUND

Approximately 20% to 40% of trauma survivors experience posttraumatic stress disorder (PTSD). The American College of Surgeons Committee on Trauma reports that early screening and referral has the potential to improve outcomes and that further study of screening and intervention for PTSD would be beneficial. This prospective randomized study screened hospitalized patients for traumatic stress reactions and assessed the effect of a brief intervention in reducing later development of PTSD.

METHODS

The Primary Care PTSD (PC-PTSD) screen was administered to admitted patients. Patients with symptoms were randomized to an intervention or control group. The brief intervention focused on symptom education and normalization, coping strategies, and utilizing supports. The control group received a 3-minute educational brochure review. Both groups completed in-hospital interviews, then 45- and 90-day telephone interviews. Follow-up collected the PTSD checklist-civilian (PCL-C) assessment and qualitative data on treatment-seeking barriers.

RESULTS

The PC-PTSD screen was successful in predicting later PTSD symptoms at both 45 days (β = 0.43, p < 0.001) and 90 days (β = 0.37, p < 0.001) even after accounting for depression. Correlations of the intervention with the PCL-C scores and factor score estimates did not reach statistical significance at either time point (p = 0.827; p = 0.838), indicating that the brief intervention did not decrease PTSD symptoms over time. Of those at or above the PCL-C cutoff at follow-ups, a minority had sought treatment for their symptoms (43.2%). Primary barriers included focusing on their injury or ongoing rehabilitation, financial concerns, or location of residence.

CONCLUSION

The PC-PTSD screen identified patients who later assess positive for PTSD using the PCL-C. The brief intervention did not reduce 45- and 90-day PTSD development. Follow-up interviews revealed lack of treatment infrastructure in the community. It will be important for trauma centers to align with community resources to address the treatment needs of at-risk patients.

LEVEL OF EVIDENCE

Prospective randomized controlled trial, level II.
A meta-analysis of the incidence of complications associated with groin access after the use of resuscitative endovascular balloon occlusion of the aorta in trauma patients
Authors: Manzano-Nunez Ramiro , Orlas Claudia P. , Herrera-Escobar Juan P. , Galvagno Samuel , DuBose Joseph , Melendez Juan J. , Serna Jose J. , Salcedo Alexander , Peña Camilo A. , Angamarca Edison , Horer Tal , Salazar Camilo J. , Lopez-Castilla Valeria , Ruiz-Yucuma Juan , Rodriguez Fernando , Parra Michael W. , Ordoñez Carlos A.
Published: May 2018

BACKGROUND

Serious complications related to groin access have been reported with the use of resuscitative endovascular balloon occlusion of the aorta (REBOA). We performed a systematic review and meta-analysis to estimate the incidence of complications related to groin access from the use of REBOA in adult trauma patients.

METHODS

We identified articles in MEDLINE and EMBASE. We reviewed all studies that involved adult trauma patients who underwent the placement of a REBOA and included only those that reported the incidence of complications related to groin access. A meta-analysis of proportions was performed.

RESULTS

We identified 13 studies with a total of 424 patients. REBOA was inserted most commonly by trauma surgeons or emergency room physicians. Information regarding puncture technique was reported in 12 studies and was available for a total of 414 patients. Percutaneous access and surgical cutdown were performed in 304 (73.4%) and 110 (26.5%) patients, respectively. Overall, complications related to groin access occurred in 5.6% of patients (n = 24/424). Lower limb amputation was required in 2.1% of patients (9/424), of which three cases (3/424 [0.7%]) were directly related to the vascular puncture from the REBOA insertion. A meta-analysis that used the logit transformation showed a 5% (95% CI 3%–9%) incidence of complications without significant heterogeneity (LR test: χ
2 = 0.73, p = 0.2, Tau-square = 0.2). In a second meta-analysis, we used the Freeman–Tukey double arcsine transformation and found an incidence of complications of 4% (95% CI 2%–7%) with low heterogeneity (I
2 = 16.3%).

CONCLUSION

We found that the incidence of complications related to groin access was of 4–5% based on a meta-analysis of 13 studies published worldwide. Currently, there are no benchmarks or quality measures as a reference to compare, and thus, further work is required to identify these benchmarks and improve the practice of REBOA in trauma surgery.

LEVEL OF EVIDENCE

Systematic review and meta-analysis, level III.
An AAST-MITC analysis of pancreatic trauma: Staple or sew? Resect or drain?
Authors: Byrge Nickolas , Heilbrun Marta , Winkler Nicole , Sommers Daniel , Evans Heather , Cattin Lindsay M. , Scalea Tom , Stein Deborah M. , Neideen Todd , Walsh Pamela , Sims Carrie A. , Brahmbhatt Tejal S. , Galante Joseph M. , Phan Ho H. , Malhotra Ajai , Stovall Robert T. , Jurkovich Gregory J. , Coimbra Raul , Berndtson Allison E. , O’Callaghan Thomas A. , Gaspard Scott F. , Schreiber Martin A. , Cook Mackenzie R. , Demetriades Demetrios , Rivera Omar , Velmahos George C. , Zhao Ting , Park Pauline K. , Machado-Aranda David , Ahmad Salman , Lewis Julie , Hoff William S. , Suleiman Ghada , Sperry Jason , Zolin Samuel , Carrick Matthew M. , Mallory Gina R. , Nunez Jade , Colonna Alexander , Enniss Toby , Nirula Ram
Published: May 2018

INTRODUCTION

Pancreatic trauma results in high morbidity and mortality, in part caused by the delay in diagnosis and subsequent organ dysfunction. Optimal operative management strategies remain unclear. We therefore sought to determine CT accuracy in diagnosing pancreatic injury and the morbidity and mortality associated with varying operative strategies.

