Miracle-dz/UniFAR-FTUs huggingface dataset:
Formation of recumbent folds during synorogenic crustal extension (Austroalpine nappes, Switzerland)

In sedimentary rocks of the Austroalpine nappes in eastern Switzerland, several generations of Alpine (Cretaceous-Tertiary) folds can be distinguished by overprinting relations. The second generation (D 2 ), probably Late Cretaceous in age, includes spectacular, kilometre-scale folds refolding the earlier formed nappe pile. D 2 folds are interpreted here as resulting from east-southeast-directed crustal extension rather than, as previously assumed, from north-south crustal shortening, for the following reasons: (1) D 2 folds are restricted to a predominantly ductile layer underlying the brittlely extended "orogenic lid," and (2) D 2 folds are associated with structures indicating extension in a direction parallel to the extension direction of the brittle layer. Before the east-southeast extension started, the layering of the rocks was already steeply inclined owing to earlier D 1 folding. The deformation producing the second-phase folds probably had a noncoaxial component with a top-to-the-east-southeast shear sense and a component of coaxial deformation leading to shortening in the vertical direction and stretching in an east-southeast, horizontal direction. The folds developed with axes oblique to parallel to the direction of bulk stretching. I suggest that folding of initially nonhorizontal layers by ductile crustal extension is an important deformation mechanism in the Austroalpine and possibly also in other parts of the Alps. Initially steep orientations of layers resulted from transpressive deformation in the obliquely convergent Alpine belt, and crustal extension parallel to the chain resulted from gravitational spreading. I propose that this process can lead to the often-encountered phenomenon of stretching parallel to the axes of folds.
Rapidly Characterizing the Fast Dynamics of RNA Genetic Circuitry with Cell-Free Transcription–Translation (TX-TL) Systems

RNA regulators are emerging as powerful tools to engineer synthetic genetic networks or rewire existing ones. A potential strength of RNA networks is that they may be able to propagate signals on timescales that are set by the fast degradation rates of RNAs. However, a current bottleneck to verifying this potential is the slow design-build-test cycle of evaluating these networks in vivo. Here we adapt an Escherichia coli-based cell-free transcription-translation (TX-TL) system for rapidly prototyping RNA networks. We used this system to measure the response time of an RNA transcription cascade to be approximately five minutes per step of the cascade. We also show that this response time can be adjusted with temperature and regulator threshold response tuning. Finally we use TX-TL to prototype a new RNA network, an RNA single input module, and show that this network temporally stages the expression of two genes in vivo.
First observations of the temporal/spatial variation of the sub‐auroral polarization stream from the SuperDARN Wallops HF radar

In this letter we present the first two‐dimensional observations of sub‐auroral ion drift (SAID) variability within the sub‐auroral polarization stream (SAPS) using a new mid‐latitude SuperDARN radar located at Wallops Island, VA. The radar data are complemented with observations from the DMSP F15, TIMED, and NOAA‐18 spacecraft to confirm that a backscatter feature observed at the equatorward edge of the auroral oval is a manifestation of SAPS/SAID. During a several hour long period on August 6, 2005, the velocity data indicate that significant changes in the SAPS flow occurred on time scales of a few minutes. The Wallops HF radar observations demonstrate that the SAPS phenomenon is a source of small‐scale irregularities extending over many hours of MLT and that the electric fields associated with SAID in particular are highly variable.
Strong Trends in the Skill of the ERA-40 and NCEP–NCAR Reanalyses in the High and Midlatitudes of the Southern Hemisphere, 1958–2001*

