Miracle-dz/UniFAR-FTUs huggingface dataset:
Parameters Governing the Community Structure and Element Turnover in Kermadec Volcanic Ash and Hydrothermal Fluids as Monitored by Inorganic Electron Donor Consumption, Autotrophic CO2 Fixation and 16S Tags of the Transcriptome in Incubation Experiments

The microbial community composition and its functionality was assessed for hydrothermal fluids and volcanic ash sediments from Haungaroa and hydrothermal fluids from the Brothers volcano in the Kermadec island arc (New Zealand). The Haungaroa volcanic ash sediments were dominated by epsilonproteobacterial Sulfurovum sp. Ratios of electron donor consumption to CO2 fixation from respective sediment incubations indicated that sulfide oxidation appeared to fuel autotrophic CO2 fixation, coinciding with thermodynamic estimates predicting sulfide oxidation as the major energy source in the environment. Transcript analyses with the sulfide-supplemented sediment slurries demonstrated that Sulfurovum prevailed in the experiments as well. Hence, our sediment incubations appeared to simulate environmental conditions well suggesting that sulfide oxidation catalyzed by Sulfurovum members drive biomass synthesis in the volcanic ash sediments. For the Haungaroa fluids no inorganic electron donor and responsible microorganisms could be identified that clearly stimulated autotrophic CO2 fixation. In the Brothers hydrothermal fluids Sulfurimonas (49%) and Hydrogenovibrio/Thiomicrospira (15%) species prevailed. Respective fluid incubations exhibited highest autotrophic CO2 fixation if supplemented with iron(II) or hydrogen. Likewise catabolic energy calculations predicted primarily iron(II) but also hydrogen oxidation as major energy sources in the natural fluids. According to transcript analyses with material from the incubation experiments Thiomicrospira/Hydrogenovibrio species dominated, outcompeting Sulfurimonas. Given that experimental conditions likely only simulated environmental conditions that cause Thiomicrospira/Hydrogenovibrio but not Sulfurimonas to thrive, it remains unclear which environmental parameters determine Sulfurimonas’ dominance in the Brothers natural hydrothermal fluids.
Impacts des changements climatiques sur les flux de carbone stimulés par la lumière dans l'Océan Arctique : quantification et suivi de la photo-oxydation de la matière organique dissoute dans la Mer de Beaufort par télédection spatiale

L’oxydation photochimique de la matiere organique dissoute coloree (CDOM), et la production de CO2 qui en resulte, est maintenant reconnue comme etant un processus majeur dans le cycle du carbone dans le systeme ocean-atmosphere. L’Ocean Arctique fait parti des environnements ou ce processus risque de jouer un role de plus en plus important dans le contexte des changements climatiques a cause de : 1) l’augmentation du CDOM d’origine terrigene transporte a l’Ocean cotier en reponse a la fonte du pergelisol et a l’augmentation du debit des rivieres; 2) la diminution du couvert de glace estivale permettant au rayonnement solaire de penetrer dans la colonne d’eau; et 3) l’augmentation du rayonnement ultraviolet (UV) dans cette region. Un modele couple « optique-photochimique » a ete utilise pour examiner le role de la photooxydation dans le cycle du carbone organique de l’Ocean Arctique. Pour calculer la photoproduction de CO2 (PDIC), l’eclairement spectral incident, incluant les UV, a ete modelise avec un modele de transfert radiatif necessitant les concentrations de glace de mer, d’ozone, d’aerosols atmospheriques et le couvert nuageux observes par satellite entre 1979 et 2004. Les rendements quantiques apparents pour calculer la PDIC ont ete determines en laboratoire sur des echantillons provenant de la Mer de Beaufort et du Fleuve Mackenzie. La contribution du CDOM au coefficient d’absorption totale ([aCDOM/at]), un parametre cle du modele, a ete determinee soit a partir des mesures in situ, soit derivee des donnees de la couleur de l’ocean a l’aide d’un nouvel algorithme empirique. Contrairement aux methodes semi-analytiques trouvees dans la litterature, l’algorithme empirique propose permet de separer, a l’echelle regionale, les coefficients d’absorption du CDOM et des particules non-algales. Cependant, l’utilisation des donnees de la couleur de l’ocean dans les hautes latitudes est souvent compromise par la presence de glace de mer qui contamine les donnees. Ce probleme a ete aborde dans le cadre de la presente etude, et une methode a ete proposee afin de detecter et eliminer les donnees contaminees par la glace de mer. Enfin, il a ete demontre que les valeurs de PDIC sont similaires aux taux de carbone organique provenant de la production primaire marine qui est sequestre dans les sediments oceaniques; et que l’augmentation des UV et la diminution de la glace de mer estivale au cours des 26 dernieres annees a conduit a une augmentation de PDIC d’environ 15%. Ces resultats indiquent que la photooxydation joue un role significatif dans le cycle du carbone actuel, et que la diminution de l'etendue de la glace de mer, prevue par les modeles climatiques, risque d'amplifier significativement la remineralisation photochimique du carbone organique dissous d'origine terrigene dans l'Ocean Arctique.
The acute respiratory distress syndrome after major cardiac surgery - Case report

