bluuebunny/crossref_metadata_2025 huggingface dataset:
Actin enhances ER-mitochondrial calcium transfer and IMM constriction during mitochondrial division
Authors: Chakrabarti Rajarshi , Ji Wei-Ke , Stan Radu V. , de Juan Sanz Jaime , Ryan Timothy A. , Higgs Henry N.
Published: September 2017

Mitochondrial division requires division of both the inner and outer mitochondrial membranes (IMM and OMM, respectively). Interaction with endoplasmic reticulum (ER) promotes OMM division by recruitment of the dynamin Drp1, but effects on IMM division are not well characterized. We previously showed that actin polymerization through the ER-bound formin INF2 stimulates Drp1 recruitment in mammalian cells. Here, we show that INF2-mediated actin polymerization stimulates a second mitochondrial response independent of Drp1: a rise in mitochondrial matrix calcium through the mitochondrial calcium uniporter. ER stores supply the increased mitochondrial calcium, and the role of actin is to increase ER-mitochondria contact. Myosin IIA is also required for this mitochondrial calcium increase. Elevated mitochondrial calcium in turn activates IMM constriction in a Drp1-independent manner. IMM constriction requires electron transport chain activity. IMM division precedes OMM division. These results demonstrate that actin polymerization independently stimulates the dynamics of both membranes during mitochondrial division: IMM through increased matrix calcium, and OMM through Drp1 recruitment.
Population-level distribution and putative immunogenicity of cancer neoepitopes
Authors: Wood Mary A. , Paralkar Mayur , Paralkar Mihir P. , Nguyen Austin , Struck Adam J. , Ellrott Kyle , Margolin Adam , Nellore Abhinav , Thompson Reid F.
Published: September 2017

Background

Tumor neoantigens are a driver of cancer immunotherapy response; however, current neoantigen prediction tools produce many candidates that require further prioritization for research/clinical applications. Additional filtration criteria and population-level understanding may help to produce refined lists of putative neoantigens. Herein, we show neoepitope immunogenicity is likely related to measures of peptide novelty and report population-level behavior of these and other metrics.

Methods

We propose four peptide novelty metrics to refine predicted neoantigenicity: tumor vs. paired normal peptide binding affinity difference, tumor vs. paired normal peptide sequence similarity, tumor vs. closest human peptide sequence similarity, and tumor vs. closest microbial peptide sequence similarity. We apply these metrics to tumor neoepitopes predicted from somatic missense mutations in The Cancer Genome Atlas (TCGA) and a cohort of melanoma patients, as well as to a group of peptides with neoepitope-specific immune response data using an extension of pVAC-Seq [1].

Results

We show neoepitope burden varies across TCGA disease sites and HLA alleles, with surprisingly low repetition of neoepitope sequences across patients or neoepitope preferences among sets of HLA alleles. Only 20.3% of predicted neoepitopes across TCGA patients displayed novel binding change based on our binding affinity difference criteria. Similarity of amino acid sequence was typically high between paired tumor-normal epitopes, but in 24.6% of cases, neoepitopes were more similar to other human peptides, or even to bacterial (56.8% of cases) or viral peptides (15.5% of cases), than their paired normal counterparts. Applied to peptides with neoepitope-specific immune response, a linear model incorporating neoepitope binding affinity, protein sequence similarity between neoepitopes and their closest viral peptides, and paired binding affinity difference was able to predict immunogenicity with an AUROC of 0.66.

Conclusions

Our proposed neoepitope prioritization criteria emphasize neoepitope novelty and refine patient neoepitope predictions for focus on biologically meaningful candidate neoantigens. We have demonstrated that neoepitopes should be considered not only with respect to their paired normal epitope, but with respect to the entire human proteome, as well as bacterial and viral peptides, with potential implications for neoepitope immunogenicity and personalized vaccines for cancer treatment. We conclude that putative neoantigens are highly variable across individuals as a function of both cancer genetics and personalized HLA repertoire, while the overall behavior of filtration criteria reflects predictable patterns.
Mechanisms of improved specificity of engineered Cas9s revealed by single molecule analysis
Authors: Singh Digvijay , Wang Yanbo , Mallon John , Yang Olivia , Fei Jingyi , Poddar Anustup , Ceylan Damon , Bailey Scott , Ha Taekjip
Published: September 2017

In microbes, CRISPR-Cas systems provide adaptive immunity against invading genetic elements. Cas9 in complex with a guide-RNA targets complementary DNA for cleavage and has been repurposed for wide-ranging biological applications. New Cas9s have been engineered (eCas9 and Cas9-HF1) to improve specificity, but how they help reduce off-target cleavage is not known. Here, we developed single molecule DNA unwinding assay to show that sequence mismatches affect cleavage reactions through rebalancing the internal unwinding/rewinding equilibrium. Increasing PAM-distal mismatches facilitate rewinding, and the associated cleavage impairment shows that cleavage proceeds from the unwound state. Engineered Cas9s depopulate the unwound state more readily upon mismatch detection. Intrinsic cleavage rate is much lower for engineered Cas9s, preventing cleavage from transiently unwound off-targets. DNA interrogation experiments showed that engineered Cas9s require about one additional base pair match for stable binding, freeing them from sites that would otherwise sequester them. Therefore, engineered Cas9s achieve their improved specificity (1) by inhibiting stable DNA binding to partially matching sequences, (2) by making DNA unwinding more sensitive to mismatches, and (3) by slowing down intrinsic cleavage reaction.
Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome
Authors: Li Cai , Lenhard Boris , Luscombe Nicholas M.
Published: September 2017

