bluuebunny/crossref_metadata_2025 huggingface dataset:
New guidelines for managing pulmonary hypertension: what the pediatrician needs to know
Authors: Abman Steven H.
Published: July 2016

Purpose of review

Pediatric pulmonary vascular disease contributes to morbidities and death in diverse clinical settings, ranging from idiopathic or heritable forms of pediatric arterial hypertension, congenital heart disease, developmental lung disorders, chronic lung disease, left heart disease, sickle cell disease, oncologic disease, and systemic disorders. Despite its impact on the clinical courses in so many diseases, information is limited on how to best approach the diagnosis and evaluation of pediatric pulmonary hypertension.

Recent findings

To address this issue, a group of clinical experts from several subspecialties, including pulmonology, cardiology, neonatology, and others, were selected to form a task force to tackle this topic with support from the American Heart Association and American Thoracic Society. A joint guidelines study presenting their findings was recently published.

This review highlights a few key topics underlying guidelines for the care of children with pulmonary hypertension that are especially important for the practicing pediatrician and others, and presents some of the major recommendations from the published guidelines report. Overall, the author emphasizes that these guidelines are based on the best current evidence and clinical experience of experts in the field, yet much more clinical research is needed to improve long-term outcomes in pediatric pulmonary hypertension.
Differences in Postprandial Lipid Response to Breast‐ or Formula‐feeding in 8‐Week‐Old Infants
Authors: Teller Inga C. , Schoen Stefanie , van de Heijning Bert , van der Beek Eline M. , Sauer Pieter J.J.
Published: July 2016

Objective:

Lipids play important roles in infant growth and development. In this exploratory observational single‐center study, we investigated postmeal responses of infants to dietary lipids and differences between breast‐feeding (BF) and formula‐feeding (FF).

Methods:

Two capillary blood samples were collected from each subject, before and randomly assigned at either 30, 60, 90, 120, 180, or 240 minutes after their respective feeding, followed by measurement of lipid‐related plasma parameter concentrations using enzyme‐linked immunosorbent assay‐based or combined enzymatic and colorimetric methods.

Results:

The intermeal interval before testing was shorter in the BF (182.91 ± 22.85 minutes, n = 33) versus FF group (214.1 ± 30.76 minutes, n = 34); BF subjects fed 5 minutes longer (BF 20.27 ± 7.7 minutes; FF 14.82 ± 3.57 minutes). Composite postmeal concentration profiles were generated from 59 plasma sample pairs with sufficient volume (BF = 30): triglyceride (TG) baselines were not different. A TG difference was indicated for BF over FF subjects at 30 minutes, for FF over BF subjects at 60 minutes when corrected for baseline. TG responses in both groups appeared and seemed to clear much faster than those reported for adults. The TG:apolipoprotein B48 (ApoB48) ratio suggests that chylomicrons in BF subjects may carry a higher fat load (P < 0.05), compensated by a higher chylomicron number in FF subjects (P < 0.05). Cholesterol in BF subjects was higher and showed an increase after feeding when corrected for baseline.

Conclusions:

Our results indicate that lipids from either BF or FF may be handled differently in young healthy infants.
Defense Mechanisms in “Pure” Anxiety and “Pure” Depressive Disorders
Authors: Colovic Olga , Lecic Tosevski Dusica , Perunicic Mladenovic Ivana , Milosavljevic Maja , Munjiza Ana
Published: July 2016

Our study was intended to test whether there are any differences in the way defense mechanisms are used by patients suffering from pure anxiety and those with pure depressive disorders. The sample size was as follows: depressive disorders without psychotic symptoms 30, anxiety disorders 30, and the healthy control group 30. The assessment of defense mechanisms was made using the DSQ-40 questionnaire. Our findings show that “pure” anxiety disorders differ from “pure” depressive disorders only in the use of immature defense mechanisms. The group with depressive disorders was significantly more prone to use immature defense mechanisms than the group with anxiety disorders (p = 0.005), primarily projection (p = 0.001) and devaluation (p = 0.003). These defense mechanisms may therefore be used both to differentiate between anxiety and depressive disorders and also to determine which symptoms (anxiety or depressive disorders) are dominant at any given stage of treatment.
The Association Between Social Capital and Depression Among Chinese Older Adults Living in Public Housing
Authors: Wu Tat Leong , Hall Brian J. , Canham Sarah L. , Lam Agnes Iok Fong
Published: July 2016

Social capital is a critical resource for physical and mental health among older adults, but few studies have investigated this relationship in Chinese populations, and specifically among those with low socioeconomic status. This study examined the association between depression and cognitive social capital (reciprocity and trust) and structural social capital (social participation) in a community sample of older adults living in public housing in Macau (SAR), China (N= 366). Multivariable linear regressions estimated the associations between dimensions of social capital and depression, while adjusting for potential confounders. Significant inverse associations were found between reciprocity and trust and depression. No association was found between social participation and depression. Poor self-reported health was a robust correlate of depression in all models tested. Future studies are needed to evaluate whether enhancing social capital may reduce depression among Chinese older adults living in poverty.
Transition of Experienced and New Graduate Nurses to a Pediatric Hospital
Authors: Klingbeil Carol , Schiffman Rachel F. , Ziebert Carolyn , Totka Joan P. , Schmitt Catherine A. , Doyle Lynn , Stelter Ashley , Stonek Alice V. , Ke Weiming , Johnson Norah
Published: July 2016