METHODS

We created a multicenter, pancreatic trauma registry from 18 Level 1 and 2 trauma centers. Adult, blunt or penetrating injured patients from 2005 to 2012 were analyzed. Sensitivity and specificity of CT scan identification of main pancreatic duct injury was calculated against operative findings. Independent predictors for mortality, adult respiratory distress syndrome (ARDS), and pancreatic fistula and/or pseudocyst were identified through multivariate regression analysis. The association between outcomes and operative management was measured.

RESULTS

We identified 704 pancreatic injury patients of whom 584 (83%) underwent a pancreas-related procedure. CT grade modestly correlated with OR grade (r2 0.39) missing 10 ductal injuries (9 grade III, 1 grade IV) providing 78.7% sensitivity and 61.6% specificity. Independent predictors of mortality were age, Injury Severity Score (ISS), lactate, and number of packed red blood cells transfused. Independent predictors of ARDS were ISS, Glasgow Coma Scale score, and pancreatic fistula (OR 5.2, 2.6–10.1). Among grade III injuries (n = 158, 22.4%), the risk of pancreatic fistula/pseudocyst was reduced when the end of the pancreas was stapled (OR 0.21, 95% CI 0.05–0.9) compared with sewn and was not affected by duct stitch placement. Drainage alone in grades IV (n = 25) and V (n = 24) injuries carried increased risk of pancreatic fistula/pseudocyst (OR 8.3, 95% CI 2.2–32.9).

CONCLUSION

CT is insufficiently sensitive to reliably identify pancreatic duct injury. Patients with grade III injuries should have their resection site stapled instead of sewn and a duct stitch is unnecessary. Further study is needed to determine if drainage alone should be employed in grades IV and V injuries.

LEVEL OF EVIDENCE

Epidemiologic/Diagnostic study, level III.
Population Health, Ethnicity, and Rate of Living Donor Kidney Transplantation
Authors: Reed Rhiannon D. , Sawinski Deirdre , Shelton Brittany A. , MacLennan Paul A. , Hanaway Michael , Kumar Vineeta , Long Dustin , Gaston Robert S. , Kilgore Meredith L. , Julian Bruce A. , Lewis Cora E. , Locke Jayme E.
Published: May 2018

Background

Living donor kidney transplantation has declined in the United States since 2004, but the relationship between population characteristics and rate of living donation is unknown. The goal of our study was to use data on general population health and socioeconomic status to investigate the association with living donation.

Methods

This cross-sectional, ecological study used population health and socioeconomic status data from the CDC Behavioral Risk Factor Surveillance System to investigate the association with living donation. Transplant centers performing 10 or greater kidney transplants reported to the Scientific Registry of Transplant Recipients in 2015 were included. Center rate of living donation was defined as the proportion of all kidney transplants performed at a center that were from living donors.

Results

In a linear mixed-effects model, a composite index of health and socioeconomic status factors was negatively associated with living donation, with a rate of living donation that was on average 7.3 percentage points lower among centers in areas with more comorbid disease and poorer socioeconomic status (95% confidence interval, −12.2 to −2.3, P = 0.004). Transplant centers in areas with higher prevalence of minorities had a rate of living donation that was 7.1 percentage points lower than centers with fewer minorities (95% confidence interval, −11.8 to −2.3, P = 0.004).

Conclusions

Center-level variation in living donation was associated with population characteristics and minority prevalence. Further examination of these factors in the context of patient and center-level barriers to living donation is warranted.
Hyperactive Rac1 drives MAPK-independent proliferation in melanoma by assembly of a mechanosensitive dendritic actin network
Authors: Mohan Ashwathi S. , Dean Kevin M. , Kasitinon Stacy Y. , Isogai Tadamoto , Siruvallur Murali Vasanth , Han Sangyoon J. , Roudot Philippe , Groisman Alex , Welf Erik , Danuser Gaudenz
Published: May 2018

