Miracle-dz/UniFAR-FTUs huggingface dataset:
Biodiversity in cities needs space: a meta-analysis of factors determining intra-urban biodiversity variation.

Understanding varying levels of biodiversity within cities is pivotal to protect it in the face of global urbanisation. In the early stages of urban ecology studies on intra-urban biodiversity focused on the urban-rural gradient, representing a broad generalisation of features of the urban landscape. Increasingly, studies classify the urban landscape in more detail, quantifying separately the effects of individual urban features on biodiversity levels. However, while separate factors influencing biodiversity variation among cities worldwide have recently been analysed, a global analysis on the factors influencing biodiversity levels within cities is still lacking. We here present the first meta-analysis on intra-urban biodiversity variation across a large variety of taxonomic groups of 75 cities worldwide. Our results show that patch area and corridors have the strongest positive effects on biodiversity, complemented by vegetation structure. Local, biotic and management habitat variables were significantly more important than landscape, abiotic or design variables. Large sites greater than 50 ha are necessary to prevent a rapid loss of area-sensitive species. This indicates that, despite positive impacts of biodiversity-friendly management, increasing the area of habitat patches and creating a network of corridors is the most important strategy to maintain high levels of urban biodiversity.
PolA1, a Putative DNA Polymerase I, Is Coexpressed with PerR and Contributes to Peroxide Stress Defenses of Group A Streptococcus

ABSTRACT The peroxide stress response regulator PerR coordinates the oxidative-stress defenses of group A Streptococcus (GAS). We now show that PerR is expressed from an operon encoding a putative DNA polymerase I (PolA1), among other GAS products. A polA1 deletion mutant exhibited wild-type growth but showed reduced capacity to repair DNA damage caused by UV light or ciprofloxacin. Mutant bacteria were hypersensitive to H2O2, compared with the wild type or a complemented mutant strain, and remained severely attenuated even after adaptation at sublethal H2O2 levels, whereas wild-type bacteria could adapt to withstand peroxide challenge under identical conditions. The hypersensitivity of the mutant was reversed when bacteria were grown in iron-depleted medium and challenged in the presence of a hydroxyl radical scavenger, results that indicated sensitivity to hydroxyl radicals generated by Fenton chemistry. The peroxide resistance of a perR polA1 double mutant following adaptation at sublethal H2O2 levels was decreased 9-fold relative to a perR single mutant, thus implicating PolA1 in PerR-mediated defenses against peroxide stress. Cultures of the polA1 mutant grown with or without prior H2O2 exposure yielded considerably lower numbers of rifampin-resistant mutants than cultures of the wild type or the complemented mutant strain, a finding consistent with PolA1 lacking proofreading activity. We conclude that PolA1 promotes genome sequence diversity while playing an essential role in oxidative DNA damage repair mechanisms of GAS, dual functions predicted to confer optimal adaptive capacity and fitness in the host. Together, our studies reveal a unique genetic and functional relationship between PerR and PolA1 in streptococci.
Clustering Suicide Attempters: Impulsive-Ambivalent, Well-Planned, or Frequent.

BACKGROUND Attempts to predict suicidal behavior within high-risk populations have so far shown insufficient accuracy. Although several psychosocial and clinical features have been consistently associated with suicide attempts, investigations of latent structure in well-characterized populations of suicide attempters are lacking. METHODS We analyzed a sample of 1,009 hospitalized suicide attempters that were recruited between 1999 and 2012. Eleven clinically relevant items related to the characteristics of suicidal behavior were submitted to a Hierarchical Ascendant Classification. Phenotypic profiles were compared between the resulting clusters. A decisional tree was constructed to facilitate the differentiation of individuals classified within the first 2 clusters. RESULTS Most individuals were included in a cluster characterized by less lethal means and planning ("impulse-ambivalent"). A second cluster featured more carefully planned attempts ("well-planned"), more alcohol or drug use before the attempt, and more precautions to avoid interruptions. Finally, a small, third cluster included individuals reporting more attempts ("frequent"), more often serious or violent attempts, and an earlier age at first attempt. Differences across clusters by demographic and clinical characteristics were also found, particularly with the third cluster whose participants had experienced high levels of childhood abuse. CONCLUSIONS Cluster analysis consistently supported 3 distinct clusters of individuals with specific features in their suicidal behaviors and phenotypic profiles that could help clinicians to better focus prevention strategies.
Drosophila spalt/spalt-related mutants exhibit Townes-Brocks' syndrome phenotypes

