Population dynamics and genetic changes of Picea abies in the South Carpathians revealed by pollen and ancient DNA analyses

Background: Studies on allele length polymorphism designate several glacial refugia for Norway spruce (Picea abies) in the South Carpathian Mountains, but infer only limited expansion from these refugia after the last glaciation. To better understand the genetic dynamics of a South Carpathian spruce lineage, we compared ancient DNA from 10,700 and 11,000-year-old spruce pollen and macrofossils retrieved from Holocene lake sediment in the Retezat Mountains with DNA extracted from extant material from the same site. We used eight primer pairs that amplified short and variable regions of the spruce cpDNA. In addition, from the same lake sediment we obtained a 15,000-years-long pollen accumulation rate (PAR) record for spruce that helped us to infer changes in population size at this site.Results: We obtained successful amplifications for Norway spruce from 17 out of 462 pollen grains tested, while the macrofossil material provided 22 DNA sequences. Two fossil sequences were found to be unique to the ancient material. Population genetic statistics showed higher genetic diversity in the ancient individuals compared to the extant ones. Similarly, statistically significant Ks and Kst values showed a considerable level of differentiation between extant and ancient populations at the same loci.Lateglacial and Holocene PAR values suggested that population size of the ancient population was small, in the range of 1/10 or 1/5 of the extant population. PAR analysis also detected two periods of rapid population growths (from ca. 11,100 and 3900 calibrated years before present (cal yr BP)) and three bottlenecks (around 9180, 7200 and 2200 cal yr BP), likely triggered by climatic change and human impact.Conclusion: Our results suggest that the paternal lineages observed today in the Retezat Mountains persisted at this site at least since the early Holocene. Combination of the results from the genetic and the PAR analyses furthermore suggests that the higher level of genetic variation found in the ancient populations and the loss of ancient allele types detected in the extant individuals were likely due to the repeated bottlenecks during the Holocene; however our limited sample size did not allow us to exclude sampling effect.This study demonstrates how past population size changes inferred from PAR records can be efficiently used in combination with ancient DNA studies. The joint application of palaeoecological and population genetics analyses proved to be a powerful tool to understand the influence of past population demographic changes on the haplotype diversity and genetic composition of forest tree species

Antiinflammatory Therapy with Canakinumab for Atherosclerotic Disease

Background: Experimental and clinical data suggest that reducing inflammation without affecting lipid levels may reduce the risk of cardiovascular disease. Yet, the inflammatory hypothesis of atherothrombosis has remained unproved. Methods: We conducted a randomized, double-blind trial of canakinumab, a therapeutic monoclonal antibody targeting interleukin-1β, involving 10,061 patients with previous myocardial infarction and a high-sensitivity C-reactive protein level of 2 mg or more per liter. The trial compared three doses of canakinumab (50 mg, 150 mg, and 300 mg, administered subcutaneously every 3 months) with placebo. The primary efficacy end point was nonfatal myocardial infarction, nonfatal stroke, or cardiovascular death. RESULTS: At 48 months, the median reduction from baseline in the high-sensitivity C-reactive protein level was 26 percentage points greater in the group that received the 50-mg dose of canakinumab, 37 percentage points greater in the 150-mg group, and 41 percentage points greater in the 300-mg group than in the placebo group. Canakinumab did not reduce lipid levels from baseline. At a median follow-up of 3.7 years, the incidence rate for the primary end point was 4.50 events per 100 person-years in the placebo group, 4.11 events per 100 person-years in the 50-mg group, 3.86 events per 100 person-years in the 150-mg group, and 3.90 events per 100 person-years in the 300-mg group. The hazard ratios as compared with placebo were as follows: in the 50-mg group, 0.93 (95% confidence interval [CI], 0.80 to 1.07; P = 0.30); in the 150-mg group, 0.85 (95% CI, 0.74 to 0.98; P = 0.021); and in the 300-mg group, 0.86 (95% CI, 0.75 to 0.99; P = 0.031). The 150-mg dose, but not the other doses, met the prespecified multiplicity-adjusted threshold for statistical significance for the primary end point and the secondary end point that additionally included hospitalization for unstable angina that led to urgent revascularization (hazard ratio vs. placebo, 0.83; 95% CI, 0.73 to 0.95; P = 0.005). Canakinumab was associated with a higher incidence of fatal infection than was placebo. There was no significant difference in all-cause mortality (hazard ratio for all canakinumab doses vs. placebo, 0.94; 95% CI, 0.83 to 1.06; P = 0.31). Conclusions: Antiinflammatory therapy targeting the interleukin-1β innate immunity pathway with canakinumab at a dose of 150 mg every 3 months led to a significantly lower rate of recurrent cardiovascular events than placebo, independent of lipid-level lowering. (Funded by Novartis; CANTOS ClinicalTrials.gov number, NCT01327846.