Abstract

Cancer cells use a variety of mechanisms to subvert growth regulation and overcome environmental challenges. Often, these same mechanisms enable cancer cells to also develop resistance to targeted therapies. Here, we describe how a hyperactivating mutation of the Rac1 GTPase (Rac1P29S) harnesses Rac1’s role as a regulator of actin polymer assembly to sustain cell cycle progression in growth limiting conditions. This proliferative advantage supports metastatic colonization of melanoma cells and confers insensitivity to inhibitors of the mitogen-activated protein kinase (MAPK) pathway, a frequent target for melanoma treatment. Rac1P29S bypasses the MAPK axis through a mechanism that necessitates cell-matrix attachment, however, does not depend on integrin-mediated focal adhesion assembly and focal adhesion kinase signaling. Even without involvement of canonical adhesion signaling, cells carrying the Rac1P29S mutation show elevated traction upon drug treatment and require mechanical resistance from their surrounding matrix to gain a proliferative advantage. We describe an alternative arm for cell mechanosensing, whereby actin polymerization against a matrix of minimal rigidity organizes biochemical cues to drive proliferative signals. Hyperactivation of Rac1 by the P29S mutation channels this pathway in melanoma through Arp 2/3-dependent formation of a constrained actin brush network that results in the inactivation of tumor suppressor NF2/Merlin. These data suggest an alternative mechanism for mechanosensitive growth regulation that can be hijacked by cancer cells to circumvent the adverse conditions of foreign microenvironments or drug treatment.
RCD1 Coordinates Chloroplastic and Mitochondrial Electron Transfer through Interaction with ANAC Transcription Factors in Arabidopsis
Authors: Shapiguzov Alexey , Vainonen Julia P. , Hunter Kerri , Tossavainen Helena , Tiwari Arjun , Järvi Sari , Hellman Maarit , Wybouw Brecht , Aarabi Fayezeh , Alseekh Saleh , Sipari Nina , Nikkanen Lauri , Der Kelen Katrien Van , Krasensky-Wrzaczek Julia , Salojärvi Jarkko , Brosché Mikael , Keinänen Markku , Tyystjärvi Esa , Rintamäki Eevi , De Rybel Bert , Fernie Alisdair R. , Breusegem Frank Van , Permi Perttu , Aro Eva-Mari , Wrzaczek Michael , Kangasjärvi Jaakko
Published: May 2018

Signaling from chloroplasts and mitochondria, both dependent on reactive oxygen species (ROS), merge at the nuclear protein RADICAL-INDUCED CELL DEATH1 (RCD1). ROS produced in the chloroplasts affect the abundance, thiol redox state and oligomerization of RCD1. RCD1 directly interactsin vivowith ANAC013 and ANAC017 transcription factors, which are the mediators of the ROS-related mitochondrial complex III retrograde signa and suppresses activity of ANAC013 and ANAC017. Inactivation ofRCD1leads to increased expression of ANAC013 and ANAC017-regulated genes belonging to the mitochondrial dysfunction stimulon (MDS), including genes for mitochondrial alternative oxidases(AOXs).Accumulating AOXs and other MDS gene products alter electron transfer pathways in the chloroplasts, leading to diminished production of chloroplastic ROS and increased protection of photosynthetic apparatus from ROS damage. RCD1-dependent regulation affects chloroplastic and mitochondrial retrograde signaling including chloroplast signaling by 3’-phosphoadenosine 5’-phosphate (PAP). Sensitivity of RCD1 to organellar ROS provides feedback control of nuclear gene expression.
The Impact of Reward on Attention in Schizophrenia
Authors: Bansal Sonia , Robinson Benjamin M. , Geng Joy J. , Leonard Carly J. , Hahn Britta , Luck Steven J. , Gold James M.
Published: May 2018

Traditionally, attention was thought to be directed by either top-down goals or bottom-up salience. Recent studies have shown that the reward history of a stimulus feature also acts as a powerful attentional cue. This is particularly relevant in schizophrenia, which is characterized by motivational and attentional deficits. Here, we examine the impact of reward on selective attention.

Forty-eight people with schizophrenia (PSZ) and 34 non-psychiatric control subject (NCS) discriminated the location of a target dot appearing inside a left circle or right circle. The circles were different colors, one of which was associated with reward via pre-training. In the first 2 blocks, targets were equally likely to appear in the left or right circle. In the last 4 blocks, the target was 75% likely on one side, thus allowing us to separately examine how attention was impacted by reward (color) and probability (location).

PSZ had slower overall reaction times (RTs) than NCS. Both groups showed robust effects of spatial probability and reward history, with faster RTs for the rewarded color and for the more probable location. These effects were similar in PSZ and NCS. Negative symptom severity correlated with overall RT slowing, but there were no correlations between symptoms and reward-associated biasing of attention.

PSZ demonstrated RT slowing but normal reward history and spatial probability-driven RT facilitation. These results are conceptually similar to prior findings showing intact implicit reward effects on response bias, and suggest that implicit processing of reward and probability is intact in PSZ.
The efficacy of a 14-day modified quadruple therapy containing amoxicillin, tetracycline and high dose metronidazole and proton-pump inhibitors as an empirical third line helicobacter pylori eradication treatment in Taiwan
Authors: Huang Hsiang Tso , Liang Chih-Ming , Lee Chen-Hsiang , Tai Wei-Chen , Wu Cheng-Kun , Yang Shih-Cheng , Huang Chih-Fang , Chiu Chien-Hua , Tsai Kai-Lung , Chang Meng-wei , Wang Hsin-Ming , Wu Keng-Liang , Hsu Ping-I , Wu Deng-Chyang , Chuah Seng-Kee ,   on behalf of Taiwan Acid-Related Disease (TARD) Study Group
Published: May 2018

