Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of Liftover Tools for the Conversion of Genome Reference Consortium Human Build 37 to Build 38 Using ClinVar Variants

Although Genome Reference Consortium Human Build 38 (GRCh38) was released with improvement over GRCh37, it has not been widely adopted. Several liftover tools have been developed as a convenient approach for GRCh38 implementation. This study aimed to investigate the accuracy of liftover tools for genome conversion. Two Variant Call Format (VCF) files aligned to GRCh37 and GRCh38 were downloaded from ClinVar (clinvar_20221217.vcf.gz). Liftover tools such as CrossMap, NCBI Remap, and UCSC liftOver were used to convert genome coordinates from GRCh37 to GRCh38. The accuracy of CrossMap, NCBI Remap, and UCSC liftOver were 99.81% (1,567,838/1,570,748), 99.69% (1,565,953/1,570,748), and 99.99% (1,570,550/1,570,748), respectively. Variants that failed conversion via all three liftover tools were all indels/duplications: a pathogenic/likely pathogenic variant (n = 1) and benign/likely benign variants (n = 7). The eight variants that failed conversion were identified in the ALMS, TTN, CFTR, SLCO, LDLR, PCNT, MID1, and GRIA3 genes, and all the variants were not in the VCF files aligned to GRCh37. This study demonstrated that three liftover tools could successfully convert reference genomes from GRCh37 to GRCh38 in more than 99% of ClinVar variants. This study takes the first step to clinically implement GRCh38 using liftover tools. Further clinical studies are warranted to compare the performance of liftover tools and to validate re-alignment approaches in routine clinical settings.
Fire and forest history of central European low mountain forest sites based on soil charcoal analysis: The case of the eastern Harz

Long-term environmental changes in some areas of Central Europe are still poorly documented due to the lack of archives suitable for well-established paleoecological approaches. However, paleorecords of such areas would provide important insights into the Holocene vegetation history of Central Europe. To contribute to fill this gap, we conducted soil charcoal analyses to investigate fire and forest history for the eastern Harz Mountains (Germany). Soil from 15 sequences at three investigation sites was analyzed, and charcoal assemblages were extracted. The taxonomic analysis shows Holocene woodland composition changes, from post-glacial pioneer woodland, dominated by pine, to broad-leaf closed forests, dominated by oak, and succeeded by beech. The temporal distribution of accelerator mass spectrometry (AMS)-14C datings of single charcoal pieces indicates that fire events occurred regionally synchronous, mainly in the late-Pleistocene/early-Holocene and late-Holocene periods. The radiocarbon dating is supported by the description of the sampled soil sequences, which permits the identification of late-Pleistocene/early-Holocene in situ formed soil horizons, as well as evidences late-Holocene erosion-sedimentation processes. Climate seems to have triggered late-Pleistocene/early-Holocene fire events. In contrast, the increase of fires, at both local and regional scales, during the late Holocene in low flammable broad-leaf forests is interpreted as related to human activities. Finally, it is highlighted that the species spectrum of the extracted charcoal assemblages and the radiocarbon ages obtained fits regional and over-regional data, also concerning the soil charcoal concentrations that appear to be included in regional and global ranges of soil charcoal pools.
Numerical age control for the Miocene-Pliocene succession at Lothagam, a hominoid-bearing sequence in the northern Kenya Rift

Lothagam, located west of Lake Turkana in northern Kenya, is an uplifted fault block comprising a gently westward-dipping sequence of volcanic and sedimentary rocks. The lower part of the sequence, lavas and coarse volcaniclastic sediments of the Nabwal Arangan beds, was deposited mainly between 14 Ma and 12 Ma (Mid-Miocene), although the uppermost basalt has a K-Ar age of 9.1 Ma. The overlying fluvial sediments of the lower Nawata Formation have yielded ages on five tuffaceous horizons ranging from 7.4 ±0.1 to 6.5 ±0.1 Ma, Late Miocene. A tuffaceous horizon in the overlying Apak Member of the Nachukui Formation, yields an age of 4.22 ± 0.03 Ma; 40Ar-39Ar age spectra on the succeeding Lothagam Basalt indicate an age of 4.20 ± 0.03 Ma for its eruption. Much of the rich faunal assemblage from the Nawata Formation derives from the tightly dated lower intervals. Two hominoid teeth from higher in the formation can only be constrained to lie between 6.5 and 5 Ma old. The hominoid mandible, KNM-LT 329, from the lower Apak Member is older than 4.2 Ma and younger than 5.0 Ma.
Framing the present through the past: Ukrainian diaspora in France, Holodomor memory and the 2014 critical juncture