Previous studies revealed widespread transcription initiation and fast turnover of transcription start sites (TSSs) in mammalian genomes. Yet how new TSSs originate and how they evolve over time remain poorly understood. To address these questions, we analyzed ∼200,000 human TSSs by integrating evolutionary and functional genomic data, particularly focusing on TSSs that emerged in the primate lineages. We found that intrinsic factors of repetitive sequences and their proximity to established regulatory modules (extrinsic factors) contribute significantly to origin of new TSSs. In early periods, young TSSs experience rapid sequence evolution driven by endogenous mutational mechanisms that reduce the instability of associated repetitive sequences. In later periods, the regulatory functions of young TSSs are gradually modified, and with evolutionary changes subject to temporal (fewer regulatory changes in younger TSSs) and spatial constraints (fewer regulatory changes in more isolated TSSs). These findings advance our understanding of how regulatory innovations arise in the genome throughout evolution and highlight the roles of repetitive sequences in these processes.
Quantifying Seasonal and Diel Variation in Anopheline and Culex Human Biting Rates in Southern Ecuador
Authors: Ryan Sadie J. , Lippi Catherine A. , Boersch-Supan Philipp H. , Heydari Naveed , Silva Mercy , Adrian Jefferson , Noblecilla Leonardo F. , Ayala Efraín B. , Encalada Mayling D. , Larsen David A. , Krisher Jesse T. , Krisher Lyndsay , Fregosi Lauren , Stewart-Ibarra Anna M.
Published: September 2017

Background

Quantifying mosquito biting rates for specific locations enables estimation of mosquito-borne disease risk, and can inform intervention efforts. Measuring biting itself is fraught with ethical concerns, so the landing rate of mosquitoes on humans is often used as a proxy measure. Southern coastal Ecuador was historically endemic for malaria (P. falciparumandP. vivax), although successful control efforts in the 2000s eliminated autochthonous transmission (since 2011). This study presents an analysis of data collected during the elimination period.

Methods

We examined human landing catch (HLC) data for three mosquito taxa: 2 malaria vectors,Anopheles albimanusandAnopheles punctimacula, and groupedCulex spp. These data were collected by the National Vector Control Service of the Ministry of Health over a 5-year time span (2007 – 2012) in five cities in southern coastal Ecuador, at multiple households, in all months of the year, during dusk-dawn (18:00-6:00) hours, often at both indoor and outdoor locations. Hurdle models were used to determine if biting activity was fundamentally different for the three taxa, and to identify spatial and temporal factors influencing bite rate. Due to the many different approaches to studying and quantifying bite rates in the literature, we also created a glossary of terms, to facilitate comparative studies in the future.

Results

Biting trends varied significantly with species and time. All taxa exhibited exophagic feeding behavior, and outdoor locations increased both the odds and incidence of bites across taxa.An. albimanuswas most frequently observed biting, with an average of 4.7 bites per hour. The highest and lowest respective months for significant biting activity were March and July forAn. albimanus,July and August forAn. punctimacula, and February and July forCulex spp.

Conclusions

Fine-scale spatial and temporal differences exist in biting patterns among mosquito taxa in southern coastal Ecuador. This analysis provides detailed information for targeting vector control and household level behavioral interventions. These data were collected as part of routine vector surveillance conducted by the Ministry of Health, but such data have not been collected since. Reinstating such surveillance measures would provide important information to aid in preventing malaria re-emergence.
Sodium valproate rescues expression ofTRANK1in iPSC-derived neural cells that carry a genetic variant associated with serious mental illness
Authors: Jiang Xueying , Detera-Wadleigh Sevilla D , Akula Nirmala , Mallon Barbara S. , Hou Liping , Xiao Tiaojiang , Felsenfeld Gary , Gu Xinglong , McMahon Francis J.
Published: September 2017

Biological characterization of genetic variants identified in genome-wide association studies (GWAS) remains a substantial challenge. Here we used human induced pluripotent stem cells (hiPSC) and their neural derivatives to characterize common variants on chromosome 3p22 that have been associated by GWAS with major mental illnesses. HiPSC-derived neural progenitor cells carrying the risk allele of the single nucleotide polymorphism (SNP), rs9834970, displayed lower baselineTRANK1expression that was rescued by chronic treatment with therapeutic dosages of valproic acid (VPA). Although rs9834970 has no known function, we demonstrated that a nearby SNP, rs90832, strongly affects binding by the transcription factor, CTCF, and that the high-affinity allele usually occurs on haplotypes carrying the rs9834970 risk allele. Decreased expression ofTRANK1perturbed expression of many genes involved in neural development and differentiation. These findings have important implications for the pathophysiology of major mental illnesses and the development of novel therapeutics.

