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1.  Effect of prophylactic non-invasive mechanical ventilation on functional capacity after heart valve replacement: a clinical trial 
Clinics  2017;72(10):618-623.
OBJECTIVE:
During cardiac surgery, several factors contribute to the development of postoperative pulmonary complications. Non-invasive ventilation is a promising therapeutic tool for improving the functionality of this type of patient. The aim of this study is to evaluate the functional capacity and length of stay of patients in a nosocomial intensive care unit who underwent prophylactic non-invasive ventilation after heart valve replacement.
METHOD:
The study was a controlled clinical trial, comprising 50 individuals of both sexes who were allocated by randomization into two groups with 25 patients in each group: the control group and experimental group. After surgery, the patients were transferred to the intensive care unit and then participated in standard physical therapy, which was provided to the experimental group after 3 applications of non-invasive ventilation within the first 26 hours after extubation. For non-invasive ventilation, the positive pressure was 10 cm H2O, with a duration of 1 hour. The evaluation was performed on the 7th postoperative day/discharge and included a 6-minute walk test. The intensive care unit and hospitalization times were monitored in both groups. Brazilian Registry of Clinical Trials (REBeC): RBR number 8bxdd3.
RESULTS:
Analysis of the 6-minute walk test showed that the control group walked an average distance of 264.34±76 meters and the experimental group walked an average distance of 334.07±71 meters (p=0.002). The intensive care unit and hospitalization times did not differ between the groups.
CONCLUSION:
Non-invasive ventilation as a therapeutic resource was effective toward improving functionality; however, non-invasive ventilation did not influence the intensive care unit or hospitalization times of the studied cardiac patients.
doi:10.6061/clinics/2017(10)05
PMCID: PMC5666445
Thoracic Surgery; Continuous Positive Airway Pressure; Walk Test
2.  Evaluation of peripheral muscle strength of patients undergoing elective cardiac surgery: a longitudinal study 
Introduction
Peripheral muscle strength has been little explored in the literature in the context of cardiac rehabilitation.
Objective
To evaluate the peripheral muscle strength of patients undergoing elective cardiac surgery.
Methods
This was a longitudinal observational study. The peripheral muscle strength was measured using isometric dynamometry lower limb (knee extensors and flexors) at three different times: preoperatively (M1), the day of discharge (M2) and hospital discharge (M3). Participants received physiotherapy pre and postoperatively during the days of hospitalization during the morning and afternoon.
Results
Twenty-two patients were evaluated. The values of peripheral muscle strength of knee extensors preoperative found were about 50% lower than those predicted for the healthy population. When comparing muscle strength prior (M1), with the remaining evaluation, found himself in a fall of 29% for the movement of knee extension and 25% for knee flexion in M2 and a decrease of 10% movement for knee extension and 13% for knee flexion in M3 when comparing with M1.
Conclusion
The values of peripheral muscle strength prior of the study patients were lower than predicted for the healthy population of the same age. After the surgical event this reduction is even more remarkable, being reestablished until the time of discharge, to values close to baseline.
doi:10.5935/1678-9741.20140043
PMCID: PMC4412325  PMID: 25372909
Muscle Strength; Muscle Strength Dynamometer; Heart Diseases
3.  Determinants of distance walked during the six-minute walk test in patients undergoing cardiac surgery at hospital discharge 
Introduction
The aim of this study was to identify the determinants of distance walked in six-minute walk test (6MWD) in patients undergoing cardiac surgery at hospital discharge.
Methods
The assessment was performed preoperatively and at discharge. Data from patient records were collected and measurement of the Functional Independence Measure (FIM) and the Nottingham Health Profile (NHP) were performed. The six-minute walk test (6MWT) was performed at discharge. Patients undergoing elective cardiac surgery, coronary artery bypass grafting or valve replacement were eligible. Patients older than 75 years who presented arrhythmia during the protocol, with psychiatric disorders, muscular or neurological disorders were excluded from the study.
Results
Sixty patients (44.26% male, mean age 51.53 ± 13 years) were assessed. In multivariate analysis the following variables were selected: type of surgery (P = 0.001), duration of cardiopulmonary bypass (CPB) (P = 0.001), Functional Independence Measure - FIM (0.004) and body mass index - BMI (0.007) with r = 0.91 and r2 = 0.83 with P < 0.001. The equation derived from multivariate analysis: 6MWD = Surgery (89.42) + CPB (1.60) + MIF (2.79 ) - BMI (7.53) - 127.90.
Conclusion
In this study, the determinants of 6MWD in patients undergoing cardiac surgery were: the type of surgery, CPB time, functional capacity and body mass index.
doi:10.1186/1749-8090-9-95
PMCID: PMC4064506  PMID: 24885130
Six-minute walk test; Exercise; Cardiac surgery; Physiotherapy
4.  Case for diagnosis*  
Anais Brasileiros de Dermatologia  2014;89(3):519-520.
We report the case of an 11-year-old male patient with a histopathological and immunohistochemical diagnosis of dermatofibroma with an atypical clinical presentation on the right forearm. Although dermatofibroma is considered a benign skin tumor, some of its differential diagnoses, such as dermatofibrosarcoma protuberans and malignant fibrous histiocytoma, are truly aggressive. Lesions with atypical clinical aspects and topology associated with specific histopathological variants are some of the criteria for complete tumor excision.
doi:10.1590/abd1806-4841.20142507
PMCID: PMC4056719  PMID: 24937835
Dermatofibrosarcoma; Histiocytoma, benign fibrous; Keloid
5.  Acute effects of physiotherapeutic respiratory maneuvers in critically ill patients with craniocerebral trauma 
Clinics  2013;68(9):1210-1214.
OBJECTIVE:
To evaluate the effects of physiotherapeutic respiratory maneuvers on cerebral and cardiovascular hemodynamics and blood gas variables.
METHOD:
A descriptive, longitudinal, prospective, nonrandomized clinical trial that included 20 critical patients with severe craniocerebral trauma who were receiving mechanical ventilation and who were admitted to the intensive care unit. Each patient was subjected to the physiotherapeutic maneuvers of vibrocompression and increased manual expiratory flow (5 minutes on each hemithorax), along with subsequent airway suctioning with prior instillation of saline solution, hyperinflation and hyperoxygenation. Variables related to cardiovascular and cerebral hemodynamics and blood gas variables were recorded after each vibrocompression, increased manual expiratory flow and airway suctioning maneuver and 10 minutes after the end of airway suctioning.
RESULTS:
The hemodynamic and blood gas variables were maintained during vibrocompression and increased manual expiratory flow maneuvers; however, there were increases in mean arterial pressure, intracranial pressure, heart rate, pulmonary arterial pressure and pulmonary capillary pressure during airway suctioning. All of the values returned to baseline 10 minutes after the end of airway suctioning.
CONCLUSION:
Respiratory physiotherapy can be safely performed on patients with severe craniocerebral trauma. Additional caution must be taken when performing airway suctioning because this technique alters cerebral and cardiovascular hemodynamics, even in sedated and paralyzed patients.
doi:10.6061/clinics/2013(09)06
PMCID: PMC3782728  PMID: 24141836
Physical Therapy Modalities; Craniocerebral Trauma; Intensive Care
6.  Have bird distributions shifted along an elevational gradient on a tropical mountain? 
Ecology and Evolution  2017;7(23):9914-9924.
Abstract
An upward shift in elevation is one of the most conspicuous species responses to climate change. Nevertheless, downward shifts and, apparently, the absences of response have also been recently reported. Given the growing evidence of multiple responses of species distributions due to climate change and the paucity of studies in the tropics, we evaluated the response of a montane bird community to climate change, without the confounding effects of land‐use change. To test for elevational shifts, we compared the distribution of 21 avian species in 1998 and 2015 using occupancy models. The historical data set was based on point counts, whereas the contemporary data set was based on acoustic monitoring. We detected a similar number of species in historical (36) and contemporary data sets (33). We show an overall pattern of no significant change in range limits for most species, although there was a significant shift in the range limit of eight species (38%). Elevation limits shifted mostly upward, and this pattern was more common for upper than lower limits. Our results highlight the variability of species responses to climate change and illustrate how acoustic monitoring provides an easy and powerful way to monitor animal populations along elevational gradients.
doi:10.1002/ece3.3520
PMCID: PMC5723601
acoustic monitoring; ARBIMON; climate change; occupancy
7.  Rama: a machine learning approach for ribosomal protein prediction in plants 
Scientific Reports  2017;7:16273.