ABSTRACT This article focuses on a rarely addressed aspect of the link between diaspora and memory construction: the use of historical analogies, i.e. the way in which the memory of a past event (the 1933 famine in Ukraine, known as the Holodomor) is used by diasporic entrepreneurs to frame current violent events (the Russian–Ukrainian conflict). Based on fieldwork conducted among the Ukrainian diaspora in France, I show that the critical juncture of 2014 was a key moment in the reinterpretation of the present through the past (and vice versa), and identify three core-framing mechanisms that construct the historical analogy: parallelism, causality and implication. This framing activity contributed to the reconstruction of the imagined Ukrainian community and its radical separation from the Russian one. More generally, the article highlights the need to understand memory and nation-building as transnational processes that are not necessarily tied to the personal histories of diasporic entrepreneurs.
Decanoic Acid Rescues Differences in AMPA-Mediated Calcium Rises in Hippocampal CA1 Astrocytes and Neurons in the 5xFAD Mouse Model of Alzheimer’s Disease

Alzheimer’s disease (AD), a devastating neurodegenerative disease characterized by cognitive dysfunctions, is associated with high levels of amyloid beta 42 (Aβ42), which is believed to play a role in cellular damage and signaling changes in AD. Decanoic acid has been shown to be therapeutic in AD. Glutamatergic signaling within neurons and astrocytes of the CA1 region of the hippocampus is critical in cognitive processes, and previous work has indicated deficiencies in this signaling in a mouse model of AD. In this study, we investigated glutamate-mediated signaling by evaluating AMPA-mediated calcium rises in female and male CA1 neurons and astrocytes in a mouse model of AD and examined the potential of decanoic acid to normalize this signaling. In brain slices from 5xFAD mice in which there are five mutations leading to increasing levels of Aβ42, AMPA-mediated calcium transients in CA1 neurons and astrocytes were significantly lower than that seen in wildtype controls in both females and males. Interestingly, incubation of 5xFAD slices in decanoic acid restored AMPA-mediated calcium levels in neurons and astrocytes in both females and males to levels indistinguishable from those seen in wildtype, whereas similar exposure to decanoic acid did not result in changes in AMPA-mediated transients in neurons or astrocytes in either sex in the wildtype. Our data indicate that one mechanism by which decanoic acid could improve cognitive functioning is through normalizing AMPA-mediated signaling in CA1 hippocampal cells.
Role of halokinesis in controlling structural styles and sediment dispersal in the Santos Basin, offshore Brazil

Abstract Salt–sediment interplay in the Santos Basin is investigated integrating seismic interpretation, kinematic restoration and analogue modelling. Deformation within the post-salt sequence results from thin-skinned gravitational gliding and spreading, driven primarily by halokinesis, greatly affected by massive sediment inflows. The impressive landward-dipping listric Cabo Frio Fault controls the major depocentres updip, whereas salt-cored folds accommodate downdip shortening. Sediment supply from confluent directions creates a complex interference pattern of superposed folds with intervening polygonal minibasins. A new structure is identified (termed the ‘Ilha Grande Gravitational Cell’), a linked system of updip extension and downdip contraction detached on salt, comprising the Cabo Frio Fault and minibasins. It moves to the SE, with eastern and western borders suggesting lateral gradients of slippage. This thin-skinned feature results from the differential load imposed by a thick prograding wedge over the ductile salt and is independent of pre-salt structures. The post-salt sequence moves basinwards due to halokinesis, thereby changing position relative to the pre-salt sequence, which implies that any present-day correspondence between pre- and post-salt structures may not attest to linkage in the past. Application of kinematic restoration techniques allows the true position and geometry of the key elements through time, improving petroleum systems assessment.
The Economics of Climate Change: The Stern Review

