julilili42/papers huggingface dataset:
The correction of linear fracture density and error analysis using underground well-logging data
2022-08-15

Fractures are favorable fluid channels and provide storage space in reservoirs, which are of great significance to the exploration and development of groundwater, petroleum, etc. Quantitative analysis of fracture density controlled by mechanical stratigraphy is of great importance to determine or predict fracture properties and statistics in a reservoir. The measurement of subsurface fracture parameters is usually limited to observations from drill cores. The semi-one dimensional drill core data require corrections, in particular the Terzaghi correction for orientation bias. The Terzaghi correction performs poorly when the angle between drill core and fractures is small. To correct this, we suggest extending Terzaghi's correction to include the diameter of the drill core. The new correction method reduces the correction error. It is particularly useful when bedding thickness is small, and fracture density is large. This study thus proposed an extension to Terzaghi's method to correct orientation bias in the quantification of linear fracture density, especially applicable to thin layers or large fracture densities. Note: This paper was accepted into the Technical Program but was not presented at IMAGE 2022 in Houston, Texas.
Let’s Take a Look at the Very Best of EAU22: Great Topics, Great Research, and Great Teamwork
2022-08-15

The European Association of Urology (EAU) delved into the very latest in urological science at the 37th Annual Congress, EAU22, on 1st–4th July in Amsterdam, the Netherlands. The four days were filled to the brim with 2,580 presentations by more than 900 speakers, and 56 courses organised by the European School of Urology (ESU). This included six Game Changing sessions, a day of live surgery, eight plenary sessions, Section meetings, Urology Beyond Europe, poster presentations, prestigious awards, patient days, and industry sessions. EAU Nurses (EAUN) also held EAUN22 during this time. The congress attracted over 8,200 participants from 124 countries, with some also opting to participate via the virtual option. The opening night not only honoured pioneering and promising urologists, it also commemorated the beginning of the 50th celebratory year of the EAU. Secretary General Frans Debruyne was awarded a bronze bust to mark his extraordinary contributions to the EAU during its 50-year existence.
Curcumin-Based Nanoformulations: A Promising Adjuvant towards Cancer Treatment
2022-08-16

Throughout the United States, cancer remains the second leading cause of death. Traditional treatments induce significant medical toxic effects and unpleasant adverse reactions, making them inappropriate for long-term use. Consequently, anticancer-drug resistance and relapse are frequent in certain situations. Thus, there is an urgent necessity to find effective antitumor medications that are specific and have few adverse consequences. Curcumin is a polyphenol derivative found in the turmeric plant (Curcuma longa L.), and provides chemopreventive, antitumor, chemo-, and radio-sensitizing properties. In this paper, we summarize the new nano-based formulations of polyphenolic curcumin because of the growing interest in its application against cancers and tumors. According to recent studies, the use of nanoparticles can overcome the hydrophobic nature of curcumin, as well as improving its stability and cellular bioavailability in vitro and in vivo. Several strategies for nanocurcumin production have been developed, each with its own set of advantages and unique features. Because the majority of the curcumin-based nanoformulation evidence is still in the conceptual stage, there are still numerous issues impeding the provision of nanocurcumin as a possible therapeutic option. To support the science, further work is necessary to develop curcumin as a viable anti-cancer adjuvant. In this review, we cover the various curcumin nanoformulations and nanocurcumin implications for therapeutic uses for cancer, as well as the current state of clinical studies and patents. We further address the knowledge gaps and future research orientations required to develop curcumin as a feasible treatment candidate.
Towards Personalized Allele-Specific Antisense Oligonucleotide Therapies for Toxic Gain-of-Function Neurodegenerative Diseases
2022-08-16

