bluuebunny/crossref_metadata_2025 huggingface dataset:
Separation of Dual Oxidase 2 and Lactoperoxidase Expression in Intestinal Crypts and Species Differences May Limit Hydrogen Peroxide Scavenging During Mucosal Healing in Mice and Humans
Authors: Rigoni Alice , Poulsom Richard , Jeffery Rosemary , Mehta Shameer , Lewis Amy , Yau Christopher , Giannoulatou Eleni , Feakins Roger , Lindsay James O , Colombo Mario P , Silver Andrew
Published: December 2017

Background

DUOX2 and DUOXA2 form the predominant H2O2-producing system in human colorectal mucosa. Inflammation, hypoxia, and 5-aminosalicylic acid increase H2O2 production, supporting innate defense and mucosal healing. Thiocyanate reacts with H2O2 in the presence of lactoperoxidase (LPO) to form hypothiocyanate (OSCN-), which acts as a biocide and H2O2 scavenging system to reduce damage during inflammation. We aimed to discover the organization of Duox2, Duoxa2, and Lpo expression in colonic crypts of Lieberkühn (intestinal glands) of mice and how distributions respond to dextran sodium sulfate (DSS)-induced colitis and subsequent mucosal regeneration.

Methods

We studied tissue from DSS-exposed mice and human biopsies using in situ hybridization, reverse transcription quantitative polymerase chain reaction, and cDNA microarray analysis.

Results

Duox2 mRNA expression was mostly in the upper crypt quintile while Duoxa2 was more apically focused. Most Lpo mRNA was in the basal quintile, where stem cells reside. Duox2 and Duoxa2 mRNA were increased during the induction and resolution of DSS colitis, while Lpo expression did not increase during the acute phase. Patterns of Lpo expression differed from Duox2 in normal, inflamed, and regenerative mouse crypts (P < 0.001). We found no evidence of LPO expression in the human gut.

Conclusions

The spatial and temporal separation of H2O2-consuming and -producing enzymes enables a thiocyanate- H2O2 “scavenging” system in murine intestinal crypts to protect the stem/proliferative zones from DNA damage, while still supporting higher H2O2 concentrations apically to aid mucosal healing. The absence of LPO expression in the human gut suggests an alternative mechanism or less protection from DNA damage during H2O2-driven mucosal healing.
Wheat Resistances to Fusarium Root Rot and Head Blight Are Both Associated with Deoxynivalenol- and Jasmonate-Related Gene Expression
Authors: Wang Qing , Shao Beiqi , Shaikh Fayaz Imamrasul , Friedt Wolfgang , Gottwald Sven
Published: December 2017

Fusarium graminearum is a major pathogen of wheat causing Fusarium head blight (FHB). Its ability to colonize wheat via seedling root infection has been reported recently. Our previous study on Fusarium root rot (FRR) has disclosed histological characteristics of pathogenesis and pathogen defense that mirror processes of spike infection. Therefore, it would be interesting to understand whether genes relevant for FHB resistance are induced in roots. The concept of similar-acting defense mechanisms provides a basis for research at broad Fusarium resistance in crop plants. However, molecular defense responses involved in FRR as well as their relation to spike resistance are unknown. To test the hypothesis of a conserved defense response, a candidate gene expression study was conducted to test the activity of selected prominent FHB defense-related genes in seedling roots, adult plant roots, spikes, and shoots. FRR was examined at seedling and adult plant stages to assess age-related pattern of disease and pathogen resistance. This study offers first evidence for a significant genetic overlap in root and spike defense responses, both in local and distant tissues. The results point to plant development-specific rather than organ-specific determinants of resistance, and suggest roots as an interesting model for studies on wheat−Fusarium interactions.
Succession of Fungal and Oomycete Communities in Glyphosate-Killed Wheat Roots
Authors: Schlatter Daniel C. , Burke Ian , Paulitz Timothy C.
Published: December 2017

The successional dynamics of root-colonizing microbes are hypothesized to be critical to displacing fungal pathogens that can proliferate after the use of some herbicides. Applications of glyphosate in particular, which compromises the plant defense system by interfering with the production of aromatic amino acids, are thought to promote a buildup of root pathogens and can result in a “greenbridge” between weeds or volunteers and crop hosts. By planting 2 to 3 weeks after spraying, growers can avoid most negative impacts of the greenbridge by allowing pathogen populations to decline, but with the added cost of delayed planting dates. However, the specific changes in microbial communities during this period of root death and the microbial taxa likely to be involved in displacing pathogens are poorly characterized. Using high-throughput sequencing, we characterized fungal and oomycete communities in roots after applications of herbicides with different modes of action (glyphosate or clethodim) and tracked their dynamics over 3 weeks in both naturally infested soil and soil inoculated with Rhizoctonia solani AG-8. We found that many unexpected taxa were present at high relative abundance (e.g., Pythium volutum and Myrmecridium species) in live and dying wheat roots and may play an under-recognized role in greenbridge dynamics. Moreover, communities were highly dynamic over time and had herbicide-specific successional patterns, but became relatively stable by 2 weeks after herbicide application. Network analysis of communities over time revealed patterns of interactions among taxa that were both common and unique to each herbicide treatment and identified two primary groups of taxa with many positive associations within-groups but negative associations between-groups, suggesting that these groups are antagonistic to one another in dying roots and may play a role in displacing pathogen populations during greenbridge dynamics.
The Multiple-Patient Simulation Toolkit: Purpose, Process, and Pilot
Authors: Beroz Sabrina , Sullivan Nancy , Kramasz Vanessa , Morgan Patricia
Published: December 2017

