julilili42/papers huggingface dataset:
Insights into the African Humid Period from fossil stromatolites and Etheria elliptica shells from the Chew Bahir Basin, southern Ethiopia
2020-03-10

&amp;lt;p&amp;gt;In the context of human evolution and dispersal in Africa, it is important to understand past climate conditions and changes as possible drivers of these processes. One of the most recent climatic events was the end of the African Humid Period (AHP) at around 5 ka BP. This was marked by a decrease in precipitation following a long wet-phase in northern and eastern Africa, which caused many lakes to decrease in size or even desiccate. Although the termination of the AHP is well known, the timing and rate of the transition from wet to dry conditions is still heavily debated. To investigate the termination of the AHP at a high temporal resolution (subdecadal and subannual), fossil stromatolites and &amp;lt;em&amp;gt;Etheria elliptica&amp;lt;/em&amp;gt; shells from paleo-shorelines in the Chew Bahir Basin, southern Ethiopia, were collected. Today, Lake Chew Bahir is a deltaic swamp, however in past pluvials a large lake was present that likely overflowed and connected to other basins similar to other amplifier lakes in the East African Rift System. Radiocarbon dating, oxygen and carbon stable isotope analyses, trace element analyses and petrographic mapping of stromatolite laminae structure were conducted. A strong correlation between &amp;amp;#948;&amp;lt;sup&amp;gt;18&amp;lt;/sup&amp;gt;O and &amp;amp;#948;&amp;lt;sup&amp;gt;13&amp;lt;/sup&amp;gt;C shows that paleo-lake Chew Bahir likely experienced highly evaporative conditions and indicate an endorheic state of the basin in times of stromatolite growth at 7.1, 5.8, 4.7 and 4.6 ka BP. Furthermore, our findings suggest highly fluctuating environmental conditions during these times and demonstrate that the transition to drier conditions was not a strictly linear trend. In summary, the stromatolites and &amp;lt;em&amp;gt;Etheria elliptica&amp;lt;/em&amp;gt; shells are an excellent environmental archive due to their high temporal resolution, precise dating (&amp;amp;#177; 30 yrs) and an indication of the paleo-lake water depth. These types of records provide insights to past changes in freshwater availability, the variability of which would have had large consequences for humans living in the region.&amp;lt;/p&amp;gt;
Lake level changes and their paleo-climatic implications at the middle Pleistocene excavation of MAR-1, southern Greece
2020-03-10

&amp;lt;p&amp;gt;In the fossil-rich sediments of the Megalopolis Basin, southern Greece, the remains of an ancient paleo-lake alternate between detrital units and lignite seams deposited during the Middle Pleistocene. The detrital sediments of MAR-1 (480-420 kyr) between two lignite seams are where lithics and elephant bones with cut-marks have been systematically excavated indicating hominin activity along a paleo-shoreline circa 440 kyr. Based on current knowledge, lignite seams formed during interglacials, while the silty-clay-rich deposits in between were deposited under glacial conditions. However, the paleoenvironmental and paleoclimatic conditions on shorter times-scales, leading to the preservation of hominin activity in the area, remain largely unknown. In order to reconstruct the paleo-environment including paleo-lake levels and thus sedimentation patterns and their governing paleo-climatic factors, we analyzed a high resolution 5-meter long sediment sequence from the archaeological site MAR-1. For the reconstruction, a multiproxy approach was applied using microfossils, grain-size, and geochemical analysis such as total organic carbon, total inorganic carbon, X-ray diffraction, and conventional X-ray fluorescence. Diatoms were often too corroded to be of use, most likely due to a combination of alkaline water conditions and the influence of silicate sponges. The results of the analyses revealed that MAR-1, located between lignite unit II and III, experienced multiple lake level oscillations mostly following insolation changes suggesting that several short-term wet-dry-wet cycles occurred during the investigated period, which must have impacted flora and fauna, including hominins, in the area. This research was conducted under the auspices of the Ephoreia of Paleoanthropology and Speleology, Greek Ministry of Culture, and was supported by the European Research Council (PaGE, CROSSROADS).&amp;lt;/p&amp;gt;
Shaping of the Female Human Brain by Sex Hormones: A Review
2020-03-11