Mutations in SALL1, the human homolog of the Drosophila spalt gene, result in Townes-Brocks' syndrome, which is characterized by hand/foot, anogenital, renal, and ear anomalies, including sensorineural deafness. spalt genes encode zinc finger transcription factors that are found in animals as diverse as worms, insects, and vertebrates. Here, we examine the effect of losing both of the spalt genes, spalt and spalt-related, in the fruit fly Drosophila melanogaster, and report defects similar to those in humans with Townes-Brocks' syndrome. Loss of both spalt and spalt-related function in flies yields morphological defects in the testes, genitalia, and the antenna. Furthermore, spalt/spalt-related mutant antennae show severe reductions in Johnston's organ, the major auditory organ in Drosophila. Electrophysiological analyses confirm that spalt/spalt-related mutant flies are deaf. These commonalities suggest that there is functional conservation for spalt genes between vertebrates and insects.
Long-term results of renal transplant from living donors aged over 60 years.

OBJECTIVES This study sought to determine whether recipients of grafts from donors aged 60 years or older achieve the same benefit as those from younger donors in the long term. MATERIALS AND METHODS Between January 2004 and July 2008, one hundred seventeen living renal transplants were performed. The patients were divided into an older donor group (aged ≥ 60 y, n=23) and a younger donor group (aged < 60 y, n=94). Characteristics and evolution of the donors and recipients were compared between the groups. RESULTS There was no statistically significant difference between the groups respecting sex, body mass index, duration on dialysis, ischemia time, human leukocyte antigen matches and incidence of primary nonfunction, delayed graft function, acute rejection, and infection (P > .05). The 1-, 3-, and 5-year graft survival for the older group versus the younger group was 95.7% versus 97.9% (P > .05), 91.3% versus 93.6% (P > .05), and 81.8% versus 83.3% (P > .05). Patient survival at 1, 3, and 5 years was 100% versus 100% (P > .05), 95.7% versus 96.8% (P > .05), and 90.9% versus 88.9% (P > .05) with no significant difference in the log-rank test for Kaplan-Meier. CONCLUSIONS Our studies suggest that in the long term, renal transplant from live donors older than 60 years it is an acceptable alternative.
Host model uncertainties in aerosol radiative forcing estimates: results from the AeroCom Prescribed intercomparison study

Abstract. Simulated multi-model "diversity" in aerosol direct radiative forcing estimates is often perceived as a measure of aerosol uncertainty. However, current models used for aerosol radiative forcing calculations vary considerably in model components relevant for forcing calculations and the associated "host-model uncertainties" are generally convoluted with the actual aerosol uncertainty. In this AeroCom Prescribed intercomparison study we systematically isolate and quantify host model uncertainties on aerosol forcing experiments through prescription of identical aerosol radiative properties in twelve participating models. Even with prescribed aerosol radiative properties, simulated clear-sky and all-sky aerosol radiative forcings show significant diversity. For a purely scattering case with globally constant optical depth of 0.2, the global-mean all-sky top-of-atmosphere radiative forcing is −4.47 Wm−2 and the inter-model standard deviation is 0.55 Wm−2, corresponding to a relative standard deviation of 12%. For a case with partially absorbing aerosol with an aerosol optical depth of 0.2 and single scattering albedo of 0.8, the forcing changes to 1.04 Wm−2, and the standard deviation increases to 1.01 W−2, corresponding to a significant relative standard deviation of 97%. However, the top-of-atmosphere forcing variability owing to absorption (subtracting the scattering case from the case with scattering and absorption) is low, with absolute (relative) standard deviations of 0.45 Wm−2 (8%) clear-sky and 0.62 Wm−2 (11%) all-sky. Scaling the forcing standard deviation for a purely scattering case to match the sulfate radiative forcing in the AeroCom Direct Effect experiment demonstrates that host model uncertainties could explain about 36% of the overall sulfate forcing diversity of 0.11 Wm−2 in the AeroCom Direct Radiative Effect experiment. Host model errors in aerosol radiative forcing are largest in regions of uncertain host model components, such as stratocumulus cloud decks or areas with poorly constrained surface albedos, such as sea ice. Our results demonstrate that host model uncertainties are an important component of aerosol forcing uncertainty that require further attention.
AN ABSTRACT OF THE THESIS OF Xu Xu for the degree of Master of Science in Computer Science presented on June 13, 2017. Title: Classifying and Synthesizing 3D Shapes of Objects using Deep Neural Networks Abstract approved:

