bluuebunny/crossref_metadata_2025 huggingface dataset:
An Anatomical Murine Model of Heterotopic Periorbital Subunit Transplantation
Authors: Gao Bowen , Yu Qingxiong , Xie Feng , Sheng Lingling , Mao Xiyuan , Li Qingfeng , Zhu Hainan
Published: October 2016

Background:

Conventional reconstructive methods fail to achieve satisfactory results in total eyelid defect cases. Vascularized composite tissue allotransplantation might provide both good appearance and function for these patients. The structure of the eyelid is exceptional because it simultaneously consists of skin, connective tissue, the striated muscle, fiber structure, aponeuroses, and mucosa. Thus, before clinical application of eyelid allotransplantation, more experiments are needed to clarify the impact of ischemia, immunal suppressive agents, and deinnervation effects on these sophisticated structures. We developed an heterotopic periorbital transplantation model in rats to facilitate further experiment in this field.

Methods:

Twenty-five inbred male Lewis rats were used for anatomy study (n=10), and as donors or recipients of the operations (n=10). In the anatomy study, the vascular distribution and innervation to the periorbital unit was identified and recorded. Then, according to the anatomy study, 10 heterotopic transplantations and 2 transplantations with pedicle ligated were performed. The posterior facial vein and the external carotid artery are selected as the graft pedicle. All transplanted eyelids were assessed daily. Micro-CT scanning and hematoxylin and eosin staining of the grafts were performed 60 days after the operation.

Results:

All recipients tolerated the operation well. All grafts without pedicles ligated survived and new hair growth was observed. All of the transplanted eyelids were pink and pliable during the entire observation period, and we did not observe any signs of arterial or venous occlusion. In the recipients with graft pedicle ligated, the grafts were necrosed and mummified within 4 to 5 days. MicroCT of the survived grafts showed good blood supply and histologic staining revealed normal histologic morphologies.

Conclusions:

Our study proved the anatomical feasibility of periorbital transplantation by establishing a heterotopic transplantation model, which might facilitate future eyelid allotransplantation-related experiments.
Haemostatic resuscitation in trauma: the next generation
Authors: Stensballe Jakob , Ostrowski Sisse R. , Johansson Pär I.
Published: October 2016

Purpose of review

To discuss the recent developments in and evolvement of next generation haemostatic resuscitation in bleeding trauma.

Recent findings

Mortality from major trauma is a worldwide problem, and massive haemorrhage remains a major cause of potentially preventable deaths. Development of coagulopathy further increases trauma mortality emphasizing that coagulopathy is a key target in the phase of bleeding. The pathophysiology of coagulopathy in trauma reflects at least three distinct mechanisms that may be present isolated or coexist: acute traumatic coagulopathy, coagulopathy associated with the lethal triad, and consumptive coagulopathy. The concepts of ‘damage control surgery’ and ‘damage control resuscitation’ have been developed to ensure early control of bleeding and coagulopathy to improve outcome in bleeding trauma. Haemostatic resuscitation aims at controlling coagulopathy and consists of a ratio driven strategy aiming at 1 : 1 : 1, using tranexamic acid according to CRASH-2, and applying haemostatic monitoring enabling a switch to a goal-directed approach when bleeding slows. Haemostatic resuscitation is the mainstay of trauma resuscitation and is associated with improved survival.

The next generation of haemostatic resuscitation aims at applying a ratio 1 : 1 : 1 driven strategy while using antifibrinolytics, haemostatic monitoring and avoiding critical fibrinogen deficiency by substitution.
Advanced extracorporeal therapy in trauma
Authors: Zonies David , Merkel Matthias
Published: October 2016

Purpose of review

The purpose is to review the current application of extracorporeal life support (ECLS) in trauma patients. In addition, programmatic development is described.

Recent findings

ECLS use is increasing among trauma patients. Several recent studies among trauma patients report survival rates of 65–79%. Despite the high bleeding risk, extracorporeal membrane oxygenation (ECMO) may be safely implemented in trauma patients based on a strict protocol-driven policy. Early implementation may improve overall outcomes. Alternative anticoagulants and heparin free periods may be well tolerated in trauma patients at high risk of hemorrhage.

ECMO is becoming a more routine option in severely injured trauma patients that develop severe respiratory failure. Well tolerated implementation and program development is possible among regional trauma centers. Although clinical knowledge gaps exist, ECMO is a promising treatment in this high-risk population.
Interferon-based hepatitis C therapy in a safety net hospital: access, efficacy, and safety
Authors: Nordstrom Eric M. , Keniston Angela , Baouchi Fafa , Martinez-Camacho Alvaro
Published: October 2016

Aims

This study assesses the efficacy, accessibility, and safety of hepatitis C virus (HCV) treatment in a safety net hospital population.

Methods

Patients at Denver Health receiving pegylated interferon for HCV infection between 2008 and 2012 were included in this retrospective study. Sociodemographic, biochemical, and virologic data were collected on each patient. The primary outcomes were the rate of sustained virologic response and early treatment discontinuation, with reason for discontinuation documented. Multivariable analyses were performed to identify factors associated with the primary outcomes.