Antisense oligonucleotides (ASOs) are single-stranded nucleic acid strings that can be used to selectively modify protein synthesis by binding complementary (pre-)mRNA sequences. By specific arrangements of DNA and RNA into a chain of nucleic acids and additional modifications of the backbone, sugar, and base, the specificity and functionality of the designed ASOs can be adjusted. Thereby cellular uptake, toxicity, and nuclease resistance, as well as binding affinity and specificity to its target (pre-)mRNA, can be modified. Several neurodegenerative diseases are caused by autosomal dominant toxic gain-of-function mutations, which lead to toxic protein products driving disease progression. ASOs targeting such mutations—or even more comprehensively, associated variants, such as single nucleotide polymorphisms (SNPs)—promise a selective degradation of the mutant (pre-)mRNA while sparing the wild type allele. By this approach, protein expression from the wild type strand is preserved, and side effects from an unselective knockdown of both alleles can be prevented. This makes allele-specific targeting strategies a focus for future personalized therapies. Here, we provide an overview of current strategies to develop personalized, allele-specific ASO therapies for the treatment of neurodegenerative diseases, such Huntington’s disease (HD) and spinocerebellar ataxia type 3 (SCA3/MJD).
Carbon fluxes within tree-crop-grass agroforestry system: 13C field labeling and tracing
2022-08-16

Agroforestry systems are characterized by a high complexity between vegetation components and niche partitioning. In a crop-grass-tree agroforestry system, rape, willow, and grasses were in situ pulse labeled separately with 13CO2 for 6 h, and 13C was traced in shoots, roots, topsoil (0–15 cm) and subsoil (15–30 cm), microbial biomass carbon (C), and dissolved organic C, as well as respiration losses (CO2) up to 28 days after labeling to investigate the effects of vegetation components on C allocation belowground. 13C recovery in roots after 28 days was 7.0% of total assimilated C for grassland, which was 3.5- and 5.2-fold higher than that for rape and willow, respectively. The larger C allocation belowground in grassland was ascribed to its higher root/shoot ratio compared to willow and rape. Grassland facilitated higher accumulation of root-derived C in soil compared to rape (9.2% of recovered 13C) and compared to willow (1.6% of 13C). Willow retained more photosynthetic C aboveground and less was allocated to roots compared to rape. Although the C allocated to the top 15-cm soil was similar between willow and rape, willow facilitated C allocation in deeper soil compared to rape (0.6% vs. 0.2%). This could be explained by the lower microbial activity and subsequent weaker decomposition of rhizodeposits in 15–30-cm depth under willow. The net belowground C inputs in grassland, willow, and rape were 0.53, 0.06, and 0.10 g C m−2 month−1 of vegetation period, including rhizodeposition of 0.24, 0.05, and 0.04 g C m−2 month−1, respectively. Overall, integrating trees and grassland within cropland facilitates higher root-derived C input into soil, thus contributing to the soil C sequestration in agroforestry systems.
A paradigm shift in pharmacogenomics: From candidate polymorphisms to comprehensive sequencing
2022-08-16

Abstract Genetic factors have long been recognized as important determinants of interindividual variability in drug efficacy and toxicity. However, despite the increasing number of established gene–drug associations, candidate polymorphisms can only explain a fraction of the genetically encoded functional variability in drug disposition. Advancements in genetic profiling methods now allow to analyse the landscape of human pharmacogenetic variations comprehensively, which opens new opportunities to identify novel factors that could explain the “missing heritability.” Here, we provide an updated overview of the landscape of pharmacogenomic variability based on recent analyses of population‐scale sequencing projects. We then summarize the current state‐of‐the‐art how the functional consequences of variants with unknown effects can be quantitatively estimated while discussing challenges and peculiarities that are specific to pharmacogenes. In the last sections, we discuss the importance of considering ethnogeographic diversity to provide equitable benefits of pharmacogenomics and summarize current roadblocks for the implementation of sequencing‐based guidance of clinical decision‐making. Based on the current state of the field, we conclude that testing is likely to gradually shift from the interrogation of selected candidate polymorphisms to comprehensive sequencing, which allows to consider the full spectrum of pharmacogenomic variations for a true personalization of genomic prescribing.
Physico-chemical properties of maize (Zea mays L.) mucilage differ with the collection system and corresponding root type and developmental stage of the plant
2022-08-16