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016) : part two

Background The immunological escape of tumors represents one of the main ob- stacles to the treatment of malignancies. The blockade of PD-1 or CTLA-4 receptors represented a milestone in the history of immunotherapy. However, immune checkpoint inhibitors seem to be effective in specific cohorts of patients. It has been proposed that their efficacy relies on the presence of an immunological response. Thus, we hypothesized that disruption of the PD-L1/PD-1 axis would synergize with our oncolytic vaccine platform PeptiCRAd. Methods We used murine B16OVA in vivo tumor models and flow cytometry analysis to investigate the immunological background. Results First, we found that high-burden B16OVA tumors were refractory to combination immunotherapy. However, with a more aggressive schedule, tumors with a lower burden were more susceptible to the combination of PeptiCRAd and PD-L1 blockade. The therapy signifi- cantly increased the median survival of mice (Fig. 7). Interestingly, the reduced growth of contralaterally injected B16F10 cells sug- gested the presence of a long lasting immunological memory also against non-targeted antigens. Concerning the functional state of tumor infiltrating lymphocytes (TILs), we found that all the immune therapies would enhance the percentage of activated (PD-1pos TIM- 3neg) T lymphocytes and reduce the amount of exhausted (PD-1pos TIM-3pos) cells compared to placebo. As expected, we found that PeptiCRAd monotherapy could increase the number of antigen spe- cific CD8+ T cells compared to other treatments. However, only the combination with PD-L1 blockade could significantly increase the ra- tio between activated and exhausted pentamer positive cells (p= 0.0058), suggesting that by disrupting the PD-1/PD-L1 axis we could decrease the amount of dysfunctional antigen specific T cells. We ob- served that the anatomical location deeply influenced the state of CD4+ and CD8+ T lymphocytes. In fact, TIM-3 expression was in- creased by 2 fold on TILs compared to splenic and lymphoid T cells. In the CD8+ compartment, the expression of PD-1 on the surface seemed to be restricted to the tumor micro-environment, while CD4 + T cells had a high expression of PD-1 also in lymphoid organs. Interestingly, we found that the levels of PD-1 were significantly higher on CD8+ T cells than on CD4+ T cells into the tumor micro- environment (p < 0.0001). Conclusions In conclusion, we demonstrated that the efficacy of immune check- point inhibitors might be strongly enhanced by their combination with cancer vaccines. PeptiCRAd was able to increase the number of antigen-specific T cells and PD-L1 blockade prevented their exhaus- tion, resulting in long-lasting immunological memory and increased median survival

Small-scale moisture availability increase during the 8.2-ka climatic event inferred from biotic proxy records in the South Carpathians (SE Romania)

In this paper, we present high-resolution early Holocene pollen, plant macrofossil, charcoal, diatom, biogenic silica, and loss-on-ignition records from a mountain lake in the South Carpathians in order to reveal ecosystem response to the 8.2-ka climatic oscillation. We found significant changes both in terrestrial vegetation and lake diatom assemblages in the northern slope of the Retezat Mts between c. 8300 and 8000 cal. yr BP. Rapid changes in relative frequencies and pollen accumulation rates of the major deciduous pollen types associated with peaks in microcharcoal accumulation rates suggested that vegetation disturbance mainly took place in the mixed-deciduous forest zone, where woodland fires partially destroyed the populations of Fraxinus excelsior, Quercus, and Corylus avellana and facilitated the establishment of Carpinus betulus in the forest openings. The diatom record furthermore showed the spread of a planktonic diatom species, Aulacoseira valida, at 8150 cal. yr BP, coincidently with a short-lived expansion of C. betulus. Since diatom blooms mainly occur in spring in the Retezat Mts, increased spring water depth and increased water turbulence were inferred from these data. The expansion of C. betulus against F. excelsior and C. avellana at the same time suggested a modest increase in available moisture during the growing season. Taken together, these data imply that during the 8.2-ka event, winter and spring season available moisture increased, while summers were characterized by alternating moist/cool and dry/warm conditions

