Miracle-dz/UniFAR-FTUs huggingface dataset:
The oldest rocks of the Holy Cross Mountains, Poland - biostratigraphy of the Cambrian Czarna Shale Formation in the vicinity of Kotuszów

Three lower Cambrian acritarch assemblages recognized in four outcrops in the vicinity of Kotuszow in the southernmost part of the Palaeozoic inlier of the Holy Cross Mountains span a stratigraphic interval from the uppermost part of the Asteridium tornatum – Comasphaeridium velvetum Assemblage Zone to the Skiagia ornata – Fimbriaglomerella membranacea Assemblage Zone (most probably its lower part). According to current views (Moczydlowska and Yin 2012), this interval corresponds to the upper part of the Fortunian and to Stage 2 of the Terreneuvian Series. The strata yielding the oldest assemblage are thus the oldest precisely documented rocks in the Palaeozoic succession of the Holy Cross Mountains, and the oldest Cambrian rocks exposed on the surface in Poland. The current biostratigraphic scheme for the pre-trilobitic part of the Cambrian System in the Holy Cross Mountains should be modified so that it is based on local acritarch interval subzones
Derivative Computation using an Adjoint-Based Goal-Oriented Iterative Multiscale Lagrangian Framework: Application to Reservoir Simulation

Even though negative effects on the use of crude oil have surfaced over the past years, our energy matrix still largely relies on this energy source. The production of oil, therefore, plays an important role in our society. Unfortunately, the process of oil production is highly uncertain. There are uncertainties associated on the production strategy, e.g. where and how many wells should be drilled and how these wells should operate because of the uncertainties associated with the limited knowledge about the subsurface. In this thesis we are dealing with the uncertainty of the rock permeability distribution. Typically, rock permeabilities in the rock vary, but from the outside this can’t be perceived. If these rock permeabilities are estimated inaccurately, they will result in inaccurate pressure solutions. Then, this can lead to faulty decisions regarding the oil exploitation. To resolve this issue, a data assimilation technique may be applied to correct these model parameters based on mismatch of simulated data and observations. For this optimization technique, often gradient information is required. Since in reservoir simulation the number of parameters generally is extremely high, computation of this information is computationally expensive. Therefore, a multiscale framework is employed to improve the computational efficiency of the forward simulation. Multiscale methods are able to solve the model equations at a computationally efficient coarse scale and can easily interpolate this solution to the fine scale resolution. Next, we use a Lagrangian set-up together with a multiscale framework to re-derive an efficient formulation for the derivative computation. However, as the multiscale method is prone to errors, this derivative computation formulation is recast in an iterative fashion, using a residual based iterative multiscale method to provide control of these errors. In this thesis we show that this method generates accurate gradients. In contract to the high accuracy of the method, this method comprises a computationally heavy smoothing step. This issue can be resolved by making smart use of the Lagrange multipliers, to re-derive an efficient iterative multiscale solution strategy. The multipliers are used to identify important domains of the region for which smoothing is required and for which regions we may neglect the smoothing. We show that the newly proposed iterative multiscale goal oriented method is computationally more efficient and we show that method is promising for efficient derivative computation, but that more work is required to fully demonstrate the benefit of this method.
Fight Ill-Posedness with Ill-Posedness: Single-shot Variational Depth Super-Resolution from Shading

We put forward a principled variational approach for up-sampling a single depth map to the resolution of the companion color image provided by an RGB-D sensor. We combine heterogeneous depth and color data in order to jointly solve the ill-posed depth super-resolution and shape-from-shading problems. The low-frequency geometric information necessary to disambiguate shape-from-shading is extracted from the low-resolution depth measurements and, symmetrically, the high-resolution photometric clues in the RGB image provide the high-frequency information required to disambiguate depth super-resolution.
The B Fields in OB Stars (BOB) Survey

Abstract The B fields in OB stars (BOB) survey is an ESO large programme collecting spectropolarimetric observations for a large number of early-type stars in order to study the occurrence rate, properties, and ultimately the origin of magnetic fields in massive stars. As of July 2014, a total of 98 objects were observed over 20 nights with FORS2 and HARPSpol. Our preliminary results indicate that the fraction of magnetic OB stars with an organised, detectable field is low. This conclusion, now independently reached by two different surveys, has profound implications for any theoretical model attempting to explain the field formation in these objects. We discuss in this contribution some important issues addressed by our observations (e.g., the lower bound of the field strength) and the discovery of some remarkable objects.
Brucellar Epididymo-Orchitis: A Retrospective Study