The antibiotics resistances to amoxicilln, tetracycline was low in Taiwan even after multiple H. pylori treatment failures and high dose metronidazole could overcome antibiotics resistance. In real world practice, susceptibility-guided treatments are not widely available. Therefore, we assessed the efficacy of 14-day modified quadruple therapy containing amoxicillin, tetracycline and high dose metronidazole and PPI as an empirical third-line rescue H. pylori treatment. This study was conducted by analyzing 70 consecutive prospectively registered patients who failed two times H. pylori eradication. All of them received endoscopy for H. pylori culture. Seven patients were lost to follow up. They were then treated according to the antibiotic susceptibility testing reports (Cultured group, n=39). Those who failed H. pylori culture were prescribed with a modified 14-day quadruple therapy containing esomeprazole 40 mg twice daily, amoxicillin 1 g twice daily, tetracycline 500 mg four times daily and metronidazole 500 mg three times daily (empirical group, n=24). Follow-up urea breath test was performed 8 weeks later. The eradication rates attained by Cultured group and empirical group were 89.7% (95% confidence interval [CI] = 72.72%-97.11%) and 58.3% (95% CI=36.61%-77.86%), in the per protocol analysis (p=0.004); 81.4%(95% CI=66.60%-91.61%) and 51.8% (95% CI=31.9%-71.29%), in the intention-to-treat analysis (p=0.014). Culture-guided therapy was the clinical factors influencing the efficacy of H. pylori eradication (OR: 0.16; 95% CI: 0.04-0.60, p=0.006). In conclusion, empirical 14-day modified 3 quadruple therapy is not acceptable as an alternative third-line rescue H. pylori treatment arobably but the success rate of the third-line susceptibility-guided treatment was only moderate (<90%).
TLR3-TRIF pathway activation by Neospora caninum RNA enhances infection control
Authors: Miranda Vanessa dos Santos , França Flávia Batista Ferreira , da Costa Mylla Spirandelli , Silva Vanessa Resende Souza , Mota Caroline Martins , Barros Patrício da Silva Cardoso , Parreira Kleber Simônio , Santiago Fernanda Maria , Mineo Jose Roberto , Mineo Tiago Wilson Patriarca
Published: May 2018

Neospora caninum is a protozoan parasite closely related to Toxoplasma gondii and has been studied for causing neuromuscular disease in dogs and abortions in cattle. It is recognized as the major cause of economic losses in bovine products. In that sense, this study aimed to evaluate the role of TLR3-TRIF dependent resistance against N. caninum infection. We observed that TLR3−/− and TRIF−/− mice presented higher parasite burden, increased inflammatory lesions and reduced production of IL-12p40, TNF, IFN-γ, and NO. Differently from T. gondii, N. caninum tachyzoites and its RNA recruited TLR3 and IRF3 to the parasitophorous vacuole (PV). We observed that N. caninum upregulated the expression of TRIF in macrophages, which by its turn upregulated IFN-α and IFN-β in the presence of the parasite. Furthermore, TRIF−/− infected macrophages produced lower levels of IL-12p40 and IFN-α replacement was able to completely restore the production of this key cytokine. Our results have shown that TLR3-TRIF signaling pathway enhances resistance against N. caninum infection, since it improves Th1 immune responses that control parasitism and tissue inflammation, which are hallmarks of the disease.
Marine sponges as Chloroflexi hot-spots: Genomic insights and high resolution visualization of an abundant and diverse symbiotic clade
Authors: Bayer Kristina , Jahn Martin T. , Slaby Beate M. , Moitinho-Silva Lucas , Hentschel Ute
Published: May 2018

Chloroflexirepresent a widespread, yet enigmatic bacterial phylum. Meta-and single cell genomics were performed to shed light on the functional gene repertoire ofChloroflexisymbionts from the HMA spongeAplysina aerophoba. Eighteen draft genomes were reconstructed and placed into phylogenetic context of which six were investigated in detail. Common genomic features ofChloroflexisponge symbionts were related to central energy and carbon converting pathways, amino acid and fatty acid metabolism and respiration. Clade specific metabolic features included a massively expanded genomic repertoire for carbohydrate degradation in Anaerolineae and Caldilineae genomes, and amino acid utilization as nutrient source by SAR202. While Anaerolineae and Caldilineae import cofactors and vitamins, SAR202 genomes harbor genes encoding for co-factor biosynthesis. A number of features relevant to symbiosis were further identified, including CRISPRs-Cas systems, eukaryote-like repeat proteins and secondary metabolite gene clusters.Chloroflexisymbionts were visualized in the sponge extracellular matrix at ultrastructural resolution by FISH-CLEM method.Chloroflexicells were generally rod-shaped and about 1 μm in length, albeit displayed different and characteristic cellular morphotypes per each class. The extensive potential for carbohydrate degradation has been reported previously forCa. Poribacteria and SAUL, typical symbionts of HMA sponges, and we propose here that HMA sponge symbionts collectively engage in degradation of dissolved organic matter, both labile and recalcitrant. Thus sponge microbes may not only provide nutrients to the sponge host, but also contribute to DOM re-cycling and primary productivity in reef ecosystems via a pathway termed the “sponge loop”.
Phenotypic and metabolic plasticity shapes life-history strategies under combinations of abiotic stresses
Authors: Shaar-Moshe Lidor , Hayouka Ruchama , Roessner Ute , Peleg Zvi
Published: May 2018

