Miracle-dz/UniFAR-FTUs huggingface dataset:
Multipartite symbioses in fungus‐growing termites (Blattodea: Termitidae, Macrotermitinae) for the degradation of lignocellulose

Fungus‐growing termites are among the most successful herbivorous animals and improve crop productivity and soil fertility. A range of symbiotic organisms can be found inside their nests. However, interactions of termites with these symbionts are poorly understood. This review provides detailed information on the role of multipartite symbioses (between termitophiles, termites, fungi, and bacteria) in fungus‐growing termites for lignocellulose degradation. The specific functions of each component in the symbiotic system are also discussed. Based on previous studies, we argue that the enzymatic contribution from the host, fungus, and bacteria greatly facilitates the decomposition of complex polysaccharide plant materials. The host–termitophile interaction protects the termite nest from natural enemies and maintains the stability of the microenvironment inside the colony.
Cholesterol Efflux Capacity and Cardiovascular Disease: The Ludwigshafen Risk and Cardiovascular Health (LURIC) Study

(1) Background and Aims: Efforts to reduce coronary artery disease (CAD) by raising high-density lipoprotein (HDL) cholesterol (HDL-C) have not been uniformly successful. A more important factor than HDL-C may be cellular cholesterol efflux mediated by HDL, which has been shown to be associated with CAD. In this report, we analyzed the influence of cardiovascular biomarkers and risk factors on cholesterol efflux in a prospective observational study of patients referred to coronary angiography. (2) Methods: HDL-mediated efflux capacity was determined for 2468 participants of the Ludwigshafen Risk and Cardiovascular Health (LURIC) study who were referred to coronary angiography at baseline between 1997 and 2000. Median follow-up time was 9.9 years. Primary and secondary endpoints were cardiovascular and all-cause mortality, respectively. (3) Results: Cholesterol efflux strongly correlated with HDL-related markers including HDL cholesterol, HDL phospholipids, and apolipoproteins AI and AII, as well as HDL particle concentration, which was not seen for low density lipoprotein (LDL) markers including LDL cholesterol and apoB. Cholesterol efflux was associated negatively with C-reactive protein (CRP), fibrinogen, interleukin-6 (IL-6), and serum amyloid A. Cardiovascular mortality was higher in patients in the lowest cholesterol efflux quartile. This association was weakened, but not fully abolished, after adjustment for HDL cholesterol. (4) Conclusions: We demonstrate that cholesterol efflux was associated with HDL-composition as well as inflammatory burden in patients referred for coronary angiography, and that this inversely predicts cardiovascular mortality independently of HDL cholesterol.
Overexpression of DDR1 Promotes Migration, Invasion, Though EMT-Related Molecule Expression and COL4A1/DDR1/MMP-2 Signaling Axis

Purpose: Discoidin domain receptor 1 (DDR1) belongs to a novel class of receptor tyrosine kinases. Previous evidence indicates that DDR1 overexpression promotes the aggressive growth of bladder cancer (BC) cells. This study aimed to investigate the molecular mechanisms by which DDR1 influences BC. Methods: DDR1 was transfected into human BC RT4 cells. DDR1, COL4A1, and MMP-2 expression in 30 BC tissues and paired adjacent tissues were examined by real-time polymerase chain reaction (RT-PCR) and immunohistochemistry. Transwell assays were conducted to determine cell migration and invasion. RT-PCR and western blot (WB) were also used to measure the DDR1, COL4A1, MMP-2, and EMT-related gene (ZEB1 and SLUG) expression in RT4 cells after DDR1 overexpression. Results: COL4A1 and MMP-2 interacted with DDR1 in the PPI network. RT-PCR and immunohistochemistry results showed that both mRNA and protein levels of DDR1 and COL4A1 were significantly increased in BC tissue, while the expression of MMP-2 was increased only at the mRNA level (P < 0.05). Overexpression of DDR1 in RT4 cells significantly promoted their migratory and invasive capabilities in vitro (P < 0.05). Moreover, overexpression of DDR1 in RT4 cells increased the mRNA and protein expression of ZEB1, SLUG, COL4A1, and MMP-2 (P < 0.01). DDR1-mediated migration and invasion of RT4 cells were reversed after COL4A1-siRNA treatment. Conclusion: DDR1 may be a potential therapeutic target in BC patients.
CITCO as an Adjuvant Facilitates CHOP-Based Lymphoma Treatment in hCAR-Transgenic Mice

