bluuebunny/crossref_metadata_2025 huggingface dataset:
La evaluación en el aula de traducción jurídica
Authors: Pontrandolfo Gianluca
Published: August 2016

El artículo propone un estudio de caso basado en la descripción y evaluación de los errores más representativos detectados en un encargo didáctico de traducción jurídica de una sentencia penal en la combinación español-italiano. El objetivo primario del trabajo es llevar a cabo un análisis cuantitativo y cualitativo de las principales tipologías de errores detectados desde una perspectiva funcional, textual y contextual. El análisis está orientado a la identificación de los problemas de traducción a los que se pueden enfrentar los alumnos en la fase de traducción de un texto judicial, dificultades que representan, básicamente, las áreas que los profesores de traducción jurídica tendrían que trabajar más para desarrollar las competencias del alumnado y mejorar la calidad de sus producciones mediante tareas específicas y unidades didácticas ad hoc en sus clases.
Exogenous TNFR2 activation protects from acute GvHD via host T reg cell expansion
Authors: Chopra Martin , Biehl Marlene , Steinfatt Tim , Brandl Andreas , Kums Juliane , Amich Jorge , Vaeth Martin , Kuen Janina , Holtappels Rafaela , Podlech Jürgen , Mottok Anja , Kraus Sabrina , Jordán-Garrote Ana-Laura , Bäuerlein Carina A. , Brede Christian , Ribechini Eliana , Fick Andrea , Seher Axel , Polz Johannes , Ottmüller Katja J. , Baker Jeanette , Nishikii Hidekazu , Ritz Miriam , Mattenheimer Katharina , Schwinn Stefanie , Winter Thorsten , Schäfer Viktoria , Krappmann Sven , Einsele Hermann , Müller Thomas D. , Reddehase Matthias J. , Lutz Manfred B. , Männel Daniela N. , Berberich-Siebelt Friederike , Wajant Harald , Beilhack Andreas
Published: August 2016

Donor CD4+Foxp3+ regulatory T cells (T reg cells) suppress graft-versus-host disease (GvHD) after allogeneic hematopoietic stem cell transplantation (HCT [allo-HCT]). Current clinical study protocols rely on the ex vivo expansion of donor T reg cells and their infusion in high numbers. In this study, we present a novel strategy for inhibiting GvHD that is based on the in vivo expansion of recipient T reg cells before allo-HCT, exploiting the crucial role of tumor necrosis factor receptor 2 (TNFR2) in T reg cell biology. Expanding radiation-resistant host T reg cells in recipient mice using a mouse TNFR2-selective agonist before allo-HCT significantly prolonged survival and reduced GvHD severity in a TNFR2- and T reg cell–dependent manner. The beneficial effects of transplanted T cells against leukemia cells and infectious pathogens remained unaffected. A corresponding human TNFR2-specific agonist expanded human T reg cells in vitro. These observations indicate the potential of our strategy to protect allo-HCT patients from acute GvHD by expanding T reg cells via selective TNFR2 activation in vivo.
Orientation-specific RAG activity in chromosomal loop domains contributes to Tcrd V(D)J recombination during T cell development
Authors: Zhao Lijuan , Frock Richard L. , Du Zhou , Hu Jiazhi , Chen Liang , Krangel Michael S. , Alt Frederick W.
Published: August 2016

T cell antigen receptor δ (Tcrd) variable region exons are assembled by RAG-initiated V(D)J recombination events in developing γδ thymocytes. Here, we use linear amplification–mediated high-throughput genome-wide translocation sequencing (LAM-HTGTS) to map hundreds of thousands of RAG-initiated Tcrd D segment (Trdd1 and Trdd2) rearrangements in CD4−CD8− double-negative thymocyte progenitors differentiated in vitro from bone marrow–derived hematopoietic stem cells. We find that Trdd2 joins directly to Trdv, Trdd1, and Trdj segments, whereas Trdd1 joining is ordered with joining to Trdd2, a prerequisite for further rearrangement. We also find frequent, previously unappreciated, Trdd1 and Trdd2 rearrangements that inactivate Tcrd, including sequential rearrangements from V(D)J recombination signal sequence fusions. Moreover, we find dozens of RAG off-target sequences that are generated via RAG tracking both upstream and downstream from the Trdd2 recombination center across the Tcrd loop domain that is bounded by the upstream INT1-2 and downstream TEA elements. Disruption of the upstream INT1-2 boundary of this loop domain allows spreading of RAG on- and off-target activity to the proximal Trdv domain and, correspondingly, shifts the Tcrd V(D)J recombination landscape by leading to predominant V(D)J joining to a proximal Trdv3 pseudogene that lies just upstream of the normal boundary.
Cuba's Agricultural Transition and Food Security in a Global Perspective
Authors: Riera Olivia , Swinnen Johan
Published: August 2016

This paper reviews the situation in the agricultural sector and food security in Cuba, and particularly the transformations that have (not) taken place since 1990. We compare the Cuban transition with transitions in other “transition countries” and show that Cuba does not easily fit into one of the transition patterns, and, in a way, has characteristics of “a bit of everything”. To conclude, we discuss the (potential) effects of the recent policy changes and the new economic reforms that were announced.
Continental versus oceanic subduction zones
Authors: Zheng Yong-Fei , Chen Yi-Xiang
Published: August 2016