Plants developed various reversible and non-reversible acclimation mechanisms to cope with the multifaceted nature of abiotic stress combinations. We hypothesized that in order to endure these stress combinations, plants elicit distinctive acclimation strategies through specific trade-offs between reproduction and defense. To investigateBrachypodium distachyonacclimation strategies to combinations of salinity, drought and heat, we applied a system biology approach, integrating physiological, metabolic and transcriptional analyses. We analyzed the trade-offs among functional and performance traits, and their effects on plant fitness. A combination of drought and heat resulted in escape strategy, while under a combination of salinity and heat, plants exhibited avoidance strategy. On the other hand, under combinations of salinity and drought, with or without heat stress, plant fitness (i.e. germination rate of subsequent generation) was severely impaired. These results indicate that under combined stresses, plants’ life-history strategies were shaped by the limits of phenotypic and metabolic plasticity and the trade-offs between traits, thereby giving raise to distinct acclimations. Our findings provide a mechanistic understanding of plant acclimations to combinations of abiotic stresses and shed light on the different life-history strategies that can contribute to grass fitness and possibly to their dispersion under changing environments.
Isotropic myosin-generated tissue tension is required for the dynamic orientation of the mitotic spindle
Authors: Lam Maxine SY , Lisica Ana , Ramkumar Nitya , Mao Yanlan , Charras Guillaume , Baum Buzz
Published: May 2018

The ability of epithelial cells to divide along their long cell axis, known as “Hertwig’s rule”, has been proposed to play an important and wide-ranging role in homogenising epithelial cell packing during tissue development and homeostasis. Since the position of the anaphase spindle defines the division plane, how divisions are oriented requires an understanding of the mechanisms that position the mitotic spindle. While many of the molecules required to orient the mitotic spindle have been identified in genetic screens, the mechanisms by which spindles read and align with the long cell axis remain poorly understood. Here, in exploring the dynamics of spindle orientation in mechanically distinct regions of the fly notum, we find that the ability of cells to properly orient their divisions depends both on cortical cues and on local tissue tension. Thus, spindles align with the long cell axis in tissues in which isotropic tension is elevated, but fail to do so in elongated cells within the crowded midline, where tension is low. Importantly, these region-specific differences in spindle behaviour can be reversed by decreasing or increasing the activity of non-muscle Myosin II. In addition, spindles in a tissue experiencing isotropic stress fail to align with the long cell axis if cells are mechanically isolated from their neighbours. These data lead us to propose that isotropic tension is required within an epithelium to provide cells with a mechanically stable substrate upon which localised cortical Dynein can pull on astral microtubules to orient the spindle.
Strange Stable Replicators Generated From Mumps Virus cDNA Clones
Authors: Bamford Connor , Wignall-Fleming Elizabeth , Randall Richard , Duprex Paul , Rima Bert
Published: May 2018

In reverse genetic experiments we have isolated recombinant mumps viruses (rMuV) based on a recent clinical isolate that carry large numbers of mutations clustered in small parts of their genome and which are not caused by biased hyper-mutation. In two separate experiments we obtained such rMuV: one virus had 19 mutations in the V/P region of the genome; the other, which also contained an extra transcription unit encoding green fluorescent protein (EGFP), had 32 mutations in the N gene. These specific constellations of mutations have not been observed in naturally occurring MuV isolates. The vast majority of the mutations (48/51) are synonymous.

On passage in Vero cells and human B-LCL cells, a B lymphocyte-like cell Line, these mutations appear stable as no reversal occurs to the original consensus sequences, though mutations in other genes occur and change in frequency during passage. Defective Interfering RNAs accumulate in passage in Vero cells but not in B-LCL cells. Interestingly, in all passaged samples the level of variation in the EGFP gene is the same as in the viral genes, though it is unlikely that this gene is under any functionality constraint. The stability in repeated high multiplicity passage indicates that the constellation of mutations is placing the virus on a fitness peak from which it cannot escape. What mechanism gave rise to these mutant viruses and their stability remain open questions of interest to a wider field than mumps reverse genetics alone.
Generation of light-producing somatic-transgenic mice using adeno-associated virus vectors
Authors: Karda Rajvinder , Rahim Ahad A. , Wong Andrew M.S. , Suff Natalie , Antinao Diaz Juan , Perocheau Dany P. , Palomar Martin Nuria , Hughes Michael , Delhove Juliette M.K.M. , Counsell John R. , Cooper Jonathan D. , Henckaerts Els , Mckay Tristan R. , Buckley Suzanne M.K. , Waddington Simon N.
Published: May 2018

We have previously designed a library of lentiviral vectors to generate somatic-transgenic rodents to monitor signalling pathways in diseased organs using whole-body bioluminescence imaging, in conscious, freely moving rodents. We have now expanded this technology to adeno-associated viral vectors. We first explored bio-distribution by assessing GFP expression after neonatal intravenous delivery of AAV8. We observed widespread gene expression in, central and peripheral nervous system, liver, kidney and skeletal muscle. Next, we selected a constitutive SFFV promoter and NFκB binding sequence for bioluminescence and biosensor evaluation.