Educating nursing students to safely care for multiple patients has become an important but challenging focus for nurse educators. New graduate nurses are expected to manage care for multiple patients in a complex and multifaceted health care system. With patient safety as a priority, multiple-patient assignments are necessary in order for nursing students to learn how to effectively prioritize and delegate care. The purpose of this project was the construction of an adaptable and flexible template for the development of multiple-patient simulations. Through utilization, the template moved to a toolkit adding an operational guide, sample-populated template, and bibliography.
Exploring Truth, Justice, Compassion, Community, and Partnership While Learning to Care for Veterans Through Study, Reflection, and Action
Authors: Crary Pamela
Published: December 2017

This article describes an innovative elective nursing course developed and implemented in a private, liberal arts school of nursing grounded in Dominican values of study, reflection, and action. Course development, course content, and highlights and lowlights of the first cohort experience and implications for the community are discussed, along with background about veteran-centered care.
Critical Care Organizations: Building and Integrating Academic Programs
Authors: Moore Jason E. , Oropello John M. , Stoltzfus Daniel , Masur Henry , Coopersmith Craig M. , Nates Joseph , Doig Christopher , Christman John , Hite R. Duncan , Angus Derek C. , Pastores Stephen M. , Kvetan Vladimir
Published: December 2017

Objective:

Academic medical centers in North America are expanding their missions from the traditional triad of patient care, research, and education to include the broader issue of healthcare delivery improvement. In recent years, integrated Critical Care Organizations have developed within academic centers to better meet the challenges of this broadening mission. The goal of this article was to provide interested administrators and intensivists with the proper resources, lines of communication, and organizational approach to accomplish integration and Critical Care Organization formation effectively.

Design:

The Academic Critical Care Organization Building section workgroup of the taskforce established regular monthly conference calls to reach consensus on the development of a toolkit utilizing methods proven to advance the development of their own academic Critical Care Organizations. Relevant medical literature was reviewed by literature search. Materials from federal agencies and other national organizations were accessed through the Internet.

Setting:

The Society of Critical Care Medicine convened a taskforce entitled “Academic Leaders in Critical Care Medicine” on February 22, 2016 at the 45th Critical Care Congress using the expertise of successful leaders of advanced governance Critical Care Organizations in North America to develop a toolkit for advancing Critical Care Organizations.

Measurements and Main Results:

Key elements of an academic Critical Care Organization are outlined. The vital missions of multidisciplinary patient care, safety, and quality are linked to the research, education, and professional development missions that enhance the value of such organizations. Core features, benefits, barriers, and recommendations for integration of academic programs within Critical Care Organizations are described. Selected readings and resources to successfully implement the recommendations are provided. Communication with medical school and hospital leadership is discussed.

Conclusions:

We present the rationale for critical care programs to transition to integrated Critical Care Organizations within academic medical centers and provide recommendations and resources to facilitate this transition and foster Critical Care Organization effectiveness and future success.
APPLICATION OF OPTICAL COHERENCE TOMOGRAPHY ANGIOGRAPHY TO ASSESS ANTI–VASCULAR ENDOTHELIAL GROWTH FACTOR THERAPY IN MYOPIC CHOROIDAL NEOVASCULARIZATION
Authors: Cheng Ying , Li Ying , Huang Xin , Qu Yi
Published: December 2017

Purpose:

Using optical coherence tomography (OCT) angiography to assess the therapeutic effect of intravitreal anti–vascular endothelial growth factor on myopic choroidal neovascularization (CNV) by detecting the changes of shape, size, and flow area.

Methods:

Our prospective case series recruited consecutive patients with myopic CNV from January 2016 to August 2016. Intravitreal injections of ranibizumab were conducted on all patients. Patients received OCT angiography on 3 different follow-ups, including before treatment, 1 week after treatment, and 1 month after treatment. At each visit, we measured the best-corrected visual acuity, central macular thickness , greatest linear dimension of CNV, selected CNV area and flow area using OCT angiography.

Results:

This study involved 13 eyes of 12 patients, in which 9 eyes were of 9 women and 4 eyes were of 3 men, with mean age of 49.92 ± 14.79 years. Best-corrected visual acuity was significantly improved with decreased central macular thickness, greatest linear dimension, intraretinal fluid, or subretinal fluid 7 days or 30 days after treatment (All P < 0.05). Myopic CNV was presented as irregular or nearly round closed mass at the level of the outer retinal layer in all eyes at the initial visit. Thirty days after treatment, the size of selected CNV area and flow area were further decreased (t = 4.012, P = 0.003).