Traditionally sex hormones have been associated with reproductive and developmental processes only. Since the 1950s we know that hormones can have organizational effects on the developing brain and initiate hormonal transition periods such as puberty. However, recent evidence shows that sex hormones additionally structure the brain during important hormonal transition periods across a woman’s life including short-term fluctuations during the menstrual cycle. However, a comprehensive review focusing on structural changes during all hormonal transition phases of women is still missing. Therefore, in this review structural changes across hormonal transition periods (i.e., puberty, menstrual cycle, oral contraceptive intake, pregnancy and menopause) were investigated in a structured way and correlations with sex hormones evaluated. Results show an overall reduction in grey matter and region-specific decreases in prefrontal, parietal and middle temporal areas during puberty. Across the menstrual cycle grey matter plasticity in the hippocampus, the amygdala as well as temporal and parietal regions were most consistently reported. Studies reporting on pre- and post-pregnancy measurements revealed volume reductions in midline structures as well as prefrontal and temporal cortices. During perimenopause, the decline in sex hormones was paralleled with a reduction in hippocampal and parietal cortex volume. Brain volume changes were significantly correlated with estradiol, testosterone and progesterone levels in some studies, but directionality remains inconclusive between studies. These results indicate that sex hormones play an important role in shaping women’s brain structure during different transition periods and are not restricted to specific developmental periods.
Role of in Situ Natural Organic Matter in Mobilizing As during Microbial Reduction of FeIII-Mineral-Bearing Aquifer Sediments from Hanoi (Vietnam)
2020-03-11

Natural organic matter (NOM) can contribute to arsenic (As) mobilization as an electron donor for microbially-mediated reductive dissolution of As-bearing Fe(III) (oxyhydr)oxides. However, to investigate this process, instead of using NOM, most laboratory studies used simple fatty acids or sugars, often at relatively high concentrations. To investigate the role of relevant C sources, we therefore extracted in situ NOM from the upper aquitard (clayey silt) and lower sandy aquifer sediments in Van Phuc (Hanoi area, Vietnam), characterized its composition, and used 100-day microcosm experiments to determine the effect of in situ OM on Fe(III) mineral reduction, As mobilization, and microbial community composition. We found that OM extracted from the clayey silt (OMC) aquitard resembles young, not fully degraded plant-related material, while OM from the sandy sediments (OMS) is more bioavailable and related to microbial biomass. Although all microcosms were amended with the same amount of C (12 mg C/L), the extent of Fe(III) reduction after 100 days was the highest with acetate/lactate (43 ± 3.5% of total Fe present in the sediments) followed by OMS (28 ± 0.3%) and OMC (19 ± 0.8%). Initial Fe(III) reduction rates were also higher with acetate/lactate (0.53 mg Fe(II) in 6 days) than with OMS and OMC (0.18 and 0.08 mg Fe(II) in 6 days, respectively). Although initially more dissolved As was detected in the acetate/lactate setups, after 100 days, higher concentrations of As (8.3 ± 0.3 and 8.8 ± 0.8 μg As/L) were reached in OMC and OMS, respectively, compared to acetate/lactate-amended setups (6.3 ± 0.7 μg As/L). 16S rRNA amplicon sequence analyses revealed that acetate/lactate mainly enriched <i>Geobacter</i>, while in situ OM supported growth and activity of a more diverse microbial community. Our results suggest that although the in situ NOM is less efficient in stimulating microbial Fe(III) reduction than highly bioavailable acetate/lactate, it ultimately has the potential to mobilize the same amount or even more As.
Pathogenic variants in SQOR encoding sulfide:quinone oxidoreductase are a potentially treatable cause of Leigh disease
2020-03-11