Acute respiratory distress syndrome (ARDS) is a severe pulmonary disease first described in 1967 by Dr. Thomas L. Petty and colleagues as a syndrome of respiratory failure that presents with progressive arterial hypoxemia refractory to oxygen therapy, severe dyspnea caused by reduction of pulmonary compliance and diffuse bilateral pulmonary infiltrations. This clinical syndrome is characterised by acute, severe and life threatening respiratory insufficiency with high mortality rate [1-3]. The definition of ALI/ARDS was recommended by the American/ European Consensus Conference since 1994 (Table 1). The standard definition classifies the patients with bilateral pulmonary infiltrates and arterial hypoxemia, who have the ratio of PaO2 / FiO2 less than 300 mmHg. However, if the ratio is less than 200 mmHg, the diagnosis of ARDS can be made. In patients with left heart disease, the pulmonary wedge pressure less that 18 mmHg is a criterion to distinguish ARDS form cardiac failure. Recently, new Berlin classification of ARDS was accepted in 2013, where the term ALI was abandoned and ARDS was categorized [3,4].
Visual Search for Feature and Conjunction Targets with an Attention Deficit

Brain-damaged subjects who had previously been identified as suffering from a visual attention deficit for contralesional stimulation were tested on a series of visual search tasks. The experiments examined the hypothesis that the processing of single features is preattentive but that feature integration, necessary for the correct perception of conjunctions of features, requires attention (Treisman & Gelade, 1980 Treisman & Sato, 1990). Subjects searched for a feature target (orientation or color) or for a conjunction target (orientation and color) in unilateral displays in which the number of items presented was variable. Ocular fixation was controlled so that trials on which
Modeling the adaptation of infrastructures to prevent the effects of climate change: An overview of existing literature

Climate change is likely to affect our infrastructures and, consequently, the way society interacts with these infrastructures. For instance, higher average temperatures increase the need for electricity delivered through the grid in the summer due to augmented air-conditioning. As the scientific consensus is that climate change effects may be severe, a next step is to divert the focus from the natural system to the effects on man-made systems. Particularly, we expect that the interconnectedness of man-made systems, especially energy, transport, ICT and water infrastructures is important with respect to cascading effects of climate change. In order to gain insight into the effects of climate change on our infrastructures and possible adaption strategies for the coming decades, we describe a literature search on the intersection of literature on infrastructures and climate change. Specifically, we search for ways to adapt our energy and transport infrastructures and make them resilient against the consequences of climate change and modeling approaches that simulate these adaption strategies for our infrastructure systems. We have found that, although there is a vast body of literature on climate change, less attention was paid to the effects of climate change on infrastructures. Our literature analysis shows that there is ample literature measuring the effects of climate change on individual technologies and parts of infrastructures. In contrast, the literature on the systems level, the adaptation of infrastructures and infrastructure interdependencies is just emerging. We anticipate that future research attention needs to be diverted from the analysis of a technical component (when will my bridge be broken) to the technical system level (how do I judge/measure when to replace a road section (including the bridge)? ) or even to one of the socio-technical system level (how can I adapt the system as a whole as to prevent the effects of a tunnel breakdown? ). We conjecture that suitable simulations and models should be developed to explore adaptation strategies at these levels of aggregation.
Identifying Critical Points of Trajectories of Depressive Symptoms From Childhood to Young Adulthood: Evidence of Sex Differences from the Avon Longitudinal Study of Parents and Children (ALSPAC)