Conclusion:

Combined with OCT B-scan, OCT angiography, a new technique, could provide sensitive and intuitive images and quantitative analysis for monitoring and evaluating the therapeutic effect of intravitreal anti–vascular endothelial growth factor for myopic CNV.
Novel Image-Based Analysis for Reduction of Clinician-Dependent Variability in Measurement of the Corneal Ulcer Size
Authors: Patel Tapan P. , Prajna N Venkatesh , Farsiu Sina , Valikodath Nita G. , Niziol Leslie M. , Dudeja Lakshey , Kim Kyeong Hwan , Woodward Maria A.
Published: December 2017

Purpose:

To assess variability in corneal ulcer measurements between ophthalmologists and reduce clinician-dependent variability using semiautomated segmentation of the ulcer from photographs.

Methods:

Three ophthalmologists measured 50 patients' eyes for epithelial defects (EDs) and the stromal infiltrate (SI) size using slit-lamp (SL) calipers. SL photographs were obtained. An algorithm was developed for semiautomatic segmenting of the ED and SI in the photographs. Semiautomatic segmentation was repeated 3 times by different users (2 ophthalmologists and 1 trainee). Clinically significant variability was assessed with intraclass correlation coefficients (ICCs) and the percentage of pairwise measurements differing by ≥0.5 mm. Semiautomatic segmentation measurements were compared with manual delineation of the image by a corneal specialist (gold standard) using Dice similarity coefficients.

Results:

Ophthalmologists' reliability in measurements by SL calipers had an ICC from 0.84 to 0.88 between examiners. Measurements by semiautomatic segmentation had an ICC from 0.96 to 0.98. SL measures of ulcers by clinical versus semiautomatic segmentation measures differed by ≥0.5 mm in 24% to 38% versus 8% to 28% (ED height); 30% to 52% versus 12% to 34% (ED width); 26% to 38% versus 10% to 32% (SI height); and 38% to 58% versus 14% to 34% (SI width), respectively. Average Dice similarity coefficients between manual and repeated semiautomatic segmentation ranged from 0.83 to 0.86 for the ED and 0.78 to 0.83 for the SI.

Conclusions:

Variability exists when measuring corneal ulcers, even among ophthalmologists. Photography and computerized methods for quantifying the ulcer size could reduce variability while remaining accurate and impact quantitative measurement endpoints.
Unilateral Posterior Interstitial Keratitis as a Clinical Presentation of Herpes Simplex Virus Disease
Authors: Farooq Asim V. , Paley Grace L. , Lubniewski Anthony J. , Gonzales John A. , Margolis Todd P.
Published: December 2017

Purpose:

To describe a case series of patients with unilateral, posterior interstitial keratitis presumed to be caused by herpes simplex virus.

Methods:

Retrospective case series.

Results:

Five patients were found to have unilateral, posterior interstitial keratitis. Three of the involved eyes had decreased corneal sensation, and 2 eyes had corneal stromal neovascularization. All patients were treated with topical steroids and an oral antiviral, and among those with long-term follow-up, clinical improvement required treatment over an extended duration. A review of the literature revealed 1 reported case with a similar clinical appearance, although that case was attributed to Lyme disease.

Conclusions:

The clinical presentation of unilateral, posterior interstitial keratitis may be a rare manifestation of herpes simplex virus keratitis.
Influence of Sex and Previous Concussion History on Postconcussive Recovery in Young Athletes
Authors: Chand Manisha R. , Kanwar Sumit , Calvo Cecilia , Peck Evan
Published: December 2017

Objective:

To determine whether concussed female athletes with a previous history of concussion have longer postconcussive recovery than that of male counterparts.

Design:

Retrospective cohort study.

Setting:

Outpatient sports medicine clinic in an academic practice.

Participants:

Male and female youth, high school, and collegiate athletes (n = 431; ages = 10-21 years) who sustained a sport-related concussion (SRC).

Interventions:

The clinical courses of young athletes treated for concussion by 1 provider at an outpatient sports medicine clinic were retrospectively reviewed.

Main Outcome Measures:

Recovery time was compared after an SRC with relationship to sex and previous concussion history.

Results:

When comparing male and female athletes with a previous history of concussion, there were no differences found (P = 0.820) in SRC recovery time. Regardless of previous concussion history, males recovered faster from an SRC compared with their female counterparts (P = 0.0002). Without regard to sex, those with no previous history of concussion recovered faster than those with a previous concussion history, although the difference was not statistically significant (P = 0.668). Athletes with a previous history of concussion were more likely to require neuropsychology referral than those with no previous concussion history (P = 0.021), and females, without regard to concussion history, were more likely to require neuropsychology referral than males (P = 0.001).

Conclusions:

A previous concussion history does not appear to significantly influence postconcussive recovery time in young athletes, although it does increase the probability of neuropsychological referral. Without regard to a previous concussion history, young female athletes recover slower than males from concussion and are also more likely to require neuropsychological referral.
Clinical Presentation and Outcomes of Diagnostic Endoscopy in Newly Presenting Children With Gastrointestinal Symptoms
Authors: Wang Shuang , Younus Osman , Rawat David , Naik Sandhia , Giles Edward , Meadows Nigel , Croft Nicholas M.
Published: December 2017

Objectives:

Paediatric endoscopy is an important diagnostic tool; however, there is little published data to guide clinicians in selecting patients for endoscopy. This study aimed to evaluate a single centre's experience of newly presenting children focusing on presenting symptoms, investigations, and diagnostic yield.