Ribosomal proteins (RPs) play a fundamental role within all type of cells, as they are major components of ribosomes, which are essential for translation of mRNAs. Furthermore, these proteins are involved in various physiological and pathological processes. The intrinsic biological relevance of RPs motivated advanced studies for the identification of unrevealed RPs. In this work, we propose a new computational method, termed Rama, for the prediction of RPs, based on machine learning techniques, with a particular interest in plants. To perform an effective classification, Rama uses a set of fundamental attributes of the amino acid side chains and applies a two-step procedure to classify proteins with unknown function as RPs. The evaluation of the resultant predictive models showed that Rama could achieve mean sensitivity, precision, and specificity of 0.91, 0.91, and 0.82, respectively. Furthermore, a list of proteins that have no annotation in Phytozome v.10, and are annotated as RPs in Phytozome v.12, were correctly classified by our models. Additional computational experiments have also shown that Rama presents high accuracy to differentiate ribosomal proteins from RNA-binding proteins. Finally, two novel proteins of Arabidopsis thaliana were validated in biological experiments. Rama is freely available at http://inctipp.bioagro.ufv.br:8080/Rama.
doi:10.1038/s41598-017-16322-4
PMCID: PMC5701237  PMID: 29176736
8.  Eukaryotic DNA Polymerases in Homologous Recombination 
Annual review of genetics  2016;50:393-421.
Homologous recombination (HR) is a central process to ensure genomic stability in somatic cells and during meiosis. HR-associated DNA synthesis determines in large part the fidelity of the process. A number of recent studies have demonstrated that DNA synthesis during HR is conservative, less processive, and more mutagenic than replicative DNA synthesis. In this review, we describe mechanistic features of DNA synthesis during different types of HR-mediated DNA repair, including synthesis-dependent strand annealing, break-induced replication, and meiotic recombination. We highlight recent findings from diverse eukaryotic organisms, including humans, that suggest both replicative and translesion DNA polymerases are involved in HR-associated DNA synthesis. Our focus is to integrate the emerging literature about DNA polymerase involvement during HR with the unique aspects of these repair mechanisms, including mutagenesis and template switching.
doi:10.1146/annurev-genet-120215-035243
PMCID: PMC5295669  PMID: 27893960
DNA synthesis; genome stability; mutagenesis; template switching
9.  A new approach by optical coherence tomography for elucidating biofilm formation by emergent Candida species 
PLoS ONE  2017;12(11):e0188020.
The majority of microorganisms present a community lifestyle, establishing biofilm ecosystems. However, little is known about its formation in emergent Candida species involved in catheter-related infections. Thus, various techniques may be used in the biofilm detection to elucidate structure and clinical impact. In this context, we report the ability of emergent Candida species (Candida haemulonii, C. lusitaniae, C. pelliculosa, C.guilliermondii, C. famata and C. ciferrii) on developing well structured biofilms with cell viability and architecture, using optical coherence tomography (OCT). This new approach was compared with XTT analyses and Scanning Electron Microscopy (SEM). A positive correlation between oxidative activity (XTT) and OCT results (r = 0.8752, p < 0.0001) was observed. SEM images demonstrated cells attachment, multilayer and morphologic characteristics of the biofilm structure. C. lusitaniae was the emergent species which revealed the highest scattering extension length and oxidative metabolism when evaluated by OCT and XTT methods, respectively. Herein, information on C. ciferri biofilm structure were presented for the first time. The OCT results are independently among Candida strains and no species-specific pattern was observed. Our findings strongly contribute for clinical management based on the knowledge of pathogenicity mechanisms involving emergent yeasts.
doi:10.1371/journal.pone.0188020
PMCID: PMC5690619  PMID: 29145445
10.  Lowland extirpation of anuran populations on a tropical mountain 
PeerJ  2017;5:e4059.
Background
Climate change and infectious diseases threaten animal and plant species, even in natural and protected areas. To cope with these changes, species may acclimate, adapt, move or decline. Here, we test for shifts in anuran distributions in the Luquillo Mountains (LM), a tropical montane forest in Puerto Rico by comparing species distributions from historical (1931–1989)and current data (2015/2016).
Methods
Historical data, which included different methodologies, were gathered through the Global Biodiversity Information Facility (GBIF) and published literature, and the current data were collected using acoustic recorders along three elevational transects.
Results
In the recordings, we detected the 12 native frog species known to occur in LM. Over a span of ∼25 years, two species have become extinct and four species suffered extirpation in lowland areas. As a consequence, low elevation areas in the LM (<300 m) have lost at least six anuran species.
Discussion
We hypothesize that these extirpations are due to the effects of climate change and infectious diseases, which are restricting many species to higher elevations and a much smaller area. Land use change is not responsible for these changes because LM has been a protected reserve for the past 80 years. However, previous studies indicate that (1) climate change has increased temperatures in Puerto Rico, and (2) Batrachochytrium dendrobatidis (Bd) was found in 10 native species and early detection of Bd coincides with anurans declines in the LM. Our study confirms the general impressions of amphibian population extirpations at low elevations, and corroborates the levels of threat assigned by IUCN.
doi:10.7717/peerj.4059
PMCID: PMC5694215
Acoustic monitoring; Occupancy; Elevation; Climate change; Infectious disease; Local extinctions; Range shift; Animal distribution; ARBIMON; Anuran
11.  Chemically Modified Polyvinyl Chloride for Removal of Thionine Dye (Lauth’s Violet) 
Materials  2017;10(11):1298.
The chemical modification of hydrophobic polymer matrices is an alternative way to elchange their surface properties. The introduction of sulfonic groups in the polymer changes the surface properties such as adhesion, wettability, catalytic ability, and adsorption capacity. This work describes the production and application of chemically modified polyvinyl chloride (PVC) as adsorbent for dyes removal. Chemical modification of PVC was evaluated by infrared spectroscopy and elemental analysis, which indicated the presence of sulfonic groups on PVC. The chemically modified PVC (PVCDS) showed an ion exchange capacity of 1.03 mmol−1, and efficiently removed the thionine dye (Lauth’s violet) from aqueous solutions, reaching equilibrium in 30 min. The adsorption kinetics was better adjusted for a pseudo second order model. This result indicates that the adsorption of thionine onto PVCDS occurs by chemisorption. Among the models for the state of equilibrium, SIPS and Langmuir exhibited the best fit to the experimental results and PVCDS showed high adsorption capacities (370 mg−1). Thus, it is assumed that the system presents homogeneous characteristics to the distribution of active sites. The modification promoted the formation of surface characteristics favorable to the dye adsorption by the polymer.
doi:10.3390/ma10111298
PMCID: PMC5706245  PMID: 29137158
poli(vinyl chloride); sulfonation; adsorption; dye; environment
12.  Mitochondrial genome of Plasmodium vivax/simium detected in an endemic region for malaria in the Atlantic Forest of Espírito Santo state, Brazil: do mosquitoes, simians and humans harbour the same parasite? 
Malaria Journal  2017;16:437.
Background
The transmission of malaria in the extra-Amazonian regions of Brazil, although interrupted in the 1960s, has persisted to the present time in some areas of dense Atlantic Forest, with reports of cases characterized by particular transmission cycles and clinical presentations. Bromeliad-malaria, as it is named, is particularly frequent in the state of Espírito Santo, with Plasmodium vivax being the parasite commonly recognized as the aetiologic agent of human infections. With regard to the spatial and temporal distances between cases reported in this region, the transmission cycle does not fit the traditional malaria cycle. The existence of a zoonosis, with infected simians participating in the epidemiology, is therefore hypothesized. In the present study, transmission of bromeliad-malaria in Espírito Santo is investigated, based on the complete mitochondrial genome of DNA extracted from isolates of Plasmodium species, which had infected humans, a simian from the genus Allouata, and Anopheles mosquitoes. Plasmodium vivax/simium was identified in the samples by both nested PCR and real-time PCR. After amplification, the mitochondrial genome was completely sequenced and compared with a haplotype network which included all sequences of P. vivax/simium mitochondrial genomes sampled from humans and simians from all regions in Brazil.