Results

Detectable HCV antibodies were found in 2912 patients, and 1630 had a detectable viral load. Eighty percent of these patients were uninsured/underinsured. Only 46% were seen in the hepatology clinic, and 8% received interferon-based HCV treatment. Of the 125 patients treated with interferon-containing regimens, 54% had genotype 1 infection. The overall rate of sustained virologic response (SVR) was 47%. Rapid virologic response, low FIB-4 score combined with age, and increasing number of days on therapy were associated with SVR in multivariable analysis. Therapy was prematurely discontinued in 43% of patients related to being lost to follow-up (30%), null response (24%), and intolerance to pegylated interferon/ribavirin (24%). Genotype 1 infection and unfavorable viral kinetics were associated with premature treatment discontinuation in multivariable analysis. There were no statistically significant associations between age, sex, ethnicity, race, diabetes, BMI, psychiatric comorbidities, income, employment status, homelessness, or insurance status and the primary outcomes.

Conclusion

An acceptable SVR rate is achievable in a safety net patient population. Addressing the barriers to care will be paramount when using direct-acting antivirals.
Preliminary Study of a Caregiver‐based Infant and Child Feeding and Swallowing Screening Tool
Authors: Barkmeier‐Kraemer Julie M. , Linn Chris , Thompson Heather L. , Byrd Robert S. , Steinfeld Mary B. , Hoffmann Raymond G. , Silverman Alan H.
Published: October 2016

Objectives:

The Infant and Child Feeding Questionnaire (ICFQ) was created to facilitate early detection of feeding and swallowing problems. This is achieved by promoting effective communication between caregivers and health care providers resulting in referral for evaluation and treatment of feeding and swallowing problems by specialists. The purpose of this pilot study was to determine whether items from the ICFQ could be used to screen for differences between children with known feeding problems (FP) and without known feeding problems (NFP).

Methods:

Caregivers of children ages 36 months or younger with FP and NFP were recruited to complete the ICFQ and demographic questions. T tests were completed to compare demographic characteristics of the research groups. Responses to ICFQ items were analyzed using receiver operating characteristic analysis and odds ratios to determine whether questionnaire items distinguished between study groups.

Results:

Sixty‐four caregivers of children with FP and 57 caregivers of NFP children were recruited. Three participants in the NFP group did not meet inclusion criteria and were excluded from analysis. A combination of 4 ICFQ questions distinguished between groups (receiver operating characteristic = 0.974). Significant odds ratios were also found for 9 feeding behaviors that distinguished between groups.

Conclusions:

A subset of items from the ICFQ showed promise for distinguishing FP from NFP groups. Future work will expand the regional representation of the participant samples and obtain equal representation of participants across all age‐adjusted questionnaires to determine whether the same combination of ICFQ items continues to distinguish between FP and NFP groups.
Rectal Suction Biopsy in Patients With Previous Anorectal Surgery for Hirschsprung Disease
Authors: Vadva Zareen , Nurko Samuel , Hehn Rebecca , Vargas Sara O.
Published: October 2016

Objectives:

The aim of the study was to determine rates of histologically positive, negative, and inconclusive rectal suction biopsies in post‐pull‐through patients with Hirschsprung disease evaluated for potential residual aganglionosis at our institution and to determine how patients were managed after a post‐pull‐through rectal suction biopsy.

Methods:

Thirty‐nine post‐pull‐through suction biopsies from our institution were reviewed. Samples, stained with H&E and often acetylcholinesterase and/or calretinin, were categorized as “histologically” positive, negative, or inconclusive for aganglionosis. Subsequent clinical action was categorized as bowel resection, no further procedure, or rebiopsy. Agreement between histologic diagnosis and clinical action was assessed.

Results:

Histologically, all biopsies were inconclusive (46%) or negative (54%) for residual aganglionosis. Postbiopsy clinical action included redo pull‐through (5%), no further procedure (59%), or rebiopsy (36%). Rebiopsy was sought in 2 of 21 histologically negative patients and in only 12 of 18 histologically indeterminate patients. Eventual redo pull‐through procedures in 6 of 39 patients showed 4 with residual aganglionosis and 2 with abnormalities suggesting residual “transition zone.”

Conclusions:

Our findings show that suction biopsy after pull‐through was frequently histologically indeterminate and never definitively positive for residual aganglionosis. When biopsy was histologically indeterminate, rebiopsy was pursued less commonly than may be expected. Our findings emphasize that suction biopsy examination is not a “criterion standard” for residual aganglionosis, but instead a component of a diagnosis that ultimately combines clinicopathologic factors, the constellation of which can sometimes spare patients from a more invasive full‐thickness biopsy.
Controversies in Persistent (Chronic) Lyme Disease
Authors: Maloney Elizabeth L.
Published: October 2016

The Centers for Disease Control and Prevention estimates that more than 300 000 new cases of Lyme disease occur each year in the United States and that 10% to 20% of these patients will remain symptomatic despite receiving appropriate antibiotic therapy. Many elements of the disease are poorly understood and have generated considerable controversy. This paper discusses the medical controversies related to posttreatment manifestations and their potential impact on infusion nurses.
Amniotic Fluid Embolism
Authors: Sundin Courtney Stanley , Mazac Lauren Bradham
Published: October 2016