This study reports on the 3-, 6-, 12-, and 18-month outcomes of 118 newly hired registered nurses (RNs) who completed a 12-month transition-to-practice program at a pediatric hospital. Experienced RNs (n = 42) and new graduate RNs (n = 76) showed improved organization, prioritization, communication, and leadership skills over time. The experienced RNs reported better communication and leadership skills than the new graduate nurses. Results inform transition program development for both new and experienced nurses.
Driver Mutation Analysis and PD-L1 Expression in Synchronous Double Primary Lung Cancer
Authors: Jia Xiaoli , Zhang Liping , Wu Wei , Zhang Wei , Wu Chunyan
Published: July 2016

Synchronous double primary lung cancer (SDPLC) is detected more frequently than in the past. However, the genetic features, diagnosis, and outcome are not well known. For diagnostic and management applications, we collected 110 lesions from 55 patients who underwent surgical resection to analyze the 5 known driver mutations (EGFR, KRAS, BRAF, EML4-ALK, and ROS1) and programmed cell death ligand 1 (PD-L1) expression in various histologic types of SDPLC. Among 110 tumor lesions, 55 (50%) tumors were found harboring EGFR mutations. In addition, there were 5 (4.55%) tumors harboring EML4-ALK fusions, and 9 (8.18%) KRAS mutations. Only 1 tumor had the coexistence of L858R mutation and EML4-ALK fusion. No BRAF or ROS1 aberrations could be detected. Combining the results for the mutation and fusion patterns, 4 (7.27%) and 47 (85.5%) patients were assessed as having the same clonality and different clonality, respectively. Strikingly, patients with EGFR mutations classified as having same clonality were commonly observed among patients aged above 65 years old (P=0.021). The frequency of PD-L1 expression was 14.54% (16/110). PD-L1 had higher positive results in male, in squamous cell carcinoma subtype, and in tumors >3 cm in diameter. Univariable analysis revealed that lymph node metastasis, smoking history, and male predict worse replase-free survival and overall survival. EGFR/KRAS mutation and EML4-ALK fusion status evaluation was an important tool to support the diagnosis of SDPLC. Following resection, these marks could be used to guide targeted treatment decisions.
IMP3 Immunohistochemical Expression Remains Consistent Among All Grades of Gastrointestinal Neuroendocrine Tumors
Authors: Agostini-Vulaj Diana , Whitney-Miller Christa L. , Gonzalez Raul S. , McMahon Loralee A. , Findeis-Hosey Jennifer J.
Published: July 2016

Insulin-like growth factor-II messenger RNA-binding protein-3 (IMP3), is an oncofetal protein whose aberrant expression has previously been detected in multiple malignant neoplasms. Pulmonary neuroendocrine carcinomas demonstrate increased expression compared with pulmonary carcinoid tumors, but this relationship has not been studied in gastrointestinal neuroendocrine tumors (GINETs). This study examined IMP3 expression in GINETs, with a focus on correlation with established grading criteria. Fifty-four GINETs were immunohistochemically studied using a monoclonal antibody against IMP3. Using established World Health Organization criteria, the cases were stratified by grade and included 31 grade 1 neuroendocrine tumors (G1 GINETs), 15 grade 2 neuroendocrine tumors (G2 GINETs), and 8 neuroendocrine carcinomas (GINECs). The majority (51/54, 94.4%) of GINETs demonstrated IMP3 staining. Thirty cases (55.6%) showed IMP3 cytoplasmic/membranous staining in 60% or greater of tumor cells, with moderate to strong staining in nearly all of these cases (29/30; 96.7%). Of the remaining 24 cases, 3 cases showed no staining, whereas 17 (81%) demonstrated weak staining. When stratified by grade, there was no statistically significant difference in IMP3 staining among the 3 grades of GINETs; of the G1 GINETs, 14 (45.2%) demonstrated staining in at least 60% of tumor cells, compared with 10 (66.7%) G2 GINETs and 6 (75%) GINECs. Hindgut neoplasms of any grade were the most likely to show significant IMP3 staining. Unlike what has been demonstrated in neuroendocrine neoplasms in the lungs, GINETs appear to have a consistent IMP3 expression profile among all tumors grades, which may be reflective of their unique tumor biology.
Adrenal Pathology in the Adult: A Urological Pathologist’s Perspective
Authors: Hansel Donna E. , Reuter Victor E.
Published: July 2016

Adrenal gland diagnostics can pose significant challenges. In most academic and community practice settings, adrenal gland resections are encountered less frequently than other endocrine or genitourinary specimens, leading to less familiarity with evolving classifications and criteria. The unique dichotomy between cortical and medullary lesions reflects the developmental evolution of these functionally independent components. Adrenal cortical lesions at resection include hyperplasia, adenoma, and carcinoma, with some cases straddling the boundary between these distinct clinical classifications. The lack of immunohistochemical or molecular markers to definitively categorize these intermediate lesions enhances the diagnostic challenge. In addition, modified terminology for oncocytic and myxoid cortical lesions has been proposed. Medullary lesions are somewhat easier to categorize; however, the prediction of aggressive behavior in pheochromocytomas remains a challenge due to a lack of reliable prognostic biomarkers. Recent work by the Cancer Genome Atlas Project and other research groups has identified a limited subset of molecular and signaling pathway alterations in these 2 major neoplastic categories. Ongoing research to better define prognostic and predictive biomarkers in cortical and medullary lesions has the potential to enhance both pathologic diagnosis and patient therapy.
MLH1-deficient Colorectal Carcinoma With Wild-type BRAF and MLH1 Promoter Hypermethylation Harbor KRAS Mutations and Arise From Conventional Adenomas
Authors: Farchoukh Lama , Kuan Shih-Fan , Dudley Beth , Brand Randall , Nikiforova Marina , Pai Reetesh K.
Published: July 2016