Methods:

Clinical factors and endoscopic plus histological findings over a 6‐month period were assessed. Only first diagnostic endoscopies were included. All biopsies were reviewed in a weekly histopathology multidisciplinary team meeting with a final agreed outcome. Abnormal histology was used as the criterion standard for reporting abnormality.

Results:

A total of 218 endoscopies were reviewed in 164 children. Approximately 65% were histologically normal (49% of children had macroscopically and histologically normal findings). Macroscopic and histological abnormalities (respectively) were 44% and 28% of oesophagogastroduodenoscopy (OGD) patients, 25% and 25% of colonoscopy alone, and 53% and 53% of those undergoing both OGD and colonoscopy (OGD&Col). For OGD‐only patients, excluding those with raised anti‐tissue transglutaminase antibodies, vomiting led to the highest rate of abnormal histology (22%). For colonoscopy‐only and OGD&Col patients, per rectum bleeding led to the highest rates of abnormal histology (14% and 29%, respectively), after excluding those with laboratory abnormalities (anaemia and raised erythrocyte sedimentation rate) suggestive of inflammatory bowel disease.

Conclusions:

This study showed that half of all first diagnostic endoscopies in our unit had neither macroscopic nor histological abnormalities. There was discrepancy between macroscopic abnormalities and histological findings in OGD. Prospective studies are needed to develop guidelines in appropriately predicting abnormality and selecting patients for endoscopy.
Human Papillomavirus (HPV)-associated Lymphoepithelioma-like Carcinoma of the Vagina and Anal Canal: A Rare Variant of Squamous Cell Carcinoma
Authors: Scott Kerry , Trainor James , McVeigh Gerard , Jamison Jackie , Loughrey Maurice B. , Kelly Paul J. , McCluggage W. Glenn
Published: December 2017

Lymphoepithelioma-like carcinoma (LELC) is an uncommon variant of squamous cell carcinoma, which is histologically identical to lymphoepithelial carcinoma of the nasopharynx. LELCs have been reported at a variety of sites, including the stomach, salivary gland, thymus, cervix, endometrium, breast, skin, bladder, and lung. We report 2 LELCs of the vagina and 1 of the anal canal, the first report of LELC at the latter site. All 3 neoplasms were diffusely positive with p16 (block-type immunoreactivity) and the anal canal lesion contained high-risk human papillomavirus type 16; the 2 vaginal neoplasms underwent human papillomavirus testing but were unsuitable for analysis. All cases were Epstein-Barr virus negative. In reporting these cases, we highlight the potential for misdiagnosis and suggest an association with human papillomavirus infection similar to LELCs in the uterine cervix.
Capsular Biofilm Formation at the Interface of Textured Expanders and Human Acellular Dermal Matrix: A Comparative Scanning Electron Microscopy Study
Authors: Danino Michel A. , Efanov Johnny I. , Dimitropoulos Georges , Moreau Maxim , Maalouf Charles , Nelea Monica , Izadpanah Ali , Giot Jean-Philippe
Published: December 2017

Background:

Despite benefits in reducing capsular contractures, textured implants have been associated with significant pitfalls, such a propensity for biofilm formation. Few studies have investigated whether the use of acellular dermal matrix on textured implants produces similar findings. This study aims to characterize biofilm formation at the capsular–acellular dermal matrix interface with scanning electron microscopy.

Methods:

The authors performed a prospective observational pilot study in patients undergoing two-stage expander-to-permanent implant exchange. Patients were inflated with Biocell or Siltex expanders, and specimens from the capsular-pectoralis interface and capsular–acellular dermal matrix interface were obtained and examined under scanning electron microscopy for capsular ingrowth and biofilm formation using the Van Herdeen Biofilm Grading System and the Biofilm Thickness Grading Scale.

Results:

Nine patients including 14 breasts (28 capsular samples in total) were examined. Thick biofilm formation was observed in all specimens from the capsular–acellular dermal matrix interface with Biocell and 25 percent of capsule-pectoralis interface, whereas no biofilm formation was found in Siltex implants. For Biocell implants, a significant difference in biofilm coverage between the upper and lower poles was observed using the Van Herdeen Biofilm Grading System (p = 0.0028) and the Biofilm Thickness Grading Scale (p = 0.0161).

Conclusions:

Biocell implants produce a significant rate of biofilm formation over acellular dermal matrix–covered capsules, which is not present in the muscular region or in Siltex implants. Further randomized controlled trials will further elucidate the clinical impact of using acellular dermal matrices with macrotextured implants.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, IV.
Critical Differences between Microscopic (MIFE) and Macroscopic (MAFE) Fat Embolism during Liposuction and Gluteal Lipoinjection
Authors: Cárdenas-Camarena Lázaro , Durán Héctor , Robles-Cervantes José Antonio , Bayter-Marin Jorge Enrique
Published: December 2017

Background:

Liposuction and gluteal lipoinjection are two of the most frequent surgical procedures in body contouring surgery, and two of the most important complications are microscopic (MIFE) and macroscopic (MAFE) fat embolism. Despite a high index of morbidity and mortality, few reports exist about these complications, and although they have the same causal agent, their etiopathogenesis, clinical evolution, treatment, prognosis, and prevention are totally different. Therefore, the authors performed a comprehensive review of the literature to exhaustively analyze both pathologic conditions and present the differences between them.