Highlights

hiPSC-derived neural cells carrying a mental illness risk allele showed lower expression ofTRANK1

Valproic acid rescuedTRANK1expression in cells carrying the risk allele

Risk haplotypes usually carry an allele that increased CTCF binding

Reduced expression ofTRANK1perturbed genes involved in neural development and differentiation

In Brief

Using neural derivatives of human induced pluripotent stem cells, Jiang et al. demonstrate that genetic variants associated with mental illness alter transcription factor binding and decrease expression of a nearby gene, an effect which is rescued by valproic acid.
A high-throughput fluorescent indicator displacement assay and principal component/cluster data analysis for determination of ligand-nucleic acid structural selectivity
Authors: del Villar-Guerra Rafael , Gray Robert D. , Trent John O. , Chaires Jonathan B.
Published: September 2017

We describe a high-throughput fluorescence indicator displacement assay (HT-FID) to evaluate the affinity and the selectivity of compounds binding to different DNA structures. We validated the assay using a library of 30 well-known nucleic acid binders containing a variety chemical scaffolds. We used a combination of principal component analysis and hierarchical clustering analysis to interpret the results obtained. This analysis classified compounds based on selectivity for AT-rich, GC-rich and G4 structures. We used the FID assay as a secondary screen to test the binding selectivity of an additional 20 compounds selected from the NCI diversity set III library that were identified as G4 binders using a thermal shift assay. The results showed G4 binding selectivity for only a few of the 20 compounds. Overall, we show that this HT-FID assay, coupled with PCA and HCA, provides a useful tool for the discovery of ligands selective for particular nucleic acid structures.
NECAPs are negative regulators of the AP2 clathrin adaptor complex
Authors: Beacham Gwendolyn M , Partlow Edward A , Lange Jeffrey J , Hollopeter Gunther
Published: September 2017

Eukaryotic cells internalize transmembrane receptors via clathrin-mediated endocytosis, but it remains unclear how the machinery underpinning this process is regulated. We recently discovered that membrane-associated muniscin proteins such as FCHo and SGIP initiate endocytosis by converting the AP2 clathrin adaptor complex to an open, active conformation that is then phosphorylated (Hollopeter et al., 2014). Here we report that loss ofncap-1, the soleC.elegansgene encoding an adaptiN Ear-binding Coat-Associated Protein (NECAP), bypasses the requirement for FCHO-1. Biochemical analyses reveal AP2 accumulates in an open, phosphorylated state inncap-1mutant worms, suggesting NECAPs promote the closed, inactive conformation of AP2. Consistent with this model, NECAPs preferentially bind open and phosphorylated forms of AP2in vitroand localize with constitutively open AP2 mutantsin vivo. NECAPs do not associate with phosphorylation-defective AP2 mutants, implying that phosphorylation precedes NECAP recruitment. We propose NECAPs function late in endocytosis to inactivate AP2.
Comprehensive survey of vitiligo patients in the northeast of China using a predesigned questionnaire
Authors: Lin Zheng , Tian Yaping , Bai Bingxue , Liu Mei , Wu Yan , Xiao Bihuan , Gao Xing‐Hua , Chen Hong‐Duo
Published: September 2017

To assess the sociodemographic data and clinical information of outpatients affected by vitiligo in the northeast of China, vitiligo patients or guardians who presented to the clinic were invited to participate in an exploratory questionnaire. The questionnaire consisted of two sections related to vitiligo, including sociodemographic data and clinical information. A total of 983 vitiligo patients answered the questionnaire. The rates of female and male patients were comparable. The investigated patients were mostly young and middle‐aged. Most patients suffered from vitiligo in childhood or young adulthood. Vitiligo vulgaris was the most common type of vitiligo in clinic and 53.0% of patients were categorized as body surface area (BSA) of 10% or less. In response to the latest treatment, 43.6% of patients achieved good response (completely stopped or almost disappeared). More patients at active stage showed good response than the patients at stable stage (χ2 = 7.866, P < 0.05). Chronic comorbid condition(s) were observed in 12.6% of patients with BSA of more than 10%, whereas those were seen in 6.0% of patients with BSA of 10% or less (χ2 = 12.969, P < 0.05). In conclusion, active vitiligo seems to respond better than stable vitiligo and complications with other autoimmune diseases more frequently observed in severe patients than mild patients. The current study presented a comprehensive understanding of vitiligo in the northeast of China.
Competition induces increased toxin production in toad larvae without allelopathic effects on heterospecific tadpoles
Authors: Bókony Veronika , Üveges Bálint , Móricz Ágnes M. , Hettyey Attila
Published: September 2017

Inducible defences are a form of phenotypic plasticity by which organisms respond to and mitigate the threat posed by predators, parasites and competitors. While anti‐predatory defences are often in trade‐off with anti‐competitor responses, chemicals that deter predators may have negative effects on competitors as well. Allelopathy is well known in plants and plant‐like animals, but whether the toxins of mobile, behaviourally and morphologically complex animals are induced by and exert allelopathic effects on competitors is poorly known.

Common toads Bufo bufo synthesize bufadienolides which make them unpalatable or toxic to many predators. However, bufadienolide content of toad tadpoles correlates positively with the density of competitors in natural populations, suggesting that they may upregulate their toxin production to inhibit their competitors, such as heterospecific tadpoles that may be vulnerable to toad toxins.

We conducted a microcosm experiment with tadpoles of common toads and agile frogs Rana dalmatina, in which we manipulated the density of conspecific and heterospecific competitors. We measured the bufadienolide content of toad tadpoles to test for competitor‐induced changes in toxin production, and we assessed the growth and development of agile frog tadpoles to test for allelopathy.

We found that toad tadpoles contained higher amounts of bufadienolides at higher densities; however, heterospecific competitors did not have a stronger effect than conspecifics. Furthermore, the presence or density of toad tadpoles had no effect on the body mass and development rate of agile frog tadpoles.

Our results demonstrate competitor‐induced plasticity in toxin production, but we found no support for an allelopathic function of bufadienolides. Instead, we suggest that inducible changes in bufadienolide production may serve to mitigate risks posed by competitors, including aggression, cannibalism or disease. Therefore, bufadienolides are intriguing candidates for multi‐purpose defences that may provide protection not only against predators but also against competitors.