There is now clear scientific evidence that emissions from economic activity, particularly the burning of fossil fuels for energy, are causing changes to the Earth´s climate. A sound understanding of the economics of climate change is needed in order to underpin an effective global response to this challenge. The Stern Review is an independent, rigourous and comprehensive analysis of the economic aspects of this crucial issue. It has been conducted by Sir Nicholas Stern, Head of the UK Government Economic Service, and a former Chief Economist of the World Bank. The Economics of Climate Change will be invaluable for all students of the economics and policy implications of climate change, and economists, scientists and policy makers involved in all aspects of climate change.
The Impact of Adding Chitosan Nanoparticles on Biofilm Formation, Cytotoxicity, and Certain Physical and Mechanical Aspects of Directly Printed Orthodontic Clear Aligners

Aligner treatment is associated with bacterial colonization, leading to enamel demineralization. Chitosan nanoparticles have been demonstrated to have antibacterial properties. This in vitro study aims to determine the effect of adding chitosan nanoparticles to directly 3D-printed clear aligner resin with regard to antibiofilm activity, cytotoxicity, degree of conversion, accuracy, deflection force, and tensile strength. Different concentrations (2%, 3%, and 5% w/w) of chitosan nanoparticles were mixed with the clear resin, and the samples were then 3D printed. Additionally, the thermoforming technique for aligner manufacturing was utilized. The obtained specimens were evaluated for antibiofilm activity against Streptococcus mutans bacteria and cytotoxicity against L929 and 3T3 cell lines. Additionally, Fourier transform infrared spectroscopy via attenuated total reflection analysis was used to assess the degree of conversion. Geomagic Control X software was utilized to analyze the accuracy. In addition, the deflection force and tensile strength were evaluated. The results indicated a notable reduction in bacterial colonies when the resin was incorporated with 3 and 5% chitosan nanoparticles. No significant changes in the cytotoxicity or accuracy were detected. In conclusion, integrating biocompatible chitosan nanoparticles into the resin can add an antibiofilm element to an aligner without compromising the material’s certain biological, mechanical, and physical qualities at specific concentrations.
Terrestrial Distribution of 14C in the Vicinity of Qinshan Nuclear Power Plant, China

We used accelerator mass spectrometry (AMS) to study radiocarbon-specific activity levels in agricultural and botanical samples (moss and pine needles) distributed within a 6.5-km radius of the Qinshan Nuclear Power Plant (NPP). The 14C-specific activity in moss samples (ranging from 265.6 to 223.0 Bq/kg C) decreased with increased distance from the stacks of Plant III (heavy water reactor) and reached the background level (223.8 Bq/kg C) at 6.5 km distance. Compared to the pine needles, the moss was a better indicator for investigating the 14C distribution near Qinshan NPP. The 14C-specific activity distribution in moss samples showed that the diffusion of 14C discharged from the Qinshan NPP was affected by both geographical and meteorological factors. Excess 14C-specific activity in the food samples ranged from 8.5 to 13.0 Bq/kg C (except for rice samples), resulting in a minimal radiation dose of 0.5 μSv per year to the public.
Investigations into soil nutrient and change in soil physical characteristics under complementary forage rotation in comparison to pasture systems for dairy cows

s and Papers presented at conferences and symposia B. Kabore, W.J. Fulkerson, SC. Garcia, P. Milham and R.W. Vervoot (2006). Investigation into soil nutrient balance and change in soil physical characteristics under an intensive complementary cropping rotation. Dairy Research Foundation Symposium, (Camden, NSW) Volume 11, 139-141. B. Kabore, W.J. Fulkerson, S.C. Garcia, P. Milham and R.W. Vervoot (2006). Investigation into soil nutrient balance and change in soil physical characteristics under an intensive complementary cropping rotation in comparison to pasture. Postgraduate Conference 2006, University of Sydney, Faculty of Veterinary Science, (Camden, NSW) pp 33. B. Kabore, W.J. Fulkerson, S.C. Garcia and P. Milham (2007). Complementary Forage Rotation as the alternative pasture production for dairy cows. Dairy Research Foundation Symposium, (Camden, NSW) Volume 12, 52-55. B. Kabore, W.J. Fulkerson, S.C. Garcia and P. Milham (2007). Sustainability of a Complementary Forage Rotation and Pasture. Postgraduate Conference 2007, University of Sydney, Faculty of Veterinary Science, (Camden, NSW) pp 31. B. Kabore, W.J. Fulkerson, SC. Garcia, P. Milham and R.W. Vervoot (2007). Nutrient Balance for Complementary Forage Rotation and Pasture Systems. Australian Society of Animal Production Conference, University of Brisbane. (Proceedings in progess).
Nature versus nurture: Functional assessment of restoration effects on wetland services using Nuclear Magnetic Resonance Spectroscopy