Methods:

A detailed search was carried out in PubMed of studies on humans from 1946 to March of 2017 in any language and including the keywords microscopic fat embolism and macroscopic fat embolism with either liposuction or gluteal lipoinjection. The articles found were selected according to the search criteria and were analyzed to provide the final data and recommendations.

Results:

Of the 1245 and 26 articles that were found on complications related to liposuction and gluteal lipoinjection, respectively, only 41 on liposuction and microscopic fat embolism and seven on gluteal lipoinjection and microscopic fat embolism met the specific criteria for inclusion in the analysis. Only two articles on liposuction and two on gluteal lipoinjection referred to macroscopic fat embolism as a complication.

Conclusion:

Although microscopic fat embolism and macroscopic fat embolism are pathologic conditions with high morbidity and mortality rates in association with liposuction and gluteal lipoinjection, few reports about them exist; therefore, the authors made recommendations based on this study for their diagnosis, prevention, and treatment.
Comparison of Two Versions of the Hospital Anxiety and Depression Scale in Assessing Depression in a Neurologic Setting
Authors: Patel Viral P. , Feinstein Anthony
Published: December 2017

Background:

The Hospital Anxiety and Depression Scale–Depression Subscale (HADS-D) is widely used to assess depression in people with multiple sclerosis (MS). Developed specifically for use in a medical setting, the scale has one item, “I feel as if I am slowed down,” that might represent a significant somatic confounder, possibly biasing the assessment.

Objective:

We sought to determine whether inclusion or exclusion of the “slowed down” item in the HADS-D affects the detection of depression and the scale’s associations with impaired cognition, fatigue, and employment status.

Methods:

A sample of 193 people with confirmed MS completed the HADS. To identify depressed participants, we used previously established cutoff scores for the HADS-D with (≥8) and without (≥6) the “slowed down” item. Linear and logistic regression models were used to determine predictors of cognition and employment status.

Results:

The HADS-D with and without the “slowed down” item detected similar rates of depression: 30.6% and 31.6%, respectively. Both versions of the HADS-D predicted processing speed and executive functioning, but not memory. Neither version predicted employment status.

Conclusions:

The HADS-D is an easy-to-use and clinically relevant self-report psychometric scale for detecting depression in MS. Removing the “slowed down” item from the HADS-D does not influence its internal consistency, and both versions have similar associations with clinical outcomes.
Leftward Bias of Visual Attention in Patients with End-Stage Renal Disease Receiving Dialysis: A Neglected Phenomenon
Authors: Mańkowska Aleksandra , Heilman Kenneth M. , Williamson John B. , Biedunkiewicz Bogdan , Dębska-Ślizień Alicja , Harciarek Michał
Published: December 2017

Background and Objective:

Patients with end-stage renal disease (ESRD) who are receiving dialysis often have cognitive and behavioral changes, including impairments in sustained attention. Impairments in sustained attention appear to be the consequence of right hemisphere dysfunction. Right hemisphere brain networks are also important for the allocation of spatial attention. Therefore, the objective of this study was to learn whether patients with ESRD receiving dialysis might also have a spatial attentional bias.

Participants and Methods:

Eighteen nondemented patients with ESRD receiving dialysis but without any neurologic diseases (age range: 20 to 60 years) and 18 demographically matched healthy controls participated in this study. Participants performed a standard line bisection task using 24 horizontal lines (24 cm long and 2 mm thick) that were sequentially placed at eye level on a white board.

Results:

Patients receiving dialysis had a significantly greater leftward bias than healthy controls.

Conclusions:

Patients with ESRD receiving dialysis appear to have an impaired ability to correctly allocate their spatial attention (spatial neglect). Although the reason for the patients’ leftward bias needs to be elucidated, ESRD and/or dialysis may have induced right frontal-subcortical dysfunction that disinhibited the right parietal lobe, producing a left-sided attentional bias. Further studies are needed to test this hypothesis.
Organs and tissues of Rhynie chert plants
Authors: Kerp Hans
Published: December 2017

The Early Devonian Rhynie chert and the nearby Windyfield chert contain the oldestin situpreserved terrestrial ecosystem. Two of the seven species of anatomically preserved land plants had naked axes, one an axis with a more or less regular pattern of short-longitudinal ribs, two species had spiny axes and one species had small leaf-like appendages. All plants mainly consist of parenchymatous tissues. In some species, conducting elements comprise uniformly thickened thick-walled cells resembling hydroids of larger bryophytes, whereas others have real tracheids with annular and/or spiral secondary wall thickenings. True phloem has never been demonstrated but in all species the thick-walled water-conducting cells are encircled by a zone of thin-walled cells without intercellular spaces. The cortex is differentiated into two or three zones and forms the major part of the axes; in one species the cells of the middle cortex are sclerified. Some species have a hypodermis. In all species the epidermis is covered by a well-developed cuticle. Sporangia are known from all species. Sporangia are spindle-shaped, lobed or kidney-shaped and attached terminally or laterally with a short stalk. Gametophytes of four species have been described. Gametophytes are unisexual, isomorphic but much smaller than the sporophytes.