Abstract The European Centre for Medium-Range Weather Forecasts (ECMWF) Re-Analysis (ERA-40) and the National Centers for Environmental Prediction–National Center for Atmospheric Research (NCEP–NCAR) reanalysis (NCEP1) data are compared with Antarctic and other mid- to high-latitude station observations for the complete years of overlap, 1958–2001. Overall, it appears that ERA-40 more closely follows the observations; however, a more detailed look at the presatellite era reveals many shortcomings in ERA-40, particularly in the austral winter. By calculating statistics in 5-yr moving windows for June–July–August (JJA), it is shown that ERA-40 correlations with observed MSLP and surface (2 m) temperatures are low and even negative during the mid-1960s. A significant trend in skill in ERA-40 is observed in conjunction with the assimilation of satellite data during winter, eventually reaching a high level of skill after 1978 that is superior to NCEP1. NCEP1 shows consistency in its correlation with observatio.
Midsummer Low-Level Circulation and Precipitation in Subtropical South America and Related Sea Surface Temperature Anomalies in the South Atlantic

Abstract The midsummer interannual variability of the low-level tropospheric circulation and of the precipitation field in subtropical South America (SA) associated to the sea surface temperature (SST) anomalies in the western subtropical South Atlantic Ocean (WSSA) is investigated using reanalyses, regional precipitation datasets, and monthly SSTs. The region of the WSSA where SST has the strongest relation with precipitation in subtropical SA was identified using canonical correlation analysis. This region extends from 20° to 30°S and from 30° to 50°W. Composites corresponding to extreme SSTs in this area show two well-differentiated patterns in the low-level circulation and in the precipitation fields. In the composite, corresponding to the more positive SST anomalies in this area, the mainstream of the low-level flow and of the moisture transport from the continental low latitudes starts to follow a southeastward direction at 10°S, and converges with the west flow at 35°S over the Atlantic Ocean. On t.
Leucocyte profiles of Arctic marine birds: correlates of migration and breeding phenology

We examined white blood cell profiles of marine birds breeding in the Arctic, as an index of stress. Within species, birds that had to migrate farther had higher heterophil:lymphocyte ratios during incubation (i.e., residual stress) than those that migrated short distances. These reference values will be important as global warming and anthropogenic activities change the Arctic marine landscape.
Linking elements in compounds: Regional variation in speech production and perception

The plural suffix -en (noot+en, ‘nuts’) is pronounced differently by speakers from different regions of the Netherlands. In this study, we compared the pronunciation of the plural suffix -en in phrases (noot+en kraken, ‘to crack nuts’) with linking en in compounds (noot+en+kraker, ‘nutcracker’), because some claim that both are similar (Schreuder, Neijt, van der Weide, & Baayen, 1998), while others claim that they are not (Verkuyl, 2007). The pronunciations of 109 participants coming from five regions of the Netherlands were therefore compared in a picture naming task. A systematic relation between the pronunciations of plural -en and linking en was detected: Speakers from the Northern and Eastern regions produced [( ) ] most often for both the linking elements and plural endings, while speakers from the Middle and Western regions produced [ ] most often for both. For speakers from the Southern region, we found no preference to pronounce either [ ] or [ ] in compounds or phrases. It is concluded that Dutch speakers often do not distinguish plural en from linking en in their speech production. Possibly, speakers of Dutch consider linking en and plural -en as the same morpheme. LINKING ELEMENTS IN COMPOUNDS 28 2.
Evolution of the Continental Margin of Western India: New Evidence from Apatite Fission-Track Dating

Apatite fission-track dating in southwestern India yields Middle Triassic to Middle Jurassic ages that correlate with the breakup of eastern Gondwanaland and Africa. The later India-Madagascar split is not recorded in the apatite ages. The apatite ages are not a reflection of thermal events in the present location of this region but are associated with uplift and erosion in the Upper Paleozoic/Early Mesozoic eastern Gondwana-Africa separation. Track length measurements indicate that cooling through the 100°C isotherm began in the Upper Paleozoic. Time-temperature modeling suggests that a period of slow cooling during the Mesozoic was followed by relatively rapid cooling to the present.
Assessing Gender Inequality among Italian Regions: The Italian Gender Gap Index

This paper aims at exploring and evaluating the geographic distribution of gender inequality across Italian regions. The purpose of the analysis is twofold. First, we build a composite indicator of gender inequality at the regional level for Italy by applying the methodology developed by the World Economic Forum for the Global Gender Gap Index. Secondly, we compute the Italian Gender Gap Index for each region in order to measure the within-country heterogeneity that characterizes Italy. We complete the analysis by presenting the correlation between the Italian Gender Gap Index and relevant socioeconomic variables.
The role of non-canonical SNAREs in synaptic vesicle recycling