Amniotic fluid embolism (AFE) is a rare but serious and potentially deadly complication of pregnancy that is unpreventable and unpredictable. Most AFE events occur during labor; however, approximately one third happen during the immediate postpartum period. Presentation is abrupt and thought to be an abnormal response to fetal materials entering maternal circulation through the placental insertion site. Care providers must recognize the signs and symptoms of AFE and react quickly to treat potential complications. This can be challenging as there are no set diagnostic criteria or specific laboratory tests. Generally, the diagnosis is based on clinical status when the classic triad of hypoxia, hypotension, and subsequent coagulopathy are noted in a laboring woman or woman who just gave birth, and no other plausible explanation can be determined. Proper treatment of AFE requires a multidisciplinary approach to decrease maternal morbidity and mortality. Knowledge, simulation, and familiarization of a Massive Obstetric Transfusion protocol can help all members of the perinatal team recognize and respond to women with AFE in a timely and effective manner. A case study is presented of a woman with a seemingly normal obstetric course that became complicated rapidly following development of an AFE.
Late Recognition of a Case of Oculo-Auriculo-Vertebral Spectrum
Authors: El Mansoury Jeylan , Mbekeani Joyce N.
Published: October 2016

Purpose

To report the late recognition of a case oculo-auriculo-vertebral spectrum (OAVS).

Case Report

A 14-year-old male patient with a history of spinal scoliosis and anal atresia presented with a right ocular growth that was increasing in size and causing irritation. He was discovered to have a right limbal dermoid and forniceal lipodermoid. All visual functions were normal and the rest of the anterior and posterior segments were unremarkable. External examination revealed facial asymmetry and ipsilateral hemifacial microsomia and a pre-auricular skin tag. A diagnosis of oculo-auriculo-vertebral spectrum (OAVS) or Goldenhar syndrome was made.

Conclusions

Growth of a limbal dermoid helped identify oculo-auriculo-vertebral spectrum, a disorder with a wide phenotypic spectrum that can affect all systems. Early recognition and syndromic designation is imperative; full pediatric survey of suspected cases will help rule out the life-threatening manifestations of the spectrum.
Distinguishing Between Hepatosplenic T-cell Lymphoma and γδ T-cell Large Granular Lymphocytic Leukemia
Authors: Yabe Mariko , Medeiros L. Jeffrey , Wang Sa A. , Tang Guilin , Bueso-Ramos Carlos E. , Jorgensen Jeffrey L. , Bhagat Govind , Chen Weina , Li Shaoying , Young Ken H. , Miranda Roberto N.
Published: October 2016

Hepatosplenic T-cell lymphoma (HSTCL) is a rare, aggressive T-cell lymphoma that can be challenging to diagnose. In particular, distinguishing HSTCL from T-cell large granular lymphocytic (T-LGL) leukemia of γδ T-cell receptor (TCR) type is difficult without examination of a splenectomy specimen. In this study, we systematically assessed a series of HSTCL cases for findings reported in the literature as supporting or not supporting the diagnosis of HSTCL. We also compared HSTCL with a group of cases of T-LGL of γδ TCR type. Criteria assessed in this study included: B-symptoms, massive splenomegaly, lymphadenopathy, extranodal involvement, peripheral lymphocytosis, lymphoma cells that expand bone marrow sinuses, lymphocyte azurophilic granules, immunophenotype, evidence of infection by Epstein-Barr virus, human immunodeficiency virus, or human T-cell leukemia virus type 1, isochromosome 7q, trisomy 8, and TCR gene rearrangement status. On the basis of the data of this study, we conclude that massive splenomegaly, bone marrow sinusoidal expansion by lymphoma cells, and lymphocytes devoid of azurophilic granules were significantly more common in HSTCL patients than in γδ T-LGL patients (P<0.0001), and these features help support the diagnosis of HSTCL.
The Incidence of Acute Kidney Injury and Its Effect on Neonatal and Pediatric Extracorporeal Membrane Oxygenation Outcomes: A Multicenter Report From the Kidney Intervention During Extracorporeal Membrane Oxygenation Study Group
Authors: Fleming Geoffrey M. , Sahay Rashmi , Zappitelli Michael , King Eileen , Askenazi David J. , Bridges Brian C. , Paden Matthew L. , Selewski David T. , Cooper David S.
Published: October 2016

Objective:

In a population of neonatal and pediatric patients on extracorporeal membrane oxygenation; to describe the prevalence and timing of acute kidney injury utilizing a consensus acute kidney injury definition and investigate the association of acute kidney injury with outcomes (length of extracorporeal membrane oxygenation and mortality).

Design:

Multicenter retrospective observational cohort study.

Setting:

Six pediatric extracorporeal membrane oxygenation centers.

Patients:

Pediatric patients (age, < 18 yr) on extracorporeal membrane oxygenation at six centers during a period of January 1, 2007, to December 31, 2011.

Interventions:

None.