Subduction zones are tectonic expressions of convergent plate margins, where crustal rocks descend into and interact with the overlying mantle wedge. They are the geodynamic system that produces mafic arc volcanics above oceanic subduction zones but high- to ultrahigh-pressure metamorphic rocks in continental subduction zones. While the metamorphic rocks provide petrological records of orogenic processes when descending crustal rocks undergo dehydration and anataxis at forearc to subarc depths beneath the mantle wedge, the arc volcanics provide geochemical records of the mass transfer from the subducting slab to the mantle wedge in this period though the mantle wedge becomes partially melted at a later time. Whereas the mantle wedge overlying the subducting oceanic slab is of asthenospheric origin, that overlying the descending continental slab is of lithospheric origin, being ancient beneath cratons but juvenile beneath marginal arcs. In either case, the mantle wedge base is cooled down during the slab–wedge coupled subduction. Metamorphic dehydration is prominent during subduction of crustal rocks, giving rise to aqueous solutions that are enriched in fluid-mobile incompatible elements. Once the subducting slab is decoupled from the mantle wedge, the slab–mantle interface is heated by lateral incursion of the asthenospheric mantle to allow dehydration melting of rocks in the descending slab surface and the metasomatized mantle wedge base, respectively. Therefore, the tectonic regime of subduction zones changes in both time and space with respect to their structures, inputs, processes and products. Ophiolites record the tectonic conversion from seafloor spreading to oceanic subduction beneath continental margin, whereas ultrahigh-temperature metamorphic events mark the tectonic conversion from compression to extension in orogens.
Climate change, air pollution, and allergic respiratory diseases: an update
Authors: D’Amato Gennaro , Vitale Carolina , Lanza Maurizia , Molino Antonio , D’Amato Maria
Published: August 2016

Purpose of review

The rising trend in prevalence of allergic respiratory disease and bronchial asthma, observed over the last decades, can be explained by changes occurring in the environment, with increasing presence of biologic, such as allergens, and chemical atmospheric trigger factors able to stimulate the sensitization and symptoms of these diseases.

Recent findings

Many studies have shown changes in production, dispersion, and allergen content of pollen and spores because of climate change with an increasing effect of aeroallergens on allergic patients.

Over the last 50 years, global earth's temperature has markedly risen likely because of growing emission of anthropogenic greenhouse gas concentrations. Major changes involving the atmosphere and the climate, including global warming induced by human activity, have a major impact on the biosphere and human environment.

Urbanization and high levels of vehicle emissions are correlated to an increase in the frequency of pollen-induced respiratory allergy prevalent in people who live in urban areas compared with those who live in rural areas. Measures of mitigation need to be applied for reducing future impacts of climate change on our planet, but until global emissions continue to rise, adaptation to the impacts of future climate variability will also be required.
The Difference Between Random and Postaccident Urine Drug Test Concentrations Among Southern Indiana, Western Kentucky, and Eastern Illinois Workers
Authors: Price James W.
Published: August 2016

Introduction:

If employee drug use plays a significant part in the incidence of workplace accidents, one would anticipate the positivity rates of postaccident drug tests to be higher than the positivity rates for random tests. Past studies examined the difference of a dichotomous outcome between 2 groups. Dichotomous (positive or negative) categorization may have been a source of systemic error, which minimized the difference between random and postaccident groups.

Methods:

This is a study exploring the difference of urine drug concentrations between random and postaccident groups. The population consists of employees from various industries in Southern Indiana, Western Kentucky, and Eastern Illinois. Normalization of drug excretion to urinary creatinine concentration was carried out. Preliminary assumption testing was done. Logarithmic transformation was completed. One-way between-groups analysis of variance was performed to investigate random and postaccident drug test differences in urine drug concentrations.

Results:

There was a statistically significant difference between test groups on the combined dependent variables. The only dependent variables to reach statistical significance, to an alpha level of 0.025, were urine opiate and urine amphetamine concentrations. Higher mean concentration of both drugs was found in the postaccident group. However, the proportion of variances explained by the reason for testing was quite small.

Conclusions:

The results of this study are consistent with studies using dichotomous dependent variables, which demonstrated a significantly higher prevalence for positive postaccident urine opiate tests. The study also identified a similar result for postaccident urine amphetamine tests which was not previously known.
Contribution of Opiate Analgesics to the Development of Infections in Advanced Cancer Patients
Authors: Shao Yue-juan , Liu Wei-shuai , Guan Bing-qing , Hao Jian-lei , Ji Kai , Cheng Xian-jiang , Wang Kun
Published: August 2016

Objectives:

Literature is limited on the relationship between opiate analgesics and the development of infections in cancer patients. This study aimed to determine whether opiate analgesics contribute to the advancement of infections and how infection rates differ among the various opiates used for cancer management.

Materials and Methods:

From January 2013 to October 2014, we analyzed retrospectively 642 consecutive advanced cancer patients who received single types of opiates, including morphine, oxycodone, or fentanyl, or a combination of these drugs, continuously for >14 days. Binominal logistic regression analysis was used to analyze the factors that may promote the development of infections.