Land‐use change has altered the ability of wetlands to provide vital services such as nutrient retention. While compensatory practices attempt to restore degraded wetlands and their functions, it is difficult to evaluate the recovery of soil biogeochemical functions that are critical for restoration of ecosystem services. Using solution 31P Nuclear Magnetic Resonance Spectroscopy, we examined the chemical forms of phosphorus (P) in soils from wetlands located across a land‐use gradient. We report that soil P diversity, a functional attribute, was lowest in farmland, and greatest in native wetlands. Soil P diversity increased with age of restoration, indicating restoration of biogeochemical function. The trend in soil P diversity was similar to documented trends in soil bacterial taxonomic composition but opposite that of soil bacterial diversity at our study sites. These findings provide insights into links between ecosystem structure and function and provide a tool for evaluating the success of ecosystem restoration efforts.
Overcoming taxonomic challenges in DNA barcoding for improvement of identification and preservation of clariid catfish species

DNA barcoding without assessing reliability and validity causes taxonomic errors of species identification, which is responsible for disruptions of their conservation and aquaculture industry. Although DNA barcoding facilitates molecular identification and phylogenetic analysis of species, its availability in clariid catfish lineage remains uncertain. In this study, DNA barcoding was developed and validated for clariid catfish. 2,970 barcode sequences from mitochondrial cytochrome c oxidase I (COI) and cytochrome b (Cytb) genes and D-loop sequences were analyzed for 37 clariid catfish species. The highest intraspecific nearest neighbor distances were 85.47%, 98.03%, and 89.10% for COI, Cytb, and D-loop sequences, respectively. This suggests that the Cytb gene is the most appropriate for identifying clariid catfish and can serve as a standard region for DNA barcoding. A positive barcoding gap between interspecific and intraspecific sequence divergence was observed in the Cytb dataset but not in the COI and D-loop datasets. Intraspecific variation was typically less than 4.4%, whereas interspecific variation was generally more than 66.9%. However, a species complex was detected in walking catfish and significant intraspecific sequence divergence was observed in North African catfish. These findings suggest the need to focus on developing a DNA barcoding system for classifying clariid catfish properly and to validate its efficacy for a wider range of clariid catfish. With an enriched database of multiple sequences from a target species and its genus, species identification can be more accurate and biodiversity assessment of the species can be facilitated.
Determining the Relationship between Resistivity, Water and Hydrocarbon Saturation of Rock Formation Using Composite Well Logs

This paper focuses on comparing the percentages of water and hydrocarbon saturation to the resistivity of formation of reservoirs in an oil well by using composite logs. The composite logs were obtained from Nigeria National petroleum co-operation (NNPC) Etete Benin branch Edo state. Eight reservoirs were considered from a well in Ambura field in Delta state. When the logs were interpreted a composite table containing values of resistivity, percentages of water and hydrocarbon saturation was produced. From the values obtained it was found that resistivity increases with hydrocarbon saturation and decreases with water saturation in each reservoir. A graph of resistivity against hydrocarbon saturation and resistivity against water saturation was plotted. In conclusion, suggestions and recommendations were made to promote further research work on the project. DOI: 10.5901/ajis.2013. v2n13p119
External geophysics, climate and environment DORIS applications for solid earth and atmospheric sciences