"Transport Me Away": Fostering Flow in Open Offices through Virtual Reality

Open offices are cost-effective and continue to be popular. However, research shows that these environments, brimming with distractions and sensory overload, frequently hamper productivity. Our research investigates the use of virtual reality (VR) to mitigate distractions in an open office setting and improve one’s ability to be in flow. In a lab study, 35 participants performed visual programming tasks in four combinations of physical (open or closed office) and virtual environments(beach or virtual office). While participants both preferred and were in flow more in a closed office without VR, in an open office, the VR environments outperformed the no VR condition in all measures of flow, performance, and preference. Especially considering the recent rapid advancements in VR, our findings illustrate the potential VR has to improve flow and satisfaction in open offices

A high-resolution Early Holocene-late MIS 3 environmental rock- and palaeomagnetic record from Lake Sf. Ana, Carpathian Mts, Romania

Lacustrine sediments are excellent sources of palaeoenvironmental and palaeoclimatic information because they usually provide continuous and high-resolution records. In centraleastern Europe however lacustrine records that extend beyond the Holocene are rather sparse.Palaeomagnetic records from this region are also insufficiently explored, and usually associated with terrestrial deposits such as loess. In this context, the lacustrine record of Lake Sf. Ana, a volcanic crater lake in the East Carpathians, Romania, provides an important archive for reconstructing past paleomagnetic secular variation in the region from early Holocene to late Marine Isotope Stage (MIS) 3.</p

How warm? How wet? Hydroclimate reconstruction of the past 7500 years in northern Carpathians, Romania

As natural and anthropogenic ecosystems are dependent on the local water availability, understanding past changes in hydroclimate represents a priority in research concerning past climate variability. Here, we used testate amoebae (TA) and chironomid analysis on a radiocarbon dated complex of small pond and peat bog sediment profiles from an ombrotrophic bog (Taut Muced, northern Carpathians, Romania) to quantitatively determine major hydrological changes and July air temperature over the last 7500 years.Wet mire surface conditions with a pH between 23 and 4.5 were inferred for the periods 4500-2700 and 1300400 cal yr BP by the occurrence of Archerella flavum, Amphitrema wrightianum and Hyalosphenia papilio. Dry phases in mire surface conditions and a pH between 2.5 and 5 were inferred for 7550-4500, 2750-1300 and 0 cal yr BP-present by the dominance of Nebela militaris, Difflugia pulex and Phryganella acropodia. The quantitative reconstruction of mean July temperature based on the chironomid communities suggests low summer temperatures for the periods 6550-5600, 4500-3150 and 1550-600 cal yr BP, while periods of slightly higher summer temperatures were observed for 5600-4500,3150-1550 and 100 cal yr BP-present. There is a generally good agreement between drier phases of the peat surface conditions with higher July temperature, suggesting that temperature may have been a controlling factor for water table fluctuation.Our quantitative reconstructions, among the first for central eastern Europe, show a relatively good agreement with other palaeohydrological studies from central eastern Europe, but contrast with others estimates from north-west Europe. Another important aspect of our study is that it provides valuable information on changes in local hydrology and the potential effect of the mean summer temperature over these changes. (C) 2017 Elsevier B.V. All rights reserved

Treeline and timberline dynamics on the northern and southern slopes of the Retezat Mountains (Romania) during the late glacial and the Holocene

