Miracle-dz/UniFAR-FTUs huggingface dataset:
Branching of hydraulic cracks enabling permeability of gas or oil shale with closed natural fractures

Significance Development of a realistic model of fracking would allow better control. It should make it possible to optimize various parameters such as the history of pumping, its rate or cycles, changes of viscosity, etc. This could lead to an increase of the percentage of gas extraction from the deep shale strata, which currently stands at about 5% and rarely exceeds 15%. While hydraulic fracturing technology, aka fracking (or fraccing, frac), has become highly developed and astonishingly successful, a consistent formulation of the associated fracture mechanics that would not conflict with some observations is still unavailable. It is attempted here. Classical fracture mechanics, as well as current commercial software, predict vertical cracks to propagate without branching from the perforations of the horizontal well casing, which are typically spaced at 10 m or more. However, to explain the gas production rate at the wellhead, the crack spacing would have to be only about 0.1 m, which would increase the overall gas permeability of shale mass about 10,000×. This permeability increase has generally been attributed to a preexisting system of orthogonal natural cracks, whose spacing is about 0.1 m. However, their average age is about 100 million years, and a recent analysis indicated that these cracks must have been completely closed by secondary creep of shale in less than a million years. Here it is considered that the tectonic events that produced the natural cracks in shale must have also created weak layers with nanocracking or microcracking damage. It is numerically demonstrated that seepage forces and a greatly enhanced permeability along the weak layers, with a greatly increased transverse Biot coefficient, must cause the fracking to engender lateral branching and the opening of hydraulic cracks along the weak layers, even if these cracks are initially almost closed. A finite element crack band model, based on a recently developed anisotropic spherocylindrical microplane constitutive law, demonstrates these findings [Rahimi-Aghdam S, et al. (2018) arXiv:1212.11023].
Blind Estimation of the PN Sequence of A DSSS Signal Using A Modified Online Unsupervised Learning Machine

Direct sequence spread spectrum (DSSS) signals are now widely used in air and underwater acoustic communications. A receiver which does not know the pseudo-random (PN) sequence cannot demodulate the DSSS signal. In this paper, firstly, the principle of principal component analysis (PCA) for PN sequence estimation of the DSSS signal is analyzed, then a modified online unsupervised learning machine (LEAP) is introduced for PCA. Compared with the original LEAP, the modified LEAP has the following improvements: (1) By normalizing the system state transition matrices, the modified LEAP can obtain better robustness when the training errors occur; (2) with using variable learning steps instead of a fixed one, the modified LEAP not only converges faster but also has excellent estimation performance. When the modified LEAP is converging, we can utilize the network connection weights which are the eigenvectors of the autocorrelation matrix of the DSSS signal to estimate the PN sequence. Due to the phase ambiguity of the eigenvectors, a novel approach which is based on the properties of the PN sequence is proposed here to exclude the wrong estimated PN sequences. Simulation results showed that the methods mentioned above can estimate the PN sequence rapidly and robustly, even when the DSSS signal is far below the noise level.
The genetic diversity and evolution of diatom-diazotroph associations highlights traits favoring symbiont integration

Abstract Diatom diazotroph associations (DDAs) are a widespread marine planktonic symbiosis between several diatom genera and di-nitrogen (N2)-fixing bacteria. Combining single cell confocal microscopy observations and molecular genetic approaches on individual field collected cells, we determined the phylogenetic diversity, distribution and evolution of the DDAs. Confocal analyses coupled with 3-D imaging re-evaluated the cellular location of DDA symbionts. DDA diversity was resolved by paired gene sequencing (18S rRNA and rbcL genes, 16S rRNA and nifH genes). A survey using the newly acquired sequences against public databases found sequences with high similarity (99–100%) to either host (18S rRNA) or symbiont (16S rRNA) in atypical regions for DDAs (high latitudes, anoxic basin and copepod gut). Concatenated phylogenies were congruent for the host and cyanobacteria sequences and implied co-evolution. Time-calibrated trees dated the appearance of N2 fixing planktonic symbiosis from 100–50Mya and were consistent with the symbiont cellular location: symbioses with internal partners are more ancient. An ancestral state reconstruction traced the evolution of traits in DDAs and highlight that the adaptive radiation to the marine environment was likely facilitated by the symbiosis. Our results present the evolutionary nature of DDAs and provide new genetic and phenotypic information for these biogeochemically relevant populations.
Iron deficiency in pulmonary arterial hypertension associated with congenital heart disease