Measurements and Main Results:

Complete data were analyzed for 832 patients on extracorporeal membrane oxygenation. Sixty percent of patients had acute kidney injury utilizing the serum creatinine Kidney Disease Improving Global Outcomes criteria (AKISCr) and 74% had acute kidney injury using the full Kidney Disease Improving Global Outcomes criteria including renal support therapy (AKISCr + RST). Of those who developed acute kidney injury, it was present at extracorporeal membrane oxygenation initiation in a majority of cases (52% AKISCr and 65% AKISCr + RST) and present by 48 hours of extracorporeal membrane oxygenation support in 86% (AKISCr) and 93% (AKISCr + RST). When adjusted for patient age, center of support, mode of support, patient complications and preextracorporeal membrane oxygenation pH, the presence of acute kidney injury by either criteria was associated with a significantly longer duration of extracorporeal membrane oxygenation support (AKISCr, 152 vs 110 hr; AKISCr + RST, 153 vs 99 hr) and increased adjusted odds of mortality at hospital discharge (AKISCr: odds ratio, 1.77; 1.22–2.55 and AKISCr + RST: odds ratio, 2.50; 1.61–3.90). With the addition of renal support therapy to the model, acute kidney injury was associated with a longer duration of extracorporeal membrane oxygenation support (AKISCr, 149 vs 121 hr) and increased risk of mortality at hospital discharge (AKISCr: odds ratio, 1.52; 1.04–2.21).

Conclusion:

Acute kidney injury is present in 60–74% of neonatal-pediatric patients supported on extracorporeal membrane oxygenation and is present by 48 hours of extracorporeal membrane oxygenation support in 86–93% of cases. Acute kidney injury has a significant association with increased duration of extracorporeal membrane oxygenation support and increased adjusted odds of mortality at hospital discharge.
A Novel Electrocardiogram Algorithm Utilizing ST-Segment Instability for Detection of Cardiopulmonary Arrest in Single Ventricle Physiology: A Retrospective Study
Authors: Vu Eric L. , Rusin Craig G. , Penny Dan J. , Kibler Kathy K. , Easley Ronald Blaine , Smith Brendan , Andropoulos Dean , Brady Ken
Published: October 2016

Objective:

We evaluated ST-segment monitoring to detect clinical decompensation in infants with single ventricle anatomy. We proposed a signal processing algorithm for ST-segment instability and hypothesized that instability is associated with cardiopulmonary arrests.

Design:

Retrospective, observational study.

Setting:

Tertiary children’s hospital 21-bed cardiovascular ICU and 36-bed step-down unit.

Patients:

Twenty single ventricle infants who received stage 1 palliation surgery between January 2013 and January 2014. Twenty rapid response events resulting in cardiopulmonary arrests (arrest group) were recorded in 13 subjects, and nine subjects had no interstage cardiopulmonary arrest (control group).

Interventions:

None.

Measurements and Main Results:

Arrest data were collected over the 4-hour time window prior to cardiopulmonary arrest. Control data were collected from subjects with no interstage arrest using the 4-hour time window prior to cardiovascular ICU discharge. A paired subgroup analysis was performed comparing subject 4-hour windows prior to arrest (prearrest group) with 4-hour windows prior to discharge (postarrest group). Raw values of ST segments were compared between groups. A 3D ST-segment vector was created using three quasi-orthogonal leads (II, aVL, and V5). Magnitude and instability of this continuous vector were compared between groups. There was no significant difference in mean unprocessed ST-segment values in the arrest and control groups. Utilizing signal processing, there was an increase in the ST-vector magnitude (p = 0.02) and instability (p = 0.008) in the arrest group. In the paired subgroup analysis, there was an increase in the ST-vector magnitude (p = 0.05) and instability (p = 0.05) in the prearrest state compared with the postarrest state prior to discharge.

Conclusions:

In single ventricle patients, increased ST instability and magnitude were associated with rapid response events that required intervention for cardiopulmonary arrest, whereas conventional ST-segment monitoring did not differentiate an arrest from control state.
Feasibility Study of an Optical Caustic Plasmonic Light Scattering Sensor for Human Serum Anti-Dengue Protein E Antibody Detection
Authors: Garcia A.A. , Franco L.S. , Pirez-Gomez M.A. , Pech-Pacheco J.L. , Mendez-Galvan J.F. , Machain-Williams C. , Talavera-Aguilar L. , Espinosa-Carrillo J.H. , Duarte-Villaseñor M.M. , Be Ortiz Ch.J. , Espinosa de los Monteros L.E. , Castillo-Pacheco A. , García-Rejon J.E. , Chavez B
Published: October 2016

