Miracle-dz/UniFAR-FTUs huggingface dataset:
Bile Acid Profiles in Primary Sclerosing Cholangitis and Their Ability to Predict Hepatic Decompensation

Altered bile acid (BA) homeostasis is an intrinsic facet of cholestatic liver diseases, but clinical usefulness of plasma BA assessment in primary sclerosing cholangitis (PSC) remains understudied. We performed BA profiling in a large retrospective cohort of patients with PSC and matched healthy controls, hypothesizing that plasma BA profiles vary among patients and have clinical utility.
Design and fabrication of a portable minicuvette system for measuring leaf photosynthesis and stomatal conductance under controlled conditions

The design specifications and some performance data for a new miniaturized cuvette system suitable for measuring photosynthesis and stomatal conductance in the field are reported. The system operates on 12-V power (dc). An electronic support module is attached by an umbilical cord to a stirred-reaction leaf chamber and a rechargeable battery pack. The chamber is heated or cooled by thermoelectric modules and humidity and CO/sub 2/ concentration are kept steady by bleeding in dry air and CO/sub 2/-enriched dry air through capillaries. Relative humidity is measured in situ by a fast-response capacitive-type humidity sensor. Carbon dioxide concentration is currently monitored by diverting exhaust gas from the chamber to a conventional infrared gas analyzer. A miniaturized, folded-path infrared gas analyzer is to be incorporated into the system as an in situ CO/sub 2/ sensor in a manner analogous to the humidity sensor. True CO/sub 2/ can be estimated using /sup 14/CO/sub 2/-labeled air. The system features solid-state pressure transducers for monitoring flow rate and digital readout for all parameters. Interfacing for data acquisition and automatic control is provided. Extensive field performance tests have shown that this instrumentation effectively replaces large cuvette systems, while it incorporates many of the desirable features ofmore » small, hand-held porometers. (ERB)« less
The value of a metabolic reprogramming-related gene signature for pancreatic adenocarcinoma prognosis prediction

Pancreatic ductal adenocarcinoma (PDAC) is one of the most fatal malignancies worldwide. Extensive enhancement of glycolysis and reprogramming of lipid metabolism are both associated with the development and progression of PDAC. Previous studies have suggested that various gene signatures could convey prognostic information about PDAC. However, the use of these signatures has some limitations, perhaps because of a lack of knowledge regarding the genetic and energy supply backgrounds of PDAC. Therefore, we conducted multi-mRNA analysis based on metabolic reprogramming to identify novel signatures for accurate prognosis prediction in PDAC patients. In this study, a three-gene signature comprising MET, ENO3 and CD36 was established to predict the overall survival of PDAC patients. The three-gene signature could divide patients into high- and low-risk groups by disparities in overall survival verified by log-rank test in two independent validation cohorts and could differentiate tumors from normal tissues with excellent accuracy in four Gene Expression Omnibus (GEO) cohorts. We also found a positive correlation between the risk score of the gene signature and inherited germline mutations in PDAC predisposition genes. A glycolysis and lipid metabolism-based gene nomogram and corresponding calibration curves showed significant performance for survival prediction in the TCGA-PDAC dataset. The high-risk designation was closely connected with oncological signatures and multiple aggressiveness-related pathways, as determined by gene set enrichment analysis (GSEA). In summary, our study developed a three-gene signature and established a prognostic nomogram that objectively predicted overall survival in PDAC. The findings could provide a reference for the prediction of overall survival and could aid in individualized management for PDAC patients.
Hemodynamic study in 3D printed stenotic coronary artery models: experimental validation and transient simulation

Abstract Atherosclerosis is a progressive disease that can significantly reduce blood supply to vital organs, being one of the main causes of death worldwide. In this work, a numerical and experimental study in 3D printed stenotic coronary arteries, considering both steady and pulsatile blood flow conditions, is presented. The results revealed that a degree of stenosis superior to 50% creates disturbed flows downstream of the contraction, with an accented increase in the wall shear stress measurements at the stenosis throat. Finally, the multiphase mixture was investigated and compared with a single-phase modelling, and only slight differences were observed right after the stenosis throat.
Cyclophilin 19 secreted in the host cell cytosol by Trypanosoma cruzi promotes ROS production required for parasite growth