Results:

A total of 303 patients were included in the final analysis. Of these patients, 85, 41, and 68 patients received only morphine, oxycodone, and fentanyl, respectively. Altogether, 87 (28.7%) patients developed infections; 20 (23.5%), 10 (24.4%), and 14 (20.6%) patients developed infections in the groups that received only morphine, oxycodone, and fentanyl, respectively (P>0.05). Logistic regression analysis found that the daily oral morphine equivalent (OME) is the an independent factor that influences the development of infection in the single-opiate group (odds ratio=1.002, P<0.01). The risk for developing infection increased by 2% per 10 mg increase in the daily OME.

Conclusions:

Our clinical results did not display any difference among the single-opiate groups in the development of infections. However, the increase in daily OME may serve as a risk factor for the development of infections in advanced cancer patients using one opiate type for pain management.
Expert Nurses' Perceptions of the Relevance of Carper's Patterns of Knowing to Junior Nurses
Authors: Terry Louise , Carr Graham , Curzio Joan
Published: August 2016

This study explored with expert nurses in the UK how nursing wisdom can be developed in new and junior nurses. Carper's patterns of knowing and Benner's novice-to-expert continuum formed the theoretical framework. Employing a constructionist research methodology with participant engagement in co-construction of findings, data were collected via 2 separate cycles comprising 4 consecutive sessions followed by a nationally advertised miniconference. Empirical, ethical, personal, and esthetic knowing was considered evident in junior nurses. Junior nurses in the UK seem to lack a previously unrecognized domain of organizational knowing without which they cannot overcome hegemonic barriers to the successful development of nursing praxis.
What's new in the world of postmenopausal sex?
Authors: Iglesia Cheryl B.
Published: August 2016

Purpose of review

The purpose of this review is to describe new terminology for vulvovaginal atrophy and female sexual dysfunction and to highlight recent findings related to vaginal moisturizers, lubricants and prescription estrogen preparations.

Recent findings

Sexual health is a marker for overall health. A minority (40%) of healthcare providers routinely ask about sexual problems and its impact on quality of life. New terminology by the American Psychiatric Association divides female sexual disorders into three categories: arousal/interest disorder, orgasmic disorder and genital pain and penetration disorder. First-line therapy for genitourinary syndrome of menopause includes over-the-counter vaginal lubricants and moisturizers, followed by topical estrogen formulations. Progesterones are generally not needed when topical low-dose estrogen is prescribed. A systemic selective estrogen receptor modulator, designed specifically for genitourinary menopausal symptoms, is an option for patients who do not tolerate local estrogen.

Female sexual dysfunction is prevalent and causes distress, particularly among women at midlife. Although hypoactive sexual desire disorder may be the most prevalent dysfunction, dyspareunia and pain, particularly related to genitourinary and vulvovaginal atrophy, are also very common. Over-the-counter lubricants and prescription strength estrogen formulations are generally effective and well tolerated.
Multiple Delayed Scalp Reconstruction for Complicated Cranial Defects
Authors: Sakamoto Yoshiaki , Arnaud Eric
Published: August 2016

In cases of skull trauma, emergency surgery for cranial decompression typically involves the shortest approach, with the incision lying directly on or immediately near the bony defect. Subsequent reconstructive plastic surgery for the skull is difficult in such cases because incisions taken on the previous scar overlying the bony defect are prone to dehiscence and infection. Herein, we describe a technique for creating a well-vascularized delayed skin flap via multistaged operation before the actual skull reconstruction. Four patients (age range, 10–25 y) were prepared for skull reconstruction using this technique. Flap elevation was performed in 3 stages, with adequate time intervals (4 wk between each stage) to allow for adequate delay. Dissection under the galea aponeurotica was performed only after initial flap elevation allowing for adequate vascularization. Skull reconstruction was then performed using custom-made implants. The patients were followed up for 6 to 12 months. No complications, including infections, exposure of the artificial bone, or flap necrosis, were observed. All the patients were satisfied with the cosmetic results. Despite the multiple stages required, we consider that our technique of using a delayed, well-vascularized bipedicled skin flap can be successfully used in the skull reconstruction of patients in whom the initial scar lies close to the bone defect. We recommend scalp incision be shifted outside of the foreseen bony flap to limit infectious risks during primary or subsequent cranial reconstruction.
Raising the Minimum Effective Dose of Serotonin Reuptake Inhibitor Antidepressants
Authors: Safer Daniel J.
Published: August 2016

This review focuses on the dose-response of serotonin reuptake inhibitor (SRI) antidepressants for efficacy and for adverse drug events (ADEs). Dose-response is identified by placebo-controlled, double-blind, fixed-dose clinical trials comparing various doses for efficacy and for ADEs. Reports from the great majority of clinical trials have consistently found that the minimum SRI effective dose is usually optimal for efficacy in the treatment of depression disorders, even though most American medical practitioners raise the dose when early antidepressant treatment results are negative or partial. To better understand this issue, the medical literature was comprehensively reviewed to ascertain the degree to which SRI medications resulted in a flat dose response for efficacy and then to identify specific ADEs that are dose-dependent. Strong evidence from fixed-dose trial data for the efficacy of nonascendant, minimum effective doses of SRIs was found for the treatment of both major depression and anxiety disorders. Particularly important was the finding that most SRI ADEs have an ascending dose-response curve. These ADEs include sexual dysfunction, hypertension, cardiac conduction risks, hyperglycemia, decreased bone density, sweating, withdrawal symptoms, and agitation. Thus, routinely raising the SRI dose above the minimum effective dose for efficacy can be counter-productive.
New apheresis indications in hematological disorders
Authors: Pham Huy P. , Schwartz Joseph
Published: August 2016