An increasing number of studies suggest that distinct pools of synaptic vesicles drive specific forms of neurotransmission. Interspersed with these functional studies are analyses of the synaptic vesicle proteome which have consistently detected the presence of so-called “non-canonical” SNAREs that typically function in fusion and trafficking of other subcellular structures within the neuron. The recent identification of certain non-canonical vesicular SNAREs driving spontaneous (e.g., VAMP7 and vti1a) or evoked asynchronous (e.g., VAMP4) release integrates and corroborates existing data from functional and proteomic studies and implies that at least some complement of non-canonical SNAREs resident on synaptic vesicles function in neurotransmission. Here, we discuss the specific roles in neurotransmission of proteins homologous to each member of the classical neuronal SNARE complex consisting of synaptobrevin2, syntaxin-1 and SNAP-25.
Homoeologous Chromosomes From Two Hordeum Species Can Recognize and Associate During Meiosis in Wheat in the Presence of the Ph1 Locus

Understanding the system of a basic eukaryotic cellular mechanism like meiosis is of fundamental importance in plant biology. Moreover, it is also of great strategic interest in plant breeding since unzipping the mechanism of chromosome specificity/pairing during meiosis will allow its manipulation to introduce genetic variability from related species into a crop. The success of meiosis in a polyploid like wheat strongly depends on regular pairing of homologous (identical) chromosomes and recombination, processes mainly controlled by the Ph1 locus. This means that pairing and recombination of related chromosomes rarely occur in the presence of this locus, making difficult wheat breeding trough the incorporation of genetic variability from related species. In this work, we show that wild and cultivated barley chromosomes associate in the wheat background even in the presence of the Ph1 locus. We have developed double monosomic wheat lines carrying two chromosomes from two barley species for the same and different homoeology chromosome group, respectively. Genetic in situ hybridization revealed that homoeologous Hordeum chromosomes recognize each other and pair during early meiosis in wheat. However, crossing over does not occur at any time and they remained always as univalents during meiosis metaphase I. Our results suggest that the Ph1 locus does not prevent chromosome recognition and pairing but crossing over between homoeologous. The role of subtelomeres in chromosome recognition is also discussed.
Seismic characterization of an Alpine site

Site amplification of earthquake ground motion can arise from local stratigraphic and morphological conditions. In this respect, a detailed geo-mechanical 2D model is needed, in particular for peculiar situations such as the ones in Alpine valleys. This paper reports a site characterization case history for seismic response analysis, where a combination of both body and surface wave seismic techniques has been used. In particular, it is shown that synergies and mutual cross-checking of information lead to a reliable 2D model for site amplification studies. The evaluation of the deep structure and the location of the seismic bedrock have been obtained through seismic reflection and combined active-passive surface wave analysis, while the shear-wave velocity profile of the sediments has been obtained by downhole measurements and surface wave tests. Furthermore, a detailed compressional wave velocity model has been retrieved by tomographic inversion of the first arrivals picked on seismic reflection records. This model is useful for geological interpretation as well as for quality control of the other methods. Surface wave analysis has also been performed on the ground roll of the seismic reflection records. The large amount of profile oriented data has made it possible to reconstruct lateral variations of the shear-wave velocity in the soil deposit. The final pseudo-2D shear-wave velocity model is the product of an innovative inversion approach, based on the integration of the Monte Carlo and laterally constrained least-squares techniques. In the laterally constrained inversion the shear-wave velocity profiles obtained from downhole tests and data from passive surface wave measurements have been used to constrain the inversion. This has greatly improved the final solution. This case history underlines the necessity of combining different seismic techniques to derive an accurate and reliable 2D model for site amplification studies. Through several different and independent analyses of the same seismic records, the cost effectiveness of the whole survey is optimized and a full exploitation of the information contained in the reflection seismic data set is achieved.
South Pole submillimeter sky opacity and correlations with radiosonde observations