This article is part of a discussion meeting issue ‘The Rhynie cherts: our earliest terrestrial ecosystem revisited’.
Evolution and palaeophysiology of the vascular system and other means of long-distance transport
Authors: Raven John A.
Published: December 2017

Photolithotrophic growth on land using atmospheric CO2inevitably involves H2O vapour loss. Embryophytes greater than or equal to 100 mm tall are homoiohydric and endohydric with mass flow of aqueous solution through the xylem in tracheophytes. Structural details in Rhynie sporophytes enable modelling of the hydraulics of H2O supply to the transpiring surface, and the potential for gas exchange with the Devonian atmosphere. Xylem carrying H2O under tension involves programmed cell death, rigid cell walls and embolism repair; fossils provide little evidence on these functions other than the presence of lignin. The phenylalanine ammonia lyase essential for lignin synthesis came from horizontal gene transfer. Rhynie plants lack endodermes, limiting regulation of the supply of soil nutrients to shoots. The transfer of organic solutes from photosynthetic sites to growing and storage tissues involves mass flow through phloem in extant tracheophytes. Rhynie plants show little evidence of phloem; possible alternatives for transport of organic solutes are discussed. Extant examples of the arbuscular mycorrhizas found in Rhynie plants exchange soil-derived nutrients (especially P) for plant-derived organic matter, involving bidirectional mass flow along the hyphae. The aquatic cyanobacteria and the charaleanPalaeonitellaat Rhynie also have long-distance (relative to the size of the organism) transport.

This article is part of a discussion meeting issue ‘The Rhynie cherts: our earliest terrestrial ecosystem revisited’.
Exploring the geochemical distribution of organic carbon in early land plants: a novel approach
Authors: Abbott Geoffrey D. , Fletcher Ian W. , Tardio Sabrina , Hack Ethan
Published: December 2017

Terrestrialization depended on the evolution of biosynthetic pathways for biopolymers including lignin, cutin and suberin, which were concentrated in specific tissues, layers or organs such as the xylem, cuticle and roots on the submillimetre scale. However, it is often difficult, or even impossible especially for individual cells, to resolve the biomolecular composition of the different components of fossil plants on such a scale using the well-established coupled techniques of gas chromatography/mass spectrometry and liquid chromatography/mass spectrometry. Here, we report the application of techniques for surface analysis to investigate the composition of
Rhynia gwynne-vaughanii
. X-ray photoelectron spectroscopy of two different spots (both 300 µm × 600 µm) confirmed the presence of carbon. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) revealed ‘chemical maps’ (imaging mode with 300 nm resolution) of aliphatic and aromatic carbon in the intact fossil that correlate with the vascular structures observed in high-resolution optical images. This study shows that imaging ToF-SIMS has value for determining the location of the molecular components of fossil embryophytes while retaining structural information that will help elucidate how terrestrialization shaped the early evolution of land plant cell wall biochemistry.

This article is part of a discussion meeting issue ‘The Rhynie cherts: our earliest terrestrial ecosystem revisited’.
Performance of serological antibody tests for bovine tuberculosis in cattle from infected herds in Northern Ireland
Authors: McCallan L. , Brooks C. , Couzens C. , Young F. , Byrne A.W. , McNair J.
Published: December 2017

The ability to accurately identify infected hosts is the cornerstone of effective disease control and eradication programs. In the case of bovine tuberculosis, caused by infection with the pathogenMycobacterium bovis, accurately identifying infected individual animals has been challenging as all available tests exhibit less than 100% discriminatory ability. Here we assess the utility of three serological tests and assess their performance relative to skin test (Single Intradermal Comparative Cervical Tuberculin; SICCT), gamma-interferon (IFNγ) and post-mortem results in a Northern Ireland setting. Furthermore, we describe a case-study where one test was used in conjunction with statutory testing.

Serological tests using samples taken prior to SICCT disclosed low proportions of animals as test positive (mean 3% positive), despite the cohort having high proportions with positive SICCT test under standard interpretation (121/921; 13%) or IFNγ (365/922; 40%) results. Furthermore, for animals with a post-mortem record (n=286), there was a high proportion with TB visible lesions (27%) or with laboratory confirmed infection (25%). As a result, apparent sensitivities within this cohort was very low (≤15%), however the tests succeeded in achieving very high specificities (96-100%). During the case-study, 7/670 (1.04%) samples from SICCT negative animals from a large chronically infected herd were serology positive, with a further 10 animals being borderline positive (17/670; 2.54%). 9/17 of these animals were voluntarily removed, none of which were found to be infected (-lesions/-bacteriology) post-mortem; 1 serology test negative animal was subsequently lesion+ andM bovisconfirmed at slaughter.