Infection by Trypanosoma cruzi, the protozoan parasite that causes Chagas disease, depends on reactive oxygen species (ROS), which has been described to induce parasite proliferation in mammalian host cells. It is unknown how the parasite manages to increase host ROS levels. Here, we found that intracellular T. cruzi forms release in the host cytosol its major cyclophilin of 19 kDa (TcCyp19). Parasites depleted of TcCyp19 by using CRISPR/Cas9 gene replacement proliferate inefficiently and fail to increase ROS, compared to wild type parasites or parasites with restored TcCyp19 gene expression. Expression of TcCyp19 in L6 rat myoblast increased ROS levels and restored the proliferation of TcCyp19 depleted parasites. These events could also be inhibited by cyclosporin A, (a cyclophilin inhibitor), and by polyethylene glycol‐linked to antioxidant enzymes. TcCyp19 was found more concentrated in the membrane leading edges of the host cells in regions that also accumulate phosphorylated p47phox, as observed to the endogenous cyclophilin A, suggesting some mechanisms involved with the translocation process of the regulatory subunit p47phox in the activation of the NADPH oxidase enzymatic complex. We concluded that cyclophilin released in the host cell cytosol by T. cruzi mediates the increase of ROS, required to boost parasite proliferation in mammalian hosts.
Morphological Integration and Modularity in the Hyperkinetic Feeding System of Aquatic-foraging Snakes

The kinetic skull is a key innovation that allowed snakes to capture, manipulate, and swallow prey exclusively using their heads using the coordinated movement of 8 bones. Despite these unique feeding behaviors, patterns of evolutionary integration and modularity within the feeding bones of snakes in a phylogenetic framework have yet to be addressed. Here, we use a dataset of 60 µCT scanned skulls and high-density geometric morphometric methods to address the origin and patterns of variation and integration in the feeding bones of aquatic-foraging snakes. By comparing alternate superimposition protocols allowing us to analyze the entire kinetic feeding system simultaneously, we find that the feeding bones are highly integrated, driven predominantly by functional selective pressures. The most supported pattern of modularity contains four modules each associated with distinct functional roles: the mandible, the palatopterygoid arch, the maxilla, and the suspensorium. Further, the morphological disparity of each bone is not linked to its magnitude of integration, indicating that integration within the feeding system does not constrain morphological evolution and that adequate biomechanical solutions to a wide range of feeding ecologies and behaviors is readily evolvable within the constraint due to integration in the snake feeding system.
Anti-Tumor Effect of Vitamin D Combined with Calcium on Lung Cancer: A Systematic Review and Meta-Analysis

Abstract Although many studies have demonstrated the impact of vitamin D and calcium on lung cancer, it remains the discrepancy for the effect of vitamin D and calcium on lung cancer. In this study, we aimed to verify the roles of vitamin D and calcium in the incidence and prognosis of lung cancer. A systematic literature search was performed by February 29, 2020. The relative risks (RRs) and hazard ratio (HRs) were pooled to evaluate the risk for the incidence and mortality of lung cancer. A total of 58,625 lung cancer cases from 40 studies were included. The risk (RR: 0.915, 95% Cl: 0.849–0.986) and mortality (RR: 0.718, 95% Cl: 0.530–0.973) of lung cancer were significantly decreased due to high circulating 25(OH)D level. Although the separate intake of vitamin D (RR: 0.909, 95% Cl: 0.801–1.031) and calcium (RR: 0.890, 95% Cl: 0.741–1.070) did not exhibit a protective effect on lung cancer, the combination supplement of vitamin D and calcium significantly decreased the incidence of lung cancer (RR: 0.811, 95% Cl: 0.659–0.999). High level of serum 25(OH)D could play the preventive role in lung cancer. Furthermore, vitamin D could be supplemented together with calcium against lung cancer.
A robust culture system to generate neural progenitors with gliogenic competence from clinically relevant induced pluripotent stem cells for treatment of spinal cord injury