Submillimeter wave-length observations of the South Pole wintertime atmospheric opacity were performed on a regular basis starting in the year 1992. The absorption spectrum of pressure broadened water vapor lines is known to dominate submillimeter atmospheric transparency, and changes in opacity should be correlated with changes in the precipitable water vapor column (PWV). Indications of PWV were derived from radiosonde observations and the expected correlation with opacity was observed. Thus submillimeter radiometry can be used to predict radiosonde derived PWV and vice versa. These comparisons can be used to help interpret radiosonde PWVs. For example, we show that the absolute calibration of one instrument type, the A.I.R. Model 5A, in use at the South Pole since February 22, 1997, is doubtful and indicates wintertime PWVs about a factor of 2 smaller than expected when compared to opacity and PWV relationships established previously. Comparisons were also made to PWVsat, the precipitable water vapor column derived by assuming saturation over ice. Radiosonde data going back to 1961 were available, and we examined long-term trends in the wintertime PWV and PWVsat. The primary emphasis here was to reveal the expected long-term site quality of the South Pole for performing ground based submillimeter astronomy. Thus we focused on wintertime conditions. Our comparisons of submillimeter opacity to PWV also provide robust determinations of the magnitude of dry air opacity, important for improving submillimeter radiative transfer models.
Detailed analysis of the isotopic composition of CO and characterization of the air masses arriving at Mount Sonnblick (Austrian Alps)

Air sampling for analysis of CO and its isotopic composition (13C, 18O, and 14C) has been performed at the alpine station Sonnblick (47°N, 13°E, 3106 m above sea level) since September 1996. A high degree of variability is observed, which is due to the wide variation in the origin of air masses sampled. On the basis of the CO and isotope results, a classification of the different samples is performed. Other data such as 7Be, O3, relative humidity, and back trajectories are used to give additional information about the air mass origin. Background values, representative of the NH midlatitudes free troposphere, are observed about 50% of the time and are used to define seasonal cycles. CO and its isotopes show a minimum in summer and a maximum in winter with extreme values of 90 and 160 ppb for CO, −30 and −25‰ for δ13C, 0 and 8‰ for δ18O, and 8 and 20 molecules cm−3 STP for 14CO. CO and stable isotope data are compared with results from a three-dimensional model (TM2). Generally good agreement supports the CO, δ13CO, and δC18O source/sink distributions inferred by the model. According to model calculations, fossil fuel combustion contributes 35% in summer and 50% in winter of total CO for such a midlatitude location. Other categories of sampled air are “subtropical,” “polluted,” and “stratospheric” and are observed 24%, 18%, and 4% of the time. Corresponding signatures of CO and its isotopic variations are presented, and some specific events are discussed.
Discovery of a small protein factor involved in the coordinated degradation of phycobilisomes in cyanobacteria