Antibody detection and accurate diagnosis of tropical diseases is essential to help prevent the spread of disease. However, most detection methods lack cost-effectiveness and field-portability, which are essential features for achieving diagnosis in a timely manner in developing countries. To address this problem, transparent 3D printed sample chambers with a total volume of 700 microliters and an oblate spheroid shape were fabricated to measure green light scattering of gold nanoparticles using an optical caustic focus to detect antibodies. Scattering signals from 90 degree scattering of 20, 40, 50, 60, 80, 100, and 200 nm gold nanoparticles using a green laser and standard quartz cuvette were compared to the scattering signals from a green LED light source with an oblate spheroid sample chamber and to Mie theory by fitting the data to a logistic curve. The change in signal from 60 nm to 120 nm decreased in the order of Mie Theory > Optical Caustic scattering > standard laser 90 degree scattering. These results suggested that conjugating 60 nm gold nanoparticles with Dengue Protein E and using an optical caustic system to detect plasmonic light scattering would result in a sensitive test for detecting human antibodies against Dengue Protein E in serum. To explore this possibility, we studied the light scattering response of protein E conjugated gold nanoparticles exposed to different concentrations of anti-protein E antibody, and posteriorly via a feasibility study consisting of 10 human serum samples using a modified dot blot protocol and a handheld optical caustic-based sensor device. The overall agreement between the benchtop light scattering and dot blot results and the handheld optical caustic sensor suggest that the new sensor concept shows promise to detect gold nanoparticle aggregation caused by the presence of the antibody using a homogeneous assay. Further testing and protocol optimization is needed in order to draw conclusions on the positive predictive and negative predictive values for this new testing system.
DNA Methylation Landscape Reflects the Spatial Organization of Chromatin in Different Cells
Authors: Zhang Ling , Xie Wen Jun , Liu Sirui , Meng Luming , Gu Chan , Gao Yi Qin
Published: October 2016

The relation between DNA methylation and chromatin structure is still largely unknown. By analyzing a large set of sequencing data, we observed a long-range power law correlation of DNA methylation with cell-class-specific scaling exponents in the range of thousands to millions of base pairs. We showed such cell-class-specific scaling exponents are caused by different patchiness of DNA methylation in different cells. By modeling the chromatin structure using Hi-C data and mapping the methylation level onto the modeled structure, we demonstrated the patchiness of DNA methylation is related to chromatin structure. The scaling exponents of the power law correlation is thus a display of the spatial organization of chromatin. Besides, the local correlation of DNA methylation is associated with nucleosome positioning and different between partially-methylated-domain and non-partially-methylated-domain, suggesting their different chromatin structures at several nucleosomes level. Our study provides a novel view of the spatial organization of chromatin structure from a perspective of DNA methylation, in which both long-range and local correlations of DNA methylation along the genome reflect the spatial organization of chromatin.
Effect of error and missing data on population structure inference using microsatellite data
Authors: Reeves Patrick A. , Bowker Cheryl L. , Fettig Christa E. , Tembrock Luke R. , Richards Christopher M.
Published: October 2016

Missing data and genotyping errors are common in microsatellite data sets. We used simulated data to quantify the effect of these data aberrations on the accuracy of population structure inference. Data sets with complex, randomly-generated, population histories were simulated under the coalescent. Models describing the characteristic patterns of missing data and genotyping error in real microsatellite data sets were used to modify the simulated data sets. Accuracy of ordination, tree-based, and model-based methods of inference was evaluated before and after data set modifications. The ability to recover correct population clusters decreased as missing data increased. The rate of decrease was similar among analytical procedures, thus no single analytical approach was preferable. For every 1% of a data matrix that contained missing genotypes, 2–4% fewer correct clusters were found. For every 1% of a matrix that contained erroneous genotypes, 1–2% fewer correct clusters were found using ordination and tree-based methods. Model-based procedures that minimize the deviation from Hardy-Weinberg equilibrium in order to assign individuals to clusters performed better as genotyping error increased. We attribute this surprising result to the inbreeding-like nature of microsatellite genotyping error, wherein heterozygous genotypes are mischaracterized as homozygous. We show that genotyping error elevates estimates of the level of genetic admixture. Overall, missing data negatively impact population structure inference more than typical genotyping errors.
Assessing sampling sufficiency of network metrics using bootstrap
Authors: Casas Grasiela , Bastazini Vinicius A.G. , Debastiani Vanderlei J. , Pillar Valério D.
Published: October 2016

Sampling the full diversity of interactions in an ecological community is a highly intensive effort. Recent studies have demonstrated that many network metrics are sensitive to both sampling effort and network size. Here, we develop a statistical framework, based on bootstrap resampling, that aims to assess sampling sufficiency for some of the most widely used metrics in network ecology, namely connectance, nestedness (NODF-nested overlap and decreasing fill) and modularity (using the QuaBiMo algorithm). Our framework can generate confidence intervals for each network metric with increasing sample size (i.e., the number of sampled interaction events, or number of sampled individuals), which can be used to evaluate sampling sufficiency. The sample is considered sufficient when the confidence limits reach stability or lie within an acceptable level of precision for the aims of the study. We illustrate our framework with data from three quantitative networks of plant and frugivorous birds, varying in size from 16 to 115 species, and 17 to 2,745 interactions. These data sets illustrate that, for the same dataset, sampling sufficiency may be reached at different sample sizes depending on the metric of interest. The bootstrap confidence limits reached stability for the two largest networks, but were wide and unstable with increasing sample size for all three metrics estimated based on the smallest network. The bootstrap method is useful to empirical ecologists to indicate the minimum number of interactions necessary to reach sampling sufficiency for a specific network metric. It is also useful to compare sampling techniques of networks in their capacity to reach sampling sufficiency. Our method is general enough to be applied to different types of metrics and networks.
An equation-free method reveals the ecological interaction networks within complex microbial ecosystems
Authors: Suzuki Kenta , Yoshida Katsuhiko , Nakanishi Yumiko , Fukuda Shinji
Published: October 2016

Mapping the network of ecological interactions is key to understanding the composition, stability, function and dynamics of microbial communities. In recent years various approaches have been used to reveal microbial interaction networks from metagenomic sequencing data, such as time-series analysis, machine learning and statistical techniques. Despite these efforts it is still not possible to capture details of the ecological interactions behind complex microbial dynamics.