Between 10% and 15% of colorectal carcinomas demonstrate sporadic DNA mismatch-repair protein deficiency as a result of MLH1 promoter methylation and are thought to arise from sessile serrated adenomas, termed the serrated neoplasia pathway. Although the presence of the BRAF V600E mutation is indicative of a sporadic cancer, up to 30% to 50% of colorectal carcinomas with MLH1 promoter hypermethylation will lack a BRAF mutation. We report the clinicopathologic and molecular features of MLH1-deficient colorectal carcinoma with wild-type BRAF and MLH1 promoter hypermethylation (referred to as MLH1-hypermethylated BRAF wild-type colorectal carcinoma, n=36) in comparison with MLH1-deficient BRAF-mutated colorectal carcinoma (n=113) and Lynch syndrome–associated colorectal carcinoma (n=36). KRAS mutations were identified in 31% of MLH1-hypermethylated BRAF wild-type colorectal carcinomas compared with 0% of MLH1-deficient BRAF-mutated colorectal carcinomas and 37% of Lynch syndrome–associated colorectal carcinomas. When a precursor polyp was identified, MLH1-hypermethylated BRAF wild-type colorectal carcinomas arose from precursor polyps resembling conventional tubular/tubulovillous adenomas in contrast to MLH1-deficient BRAF-mutated colorectal carcinomas, which arose from precursor sessile serrated adenomas (P<0.001). Both MLH1-hypermethylated BRAF wild-type colorectal carcinoma and MLH1-deficient BRAF-mutated colorectal carcinoma had a predilection for the right colon compared with Lynch syndrome–associated colorectal carcinoma (86% vs. 92% vs. 49%, P<0.001). There was no significant difference in mucinous differentiation, tumor-infiltrating lymphocytes, Crohn-like reaction, and medullary differentiation between the 3 tumor groups. Using Kaplan-Meier survival functions, there was no significant difference in disease-specific survival between the 3 patient groups (P>0.05). In conclusion, our results indicate that MLH1-hypermethylated BRAF wild-type colorectal carcinomas can harbor KRAS mutations and arise from precursor polyps resembling conventional tubular/tubulovillous adenomas.
The Effect of Same-Day Observed Initiation of Antiretroviral Therapy on HIV Viral Load and Treatment Outcomes in a US Public Health Setting
Authors: Pilcher Christopher D. , Ospina-Norvell Clarissa , Dasgupta Aditi , Jones Diane , Hartogensis Wendy , Torres Sandra , Calderon Fabiola , Demicco Erin , Geng Elvin , Gandhi Monica , Havlir Diane V. , Hatano Hiroyu
Published: July 2016

Background:

Antiretroviral therapy (ART) is typically begun weeks after HIV diagnosis. We assessed the acceptability, feasibility, safety, and efficacy of initiating ART on the same day as diagnosis.

Methods:

We studied a clinic-based cohort consisting of consecutive patients who were referred with new HIV diagnosis between June 2013 and December 2014. A subset of patients with acute or recent infection (<6 months) or CD4 <200 were managed according to a “RAPID” care initiation protocol. An intensive, same-day appointment included social needs assessment; medical provider evaluation; and a first ART dose offered after laboratories were drawn. Patient acceptance of ART, drug toxicities, drug resistance, and time to viral suppression outcomes were compared between RAPID participants and contemporaneous patients (who were not offered the program), and with an historical cohort.

Results:

Among 86 patients, 39 were eligible and managed on the RAPID protocol. Thirty-seven (94.9%) of 39 in RAPID began ART within 24 hours. Minor toxicity with the initial regimen occurred in 2 (5.1%) of intervention patients versus none in the nonintervention group. Loss to follow-up was similar in intervention (10.3%) and nonintervention patients (14.9%) during the study. Time to virologic suppression (<200 copies HIV RNA/mL) was significantly faster (median 1.8 months) among intervention-managed patients when compared with patients treated in the same clinic under prior recommendations for universal ART (4.3 months; P = 0.0001).