Abstract Hydrogen sulfide, a signaling molecule formed mainly from cysteine, is catabolized by sulfide:quinone oxidoreductase (gene SQOR ). Toxic hydrogen sulfide exposure inhibits complex IV. We describe children of two families with pathogenic variants in SQOR . Exome sequencing identified variants; SQOR enzyme activity was measured spectrophotometrically, protein levels evaluated by western blotting, and mitochondrial function was assayed. In family A, following a brief illness, a 4‐year‐old girl presented comatose with lactic acidosis and multiorgan failure. After stabilization, she remained comatose, hypotonic, had neurostorming episodes, elevated lactate, and Leigh‐like lesions on brain imaging. She died shortly after. Her 8‐year‐old sister presented with a rapidly fatal episode of coma with lactic acidosis, and lesions in the basal ganglia and left cortex. Muscle and liver tissue had isolated decreased complex IV activity, but normal complex IV protein levels and complex formation. Both patients were homozygous for c.637G &gt; A, which we identified as a founder mutation in the Lehrerleut Hutterite with a carrier frequency of 1 in 13. The resulting p.Glu213Lys change disrupts hydrogen bonding with neighboring residues, resulting in severely reduced SQOR protein and enzyme activity, whereas sulfide generating enzyme levels were unchanged. In family B, a boy had episodes of encephalopathy and basal ganglia lesions. He was homozygous for c.446delT and had severely reduced fibroblast SQOR enzyme activity and protein levels. SQOR dysfunction can result in hydrogen sulfide accumulation, which, consistent with its known toxicity, inhibits complex IV resulting in energy failure. In conclusion, SQOR deficiency represents a new, potentially treatable, cause of Leigh disease.
Importance of radiative effects in gap opening by planets in protoplanetary disks
2020-03-11

Recent ALMA observations revealed concentric annular structures in several young class-II objects. In an attempt to produce the rings and gaps in some of these systems, they have been modeled numerically with a single embedded planet assuming a locally isothermal equation of state. This is often justified by observations targeting the irradiation-dominated outer regions of disks (approximately 100 au). We test this assumption by conducting hydrodynamics simulations of embedded planets in thin locally isothermal and radiative disks that mimic the systems HD 163296 and AS 209 in order to examine the effect of including the energy equation in a seemingly locally isothermal environment as far as planet–disk interaction is concerned. We find that modeling such disks with an ideal equation of state makes a difference in terms of the number of produced rings and the spiral arm contrast in the disk. Locally isothermal disks produce sharper annular or azimuthal features and overestimate a single planet’s gap-opening capabilities by producing multiple gaps. In contrast, planets in radiative disks carve a single gap for typical disk parameters. Consequently, for accurate modeling of planets with semimajor axes up to about 100 au, radiative effects should be taken into account even in seemingly locally isothermal disks. In addition, for the case of AS 209, we find that the primary gap is significantly different between locally isothermal and radiative models. Our results suggest that multiple planets are required to explain the ring-rich structures in such systems.
Reference curves for refraction in a German cohort of healthy children and adolescents
2020-03-11

Our analysis presents the first reference curve for refraction in central Europe. In comparison to data from China and Korea, there is only little difference at the age of 5 years in all centiles which then increases continuously. For all ethnicities, a trend towards myopia with increasing age could be observed, but myopia progression is much higher in China and Korea than in Germany. The most marked differences can be seen in the lower centiles. Further investigations should clarify whether commencement of preschool activities with prolonged near-work initiates the divergence in refractive development.
Targets of cGMP/cGKI in Cardiac Myocytes
2020-03-11

Abstract: The 3′,5′-cyclic guanosine monophosphate (cGMP)-dependent protein kinase type I (cGKI aka PKGI) is a major cardiac effector acting downstream of nitric oxide (NO)-sensitive soluble guanylyl cyclase and natriuretic peptides (NPs), which signal through transmembrane guanylyl cyclases. Consistent with the wide distribution of the cGMP-generating guanylyl cyclases, cGKI, which usually elicits its cellular effects by direct phosphorylation of its targets, is present in multiple cardiac cell types including cardiomyocytes (CMs). Although numerous targets of cGMP/cGKI in heart were identified in the past, neither their exact patho-/physiological functions nor cell-type specific roles are clear. Herein, we inform about the current knowledge on the signal transduction downstream of CM cGKI. We believe that better insights into the specific actions of cGMP and cGKI in these cells will help to guide future studies in the search for predictive biomarkers for the response to pharmacological cGMP pathway modulation. In addition, targets downstream of cGMP/cGKI may be exploited for refined and optimized diagnostic and therapeutic strategies in different types of heart disease and their causes. Importantly, key functions of these proteins and particularly sites of regulatory phosphorylation by cGKI should, at least in principle, remain intact, although upstream signaling through the second messenger cGMP is impaired or dysregulated in a stressed or diseased heart state.
Enhancement of the second harmonic signal of nonlinear crystals by self-assembled gold nanoparticles
2020-03-11