We developed the sparse S-map method (SSM), which generates a sparse interaction network from a multivariate ecological time-series without presuming any mathematical formulation for the underlying microbial processes. The advantage of the SSM over alternative methodologies is that it fully utilizes the observed data using a framework of empirical dynamic modelling. This makes the SSM robust to non-equilibrium dynamics and underlying complexity (nonlinearity) in microbial processes.

We showed that an increase in dataset size or a decrease in observational error improved the accuracy of SSM whereas, the accuracy of a comparative equation-based method was almost unchanged for both cases and equivalent to the SSM at best. Hence, the SSM outperformed a comparative equation-based method when datasets were large and the magnitude of observational errors were small. The results were robust to the magnitude of process noise and the functional forms of inter-specific interactions that we tested. We applied the method to a microbiome data of six mice and found that there were different microbial interaction regimes between young to middle age (4-40 week-old) and middle to old age (36-72 week-old) mice.

The complexity of microbial relationships impedes detailed equation-based modeling. Our method provides a powerful alternative framework to infer ecological interaction networks of microbial communities in various environments and will be improved by further developments in metagenomics sequencing technologies leading to increased dataset size and improved accuracy and precision.
Towards high-flux X-ray beam compressing channel-cut monochromators
Authors: Végsö Karol , Jergel Matej , Šiffalovič Peter , Majková Eva , Korytár Dušan , Zápražný Zdenko , Mikulík Petr , Vagovič Patrik
Published: October 2016

The issue of a high-flux X-ray beam compressing channel-cut monochromator for applications in X-ray metrology is addressed. A Ge(111) compressor with compression ratio 20.3 was designed on the principle of a combination of symmetric and highly asymmetric diffractions. A pilot application of the single-point diamond technology (SPDT) to finish active surfaces of X-ray optics was tested, providing 50% flux enhancement as compared to a Ge(220) counterpart prepared by traditional surface treatment. This is much more than the theoretical 22% forecast and shows the potential of SPDT for preparation of high-flux X-ray compressors with a high compression ratio, where highly asymmetric diffraction with a very low exit angle is inevitable. The implications for efficient collection of X-rays from microfocus X-ray sources are discussed. A comparison of Ge compressors with Ge parallel channel-cut monochromators combined with a 50 µm slit shows the several times higher flux of the former, making them applicable in X-ray diffraction experiments at medium resolution. Furthermore, the Ge(111) compressor was tested as a collimator in high-resolution grazing-incidence small-angle X-ray scattering (GISAXS) measurements of surface gratings, providing experimental resolution close to 400 nm. This is ∼100 nm smaller than that achieved with the Ge(220) compressor but still approximately twice that of commercial SAXS/GISAXS laboratory setups.
7,9-Didodecyl-6-methyl-3H,7H,8H,9H,9aH-[1,2,4]triazolo[4,3-b][1,2,4]triazepin-8-one
Authors: El Bakri Youness , Harmaoui Abdallah , Sebhaoui Jihad , Ramli Youssef , Essassi El Mokhtar , Mague Joel T.
Published: October 2016

The title compound, C30H55N5O, forms a micellar structure in the crystal with the dodecyl chains intercalating and the bicyclic cores forming dimers across centres of symmetry, via weak C—H...N hydrogen bonds, and slipped π-stacking interactions between the five-membered rings.
(E)-4-Nitro-2-[(phenylimino)methyl]phenol
Authors: Ida Malarselvi R. , Ramachandra Raja C. , Thiruvalluvar A. , Priscilla J. , Panneer Selvam K.
Published: October 2016

In the title compound, C13H10N2O3, the dihedral angle between the planes of the two aryl rings is 7.42 (10)°. An intramolecular O—H...N hydrogen bond generates an S(6) ring. The crystal structure features C—H...O hydrogen bonds.
An experimental periodicals checking list
Authors: Enright B.J. , Hanson D.G.
Published: October 2016

The use of an ICT 1905 computer for the mechanization of library procedures at The City University was considered as part of the library reorganization prior to the acquisition of University status. In view of the smallness of the library staff and the pressure of work it seemed essential to select an area which would quickly lead to relieving staff of tedious routine work, and at the same time provide useful training in computer applications. There seemed no point in attempting to duplicate exercises which were being currently tackled by larger libraries e.g. cataloguing, and the volume of loans hardly justified mechanization of circulation records at the present time.
On‐line Information Retrieval: a Method of Query Formulation using a Video Terminal
Authors: Hall J.L. , Negus A.E. , Dancy D.J.
Published: October 2016

This paper discusses some particularly desirable features of the user‐computer dialogue involved in query formulation in an on‐line information retrieval system. The methods used in the Culham RIOT II system, designed to give on‐line access to a data base of 25, 000–50, 000 references, are described. To facilitate query formulation a matrix technique is employed and the most recent titles may be displayed while the query statement is under construction and before a full search is requested.
Comparing the responses of bryophytes and short‐statured vascular plants to climate shifts and eutrophication
Authors: Virtanen Risto , Eskelinen Anu , Harrison Susan
Published: October 2016

Few experimental studies have tested how abundance and diversity of grassland bryophytes respond to global environmental changes such as climate shifts and eutrophication. Because bryophytes in grasslands are low‐statured, and because plant height is a key functional trait governing plant responses to resource gradients, their responses to these factors could resemble those of better‐studied small vascular plants. Alternatively, traits unique to bryophytes could lead to qualitatively different responses than those of small vascular plants.