Results
The haplotype network indicates that humans and simians from the Atlantic Forest become infected by the same haplotype, but some isolates from humans are not identical to the simian isolate. In addition, the plasmodial DNA extracted from mosquitoes revealed sequences different from those obtained from simians, but similar to two isolates from humans.
Conclusions
These findings strengthen support for the hypothesis that in the Atlantic Forest, and especially in the state with the highest frequency of bromeliad-malaria in Brazil, parasites with similar molecular backgrounds are shared by humans and simians. The recognized identity between P. vivax and P. simium at the species level, the sharing of haplotypes, and the participation of the same vector in transmitting the infection to both host species indicate interspecies transference of the parasites. However, the intensity, frequency and direction of this transfer remain to be clarified.
Electronic supplementary material
The online version of this article (10.1186/s12936-017-2080-9) contains supplementary material, which is available to authorized users.
doi:10.1186/s12936-017-2080-9
PMCID: PMC5663072  PMID: 29084553
Anopheles; Malaria; Epidemiology; Real-time polymerase chain reaction; DNA, mitochondrial; Sequence analyses, DNA; Zoonoses
13.  Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent 
PLoS Genetics  2017;13(10):e1007065.
With the rapidly increasing abundance and accessibility of genomic data, there is a growing interest in using population genetic approaches to characterize fine-scale dispersal of organisms, providing insight into biological processes across a broad range of fields including ecology, evolution and epidemiology. For sexually recombining haploid organisms such as the human malaria parasite P. falciparum, however, there have been no systematic assessments of the type of data and methods required to resolve fine scale connectivity. This analytical gap hinders the use of genomics for understanding local transmission patterns, a crucial goal for policy makers charged with eliminating this important human pathogen. Here we use data collected from four clinics with a catchment area spanning approximately 120 km of the Thai-Myanmar border to compare the ability of divergence (FST) and relatedness based on identity by descent (IBD) to resolve spatial connectivity between malaria parasites collected from proximal clinics. We found no relationship between inter-clinic distance and FST, likely due to sampling of highly related parasites within clinics, but a significant decline in IBD-based relatedness with increasing inter-clinic distance. This association was contingent upon the data set type and size. We estimated that approximately 147 single-infection whole genome sequenced parasite samples or 222 single-infection parasite samples genotyped at 93 single nucleotide polymorphisms (SNPs) were sufficient to recover a robust spatial trend estimate at this scale. In summary, surveillance efforts cannot rely on classical measures of genetic divergence to measure P. falciparum transmission on a local scale. Given adequate sampling, IBD-based relatedness provides a useful alternative, and robust trends can be obtained from parasite samples genotyped at approximately 100 SNPs.
Author summary
The spatiotemporal dispersal of organisms can inform efforts to conserve endangered species, to contain the spread of drug resistance, and to eliminate disease. As genomic data become increasingly more affordable and accessible via public depositories, the demand for methods capable of extracting fine-scale population structure from genomic data grows. However, to the best of our knowledge, there are no guidelines regarding the type of data and methods required to resolve local spatial trends over sexually recombining haploid organisms, such as the malaria parasite. The approach we present here compares relatedness based on identity by descent, which accounts for recombination while distinguishing genetic identity due to inheritance from genetic identity due to chance, to a classic population genetic measure of divergence, using data from sexually recombining malaria parasites. Using identity by descent, we uncover a significant decrease in highly related malaria parasites collected from proximal clinics on the Thai-Myanmar border, a region where human mobility is high. Our results demonstrate the power of analyses based on identity by descent to detect recent and local trends. Similar analyses could be used to inform the molecular epidemiology of other sexually recombining organisms.
doi:10.1371/journal.pgen.1007065
PMCID: PMC5678785  PMID: 29077712
14.  Environmental and behavioral changes may influence the exposure of an Arctic apex predator to pathogens and contaminants 
Scientific Reports  2017;7:13193.
Recent decline of sea ice habitat has coincided with increased use of land by polar bears (Ursus maritimus) from the southern Beaufort Sea (SB), which may alter the risks of exposure to pathogens and contaminants. We assayed blood samples from SB polar bears to assess prior exposure to the pathogens Brucella spp., Toxoplasma gondii, Coxiella burnetii, Francisella tularensis, and Neospora caninum, estimate concentrations of persistent organic pollutants (POPs), and evaluate risk factors associated with exposure to pathogens and POPs. We found that seroprevalence of Brucella spp. and T. gondii antibodies likely increased through time, and provide the first evidence of exposure of polar bears to C. burnetii, N. caninum, and F. tularensis. Additionally, the odds of exposure to T. gondii were greater for bears that used land than for bears that remained on the sea ice during summer and fall, while mean concentrations of the POP chlordane (ΣCHL) were lower for land-based bears. Changes in polar bear behavior brought about by climate-induced modifications to the Arctic marine ecosystem may increase exposure risk to certain pathogens and alter contaminant exposure pathways.
doi:10.1038/s41598-017-13496-9
PMCID: PMC5643432  PMID: 29038498
15.  Cognitive appraisal of environmental stimuli induces emotion-like states in fish 
Scientific Reports  2017;7:13181.
The occurrence of emotions in non-human animals has been the focus of debate over the years. Recently, an interest in expanding this debate to non-tetrapod vertebrates and to invertebrates has emerged. Within vertebrates, the study of emotion in teleosts is particularly interesting since they represent a divergent evolutionary radiation from that of tetrapods, and thus they provide an insight into the evolution of the biological mechanisms of emotion. We report that Sea Bream exposed to stimuli that vary according to valence (positive, negative) and salience (predictable, unpredictable) exhibit different behavioural, physiological and neuromolecular states. Since according to the dimensional theory of emotion valence and salience define a two-dimensional affective space, our data can be interpreted as evidence for the occurrence of distinctive affective states in fish corresponding to each the four quadrants of the core affective space. Moreover, the fact that the same stimuli presented in a predictable vs. unpredictable way elicited different behavioural, physiological and neuromolecular states, suggests that stimulus appraisal by the individual, rather than an intrinsic characteristic of the stimulus, has triggered the observed responses. Therefore, our data supports the occurrence of emotion-like states in fish that are regulated by the individual’s perception of environmental stimuli.