An intravenous injection of AAV8 containing firefly luciferase and eGFP under transcriptional control of either element resulted in strong and persistent widespread luciferase expression. A single dose of LPS-induced a 10-fold increase in luciferase expression in AAV8-NFκB mice and immunohistochemistry revealed GFP expression in cells of astrocytic and neuronal morphology. Importantly, whole-body bioluminescence persisted up to 240 days.

To further restrict biosensor activity to the CNS, we performed intracerebroventricular injection of each vector. We observed greater restriction of bioluminescence to the head and spine with both vectors. Immunohistochemistry revealed strongest expression in cells of neuronal morphology. LPS administration stimulated a 4-fold increase over baseline bioluminescence.

We have validated a novel biosensor technology in an AAV system by using an NFκB response element and revealed its potential to monitor signalling pathway in a non-invasive manner using a model of LPS-induced inflammation. This technology employs the 3R’s of biomedical animal research, complements existing germline-transgenic models and may be applicable to other rodent disease models with the use of different response elements.
Theoretical Tool Bridging Cell Polarities with Development of Robust Morphologies
Authors: Nissen Silas Boye , Rønhild Steven , Trusina Ala , Sneppen Kim
Published: May 2018

Despite continual renewal and damages, a multicellular organism is able to maintain its complex morphology. How is this stability compatible with the complexity and diversity of living forms? Looking for answers at protein level may be limiting as diverging protein sequences can result in similar morphologies. Inspired by the progressive role of apical-basal and planar cell polarity in development, we propose that stability, complexity, and diversity are emergent properties in populations of proliferating polarized cells. We support our hypothesis by a theoretical approach, developed to effectively capture both types of polar cell adhesions. When applied to specific cases of development gastrulation and the origins of folds and tubes our theoretical tool suggests experimentally testable predictions pointing to the strength of polar adhesion, restricted directions of cell polarities, and the rate of cell proliferation to be major determinants of morphological diversity and stability.
Reciprocal Modulation Between Amyloid Precursor Protein and Synaptic Membrane Cholesterol Revealed By Live Cell Imaging
Authors: DelBove Claire E. , Strothman Claire E. , Lazarenko Roman M. , Huang Hui , Sanders Charles R. , Zhang Qi
Published: May 2018

The amyloid precursor protein (APP) has been extensively studied because of its association with Alzheimer’s disease (AD). However, APP distribution across different subcellular membrane compartments and its function in neurons remains unclear. We generated an APP fusion protein with a pH-sensitive green fluorescent protein at its ectodomain and a pH-insensitive blue fluorescent protein at its cytosolic domain and used it to measure APP’s distribution, subcellular trafficking and cleavage in live neurons. This reporter, closely resembling endogenous APP, revealed only a limited correlation between synaptic activities and APP trafficking. However, the synaptic surface distribution of APP was inversely correlated to membrane cholesterol levels, a phenomenon that involves APP’s cholesterol-binding site. Mutations within this site not only altered surface APP and cholesterol levels in a dominant negative manner, but also increased synaptic vulnerability to moderate membrane cholesterol reduction. Our results reveal reciprocal modulation of APP and membrane cholesterol levels at synaptic boutons.
Tendon slack length is the primary determinant of plantarflexor muscle-tendon function in computational simulations of gait
Authors: Baxter Josh R. , Hast Michael W.
Published: May 2018

1

Background: Locomotion is partly dictated by plantarflexor function and structure. Computational simulations are powerful tools capable of testing the isolated effects of muscle-tendon structure on gait function.Research Question: The purpose of this study was to characterize the sensitivity of plantarflexor muscle function based on muscle-tendon unit (MTU) parameters. We hypothesized that plantarflexor metabolics and shortening dynamics would be sensitive to MTU parameters.Methods: Stance phase of gait was simulated using a musculoskeletal model and computed muscle control algorithm. Optimal muscle fiber length, tendon slack length, and tendon stiffness parameters were systematically changed to test the effects on plantarflexor metabolics and shortening dynamics.Results and Significance: Plantarflexor metabolic demands were 8 and 28 times more sensitive to muscle fiber and tendon slack lengths, respectively, compared to the effect of tendon stiffness. Shortened tendon slack lengths induced a large passive plantarflexion moment during early stance, which required non-physiologic dorsiflexor contractions. Conversely, longer muscle fiber and tendon slack lengths increased the shortening demands of the plantarflexors to account for the added length of the MTU. These findings highlight the importance of carefully selecting MTU parameters when modeling gait with musculoskeletal models, especially in pathologic or high-performance athlete populations.
The Roles of Different Spatial Frequency Channels in Real-World Visual Motion Perception
Authors: Shi Cong , Pundlik Shrinivas , Luo Gang
Published: May 2018

Speed perception is an important task performed by our visual system in various daily life tasks. In various psychophysical tests, relationship between spatial frequency, temporal frequency, and speed has been examined in human subjects. The role of vision impairment in speed perception has also been previously examined. In this work, we examine the inter-relationship between speed, spatial frequency, low vision conditions, and the type of input motion stimuli in motion perception accuracy. For this purpose, we propose a computational model for speed perception and evaluate it in custom generated natural and stochastic sequences by simulating low-vision conditions (low pass filtering at different cutoff frequencies) as well as complementary vision conditions (high pass versions at the same cutoff frequencies). Our results show that low frequency components are critical for accurate speed perception, whereas high frequencies do not play any important role in speed estimation. Since perception of low frequencies may not be impaired in visual acuity loss, speed perception was not found to be impaired in low vision conditions compared to normal vision condition. We also report significant differences between natural and stochastic stimuli, notably an increase in speed estimation error when using stochastic stimuli compared to natural sequences, emphasizing the use of natural stimuli when performing future psychophysical studies for speed perception.
A Generative Bayesian Approach for Incorporating Biosurveillance Sources into Epidemiological Models
Authors: Manheim David
Published: May 2018