Abstract Purpose Mucilage plays crucial roles in root-soil interactions. Collection systems for maize ( Zea mays L.) use primary and seminal roots of aeroponically-grown seedlings (CS A ), or brace roots of soil-grown plants (CS B ). While each method represents specific plant developmental stages, and root types growing in specific (micro-)environments, these factors are rarely considered. It is unclear whether mucilage exhibits distinct physico-chemical properties related to collection system-inherent factors. Methods Mucilage of maize genotype B73 was collected from systems CS A and CS B . Chemical composition was assessed by pH, nutrient contents, neutral sugar composition, and polysaccharide polymer length. Viscosity, surface tension and contact angle represented physical properties. Results The share of hexoses among total polysaccharides was 11% higher in CS B than in CS A , whereas pentoses were predominant in CS A , together with higher nutrient concentrations and pH values. Mannose was detected only in CS B , which also exhibited higher surface tension, viscosity and contact angle compared to CS A . Conclusions Physico-chemical differences between the two mucilages are related to root type functions, environmental root growth conditions, and plant developmental state. Higher fractions of pentoses in CS A mucilage seem related to semi-sterile system conditions. Higher viscosity of CS B mucilage might reflect the need for enhanced water holding capacity of brace roots growing in drier conditions. A strong influence of environmental factors on mucilage properties even for a single genotype might play additional roles e.g. in the attraction of microbiomes. These aspects are relevant when assessing the role of mucilage in the rhizosphere, or when developing models of rhizosphere processes.
Genome Assembly and Genetic Traits of the Pleuromutilin-Producer Clitopilus passeckerianus DSM1602
2022-08-16

The gilled mushroom Clitopilus passeckerianus (Entolomataceae, Agaricales, Basidiomycota) is well known to produce the terpenoid pleuromutilin, which is the biotechnological basis for medically important antibiotics such as lefamulin and retapamulin. Their unique mode of action and good tolerance entails an increasing demand of pleuromutilin-derived antibiotics in veterinary and human health care. Surprisingly, despite their pharmaceutical importance, no genome sequence is available of any pleuromutilin-producing fungus. Here, we present the high-quality draft genome sequence of the pleuromutilin-producer C. passeckerianus DSM1602 including functional genome annotation. More precisely, we employed a hybrid assembly strategy combining Illumina sequencing and Nanopore sequencing to assemble the mitochondrial genome as well as the nuclear genome. In accordance with the dikaryotic state of the fungus, the nuclear genome has a diploid character. Interestingly, the mitochondrial genome appears duplicated. Bioinformatic analysis revealed a versatile secondary metabolism with an emphasis on terpenoid biosynthetic enzymes in C. passeckerianus and also in related strains. Two alleles of biosynthetic gene clusters for pleuromutilin were found in the genome of C. passeckerianus. The pleuromutilin genes were reassembled with yeast-specific elements for heterologous expression in Saccharomyces cerevisiae. Our work lays the foundation for metabolic strain engineering towards higher yields of the valuable compound pleuromutilin.
Finite Element Model of a Piezo-Electric Actuator Coupled to the Middle Ear
2022-08-16

Abstract The hearing contact lens® (HCL) is a new type of hearing aid devices. One of its main components is a piezo-electric actuator. In order to evaluate and maximize the HCL's performance, a model of the HCL coupled to a middle-ear model was developed using finite element approach. The model was validated step by step starting with the HCL only. To validate the HCL model, vibrational measurements on the HCL were performed using a laser-doppler-vibrometer (LDV). Then, a silicone cap was placed onto the HCL to provide an interface between the HCL and the tympanic membrane of the middle-ear model, and additional LDV measurements on temporal bones were performed to validate the coupled model that was used to evaluate the equivalent sound pressure of the HCL. Moreover, a de-eper insight was gained into the contact between the HCL and tympanic membrane and its effects on the HCL performance. The model can be used to investigate the sensitivity of geometrical and material parameters with respect to performance measures of the HCL and evaluate the feedback behavior.
The Azithromycin Pro-Drug CSY5669 Boosts Bacterial Killing While Attenuating Lung Inflammation Associated with Pneumonia Caused by Methicillin-Resistant Staphylococcus aureus
2022-08-16