doi:10.1038/s41598-017-13173-x
PMCID: PMC5640617  PMID: 29030568
16.  Performance of the ATLAS track reconstruction algorithms in dense environments in LHC Run 2 
Aaboud, M. | Aad, G. | Abbott, B. | Abdallah, J. | Abdinov, O. | Abeloos, B. | Abidi, S. H. | AbouZeid, O. S. | Abraham, N. L. | Abramowicz, H. | Abreu, H. | Abreu, R. | Abulaiti, Y. | Acharya, B. S. | Adachi, S. | Adamczyk, L. | Adelman, J. | Adersberger, M. | Adye, T. | Affolder, A. A. | Agatonovic-Jovin, T. | Agheorghiesei, C. | Aguilar-Saavedra, J. A. | Ahlen, S. P. | Ahmadov, F. | Aielli, G. | Akatsuka, S. | Akerstedt, H. | Åkesson, T. P. A. | Akimov, A. V. | Alberghi, G. L. | Albert, J. | Albicocco, P. | Alconada Verzini, M. J. | Aleksa, M. | Aleksandrov, I. N. | Alexa, C. | Alexander, G. | Alexopoulos, T. | Alhroob, M. | Ali, B. | Aliev, M. | Alimonti, G. | Alison, J. | Alkire, S. P. | Allbrooke, B. M. M. | Allen, B. W. | Allport, P. P. | Aloisio, A. | Alonso, A. | Alonso, F. | Alpigiani, C. | Alshehri, A. A. | Alstaty, M. | Alvarez Gonzalez, B. | Álvarez Piqueras, D. | Alviggi, M. G. | Amadio, B. T. | Amaral Coutinho, Y. | Amelung, C. | Amidei, D. | Santos, S. P. Amor Dos | Amorim, A. | Amoroso, S. | Amundsen, G. | Anastopoulos, C. | Ancu, L. S. | Andari, N. | Andeen, T. | Anders, C. F. | Anders, J. K. | Anderson, K. J. | Andreazza, A. | Andrei, V. | Angelidakis, S. | Angelozzi, I. | Angerami, A. | Anisenkov, A. V. | Anjos, N. | Annovi, A. | Antel, C. | Antonelli, M. | Antonov, A. | Antrim, D. J. | Anulli, F. | Aoki, M. | Aperio Bella, L. | Arabidze, G. | Arai, Y. | Araque, J. P. | Araujo Ferraz, V. | Arce, A. T. H. | Ardell, R. E. | Arduh, F. A. | Arguin, J.-F. | Argyropoulos, S. | Arik, M. | Armbruster, A. J. | Armitage, L. J. | Arnaez, O. | Arnold, H. | Arratia, M. | Arslan, O. | Artamonov, A. | Artoni, G. | Artz, S. | Asai, S. | Asbah, N. | Ashkenazi, A. | Asquith, L. | Assamagan, K. | Astalos, R. | Atkinson, M. | Atlay, N. B. | Augsten, K. | Avolio, G. | Axen, B. | Ayoub, M. K. | Azuelos, G. | Baas, A. E. | Baca, M. J. | Bachacou, H. | Bachas, K. | Backes, M. | Backhaus, M. | Bagnaia, P. | Bahrasemani, H. | Baines, J. T. | Bajic, M. | Baker, O. K. | Baldin, E. M. | Balek, P. | Balli, F. | Balunas, W. K. | Banas, E. | Banerjee, Sw. | Bannoura, A. A. E. | Barak, L. | Barberio, E. L. | Barberis, D. | Barbero, M. | Barillari, T. | Barisits, M.-S. | Barklow, T. | Barlow, N. | Barnes, S. L. | Barnett, B. M. | Barnett, R. M. | Barnovska-Blenessy, Z. | Baroncelli, A. | Barone, G. | Barr, A. J. | Barranco Navarro, L. | Barreiro, F. | Barreiro Guimarães da Costa, J. | Bartoldus, R. | Barton, A. E. | Bartos, P. | Basalaev, A. | Bassalat, A. | Bates, R. L. | Batista, S. J. | Batley, J. R. | Battaglia, M. | Bauce, M. | Bauer, F. | Bawa, H. S. | Beacham, J. B. | Beattie, M. D. | Beau, T. | Beauchemin, P. H. | Bechtle, P. | Beck, H. P. | Becker, K. | Becker, M. | Beckingham, M. | Becot, C. | Beddall, A. J. | Beddall, A. | Bednyakov, V. A. | Bedognetti, M. | Bee, C. P. | Beermann, T. A. | Begalli, M. | Begel, M. | Behr, J. K. | Bell, A. S. | Bella, G. | Bellagamba, L. | Bellerive, A. | Bellomo, M. | Belotskiy, K. | Beltramello, O. | Belyaev, N. L. | Benary, O. | Benchekroun, D. | Bender, M. | Bendtz, K. | Benekos, N. | Benhammou, Y. | Benhar Noccioli, E. | Benitez, J. | Benjamin, D. P. | Benoit, M. | Bensinger, J. R. | Bentvelsen, S. | Beresford, L. | Beretta, M. | Berge, D. | Bergeaas Kuutmann, E. | Berger, N. | Beringer, J. | Berlendis, S. | Bernard, N. R. | Bernardi, G. | Bernius, C. | Bernlochner, F. U. | Berry, T. | Berta, P. | Bertella, C. | Bertoli, G. | Bertolucci, F. | Bertram, I. A. | Bertsche, C. | Bertsche, D. | Besjes, G. J. | Bessidskaia Bylund, O. | Bessner, M. | Besson, N. | Betancourt, C. | Bethani, A. | Bethke, S. | Bevan, A. J. | Beyer, J. | Bianchi, R. M. | Biebel, O. | Biedermann, D. | Bielski, R. | Biesuz, N. V. | Biglietti, M. | Billoud, T. R. V. | Bilokon, H. | Bindi, M. | Bingul, A. | Bini, C. | Biondi, S. | Bisanz, T. | Bittrich, C. | Bjergaard, D. M. | Black, C. W. | Black, J. E. | Black, K. M. | Blair, R. E. | Blazek, T. | Bloch, I. | Blocker, C. | Blue, A. | Blum, W. | Blumenschein, U. | Blunier, S. | Bobbink, G. J. | Bobrovnikov, V. S. | Bocchetta, S. S. | Bocci, A. | Bock, C. | Boehler, M. | Boerner, D. | Bogavac, D. | Bogdanchikov, A. G. | Bohm, C. | Boisvert, V. | Bokan, P. | Bold, T. | Boldyrev, A. S. | Bolz, A. E. | Bomben, M. | Bona, M. | Boonekamp, M. | Borisov, A. | Borissov, G. | Bortfeldt, J. | Bortoletto, D. | Bortolotto, V. | Boscherini, D. | Bosman, M. | Bossio Sola, J. D. | Boudreau, J. | Bouffard, J. | Bouhova-Thacker, E. V. | Boumediene, D. | Bourdarios, C. | Boutle, S. K. | Boveia, A. | Boyd, J. | Boyko, I. R. | Bracinik, J. | Brandt, A. | Brandt, G. | Brandt, O. | Bratzler, U. | Brau, B. | Brau, J. E. | Breaden Madden, W. D. | Brendlinger, K. | Brennan, A. J. | Brenner, L. | Brenner, R. | Bressler, S. | Briglin, D. L. | Bristow, T. M. | Britton, D. | Britzger, D. | Brochu, F. M. | Brock, I. | Brock, R. | Brooijmans, G. | Brooks, T. | Brooks, W. K. | Brosamer, J. | Brost, E. | Broughton, J. H | de Renstrom, P. A. Bruckman | Bruncko, D. | Bruni, A. | Bruni, G. | Bruni, L. S. | Brunt, BH | Bruschi, M. | Bruscino, N. | Bryant, P. | Bryngemark, L. | Buanes, T. | Buat, Q. | Buchholz, P. | Buckley, A. G. | Budagov, I. A. | Buehrer, F. | Bugge, M. K. | Bulekov, O. | Bullock, D. | Burch, T. J. | Burckhart, H. | Burdin, S. | Burgard, C. D. | Burger, A. M. | Burghgrave, B. | Burka, K. | Burke, S. | Burmeister, I. | Burr, J. T. P. | Busato, E. | Büscher, D. | Büscher, V. | Bussey, P. | Butler, J. M. | Buttar, C. M. | Butterworth, J. M. | Butti, P. | Buttinger, W. | Buzatu, A. | Buzykaev, A. R. | Cabrera Urbán, S. | Caforio, D. | Cairo, V. M. | Cakir, O. | Calace, N. | Calafiura, P. | Calandri, A. | Calderini, G. | Calfayan, P. | Callea, G. | Caloba, L. P. | Calvente Lopez, S. | Calvet, D. | Calvet, S. | Calvet, T. P. | Camacho Toro, R. | Camarda, S. | Camarri, P. | Cameron, D. | Caminal Armadans, R. | Camincher, C. | Campana, S. | Campanelli, M. | Camplani, A. | Campoverde, A. | Canale, V. | Cano Bret, M. | Cantero, J. | Cao, T. | Capeans