Conclusions:

Treatment for HIV infection can be started on the day of diagnosis without impacting the safety or acceptability of ART. Same-day ART may shorten the time to virologic suppression.
Update on the Role of Cardiac Magnetic Resonance in Acquired Nonischemic Cardiomyopathies
Authors: Rajiah Prabhakar , Raza Samreen , Saboo Sachin S. , Ghoshhajra Brian , Abbara Suhny
Published: July 2016

Cardiomyopathies refer to a variety of myocardial disorders without underlying coronary artery disease, valvular heart disease, hypertension, or congenital heart disease. Several imaging modalities are available, but cardiac magnetic resonance (CMR) has now established itself as a crucial imaging technique in the evaluation of several cardiomyopathies. It not only provides comprehensive information on structure and function, but also can perform tissue characterization, which helps in establishing the etiology of cardiomyopathy. CMR is also useful in establishing the diagnosis, providing guidance for endomyocardial biopsy, accurate quantification of function, volumes, and fibrosis, prognostic determination, risk stratification, and monitoring response to therapy. In this article, we review the current role of CMR in the evaluation of several acquired nonischemic cardiomyopathies, particularly focusing on recent advances in knowledge. We also discuss in detail a select group of common acquired nonischemic cardiomyopathies.
Nonintubated Needlescopic Thoracic Sympathectomy for Primary Palmar Hyperhidrosis: A Randomized Controlled Trial
Authors: Chen Jian-Feng , Lin Min , Chen Ping , Quan Du , Li Xu , Lai Fan-Cai , Tu Yuan-Rong
Published: July 2016

Background:

Conventional endoscopic thoracic sympathectomy (ETS) is usually performed with 5-mm thoracoscope under general anesthesia with endotracheal intubation. Needlescopic thoracic sympathectomy under total intravenous anesthesia without intubation has rarely been attempted. This randomized controlled trial assesses the feasibility and safety of this minimally invasive therapeutic procedure in managing primary palmar hyperhidrosis.

Methods:

From July 2012 to July 2014, 221 patients with severe primary palmar hyperhidrosis underwent bilateral ETS and were randomly allocated to group A or group B. Patients in group A (n=108) underwent nonintubated ETS using a needle endoscope, whereas those in group B (n=113) underwent traditional transaxillary single-port ETS using a 5-mm thoracoscope.

Results:

ETS was successfully performed in all patients. The palms of all patients became dry and warm immediately after surgery. The mean resuscitation time was significantly shorter in nonintubated patients than in intubated patients (P<0.01). Postoperative sore throat occurred in 37 patients in group B, whereas none of the patients in group A complained about sore throat after surgery (P<0.01). The mean incision length was 5.1±0.1 mm with needle endoscope and 11.0±0.8 mm with traditional thoracoscope (P<0.01). The mean postoperative pain score was 1.1±0.8 in group A and 3.2±0.8 in group B (P<0.01). The mean cost of anesthesia was considerably lower in nonintubated patients than in intubated patients (P<0.01). Follow-up was 100% completed. The mean cosmetic scores were higher in group A than in group B (P<0.01). Residual pain occurred in 2 patients in group A and in 18 patients in group B (P<0.01).

Conclusions:

Nonintubated needlescopic thoracic sympathectomy is a safe, effective, and minimally invasive therapeutic procedure, which has the advantages of a smaller incision with less pain, shorter resuscitation time, and better cosmetic results.
The Most Minimally Invasive Lobectomy: Videomediastinoscopic Lobectomy
Authors: Tezel Cagatay , Dogruyol Talha , Baysungur Volkan , Yalcinkaya Irfan
Published: July 2016

Transcervical approaches are well-described procedures. However, they are performed in a limited number of experienced centers. Transcervical lobectomies are even rarer. However, these lobectomy cases defined in the literature are performed through a collar incision with the aid of a sternal retractor. The case presented here describes the first right upper lobectomy through videomediastinoscopy without sternal elevation.
Synthetic consciousness: the distributed adaptive control perspective
Authors: Verschure Paul F. M. J.
Published: July 2016

Understanding the nature of consciousness is one of the grand outstanding scientific challenges. The fundamental methodological problem is how phenomenal first person experience can be accounted for in a third person verifiable form, while the conceptual challenge is to both define its function and physical realization. The distributed adaptive control theory of consciousness (DACtoc) proposes answers to these three challenges. The methodological challenge is answered relative to the hard problem and DACtoc proposes that it can be addressed using a convergent synthetic methodology using the analysis of synthetic biologically grounded agents, or quale parsing. DACtoc hypothesizes that consciousness in both its primary and secondary forms serves the ability to deal with the hidden states of the world and emerged during the Cambrian period, affording stable multi-agent environments to emerge. The process of consciousness is an autonomous virtualization memory, which serializes and unifies the parallel and subconscious simulations of the hidden states of the world that are largely due to other agents and the self with the objective to extract norms. These norms are in turn projected as value onto the parallel simulation and control systems that are driving action. This functional hypothesis is mapped onto the brainstem, midbrain and the thalamo-cortical and cortico-cortical systems and analysed with respect to our understanding of deficits of consciousness. Subsequently, some of the implications and predictions of DACtoc are outlined, in particular, the prediction that normative bootstrapping of conscious agents is predicated on an intentionality prior. In the view advanced here, human consciousness constitutes the ultimate evolutionary transition by allowing agents to become autonomous with respect to their evolutionary priors leading to a post-biological Anthropocene.