approved: Sinisa Todorovic Reasoning about 3D shape of objects is important for successful computer vision applications in robotics, 3D rendering and modeling. In this thesis, we address two problems – First, given an image, we generate 3D shape of the foreground object that appears in the image. Second, we predict the class label of the input 3D object shape. Recent work uses convolutional neural networks (CNNs) for these problems. However, their training is difficult, since it requires a large amount of training data. Also, in 3D shape generation, existing approaches can not generate realistic 3D shapes and have limited variations in generated 3D shapes. This thesis addresses these issues. We present two novel approaches, one for each problem. First, for 3D classification, we formulate CNN learning as a beam search aimed at identifying an optimal CNN architecture as well as estimating parameters of such an optimal CNN. This model pursuit approach is evaluated on 3D ShapeNet dataset. Second, we introduce a 3D-VAE-GAN (3D Variational AutoEncoder Generative Adversarial Network) model to synthesize high-quality 3D objects from 2D images in ObjectNet3D dataset. Our experimental evaluation shows that our new CNN learning achieves the state-of-the-art results with better modeling efficiency, i.e., with fewer parameters which are much easier to train. Also, in 3D shape synthesis, we achieve larger variability in shapes. c ©Copyright by Xu Xu June 13, 2017 All Rights Reserved Classifying and Synthesizing 3D Shapes of Objects using Deep Neural Networks
Climatological diurnal variability in sea surface temperature characterized from drifting buoy data

Drifting buoy sea‐surface temperature (SST) records have been used to characterize the diurnal variability of ocean temperature at a depth of order 20 cm. We use measurements covering the period 1986–2012 from the International Comprehensive Ocean‐Atmosphere Data Set (ICOADS) version 2.5, which is a collection of marine surface observations that includes individual SST records from drifting buoys. Appropriately transformed, this dataset is well suited for estimation of the diurnal cycle, since many drifting buoys have high temporal coverage (many reports per day), and are globally distributed. For each drifter for each day, we compute the local‐time daily SST variation relative to the local‐time daily mean SST. Climatological estimates of subdaily SST variability are found by averaging across various strata of the data: in 10° latitudinal bands as well as globally; and stratified with respect to season, wind speed and cloud cover. A parameterization of the diurnal variability is fitted as a function of the variables used to stratify the data, and the coefficients for this fit are also provided with the data. Results are consistent with expectations based on the previous work: the diurnal temperature cycle peaks in early afternoon (circa 2 pm local time); there is an increase in amplitude and a decrease in seasonality towards the equator. Generally, the ocean at this depth cools on windy days and warms on calm days, so that a component of subdaily variability is the SST tendency on slower timescales. By not ‘closing’ the diurnal cycle when stratified by environmental conditions, this dataset differs from previously published diurnal‐cycle parameterizations. This thorough characterization of the SST diurnal cycle will assist in interpreting SST observations made at different local times of day for climatological purposes, and in testing and constraining models of the diurnal‐cycle and air‐sea interaction at high temporal resolution.
Atrial and ventricular septal defects – epidemiology and spontaneous closure