Cell‐based therapy targeting spinal cord injury (SCI) is an attractive approach to promote functional recovery by replacing damaged tissue. We and other groups have reported the effectiveness of transplanting neural stem/progenitor cells (NS/PCs) derived from human induced pluripotent stem cells (hiPSCs) in SCI animal models for neuronal replacement. Glial replacement is an additional approach for tissue repair; however, the lack of robust procedures to drive iPSCs into NS/PCs which can produce glial cells has hindered the development of glial cell transplantation for the restoration of neuronal functions after SCI. Here, we established a method to generate NS/PCs with gliogenic competence (gNS/PCs) optimized for clinical relevance and utilized them as a source of therapeutic NS/PCs for SCI. We could successfully generate gNS/PCs from clinically relevant hiPSCs, which efficiently produced astrocytes and oligodendrocytes in vitro. We also performed comparison between gNS/PCs and neurogenic NS/PCs based on single cell RNA‐seq analysis and found that gNS/PCs were distinguished by expression of several transcription factors including HEY2 and NFIB. After gNS/PC transplantation, the graft did not exhibit tumor‐like tissue formation, indicating the safety of them as a source of cell therapy. Importantly, the gNS/PCs triggered functional recovery in an SCI animal model, with remyelination of demyelinated axons and improved motor function. Given the inherent safety of gNS/PCs and favorable outcomes observed after their transplantation, cell‐based medicine using the gNS/PCs‐induction procedure described here together with clinically relevant iPSCs is realistic and would be beneficial for SCI patients.
金属内包フラーレン生成の分子動力学シミュレーション ( マイクロスケールの流体・熱流動現象)

The growth process of metal-containing fullerene was studied using the molecular dynamics method. As for metalcontaining fullerene, only the metal atoms such as La, Y or Sc are experimentally assigned to be contained inside the carbon cage. In this paper, the difference of growth process and structures of metal-attached carbon clusters were examined using lanthanum and nickel as the additional metal atoms to clarify the effect of the metal atoms. In order to model the potential function between carbon and metal atoms appropriate for the classical MD simulation, the binding energy and charge state of various forms of small clusters MCn (M: La,Ni; n =1-3) were calculated with the density functional theory. A multi-body potential function was constructed as a function of coordinate number of a scandium atom. Here, the Coulomb term and the Morse-type term were separately described considering the large charge transfer from a lanthanum atom to carbon atoms. By using the potential function, the clustering process starting from 500 isolated carbon atoms and 5 metal atoms in a 342 A cubic cell was simulated under the controlled temperature condition at Tc = 3000 K, and the growth history of metal-attached clusters was studied in detail. Figure A-1 shows the growth process of La attached clusters obtained in the simulation. The fan-type structure and mono-cyclic or bi-cyclic rings were reproduced around the metal atom for LaCn (n<20). An open cap structure surrounding the La atom was formed for LaCn (20<n<50) due to the strong Coulomb interaction, and that resulted in the lanthanum-containing caged cluster. When Ni atoms were applied as shown in Figure A-2, the structures of small clusters up to NiC n (n<20) were similar to LaCn (n<20), while tangled-poly-cyclic structures and random cage were dominant for NiCn (20<n<50). The nickel atom attached on one face of the caged structure, and could not stay stably inside the carbon cage structure.
The Truth Is Out There: Accuracy in Recall of Verifiable Real-World Events