Biosurveillance “systematically collects and analyzes data for the purpose of detecting cases of disease, [and] outbreaks of disease.” (Wagner, Moore and Aryel, 2006) This typically involves using a set of known sources of epidemiological data, instead of opportunistically using the data sources which become available over time. This work attempts to partially remedy that limitation by using an easily adapted generative Bayesian econometric model to allow incorporation of novel data sources. This is done by building a generative model of the information sources, then using Bayesian Markov-chain Monte-Carlo to find the relationships between data and actual caseloads to use in an epidemiological model1.While the application presented is limited to three data sources for a single disease (influenza), the methodology is potentially widely applicable, and enables rapid incorporation of a variety of sources and source types.
Biophysical Principles of Lineage Factor PU.1 Binding Revealed by NextPBMs
Authors: Mohaghegh Nima , Bray David , Keenan Jessica , Penvose Ashley , Andrilenas Kellen K. , Ramlall Vijendra , Siggers Trevor
Published: May 2018

Determining the biophysical principles that shape transcription factor (TF) binding in a cell-specific manner is key to quantitative models of gene expression. High-throughput (HT)in vitromethods measuring protein-DNA binding are invaluable for relating TF binding affinity to genome-wide binding; however, the impact of cell-specific post-translational modifications (PTMs) and cofactors are not routinely assessed. To address these limitations, we describe a new HT approach, called nextPBMs (nuclearextractprotein-bindingmicroarrays), to characterize TF binding that accounts for PTMs and endogenous cofactors. We use nextPBMs to examine the DNA binding of the lineage factor PU.1/Spi1 and IRF8 in human monocytes. We identify two binding modes for PU.1 in monocytes – autonomous binding unaffected by PTMs and cooperative binding with IRF8, and identify a single cooperative mode for IRF8. We characterize the DNA binding of PU.1:IRF8 complexes, and show how nextPBMs can be used to discover cell-specific cofactors and characterize TF cooperativity at single-nucleotide resolution. We show that chromatin state and cofactors both influence the affinity requirements for PU.1 binding sites. Furthermore, we find that the influences of cooperative (IRF8) and collaborative (C/EBPα) cofactors on PU.1-binding-site affinity are independent and additive.
A Deep Learning Approach for Learning Intrinsic Protein-RNA Binding Preferences
Authors: Ben-Bassat Ilan , Chor Benny , Orenstein Yaron
Published: May 2018

Motivation

The complexes formed by binding of proteins to RNAs play key roles in many biological processes, such as splicing, gene expression regulation, translation, and viral replication. Understanding protein-RNA binding may thus provide important insights to the functionality and dynamics of many cellular processes. This has sparked substantial interest in exploring protein-RNA binding experimentally, and predicting it computationally. The key computational challenge is to efficiently and accurately infer RNA-binding models that will enable prediction of novel protein-RNA interactions to additional transcripts of interest.

Results

We developed DLPRB, a new deep neural network (DNN) approach for learning protein-RNA binding preferences and predicting novel interactions. We present two different network architectures: a convolutional neural network (CNN), and a recurrent neural network (RNN). The novelty of our network hinges upon two key aspects: (i) the joint analysis of both RNA sequence and structure, which is represented as a probability vector of different RNA structural contexts; (ii) novel features in the architecture of the networks, such as the application of RNNs to RNA-binding prediction, and the combination of hundreds of variable-length filters in the CNN. Our results in inferring accurate RNA-binding models from high-throughput in vitro data exhibit substantial improvements, compared to all previous approaches for protein-RNA binding prediction (both DNN and non-DNN based). A highly significant improvement is achieved for in vitro binding prediction, and a more modest, yet statistically significant,improvement for in vivo binding prediction. When incorporating experimentally-measured RNA structure compared to predicted one, the improvement on in vivo data increases. By visualizing the binding specificities, we can gain novel biological insights underlying the mechanism of protein RNA-binding.

Availability

The source code is publicly available at https://github.com/ilanbb/dlprb.