Purpose of review

Therapeutic apheresis can be used to treat many diseases. The American Society for Apheresis (ASFA) publishes Guidelines on the use of therapeutic apheresis every 3 years with the goal of providing the best available evidence for apheresis practice as well as clinical expertise. The 2016 (7th ed.) ASFA Guidelines contain 87 diseases (up from 78 in the 6th ed.) and 179 indications. This review outlines three new therapeutic apheresis indications for hematological disorders.

Recent findings

The three new nonmalignant and nontransplant-related hematological disorders discussed are therapeutic plasma exchange procedures for hemophagocytic syndrome, hemolysis, elevated liver enzymes, and low platelets syndrome, and red blood cell exchange to prevent alloimmunization after exposure to rhesus (D)-positive red blood cells. All three indications are ASFA category III indications (i.e., optimal role of apheresis therapy is not established) with Grade 2C recommendation (weak recommendation, low-quality evidence).

Although the three new therapeutic apheresis indications related to hematological disorders are ASFA category III with Grade 2C recommendations, along with other ASFA category III with Grade 2C recommendations, they may form the list of diseases for which basic, translational, and clinical research is needed to provide better evidence for clinical practice.
Histology of the Transition Zone in Hirschsprung Disease
Authors: Kapur Raj P.
Published: August 2016

Surgical management of Hirschsprung disease requires resection of the aganglionic bowel and transition zone, a length of ganglionic bowel, immediately proximal to the aganglionic segment, with neuropathologic features that seem to correlate with dysmotility. Pathologists must be able to recognize histopathologic features of the transition zone in hematoxylin and eosin–stained sections in order to interpret intraoperative frozen sections and ensure adequate resection. The proximal ganglionic portions of colonic resection specimens from 59 patients with distal aganglionosis were analyzed with closely spaced transverse sections to map the distribution of the 3 most commonly referenced features of transition zone (partial circumferential aganglionosis, myenteric hypoganglionosis, and submucosal nerve hypertrophy). Each of these “primary” findings was restricted to a region ≤5 cm proximal to the aganglionic segment in the overwhelming majority of patients. Exceptions were more common with longer aganglionic segments. Three other neuroanatomic phenotypes (gangliosclerosis, ectopic myenteric ganglia, and eosinophilic ganglionitis) of uncertain clinical significance were distributed more irregularly and often over much longer distances. Routine resection of at least 5 cm of ganglionic bowel proximal to the aganglionic segment may reduce the incidence of transition zone pull-through. However, routine intraoperative frozen section examination of the proximal resection margin to exclude the 3 primary forms of hematoxylin and eosin neuropathology described in this study is strongly advised.
Spectrum of Magnetic Resonance Imaging Features in Unilateral Optic Tract Dysfunction
Authors: Kowal Kristopher M. , Rivas Rodriguez Francisco F. , Srinivasan Ashok , Trobe Jonathan D.
Published: August 2016

Background:

Optic tract dysfunction may be the predominant or only clinical manifestation of an intracranial disorder including mass legion, ischemic infarct, inflammatory disease, and trauma. Documentation of the neuroimaging features of these lesions is limited to reports mostly published before the availability of MRI. This study was undertaken to document the spectrum of MRI features in patients presenting with optic tract dysfunction.

Methods:

A retrospective study from 2004 to 2015 at a single tertiary care neuro-ophthalmology service of 24 patients who had unilateral optic tract dysfunction defined by a homonymous hemianopia and a relative afferent pupil defect that could not be attributed to optic neuropathy or retinopathy. Two institutional neuroradiologists, who were privy to the presence of optic tract dysfunction but not to its side or cause, independently documented the MRI abnormalities on a standard data collection form and then convened for a consensus review of the imaging abnormalities with the 2 clinician authors.

Results:

The clinical diagnoses were 6 ischemic strokes, 5 malignant brain tumors, 5 postoperative neurosurgical cases, 4 intracranial hemorrhages, 2 traumatic brain injuries, 1 midbrain/optic tract primary demyelination, and 1 temporal lobe herpes simplex encephalitis. In their independent review, both neuroradiologists identified MRI abnormalities in 20 (83%) cases that were extrinsic to the optic tract in the neighboring temporal lobe, midbrain, thalamus, basal ganglia, or suprasellar space. In 5 of those cases, the extrinsic abnormality included features suggesting compression of the optic tract, but these compressive features were not appreciated by either neuroradiologist until the consensus conference. In 15 cases, MRI abnormalities intrinsic to the optic tract itself were eventually identified, including T2 or fluid-attenuated inversion recovery image (FLAIR) hyperintensity (9 cases) or hypointensity (1 case), thinning (6 cases), thickening (2 cases), and contrast enhancement (1 case). However, none of these intrinsic MRI abnormalities was identified during the independent review, being detected only in the consensus conference.