Objectives: Epididymo-orchitis is a focal form of human brucellosis described in 2-20% of patients with brucellosis. Patients and Methods: In this retrospective study, the records of 190 adult male patients (mean age 27.5 years; range 17 to 71 years) with brucellosis were evaluated. Ten of these cases presented with epididymo-orchitis. Among these cases, epididymitis or epididymo-orchitis were diagnosed on the basis of a typical history of gradual onset of scrotal pain and findings of enlarged tender testes and/or epididymis. Results: The most common symptoms were fever, scrotal pain, and swelling (100%). There were different focal Brucellar involvements other than the epididymoorchitis in eight patients (80%). All of the patients had unilateral epididymo-orchitis. A testicular abscess was detected in one patient. Combined antibiotic therapy was started and continued for 6-8 weeks. Orchiectomy was required for one patient (10%) and granulomatous orchitis was detected in the resected specimens. Relapse was not observed in any patient. Conclusion: Brucellosis should be considered in the diagnosis of scrotal diseases in endemic areas. Clinical and serological data are sufficient for the diagnosis. Conservative management combined with antibiotic therapy is adequate for managing brucellar epididymo-orchitis.
Hybrid Laminate for Haptic Input Device with Integrated Signal Processing

Achieving lightweight construction through only material substitution does not realize the full potential of producing a lightweight material, hence, it is no longer sufficient. Weight-saving goals are best achieved through additional function integration. In order to implement this premise for mass production, a manufacturing process for joining and forming hybrid laminates using a new tool concept is presented. All materials used are widely producible and processable. The manufactured cover of an automotive center console serves to demonstrate a human interface device with impact detection and action execution. This is only possible through a machine learning system, which is implemented on a small—and thus space- and energy-saving—embedded system. The measurement results confirm the objective and show that localization was sufficiently accurate.
The broad-band properties of the intermediate synchrotron peaked BL Lac S2 0109+22 from radio to VHE gamma-rays

The Major Atmospheric Gamma-ray Imaging Cherenkov (MAGIC) telescopes observed S2 0109+22 in 2015 July during its flaring activity in high-energy gamma-rays observed by Fermi-Large Area Telescope. We analyse the MAGIC data to characterize the very high energy (VHE) gamma-ray emission of S2 0109+22, which belongs to the subclass of intermediate synchrotron peak (ISP) BL Lacertae (BL Lac) objects. We study the multifrequency emission in order to investigate the source classification. Finally, we compare the source long-term behaviour to other VHE gamma-ray emitting (TeV) blazars. We performed a temporal and spectral analysis of the data centred around the MAGIC interval of observation (MJD 57225-57231). Long-term radio and optical data have also been investigated using the discrete correlation function. The redshift of the source is estimated through optical host-galaxy imaging and also using the amount of VHE gamma-ray absorption. The quasi-simultaneous multifrequency spectral energy distribution (SED) is modelled with the conventional one-zone synchrotron self-Compton (SSC) model. MAGIC observations resulted in the detection of the source at a significance level of 5.3 sigma. The VHE gamma-ray emission of S2 0109+22 is variable on a daily time scale. VHE gamma-ray luminosity of the source is lower than the average of TeV BL Lacs. The optical polarization and long-term optical/radio behaviour of the source are different from the general population of TeV blazars. All these findings agree with the classification of the source as an ISP BL Lac object. We estimate the source redshift as z = 0.36 +/- 0.07. The SSC parameters describing the SED are rather typical for blazars.
Item-specific delay activity demonstrates concurrent storage of multiple items in working memory

Abstract A longstanding view holds that information is maintained in working memory (WM) via persistent neural activity that encodes the content of WM. Recent work, however, has challenged the view that all items stored in WM are actively maintained. Instead, “activity-silent” models propose that items can be maintained in WM without the need for persistent neural activity, raising the possibility that only a subset of items – perhaps just a single item – may be actively represented at a given time. While past studies have successfully decoded multiple items stored in WM, these studies cannot rule out an active switching account in which only a single item is actively represented at a time. Here, we directly tested whether multiple representations can be held concurrently in an active state. We tracked spatial representations in WM using alpha-band (8–12 Hz) activity, which encodes spatial positions held in WM. Human observers (male and female) remembered one or two positions over a short delay while we recorded EEG. Using a spatial encoding model, we reconstructed stimulus-specific working memory representations (channel tuning functions, CTFs) from the scalp distribution of alphaband power. Consistent with past work, we found the selectivity of spatial CTFs was lower when two items were stored than when one item was stored. Critically, data-driven simulations revealed that the selectivity of spatial representations in the two-item condition could not be explained by models restricting storage to a single item at a time. Thus, our findings provide robust evidence for the concurrent storage of multiple items in visual working memory. Author Summary Working memory (WM) is a mental workspace where we temporarily hold information “online” in pursuit of our current goals. However, recent activity-silent models of WM have challenged the view that all items are held in an “online” state, instead proposing that only a subset of representations in WM – perhaps just one item – are represented by persistent activity at a time. To directly test a single-item model of persistent activity, we used a spatial encoding model to read out the strength of two representations from alpha-band (8–12 Hz) power in the human EEG signal. We provide direct evidence that both locations were maintained concurrently, ruling out the possibility that declines in stimulus-specific activity are due to storing one of two items in an activity-silent state.
Effects of Silvopasture Establishment on Aqueous and Gaseous Soil N Losses at the University of New Hampshire Organic Dairy Research Farm