Depression is a common mental illness associated with increased substance misuse and risk of suicide. Potential risk factors for depression include sex and depressive symptoms in early life, however the mechanisms responsible are not yet understood. Research has focused on late childhood and adolescence as this developmental period may be a modifiable risk factor that prevents or reduces depression at a later stage. It is also important to establish at what ages the level of depression is changing as this will help identify critical points to intervene with treatment. We used multilevel growth-curve models to explore adolescent trajectories of depressive symptoms in the Avon Longitudinal Study of Parents and Children, a UK based pregnancy cohort. Using data from 9301 individuals, trajectories of depressive symptoms were constructed for males and females between 10.6 and 22.8 years old. We calculated the age of peak velocity for depressive symptoms (the age at which depressive symptoms increases most rapidly) and the age of maximum depressive symptoms. Adjusted results suggested that being female was associated with a steeper trajectory compared to being male (per 1 year increase in relation to depressive symptoms: 0.128, SE = 0.035, [95% CI: 0.059, 0.198]; p <0.001). We found evidence suggesting that females had an earlier age of peak velocity of depressive symptoms (females 13.7 years old, SE = 0.321, [95% CI: 12.9, 14.4] and males 16.4 years old, SE = 0.096, [95% CI: 16.2, 16.6]; p <0.001), but weak evidence of an earlier age of maximum depressive symptoms (p = 0.125). Possible mechanisms that underlie this sex difference include the roles of pubertal development and timing. Using multilevel growth curve models to estimate the age of peak velocity and maximum depressive symptoms for different population subgroups may provide useful knowledge for treating and preventing later depression.
Changes in Intraocular Pressure and Anterior Chamber Depth after Phacoemulsification in Non-Glaucomatous Patients

Aims: To evaluate changes in intraocular pressure (IOP) and anterior chamber depth (ACD) after uneventful phacoemulsification with intraocular lens (IOL) implantation. Study Design: Prospective interventional comparative study. Place and Duration of Study: Department of Ophthalmology, Assuit University Hospital, Assuit, Egypt between September 2016 and October 2017. Methodology: 100 Patients with visually significant cataract (39 males (39%) and 61 females (61%). All patients underwent uneventful phacoemulsification. Intraocular pressure and ACD were measured preoperatively by using Goldmann applanation tonometer and Ultrasonography respectively, and at 1 week, 1 month, and 3 months postoperatively. Results: The postoperative ACD was higher than the preoperative value by 0.26± 0.06 mm at 1 week, 0.45±0.06 mm at 1 month, and 0.59±0.08 mm at 3 months postoperatively (P=.000). P < 0.05 was considered to indicate a statistically significant difference. The IOP at 1 week, 1 month, and 3 months postoperatively was lower than the preoperative value by 1.03±0.3 mmHg, 1.52±0.46 mmHg, and 2.14±0.62 mmHg, respectively (P=.001). Conclusion: This study revealed that there was a decrease in IOP and increase in ACD after cataract extraction by phacoemulsification. Patients with ocular hypertension, open-angle glaucoma, and narrow-angle glaucoma may benefit from cataract extraction.
Amphibians of grasslands in the state of Paraná, southern Brazil ( Campos Sulinos ).

Amphibian conservation depends on knowledge about species composition and distribution. This emphasizes the need for inventories, especially in poorly sampled areas. This is the case of Southern grasslands ( Campos Sulinos ) associated with Araucaria forest in the state of Parana, southern Brazil. We sampled amphibians in 105 environments from 2004 to 2013 using transect sampling, active search and surveys at breeding sites. We found 61 anuran species and two caecilians. This is the first comprehensive list of amphibian species inhabiting grasslands in Parana. This landscape deserves high conservation priority before these natural grasslands vanish.
The Stata Journal Editors’ Prize 2018: Federico Belotti