Conclusions:

Neuroradiologists aware of unilateral optic tract dysfunction but not of its side detected extrinsic (neighborhood) MRI abnormalities in most cases but did not appreciate that these extrinsic features sometimes included compression of the optic tract. MRI abnormalities intrinsic to the optic tract were entirely overlooked during independent review, being recognized only in a consensus conference with clinician authors. Neuroradiologists are more likely to detect MRI abnormalities pertinent to optic tract dysfunction once they have more complete clinical information and with higher resolution imaging, especially T1 postcontrast axial and coronal sequences and T2 or FLAIR coronal scans.
Whole genome sequencing ofPlasmodium falciparumfrom dried blood spots using selective whole genome amplification
Authors: Oyola Samuel O. , Ariani Cristina V. , Hamilton William L. , Kekre Mihir , Amenga-Etego Lucas N. , Ghansah Anita , Rutledge Gavin G. , Redmond Seth , Manske Magnus , Jyothi Dushyanth , Jacob Chris G. , Otto Thomas D. , Rockett Kirk , Newbold Chris I. , Berriman Matthew , Kwiatkowski Dominic P.
Published: August 2016

Translating genomic technologies into healthcare applications for the malaria parasitePlasmodium falciparumhas been limited by the technical and logistical difficulties of obtaining high quality clinical samples from the field. Sampling by dried blood spot (DBS) finger-pricks can be performed safely and efficiently with minimal resource and storage requirements compared with venous blood (VB). Here, we evaluate the use of selective whole genome amplification (sWGA) to sequence theP. falciparumgenome from clinical DBS samples, and compare the results to current methods using leucodepleted VB. Parasite DNA with high (> 95%) human DNA contamination was selectively amplified by Phi29 polymerase using short oligonucleotide probes of 8-12 mers as primers. These primers were selected on the basis of their differential frequency of binding the desired (P. falciparumDNA) and contaminating (human) genomes. Using sWGA method, we sequenced clinical samples from 156 malaria patients, including 120 paired samples for head-to-head comparison of DBS and leucodepleted VB. Greater than 18-fold enrichment ofP. falciparumDNA was achieved from DBS extracts. The parasitaemia threshold to achieve >5x coverage for 50% of the genome was 0.03% (40 parasites per 200 white blood cells). Over 99% SNP concordance between VB and DBS samples was achieved after excluding missing calls. The sWGA methods described here provide a reliable and scalable way of generatingP. falciparumgenome sequence data from DBS samples. Our data indicate that it will be possible to get good quality sequence data on most if not all drug resistance loci from the majority of symptomatic malaria patients. This technique overcomes a major limiting factor inP. falciparumgenome sequencing from field samples, and paves the way for large-scale epidemiological applications.
Bootstrat: Population Informed Bootstrapping for Rare Variant Tests
Authors: Huang Hailiang , Peloso Gina M. , Howrigan Daniel , Rakitsch Barbara , Simon-Gabriel Carl Johann , Goldstein Jacqueline I. , Daly Mark J. , Borgwardt Karsten , Neale Benjamin M.
Published: August 2016

Recent advances in genotyping and sequencing technologies have made detecting rare variants in large cohorts possible. Various analytic methods for associating disease to rare variants have been proposed, including burden tests, C-alpha and SKAT. Most of these methods, however, assume that samples come from a homogeneous population, which is not realistic for analyses of large samples. Not correcting for population stratification causes inflated p-values and false-positive associations. Here we propose a population-informed bootstrap resampling method that controls for population stratification (Bootstrat) in rare variant tests. In essence, the Bootstrat procedure uses genetic distance to create a phenotype probability for each sample. We show that this empirical approach can effectively correct for population stratification while maintaining statistical power comparable to established methods of controlling for population stratification. The Bootstrat scheme can be easily applied to existing rare variant testing methods with reasonable computational complexity.

Author Summary

Recent technology advances have enabled large-scale analysis of rare variants, but properly testing rare variants remains a significant challenge as most rare variant testing methods assume a sample of homogenous ethnicity, an assumption often not true for large cohorts. Failure to account for this heterogeneity increases the type I error rate. Here we propose a bootstrap scheme applicable to most existing rare variant testing methods to control for population heterogeneity. This scheme uses a randomization layer to establish a null distribution of the test statistics while preserving the sample genetic relationships. The null distribution is then used to calculate an empirical p-value that accounts for population heterogeneity. We demonstrate how this scheme successfully controls the type I error rate without loss of statistical power.
ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions
Authors: Latif Haythem , Federowicz Stephen , Ebrahim Ali , Tarasova Janna , Szubin Richard , Utrilla Jose , Zengler Karsten , Palsson Bernhard O.
Published: August 2016