Garrido, M. D. M. | Caprini, I. | Caprini, M. | Capua, M. | Carbone, R. M. | Cardarelli, R. | Cardillo, F. | Carli, I. | Carli, T. | Carlino, G. | Carlson, B. T. | Carminati, L. | Carney, R. M. D. | Caron, S. | Carquin, E. | Carrá, S. | Carrillo-Montoya, G. D. | Carvalho, J. | Casadei, D. | Casado, M. P. | Casolino, M. | Casper, D. W. | Castelijn, R. | Castillo Gimenez, V. | Castro, N. F. | Catinaccio, A. | Catmore, J. R. | Cattai, A. | Caudron, J. | Cavaliere, V. | Cavallaro, E. | Cavalli, D. | Cavalli-Sforza, M. | Cavasinni, V. | Celebi, E. | Ceradini, F. | Cerda Alberich, L. | Cerqueira, A. S. | Cerri, A. | Cerrito, L. | Cerutti, F. | Cervelli, A. | Cetin, S. A. | Chafaq, A. | Chakraborty, D. | Chan, S. K. | Chan, W. S. | Chan, Y. L. | Chang, P. | Chapman, J. D. | Charlton, D. G. | Chau, C. C. | Chavez Barajas, C. A. | Che, S. | Cheatham, S. | Chegwidden, A. | Chekanov, S. | Chekulaev, S. V. | Chelkov, G. A. | Chelstowska, M. A. | Chen, C. | Chen, H. | Chen, S. | Chen, S. | Chen, X. | Chen, Y. | Cheng, H. C. | Cheng, H. J. | Cheplakov, A. | Cheremushkina, E. | Cherkaoui El Moursli, R. | Chernyatin, V. | Cheu, E. | Chevalier, L. | Chiarella, V. | Chiarelli, G. | Chiodini, G. | Chisholm, A. S. | Chitan, A. | Chiu, Y. H. | Chizhov, M. V. | Choi, K. | Chomont, A. R. | Chouridou, S. | Christodoulou, V. | Chromek-Burckhart, D. | Chu, M. C. | Chudoba, J. | Chuinard, A. J. | Chwastowski, J. J. | Chytka, L. | Ciftci, A. K. | Cinca, D. | Cindro, V. | Cioara, I. A. | Ciocca, C. | Ciocio, A. | Cirotto, F. | Citron, Z. H. | Citterio, M. | Ciubancan, M. | Clark, A. | Clark, B. L. | Clark, M. R. | Clark, P. J. | Clarke, R. N. | Clement, C. | Coadou, Y. | Cobal, M. | Coccaro, A. | Cochran, J. | Colasurdo, L. | Cole, B. | Colijn, A. P. | Collot, J. | Colombo, T. | Conde Muiño, P. | Coniavitis, E. | Connell, S. H. | Connelly, I. A. | Constantinescu, S. | Conti, G. | Conventi, F. | Cooke, M. | Cooper-Sarkar, A. M. | Cormier, F. | Cormier, K. J. R. | Corradi, M. | Corriveau, F. | Cortes-Gonzalez, A. | Cortiana, G. | Costa, G. | Costa, M. J. | Costanzo, D. | Cottin, G. | Cowan, G. | Cox, B. E. | Cranmer, K. | Crawley, S. J. | Creager, R. A. | Cree, G. | Crépé-Renaudin, S. | Crescioli, F. | Cribbs, W. A. | Cristinziani, M. | Croft, V. | Crosetti, G. | Cueto, A. | Cuhadar Donszelmann, T. | Cukierman, A. R. | Cummings, J. | Curatolo, M. | Cúth, J. | Czirr, H. | Czodrowski, P. | D’amen, G. | D’Auria, S. | D’eramo, L. | D’Onofrio, M. | Da Cunha Sargedas De Sousa, M. J. | Via, C. Da | Dabrowski, W. | Dado, T. | Dai, T. | Dale, O. | Dallaire, F. | Dallapiccola, C. | Dam, M. | Dandoy, J. R. | Daneri, M. F. | Dang, N. P. | Daniells, A. C. | Dann, N. S. | Danninger, M. | Hoffmann, M. Dano | Dao, V. | Darbo, G. | Darmora, S. | Dassoulas, J. | Dattagupta, A. | Daubney, T. | Davey, W. | David, C. | Davidek, T. | Davies, M. | Davis, D. R. | Davison, P. | Dawe, E. | Dawson, I. | De, K. | de Asmundis, R. | De Benedetti, A. | De Castro, S. | De Cecco, S. | De Groot, N. | de Jong, P. | De la Torre, H. | De Lorenzi, F. | De Maria, A. | De Pedis, D. | De Salvo, A. | De Sanctis, U. | De Santo, A. | De Vasconcelos Corga, K. | De Vivie De Regie, J. B. | Dearnaley, W. J. | Debbe, R. | Debenedetti, C. | Dedovich, D. V. | Dehghanian, N. | Deigaard, I. | Del Gaudio, M. | Del Peso, J. | Prete, T. Del | Delgove, D. | Deliot, F. | Delitzsch, C. M. | Dell’Acqua, A. | Dell’Asta, L. | Dell’Orso, M. | Della Pietra, M. | della Volpe, D. | Delmastro, M. | Delporte, C. | Delsart, P. A. | DeMarco, D. A. | Demers, S. | Demichev, M. | Demilly, A. | Denisov, S. P. | Denysiuk, D. | Derendarz, D. | Derkaoui, J. E. | Derue, F. | Dervan, P. | Desch, K. | Deterre, C. | Dette, K. | Devesa, M. R. | Deviveiros, P. O. | Dewhurst, A. | Dhaliwal, S. | Di Bello, F. A. | Di Ciaccio, A. | Di Ciaccio, L. | Di Clemente, W. K. | Di Donato, C. | Di Girolamo, A. | Di Girolamo, B. | Di Micco, B. | Di Nardo, R. | Di Petrillo, K. F. | Di Simone, A. | Di Sipio, R. | Di Valentino, D. | Diaconu, C. | Diamond, M. | Dias, F. A. | Diaz, M. A. | Diehl, E. B. | Dietrich, J. | Díez Cornell, S. | Dimitrievska, A. | Dingfelder, J. | Dita, P. | Dita, S. | Dittus, F. | Djama, F. | Djobava, T. | Djuvsland, J. I. | do Vale, M. A. B. | Dobos, D. | Dobre, M. | Doglioni, C. | Dolejsi, J. | Dolezal, Z. | Donadelli, M. | Donati, S. | Dondero, P. | Donini, J. | Dopke, J. | Doria, A. | Dova, M. T. | Doyle, A. T. | Drechsler, E. | Dris, M. | Du, Y. | Duarte-Campderros, J. | Dubreuil, A. | Duchovni, E. | Duckeck, G. | Ducourthial, A. | Ducu, O. A. | Duda, D. | Dudarev, A. | Dudder, A. Chr. | Duffield, E. M. | Duflot, L. | Dührssen, M. | Dumancic, M. | Dumitriu, A. E. | Duncan, A. K. | Dunford, M. | Duran Yildiz, H. | Düren, M. | Durglishvili, A. | Duschinger, D. | Dutta, B. | Dyndal, M. | Eckardt, C. | Ecker, K. M. | Edgar, R. C. | Eifert, T. | Eigen, G. | Einsweiler, K. | Ekelof, T. | Kacimi, M. El | Kosseifi, R. El | Ellajosyula, V. | Ellert, M. | Elles, S. | Ellinghaus, F. | Elliot, A. A. | Ellis, N. | Elmsheuser, J. | Elsing, M. | Emeliyanov, D. | Enari, Y. | Endner, O. C. | Ennis, J. S. | Erdmann, J. | Ereditato, A. | Ernis, G. | Ernst, M. | Errede, S. | Escalier, M. | Escobar, C. | Esposito, B. | Estrada Pastor, O. | Etienvre, A. I. | Etzion, E. | Evans, H. | Ezhilov, A. | Ezzi, M. | Fabbri, F. | Fabbri, L. | Facini, G. | Fakhrutdinov, R. M. | Falciano, S. | Falla, R. J. | Faltova, J. | Fang, Y. | Fanti, M. | Farbin, A. | Farilla, A. | Farina, C. | Farina, E. M. | Farooque, T. | Farrell, S. | Farrington, S. M. | Farthouat, P. | Fassi, F. | Fassnacht, P. | Fassouliotis, D. | Faucci Giannelli, M. | Favareto, A. | Fawcett, W. J. | Fayard, L. | Fedin, O. L. | Fedorko, W. | Feigl, S. | Feligioni, L. | Feng, C. | Feng, E. J. | Feng, H. | Fenton, M. J. | Fenyuk, A. B. | Feremenga, L. | Fernandez Martinez, P. | Fernandez Perez, S. | Ferrando, J. | Ferrari, A. | Ferrari, P. | Ferrari, R. | Ferreira de Lima, D. E. | Ferrer, A. | Ferrere, D. | Ferretti, C. | Fiedler, F. | Filipčič, A. | Filipuzzi, M. | Filthaut, F. | Fincke-Keeler, M. | Finelli, K. D. | Fiolhais, M. C. N. | Fiorini, L. | Fischer, A. | Fischer, C. | Fischer, J. | Fisher, W. C. | Flaschel, N. | Fleck, I. | Fleischmann, P. | Fletcher, R. R. M. | Flick, T. | Flierl, B. M. | Flores