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Do instability markers predict satisfactory reduction and requirement for later surgery in emergency department patients with wrist fracture?
Authors: Winayak Amar , Gossat Alyza , Cooper Jenny , Ritchie Peter , Lim Wei , Klim Sharon , Kelly Anne‐Maree
Published: September 2017

Objective

Research suggests that the presence of instability markers in patients with displaced distal radial fractures is associated with poorer outcome. Our aims were to determine whether the presence of previously defined instability markers could predict the likelihood of successful ED reduction and requirement for a secondary procedure after ED reduction.

Methods

Retrospective cohort study performed by medical record review. Adult ED patients coded as having an isolated wrist fracture and having fracture reduction in ED were eligible for inclusion. Data collected included demographics, history of osteoporosis, mechanism of injury, radiological features on X‐rays and performance of a secondary procedure. Outcomes of interest were the rate of successful fracture reduction in ED (against defined radiological criteria), the rate of secondary procedures and the association between the number of defined instability risk factors and successful reduction and performance of a secondary surgical procedure. Analysis was by χ2 test, receiver operating characteristic curve, logistic regression analyses.

Results

Three hundred and nineteen patients were studied; median age 62 years, 77% female. Sixty‐five per cent of patients had satisfactory fracture reduction in ED (95% CI 59%–70%). Eighty‐six patients underwent a secondary procedure to reduce/stabilise their fracture (28%, 95% CI 23%–33%). Younger age, lack of satisfactory ED reduction and increased number of instability factors were independently predictive of the performance of a secondary procedure.

Conclusion

Instability risk factors are common in patients with wrist fractures requiring reduction in ED. The number of instability factors is not a strong predictor of the performance of secondary procedures.
Characteristics of the local recurrence pattern after curative resection and values in target region delineation in postoperative radiotherapy for lower thoracic esophageal squamous cell cancer
Authors: Liu Jun , Cai Xuwei , Liu Qi , Li Hongxuan , Cheng Yan , Fu Xiaolong
Published: September 2017

Background

The aim of this study was to investigate the patterns and influencing factors of local‐regional recurrence of lower thoracic esophageal squamous cell carcinoma (TESCC) after curative resection and to delineate the clinical target volume (CTV) of postoperative radiotherapy (PORT).

Methods

From January 2009 to December 2013, the clinical data of patients who experienced local‐regional recurrence after curative esophagectomy were collected and analyzed to determine local‐regional recurrence patterns and to evaluate whether a proposed T‐shaped PORT CTV could cover regions of local‐regional failure.

Results

A total of 108 patients were eligible for this study. All patients experienced postoperative recurrence of lower TESCC. The time to local‐regional failure varied from one to 52 months (average 13.4 ± 11.0). Among the 108 patients, 127 recurrence sites were detected as the first recurrence event: 37 cases in the bilateral supraclavicular region, 56 in the upper mediastinum, 14 in the middle mediastinum, 15 in the upper abdominal lymph nodes, and five cases of anastomotic recurrence. The proposed PORT CTV could successfully cover 89 (82.4%) out of the 108 recurrences and 84.2% of the sites (107/127) of recurrence in our sample.

Conclusion

Local‐regional recurrence of lower TESCC is mainly distributed in the supraclavicular, upper‐middle mediastinum, anastomotic stoma, and upper abdominal lymph node regions. The proposed T‐shaped PORT CTV field could cover over 80% of local‐regional failure in our sample; therefore, we suggest that PORT should focus on this area.
Measuring Emergency Department Acuity
Authors: Yiadom Maame Yaa A. B. , Baugh Christopher W. , Barrett Tyler W. , Liu Xulei , Storrow Alan B. , Vogus Timothy J. , Tiwari Vikram , Slovis Corey M. , Russ Stephan , Liu Dandan ,   The ED Operations Study Group 2015
Published: September 2017

Background

Emergency department (ED) acuity is the general level of patient illness, urgency for clinical intervention, and intensity of resource use in an ED environment. The relative strength of commonly used measures of ED acuity is not well understood.

Methods

We performed a retrospective cross‐sectional analysis of ED‐level data to evaluate the relative strength of association between commonly used proxy measures with a full spectrum measure of ED acuity. Common measures included the percentage of patients with Emergency Severity Index (ESI) scores of 1 or 2, case mix index (CMI), academic status, annual ED volume, inpatient admission rate, percentage of Medicare patients, and patients seen per attending‐hour. Our reference standard for acuity is the proportion of high‐acuity charts (PHAC) coded and billed according to the Centers for Medicare and Medicaid Service's Ambulatory Payment Classification (APC) system. High‐acuity charts included those APC 4 or 5 or critical care. PHAC was represented as a fractional response variable. We examined the strength of associations between common acuity measures and PHAC using Spearman's rank correlation coefficients (rs) and regression models including a quasi‐binomial generalized linear model and linear regression.

Results

In our univariate analysis, the percentage of patients ESI 1 or 2, CMI, academic status, and annual ED volume had statistically significant associations with PHAC. None explained more than 16% of PHAC variation. For regression models including all common acuity measures, academic status was the only variable significantly associated with PHAC.

Conclusion

Emergency Severity Index had the strongest association with PHAC followed by CMI and annual ED volume. Academic status captures variability outside of that explained by ESI, CMI, annual ED volume, percentage of Medicare patients, or patients per attending per hour. All measures combined only explained only 42.6% of PHAC variation.
Sexual identity differences in high‐intensity binge drinking: findings from a US national sample
Authors: Fish Jessica N. , Hughes Tonda L. , Russell Stephen T.
Published: September 2017

Aim

To estimate sexual identity differences in high‐intensity binge drinking.