In second harmonic generation (SHG), the energy of two incoming photons, e.g., from a femtosecond laser, can be combined in one outgoing photon of twice the energy, e.g., by means of a nonlinear crystal. The SHG efficiency, however, is limited. In this work, the harvested signal is maximized by composing a hybrid system consisting of a nonlinear crystal with a dense coverage of plasmonic nanostructures separated by narrow gaps. The method of self-assembled diblock-copolymer-based micellar lithography with subsequent electroless deposition is employed to cover the whole surface of a lithium niobate (LiNbO3) crystal. The interaction of plasmonic nanostructures with light leads to a strong electric near-field in the adjacent crystal. This near-field is harnessed to enhance the near-surface SHG signal from the nonlinear crystal. At the plasmon resonance of the gold nanoparticles, a pronounced enhancement of about 60-fold SHG is observed compared to the bare crystal within the confocal volume of a laser spot.
Studying the Effect of Maternal Pregestational Diabetes on Fetal Neurodevelopment Using Magnetoencephalography
2020-03-11

Background. Developmental origin of health and disease states that an adverse intrauterine environment can lead to different diseases in later life. In this study, we aimed to explore the effect of maternal pregestational diabetes on the fetal brain activity using magnetoencephalography (MEG). Methods. Forty participants were included in an observational study with 9 type 1 and 19 type 2 diabetic pregnant women compared with data from 12 nondiabetic participants. Spontaneous fetal MEG signals were recorded and power spectral density was computed in 4 standard frequency bands. Group differences were investigated using analysis of covariance. Results. Our results showed that type 1 group was significantly different ( P &lt; .05) from the reference group for 3 of the 4 brain activity frequency bands, while in type 2 group, 2 bands exhibited this trend. When dichotomized based on the maternal glycemic control, significant differences in all bands were observed between the poor-control and reference groups. Conclusion. The fetal background brain activity parameters appear to be altered in diabetic pregnancy in comparison with the reference low-risk group. The study showed that maternal pregestational diabetes could potentially influence in utero neurodevelopment.
Two new species in a new genus and a critical revision of Brachybasidiaceae (Exobasidiales, Basidiomycota) in honor of Franz Oberwinkler
2020-03-11

Abstract The Brachybasidiaceae are a family of 22 known species of plant-parasitic microfungi belonging to Exobasidiales, Basidiomycota. Within this family, species of the largest genus Kordyana develop balls of basidia on top of stomatal openings. Basidial cells originate from fungal stroma filling substomatal chambers. Species of Kordyana typically infect species of Commelinaceae. During fieldwork in the neotropics, fungi morphologically similar to Kordyana spp. were found on Goeppertia spp. (syn. Calathea spp., Marantaceae), namely on G. panamensis in Panama and on G. propinqua in Bolivia. These specimens are proposed as representatives of a genus new to science, Marantokordyana , based on the distinct host family and molecular sequence data of ITS and LSU rDNA regions. The specimens on the two host species represent two species new to science, M. oberwinkleriana on G. panamensis and M. boliviana on G. propinqua . They differ by the size and shape of their basidia, molecular sequence data of ITS and LSU rDNA regions, and host plant species. In the past, the understanding of Brachybasidiaceae at order and family level was significantly improved by investigation realized by Franz Oberwinkler and his collaborators at the University of Tübingen, Germany. On species level, however, our knowledge is still very poor due to incomplete species descriptions of several existing names in literature, scarceness of specimens, as well as sequence data lacking for many taxa and for further barcode regions. Especially species of Kordyana and species of Dicellomyces are in need of revision.
Total Synthesis of the Natural Herbicide MBH‐001 and Analogues
2020-03-11