Federico Belotti was born in Rome in 1976 and grew up there. He received a bachelor’s degree in economics in 2004 and a master’s in quantitative methods in 2005 from the University of Rome Tor Vergata. After spending two years working at the Italian National Institute of Statistics, he went back to academia and was awarded a PhD in econometrics and empirical economics, also by the University of Rome Tor Vergata. His thesis was awarded the prize for the best PhD thesis in 2011 in applied statistics and demography by the Italian Statistical Society.
Novel Respiratory Impedance-Based Phenotypes Reflect Different Pathophysiologies in Chronic Obstructive Pulmonary Disease Patients

Purpose The forced oscillation technique (FOT) is a non-invasive method to measure respiratory impedance, the respiratory resistance (Rrs) and reactance (Xrs). The disease probability measure (DPM) is a useful computed tomography (CT) imaging variable for the assessment of gas trapping and emphysema in patients with chronic obstructive pulmonary disease (COPD) using pairs of inspiratory and expiratory CT images. We aimed to develop FOT-based phenotypes and determine whether the phenotypes and their imaging characteristics could facilitate the understanding of COPD pathophysiology. Patients and methods FOT and spirometry were examined in 164 COPD patients and 22 non-COPD smokers. COPD patients were divided into four FOT-based phenotypes (NL, normal group; RD, resistance-dominant group; XD, reactance-dominant group; and MIX, mixed group) based on the 3rd quartile values of R5 (Rrs at 5Hz) and X5 (Xrs at 5Hz) in the non-COPD group. The emphysematous lesions and the airway lesions were quantitatively assessed in CT images by low attenuation volume and the square root of the wall area of a hypothetical airway with an internal perimeter of 10 mm (√Aaw at Pi10), respectively. DPM imaging analysis was also performed in 131 COPD patients. We investigated the differences in COPD parameters between the FOT-based phenotypes. Results √Aaw at Pi10 were significantly higher in the RD, XD, and MIX groups than in the NL group. The XD group showed lower pulmonary function and higher dyspnea scores than the RD group. No significant changes in DPM values were observed between the RD and the NL groups. The gas-trapping area was significantly higher in the XD group than in the NL group. The MIX group showed the highest dyspnea score, most emphysematous lesions, and the lowest forced expiratory volume in 1 s % predicted value. Conclusion The FOT-based phenotyping may be useful to assess pathophysiological changes of COPD with CT assessments.
A New Approach to Collaborative Filtering : Operator Estimation with Spectral Regularization

Collaborative filtering (CF) refers to the task of predicting preferences of a given “user” for some “objects” (e.g., books, music, products, people, etc.) based on his/her previously revealed preferences – typically in the form of ratings – as well as the revealed preferences of other users. In a book recommender system, for example, one would like to suggest new books to someone based on what he and other users have recently purchased or rated. The ultimate goal of CF is to infer the preferences of users for new to them objects. Recently there has been interest in CF using regularization based methods [2]. These methods assume that the only data available are the revealed preferences, and no other information such as background information on the objects or users is given. In this case, one may formulate the problem as that of filling a matrix with users as rows, objects (e.g., books) as columns, and missing entries as currently unknown preferences. To make useful predictions within this setting, regularization based CF methods make certain assumptions about the relatedness of the objects and users. The most common assumption is that preferences can be decomposed into a small number of factors, both for users and objects, resulting in the search for a low-rank matrix which approximates the partially observed matrix of preferences [2]. The rank constraint can be interpreted as a regularization on the hypothesis space. Since the rank constraint gives rise to a non-convex set of matrices, the associated optimization problem will be a difficult non-convex problem for which only heuristic algorithms exist [2]. An alternative formulation, proposed by [3], suggests penalizing the predicted matrix by its trace norm, i.e., the sum of its singular values. An added benefit of the trace norm regularization is that, with a sufficiently large regularization parameter, the final solution will be low-rank [1]. However, a key limitation of current regularization based CF methods is that they do not take advantage of information, such as attributes of users (e.g., gender, age) or objects (e.g., book’s author, genre), which is often available. Intuitively, such information might be useful to guide the inference of preferences, in particular for users and objects with very few known ratings. For example, at the extreme, users and objects with no prior ratings can not be considered in the standard CF formulation, while their attributes alone could provide some basic preference inference.
An expert panel review of clinical challenges in psychiatry CLINICAL CONSIDERATIONS WITH ATYPICAL ANTIPSYCHOTIC AUGMENTATION