The expansion of local agriculture in the New England region is putting increased pressure on farmers to expand their arable land base. While clear-cutting is a traditional method of converting forested land to agriculture, it is known for having adverse ecological impacts. To minimize these impacts, farmers can create a silvopasture which incorporates a portion of the original forest canopy into pastures or crop fields. This study evaluates the impact of land-use changes for agriculture on soil nitrogen (N) retention. In particular, this study investigates the differences in soil N turnover, gaseous loss, and aqueous loss among an established forest, established pasture, clear-cut converted pasture, and converted silvopasture systems over a 30day incubation period. We found significant differences in N mineralization, immobilization, and denitrification among treatments, with evidence that a forest-to-silvopasture conversion can successfully support soil N retention within the first two years of implementation. This may have been due to the presence of coarse woody debris inputs from forest cutting and its effect on the soil carbon (C) to N ratio. Nitrogen retention in silvopastures may also result from partial preservation of the forest canopy. Our results suggest that farmers looking to expand their agricultural land base through forest clearing may be able to use silvopastures for as a way of retaining soil nutrients while at the same time putting land into production.
GraphBit: Bitwise Interaction Mining via Deep Reinforcement Learning

In this paper, we propose a GraphBit method to learn deep binary descriptors in a directed acyclic graph unsupervisedly, representing bitwise interactions as edges between the nodes of bits. Conventional binary representation learning methods enforce each element to be binarized into zero or one. However, there are elements lying in the boundary which suffer from doubtful binarization as "ambiguous bits". Ambiguous bits fail to collect effective information for confident binarization, which are unreliable and sensitive to noise. We argue that there are implicit inner relationships between bits in binary descriptors, where the related bits can provide extra instruction as prior knowledge for ambiguity elimination. Specifically, we design a deep reinforcement learning model to learn the structure of the graph for bitwise interaction mining, reducing the uncertainty of binary codes by maximizing the mutual information with inputs and related bits, so that the ambiguous bits receive additional instruction from the graph for confident binarization. Due to the reliability of the proposed binary codes with bitwise interaction, we obtain an average improvement of 9.64%, 8.84% and 3.22% on the CIFAR-10, Brown and HPatches datasets respectively compared with the state-of-the-art unsupervised binary descriptors.
Cancer ‐ associated fibroblasts regulate the biological behavior of cancer cells and stroma in gastric cancer ( Review )

Gastric cancer (GC) is a frequently diagnosed type of cancer in China, and is associated with a high mortality rate. The biological behavior of GC requires investigation in order to provide an evidence base for the development of strategies to prevent and treat GC. For this purpose, the present review outlines the process of tumor microenvironment (TME) evolution, including the dynamic biological behavior of different types of cancer cell and stroma. Cancer‐associated fibroblasts (CAFs) serve as prominent stromal cellular components in the GC TME, and exhibit an essential function in GC progression. In the present study, the function of CAFs in cancer cell proliferation, cell migration, invasion, extracellular matrix remodeling, pathological angiogenesis and immune cell infiltration were investigated. The studies discussed in the present review demonstrate that the cross-talk between CAF, cancer cells and tumor stroma promotes GC progression.
Recent studies on the Silurian of the western part of Ukraine