Castillo, L. R. | Flowerdew, M. J. | Forcolin, G. T. | Formica, A. | Förster, F. A. | Forti, A. | Foster, A. G. | Fournier, D. | Fox, H. | Fracchia, S. | Francavilla, P. | Franchini, M. | Franchino, S. | Francis, D. | Franconi, L. | Franklin, M. | Frate, M. | Fraternali, M. | Freeborn, D. | Fressard-Batraneanu, S. M. | Freund, B. | Froidevaux, D. | Frost, J. A. | Fukunaga, C. | Fusayasu, T. | Fuster, J. | Gabaldon, C. | Gabizon, O. | Gabrielli, A. | Gabrielli, A. | Gach, G. P. | Gadatsch, S. | Gadomski, S. | Gagliardi, G. | Gagnon, L. G. | Galea, C. | Galhardo, B. | Gallas, E. J. | Gallop, B. J. | Gallus, P. | Galster, G. | Gan, K. K. | Ganguly, S. | Gao, Y. | Gao, Y. S. | Garay Walls, F. M. | García, C. | García Navarro, J. E. | Garcia-Sciveres, M. | Gardner, R. W. | Garelli, N. | Garonne, V. | Gascon Bravo, A. | Gasnikova, K. | Gatti, C. | Gaudiello, A. | Gaudio, G. | Gavrilenko, I. L. | Gay, C. | Gaycken, G. | Gazis, E. N. | Gee, C. N. P. | Geisen, J. | Geisen, M. | Geisler, M. P. | Gellerstedt, K. | Gemme, C. | Genest, M. H. | Geng, C. | Gentile, S. | Gentsos, C. | George, S. | Gerbaudo, D. | Gershon, A. | Geßner, G. | Ghasemi, S. | Ghneimat, M. | Giacobbe, B. | Giagu, S. | Giannetti, P. | Gibson, S. M. | Gignac, M. | Gilchriese, M. | Gillberg, D. | Gilles, G. | Gingrich, D. M. | Giokaris, N. | Giordani, M. P. | Giorgi, F. M. | Giraud, P. F. | Giromini, P. | Giugni, D. | Giuli, F. | Giuliani, C. | Giulini, M. | Gjelsten, B. K. | Gkaitatzis, S. | Gkialas, I. | Gkougkousis, E. L. | Gkountoumis, P. | Gladilin, L. K. | Glasman, C. | Glatzer, J. | Glaysher, P. C. F. | Glazov, A. | Goblirsch-Kolb, M. | Godlewski, J. | Goldfarb, S. | Golling, T. | Golubkov, D. | Gomes, A. | Gonçalo, R. | Goncalves Gama, R. | Goncalves Pinto Firmino Da Costa, J. | Gonella, G. | Gonella, L. | Gongadze, A. | González de la Hoz, S. | Gonzalez-Sevilla, S. | Goossens, L. | Gorbounov, P. A. | Gordon, H. A. | Gorelov, I. | Gorini, B. | Gorini, E. | Gorišek, A. | Goshaw, A. T. | Gössling, C. | Gostkin, M. I. | Gottardo, C. A. | Goudet, C. R. | Goujdami, D. | Goussiou, A. G. | Govender, N. | Gozani, E. | Graber, L. | Grabowska-Bold, I. | Gradin, P. O. J. | Gramling, J. | Gramstad, E. | Grancagnolo, S. | Gratchev, V. | Gravila, P. M. | Gray, C. | Gray, H. M. | Greenwood, Z. D. | Grefe, C. | Gregersen, K. | Gregor, I. M. | Grenier, P. | Grevtsov, K. | Griffiths, J. | Grillo, A. A. | Grimm, K. | Grinstein, S. | Gris, Ph. | Grivaz, J.-F. | Groh, S. | Gross, E. | Grosse-Knetter, J. | Grossi, G. C. | Grout, Z. J. | Grummer, A. | Guan, L. | Guan, W. | Guenther, J. | Guescini, F. | Guest, D. | Gueta, O. | Gui, B. | Guido, E. | Guillemin, T. | Guindon, S. | Gul, U. | Gumpert, C. | Guo, J. | Guo, W. | Guo, Y. | Gupta, R. | Gupta, S. | Gustavino, G. | Gutierrez, P. | Gutierrez Ortiz, N. G. | Gutschow, C. | Guyot, C. | Guzik, M. P. | Gwenlan, C. | Gwilliam, C. B. | Haas, A. | Haber, C. | Hadavand, H. K. | Haddad, N. | Hadef, A. | Hageböck, S. | Hagihara, M. | Hakobyan, H. | Haleem, M. | Haley, J. | Halladjian, G. | Hallewell, G. D. | Hamacher, K. | Hamal, P. | Hamano, K. | Hamilton, A.
With the increase in energy of the Large Hadron Collider to a centre-of-mass energy of 13 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\text {TeV}$$\end{document}TeV for Run 2, events with dense environments, such as in the cores of high-energy jets, became a focus for new physics searches as well as measurements of the Standard Model. These environments are characterized by charged-particle separations of the order of the tracking detectors sensor granularity. Basic track quantities are compared between 3.2 fb\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$^{-1}$$\end{document}-1 of data collected by the ATLAS experiment and simulation of proton–proton collisions producing high-transverse-momentum jets at a centre-of-mass energy of 13 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\text {TeV}$$\end{document}TeV. The impact of charged-particle separations and multiplicities on the track reconstruction performance is discussed. The track reconstruction efficiency in the cores of jets with transverse momenta between 200 and 1600 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\text {GeV}$$\end{document}GeV is quantified using a novel, data-driven, method. The method uses the energy loss, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\text { d}}{} \textit{E}/d\textit{x}$$\end{document}dE/dx, to identify pixel clusters originating from two charged particles. Of the charged particles creating these clusters, the measured fraction that fail to be reconstructed is \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$0.061 \pm 0.006\ {\text {(stat.)}} \pm 0.014\ {\text {(syst.)}}$$\end{document}0.061±0.006(stat.)±0.014(syst.) and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$0.093 \pm 0.017\ {\text {(stat.)}}\pm 0.021\ {\text {(syst.)}}$$\end{document}0.093±0.017(stat.)±0.021(syst.) for jet transverse momenta of 200–400 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\text {GeV}$$\end{document}GeV and 1400–1600 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\text {GeV}$$\end{document}GeV, respectively.
doi:10.1140/epjc/s10052-017-5225-7
PMCID: PMC5638380
17.  Depression in medical students: insights from a longitudinal study 
BMC Medical Education  2017;17:184.
Background
Factors associated with depression of medical students are poorly understood. The purpose of this study is to determine the prevalence of depression in medical students, its change during the course, if depression persists for affected students, what are the factors associated with depression and how these factors change over time.
Methods
A prospective, longitudinal observational study was conducted at the Medical School of the University of Minho, Portugal, between academic years 2009–2010 to 2012–2013. We included students who maintained their participation by annually completing a questionnaire including Beck Depression Inventory (BDI). Anxiety and burnout were assessed using the State Trait Anxiety Inventory and Maslach Burnout Inventory. Surveys on socio-demographic variables were applied to evaluate potential predictors, personal and academic characteristics and perceived difficulties. ANOVA with multiple comparisons were used to compare means of BDI score. The medical students were organized into subgroups by K-means cluster analyses. ANOVA mixed-design repeated measurement was performed to assess a possible interaction between variables associated with depression.