Significance During genome analysis, genes encoding small proteins are frequently neglected. Accordingly, small proteins have remained underinvestigated in all domains of life. Based on a previous systematic search for such genes, we present the functional analysis of the 66 amino acids protein NblD in a photosynthetic cyanobacterium. We show that NblD plays a crucial role during the coordinated dismantling of phycobilisome light-harvesting complexes. This disassembly is triggered when the cells become starved for nitrogen, a condition that frequently occurs in nature. Similar to NblA that tags phycobiliproteins for proteolysis, NblD binds to phycocyanin polypeptides but has a different function. The results show that, even in a well-investigated process, crucial new players can be discovered if small proteins are taken into consideration. Phycobilisomes are the major pigment–protein antenna complexes that perform photosynthetic light harvesting in cyanobacteria, rhodophyte, and glaucophyte algae. Up to 50% of the cellular nitrogen can be stored in their giant structures. Accordingly, upon nitrogen depletion, phycobilisomes are rapidly degraded following an intricate genetic program. Here, we describe the role of NblD, a cysteine-rich, small protein in this process in cyanobacteria. Deletion of the nblD gene in the cyanobacterium Synechocystis sp. PCC 6803 prevented the degradation of phycobilisomes, leading to a nonbleaching (nbl) phenotype, which could be complemented by a plasmid-localized gene copy. Competitive growth experiments between the ΔnblD and the wild-type strain provided direct evidence for the physiological importance of NblD under nitrogen-limited conditions. Ectopic expression of NblD under nitrogen-replete conditions showed no effect, in contrast to the unrelated proteolysis adaptors NblA1 and NblA2, which can trigger phycobilisome degradation. Transcriptome analysis indicated increased nblA1/2 transcript levels in the ΔnblD strain during nitrogen starvation, implying that NblD does not act as a transcriptional (co)regulator. However, immunoprecipitation and far-western experiments identified the chromophorylated (holo form) of the phycocyanin β-subunit (CpcB) as its target, while apo-CpcB was not bound. The addition of recombinant NblD to isolated phycobilisomes caused a reduction in phycocyanin absorbance and a broadening and shifting of the peak to lower wavelengths, indicating the occurrence of structural changes. These data demonstrate that NblD plays a crucial role in the coordinated dismantling of phycobilisomes and add it as a factor to the genetically programmed response to nitrogen starvation.
Student feedback about The Skeptic Doctor, a module on pharmaceutical promotion

Pharmaceutical promotion is an integral part of modern medical practice. Surveys show that medical students have a positive attitude towards promotion. Pharmaceutical promotion is not adequately taught in medical schools. A module based on the manual produced by Health Action International was conducted for second year medical students at KIST Medical College, Lalitpur, Nepal. Student feedback on various aspects of the module was obtained using a semi-structured questionnaire. Eighty-six of the 100 students (86%) provided feedback about the module. Forty-five (52.3%) were female and 39 (45.3%) were male. Participant feedback about the module was positive. Small group work and role plays were appreciated, and the ratings of the module and the manual were satisfactory. Respondents felt pharmaceutical promotion will play an important role in their future practice and that the module prepared them to respond appropriately to promotion and select and use medicines properly. The module further developed on issues covered during pharmacology practical and majority felt the module was of relevance to Nepal. Students appreciated the module though there were suggestions for improvement. The module should be considered during the years of clinical training (third and fourth years) and internship and in other medical schools.
Rosa26-GFP Direct Repeat (RaDR-GFP) Mice Reveal Tissue- and Age-Dependence of Homologous Recombination in Mammals In Vivo

Homologous recombination (HR) is critical for the repair of double strand breaks and broken replication forks. Although HR is mostly error free, inherent or environmental conditions that either suppress or induce HR cause genomic instability. Despite its importance in carcinogenesis, due to limitations in our ability to detect HR in vivo, little is known about HR in mammalian tissues. Here, we describe a mouse model in which a direct repeat HR substrate is targeted to the ubiquitously expressed Rosa26 locus. In the Rosa26 Direct Repeat-GFP (RaDR-GFP) mice, HR between two truncated EGFP expression cassettes can yield a fluorescent signal. In-house image analysis software provides a rapid method for quantifying recombination events within intact tissues, and the frequency of recombinant cells can be evaluated by flow cytometry. A comparison among 11 tissues shows that the frequency of recombinant cells varies by more than two orders of magnitude among tissues, wherein HR in the brain is the lowest. Additionally, de novo recombination events accumulate with age in the colon, showing that this mouse model can be used to study the impact of chronic exposures on genomic stability. Exposure to N-methyl-N-nitrosourea, an alkylating agent similar to the cancer chemotherapeutic temozolomide, shows that the colon, liver and pancreas are susceptible to DNA damage-induced HR. Finally, histological analysis of the underlying cell types reveals that pancreatic acinar cells and liver hepatocytes undergo HR and also that HR can be specifically detected in colonic somatic stem cells. Taken together, the RaDR-GFP mouse model provides new understanding of how tissue and age impact susceptibility to HR, and enables future studies of genetic, environmental and physiological factors that modulate HR in mammals.