The paper summarises the effects of recent studies carried out by a team from the Department of Historical and Regional Geology of the Faculty of Geology, University of Warsaw on the upper Silurian of Podolia (western part of Ukraine). The sedimentary history of the Silurian succession of Podolia is characterised by its cyclic pattern, with shallowing-upward cyclothems. In the traditional interpretation, the occurrence of stromatoporoid beds within each cyclothem marks the deepest (or most open-marine) sedimentary environment within the cycle. According to the results of recent studies, their occurrence is connected rather with a relatively shallow-water environment and with high energy phenomena. A substantial reinterpretation of the main sedimentary processes governing the deposition and facies distribution on the shelf is presented. Particularly, there are recognised and described high-energy sedimentary events repeatedly punctuating the generally calm sedimentation that prevailed in the lagoonal settings, some of which are interpreted as tsunami induced. Further perspectives for studies on the Silurian successions of Podolia are also discussed. The main problem is the precise correlation of particular sections that are scattered over vast distances and developed in similar facies associations.
Recent Advances on Detection and Characterization of Fruit Tree Viruses Using High-Throughput Sequencing Technologies

Perennial crops, such as fruit trees, are infected by many viruses, which are transmitted through vegetative propagation and grafting of infected plant material. Some of these pathogens cause severe crop losses and often reduce the productive life of the orchards. Detection and characterization of these agents in fruit trees is challenging, however, during the last years, the wide application of high-throughput sequencing (HTS) technologies has significantly facilitated this task. In this review, we present recent advances in the discovery, detection, and characterization of fruit tree viruses and virus-like agents accomplished by HTS approaches. A high number of new viruses have been described in the last 5 years, some of them exhibiting novel genomic features that have led to the proposal of the creation of new genera, and the revision of the current virus taxonomy status. Interestingly, several of the newly identified viruses belong to virus genera previously unknown to infect fruit tree species (e.g., Fabavirus, Luteovirus) a fact that challenges our perspective of plant viruses in general. Finally, applied methodologies, including the use of different molecules as templates, as well as advantages and disadvantages and future directions of HTS in fruit tree virology are discussed.
Protective Effects of Ibuprofen and L-Carnitine Against Whole Body Gamma Irradiation-Induced Duodenal Mucosal Injury

Objective: Ibuprofen and L-carnitine have been demonstrated to provide radioprotective activity to the hamster against whole body sublethal irradiation. The purpose of this study is to test those antioxidant drugs, each of which has the capacity of inhibiting mucosal injury, as topical radioprotectants for the intestine. Material and Methods: The male hamsters were divided into the following four groups (n=6): group 1: control group, received saline, 1 ml/100 g by gavage, as placebo. Group 2: irradiated-control group, received whole body irradiation of 8 Gy as a single dose plus physiological saline. The animals in groups 3 and 4 were given a daily dose of 10 mg/kg of ibuprofen and 50 mg/kg of L-carnitine for 15 days respectively, before irradiation with a single dose of 8 Gy. Twenty-four hours after radiation exposure, the hamsters were sacrificed and samples were taken from the duodenum, and the histopatological determinations were carried out. Results: Morphologically, examination of the gamma irradiated duodenum revealed the presence of shortening and thickening of villi and flattening of enterocytes, massive subepithelial lifting. Pretreatment of ibuprofen and L-carnitine with irradiation reduced these histopathological changes. Conclusion: Ibuprofen and L-carnitine administrated by the oral route may be a good radioprotector against small intestinal damage in patients undergoing radiotherapy
S 1 Text : Details on the stochastic model for the Pom cluster dynamics 1

Due to the similarities between the Pom system and Par systems for plasmid and chromosome segregation, we thought about whether an existing model for positioning by the Par system might also explain the observed Pom cluster dynamics. However, there is no experimental evidence that PomZ forms filaments [1] and therefore we did not consider filament-based models. Also, several experimental observations in M. xanthus cells [2] speak against a diffusion-ratchet mechanism [3–5]: (i) time-lapse experiments show that the Pom cluster is more mobile if PomZ is present than without PomZ, (ii) FRAP experiments indicate that the PomZ dynamics is fast (in the cytosol and on the nucleoid) compared to the cluster dynamics, and (iii) no clear depletion zone in PomZ in the wake of the cluster is visible. The fast PomZ dynamics on the nucleoid is also in contrast to the DNA-relay model [6, 7], where nucleoid-bound ParA dimers are spatially restricted in their movement, similar to a Brownian particle in a trap. In the directed motion model, suggested by Ietswaart et al. [8], ParA dimers can polymerize along the long cell axis and thereby form structures that bias the movement of the plasmids towards equally-spaced positions on the nucleoid. This assumption is in contrast to the Pom system, where no evidence for filament formation is found. The Pom system also differs from several Par systems by an accumulation of PomZ at the cluster consisting of PomX and PomY proteins and the large cluster size. These experimental observations need to be accounted for in a model for the Pom cluster dynamics. Overall, this necessitates a new model to describe the Pom cluster dynamics.