The first total synthesis of the natural herbicide MBH‐001 ( 1 ) is reported. Structurally it is a 2‐methyloxazol‐5(2 H )‐one with a (1‐hydroxyethyl) substituent at the 2‐position. By relying on cyclic nitrones, a flexible route to MBH‐001 and relevant analogues was developed. Key steps include the reaction of a 2‐hydroxyimino ester with an aldehyde to form a 5‐oxo‐2,5‐dihydrooxazole 3‐oxide. In an aldol‐type reaction, the anion of these cyclic nitrones reacted with an aldehyde at the 2‐position. A final reduction of the nitrone to the corresponding imine using zinc led to the target compounds. The cyclic nitrones are also accessible by reacting an α‐keto acid with an oxime. These two versatile synthetic routes enabled us to prepare the first MBH‐001 analogues for structure activity relationship analysis of the herbicidal efficacy. Thus, furthering our aim of developing new herbicides to tackle the ever‐growing problem of weed resistance.
LED Zappelin’: An open source LED controller for arbitrary spectrum visual stimulation and optogenetics during 2-photon imaging
2020-03-11

Abstract Two-photon (2P) microscopy is a cornerstone technique in neuroscience research. However, combining 2P imaging with spectrally arbitrary light stimulation can be challenging due to crosstalk between stimulation light and fluorescence detection. To overcome this limitation, we present a simple and low-cost electronic solution based on an ESP32 microcontroller and a TLC5947 LED driver to rapidly time-interleave stimulation and detection epochs during scans. Implemented for less than $100, our design can independently drive up to 24 arbitrary spectrum LEDs to meet user requirements. We demonstrate the utility of our stimulator for colour vision experiments on the in vivo tetrachromatic zebrafish retina and for optogenetic circuit mapping in Drosophila . https://github.com/BadenLab/LED-Zappelin
Loss of kidney function due to proteinuria, common problem with a rare cause: Answer
2020-03-11

Steroid-resistant nephrotic syndrome (SRNS) remains a challenge for paediatric nephrologists. SRNS is viewed as a heterogeneous disease entity including immune-based and monogenic aetiologies. Because SRNS is rare, treatment strategies are individualized and vary among centres of expertise. Calcineurin inhibitors (CNI) have been effectively used to induce remission in patients with immune-based SRNS; however, there is still no consensus on treating children who become either CNI-dependent or CNI-resistant. Rituximab is a steroid-sparing agent for patients with steroid-sensitive nephrotic syndrome, but its efficacy in SRNS is controversial. Recently, several novel monoclonal antibodies are emerging as treatment option, but their efficacy remains to be seen. Non-immune therapies, such as angiotensin-converting enzyme inhibitors or angiotensin II receptor blockers, have been proven efficacious in children with SRNS and are recommended as adjuvant agents. This review summarizes and discusses our current understandings in treating children with idiopathic SRNS.
Essence, modality, and intrinsicality
2020-03-12

Abstract Kit Fine (Philos Perspect 8:1–16, 1994) famously objected against the idea that essence can be successfully analyzed in terms of de re necessity. In response, I want to explore a novel, interesting, but controversial modal account of essence in terms of intrinsicality and grounding . In the first section, I will single out two theoretical requirements that any essentialist theory should meet—the essentialist desideratum and the essentialist challenge —in order to clarify Fine’s objections. In the second section, I will assess Denby’s improved modal account, which appeals to the notion of intrinsicality, and argue that it is untenable. In the third section, I will explain how, when combined with a modal-existential criterion, a hyperintensional account of intrinsicality—in the same vein as Bader (J Philos 110(10):525–563, 2013) and Rosen (in: Hale and Hoffman (eds) Modality: Metaphysics, logic, and epistemology, Oxford, OUP, 2010)—can help successfully address Fine’s counterexamples. In the fourth section, I will evaluate how this novel analysis of essence stands with respect to sortal, origin, and natural kinds essentialism and discuss potential objections and difficulties.
Mammuthus meridionalis (Nesti, 1825) from Apollonia-1 (Mygdonia Basin, Northern Greece) and its importance within the Early Pleistocene mammoth evolution in Europe
2020-03-12

Konidaris, George E., Kostopoulos, Dimitris S., Koufos, George D. (2020): Mammuthus meridionalis (Nesti, 1825) from Apollonia- 1 (Mygdonia Basin, Northern Greece) and its importance within the Early Pleistocene mammoth evolution in Europe. Geodiversitas 42 (6): 69-91, DOI: 10.5252/geodiversitas2020v42a6