Abstract Objectives. We aimed to investigate the prevalence of iron deficiency (ID) in congenital heart disease associated with pulmonary arterial hypertension (CHD-PAH) and to explore the influence of ID on CHD-PAH patients. What was associated with ID in these patients was also looked into. Design. One hundred and fifty-three patients who were newly diagnosed with CHD-PAH were enrolled. Patients were divided into iron-deficient and iron-replete groups according to the following criteria. ID was defined as transferrin saturation <20% in male and transferrin saturation <25% in female. Clinical data of all participants were collected and compared. Logistic regression was performed to explore factors associated with ID in CHD-PAH. Results. Thirty-nine percent of 153 CHD-PAH patients were founded with ID. Iron-deficient group had greater proportion of female patients, shorter six minutes walking distance (6-MWD), higher N-terminal pro-brain natriuretic peptide levels, lower creatinine levels, greater ratio of diastolic right ventricle diameter to left ventricle diameter. Female (OR = 15.44, 95%CI 4.91–48.54, p < .01), 6-MWD (OR = 0.99, 95%CI 0.98–1.00, p = .02) and mean right atrial pressure (OR = 1.13, 95%CI 1.02–1.26, p = .02) were independently associated with ID in the overall CHD-PAH patients. Menstruation was independently associated with ID in the female subgroup (OR = 3.88, 95%CI 1.09–13.84, p = .04). Conclusions. ID was highly prevalent in CHD-PAH patients. Worse exercise tolerance and right heart function were observed in iron-deficient patients with CHD-PAH. Female, 6-MWD, mean right atrial pressure and menstruation are important variables indicating the presence of ID in CHD-PAH.
Molecular characteristics of early-stage female germ cells revealed by RNA sequencing of low-input cells and analysis of genome-wide DNA methylation

Abstract High-throughput stage-specific transcriptomics provides an unbiased approach for understanding the process of cell development. Here, we report transcriptome analysis of primordial germ cell, female germline stem cell (FGSC), germinal vesicle and mature oocyte by performing RNA sequencing of freshly isolated cells in mice. As expected, these stages and gene-expression profiles are consistent with developmental timing. Analysis of genome-wide DNA methylation during female germline development was used for confirmation. By pathway analysis and blocking experiments, we demonstrate PI3K-AKT pathway is critical for FGSC maintenance. We also identify functional modules with hub genes and lncRNAs, which represent candidates for regulating FGSC self-renewal and differentiation. Remarkably, we note alternative splicing patterns change dramatically during female germline development, with the highest occurring in FGSCs. These findings are invaluable resource for dissecting the molecular pathways and processes into oogenesis and will be wider applications for other types of stem cell research.
Social threat attentional bias in childhood: Relations to aggression and hostile intent attributions

The goal of this study was to examine the ways attentional bias to social threat-measured across multiple attentional processes-is related to both child aggression and a well-established cognitive correlate of aggression (namely, hostile intent attributions). A community sample of 211 children (51% male; 9-12 years; 55% Caucasian) participated in our cross-sectional correlational design. Social threat attentional bias was measured through task performance on dot-probe, attentional shifting, and temporal order judgment tasks; each task measured different attentional processes. Aggression was measured by parent- and child-report. Hostile intent attributions were measured through child responses to vignettes involving peer conflict or rejection. Attentional bias to social threat within early phases of attentional processing (i.e., attentional prioritization; stimuli presented for <200 ms in temporal order judgment task) was significantly and positively related to both aggression and hostile intent attributions. Attentional bias to social threat within attentional orienting (stimuli presented for 500 ms in dot-probe task) was positively and significantly related to hostile intent attributions. Attentional bias to social threat within attentional shifting (stimuli presented for multiple seconds) was not significantly related to aggression or hostile intent attributions. Higher levels of aggression and of hostile intent attributions were associated with an attentional bias to social threat within early, but not later, phases of attentional processing. These results suggest specificity in identifying dysfunctional attentional processes that may underlie aggression and aggression-related cognitive biases.
Rho GTPase Activating Protein 24 (ARHGAP24) Silencing Promotes Lung Cancer Cell Migration and Invasion by Activating β-Catenin Signaling