This article is part of the themed issue ‘The major synthetic evolutionary transitions’.
Major transitions in information technology
Authors: Valverde Sergi
Published: July 2016

When looking at the history of technology, we can see that all inventions are not of equal importance. Only a few technologies have the potential to start a new branching series (specifically, by increasing diversity), have a lasting impact in human life and ultimately became turning points. Technological transitions correspond to times and places in the past when a large number of novel artefact forms or behaviours appeared together or in rapid succession. Why does that happen? Is technological change continuous and gradual or does it occur in sudden leaps and bounds? The evolution of information technology (IT) allows for a quantitative and theoretical approach to technological transitions. The value of information systems experiences sudden changes (i) when we learn how to use this technology, (ii) when we accumulate a large amount of information, and (iii) when communities of practice create and exchange free information. The coexistence between gradual improvements and discontinuous technological change is a consequence of the asymmetric relationship between complexity and hardware and software. Using a cultural evolution approach, we suggest that sudden changes in the organization of ITs depend on the high costs of maintaining and transmitting reliable information.

This article is part of the themed issue ‘The major synthetic evolutionary transitions’.
Transition from environmental to partial genetic sex determination inDaphniathrough the evolution of a female-determining incipient W-chromosome
Authors: Reisser Céline M.O. , Fasel Dominique , Hürlimann Evelin , Dukič Marinela , Haag-Liautard Cathy , Thuillier Virginie , Galimov Yan , Haag Christoph
Published: July 2016

Sex chromosomes can evolve during the evolution of genetic sex determination (GSD) from environmental sex determination (ESD). Despite theoretical attention, early mechanisms involved in the transition from ESD to GSD have yet to be studied in nature. No mixed ESD-GSD animal species have been reported, except for some species ofDaphnia, small freshwater crustaceans in which sex is usually determined solely by the environment, but in which a dominant female sex-determining locus is present in some populations. This locus follows Mendelian single-locus inheritance, but has otherwise not been characterized genetically. We now show that the sex-determining genomic region maps to the same low-recombining peri-centromeric region of linkage group 3 (LG3) in three highly divergent populations ofD. magna, and spans 3.6 Mb. Despite low levels of recombination, the associated region contains signs of historical recombination, suggesting a role for selection acting on several genes thereby maintaining linkage disequilibrium among the 36 associated SNPs. The region carries numerous genes involved in sex differentiation in other taxa, includingtransformer2andsox9. Taken together, the region determining the NMP phenotype shows characteristics of a sex-related supergene, suggesting that LG3 is potentially an incipient W chromosome despite the lack of significant additional restriction of recombination between Z and W. The occurrence of the female-determining locus in a pre-existing low recombining region illustrates one possible form of recombination suppression in sex chromosomes.D. magnais a promising model for studying the evolutionary transitions from ESD to GSD and early sex chromosome evolution.
Architectures of lipid transport systems for the bacterial outer membrane
Authors: Ekiert Damian C. , Bhabha Gira , Greenan Garrett , Ovchinnikov Sergey , Cox Jeffery S. , Vale Ronald D.
Published: July 2016

How phospholipids are trafficked between the bacterial inner and outer membranes through the intervening hydrophilic space of the periplasm is not known. Here we report that members of the mammalian cell entry (MCE) protein family form structurally diverse hexameric rings and barrels with a central channel capable of mediating lipid transport. TheE. coliMCE protein, MlaD, forms a ring as part of a larger ABC transporter complex in the inner membrane, and employs a soluble lipid-binding protein to ferry lipids between MlaD and an outer membrane protein complex. In contrast, EM structures of two otherE. coliMCE proteins show that YebT forms an elongated tube consisting of seven stacked MCE rings, and PqiB adopts a syringe-like architecture. Both YebT and PqiB create channels of sufficient length to span the entire periplasmic space. This work reveals diverse architectures of highly conserved protein-based channels implicated in the transport of lipids between the inner and outer membranes of bacteria and some eukaryotic organelles.

HIGHLIGHTS

MCE proteins adopt diverse architectures for transporting lipids across the bacterial periplasm

Cryo-EM and X-ray structures reveal how the MlaFEDB complex, along with MlaC, might shuttle lipids across the periplasm

3.9 Å cryo-EM structure of PqiB reveals a syringe-like architecture with a continuous central channel

YebT forms a a segmented tube-like structure, and YebT and PqiB are poised to directly link the inner and outer membranes to facilitate lipid transport.
Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition
Authors: Knudsen Berith E. , Bergmark Lasse , Munk Patrick , Lukjancenko Oksana , Priemé Anders , Aarestrup Frank M. , Pamp Sünje J.
Published: July 2016

Explorations of complex microbiomes using genomics greatly enhance our understanding about their diversity, biogeography, and function. The isolation of DNA from microbiome specimens is a key prerequisite for such examinations, but challenges remain in obtaining sufficient DNA quantities required for certain sequencing approaches, achieving accurate genomic inference of microbiome composition, and facilitating comparability of findings across specimen types and sequencing projects. These aspects are particularly relevant for the genomics-based global surveillance of infectious agents and antimicrobial resistance from different reservoirs. Here, we compare in a stepwise approach a total of eight commercially available DNA extraction kits and 16 procedures based on these for three specimen types (human feces, pig feces, and hospital sewage). We assess DNA extraction using spike-in controls, and different types of beads for bead-beating facilitating cell lysis. We evaluate DNA concentration, purity, and stability, and microbial community composition using 16S rRNA gene sequencing and for selected samples using shotgun metagenomic sequencing. Our results suggest that inferred community composition was dependent on inherent specimen properties as well as DNA extraction method. We further show that bead-beating or enzymatic treatment can increase the extraction of DNA from Gram-positive bacteria. Final DNA quantities could be increased by isolating DNA from a larger volume of cell lysate compared to standard protocols. Based on this insight, we designed an improved DNA isolation procedure optimized for microbiome genomics that can be used for the three examined specimen types and potentially also for other biological specimens. A standard operating procedure is available from: https://dx.doi.org/10.6084/m9.figshare.3475406.