Objective. To present data on the epidemiology and spontaneous closure for septal defects (secundum atrial septal defect (ASD) and/or ventricular septal defect (VSD)). Methods. Data from the EUROCAT Registry of Congenital Malformations for Funen County, Denmark were analyzed. All infants born from 1986 to 1998, diagnosed with a secundum ASD and/or a VSD as the only cardiac malformation, were included. Results. There were 78 infants with an ASD, 195 with a VSD, and 19 had both an ASD and a VSD. The overall prevalence of septal defects was 4.1 per 1000 livebirths. Among the VSDs 45% were perimembranous and 55% were muscular defects. Associated non-cardiac malformations, syndromes, or karyotype anomalies were present in 54 cases (19% of total) but with a significantly lower proportion among cases with muscular VSDs (7%, p < 0.05). Eighty-one percent of the cases had an isolated cardiac malformation. Five of 61 cases (8%) with isolated ASD were closed surgically before five years of age and 43 (70%) closed spontaneously within the first five years of life. Of the 65 cases with isolated perimembranous VSDs, 13 were closed surgically (20%) and 13 closed spontaneously (20%). Of the 99 cases with isolated muscular VSDs no defects were closed by surgery and 64 (65%) closed spontaneously. The rate of spontaneous closure for perimembranous and muscular VSDs were significantly different (p < 0.0001). Conclusions. Secundum ASD has a high rate of spontaneous closure. Perimembranous and muscular VSDs seem to be two different diseases with different epidemiology and natural history.
Integrating vegetation phenology in soil moisture change detection from ASAR wide swath images

Multitemporal processing of synthetic aperture radar imagery, e.g. for the extraction of a soil moisture index, requires normalization of acquisitions from different locations in space to a common incidence angle. Incidence angle dependence of backscatter is known to depend on the amount of aboveground vegetation, and can thus be expected to vary seasonally as a result of vegetation phenology. This study tries to assess the impact of vegetation phenology on the angular dependence, and the effect on a soil moisture index derived using a change detection method. It is found that soil moisture accuracy overall decreases when seasonality in the angular dependence of backscatter is ignored.
Rescaling inequality? Welfare reform and local variation in social assistance payments

Social assistance and other means tested benefits are the last resort in national social protection systems and variation in benefit receipt are in part a direct consequence of differences in means and needs. Variation may however also be related to local discretion over implementation of national legislation, implying inequality unintended by legislators. Such discretion is generally believed to have increased following decentralizing reforms in the 1990s, an international trend frequently referred to as devolution. More recent reforms have instead often implied recentralization and/or involved institutional cooperation of welfare agencies located at different vertical levels. Little is however known regarding the extent to which shifting divisions of power influences benefit receipt. Using individual level register data, multi-level modelling and a difference-in-difference approach we attempt to link changes in legislation to changes in inter-municipal differences in social assistance payments in the Nordic countries during the period 1990 to 2010. Somewhat simplified, the assumption is that the more detailed the regulation the less variation is possible and vice versa. The results show the changes in inequality in the wake of the reforms to be heterogeneous, both in accordance with and contradictory to the starting hypothesis. Although some of the unexpected results are difficult to account for, others may be explained by the character or implementation of the reforms.
Sex Differences in the Attractiveness Halo Ef- fect in the Online Dating Environment

The following study with 113 participants analyzes the evaluation bias effects that happen when people are confronted with a typical profile of a online dating service that contains a false photo, i.e. a photo that obviously does not portray the profile owner. It is known that profile photos have a great impact how the profile owner is judged. As predicted by the attractiveness halo effect, an attractive photo leads to better evaluations of the displayed person than an unattractive photo. The results of this study show that even if the evaluator knows that the photo does not actually portray the profile owner, he is nevertheless influenced by the perceived attractiveness of the displayed person. But this is only the case for men judging women. Women seem to be more resistant against this automatic evaluation bias. The findings are fully in line with other empirical findings that support an evolutionary perspective, namely that men ascribe a higher value to physical attractiveness in judging women than women do in judging men.
Human immunodeficiency virus type 1 viral protein R localization in infected cells and virions