How accurate is memory? Although people implicitly assume that their memories faithfully represent past events, the prevailing view in research is that memories are error prone and constructive. Yet little is known about the frequency of errors, particularly in memories for naturalistic experiences. Here, younger and older adults underwent complex real-world experiences that were nonetheless controlled and verifiable, freely recalling these experiences after days to years. As expected, memory quantity and the richness of episodic detail declined with increasing age and retention interval. Details that participants did recall, however, were highly accurate (93%–95%) across age and time. This level of accuracy far exceeded comparatively low estimations among memory scientists and other academics in a survey. These findings suggest that details freely recalled from one-time real-world experiences can retain high correspondence to the ground truth despite significant forgetting, with higher accuracy than expected given the emphasis on fallibility in the field of memory research.
Molecules in galaxies

The main achievements, current developments and prospects of molecular studies in external galaxies are reviewed. They are put in the context of the results of several decades of studies of molecules in local interstellar medium, their chemistry and their importance for star formation. CO observations have revealed the gross structure of molecular gas in galaxies. Together with other molecules, they are among the best tracers of star formation at galactic scales. Our knowledge about molecular abundances in various local galactic environments is progressing. They trace physical conditions and metallicity, and they are closely related to dust processes and large aromatic molecules. Major recent developments include mega-masers, and molecules in Active Galactic Nuclei; millimetre emission of molecules at very high redshift; and infrared H2 emission as tracer of warm molecular gas, shocks and photodissociation regions. The advent of sensitive giant interferometers from the centimetre to submillimetre range, especially ALMA in the near future in the mm/submm range, will open a new area for molecular studies in galaxies and their use to trace star formation at all distances. Molecules in Galaxies 2
Risk of latent and active tuberculosis infection in travellers: a systematic review and meta-analysis.

INTRODUCTION Achieving tuberculosis (TB) elimination in low TB incidence countries requires identification and treatment of individuals at risk for latent TB infection (LTBI). Persons travelling to high TB incidence countries are potentially at risk for TB exposure. This systematic review and meta-analysis estimates incident LTBI and active TB among individuals travelling from low to higher TB incidence countries. METHODS Five electronic databases were searched from inception to 18th February, 2020. We identified incident LTBI and active TB among individuals travelling from low (<10 cases/100000 population) to intermediate (10-100/100000) or high (>100/100000) TB incidence countries. We conducted a meta-analysis and meta-regression using a random effects model of log-transformed proportions (cumulative incidence). Subgroup analyses investigated the impact of travel duration, travel purpose, and TB incidence in the destination country. RESULTS Our search identified 799 studies, 120 underwent full-text review, and 10 studies were included. These studies included 1 154 673 travellers observed between 1994 and 2013, comprising 443 health care workers (HCW), 1 068 636 military personnel, and 85 594 general travellers/volunteers. We did not identify any studies that estimated incidence of LTBI or active TB among people travelling to visit friends and relatives (VFRs). The overall cumulative incidence of LTBI was 2.3%, with considerable heterogeneity. Among individuals travelling for a mean/median of up to 6 months, HCWs had the highest cumulative incidence of LTBI (4.3%), while the risk was lower for military (2.5%) and general travellers/volunteers (1.6%). Meta-regression did not identify a difference in incident LTBI based on travel duration and TB incidence in the destination country. Five studies reported cases of active TB, with an overall pooled estimate of 120.7 cases per 100 000 travellers. CONCLUSIONS We found that travelling HCWs were at highest risk of developing LTBI. Individual risk activities and travel purpose were most associated with risk of TB infection acquired during travel.
Corrosion rate evaluations of structural materials for a iodine-sulfur thermochemical water-splitting cycle