IMPORTANCE

Sequencing-based analyses of microbiomes may lead to a breakthrough in our understanding of the microbial world associate with humans, animals, and the environment. Such insight could further the development of innovative ecosystem management approaches for the protection of our natural resources, and the design of more effective and sustainable solutions to prevent and control infectious diseases. Genome sequence information is an organism- (pathogen-) independent language that can be used across sectors, space, and time. Harmonized standards, protocols, and workflows for sample processing and analysis can facilitate the generation of such actionable information. In this study, we assessed several procedures for the isolation of DNA for next-generation sequencing. Our study highlights several important aspects to consider in the design and conduction of sequence-based analysis of microbiomes. We provide a standard operating procedure for the isolation of DNA from a range of biological specimens particularly relevant in clinical diagnostics and epidemiology.
Microwave Mutagenesis of Brevibacillus Parabrevis for Enhanced Cellulase Production, and Investigation on Thermostability of this Cellulase
Authors: Khambhala Pinakin , Paliwal Purva , Kothari Vijay
Published: July 2016

Microwave mutagenesis ofBrevibacillus parabrevisfor enhanced cellulase production was attempted. Though microwave treatment could alter the cellulase activity of the test bacterium, none of the mutants obtained were found to be genetically stable, indicating the reversible nature of microwave-induced mutation(s). Thermal stability of theB. parabreviscellulase was also investigated. This enzyme was found to be capable of retaining its activity even after heat treatment (50-121°C, for 30-60 min). Fluorescence spectrum revealed ared shiftin the emission maxima of the heat-treated enzyme preparations, indicating some structural change upon heating, but no major loss of activity was observed. This enzyme was found to be active over a broad temp range, with 90°C as the optimum temp, which is interesting as the producing organism is a mesophile.
Local chromosome context is a major determinant of crossover pathway biochemistry during budding yeast meiosis
Authors: Medhi Darpan , Goldman Alastair S. H. , Lichten Michael
Published: July 2016

Meiotic chromosomes are divided into regions of enrichment and depletion for meiotic chromosome axis proteins, in budding yeast Hop1 and Red1. These proteins are important for formation of Spo11-catalyzed DSB, but their contribution to crossover recombination is undefined. By studying meiotic recombination initiated by the sequence-specificVMA1-derived endonuclease (VDE), we show that meiotic chromosome structure helps to determine the biochemical mechanism by which recombination intermediates are resolved to form crossovers. At a Hop1-enriched locus, most VDE-initiated crossovers required the MutLγ resolvase, which forms most Spo11-initiated crossovers. In contrast, at a locus with lower Hop1 occupancy, most VDE-initiated crossovers were MutLγ-independent. Inpch2mutants, the two loci displayed similar Hop1 occupancy levels, and also displayed similar MutLγ-dependence of VDE-induced crossovers. We suggest that meiotic and mitotic recombination pathways coexist within meiotic cells, with features of meiotic chromosome structure partitioning the genome into regions where one pathway or the other predominates.
Crystal structure of 2-isopropyl-5,7′-dimethyl-1′,3′,3a',6′,8a',8b'-hexahydrospiro[cyclohexane-1,6′-furo[3,4-d]imidazo[1,5-b]isoxazol]-8′(7′H)-one
Authors: Abda Heithem , Ezzayani Khaireddine , Aouadi Kaiss , Guerfel Taha , Vidal Sebastien , Msaddek Moncef
Published: July 2016

In the title compound, C17H28N2O3, the isoxazolidine ring adopts an envelope conformation with the O atom deviating from the mean plane of the other four ring atoms by 0.617 (1) Å. In the crystal, molecules are linkedviaweak C—H...O hydrogen bonds, forming chains which extend along theb-axis direction.
Distinct coordination geometries in bis[N,N-bis(2-methoxyethyl)dithiocarbamato-κ2S,S′]diphenyltin(IV) and bis[N-(2-methoxyethyl)-N-methyldithiocarbamato-κ2S,S′]diphenyltin(IV): crystal structures and Hirshfeld surface analysis
Authors: Mohamad Rapidah , Awang Normah , Jotani Mukesh M. , Tiekink Edward R. T.
Published: July 2016