AbstractDORISisaFrenchprecise orbitdetermination system.However,inthepastfouryears,throughthecreationoftheInternationalDORIS Service, a larger international cooperation was involved. Furthermore, the precision of its scientiﬁc applications (geodesy,geophysics) gradually improved and expanded to new ﬁelds (atmospheric sciences), leading, for example, to the publication of aspecial issue of the Journal of Geodesy. The goal of this manuscript is to present and explain these changes and to put them inperspectivewithcurrent results obtained withother spacegeodetic techniques, such asGPS or Satellite Laser Ranging. To cite thisarticle: P. Willis et al., C. R. Geoscience 339 (2007). # 2007 Academie des sciences. Published by Elsevier Masson SAS. All rights reserved.ResumeApplications DORIS aux sciences de la Terre solide et aux sciences de l’atmosphere. DORIS est un systeme francaisd’orbitographie precise. Toutefois, au cours des quatre dernieres annees, grâce a la creation de l’International DORIS Service, unecooperation internationale plus large a ete mise en place. De plus, la precision de ses applications scientiﬁques (geodesie,geophysique) s’est progressivement amelioree et etendue a de nouveaux champs d’applications dans le domaine des sciences del’atmosphere,conduisant,parexemple,alapublicationd’unnumerospecialDORISduJournal of Geodesy.Lebutdecetarticleestde presenter et d’expliquer ces evolutions et de les mettre en perspective avec les resultats obtenus par d’autres techniques degeodesie spatiale, telles que le GPS ou la technique Laser satellite. Pour citer cet article : P. Willis et al., C. R. Geoscience 339(2007). # 2007 Academie des sciences. Published by Elsevier Masson SAS. All rights reserved.
Evaluation of Role of Prognostic Factors on Hearing Outcome in Unilateral Idiopathic Sudden Onset Sensorineural Hearing Loss

Introduction: Owing to its uncertain and multiple possible etiologies, use of multiple empirical treatment regimens and possibility of spontaneous recovery, it becomes important to look for the possible prognostic factors affecting the outcome of sudden sensorineural hearing loss (SSNHL). Material and methods: This prospective observational study was conducted with the primary aim of analyzing the role of various possible prognostic factors on the outcome of idiopathic SSNHL including demographic (Age, gender), audio-vestibular (Pre-treatment hearing loss in the affected ear, hearing in the contralateral ear, time elapse between onset of hearing loss and start of treatment, type of hearing loss in term of frequencies affected), presence of tinnitus / vertigo and Comorbidities (Diabetes, Hypothyroidism & Deranged lipid profile/ dyslipidemia). Result: The absence of vertigo and tinnitus led to better hearing outcomes while raised HbA1c levels, deranged lipids and thyroid profiles adversely affected the outcome. Conclusion: Vertigo, tinnitus, raised HbA1c levels, deranged lipids and thyroid profiles are possible negative prognostic factors. Better pretreatment hearing levels in the affected and unaffected ears prompted improved recovery.
The Origin of the Double Maximum Pattern of Optic Axes in Quartzite Mylonite

The double maximum pattern of optic axes is found in quartzite mylonites that have undergone extensive plastic deformation and partial recrystallization as shown by highly elongate grains with small strain free grains along the grain boundaries. The optic axis pattern is characterized by two maxima of [0001] at 45° to the foliation and perpendicular to the lineation. The pattern has orthorhombic symmetry. However, X-ray analysis of a specimen from the Moine thrust zone in N.W. Scotland has revealed that the actual symmetry of the specimen is monoclinic and that {1011} is parallel to foliation and poles to {4041} are parallel to the direction of maximum elongation (= lineation). As both the texture and preferred orientation correspond to those observed by Tullis et al. (1973) in experimentally produced mylonites (although the symmetries are different), it is concluded that basal slip, prismatic slip, Dauphiné twinning, subsidiary syntectonic recrystallization and loss of strength due to water weakening observed in the laboratory also occurred in this naturally deformed mylonite. The orientation distribution function (ODF), used to specify the complete orientation of the grains, contains rods of high density corresponding to families of grain orientations. These rods are analogous to the high density rods found in the ODF's for cold rolled sheets of steel or copper. Monoclinic symmetry and 10:1:0.1 grain shapes are consistent with large heterogeneous simple shear as the mode of deformation, and the deduced displacement direction is consistent with underthrusting of the foreland to the ESE under the Moine nappe.