Design and setting

Cross‐sectional US adult health survey from 2014 and 2015.

Participants

US adults aged 18 and older (n = 215 684; n = 203 562 heterosexual, n = 2784 lesbian/gay, n = 2892 bisexual, n = 686 ‘other’ and n = 1947 don't know/unsure).

Measurements

Self‐reported past 30‐day standard binge and high‐intensity binge drinking. Standard binge drinking cut‐off values were 4+/5+ drinks for women and men, respectively. High‐intensity binge drinking was measured as two and three times the standard level (8+ and 12+ drinks for women and 10+ and 15+ drinks for men).

Findings

Lesbian and bisexual women were more likely than heterosexual women to report consuming 4+ drinks (adjusted odds ratio [aOR] =1.57, confidence interval [CI] = 1.18, 2.09 and aOR = 1.83, CI = 1.45, 2.30 for lesbian and bisexual women, respectively); 8+ drinks (aOR = 3.86, CI = 2.39, 6.24, aOR = 2.07, CI = 1.39, 3.07); and 12+ drinks (aOR = 3.81, CI = 1.77, 8.19, aOR = 2.54, CI = 1.25, 5.14) on a single occasion in the past 30 days. Generally, gay and bisexual men were no more likely than heterosexual men to report standard or high‐intensity binge drinking. However, bisexual men were more likely than heterosexual men to consume 15+ drinks (aOR = 1.76, 95% CI = 1.01, 3.06). Rates of standard and high‐intensity binge drinking were similar between heterosexual and unsure men and women. Men and women who indicated ‘other’ sexual identities were generally less likely than heterosexuals to report standard and high‐intensity binge drinking, with the exception of 4+ drinks for women and 10+ drinks for men.

Conclusions

In the United States, sexual minority women are more likely, and sexual minority men are equally likely, to drink at standard and high‐intensity binge drinking levels as their heterosexual counterparts.
Symptom management and psychological support for families are the cornerstones of end‐of‐life care for children with spinal muscular atrophy type 1
Authors: Di Pede Chiara , Agosto Caterina , De Tommasi Valentina , De Gregorio Alessandra , Benini Franca
Published: September 2017

Aim

This study described end‐of‐life care for children affected by spinal muscular atrophy type 1 (SMA1), which is characterised by progressive muscle weakness and develops in the first six months of life.

Methods

We retrospectively analysed 17 children (13 boys) who attended the University of Padua's paediatric palliative care centre in Italy from March 2000 to March 2015. All the children received supportive care without proactive respiratory intervention to prolong survival.

Results

The median age at admission was 3.57 months, and the median age at death was 6.80 months. The most frequent symptoms were dyspnoea and pain. In the last 72 hours of life, 15/17 children required more intense doses of morphine and, or, benzodiazepines for intractable dyspnoea and pain, but deep palliative sedation was not needed. Airway suction to manage secretions and nasogastric tubes was required in all cases. The place of death was previously planned by the parents in all cases – home, hospital or hospice – and 15/17 deaths occurred in that place. We also interviewed 16 of the 17 parents after their child died.

Conclusion

Our study found that symptom management and psychological support for families were the cornerstones of end‐of‐life care for children with SMA1.
Performing a urine dipstick test with a clean‐catch urine sample is an accurate screening method for urinary tract infections in young infants
Authors: Herreros María Luisa , Tagarro Alfredo , García‐Pose Araceli , Sánchez Aida , Cañete Alfonso , Gili Pablo
Published: September 2017

Aim

This study evaluated using urine dipstick tests with the clean‐catch method to screen for urinary tract infection (UTI) in febrile infants under 90 days of age.

Methods

We carried out a comparative diagnostic accuracy study of infants under 90 days old, who were studied for unexplained fever without any source, in the emergency room of a hospital in Madrid from January 2011 to January 2013. We obtained matched samples of urine using two different methods: a clean‐catch, standardised stimulation technique and catheterisation collection. The results of the leucocyte esterase test and nitrite test were compared with their urine cultures.

Results

We obtained 60 pairs of matched samples. A combined analysis of leukocyte esterase and, or, nitrites yielded a sensitivity of 86% and a specificity of 80% for the diagnosis of UTIs in clean‐catch samples. The sensitivity of leukocyte esterase and, or, nitrites in samples obtained by catheterisation were not statistically different to the clean‐catch samples (p = 0.592).

Conclusion

Performing urine dipstick tests using urine samples obtained by the clean‐catch method was an accurate screening test for diagnosing UTIs in febrile infants of less than 90 days old. This provided a good alternative to bladder catheterisation when screening for UTIs.
Molecular mechanisms regulating perivascular adipose tissue – potential pharmacological targets?
Authors: Kennedy Simon , Salt Ian P
Published: September 2017

Linked Articles

This article is part of a themed section on Molecular Mechanisms Regulating Perivascular Adipose Tissue – Potential Pharmacological Targets? To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.20/issuetoc
Lon protease: a novel mitochondrial matrix protein in the interconnection between drug‐induced mitochondrial dysfunction and endoplasmic reticulum stress
Authors: Polo Miriam , Alegre Fernando , Moragrega Angela B , Gibellini Lara , Marti‐Rodrigo Alberto , Blas‐Garcia Ana , Esplugues Juan V , Apostolova Nadezda
Published: September 2017

Background and Purpose

Mitochondria‐associated membranes (MAMs) are specific endoplasmic reticulum (ER) domains that enable it to interact directly with mitochondria and mediate metabolic flow and Ca2+ transfer. A growing list of proteins have been identified as MAMs components, but how they are recruited and function during complex cell stress situations is still not understood, while the participation of mitochondrial matrix proteins is largely unrecognized.