Non-Hodgkin’s lymphoma (NHL) is a malignant cancer originating in the lymphatic system with a 25–30% mortality rate. CHOP, consisting of cyclophosphamide (CPA), doxorubicin, vincristine, and prednisone, is a first-generation chemotherapy extensively used to treat NHL. However, poor survival rates among patients in advanced stages of NHL shows a need to improve this standard of care treatment. CPA, an integral component of CHOP, is a prodrug that requires CYP2B6-mediated bioactivation to 4-hydroxy-CPA (4-OH-CPA). The expression of CYP2B6 is transcriptionally regulated by the constitutive androstane receptor (CAR, NRi13). We have previously demonstrated that the induction of hepatic CYP2B6 by CITCO, a selective human CAR (hCAR) agonist, results in CHOP’s enhanced antineoplastic effects in vitro. Here, we investigate the in vivo potential of CITCO as an adjuvant of CPA-based NHL treatment in a hCAR-transgenic mouse line. Our results demonstrate that the addition of CITCO to the CHOP regimen leads to significant suppression of the growth of EL-4 xenografts in hCAR-transgenic mice accompanied by reduced expression of cyclin-D1, ki67, Pcna, and increased caspase 3 fragmentation in tumor tissues. CITCO robustly induced the expression of cyp2b10 (murine ortholog of CYP2B6) through hCAR activation and increased plasma concentrations of 4-OH-CPA. Comparing to intraperitoneal injection, oral gavage of CITCO results in optimal hepatic cyp2b10 induction. Our in vivo studies have collectively uncovered CITCO as an effective facilitator for CPA-based NHL treatment with a pharmacokinetic profile favoring oral administration, promoting CITCO as a promising adjuvant candidate for CPA-based regimens.
Cerebellar-limbic neurocircuit is the novel biosignature of physio-cognitive decline syndrome

Both physical and cognitive deficits occur in the aging process. We operationally defined the phenomenon as physio-cognitive decline syndrome (PCDS) and aimed to decipher its corresponding neuroanatomy patterns and neurocircuit. High resolution 3T brain magnetic resonance imaging (MRI) images from a community-dwelling longitudinal aging cohort were analysed. PCDS was defined as weakness (handgrip strength) and/or slowness (gait speed) concomitant with impairment in any cognitive domain (defined by 1.5 standard deviation below age, sex-matched norms), but without dementia or disability. Among 1196 eligible ≥ 50-year-old (62±9 years, 47.6%men) subjects, 15.9% had PCDS. Compared to the other participants, individuals with PCDS had significantly lower gray-matter volume (GMV) in the bilateral amygdala and thalamus, right hippocampus, right temporo-occipital cortex, and left cerebellum VI and V regions. The regions of reduced GMV in people with PCDS were similar between the middle-aged and older adults; whereas larger clusters with more extensive GMV-depleted regions were observed in ≥65-year-olds with PCDS. Diffusion-weighted tractography showed disrupted hippocampus-amygdala-cerebellum connections in subjects with PCDS. The neuroanatomic characteristics revealed by this study provide evidence for pathophysiological processes associated with concomitant physio-cognitive decline in the elderly. This neurocircuit might constitute a target for future preventive interventions.
Fem Simulation of Non-Isothermal Viscoelastic Fluids

Thermo-mechanically coupled transport processes of viscoelastic fluids are important components in many applications in mechanical and chemical engineering. The aim of this thesis is the development of efficient numerical techniques for incompressible, non-isothermal, viscoelastic fluids which take into account the multiscale behaviour in space and time, the multiphase character and significant geometrical changes. Based on special CFD techniques including adaptivity/local grid alignment in space/time and fast hierarchical FEM techniques, the result shall be a new CFD tool which has to be evaluated w.r. t. well-known benchmarks and experimental results. The advantages of such a method are numerous and lead to efficient and accurate solution with respect to different rheological models and type of nonlinearities. In addition, it gives us a great deal of flexibility not only in dealing with well known difficulties such as High Weissenberg Number Problem (HWNP) but also in treating any new rheological models in the coming future. Several benchmark problems of interest to industrial purposes are also proposed in validating the state of the art of the numerical method. keyword Monolithic Newton-multigrid, FEM, Non-isothermal, Viscoelastic flow, Oldroyd-B, Giesekus, Log-conformation reformulation (LCR).
Association between Household Exposure to Secondhand Smoke and Dental Caries among Japanese Young Adults: A Cross-Sectional Study