In a semi‐arid Californian grassland system, where bryophytes are at relatively low abundance and their ecology has been little studied, we compared changes in cover and species richness of bryophytes and short‐statured vascular plants in response to 5 years of experimental fertilization, springtime watering and fertilization + watering, which produced strong gradients in vascular plant biomass.

Supporting our hypotheses, the cover and richness of both bryophytes and short vascular plants were negatively related to total community biomass and tall vascular plant cover, and declined in response to the fertilization + watering treatment, in which the cover of tall vascular plants most strongly increased.

Two divergent responses were also observed as follows: watering alone increased the cover of bryophytes but not short vascular plants, while fertilization alone reduced the cover of short vascular plants but not bryophytes.

Bryophytes and short‐statured vascular plants in grasslands both may be expected to decline under projected global changes in climate and nutrient deposition that enhance total community biomass and competitive pressure. However, shifts in either precipitation or eutrophication regimes alone may have differential effects on bryophytes and short vascular plants in grasslands, and organism‐specific plant functional traits must also be considered.

A lay summary is available for this article.
Optimizing management to enhance multifunctionality in a boreal forest landscape
Authors: Triviño María , Pohjanmies Tähti , Mazziotta Adriano , Juutinen Artti , Podkopaev Dmitry , Le Tortorec Eric , Mönkkönen Mikko
Published: October 2016

The boreal biome, representing approximately one‐third of remaining global forests, provides a number of crucial ecosystem services. A particular challenge in forest ecosystems is to reconcile demand for an increased timber production with provisioning of other ecosystem services and biodiversity. However, there is still little knowledge about how forest management could help solve this challenge. Hence, studies that investigate how to manage forests to reduce trade‐offs between ecosystem services and biodiversity are urgently needed to help forest owners and policy makers take informed decisions.

We applied seven alternative forest management regimes using a forest growth simulator in a large boreal forest production landscape. First, we estimated the potential of the landscape to provide harvest revenues, store carbon and maintain biodiversity across a 50‐year time period. Then, we applied multiobjective optimization to identify the trade‐offs between these three objectives and to identify the optimal combination of forest management regimes to achieve these objectives.

It was not possible to achieve high levels of either carbon storage or biodiversity if the objective of forest management was to maximize timber harvest revenues. Moreover, conflicts between biodiversity and carbon storage became stronger when simultaneously targeting high levels of timber revenues. However, with small reductions in timber revenues, it was possible to greatly increase the multifunctionality of the landscape, especially the biodiversity indicators.

Forest management actions, alternative to business‐as‐usual management, such as reducing thinnings, extending the rotation period and increasing the amount of area set aside from forestry may be necessary to safeguard biodiversity and non‐timber ecosystem services in Fennoscandia.

Synthesis and applications. Our results show that no forest management regime alone is able to maximize timber revenues, carbon storage and biodiversity individually or simultaneously and that a combination of different regimes is needed to resolve the conflicts among these objectives. We conclude that it is possible to reduce the trade‐offs between different objectives by applying diversified forest management planning at the boreal landscape level and that we need to give up the all‐encompassing objective of very intensive timber production, which is prevailing particularly in Fennoscandian countries.
Increasing the germination envelope under water stress improves seedling emergence in two dominant grass species across different pulse rainfall events
Authors: Lewandrowski Wolfgang , Erickson Todd E. , Dixon Kingsley W. , Stevens Jason C.
Published: October 2016

Demographic recruitment processes, such as seed germination and seedling emergence, are critical transitional phases to the re‐establishment of degraded plant populations, but often fail due to rainfall not supporting plant requirements. Using species from the widespread arid Australian perennial grass genus Triodia, we investigated the interactions of seeds in different dormancy states and their functional germination envelope in response to water stress after simulated pulse rainfall events.

Seed dormancy was alleviated in Triodia species to varying degrees by wet/dry cycling or by removing floret structures from seeds. The seeds were then exposed to different rainfall frequency and quantity events mimicking the 25th, median, 75th and 95th percentile rainfall events found in natural habitats for the study species in the north‐west Australian arid zone.

Under 95th percentile rainfall conditions recruitment was highest, but still limited to 35% germination and 10% emergence of cleaned seeds (i.e. the least dormant state evaluated). This was related to the functional germination envelope as indicated by more negative base water potential thresholds (Ψb50) for cleaned seeds (≥ −0·33 MPa) compared to intact florets (≥ −0·26 MPa). As a result, the maximum cumulative time where soil water potentials were optimal for germination (Ψsoil ≥ Ψb50) was 1·6–2·6 times longer for cleaned seeds in large frequent rainfall events when compared to intact florets. Furthermore, seed dormancy, that usually prolongs seed survival, was linked to a short‐term reduction in seed viability, which may further reduce recruitment rates.