Antibiotic resistance is a major problem, with methicillin-resistant Staphylococcus aureus (MRSA) being a prototypical example in surgical and community-acquired infections. S. aureus , like many pathogens, is immune evasive and able to multiply within host immune cells. Consequently, compounds that aid host immunity (e.g., by stimulating the host-mediated killing of pathogens) are appealing alternatives or adjuncts to classical antibiotics.
Fludarabine/TBI 8 Gy versus fludarabine/treosulfan conditioning in patients with AML in first complete remission: A Study from the Acute Leukemia Working Party of the EBMT
2022-08-16

<title>Abstract</title> The optimal reduced intensity conditioning (RIC) regimen is a matter of debate. We retrospectively compared conditioning with fludarabine plus fractionated total body irradiation of 8 Gy (FluTBI) and fludarabine plus treosulfan 30, 36 or 42 g/m<sup>2</sup> (FluTreo) in 754 patients with AML above the age of 40 years undergoing an allogeneic hematopoietic stem cell transplant (HSCT) in first complete remission (CR). In a multivariate analysis, FluTBI was associated with a significantly lower probability of relapse than FluTreo (hazard ratio (HR) 0.59 [95% CI, 0.38–0.93], p = 0.023). There was no significant difference in leukemia-free survival (LFS), overall survival (OS), graft-versus-host disease-free and relapse-free survival (GRFS), or acute and chronic graft-versus-host disease (GVHD). After balancing patient characteristics by propensity score matching of 115 patients in each group, FluTBI retained its significantly lower probability of relapse compared to FluTreo (18.3% vs. 34.7%, p = 0.018) which was counteracted by a higher non-relapse mortality (16.8 vs. 5.3%, p = 0.02). Thus, OS and GRFS at 2 years were similar between groups (OS 66.9% vs. 67.8%, GRFS 50.3% vs. 45.6%). We conclude that both conditioning regimens are effective and safe, but FluTBI may better be reserved for younger patients below the age of 55 years.
Paradigmatic and Syntagmatic Effects in Estonian Spontaneous Speech
2022-08-16

Recent evidence indicates that a word’s paradigmatic neighbors affect production. However, these findings have mostly been obtained in careful laboratory settings using words in isolation, and thus ignoring potential effects that may arise from the syntagmatic context, which is typically present in spontaneous speech. The current corpus analysis investigates paradigmatic and syntagmatic effects in Estonian spontaneous speech. Following work on English, we focus on the duration of inflected and uninflected word-final /-s/ in content words, while simultaneously investigating whole words. Our analyses reveal three points. First, we find an effect of realized inflectional paradigm size, such that smaller paradigms actively used by the speakers lead to longer durations. Second, higher conditional probability is associated with shorter word forms and shorter segments. Finally, we do not directly replicate previous work on effects of inflectional status as in English word-final /-s/. Instead, we find that inflectional status interacts with conditional probability. We discuss the results in light of models of speech production and how they account for morphologically complex words and their paradigmatic neighbors.
The Magic, Memory, and Curiosity fMRI Dataset of People Viewing Magic Tricks
2022-08-16

Videos of magic tricks offer lots of opportunities to study the human mind. They violate the expectations of the viewer (i.e., causing strong prediction errors), misdirect attention, and elicit a variety of epistemic emotions such as surprise and curiosity. Herein we describe and share the Magic, Memory, and Curiosity (MMC) dataset where 50 participants watched 36 magic tricks which were filmed and edited specifically for functional magnetic imaging (fMRI) experiments. The MMC dataset includes contextual incentive manipulation, curiosity ratings for the magic tricks, as well as incidental memory performance tested a week later. fMRI data were acquired before, during, and after learning. We show that both behavioural and fMRI data are of high quality, as indicated by basic validation analysis, i.e., variance decomposition as well as intersubject correlation and seed-based functional connectivity, respectively. The richness and complexity of the MMC dataset will allow researchers to explore dynamic cognitive and motivational processes from various angles.
Emotion as Feeling Towards Value: A Theory of Emotional Experience, by Jonathan Mitchell
2022-08-16