Background Rho GTPase activating protein (RhoGAPs) is an important negative regulator of the Rho signaling pathway that is involved in tumorigenesis in liver, colon, and renal cancer. However, the mechanism by which Rho GTPase activating protein 24 (ARHGAP24) regulates cell invasion and migration of lung cancer has not been fully explained. Material/Methods In this study, ARHGAP24 expression in lung cancer tissues and cell lines was measured by immunohistochemical and Western blot analysis. Transwell or wound healing analysis was performed to detect the cell migration and invasion of ARHGAP24 modulated A549 and NCI-H1975 cells with β-catenin inhibitor XAV-939 (10 μM) treatment, and the expression of MMP9, VEGF, and β-catenin protein was measured by Western blotting. Results Our results showed that ARHGAP24 expression was downregulated in lung cancer tissues and cell lines. pLVX-Puro-ARHGAP24 transfection in A549 cells significantly inhibited cell invasion and migration, along with increased E-cadherin and decreased MMP9, VEGF, Vimentin, and β-catenin protein expression. pLKO.1-ARHGAP24-shRNA transfection in NCI-H1975 cells significantly promoted cell invasion and migration, accompanied with decreased E-cadherin and increased MMP9, VEGF, and β-catenin protein expression. Moreover, NCI-H1975 cells with XAV-939 treatment showed decreased cell invasion and migration when compared with pLKO.1-ARHGAP24-shRNA transfection. ARHGAP24 silencing promoted the transcriptional activity of β-catenin in NCI-H1975 cells. Conclusions Our findings indicate that ARHGAP24 silencing promotes lung cancer cell migration and invasion through activating β-catenin signaling.
Impact of p85α Alterations in Cancer

The phosphatidylinositol 3-kinase (PI3K) pathway plays a central role in the regulation of cell signaling, proliferation, survival, migration and vesicle trafficking in normal cells and is frequently deregulated in many cancers. The p85α protein is the most characterized regulatory subunit of the class IA PI3Ks, best known for its regulation of the p110-PI3K catalytic subunit. In this review, we will discuss the impact of p85α mutations or alterations in expression levels on the proteins p85α is known to bind and regulate. We will focus on alterations within the N-terminal half of p85α that primarily regulate Rab5 and some members of the Rho-family of GTPases, as well as those that regulate PTEN (phosphatase and tensin homologue deleted on chromosome 10), the enzyme that directly counteracts PI3K signaling. We highlight recent data, mapping the interaction surfaces of the PTEN–p85α breakpoint cluster region homology (BH) domain, which sheds new light on key residues in both proteins. As a multifunctional protein that binds and regulates many different proteins, p85α mutations at different sites have different impacts in cancer and would necessarily require distinct treatment strategies to be effective.
Elastography detected solid organ stiffness increased in patients with acromegaly

Abstract Elastography is a method to examine the increase in solid organs stiffness (SOS), and there is no data in the literature regarding to its use in patients with acromegaly. In this study, we aimed to investigate the change of SOS in patients with acromegaly and to determine the parameters closely related to SOS in same patient groups. We included 40 subjects with acromegaly and 40 healthy control subjects. In addition to routine renal, liver and thyroid ultrasonography (USG), SOS for 3 solid organs were measured by elastography. The participants of the study were divided into 3 groups as the control (Group-I), acromegaly patients with remission (Group-II), and acromegaly patients without remission (Group-III). Insulin growth factor-1 (IGF-1) level significantly increased from Group-I to Group-III. Glucose, creatinine, albuminuria, alkaline phosphatase, TSH, and growth factor levels were highest in Group-III and statistically significance was found only between Group-I and Group-III. Liver, kidney and thyroid size and echogenicity were increased from Group-I to Group-III. Liver and renal stiffness and thyroid gland strain ratio significantly increased from Group-I to Group-III and these parameters were statistically different between all groups. In linear regression analysis, IGF-1 levels were independent determinants of SOS. SOS values of acromegaly patients with active disease were significantly increased compared to both the control group and the acromegaly patients in remission phase. Serum IGF-1 levels were independently associated with SOS in these patients. SOS measurement should be part of a routine USG examination in patients with acromegaly, especially in patients during active disease.
The Effect of the Isomeric Chlorine Substitutions on the Honeycomb-Patterned Films of Poly(x-chlorostyrene)s/Polystyrene Blends and Copolymers via Static Breath Figure Technique