Importance

Eradication of bovine tuberculosis (bTB; caused byMycobacterium bovis) has remained elusive in a number of countries despite long-term coordinated test and cull programs. This can partially be explained by the limitations of available statutory tests; therefore supplementary test platforms that identify additional infected animals would be of significant utility. Overall, during our study three serological tests did not disclose a high proportion of animals as infected in high-risk cattle herds, and exhibited limited ability to disclose animals that were positive to the statutory skin test, the gamma interferon test (IFNγ), or were post-mortem confirmed withM. bovis. These serological tests could be used in a supplementary fashion to the statutory tests in particular circumstances; but may be of limited advantage where parallel use of IFNγ and skin testing is performed, as these tests together tended to disclose the majority of animals with post-mortem evidence of infection in our study cohort.
ACI-1 class A beta-lactamase is widespread across human gut microbiomes due to transposons harboured by tailed prophages
Authors: Rands Chris M , Starikova Elizaveta V , Brüssow Harald , Kriventseva Evgenia V , Govorun Vadim M , Zdobnov Evgeny M
Published: December 2017

Antibiotic resistance is increasing among pathogens at unprecedented rates and the human body contains a large pool of antibiotic resistance genes that can be spread among bacteria by mobile genetic elements. Acidaminococcus intestini, a bacterium found in the human gut that belongs to the class of Negativicutes, is the first gram-negative coccus shown to be resistant to beta-lactam antibiotics. Resistance is conferred by aci1, a gene encoding the ACI-1 class A beta-lactamase, but the evolutionary history of aci1 and its distribution across other Negativicutes and in the human gut microbiota remains obscure. We discovered that ACI-1 proteins are phylogenetically distinct from class A beta-lactamases of gram-positive Firmicutes and that the aci1 gene occurs in bacteria scattered across the Negativicutes clade, suggesting possible mobilization. In the reference A. intestini RyC-MR95 strain, we found that aci1 is surrounded by mobile DNA, transposon derived sequences directly flank aci1 and are likely the vehicle for its mobility. These transposon sequences reside within a prophage context consisting of two likely degraded tailed prophages, the first prophages to be characterised in A. intestini. We found aci1 in at least 56 (4.4%) out of 1,267 human gut metagenome samples, mostly hosted within A. intestini, and, where could be determined, mostly within a similar constellation of mobile elements to that found in the reference A. intestini genome. These human samples are from individuals in Europe, China and the USA, showing that aci1 is widely distributed globally. Additionally, we examined the nine different Negativicute genome assemblies that contain aci1, and found that only two of these strains show a similar mobile element context around aci1 to the reference A. intestini with transposons adjacent to a tailed prophage. However, in all nine cases aci1 is flanked by transposon derived sequences, and these sequences are diverse, suggesting the activity and degradation of multiple transposons. Overall, we show that ACI-1 proteins form a distinct class A beta lactamase family, and that the aci1 gene is present in human guts worldwide within Negativicute bacterial hosts, due to transposons, sometimes inserted into tailed prophages.
A potential link between gambling addiction severity and central dopamine levels – evidence from spontaneous eye blink rates in gamblers and controls
Authors: Mathar David , Wiehler Antonius , Chakroun Karima , Goltz Dominique , Peters Jan
Published: December 2017

Accumulating evidence points at similarities between substance use disorders and pathological gambling on the behavioral and neural level. In substance addiction, dysregulation of striatal dopamine transmission has been consistently revealed. Due to the neurotoxicity of stimulating substances, it is still debated if this constitutes mainly a consequence of recurrent substance abuse or a vulnerability marker for addiction disorders. For gambling addiction, no clear association with striatal dopamine levels has been unveiled so far. With its presumably negligible dopaminergic toxicity, possible differences in striatal dopamine transmission in gambling addiction might therefore constitute a vulnerability marker.

Spontaneous eye blink rate (sEBR) is controversially discussed as a potential proxy measure for striatal dopamine levels. Here we examined sEBR in 21 male problem gamblers and 20 healthy control participants. In addition, participants completed a screening questionnaire for overall psychopathology and self-reported measures of alcohol and nicotine consumption. We found no significant difference in sEBR between gamblers and controls. However, in gamblers, sEBR was negatively associated with addiction severity and positively associated with psychopathology. A final exploratory analysis revealed that healthy controls with low sEBR displayed higher alcohol and nicotine consumption than healthy participants with high sEBR. Although the association between dopamine transmission and sEBR is still debated, our findings reveal that sEBR is sensitive to inter-individual differences in addiction severity in problem gamblers.
Identifying (un)controllable dynamical behavior in complex networks
Authors: Rozum Jordan C , Albert Réka
Published: December 2017

We present a technique applicable in any dynamical framework to identify control-robust subsets of an interacting system. These robust subsystems, which we call stable modules, are characterized by constraints on the variables that make up the subsystem. They are robust in the sense that if the defining constraints are satisfied at a given time, they remain satisfied for all later times, regardless of what happens in the rest of the system, and can only be broken if the constrained variables are externally manipulated. We identify stable modules as graph structures in an expanded network, which represents causal links between variable constraints. A stable module represents a system “decision point”, or trap subspace. Using the expanded network, small stable modules can be composed sequentially to form larger stable modules that describe dynamics on the system level. Collections of large, mutually exclusive stable modules describe the system’s repertoire of long-term behaviors. We implement this technique in a broad class of dynamical systems and illustrate its practical utility via examples and algorithmic analysis of two published biological network models. In the segment polarity gene network of Drosophila melanogaster, we obtain a state-space visualization that reproduces by novel means the four possible cell fates and predicts the outcome of cell transplant experiments. In the T-cell signaling network, we identify six signaling elements that determine the high-signal response and show that control of an element connected to them cannot disrupt this response.