The crystal and molecular structures of two diphenyltin bis(dithiocarbamate)s, [Sn(C6H5)2(C5H10NOS2)2], (I), and [Sn(C6H5)2(C7H14NO2S2)2], (II), are described. In (I), in which the metal atom lies on a twofold rotation axis, the dithiocarbamate ligand coordinates with approximately equal Sn—S bond lengths and theipso-C atoms of the Sn-bound phenyl groups occupycis-positions in the resulting octahedral C2S4donor set. A quite distinct coordination geometry is noted in (II), arising as a result of quite disparate Sn—S bond lengths. Here, the four S-donors define a trapezoidal plane with theipso-C atoms lying over the weaker of the Sn—S bonds so that the C2S4donor set defines a skewed trapezoidal bipyramid. The packing of (I) features supramolecular layers in theabplane sustained by methylene-C—H...π(Sn–aryl) interactions; these stack along thec-axis direction with no specific interactions between them. In (II), supramolecular chains along theb-axis direction are formed by methylene-C—O(ether) interactions; these pack with no directional interactions between them. A Hirshfeld surface analysis was conducted on both (I) and (II) and revealed the dominance of H...H interactions contributing to the respective surfaces,i.e. >60% in each case, and other features consistent with the description of the molecular packing above.
YCu(TeO3)2(NO3)(H2O)3: a novel layered tellurite
Authors: Mills Stuart J. , Dunstan Maja A. , Christy Andrew G.
Published: July 2016

A new hydrated yttrium copper tellurite nitrate, yttrium(III) copper(II) bis[trioxidotellurate(IV)] nitrate trihydrate, has been synthesized hydrothermally in a Teflon-lined autoclave and structurally determined using synchrotron radiation. The new phase is the first example containing yttrium, copper and tellurium in one structure. Its crystal structure is unique, with relatively strongly bound layers extending parallel to (020), defined by YO8, CuO4and TeO3polyhedra, while the NO3−anions and one third of the water molecules lie between those layers. The structural unit consists of [Cu2(TeO3)4]4−loop-branched chains of {Cu...Te...Cu...Te} squares running parallel to [001], which are linked further into layers only through Y(O,H2O)8polyhedra. Weak `secondary' Te bonds and O—H...O hydrogen-bonding interactions, involving water molecules and layer O atoms, link the layers and interlayer species. IR spectroscopic data are also presented.
The crystal structures of two chalcones: (2E)-1-(5-chlorothiophen-2-yl)-3-(2-methylphenyl)prop-2-en-1-one and (2E)-1-(anthracen-9-yl)-3-[4-(propan-2-yl)phenyl]prop-2-en-1-one
Authors: Girisha Marisiddaiah , Yathirajan Hemmige S. , Jasinski Jerry P. , Glidewell Christopher
Published: July 2016

In the crystal of compound (I), C14H11ClOS, molecules are linked by C—H...O hydrogen bonds to form simpleC(5) chains. Compound (II), C26H22O, crystallizes withZ′ = 2 in space groupP-1; one of the molecules is fully ordered but the other is disordered over two sets of atomic sites having occupancies 0.644 (3) and 0.356 (3). The two disordered components differ from one another in the orientation of the isopropyl substituents, and both differ from the ordered molecules in the arrangement of the central propenone spacer unit, so that the crystal of (II) contains three distinct conformers. The ordered and disordered conformers each form aC(8) chain built from a single type of C—H...O hydrogen bond but those formed by the disordered conformers differ from that formed by the ordered form.
2-Amino-3-methylpyridinium 4-methoxybenzoate
Authors: Sivakumar P. , Devi R. Niranjana , Israel S. , Chakkaravarthi G.
Published: July 2016

In the title molecular salt, C6H9N2+·C8H7O3−, the cation is protonated at its pyridine N atom and is inclined by 3.39 (9)° to the benzene ring of the anion, which is deprotonated at the carboxyl group. The methoxy group is twisted with respect to the benzene ring to which it is attached, the methyl C atom deviating from the ring plane by 0.023 (2) Å. In the crystal, the anions and cations are linked by two N—H...O hydrogen bonds, forming anR22(8) ring motif. They are also linked by a weak offset π–π interaction [centroid-to-centroid distance = 3.890 (1) Å]. The anions and cations are further connected through N—H...O and C—H...O hydrogen bonds, forming slabs parallel to (001).
Bis[S-hexyl 3-(thiophen-2-ylmethylidene)dithiocarbazato-κ2N3,S]palladium(II)
Authors: Begum K. , Sheikh M. C. , Miyatake R. , Zangrando E. , Begum M. S.
Published: July 2016

In the title complex, [Pd(C12H17N2S3)2], the PdIIatom exhibits a square-planar coordination geometry with theN,S-chelating ligands arranged in atransconfiguration. Intramolecular C—H...S hydrogen bonds are observed. In the crystal, molecules are linked by weak C—H...N hydrogen-bond interactions, forming chains parallel to thebaxis.
Scale development for consumer protection and its determinants: evidence from Nigeria
Authors: Usman Dahiru Jafaru , Yaacob Nurli , Rahman Aspalella A.
Published: July 2016

Purpose

This paper aims to develop an instrument for measuring Consumer Protection and its Determinants (CP&Ds). This is because literature on an instrument to measure CP&Ds is scarce.

Design/methodology/approach

In Nigeria, 53 questionnaires were distributed to legal practitioners. The study used 24 items to operationalize the CP&Ds. The research data were coded and scored, and the exploratory factor analysis (EFA) was conducted using SPSS version 22. The Bartlett’s test of sphericity, Kaiser–Meyer–Olkin, Cronbach’s alpha and Pearson’s correlation coefficient were used for the EFA, internal consistency reliability and multicollinearity, respectively.

Findings

The EFA produced seven factors, and each determinant was found reliable with its measure of internal consistency.

Research limitations/implications

The research result may not be generalized across jurisdiction because of the limited sample size and the fact that the data were collected from Nigerian legal practitioners.