The subcellular localization of human immunodeficiency virus type 1 (HIV-1) viral protein R (Vpr) was examined by subcellular fractionation. In HIV-1-infected peripheral blood mononuclear cells, Vpr was found in the nuclear and membrane fractions as well as the conditioned medium. Expression of Vpr without other HIV-1 proteins, in two different eukaryotic expression systems, demonstrated a predominant localization of Vpr in the nuclear matrix and chromatin extract fractions. Deletion of the carboxyl-terminal 19-amino-acid arginine-rich sequence impaired Vpr nuclear localization. Indirect immunofluorescence confirmed the nuclear localization of Vpr and also indicated a perinuclear location. Expression of Vpr alone did not result in export of the protein from the cell, but when coexpressed with the Gag protein, Vpr was exported and found in virus-like particles. A truncated Gag protein, missing the p6 sequence and a portion of the p9 sequence, was incapable of exporting Vpr from the cell. Regulation of Vpr localization may be important in the influence of this protein on virus replication.
Centipede envenomation

Five episodes of envenomation by centipedes in 2 patients are reported. These arthropods are fast-moving, frightening in appearance to some, and may display aggressive behavior. However, stings from these centipedes, like most found worldwide, caused no serious morbidity or mortality. Common effects included intense local pain, erythema, induration, and necrosis, as well as mild constitutional symptoms. All resolved without sequelae. Treatment included pain control, wound care, and tetanus immunization.
Different states of clinical control are associated with changes in IGF‐I and IGFBPs in children with congenital adrenal hyperplasia due to 21‐hydroxylase deficiency

objective Congenital adrenal hyperplasia (CAH) due to 21‐hydroxylase deficiency (21‐OHD) is characterized by high androgen levels, ambiguous genitalia or premature pubarche, increased height velocity and skeletal maturation. Considering the possibility of changes in the IGF system components depending on the state of clinical control, the objective of the present study was to analyse serum IGF‐I, IGF‐II and IGFBP levels in children with 21‐OHD under two states of clinical control.
ACE inhibitors and persistent left ventricular hypertrophy after renal transplantation: a randomized clinical trial.

BACKGROUND Interventional studies of left ventricular hypertrophy (LVH) in renal transplant recipients are scarce and to date evaluated only patients immediately after renal transplantation. STUDY DESIGN Randomized controlled trial that assessed the effectiveness of angiotensin-converting enzyme (ACE) inhibitors in regressing persistent LVH after successful transplantation. SETTING & PARTICIPANTS 70 renal transplant recipients (47 men; age, 30 to 68 years) without diabetes previously randomly assigned to either cyclosporine or tacrolimus therapy, with LVH persisting 3 to 6 months after transplantation. INTERVENTION Subjects were randomly assigned to either lisinopril (ACE-inhibitor group; 36 patients) or no therapy (control group; 34 subjects). OUTCOMES Main outcome was change in left ventricular mass index (LVMi) at month 18. RESULTS A consistent decrease in both systolic (SBP) and diastolic blood pressure (DBP) was observed in both groups (between-group differences, -1.7 +/- 3.3 mm Hg; 95% confidence interval [CI], -4.8 to 8.2; P = 0.6 for SBP; 0.3 +/- 2.2 mm Hg; 95% CI, -4.8 to 4.1; P = 0.9 for DBP), whereas LVMi regressed more in the ACE-inhibitor group (between-group difference, 10.1 +/- 16.3 g/m(2.7); 95% CI, 4.2 to 16.1; P < 0.01). A significant interaction of ACE inhibitors with cyclosporine in affecting LVMi change was shown by means of post hoc multiple regression analysis (P < 0.01; differences between cyclosporine and tacrolimus group, 13.3 +/- 3.9 g/m(2.7); 95% CI, 5.3 to 21.2; P < 0.01 in the ACE-inhibitor group; 3.7 +/- 4.2 g/m(2.7); 95% CI, -4.7 to 12.2; P = 0.4 in the control group). LIMITATIONS Single-center study with small sample size. Interaction of ACE inhibitors with cyclosporine treatment emerged from post hoc analysis. CONCLUSION A prolonged course of ACE-inhibitor therapy is effective in regressing the persistent LVH of renal transplant recipients by mechanisms independent of effects on BP. This regression seems to be at least in part the effect of an interaction between ACE inhibitors and cyclosporine.