© 2017 Elsevier Ltd and INQUA To investigate treeline and timberline dynamics in the Retezat Mountains (Romanian Carpathians), late glacial and Holocene sediment sequences from four lakes were studied. The south and north slopes of the mountain range were compared using two lakes from the north flank (Lake Brazi, 1740 m a.s.l. and Lake Gales, 1990 m a.s.l) and two from the south flank (Lake Lia, 1910 m a.s.l. and Lake Bucura, 2040 m a.s.l.). Macrofossil and stomata analyses were performed to assess changes in the local vegetation, supplemented by pollen, charcoal and loss-on-ignition analyses. Our results show that treeline reached Lake Brazi on the northern side during the late glacial (ca. 14,000 cal yr BP) and then Lake Gales between 11,000 and 10,800 cal yr BP. During the early Holocene the upper limit of closed forest, the timberline, reached and passed Lake Brazi and has stayed above it since, but it has never reached Lake Gales at 1990 m a.s.l. The expansion of Larix decidua in the late glacialand early Holocene around Lake Brazi is unique. Stomata and macrofossils of Abies alba are also more abundant in the northern records. On the southern flank, treeline reached Lake Lia at around 12,000 cal yr BP, and was either very close to or at the elevation of Lake Bucura between ca. 8600 and 3000 cal yr BP. Timberline reached Lake Lia at ca. 8000 cal yr BP, some 3000 years after Lake Brazi, only 170 m lower on the north slope. Local fire events delayed the advance of timberline around Lake Lia in the early Holocene in a dry continental climate. The surrounding forest was dominated by Picea abies with individuals of Pinus cembra and stands of P. mugo until about 3000 cal yr BP when timberline retreated below the lake. Maximum elevation of timberline was attained between ca. 8000 and 3000 cal yr BP, after which it descended in response to climate cooling. Regional climate change appears to be the main driver of treeline dynamics, but it was modified by local climatic differences due to slope aspect. The first signs of human disturbance appeared ca. 4200 cal yr BP, when naturally open areas were used as alpine pastures. Human impact in the treeline ecotone, mainly burning and grazing, was intensified after ca. 2600 cal yr BP, contributing to the widening of the ecotone and the lowering of the timberline.status: publishe

Toward Developing Techniques─Agnostic Machine Learning Classification Models for Forensically Relevant Glass Fragments

Glass fragments found in crime scenes may constitute important forensic evidence when properly analyzed, for example, to determine their origin. This analysis could be greatly helped by having a large and diverse database of glass fragments and by using it for constructing reliable machine learning (ML)-based glass classification models. Ideally, the samples that make up this database should be analyzed by a single accurate and standardized analytical technique. However, due to differences in equipment across laboratories, this is not feasible. With this in mind, in this work, we investigated if and how measurement performed at different laboratories on the same set of glass fragments could be combined in the context of ML. First, we demonstrated that elemental analysis methods such as particle-induced X-ray emission (PIXE), laser ablation induct i v e l y coupled plasma mass spectrometry (LA-ICP-MS), scanning electron microscopy with energy-dispersive X-ray spectrometry (SEM-EDS), particle-induced Gamma-ray emission (PIGE), instrumental neutron activation analysis (INAA), and prompt Gamma-ray neutron activation analysis (PGAA) could each produce lab-specific ML-based classification models. Next, we determined rules for the successf u l combinations of data from different laboratories and techniques and demonstrated that when followed, they give rise to improved models, and conversely, poor combinations wi l l lead to poor-performing models. Thus, the combination of PIXE and LA-ICP-MS improves the performances by similar to 10-15%, while combining PGAA with other techniques provides poorer performances in comparison with the lab-specific models. Finally, we demonstrated that the poor performances of the SEM-EDS technique, sti l l in use by law enforcement agencies, could be greatly improved by replacing SEM-EDS measurements for Fe and Ca by PIX E measurements for these elements. These findings suggest a process whereby forensic laboratories using different elemental analysis techniques could upload their data into a unified database and get reliable classification based on lab-agnostic models. This in tur n brings us closer to a more exhaustive extraction of information from glass fragment evidence and furthermore may form the basis for international-wide collaboration between law enforcement agencies.Peer reviewe