Recent work in the philosophy of emotion is characterized by a broad consensus that emotions possess both a phenomenal or felt character and directedness or intentionality. In being glad, jealous or angry, there is a characteristic way we feel; moreover, our emotion is directed or has an intentional object: we are glad, jealous or angry about something. In line with broader developments in the philosophy of mind, the past two decades have seen an increasing interest in the relation between these two aspects of emotion. More specifically, a further consensus is starting to form to the effect that the phenomenal and the intentional aspects of emotions are essentially intertwined: emotions are intentional feelings. At the same time, those who are party to this consensus offer competing views of the character of these feelings and the precise sense in which they are directed. While some suppose emotional feelings are intentional experiences of the same type as (or at least analogous to) perceptual experiences (for instance, Tappolet 2002; Döring 2007), others argue that the phenomenal dimension of emotion displays a reactive character that distinguishes it from perceptual experience (for instance, Deonna and Teroni 2015; Müller 2019). These opposing views come with different conceptions of the broader psychological role of emotional experiences: do they provide (quasi-)perceptual access to specific features of their intentional objects or are they attitudes or ‘stances’ we take towards those objects on the basis of prior awareness of what these objects are like? For example, does the way I feel in being outraged about Russia’s attack on Ukraine constitute (quasi-)perceptual awareness of the offensive character of Russia’s attack or is it more aptly conceived as a negative stance (of disapproval, say) which I take towards the attack in light of its offensiveness?
X-ray spectral and flux variability of the microquasar GRS 1758−258 on timescales from weeks to years
2022-08-16

We present the spectral and timing evolution of the persistent black hole X-ray binary GRS 1758−258 based on almost 12 years of observations using the Rossi X-ray Timing Explorer Proportional Counter Array. While the source was predominantly found in the hard state during this time, it entered the thermally dominated soft state seven times. In the soft state GRS 1758−258 shows a strong decline in flux above 3 keV rather than the pivoting flux around 10 keV more commonly shown by black hole transients. In its 3–20 keV hardness intensity diagram, GRS 1758−258 shows a hysteresis of hard and soft state fluxes typical for transient sources in outburst. The RXTE-PCA and RXTE-ASM long-term light curves do not show any orbital modulations in the range of 2–30 d. However, in the dynamic power spectra significant peaks drift between 18.47 and 18.04 d for the PCA data, while less significant signatures between 19 d and 20 d are seen for the ASM data as well as for the Swift/BAT data. We discuss different models for the hysteresis behavior during state transitions as well as possibilities for the origin of the long term variation in the context of a warped accretion disk.
MASSA Algorithm: automated rational sampling of training and test subsets for QSAR modelling
2022-08-16

The use of computer-aided drug design has become an essential part of drug development. In this context, QSAR models capable of predicting biological activities, toxicity, and pharmacokinetic properties were widely used to search bioactive molecules in chemical databases for lead compounds. The preparation of dataset used to build these models has a strong influence on the quality of the generated models, and sampling these data requires that the original dataset be divided into training (used for model training) and test sets (used to further evaluate the predictability of the model). This sampling can be done randomly or rationally, but the rational or purposeful division is superior to the random method. In this paper, we present MASSA Algorithm ("Molecular dAta Set SAmpling Algorithm"), an open-source, user-friendly Python tool that can be used to perform automatic sampling of datasets of molecules into training and test sets by exploring the biological, physicochemical, and structural spaces of molecules using Principal Component Analysis, Hierarchical Clustering Analysis, and K-modes clustering. This proposed algorithm is very useful when the variables for QSAR model generation is not available or to construct multiple QSAR models with the same training and test sets. When compared to random sampling, the presented algorithm produces models with lower variability and higher values across multiple replicates for validation metrics. These results were obtained even when the descriptors used in the QSAR/QSPR were different from those used in the separation of training and test sets, indicating that this tool can be used to build models for more than one QSAR/QSPR technique. Finally, the tool also generates useful graphical representations of the distribution that can provide insights into the data.