The long-term effects of secondhand smoke (SHS) on dental caries among Japanese young adults remain unclear. The purpose of this cross-sectional study was to evaluate whether household exposure to SHS is associated with dental caries in permanent dentition among Japanese young adults. The study sample included 1905 first-year university students (age range: 18–19 years) who answered a questionnaire and participated in oral examinations. The degree of household exposure to SHS was categorized into four levels according to the SHS duration: no experience (−), past, current SHS < 10 years, and current SHS ≥ 10 years. Dental caries are expressed as the total number of decayed, missing, and filled teeth (DMFT) score. The relationships between SHS and dental caries were determined by logistic regression analysis. DMFT scores (median (25th percentile, 75th percentile)) were significantly higher in the current SHS ≥ 10 years (median: 1.0 (0.0, 3.0)) than in the SHS—(median: 0.0 (0.0, 2.0)); p = 0.001). DMFT ≥ 1 was significantly associated with SHS ≥ 10 years (adjusted odds ratio: 1.50, 95% confidence interval: 1.20–1.87, p < 0.001). Long-term exposure to SHS (≥10 years) was associated with dental caries in permanent dentition among Japanese young adults.
Isotope Fractionation during Gas Chromatography Can Enhance Mass Spectrometry-Based Measures of 2H-Labeling of Small Molecules

Stable isotope tracers can be used to quantify the activity of metabolic pathways. Specifically, 2H-water is quite versatile, and its incorporation into various products can enable measurements of carbohydrate, lipid, protein and nucleic acid kinetics. However, since there are limits on how much 2H-water can be administered and since some metabolic processes may be slow, it is possible that one may be challenged with measuring small changes in isotopic enrichment. We demonstrate an advantage of the isotope fractionation that occurs during gas chromatography, namely, setting tightly bounded integration regions yields a powerful approach for determining isotope ratios. We determined how the degree of isotope fractionation, chromatographic peak width and mass spectrometer dwell time can increase the apparent isotope labeling. Relatively simple changes in the logic surrounding data acquisition and processing can enhance gas chromatography-mass spectrometry measures of low levels of 2H-labeling, this is especially useful when asymmetrical peaks are recorded at low signal:background. Although we have largely focused attention on alanine (which is of interest in studies of protein synthesis), it should be possible to extend the concepts to other analytes and/or hardware configurations.
LINC00473 rescues human bone marrow mesenchymal stem cells from apoptosis induced by dexamethasone through the PEBP1-mediated Akt/Bad/Bcl-2 signaling pathway

The inhibition of the proliferation and apoptosis of bone marrow-derived mesenchymal stem cells (BMSCs) triggered by the excessive use of glucocorticoids, is considered a potential mechanism for the pathogenesis of steroid-induced osteonecrosis of the femoral head (SONFH). Long non-coding RNAs (lncRNAs) have been proven to influence the proliferation, apoptosis and differentiation of BMSCs by regulating the expression of critical genes. A previous microarray analysis by the authors confirmed the significant downregulation of LINC00473 in human BMSCs (hBMSCs) from patients with SONFH. However, the underlying role and molecular mechanisms of LINC00473 on dexamethasone (Dex)-stimulated hBMSCs remains unknown. In the present study, the expression of LINC00473 was determined in the hBMSCs of patients with SONFH and control patients. In addition, the protective effects and underlying molecular mechanisms of LINC00473 in Dex-stimulated hBMSCs were investigated. The results revealed that LINC00473 expression was significantly down-regulated in hBMSCs from patients with SONFH compared with the controls, and that the upregulation of LINC00473 attenuated the inhibitory effects exerted by 1 µM Dex on the proliferation and apoptosis of hBMSCs. Moreover, the upregulation of LINC00473 significantly promoted the protein expression of phosphorylated (p-)Akt, p-Bcl-2-associated death promoter (p-Bad) and B-cell lymphoma 2 (Bcl-2), whereas it decreased the cleavage of caspase-3, thus preventing the Dex-induced apoptosis of hBMSCs. Of note, the regulatory effects of LINC00473 on the Akt/Bad/Bcl-2 signaling pathway and its anti-apoptotic effects were similar to those of SC79 (an Akt activator), and were inhibited by MK-2206 (an Akt inhibitor). In further experiments, it was found that the upregulation of LINC00473 markedly promoted the phosphorylation of Akt in Dex-stimulated hBMSCs, and increased the protein level of phosphatidylethanolamine-binding protein 1 (PEBP1). Alternatively, the promoting effect on Akt phosphorylation induced by LINC00473 was significantly attenuated following the knockdown of PEBP1. Furthermore, the upregulation of PEBP1 triggered a marked increase in the levels of Akt phosphorylation in Dex-stimulated hBMSCs, which was line with the upregulation of LINC00473. Taken together, the results of the present study demonstrate that LINC00473 has the ability to rescue hBMSCs from Dex-induced apoptosis through the PEBP1-mediated activation of the Akt/Bad/Bcl-2 signaling pathway.
Molecular evidence for the subfamilial status of Tetralobinae (Coleoptera: Elateridae), with comments on parallel evolution of some phenotypic characters