Results
The response rate was 84, 92, 88 and 81% for academic years 2009–2010, 2010–2011,2011-2012 and 2012/2013, respectively. Two hundred thirty-eight medical students were evaluated longitudinally. For depression the prevalence ranged from 21.5 to 12.7% (academic years 2009/2010 and 2012/2013). BDI scores decreased during medical school. 19.7% of students recorded sustained high BDI over time. These students had high levels of trait-anxiety and choose medicine for anticipated income and prestige, reported more relationship issues, cynicism, and decreased satisfaction with social activities. Students with high BDI scores at initial evaluation with low levels of trait-anxiety and a primary interest in medicine as a career tended to improve their mood and reported reduced burnout, low perceived learning problems and increased satisfaction with social activities at last evaluation. No difference was detected between men and women in the median BDI score over time.
Conclusions
Our findings suggest that personal factors (anxiety traits, medicine choice factors, relationship patterns and academic burnout) are relevant for persistence of high levels of BDI during medical training. Medical schools need to identity students who experience depression and support then, as early as possible, particularly when depression has been present over time.
doi:10.1186/s12909-017-1006-0
PMCID: PMC5633876  PMID: 29017594
Medical student; Distress; Depression; Anxiety; Burnout
18.  Emergence and loss of spliceosomal twin introns 
Background
In the primary transcript of nuclear genes, coding sequences—exons—usually alternate with non-coding sequences—introns. In the evolution of spliceosomal intron–exon structure, extant intron positions can be abandoned and new intron positions can be occupied. Spliceosomal twin introns (“stwintrons”) are unconventional intervening sequences where a standard “internal” intron interrupts a canonical splicing motif of a second, “external” intron. The availability of genome sequences of more than a thousand species of fungi provides a unique opportunity to study spliceosomal intron evolution throughout a whole kingdom by means of molecular phylogenetics.
Results
A new stwintron was encountered in Aspergillus nidulans and Aspergillus niger. It is present across three classes of Leotiomyceta in the transcript of a well-conserved gene encoding a putative lipase (lipS). It occupies the same position as a standard intron in the orthologue gene in species of the early divergent classes of the Pezizomycetes and the Orbiliomycetes, suggesting that an internal intron has appeared within a pre-extant intron. On the other hand, the stwintron has been lost from certain taxa in Leotiomycetes and Eurotiomycetes at several occasions, most likely by a mechanism involving reverse transcription and homologous recombination. Another ancient stwintron present across whole Pezizomycotina orders—in the transcript of the bifunctional biotin biosynthesis gene bioDA—occurs at the same position as a standard intron in many species of non-Dikarya. Nevertheless, also the bioDA stwintron has disappeared from certain lineages within the taxa where it occurs, i.e., Sordariomycetes and Botryosphaeriales. Intriguingly, only the internal intron was lost from the Sordariomycetes bioDA stwintron at all but one occasion, leaving a standard intron in the same position, while where the putative lipase stwintron was lost, no intronic sequences remain.
Conclusions
Molecular phylogeny of the peptide product was used to monitor the existence and fate of a stwintron in the transcripts of two neatly defined fungal genes, encoding well conserved proteins. Both defining events—stwintron emergence and loss—can be explained with extant models for intron insertion and loss. We thus demonstrate that stwintrons can serve as model systems to study spliceosomal intron evolution.
Electronic supplementary material
The online version of this article (doi:10.1186/s40694-017-0037-y) contains supplementary material, which is available to authorized users.
doi:10.1186/s40694-017-0037-y
PMCID: PMC5639578
Spliceosomal twin introns; Spliceosomal intron evolution; Intron gain; Intron loss; Molecular phylogenetics; Pezizomycotina; Aspergillus nidulans
19.  Reduction of venous pressure during the resection of liver metastases compromises enteric blood flow: IGFBP-1 as a novel biomarker of intestinal barrier injury 
Clinics  2017;72(10):645-648.
OBJECTIVES:
Disruption of the intestinal barrier and bacterial translocation commonly occur when intestinal blood flow is compromised. The aim of this study was to determine whether liver resection induces intestinal damage.
METHODS:
We investigated intestinal fatty-acid binding protein and insulin-like growth factor binding protein levels in the plasma of patients who underwent liver resection.
RESULTS:
We show that liver resection is associated with significant intestinal barrier injury, even if the Pringle maneuver is not performed.
CONCLUSION:
We propose the use of insulin-like growth factor binding protein-1 as a novel biomarker of intestinal damage in such situations.
doi:10.6061/clinics/2017(10)10
PMCID: PMC5666439
Liver; Inflammation; Intestinal Barrier; Bacterial Translocation; IGFBP-1
20.  Fangorn Forest (F2): a machine learning approach to classify genes and genera in the family Geminiviridae 
BMC Bioinformatics  2017;18:431.
Background
Geminiviruses infect a broad range of cultivated and non-cultivated plants, causing significant economic losses worldwide. The studies of the diversity of species, taxonomy, mechanisms of evolution, geographic distribution, and mechanisms of interaction of these pathogens with the host have greatly increased in recent years. Furthermore, the use of rolling circle amplification (RCA) and advanced metagenomics approaches have enabled the elucidation of viromes and the identification of many viral agents in a large number of plant species. As a result, determining the nomenclature and taxonomically classifying geminiviruses turned into complex tasks. In addition, the gene responsible for viral replication (particularly, the viruses belonging to the genus Mastrevirus) may be spliced due to the use of the transcriptional/splicing machinery in the host cells. However, the current tools have limitations concerning the identification of introns.
Results
This study proposes a new method, designated Fangorn Forest (F2), based on machine learning approaches to classify genera using an ab initio approach, i.e., using only the genomic sequence, as well as to predict and classify genes in the family Geminiviridae. In this investigation, nine genera of the family Geminiviridae and their related satellite DNAs were selected. We obtained two training sets, one for genus classification, containing attributes extracted from the complete genome of geminiviruses, while the other was made up to classify geminivirus genes, containing attributes extracted from ORFs taken from the complete genomes cited above. Three ML algorithms were applied on those datasets to build the predictive models: support vector machines, using the sequential minimal optimization training approach, random forest (RF), and multilayer perceptron. RF demonstrated a very high predictive power, achieving 0.966, 0.964, and 0.995 of precision, recall, and area under the curve (AUC), respectively, for genus classification. For gene classification, RF could reach 0.983, 0.983, and 0.998 of precision, recall, and AUC, respectively.
Conclusions
Therefore, Fangorn Forest is proven to be an efficient method for classifying genera of the family Geminiviridae with high precision and effective gene prediction and classification. The method is freely accessible at www.geminivirus.org:8080/geminivirusdw/discoveryGeminivirus.jsp.
Electronic supplementary material
The online version of this article (10.1186/s12859-017-1839-x) contains supplementary material, which is available to authorized users.
doi:10.1186/s12859-017-1839-x
PMCID: PMC5622471  PMID: 28964254
Geminivirus; machine learning; Gene classification; Genus classification; Random Forest; Multilayer perceptron; Support vector machines
21.  Comparative study of representations of professional autonomy produced by first and last-period undergraduate nursing students 1  
ABSTRACT
Objective:
to compare the social representations of professional nurse autonomy produced by first and last-period undergraduate nursing students.
Method:
qualitative, descriptive and exploratory study, based on the structural approach of social representations, the Central Core Theory, carried out with 171 students from three federal public universities, using the free association technique on the object “professional nurse autonomy”. The data were submitted to EVOC 2005 software and to similarity analysis.
Results:
care was the central core of the representational structure identified among the students of the first period. Among last-period students, knowledge stood out as a core element. The term responsibility was identified as common to both central cores.
Conclusion:
regarding professional autonomy, the results point to an overlapping process of the reified and consensual universes during the undergraduate course. However, responsibility, inherent in the profession, remains cross-sectional. For the first period students, autonomy is resignified in a practical and attitudinal way, whereas for the last period students, the knowledge acquired stimulates them to assign meaning to professional autonomy with a cognitive and attitudinal representation. The data can support the use of innovative teaching practices in nursing undergraduate courses.
doi:10.1590/1518-8345.1919.2927
PMCID: PMC5614237
Professional Autonomy; Nursing; Education, Nursing; Social, Psychology; Work; Nurse’s Role
22.  Comparative study of sickle cell anemia and hemoglobin SC disease: clinical characterization, laboratory biomarkers and genetic profiles 
BMC Hematology  2017;17:15.