Experimental Approach

This work compares mitochondrial/ER contact during combined ER stress/mitochondrial dysfunction using a model of human hepatoma cells (Hep3B cell line) treated for 24 h with classic pharmacological inducers of ER stress (thapsigargin), mitochondrial dysfunction (carbonyl cyanide m‐chlorophenyl hydrazone or rotenone) or both (the antiretroviral drug efavirenz used at clinically relevant concentrations).

Key Results

Markers of mitochondrial dynamics (dynamin‐related protein 1, optic atrophy 1 and mitofusin 2) were expressed differently with these stimuli, pointing to a specificity of combined ER/mitochondrial stress. Lon, a matrix protease involved in protein and mtDNA quality control, was up‐regulated at mRNA and protein levels under all conditions. However, only efavirenz decreased the mitochondrial content of Lon while increasing its extramitochondrial presence and its localization to MAMs. This latter effect resulted in an enhanced mitochondria/ER interaction, as shown by co‐immunoprecipitation experiments of MAMs protein partners and confocal microscopy imaging.

Conclusion and Implications

A specific dual drug‐induced mitochondria‐ER effect enhances the MAMs content of Lon and its extramitochondrial expression. This is the first report of this phenomenon and suggests a novel MAMs‐linked function of Lon protease.
Molecular modeling studies of pseudouridine isoxazolidinyl nucleoside analogues as potential inhibitors of the pseudouridine 5ʹ‐monophosphate glycosidase
Authors: Floresta Giuseppe , Pistarà Venerando , Amata Emanuele , Dichiara Maria , Damigella Arcangelo , Marrazzo Agostino , Prezzavento Orazio , Punzo Francesco , Rescifina Antonio
Published: September 2017

In this paper, we investigated the hypothesis that pseudouridine isoxazolidinyl nucleoside analogues could act as potential inhibitors of the pseudouridine 5ʹ‐monophosphate glycosidase. This purpose was pursued using molecular modeling and in silico ADME‐Tox profiling. From these studies emerged that the isoxazolidinyl derivative 1 5ʹ‐monophosphate can be effectively accommodated within the active site of the enzyme with a ligand efficiency higher than that of the natural substrate. In this context, the poor nucleofugality of the N‐protonated isoxazolidine prevents or slows down, the first mechanistic step proposed for the degradation of the pseudouridine 5ʹ‐monophosphate glycosidase, leading to the enzyme inhibition. Finally, the results of the physicochemical and ADME‐Tox informative analysis pointed out that compound 1 is weakly bounded to plasma protein, only moderately permeate the blood–brain barrier, and is non‐carcinogen in rat and mouse. To the best of our knowledge, this is the first paper that introduces the possibility of inhibition of pseudouridine 5ʹ‐monophosphate glycosidase by a molecule that competing with the natural substrate hinders the glycosidic C–C bond cleavage.
Complement regulatory proteins in kidneys of patients with anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis
Authors: Cheng L , Gou S-J , Qiu H-Y , Ma L , Fu P
Published: September 2017

The complement system activation is involved in the development of anti-neutrophil cytoplasmic antibody-associated vasculitis (AAV). The study aimed to investigate the expression of complement regulatory proteins (CRPs) CD46, CD55 and CD59 in kidneys of 51 AVV patients. The expression of CD46, CD55 and CD59 in kidneys was detected by immunohistochemistry and double immunofluorescence staining. The immunohistochemical examination revealed that expression of the three CRPs could be detected in the glomeruli and tubules of both AAV patients and normal controls. The expression levels of the three CRPs in glomeruli of patients with AAV were significantly lower than those of normal controls. The scores of CD46 and CD55 expression in the tubules of AAV patients were significantly lower than those of normal controls, while there was no significant difference between the scores of CD59 expression in tubules of AAV patients and those of normal controls. Among AAV patients, the expression level of CD46 in glomeruli correlated inversely with the proportion of normal glomeruli, while it correlated with tubular atrophy in renal interstitium (r = –0·305, P = 0·026; r = 0·330, P = 0·023, respectively). The expression levels of CD55 and CD59 in glomeruli correlated with the proportion of total crescents (r = 0·384, P = 0·006; r = 0·351, P = 0·011, respectively). Double immunofluorescence staining indicated that all three CRPs were expressed on endothelial cells, podocytes and mesangial cells in glomeruli. The expression levels of the three CRPs were dysregulated in kidneys of patients with AAV. The expression levels of CD46, CD55 and CD59 were associated with the severity of renal injury of AAV patients.
An increased CD25-positive intestinal regulatory T lymphocyte population is dependent upon Cox-2 activity in the Apcmin/+ model
Authors: Faluyi O O , Fitch P , Howie S E M
Published: September 2017