Numerousin vitrostudies have yielded a refined picture of the structural and molecular associations between Cyclic-AMP receptor protein (Crp), the DNA motif, and RNA polymerase (RNAP) holoenzyme. In this study, high-resolution ChIP-exonuclease (ChIP-exo) was applied to study Crp bindingin vivoand at genome-scale. Surprisingly, Crp was found to provide little to no protection of the DNA motif under activating conditions. Instead, Crp demonstrated binding patterns that closely resembled those generated by σ70. The binding patterns of both Crp and σ70are indicative of RNAP holoenzyme DNA footprinting profiles associated with stages during transcription initiation that occur post-recruitment. This is marked by a pronounced advancement of the template strand footprint profile to the +20 position relative to the transcription start site and a multimodal distribution on the nontemplate strand. This trend was also observed in the familial transcription factor, Fnr, but full protection of the motif was seen in the repressor ArcA. Given the time-scale of ChIP studies and that the rate-limiting step in transcription initiation is typically post recruitment, we propose a hypothesis where Crp is absent from the DNA motif but remains associated with RNAP holoenzyme post-recruitment during transcription initiation. The release of Crp from the DNA motif may be a result of energetic changes that occur as RNAP holoenzyme traverses the various stable intermediates towards elongation complex formation.
Rapid evolution of distinctHelicobacter pylorisubpopulations in the Americas
Authors: Thorell Kaisa , Yahara Koji , Berthenet Elvire , Lawson Daniel J. , Kato Ikuko , Mendez Alfonso , Canzian Federico , Bravo María Mercedes , Suzuki Rumiko , Yamaoka Yoshio , Torres Javier , Sheppard Samuel K , Falush Daniel
Published: August 2016

For the last 500 years, the Americas have been a melting pot both for genetically diverse humans and for the pathogenic and commensal organisms associated with them. One such organism is the stomach dwelling bacteriumHelicobacter pylori, which is highly prevalent in Latin America where it is a major current public health challenge because of its strong association with gastric cancer. By analyzing the genome sequence ofH. pyloriisolated in North, Central and South America, we found evidence for admixture betweenH. pyloriof European and African origin throughout the Americas, without substantial input from pre-Columbian (hspAmerind) bacteria. In the US, strains of African and European origin have remained genetically distinct, while in Colombia and Nicaragua, bottlenecks and rampant genetic exchange amongst isolates have led to the formation of national gene pools. We found four outer membrane proteins with atypical levels of Asian ancestry in American strains, including the adhesion factor AlpB, suggesting a role for the ethnic makeup of hosts in the colonization of incoming strains. Our results show that newH. pylorisubpopulations can rapidly arise, spread and adapt during times of demographic flux, and suggest that differences in transmission ecology between high and low prevalence areas may substantially affect the composition of bacterial populations.

Author Summary

Helicobacter pyloriis one of the best studied examples of an intimate association between bacteria and humans, due to its ability to colonize the stomach for decades and to transmit from generation to generation. A number of studies have sought to link diversity inH. pylorito human migrations but there are some discordant signals such as an “out of Africa” dispersal within the last few thousand years that has left a much stronger signal in bacterial genomes than in human ones. In order to understand how such discrepancies arise, we have investigated the evolution ofH. pyloriduring the recent colonization of the Americas. We find that bacterial populations evolve quickly and can spread rapidly to people of different ethnicities. Distinct new bacterial subpopulations have formed in Colombia from a European source and in Nicaragua and the US from African sources. Genetic exchange between bacterial populations is rampant within Central and South America but is uncommon within North America, which may reflect differences in prevalence. Our results also suggest that adaptation of bacteria to particular human ethnic groups may be confined to a handful of genes involved in interaction with the immune system.
IMMAN: an R/Bioconductor package for Interolog protein network reconstruction, Mapping and Mining ANalysis
Authors: Ashtinai Minoo , Nickchi Payman , Jahangiri-Tazehkand Soheil , Safari Abdollah , Mirzaie Mehdi , Jafari Mohieddin
Published: August 2016

IMMAN is a software for reconstructing Interolog Protein Network (IPN) by integrating several Protein-protein Interaction Networks (PPIN). Users can unify different PPINs to mine conserved common network among species. IMMAN helps to retrieve IPNs with different degrees of conservation to engage for protein function prediction analysis based on protein networks.

Availability

IMMAN is freely available athttps://bioconductor.org/packages/IMMAN,http://profiles.bs.ipm.ir/softwares/IMMAN/.

Contact

mirzie@ipm.ir,mjafari@ipm.ir,asafari@sfu.ca

Supplementary information

Supplementary data are available online.
CAMSA: a Tool for Comparative Analysis and Merging of Scaffold Assemblies
Authors: Aganezov Sergey S. , Alekseyev Max A.
Published: August 2016

Motivation

Despite the recent progress in genome sequencing and assembly, many of the currently available assembled genomes come in a draft form. Such draft genomes consist of a large number of genomic fragments (scaffolds), whose positions and orientations along the genome are unknown. While there exists a number of methods for reconstruction of the genome from its scaffolds, utilizing various computational and wet-lab techniques, they often can produce only partial error-prone scaffold assemblies. It therefore becomes important to compare and merge scaffold assemblies produced by different methods, thus combining their advantages and highlighting present conflicts for further investigation. These tasks may be labor intensive if performed manually.

Results

We present CAMSA—a tool for comparative analysis and merging of two or more given scaffold assemblies. The tool (i) creates an extensive report with several comparative quality metrics; (ii) constructs the most confident merged scaffold assembly; and (iii) provides an interactive framework for a visual comparative analysis of the given assemblies. Among the CAMSA features, only scaffold merging can be evaluated in comparison to existing methods. Namely, it resembles the functionality of assembly reconciliation tools, although their primary targets are somewhat different. Our evaluations show that CAMSA produces merged assemblies of comparable or better quality than existing assembly reconciliation tools while being the fastest in terms of the total running time.