Author summary

We show how to uncover the causal relationships between qualitative statements about the values of variables in ODE systems. We then show how these relationships can be used to identify subsystem behaviors that are robust to outside interventions. This informs potential system control strategies (e.g., in identifying drug targets). Typical analytical properties of biomolecular systems render them particularly amenable to our techniques. Furthermore, due to their often high dimension and large uncertainties, our results are particularly useful in biomolecular systems. We apply our methods to two quantitative biological models: the segment polarity gene network of Drosophila melanogaster and the T-cell signal transduction network.
Gratings for synchrotron and FEL beamlines: a project for the manufacture of ultra-precise gratings at Helmholtz Zentrum Berlin
Authors: Siewert F. , Löchel B. , Buchheim J. , Eggenstein F. , Firsov A. , Gwalt G. , Kutz O. , Lemke St. , Nelles B. , Rudolph I. , Schäfers F. , Seliger T. , Senf F. , Sokolov A. , Waberski Ch. , Wolf J. , Zeschke T. , Zizak I. , Follath R. , Arnold T. , Frost F. , Pietag F. , Erko A.
Published: December 2017

Blazed gratings are of dedicated interest for the monochromatization of synchrotron radiation when a high photon flux is required, such as, for example, in resonant inelastic X-ray scattering experiments or when the use of laminar gratings is excluded due to too high flux densities and expected damage, for example at free-electron laser beamlines. Their availability became a bottleneck since the decommissioning of the grating manufacture facility at Carl Zeiss in Oberkochen. To resolve this situation a new technological laboratory was established at the Helmholtz Zentrum Berlin, including instrumentation from Carl Zeiss. Besides the upgraded ZEISS equipment, an advanced grating production line has been developed, including a new ultra-precise ruling machine, ion etching technology as well as laser interference lithography. While the old ZEISS ruling machine GTM-6 allows ruling for a grating length up to 170 mm, the new GTM-24 will have the capacity for 600 mm (24 inch) gratings with groove densities between 50 lines mm−1 and 1200 lines mm−1. A new ion etching machine with a scanning radiofrequency excited ion beam (HF) source allows gratings to be etched into substrates of up to 500 mm length. For a final at-wavelength characterization, a new reflectometer at a new Optics beamline at the BESSY-II storage ring is under operation. This paper reports on the status of the grating fabrication, the measured quality of fabricated items by ex situ and in situ metrology, and future development goals.
Separation of superimposed images with subpixel shift
Authors: Jailin Clément , Poncelet Martin , Roux Stéphane
Published: December 2017

The problem of the separation of superimposed images is considered in the particular case of a steady background and a foreground that is composed of different patterns separated in space, each with a compact support. Each pattern of the foreground may move in time independently. A single pair of these superimposed images is assumed to be available, and the displacement amplitude is typically smaller than the pixel size. Further, assuming that the background is smoothly varying in space, an original algorithm is proposed. To illustrate the performance of the method, a real test case of X-ray tomographic radiographs with moving patterns due to dust particles or surface scratches of optical elements along the beam is considered. Finally an automatic and simple treatment is proposed to erase the effects of such features.
Access over ownership: meeting facilities in Lyngby-Taarbæk Knowledge City
Authors: Nielsen Susanne Balslev , Brinkø Rikke
Published: December 2017

Purpose

This study aims to investigate the attitude towards shared space in an urban context with a particular focus on meeting facilities. The Lyngby-Taarbæk City of Knowledge is used as a case, as this organisation has a vision of sharing facilities to stimulate regional development.

Design/methodology/approach

The attitude towards shared space in the Lyngby-Taarbæk City of Knowledge is studied in a three-step qualitative research process. An initial survey investigated the City of Knowledge’s members’ attitude towards shared space in general, a workshop further explored motivations and practical needs and a second survey investigated the attitude towards shared meeting facilities. The Brinkø Typology of Shared Use of Space and Facilities is used as the theoretical framework for the study (Brinkø et al., 2015).

Findings

This study shows that the respondents are very positive towards the concept of shared space but more reluctant when it comes to sharing own facilities. A majority of the informants are often using externally owned facilities for meetings and events and prefer professional meeting facilities to schools, universities and sports facilities. This points to a need for developing relevant service concepts, if a shared space strategy with focus on meeting facilities were to be used to increase the use rate of existing buildings not already intended for this use.

Originality/value

This study adds to the so far limited amount of scientific knowledge on the topic of shared space, by investigating the attitude towards shared space among a specific group of people, in relation to the use of external meeting facilities.