Only mismatch repair (MMR)-deficient colorectal cancer (CRC) appears to respond well to programmed death (PD)-1 inhibition at the present time. Emerging evidence suggests a role for micro-environmental factors such as CD25+ cells modulating response to PD-1 inhibition. In the ApcMin/+ model of familial adenomatous polyposis (MMR-proficient CRC), increased Cyclooxygenase-2 (Cox-2) expression by cells which include alternatively activated mononuclear phagocytes promotes intestinal tumorigenesis by mechanisms which may include immune suppression. To gain insight into this, we compared regulatory T cell (Treg) populations between ApcMin/+ and wild-type mice prior to and after the phase of increased intestinal Cox-2-dependent prostaglandin E2 (PGE2) production. There was no difference in systemic Treg function or numbers between ApcMin/+ and wild-type mice. However, increased numbers of small intestinal CD25+ Tregs were observed with increased Cox-2 activity in the absence of any difference in the expression of Tgf-β or Tslp between ApcMin/+ and wild-type mice. Cox-2 inhibitor therapy (Celecoxib) reversed the increase in ApcMin/+ intestinal CD25+ Treg numbers, without decreasing numbers of CD25+ systemic Tregs. Forkhead box protein 3 (FoxP3+) and Cox-2+ cells were co-localized to the interstitium of adenomas of Apcmin/+ mice. These results suggest selective dependence of an ‘activated Treg’ phenotype on paracrine Cox-2 activity in ApcMin/+ small intestine. For therapeutic potential, further studies are required to evaluate the relevance of these findings to human cancer as well as the functional significance of CD25+ intestinal Tregs in cancer.
Autoantibodies against the calcium‐sensing receptor and cytokines in autoimmune polyglandular syndromes types 2, 3 and 4
Authors: Kemp E. Helen , Kahaly George J. , Porter Julie A. , Frommer Lara , Weetman Anthony P.
Published: September 2017

Objective

The frequency of autoimmunity against the parathyroid glands in patients with polyglandular autoimmunity that is not due to autoimmune polyendocrine syndrome type 1 (APS1) is unclear. To investigate this, this study aimed to determine the prevalence of autoantibodies against parathyroid autoantigens, calcium‐sensing receptor (CaSR) and NACHT leucine‐rich‐repeat protein 5 (NALP5), in a large group of patients with non‐APS1 polyendocrine autoimmunity. Possible occult APS1 was investigated by cytokine autoantibody measurement and AIRE gene analysis.

Design, Subjects and Measurements

Subjects were 178 patients with APS2, 3 or 4, and 80 healthy blood donors. Autoantibodies against the CaSR, NALP5 and cytokines were measured by immunoprecipitation, radioligand binding assays or ELISA, respectively.

Results

Four patient samples (2.2%), but none of the controls, were positive for CaSR autoantibodies. NALP5 autoantibodies were not detected in any participant. Eleven patients (6.2%) had cytokine autoantibodies, but none of the control samples was positive. None of the patients with cytokine autoantibodies had any known or novel mutations in the AIRE gene.

Conclusions

The low prevalence of CaSR autoantibodies indicate a very low level of subclinical parathyroid autoimmunity in APS types 2, 3 and 4. In addition, autoantibodies against cytokines constitute an uncommon feature of non‐APS1 polyglandular autoimmunity.
Prediction of cerebral infarction and patient outcome in aneurysmal subarachnoid hemorrhage: comparison of new and established radiographic, clinical and combined scores
Authors: Dengler N. F. , Sommerfeld J. , Diesing D. , Vajkoczy P. , Wolf S.
Published: September 2017

Background and purpose

There are numerous grading scales to describe the severity of aneurysmal subarachnoid hemorrhage (aSAH) and to predict outcome. Historically, outcome measures are heterogeneous and the comparability of grading scales is therefore limited. We designed this study to compare radiographic, clinical and combined grading systems in aSAH.

Methods

Data from 423 consecutive patients with aSAH were analyzed. Modified Fisher (mFish), Barrow Neurological Institute (BNI), Hunt and Hess (HH), World Federation of Neurosurgical Societies (WFNS), VASOGRADE (VG) and HAIR scores were calculated from clinical and radiographic data or the combination of both. Outcome measures included the development of new cerebral infarction (CI) and functional patient outcome assessed by the modified Rankin scale.

Results

Cerebral infarction and unfavorable outcome were predicted by radiographic, clinical and combined measures (each with P ≤ 0.001). Clinical (HH, WFNS) and combined (VG, HAIR) scores had superior predictive power for CI compared with mFish grading but not BNI [area under the curve (AUC)mFish 0.612, AUCBNI 0.616, AUCWFNS 0.672, AUCHH 0.673, AUCVG 0.674, AUCHAIR 0.638]. Predictive performances of clinical gradings (HH, WFNS) for patient outcome were superior to radiographic measures and of similar quality or better than combined systems (AUCBNI 0.628, AUCmFish 0.654, AUCWFNS 0.736, AUCHH 0.749, AUCVG 0.711, AUCHAIR 0.739).

Conclusions

Knowledge of the merits and limitations of clinical, radiographic and combined scores is necessary in routine clinical practice. The new combined grading systems (HAIR, VG) showed no superiority compared with the established clinical measures (WFNS, HH) in predicting CI and unfavorable patient outcome.
Long‐term effects of cognitive rehabilitation on brain, functional outcome and cognition in Parkinson's disease
Authors: Díez‐Cirarda M. , Ojeda N. , Peña J. , Cabrera‐Zubizarreta A. , Lucas‐Jiménez O. , Gómez‐Esteban J. C. , Gómez‐Beldarrain M. Á. , Ibarretxe‐Bilbao N.
Published: September 2017

Background and purpose

Cognitive rehabilitation has demonstrated efficacy in producing short‐term cognitive and brain changes in patients with Parkinson's disease (PD). To date, no study has assessed the long‐term effects of cognitive rehabilitation using neuroimaging techniques in PD. The aim was to assess the longitudinal effects of a 3‐month cognitive rehabilitation programme evaluating the cognitive, behavioural and neuroimaging changes after 18 months.