Tetralobinae is a distinct click-beetle lineage containing 78 species in seven genera. Adults are large-bodied, and larvae live in termite nests and are grub-like unlike typical elaterid wireworms. Their taxonomic position in the Elateridae has been unstable and they were treated either as a separate elaterid subfamily or a tribe within Agrypninae. Here, we provide the first molecular investigation of Tetralobinae to test their phylogenetic position using two nuclear and two mitochondrial molecular markers from three total taxa, one from each of the following genera: Tetralobus Lepeletier & Audinet-Serville, Sinelater Laurent, and Pseudotetralobus Schwarz. Two different datasets were analyzed, Elateridae (181 terminals) and Elateroidea (451 terminals), both composed by the earlier published datasets supplemented with the newly produced tetralobine sequences. The results suggest that Tetralobinae is the sister lineage to the remaining Elateridae and that warrants the subfamilial status instead of an subordinate position in the Agrypninae. Pseudotetralobus (Australia) was sister to the Tetralobus (Africa) + Sinelater (China) consistent with previously published morphological analysis. Additionally, we discuss the homoplastic phenotypic characters which were used for building the earlier click-beetle classification, and which indicated the relationships between Tetralobinae and Agrypninae.
A Look at Robustness and Stability of 1-versus 0-Regularization : Discussion of Papers by Bertsimas et al . and Hastie et al .

We congratulate the authors Bertsimas, Pauphilet and van Parys (hereafter BPvP) and Hastie, Tibshirani and Tibshirani (hereafter HTT) for providing fresh and insightful views on the problem of variable selection and prediction in linear models. Their contributions at the fundamental level provide guidance for more complex models and procedures.
8.4 RADIATIVE TRANSFER VALIDATION STUDIES USING AIRBORNE MEASUREMENTS OF THERMAL INFRARED RADIANCES

The launch of new satellite instruments such as the Atmospheric Infrared Sounder (AIRS) and the Infrared Atmospheric Sounding Interferometer (IASI) will allow the routine measurement of high spectral resolution thermal infrared radiances for the first time. With the high information content of these observations, increased accuracy in retrievals of important atmospheric properties such as temperature and humidity profiles becomes possible. However, a sophisticated understanding of the radiative transfer properties of the atmosphere is required for operational fast models, which are underpinned by a knowledge of the spectroscopic properties of atmospheric gas species. The HITRAN database (Rothman et al., 1998) is widely used as a comprehensive source of fundamental parameters such as transition line strengths, positions and widths. The verification of databases against observational data is critical to establish their validity in radiative transfer applications, and so we have sought to quantify differences between HITRAN 96 and the most recent edition HITRAN 2000 (http://www.hitran.com) in the infrared region. The performance of each database can be judged by the success of line-by-line radiative transfer calculations in reproducing observed spectral radiances. For such comparisons to be meaningful it is essential that simultaneous measurements of radiances and atmospheric profiles of temperature and constituent gas concentrations are made. We have utilized data collected during the Measurement of Tropospheric Humidity (MOTH) campaign, using the extensive instrumentation installed on the Met Office C-130 aircraft. Infrared radiances were recorded with the Airborne Research Interferometer Evaluation System (ARIES), while aircraft atmospheric profiles were used as input to the GENLN2 line-by-line radiative transfer code (Edwards, 1992). Accurate simulations are also dependent on a sophisticated model of the water vapor continuum, which plays a significant role across the infrared spectrum. The CKD 2.4 continuum model as formulated by Clough et al. (1989) is widely used for this purpose. Comparisons between ARIES spectra and GENLN2 calculations allow the effectiveness of the continuum model to be judged.
Industrial Policies and Economic Development