Introduction: Practical Clinical Applications In spite of the tremendous advances made in developing antidepressant treatments and exploring augmentation with second-generation antipsychotics (SGAs), significant obstacles remain for psychiatrists: How should clinicians make use of cutting-edge augmentation studies? How should they use the antipsychotics in their treatment algorithm? How should they think about dosing and side effects? The first major problem is there have been no great algorithmic studies on adjunctive strategies. In fact, the most useful algorithmic study was the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study, from which SGAs were entirely absent. The second problem is that STAR*D showed a clear pattern in which the efficacy of an augmentation agent depended on its placement in the algorithm. Those agents occurring later in the algorithm, such as monoamine oxidase inhibitors (MAOIs), adjunctive triiodothyronine (T3), and adjunctive lithium, appeared to be less effective than adjunctive buspirone, which occurred earlier in the algorithm. This was not the result of a direct comparison. Because of these two problems, it is therefore difficult to determine how to rank the efficacy of SGAs among the agents investigated by the STAR*D study. Among clinical treatment strategies, SGAs might appear toward the end of first-line strategies, perhaps after combinations and stimulants but before buspirone. As a field, we also know very little about optimal dosing of SGAs when used as adjunctive treatments for depression. In general, however, doses used in adjunctive strategies are lower than those used for either acute mania or acute psychotic states. These are usually dosed in the range of 2.5-10 mg for aripiprazole, 20-60 mg for ziprasidone, 2.510 mg forolanzapine, 0.5-3 mg for risperidone, and 50-200 mg for quetiapine. However, these doses are based more on clinical experience than evidence-based data.
Seventh Annual Conference of in VIVO Planetary Health on Transforming Life : Unify Personal , Public , and Planetary Health

inVIVO Planetary Health is a progressive, humanist scientific movement promoting both evidence and advocacy around concepts of planetary health which denote the interdependence between human health and place at all scales. Our seventh annual conference was held in Canmore, Alberta 4-6th April 2018, themed “Transforming Life: Unify Personal, Public, and Planetary Health” included diverse topics and perspectives to emphasise the interdependent vitality of all natural and anthropogenic ecosystems—social, political and otherwise. A key outcome of this meeting was the The Canmore Declaration: Statement of Principles for Planetary Health (published separately) which underscores that improving the health of all systems depends on: mutualistic values; planetary consciousness; advocacy; unity of purpose; recognition of biopsychosocial interdependence; emotional bonds between people and the land; efforts to counter elitism, social dominance and marginalization; meaningful cross-sectoral and cross-cultural narrative; self-awareness; and a personal commitment to shaping new normative attitudes and behaviors. Here we present the collection of abstracts of invited lectures and oral communications presented during the meeting. These formed the foundations and direction for discussions that became the basis of The Canmore Declaration.
Community health workers' involvement in mother–child care during the 1st year after birth, in Kaya health district, Burkina Faso: A contribution analysis

Introduction Maternal and infant morbidity and mortality remain high in sub-Saharan Africa. However, actions to strengthen postpartum care are still weak and mainly limited to health facilities (HFs). In Kaya health district, Burkina Faso, community health workers (CHWs) were involved in mother and child care during the 1st year postpartum through home visits, outreach sessions and accompanying mothers to health facilities. The aim of this study was to assess the contribution of CHWs to postpartum women's attendance at the health facilities. Methods We conducted an effect assessment using Mayne and Lemire's contribution analysis framework. Qualitative and quantitative data were collected through project documents review and individual semi-structured interviews with key-informants. Results All the participants interviewed acknowledged that the number of women, who came to postpartum care, had increased since the implementation of the project activities. Postpartum consultation rates within the 1st week postpartum increased from 29% in 2011 to 80% in 2015 and from 19 to 50% within 6 weeks. Others interventions such as Performance based financing, Save The Children nutritional project and the health services component of Missed Opportunities in Mother and Infant Health (MOMI) were the alternative explanations. Conclusions CHWs involvement in women care contributed to improve their adherence to postpartum consultations in Kaya health district.