Methods

Fifteen patients with PD underwent a cognitive, behavioural and neuroimaging assessment at pre‐treatment (T0), post‐treatment (T1) and after 18 months (T2). This study examined the long‐term effects (from T0 to T2) and the maintenance of the changes (from T1 to T2). T1‐weighted, diffusion‐weighted, functional magnetic resonance imaging during both a resting‐state and a memory paradigm were acquired. Voxel‐based morphometry and tract‐based spatial statistics were used for grey and white matter analyses. A region‐of‐interest‐to‐region‐of‐interest approach was used for resting‐state functional connectivity (FC) and a model‐based approach was used for brain activation during the memory paradigm.

Results

Patients with PD showed increased cognitive performance, decreased functional disability, increased brain FC and activation at T2 compared with T0 (P < 0.05, FDR). Moreover, patients showed maintenance of the improvements in cognition and functionality, and maintenance of the increased brain FC and activation at T2 compared with T1. However, significant grey matter reduction and alterations of white matter integrity were found at T2 (P < 0.05, FWE).

Conclusions

Findings suggest that the improved cognitive performance and increased brain FC and activation after cognitive rehabilitation were significantly maintained after 18 months in patients with PD, despite the structural brain changes, consistent with a progression of neurodegenerative processes.
Comparison of the use of a braided multifilament transfixation suture for field castration with other castration techniques
Authors: Koenig J. B. , Sinclair M. , Sorge U. S.
Published: September 2017

Complications with castrations occur commonly and are usually not life‐threatening, with the exception of evisceration or haemorrhage, which are uncommon. Primary closure castration (closing deeper tissue layers and skin) or use of a transfixation ligature alone to prevent evisceration has been recommended. The goal of this study was to investigate the use of a closed technique with multifilament suture for transfixation of the spermatic cord alone in field castrations. The results of this study support our hypothesis that a closed castration technique with a multifilament, transfixing ligature (No. 2 polyglactin 910) did not result in additional post‐operative complications when compared with a closed castration technique without ligature placement or a primary closure castration technique in a hospital setting.
PCRfor antigen receptor rearrangement (PARR) clonality testing in a horse with a solitary retropharyngeal lymphoma
Authors: Collar E. M. , Parker J. E. , Gorman E. M. , Russell D. S. , Valentine B. A.
Published: September 2017

A 19‐year‐old Quarter Horse gelding was evaluated for respiratory distress and a rapidly enlarging retropharyngeal mass. Initial evaluation revealed severe respiratory distress, and a large, firm mass, visibly appreciable as 12 × 12 cm, in the left retropharyngeal and perilaryngeal region, with surrounding left and right retropharyngeal swelling. No significant abnormalities were present on complete blood count and serum biochemistry analyses. Endoscopy revealed severe pharyngeal collapse restricting airflow without gross abnormalities of the pharyngeal mucosa other than inflammation and irritation. A multilobular retropharyngeal mass, diffusely heterogeneous in echogenicity, was present adjacent to, but not occluding, the carotid artery as assessed by ultrasonography. Initial needle aspirate suggested lymphoma. Tissue biopsy and histopathology confirmed a round cell tumour. A temporary tracheotomy was performed to provide respiratory relief, and the horse was managed on oral antibiotics and anti‐inflammatory medications while awaiting histopathological results. The decision was made to humanely euthanise the horse after biopsy results indicated lymphoma. Definitive diagnosis of T cell rich, large B cell lymphoma was made by combination of cytology, immunohistochemistry and molecular clonality PCR (PARR) testing. Lymphoma should be considered in horses with focal masses of the retropharyngeal region. Although treatment was not pursued, PARR testing was successful in this case and may be helpful for accurate characterisation of lymphoma in horses to more precisely determine prognosis and the most effective treatment plans, as it has been in human patients and small animals.
Transglutaminases in autoimmune and inherited skin diseases: The phenomena of epitope spreading and functional compensation
Authors: Kárpáti Sarolta , Sárdy Miklós , Németh Krisztián , Mayer Balázs , Smyth Neil , Paulsson Mats , Traupe Heiko
Published: September 2017

Transglutaminases (TGs) are structurally and functionally related enzymes that modify the post‐translational structure and activity of proteins or peptides, and thus are able to turn on or switch off their function. Depending on location and activities, TGs are able to modify the signalling, the function and the fate of cells and extracellular connective tissues. Besides mouse models, human diseases enable us to appreciate the function of various TGs. In this study, skin diseases induced by genetic damages or autoimmune targeting of these enzymes will be discussed. TG1, TG3 and TG5 contribute to the cutaneous barrier and thus to the integrity and function of epidermis. TGM1 mutations related to autosomal recessive ichthyosis subtypes, TGM5 mutations to a mild epidermolysis bullosa phenotype and as novelty TGM3 mutation to uncombable hair syndrome will be discussed. Autoimmunity to TG2, TG3 and TG6 may develop in a few of those genetically determined individuals who lost tolerance to gluten, and manifest as coeliac disease, dermatitis herpetiformis or gluten‐dependent neurological symptoms, respectively. These gluten responder diseases commonly occur in combination. In autoimmune diseases, the epitope spreading is remarkable, while in some inherited pathologies, a unique compensation of the lost enzyme function is noted.