Synthesis and applications. Our findings indicate that large frequent rainfall events raised soil water potentials above critical thresholds for germination and are important for successful plant establishment. If recruitment bottlenecks are a result of seed dormancy and variable rainfall for arid grass species, then this study shows benefits for alleviating seed dormancy prior to seeding in restoration sites, as this increases the environmental envelope for germination.
Separating sources of density‐dependent and density‐independent establishment limitation in invading species
Authors: Spotswood Erica N. , Mariotte Pierre , Farrer Emily C. , Nichols Liana , Suding Katharine N.
Published: October 2016

Successful colonization by invasive species depends on both the ability to disperse seeds to a site and an ability to establish once seeds have arrived. While seed and establishment limitation are known to jointly influence colonization, decomposing establishment limitation into density‐dependent and density‐independent components has remained challenging.

Here, we couple theoretical models of recruitment with a multispecies invasion experiment conducted within a natural gradient of soil moisture and productivity to assess how variation in establishment limitation shapes outcomes for invasion.

Recruitment was affected by both density‐dependent and density‐independent sources of establishment limitation in three of four species. Soil moisture stress and productivity both increased density‐independent mortality in one species, whereas density‐dependent mortality increased in locations with favourable soil moisture.

Synthesis. Successful establishment of invading species can be limited by both density‐dependent and density‐independent mechanisms. In particular, the strength of density‐independent limitation may depend on natural gradients in abiotic factors. The varying strengths of establishment limitation suggest that patterns of invasion are likely to be uneven both in space and in time. Understanding how intraspecific competitive constraints and density‐independent limitation vary with abiotic gradients can assist with predicting when invasions are likely to occur, information that can be harnessed in the development of better methods for control.
Let the earth forever remain! Landscape legacies and the materiality of history in the northern Basin of Mexico
Authors: Morehart Christopher T.
Published: October 2016

This article examines the landscape as an enduring protagonist in the northern Basin of Mexico over the past 1,000 years in communities north of Mexico City. Viewing materiality as the mutual constitution between social and physical worlds, I discuss the production and inheritance of landscape legacies. The manner in which legacies are inherited is tied to changing political, economic, and social conditions. This project integrates multiple sources of information (archaeological, ethnographic, historical, and ecological) to understand transforming connections between people and the landscape in this region, from the ancient state of Xaltocan to the Aztec and Spanish empires, continuing into the struggle for a modern nation. It reveals relationships that are apparent only via a perspective in dialogue with the landscape's materiality over time. In so doing, this article asserts archaeologists' unique contribution to the study of not only long‐term change but also historical processes inherited by and relevant to the contemporary world.
Politicizing Undocumented Immigrants One Corner at a Time: How Day Laborers Became a Politically Contentious Group
Authors: Nicholls Walter
Published: October 2016

This article examines how undocumented immigrants become politicized and evolved into a relatively powerful group in the United States. It does so by examining the evolution of day laborers from their humble beginnings in a Los Angeles suburb in the early 1990s into an important component of the national immigrant rights movement today. It addresses the issue by examining the strategic importance of the ‘urban' in enabling stigmatized individuals like undocumented day laborers to overcome major barriers and establish themselves as a vocal and potent group in the public sphere. It suggests that once this group gained a foothold and a sense of itself through urban relational spaces, it experienced enhanced capacities to make rights claims in local and national political arenas. The article uses a case study of immigrant activism in Pasadena and Los Angeles, California, and draws special attention to the evolution of the National Day Labor Organizing Network (NDLON).
Characterizing Soy Sauce Moromi Manufactured by High‐Salt Dilute‐State and Low‐Salt Solid‐State Fermentation Using Multiphase Analyzing Methods
Authors: Zhang Liqiang , Zhou Rongqing , Cui Ruiying , Huang Jun , Wu Chongde
Published: October 2016

Present study was to characterize the physiochemical properties, free amino acids (FAAs), volatiles and microbial communities of various moromi, respectively sampled from different stages of high‐salt dilute‐state (HSDS) and low‐salt solid‐state (LSSS) fermentation, using multiphase analyzing methods. Phospholipid fatty acids (PLFA) analysis indicated that Gram‐positive bacteria were dominant bacteria and fungi were principal microbes. For DGGE analysis, dominant microbes in moromi were mainly fell into Weissella, Tetragenococcus, Candida, Pichia, and Zygosaccharomyces. During fermentation, the dominant microbes shifted from nonhalophilic and less acid‐tolerant species to halophilic and acid‐tolerant species. Total of 15 FAAs and 44 volatiles were identified in moromi, mainly Glu, Asp, Tyr, and acids, alcohols, esters, aldehydes, respectively. Odor activity values analysis suggested that the final moromi of LSSS fermentation had more complicated odors than that of HSDS fermentation. Conclusively, technological parameters, microbial communities, raw materials and fermentation process may result in the discrepancy of HSDS and LSSS moromi.