Background
In this study, we evaluate the association of different clinical profiles, laboratory and genetic biomarkers in patients with sickle cell anemia (SCA) and hemoglobin SC disease (HbSC) in attempt to characterize the sickle cell disease (SCD) genotypes.
Methods
We conducted a cross-sectional study from 2013 to 2014 in 200 SCD individuals (141 with SCA; 59 with HbSC) and analyzed demographic data to characterize the study population. In addition, we determined the association of hematological, biochemical and genetic markers including the βS-globin gene haplotypes and the 3.7 Kb deletion of α-thalassemia (−α3.7Kb-thal), as well as the occurrence of clinical events in both SCD genotypes.
Results
Laboratory parameters showed a hemolytic profile associated with endothelial dysfunction in SCA individuals; however, the HbSC genotype was more associated with increased blood viscosity and inflammatory conditions. The BEN haplotype was the most frequently observed and was associated with elevated fetal hemoglobin (HbF) and low S hemoglobin (HbS). The -α3.7Kb-thal prevalence was 0.09 (9%), and it was associated with elevated hemoglobin and hematocrit concentrations. Clinical events were more frequent in SCA patients.
Conclusions
Our data emphasize the differences between SCA and HbSC patients based on laboratory parameters and the clinical and genetic profile of both genotypes.
doi:10.1186/s12878-017-0087-7
PMCID: PMC5602866  PMID: 28932402
Sickle cell anemia; Hemoglobin SC disease; Biomarkers; Genetic profile
23.  Cross-species conservation of episome maintenance provides a basis for in vivo investigation of Kaposi's sarcoma herpesvirus LANA 
PLoS Pathogens  2017;13(9):e1006555.
Many pathogens, including Kaposi’s sarcoma herpesvirus (KSHV), lack tractable small animal models. KSHV persists as a multi-copy, nuclear episome in latently infected cells. KSHV latency-associated nuclear antigen (kLANA) binds viral terminal repeat (kTR) DNA to mediate episome persistence. Model pathogen murine gammaherpesvirus 68 (MHV68) mLANA acts analogously on mTR DNA. kLANA and mLANA differ substantially in size and kTR and mTR show little sequence conservation. Here, we find kLANA and mLANA act reciprocally to mediate episome persistence of TR DNA. Further, kLANA rescued mLANA deficient MHV68, enabling a chimeric virus to establish latent infection in vivo in germinal center B cells. The level of chimeric virus in vivo latency was moderately reduced compared to WT infection, but WT or chimeric MHV68 infected cells had similar viral genome copy numbers as assessed by immunofluorescence of LANA intranuclear dots or qPCR. Thus, despite more than 60 Ma of evolutionary divergence, mLANA and kLANA act reciprocally on TR DNA, and kLANA functionally substitutes for mLANA, allowing kLANA investigation in vivo. Analogous chimeras may allow in vivo investigation of genes of other human pathogens.
Author summary
KSHV latently infects cells and persists as a multi-copy, nuclear episome. KSHV LANA (kLANA) maintains episomes by acting on viral terminal repeat (kTR) elements. Model pathogen MHV68 mLANA acts analogously on mTR DNA. To date, KSHV investigation has been limited by lack of a tractable, small animal model. Here, we find that despite 60 Ma of evolutionary divergence, kLANA and mLANA exhibit inter-species functionality, acting reciprocally on TR DNA to mediate episome persistence. Further, kLANA rescued mLANA deficient MHV68, allowing chimeric virus to establish latent infection in vivo. The level of in vivo latency was moderately lower for kLANA chimeric virus compared to that of WT, but chimeric and WT virus infected cells had similar virus genome copy numbers. These results now provide a tractable model to investigate kLANA in vivo. This chimeric approach has the potential to be broadly applied to other small animal models for human pathogens.
doi:10.1371/journal.ppat.1006555
PMCID: PMC5599060  PMID: 28910389
24.  Stacking transgenic event DAS‐Ø15Ø7‐1 alters maize composition less than traditional breeding 
Plant Biotechnology Journal  2017;15(10):1264-1272.
Summary
The impact of crossing (‘stacking’) genetically modified (GM) events on maize‐grain biochemical composition was compared with the impact of generating nonGM hybrids. The compositional similarity of seven GM stacks containing event DAS‐Ø15Ø7‐1, and their matched nonGM near‐isogenic hybrids (iso‐hybrids) was compared with the compositional similarity of concurrently grown nonGM hybrids and these same iso‐hybrids. Scatter plots were used to visualize comparisons among hybrids and a coefficient of identity (per cent of variation explained by line of identity) was calculated to quantify the relationships within analyte profiles. The composition of GM breeding stacks was more similar to the composition of iso‐hybrids than was the composition of nonGM hybrids. NonGM breeding more strongly influenced crop composition than did transgenesis or stacking of GM events. These findings call into question the value of uniquely requiring composition studies for GM crops, especially for breeding stacks composed of GM events previously found to be compositionally normal.
doi:10.1111/pbi.12713
PMCID: PMC5595772  PMID: 28218975
composition; breeding stacks; equivalence
25.  Epidemiological and ecological determinants of Zika virus transmission in an urban setting 
eLife  null;6:e29820.
The Zika virus has emerged as a global public health concern. Its rapid geographic expansion is attributed to the success of Aedes mosquito vectors, but local epidemiological drivers are still poorly understood. Feira de Santana played a pivotal role in the Chikungunya epidemic in Brazil and was one of the first urban centres to report Zika infections. Using a climate-driven transmission model and notified Zika case data, we show that a low observation rate and high vectorial capacity translated into a significant attack rate during the 2015 outbreak, with a subsequent decline in 2016 and fade-out in 2017 due to herd-immunity. We find a potential Zika-related, low risk for microcephaly per pregnancy, but with significant public health impact given high attack rates. The balance between the loss of herd-immunity and viral re-importation will dictate future transmission potential of Zika in this urban setting.
eLife digest
Mosquitoes can transmit viruses that cause Zika, dengue and several other tropical diseases that affect humans. Zika virus usually causes mild symptoms, but it is thought that infection during pregnancy can lead to brain abnormalities, including microcephaly, where babies are born with an abnormally small head. Recent studies have shed light on how the Zika virus spread from Africa to reach South America, the Caribbean and North America. However, much less is known about the ecological factors that contribute to the spread of the virus within towns, cities and other local areas.
In 2015, Brazil was struck by an outbreak of the Zika virus that led to an international public health emergency. Lourenço et al. used a mathematical model to explore the local conditions within Feira de Santana (a major urban center in Brazil) that contributed to the outbreak. The model took into account numerous factors, including temperature, humidity, rainfall and the mosquito life-cycle, which made it possible to reconstruct the history of the virus over the past three years and to make projections for the next decades.
It revealed that most of the infections occured during 2015, with approximately 65% of the population infected. The incidences of new infections declined in 2016, as increasing numbers of local people had already been exposed to the virus and became immune. Temperature and humidity appeared to have played a critical role in sustaining the mosquito population carrying the Zika virus.
Further analysis suggests that the risk of Zika virus causing microcephaly is very low – only 0.3–0.5% of the pregnant women in Feira de Santana who were infected with Zika gave birth to a baby with the condition. What therefore makes Zika a public health concern is the combination of a low risk with very high infection rates, which can affect a large number of pregnancies.
This study will help researchers and policy makers to predict how the Zika virus will behave in the coming years. It also highlights the limitations and successes of the current system of surveillance. Moreover, it will help to identify critical time periods in the year when mosquito control strategies should be implemented to limit the spread of this virus. In future, this could help shape new local strategies to control Zika virus, dengue and other diseases carried by mosquitoes.
doi:10.7554/eLife.29820
PMCID: PMC5638629  PMID: 28887877
Zika; herd-immunity; mathematical model; Virus

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