Polymeric thin films patterned with honeycomb structures were prepared from poly(x-chlorostyrene) and statistical poly(x-chlorostyrene-co-styrene) copolymers by static breath figure method. Each polymeric sample was synthesized by free radical polymerization and its solution in tetrahydrofuran cast on glass wafers under 90% relative humidity (RH). The effect of the chorine substitution in the topography and conformational entropy was evaluated. The entropy of each sample was calculated by using Voronoi tessellation. The obtained results revealed that these materials could be a suitable toolbox to develop a honeycomb patterns with a wide range of pore sizes for a potential use in contact guidance induced culture.
Radiogenomics in Clear Cell Renal Cell Carcinoma: Machine Learning-Based High-Dimensional Quantitative CT Texture Analysis in Predicting PBRM1 Mutation Status.

OBJECTIVE The purpose of this study is to evaluate the potential value of machine learning (ML)-based high-dimensional quantitative CT texture analysis in predicting the mutation status of the gene encoding the protein polybromo-1 (PBRM1) in patients with clear cell renal cell carcinoma (RCC). MATERIALS AND METHODS In this retrospective study, 45 patients with clear cell RCC (29 without the PBRM1 mutation and 16 with the PBRM1 mutation) were identified in The Cancer Genome Atlas-Kidney Renal Clear Cell Carcinoma database. To create stable ML models and balanced classes, the data were augmented to a total of 161 labeled segmentations (87 without the PBRM1 mutation and 74 with the PBRM1 mutation) by obtaining three to five different samples per patient. Texture features were extracted from corticomedullary phase contrast-enhanced CT images with the use of an open-source software package for the extraction of radiomic data from medical images. Reproducibility analysis (intraclass correlation) was performed by two radiologists. Attribute selection and model optimization were done using a wrapper-based classifier-specific algorithm with nested cross-validation. ML classifiers were an artificial neural network (ANN) algorithm and a random forest (RF) algorithm. The models were validated using 10-fold cross-validation. The reference standard was the PBRM1 mutation status. The main performance metric was the AUC value. RESULTS Of 828 extracted texture features, 759 had excellent reproducibility. Using 10 selected features, the ANN algorithm correctly classified 88.2% (142 of 161) of the clear cell RCCs in terms of PBRM1 mutation status (AUC value, 0.925). Using five selected features, the RF algorithm correctly classified 95.0% (153 of 161) of the clear cell RCCs (AUC value, 0.987). Overall, the RF algorithm performed better than the ANN algorithm (z score = -2.677; p = 0.007). CONCLUSION ML-based high-dimensional quantitative CT texture analysis might be a feasible and potential method for predicting PBRM1 mutation status in patients with clear cell RCC.
Risk Factors for Low CD4+ Count Recovery Despite Viral Suppression Among Participants Initiating Antiretroviral Treatment With CD4+ Counts > 500 Cells/mm3: Findings From the Strategic Timing of AntiRetroviral Therapy (START) Trial