Many currently and previously developing countries have adopted industrial policies that push resources towards certain "strategic" sectors, and the economic reasoning behind such polices is not well understood. In this paper, I construct a model of a production network where firms purchase intermediate goods from each other in the presence of credit constraints. These credit constraints distort input choices, thereby reducing equilibrium demand for upstream goods and creating a wedge between the potential sales (“influence”) and actual sales by upstream sectors. I analyze policy interventions and show that, under weak functional form restrictions, the ratio between a sector’s influence and sales is a sufficient statistic that guides the choice of production and credit subsidies. Using firmlevel production data from China, I estimate my sufficient statistic for each sector and show that it correlates with proxy measures of government interventions into the sector. Using a panel of crosscountry input-output tables and sectoral production tax rates, I show that the tax rates for developing countries in Asia also correlate with the model-implied intervention measure. *Department of Economics, MIT. Email: liuer@mit.edu. †I am indebted to Daron Acemoglu and Abhijit Banerjee for their guidance and support throughout this project. I also thank Marios Angeletos, David Atkin, Vivek Bhattacharya, May Bunsupha, Esther Duflo, Sebastian Fanelli, John Firth, Greg Howard, Yan Ji, Pooya Molavi, Scott Nelson, Harry Di Pei, Jeff Picel, Frank Schilbach, Ludwig Straub, Tavneet Suri, Linh Tô, Ivan Werning, and especially Arnaud Costinot, Daniel Green, Alp Simsek, Jesse Shapiro, and Rob Townsend for conversations and helpful comments. All errors are of course my own.
Batch Normalized Convolution Neural Network for Liver Segmentation

With the huge innovative improvement in all lifestyles, it has been important to build up the clinical fields, remembering the finding for which treatment is done; where the fruitful treatment relies upon the preoperative. Models for the preoperative, for example, planning to understand the complex internal structure of the liver and precisely localize the liver surface and its tumors; there are various algorithms proposed to do the automatic liver segmentation. In this paper, we propose a Batch Normalization After All - Convolutional Neural Network (BATA-Convnet) model to segment the liver CT images using Deep Learning Technique. The proposed liver segmentation model consists of four main steps: pre-processing, training the BATA-Convnet, liver segmentation, and the postprocessing step to maximize the result efficiency. Medical Image Computing and Computer Assisted Intervention (MICCAI) dataset and 3DImage Reconstruction for Comparison of Algorithm Database (3D-IRCAD) were used in the experimentation and the average results using MICCAI are 0.91% for Dice, 13.44% for VOE, 0.23% for RVD, 0.29mm for ASD, 1.35mm for RMSSD and 0.36mm for MaxASD. The average results using 3DIRCAD dataset are 0.84% for Dice, 13.24% for VOE, 0.16% for RVD, 0.32mm for ASD, 1.17mm for RMSSD and 0.33mm for MaxASD.
Drivers of Market-Oriented Land Use Decisions Among Farm Households in Nigeria

In recent times, the Nigerian Government has devised strategies aimed at intensifying smallholder transformation for enhanced food security, employment creation and poverty reduction. However, despite these efforts, the process of agricultural commercialisation in Nigeria has not progressed as fast as expected. Consequently, this study examines agricultural commercialisation in Nigeria with the aim of establishing factors that are constraining commercialisation and identifying potential policy levers that can be used to fast-track the process
Volatile organic compounds in the atmosphere

Sources, Distributions, and Fates of VOCs in the Atmosphere Atmospheric VOCs from Natural Sources The UK Hydrocarbon Monitoring Network Source Inventories and Control Strategies for VOCs Gas Phase Tropospheric Chemistry of Organic Compounds Alternatives to CFCs and their Behaviour in the Atmosphere Volatile Organic Compounds in Indoor Air Volatile Organic Compounds: The Development of UK Policy Subject Index.
An Investigation into the Effects of Traumatic Brain Injury on Speech and Gait

Even mild traumatic brain injury (TBI) can lead to permanent damage if not treated immediately. In order to provide faster and more convenient methods to monitor TBI, speech and gait were explored as concussion indicators. Smartphones were used as sensors to record audio and acceleration data on the speech and gait of ten concussed and twelve non-concussed participants. Data from the two groups was statistically analyzed to determine significant differences with the hope that it could eventually lead to a more efficient method of diagnosing concussions. Although collecting speech and gait data through the smartphone was quick and convenient, there were no statistically significant differences found between the means, standard deviation, kurtosis, and skewness of the two groups. An Investigation into the Effects of Traumatic Brain Injury on Speech and Gait 3