Availability

CAMSA is distributed under the MIT license and is available athttp://cblab.org/camsa/.
Thermal niche evolution across replicatedAnolislizard adaptive radiations
Authors: Gunderson Alex R. , Mahler D. Luke , Leal Manuel
Published: August 2016

Elucidating how ecological and evolutionary mechanisms interact to produce and maintain biodiversity is a fundamental problem in evolutionary ecology. We investigate this issue by focusing on how physiological evolution affects performance and species coexistence along the thermal niche axis in replicated radiations ofAnolislizards, groups best known for resource partitioning based on morphological divergence. We find repeated divergence in thermal physiology within these radiations, and that this divergence significantly affects performance within natural thermal environments. Morphologically similar species that co-occur invariably differ in their thermal physiology, providing evidence that physiological divergence facilitates species co-existence within anole communities. Despite repeated divergence in traits of demonstrable ecological importance, phylogenetic comparative analyses indicate that physiological traits have evolved more slowly than key morphological traits related to the structural niche. Phylogenetic analyses also reveal that physiological divergence is correlated with divergence in broad-scale habitat climatic features commonly used to estimate thermal niche evolution, but that the latter incompletely predicts variation in the former. We provide comprehensive evidence for repeated adaptive evolution of physiological divergence withinAnolisadaptive radiations, including the complementary roles of physiological and morphological divergence in promoting community-level diversity. We recommend greater integration of performance-based traits into analyses of climatic niche evolution, as they facilitate a more complete understanding of the phenotypic and ecological consequences of climatic divergence.
Clinical Utility of Expanded Carrier Screening: Reproductive Behaviors of At-Risk Couples
Authors: Ghiossi Caroline , Goldberg James D. , Haque Imran S. , Lazarin Gabriel A. , Wong Kenny K.
Published: August 2016

Purpose

Expanded carrier screening (ECS) analyzes dozens or hundreds of recessive genes for determining reproductive risk. Data on clinical utility of screening conditions beyond professional guidelines is scarce.

Methods

Individuals underwent ECS for up to 110 genes. 537 at-risk couples (ARC), those in which both partners carry the same recessive disease, were invited to a retrospective IRB-approved survey of their reproductive decision making after receiving ECS results.

Results

64 eligible ARC completed the survey. Of 45 respondents screened preconceptionally, 62% (n=28) planned IVF with PGD or prenatal diagnosis (PNDx) in future pregnancies. 29% (n=13) were not planning to alter reproductive decisions. The remaining 9% (n=4) of responses were unclear.

Of 19 pregnant respondents, 42% (n=8) elected PNDx, 11% (n=2) planned amniocentesis but miscarried, and 47% (n=9) considered the condition insufficiently severe to warrant invasive testing. Of the 8 pregnancies that underwent PNDx, 5 were unaffected and 3 were affected. 2 of 3 affected pregnancies were terminated.

Disease severity was found to have significant association (p=0.000145) with changes in decision making, whereas guideline status of diseases, controlled for severity, was not (p=0.284).

Conclusion

Most ARC altered reproductive planning, demonstrating the clinical utility of ECS. Severity of conditions factored into decision making.
Gas-sensitive biological crystals processed in pressurized oxygen and krypton atmospheres: deciphering gas channels in proteins using a novel `soak-and-freeze' methodology
Authors: Lafumat Bénédicte , Mueller-Dieckmann Christoph , Leonard Gordon , Colloc'h Nathalie , Prangé Thierry , Giraud Thierry , Dobias Fabien , Royant Antoine , van der Linden Peter , Carpentier Philippe
Published: August 2016

Molecular oxygen (O2) is a key player in many fundamental biological processes. However, the combination of the labile nature and poor affinity of O2 often makes this substrate difficult to introduce into crystals at sufficient concentrations to enable protein/O2 interactions to be deciphered in sufficient detail. To overcome this problem, a gas pressure cell has been developed specifically for the `soak-and-freeze' preparation of crystals of O2-dependent biological molecules. The `soak-and-freeze' method uses high pressure to introduce oxygen molecules or krypton atoms (O2 mimics) into crystals which, still under high pressure, are then cryocooled for X-ray data collection. Here, a proof of principle of the gas pressure cell and the methodology developed is demonstrated with crystals of enzymes (lysozyme, thermolysin and urate oxidase) that are known to absorb and bind molecular oxygen and/or krypton. The successful results of these experiments lead to the suggestion that the soak-and-freeze method could be extended to studies involving a wide range of gases of biological, medical and/or environmental interest, including carbon monoxide, ethylene, methane and many others.
Love is all around us in the workplace
Authors: Wheatcroft John
Published: August 2016

Purpose

The paper examines relationships in the workplace. It considers issues such as employee engagement, decisions to be in a relationship with a co-worker and its effects on commitment certainty in a sample of adults. They all said they were currently working with their romantic partner.

Design/methodology/approach

Bearing in mind that workplace romance can be a taboo topic, the researchers recruited participants anonymously from online social media websites.