Background: Low CD4+ recovery among HIV-positive individuals who achieve virologic suppression is common but has not been studied among individuals initiating treatment at CD4+ counts of >500 cells/mm3. Setting: United States, Africa, Asia, Europe and Israel, Australia, Latin America. Methods: Among participants randomized to immediate antiretroviral therapy (ART) in the Strategic Timing of AntiRetroviral Therapy trial, low CD4+ recovery was defined as a CD4+ increase of <50 cells/mm3 from baseline after 8 months despite viral load of ⩽200 copies/mL. Risk factors for low recovery were investigated with logistic regression. Results: Low CD4+ recovery was observed in 39.7% of participants. Male sex [odds ratio (OR), 1.53; P = 0.007], lower screening CD4+ cell counts (OR, 1.09 per 100 fewer cells/mm3; P = 0.004), higher baseline CD8+ cell counts (OR, 1.05 per 100 more cells/mm3; P < 0.001), and lower HIV RNA levels (OR, 1.93 per log10 decrease; P < 0.001) were associated with low CD4+ recovery. D-dimer had a quadratic association with low CD4+ recovery, with lowest odds occurring at 0.32 &mgr;g/mL. At lower HIV RNA levels, the odds of low CD4+ recovery were elevated across the levels of screening CD4+ count; but at higher HIV RNA levels, the odds of low CD4+ recovery were higher among those with lower vs. higher screening CD4+. Conclusions: Low CD4+ recovery is frequent among participants starting ART at high CD4+ counts. Risk factors include male sex, lower screening CD4+ cell counts, higher CD8+ cell counts, and lower HIV RNA levels. More follow-up is required to determine the impact of low CD4+ recovery on clinical outcomes.
The IASP classification of chronic pain for ICD-11: chronic secondary musculoskeletal pain

Abstract Chronic musculoskeletal pain is defined as chronic pain arising from musculoskeletal structures such as bones or joints. Although comprising the most prevalent set of chronic pain conditions, it was not represented appropriately in the 10th edition of the International Classification of Diseases (ICD-10), which was organized mainly according to anatomical sites, was strongly focused on musculoskeletal disease or local damage, and did not consider the underlying mechanisms of pain. The new ICD-11 classification introduces the concept of chronic primary and secondary musculoskeletal pain, and integrates the biomedical axis with the psychological and social axes that comprise the complex experience of chronic musculoskeletal pain. Chronic primary musculoskeletal pain is a condition in its own right, not better accounted for by a specific classified disease. Chronic secondary musculoskeletal pain is a symptom that arises from an underlying disease classified elsewhere. Such secondary musculoskeletal pain originates in persistent nociception in musculoskeletal structures from local or systemic etiologies, or it may be related to deep somatic lesions. It can be caused by inflammation, by structural changes, or by biomechanical consequences of diseases of the nervous system. It is intended that this new classification will facilitate access to patient-centered multimodal pain management and promote research through more accurate epidemiological analyses.
The Use of Dietary Interventions in Pediatric Patients

Complementary and alternative treatment approaches are becoming more common among children with chronic conditions. The prevalence of CAM use among US adults was estimated to be around 42% in 2015 and around 44% to 50% among adults with neurologic disorders. Studies demonstrate that children with certain chronic illnesses such as asthma, cancer, genetic disorders, attention-deficit/hyperactivity disorder (ADHD), and other neurodevelopmental disorders are treated with complementary and alternative treatments at higher rates. Dietary therapies are gaining increasing popularity in the mainstream population. Although the majority of “fad” diets do not have enough supporting evidence, some dietary therapies have been utilized for decades and have numerous published studies. The objective of this review is to describe the dietary interventions used in children with the specific chronic conditions, to evaluate their efficacy based on published data and to encourage pharmacist involvement in the management and care of such patients.
Transparent Conductive Electrodes Based on Graphene-Related Materials

Transparent conducting electrodes (TCEs) are the most important key component in photovoltaic and display technology. In particular, graphene has been considered as a viable substitute for indium tin oxide (ITO) due to its optical transparency, excellent electrical conductivity, and chemical stability. The outstanding mechanical strength of graphene also provides an opportunity to apply it as a flexible electrode in wearable electronic devices. At the early stage of the development, TCE films that were produced only with graphene or graphene oxide (GO) were mainly reported. However, since then, the hybrid structure of graphene or GO mixed with other TCE materials has been investigated to further improve TCE performance by complementing the shortcomings of each material. This review provides a summary of the fabrication technology and the performance of various TCE films prepared with graphene-related materials, including graphene that is grown by chemical vapor deposition (CVD) and GO or reduced GO (rGO) dispersed solution and their composite with other TCE materials, such as carbon nanotubes, metal nanowires, and other conductive organic/inorganic material. Finally, several representative applications of the graphene-based TCE films are introduced, including solar cells, organic light-emitting diodes (OLEDs), and electrochromic devices.