The iodine-sulfur thermochemical cycle for hydrogen production takes place in very corrosive environments. To evaluate the corrosion rate of structural materials, corrosion tests on Bunsen reaction environments were conducted using glass apparatus, which focused on welded area corrosions and crevice corrosions for the fabrication of equipment. Prepared test specimens of tantalum and zirconium were exposed to solutions consisting of HI, H{sub 2}SO{sub 4}, I{sub 2} and H{sub 2}O at 120 degrees C for 100 or 500 hours at the atmospheric pressure. Two types of solutions were employed to simulate the process environments of the Bunsen reaction. The compositions of the solutions were H{sub 2}SO{sub 4}:HI:H{sub 2}O:I{sub 2}=0.50:0.001:0.498:0.001 (weight ratio, H{sub 2}SO{sub 4}-rich phase) and H{sub 2}SO{sub 4}:HI:H{sub 2}O:I{sub 2}=0.001:0.10:0.099:0.8 (weight ratio, HI-rich phase). After the exposure, the corrosion rates were obtained by the weight loss of each specimen. For the tantalum, their welded area corrosions and crevice corrosions exhibit appropriate corrosion resistance (below 0.02 g/m{sup 2} hr) in both solutions. As for the zirconium, higher corrosion rates (0.02 to 0.05 g/m{sup 2} hr) were observed in the HI-rich phase on the crevice corrosions. Additionally, pitting corrosions were found on Zr after 500 hours of immersion. (authors)
An isomorphic three‐dimensional cortical model of the pig rostrum

Physiological studies of the last century mapped a somatosensory cortical gyrus representing the pig's rostrum. Here, we describe the extraordinary correspondence of this gyrus to the rostrum. The pig rostrum is packed with microvibrissae (~470 per hemi‐rostrum) and innervated by a prominent infraorbital nerve, containing about 80,000 axons. The pig's rostrum has three major skin‐folds. The nostrils have a rectangular medial wall and a funnel‐like lateral opening, nasal channels run obliquely from lateral (surface) to medial (inside). The rostrum gyrus mimics rostrum geometry in great detail. The putative representation of skin folds coincides with blood sinus and folds of the rostrum gyrus. The putative nostril representation is an oblique sulcus running from lateral (surface) to medial (inside). As observed in rodents, Layer 4 is thin in the nostril sulcus. The side of the nostril sulcus representing the medial wall of the nostril is rectangular, whereas the side of the nostril sulcus representing the lateral wall is funnel‐like. Proportions and geometry of the rostrum and the rostrum gyrus are similar, albeit with a collapsed nostril and a larger interindividual variability in the gyrus. The pig's cortical rostrum gyrus receives dense thalamic innervation, has a thin Layer 1 and contains roughly 8 million neurons. With all that, the rostrum gyrus looks like a model of the pig rostrum at a scale of ~1:2. Our findings are reminiscent of the raccoon cortex with its forepaw‐like somatosensory forepaw‐representation. Representing highly relevant afferents in three‐dimensional body‐part‐models might facilitate isomorphic cortical computations in large‐brained tactile specialists.
A Computationally Based Study of Polycyclic Nitramines and Their Precursors: Comparisons between Known and Notional Compounds

Abstract : A computationally based study was conducted to assess the potential viability of schemes proposed for employing cucurbiturils as precursors for the synthesis of polycyclic nitramines (PCNAs). One scheme involved reducing cucurbiturils to cucurbitaminals, then nitrolyzing them. The other involved hydrolyzing the cucurbiturils, then nitrating the secondary amine groups of the product. To assess the schemes viabilities, an attempt was made to establish correlations between properties of equilibrium molecular structures and stability for known compounds, then employ the correlations to predict the stabilities of intermediates and targets. However, strong correlations were not found. Moreover, even if more evidence supporting hypothesized correlations had been found, results for the intermediates and targets of interest suggest that the yields of these schemes are likely to be low (at best) and that the targets will be unstable. The attempt to answer questions regarding the feasibility of producing PCNAs from cucurbiturils prompted the design and modeling of other notional PCNAs. Two appear to warrant further investigation. One is 2,6,7-trinitro-2,6,7-triaza[2.2. 2]octane. It has a tris(nitramino) group. The other is a CL-20 analog with 4 C(H)C(H) groups and 4 nitramine groups.