Practical implications

This study can be used by policymakers and even private electricity companies in the deregulated electricity sector in Nigeria for policy design and effective consumer protection.

Originality/value

From the extensive literature review none was identified on the scale development for measuring CP&Ds. This exploratory research is the first attempt to develop an instrument for measuring CP&Ds.
Corporate governance in Malaysia: has MCCG made a difference
Authors: Bhatt Padmanabha Ramachandra
Published: July 2016

Purpose

The purpose of this paper is to study the effect of Malaysian Code on Corporate Governance (MCCG) on the performance of the listed companies in Malaysia.

Design/methodology/approach

Panel data estimation techniques were used to run the regression in this study, following Baltagi (1995). The authors have selected 116 listed companies to Bursa Malaysia during the period 1996-2014, to study the effect of corporate governance on firm performance. Listed companies in Malaysia are mandatory to comply with MCCG rules and regulations.

Findings

It was found that there was a significant improvement in the performance of listed companies after Malaysian Government’s implementation of MCCG (2000) which means that MCCG matters for firm performance in Malaysia. It was also found that there was no significance difference in the overall impact of implementation of MCCG on performance level between government-linked companies (GLCs) and private companies (PCs).

Research limitations/implications

The authors have selected only 116 listed companies to Bursa Malaysia during the period 1996-2014, to study the effect of corporate governance on firm performance. The selection of the data was based on the availability of data in Thomson data stream.

Originality/value

The findings had contributed to the understanding that the MCCG has improved significantly the performance of listed companies in Malaysia.
Operational ethical banking in Rastin Banking
Authors: Bidabad Bijan , Sherafati Mahshid
Published: July 2016

Purpose

This paper aims to discuss some of the operational Islamic banking features considered in ethical banking as the aspects of Rastin Banking. Ethical banking is a branch of “ethic economics” and a narrow expression of a number of Islamic banking aspects.

Design/methodology/approach

These features are often involved in the discussions under the topic of internal control and describe the operational characteristics of ethical banking within the framework of Rastin Banking.

Findings

This study refers to the principles of Rastin Banking, including operational, financial, economic, ethical, social, legal, international and organizational principles. Additionally, it takes into account some of the internal control systems.

Research limitations/implications

Converting ethical codes into executable laws and regulations needs sophistication, and the art of codification in this subject can be observed in the present paper.

Practical implications

As far as the ethical behaviour of the assessor and trustee is concerned, the necessities of honesty, belief, virtuosity, rectitude and compliance with moral values, as well as reward and punishment mechanisms, are operationally examined. Transparency, governance and disclosure of information are the other components. The methods of auditing, accounting, inspection and preservation of Rastin Banking achievements are amongst the other matters of concern.

Social implications

An assiduous attention to the operational details of each of the above-said discussions revealed that the Islamic banking components are capable of covering the topics and discussions beyond ethical banking.

Originality/value

This paper fulfils an identified need to solve the practical ethical problem in operational banking.
Faith (re)engages with business: cultural, legal, and managerial dimensions
Authors: Morgan James Frederick
Published: July 2016

Purpose

This paper aims to explore the changing nature of religion (also described in terms of faith or spirituality) as experienced in the USA, particularly regarding the interrelationship between business and religion within the contexts of culture, law and management. With a solid understanding of these subjects, business leaders, judges and public policy officials will be able to more effectively deal with issues arising from a more religious workplace.

Design/methodology/approach

This paper begins by examining the religious nature of the USA, with attention paid to the embrace of religious tolerance from a cultural perspective and religious liberty from a legal perspective. The piece then looks at the characteristics associated with religious vibrancy. Then, the paper delves into the impact of religion on business, both yesterday and today. Legal and managerial literature, studies and perspectives are used to determine how business can respond and perhaps even embrace a more religious business environment.

Findings

After describing and critiquing cultural, legal and managerial dimensions associated with an increasingly religious business environment at worker and owner levels, this paper suggests there exists currently an adequate legal structure to serve the needs of religious workers and owners, if properly managed. More research is needed to find solutions to situations where competing interests conflict, but this paper provides a foundation upon which further study can be conducted.

Originality/value

This paper draws from cultural, legal and management sources to provide an understanding of the current religious environment facing business, legal and public policy leaders.
Strategic predisposition in communication management
Authors: Kim Soojin
Published: July 2016

Purpose

– The purpose of this paper is to identify factors influencing an organization’s predisposition to bridging strategy, and tests relationships between those factors and bridging strategy.

Design/methodology/approach

– Online survey was conducted in South Korea. Hierarchical regression was used.

Findings

– Identified factors are environmental complexity, top management attitude toward stakeholders, analysis orientation, and authoritarian culture.

Research limitations/implications

– By adopting the concept and measures of bridging as an organization’s public-engagement strategy, this study was able to capture an organization’s strategic approach for problem-solving in communication management.

Practical implications

– Strong analysis orientation allows organizations to look into problems in their complex environments affecting their performance and their key stakeholders before deciding on strategies; resultantly, they are more likely to reduce problems and to improve their performance. In contrast, authoritarian culture discourages an organization’s adoption of bridging strategy.

Originality/value

– This study is the first empirical study investigating the dynamics of factors influencing organizations’ strategic predisposition in communication management.