Contact

yaronore@bgu.ac.il

Supplementary information

Supplementary data are available at Bioinformatics online.
Earlyin plantadetection ofXanthomonas axonopodispv.punicaein pomegranate using enhanced loop-mediated isothermal amplification assay
Authors: PrasannaKumar M.K. , Parivallal P. Buela , Manjunath C. , Mahesh H.B. , Narayan Karthik S , Babu Gopal Venkatesh , Priyanka K. , Puneeth M.E. , Rangaswamy K.T.
Published: May 2018

Bacterial blight in pomegranate caused byXanthomonas axonopodispv.punicae(Xap) is an increasing threat for pomegranate cultivation in India. To prevent the economic losses, it is pivotal to detect the infection in latent stages rather than in later stages. We have developed an enhanced method termed as loop-mediated isothermal amplification (LAMP) technique to evaluate for the latent detection of Xap in pomegranate using six set of specific primers. Three DNA intercalating dyes were used, such as Ethidium bromide, hydroxynaphthol blue (HNB) and SYBR Green resulted in visualising the positivity for LAMP assay. The reaction time and temperature were to be 65°C from 30 min onwards, for the dyes and its sensitivity was observed up to 10−7ng in the LAMP assay. For field applicability, LAMP assay detected Xap on 7thday post infection while the PCR amplified Xap after 11thday post infection. Finally, the specificity of LAMP assay was validated to be positive with ten Xap isolates for its accuracy and 29 non-Xap bacterial isolates showed negative results. Moreover, this method could be used as a better alternative to PCR based methods, for early detection of the pathogens.
Merle phenotypes in dogs - SILV SINE insertions from Mc to Mh
Authors: Mary Langevin , Synkova Helena , Jancuskova Tereza , Pekova Sona
Published: May 2018

It has been recognized that the Merle coat pattern is not only a visually interesting feature, but it also exerts an important biological role, in terms of hearing and vision impairments. In 2006, the Merle (M) locus was mapped to the SILV gene with a SINE element in it, and the inserted retroelement was proven causative to the Merle phenotype. Mapping of the M locus was a genetic breakthrough and many breeders started implementing SILV SINE testing in their breeding programs. Unfortunately, the situation turned out complicated as genotypes of Merle tested individuals did not always correspond to expected phenotypes, sometimes with undesired health consequences in offspring. Two variants of SILV SINE, allelic to the wild type sequence, have been described so far - Mc and M.

Here we report a significantly larger portfolio of existing Merle alleles (Mc, Mc+, Ma, Ma+, M, Mh) in Merle dogs, which are associated with unique coat color features and stratified health impairment risk. The refinement of allelic identification was made possible by systematic, detailed observation of Merle phenotypes in a cohort of 181 dogs from known Merle breeds, by many breeders worldwide, and the use of advanced molecular technology enabling the discrimination of individual Merle alleles with significantly higher precision than previously available.

We also show that mosaicism of Merle alleles is an unexpectedly frequent phenomenon, which was identified in 30 out of 181 (16.6%). dogs in our study group. Importantly, not only major alleles, but also minor Merle alleles can be inherited by the offspring. Thus, mosaic findings cannot be neglected and must be reported to the breeder in their whole extent.

In light of negative health consequences that may be attributed to certain Merle breeding strategies, we strongly advocate implementation of the refined Merle allele testing for all dogs of Merle breeds to help the breeders in selection of suitable mating partners and production of healthy offspring.
A new polymorph of the gastrokinetic drug cisapride monohydrate
Authors: Zhou Xin-Bo , Zhu Jian-Rong , Gu Jian-Ming , Hu Xiu-Rong
Published: May 2018

Cisapride monohydrate (systematic name: 4-amino-5-chloro-N-{(3RS,4SR)-1-[3-(4-fluorophenoxy)propyl]-3-methoxypiperidin-4-yl}-2-methoxybenzamide monohydrate), C23H29ClFN3O4·H2O, is a nondopamine-blocking gastrokinetic drug. A new polymorph of cisapride monohydrate has been reported nearly three decades after the report of its first known crystal structure [Collin et al. (1989). J. Mol. Struct.
214, 159–175]. The second polymorph is also monoclinic, but with different unit-cell parameters. A comparison of both polymorphic forms shows that the difference is thus not in the molecular conformation but in the arrangements of molecules in the crystal packing. The crystal morphology of two forms was predicted with the BFDH model in Materials Studio and inferred that the powder of the new polymorph has better flowability than the original polymorph. The results of DSC (differential scanning calorimetry) analysis and slurry experiments show that both polymorphs are stable at room temperature.
Crystal structures of binary compounds of meldonium 3-(1,1,1-trimethylhydrazin-1-ium-2-yl)propanoate with sodium bromide and sodium iodide
Authors: Nazarenko Alexander Y
Published: May 2018

3-(1,1,1-Trimethylhydrazin-1-ium-2-yl)propanoate (C6H14N2O2, M, more commonly known under its commercial names Meldonium or Mildronate) co-crystalizes with sodium bromide and sodium iodide forming polymeric hydrates poly[[tetra-μ-aqua-diaquabis[3-(1,1,1-trimethylhydrazin-1-ium-2-yl)propanoate]disodium] dibromide tetrahydrate], [Na2(C6H14N2O2)2(H2O)6]Br2·4H2O, and poly[[di-μ-aqua-diaqua[μ-3-(1,1,1-trimethylhydrazin-1-ium-2-yl)propanoate]disodium] diiodide], [Na2(C6H14N2O2)2(H2O)4]I2. The coordination numbers of the sodium ions are 6; the coordination polyhedra can be described as distorted octahedra. Metal ions and M zwitterions are assembled into infinite layers via electrostatic interactions and hydrogen-bonded networks. These layers are connected via electrostatic attraction between halogenide ions and positive trimethylhydrazinium groups into a three-dimensional structure.