Findings

Some participants said that they were motivated to be in a romantic relationship with a co-worker to increase status. They tended to report lower levels of engagement. However, when relationships hit a tricky patch and/or they felt uncertainty about the relationship, these participants tended to commit themselves more, rather than less to their work.

Originality/value

This is the first study to examine the influence of workplace romantic relationships in the context of employee engagement. It also documents links between workplace relationships and performance variables.
The mediating effect of management accounting system on the relationship between competition and managerial performance
Authors: Ghasemi Reza , Azmi Mohamad Noor , Karami Meisam , Hafiz Bajuri Norkhairul , Asgharizade Ezzatollah
Published: August 2016

Purpose

This study aims to examine the effect of interaction between market competition and management accounting system (MAS) characteristics on managerial performance. Scope of the study is concentrated on Iranian financial organizations and managers of these organizations were identified as respondents for the questionnaire survey.

Design/methodology/approach

This study used the SmartPLS to analyze the data, and the model of the study was estimated with structural equation modeling (SEM). It follows the recommended two-stage analytical procedures of SEM: assessing confirmatory measurement models (factor analysis) and confirmatory structural models (path analysis).

Findings

The study uncovered the existence of direct relationships between competition and MAS, and between MAS and managerial performance. The study also confirmed that the relationship between competition and managerial performance is mediated by MAS.

Research limitations/implications

The findings provide valuable insights to guide managers in financial organizations to improve their performance through suitable MAS by considering internal and environmental factors. Recommendations on how to improve MAS and managerial performance are provided accordingly.

Originality/value

Prior researches confirm that there is no unique and universal MAS for all organizations, as this depends on internal firm characteristics and environmental features. However, there has been a lack of empirical evidence on MAS researches in the service organizations.
IFRS and accounting quality: legal origin, regional, and disclosure impacts
Authors: Dayanandan Ajit , Donker Han , Ivanof Mike , Karahan Gökhan
Published: August 2016

Purpose

The purpose of this study is to examine whether the quality of financial reporting has improved after the adoption of International Financial Reporting Standards (IFRS) in Europe and across the world. The study investigates the impact of IFRS on income smoothing and earnings management in different geographic regions under different legal origins and disclosure environments.

Design/methodology/approach

To measure income smoothing in the pre- and post-IFRS periods, the authors use the coefficient of variation and the panel unit root model proposed by Im et al. (2003) for testing whether net income is stationary throughout the sample period. The study uses a dynamic panel estimation framework, as it captures the dynamics of IFRS on discretionary accruals efficiently. Discretionary accruals are used to measure earnings management.

Findings

The results suggest that the adoption of high quality standards, such as IFRS, reduces income smoothing and earnings management. In addition, the study finds that earnings management has decreased in the post-IFRS period, in particular, for French and Scandinavian civil law countries, but not for German civil law countries and common law countries. The latter can be explained by the fact that common law countries have strong investor protection laws, strict law enforcement and high disclosure levels of financial information. The study also finds empirical evidence that the adoption of IFRS reduces earnings management in countries with high levels of financial disclosure. Overall, the study shows that the adoption of IFRS improved the quality of financial reporting.

Originality/value

This study is useful for accounting standard setters across the world, including those countries that have not yet decided to adopt IFRS. The study contributes to the literature by examining the adoption of IFRS in income smoothing and earnings management under different legal regimes and disclosure environments by using advanced empirical methodologies.
Fluctuating capacity and impulsiveness in acquired brain injury: the dilemma of “unwise” decisions under the Mental Capacity Act
Authors: Lennard Chris
Published: August 2016

Purpose

– The purpose of this paper is to examine the dilemma at the heart of nursing care – the striving for empowerment of people in nurses’ care with the responsibility to protect vulnerable adults from harm. In doing so, it argues that in difficult and borderline cases, capacity assessment is complex and ultimately based on a judgment involving interpretation, and welcomes the views of clinicians who have challenged the procedural test of capacity in the Mental Capacity Act (MCA).

Design/methodology/approach

– It presents an illustrative study of a person with acquired brain injury (ABI) resident in a nursing home, who had been assessed under the MCA and judged to have capacity regarding health and welfare decisions, who subsequently displayed a persistent and impulsive desire to leave the unit without thought of risk and vulnerability to herself, prompting safeguarding concerns, and a reassessment of her capacity.

Findings

– The paper asserts that supporting people with ABI during capacity assessments, as the MCA decrees, in a very structured way can create a false sense of “capacity”. It maintains that executive impairments in ABI, being difficult to assess in formal settings, are best undertaken over time, in real-life settings, with evidence from third parties. It welcomes the MCA’s desire to protect individual autonomy and avoid undue paternalism, through ensuring people are not deemed to lack capacity simply because they make an unwise decision.

Originality/value

– But it goes on to argue that in ABI it is often the fact of unwise decision making that is the prominent factor and main concern, particularly in regard to impulsive decision making. If nurses have to make a judgment as to how unwise decisions made with decision-making capacity are to be distinguished from unwise decisions made without it in people with ABI, then, the author concludes, a major area of difficulty for nurses is ascertaining when the presumption of capacity should be challenged, an area that an updated code of practice needs to clarify.