Miracle-dz/UniFAR-FTUs huggingface dataset:
High-Resolution Transcriptomic Analyses of Sinorhizobium sp. NGR234 Bacteroids in Determinate Nodules of Vigna unguiculata and Indeterminate Nodules of Leucaena leucocephala

The rhizobium-legume symbiosis is a model system for studying mutualistic interactions between bacteria and eukaryotes. Sinorhizobium sp. NGR234 is distinguished by its ability to form either indeterminate nodules or determinate nodules with diverse legumes. Here, we presented a high-resolution RNA-seq transcriptomic analysis of NGR234 bacteroids in indeterminate nodules of Leucaena leucocephala and determinate nodules of Vigna unguiculata. In contrast to exponentially growing free-living bacteria, non-growing bacteroids from both legumes recruited several common cellular functions such as cbb3 oxidase, thiamine biosynthesis, nitrate reduction pathway (NO-producing), succinate metabolism, PHB (poly-3-hydroxybutyrate) biosynthesis and phosphate/phosphonate transporters. However, different transcription profiles between bacteroids from two legumes were also uncovered for genes involved in the biosynthesis of exopolysaccharides, lipopolysaccharides, T3SS (type three secretion system) and effector proteins, cytochrome bd ubiquinol oxidase, PQQ (pyrroloquinoline quinone), cytochrome c550, pseudoazurin, biotin, phasins and glycolate oxidase, and in the metabolism of glutamate and phenylalanine. Noteworthy were the distinct expression patterns of genes encoding phasins, which are thought to be involved in regulating the surface/volume ratio of PHB granules. These patterns are in good agreement with the observed granule size difference between bacteroids from L. leucocephala and V. unguiculata.
Cyber-deception and attribution in capture-the-flag exercises

Attributing the culprit of a cyber-attack is widely considered one of the major technical and policy challenges of cyber-security. The lack of ground truth for an individual responsible for a given attack has limited previous studies. Here, we overcome this limitation by leveraging DEFCON capture-the-flag (CTF) exercise data where the actual ground-truth is known. In this work, we use various classification techniques to identify the culprit in a cyberattack and find that deceptive activities account for the majority of misclassified samples. We also explore several heuristics to alleviate some of the misclassification caused by deception.
Acceleration of vegetation turnover and element cycling by mammalian herbivory in riparian ecosystems

1 We examined the effects of browsing by moose and snowshoe hares on vegetation structure, species composition, plant demography and element cycling in 25 riparian (willow) vegetation stands along the Tanana River, interior Alaska, across a 250‐km gradient that represented a fivefold range in moose densities (0.2–1.0 km−2). 2 Browsing frequency was much greater in areas with high moose densities. The combined browsing pressure (% of annual browse production consumed by herbivores) of moose (Alces alces) and snowshoe hares (Lepus americanus) on forage species was over fivefold greater in the high moose density areas (33%) than the low moose density areas (6%), reflecting the fivefold difference in moose densities. 3 Above‐ground biomass of preferred willow species was lower in high moose density areas, and the age structure of the vegetation was significantly skewed towards younger age classes. This shift in age structure was accompanied by higher proportion of dead to live ramets, indicating higher mortality under increased browsing pressure. Increasing browsing pressure favoured later‐successional species (Alnus tenuifolia and Populus balsamifera) on the landscape, as shown by both a reduction in the number and size of willow stands in high‐density areas. 4 High rates of fecal input resulted in a doubling of above‐ground N input in high moose density areas. The rates of carbon and nitrogen input from willow communities to the soil as mediated by moose herbivory were approximately fivefold and eightfold greater in high moose density areas than in low moose density areas, respectively. 5 Synthesis. The effects of herbivory were manifested at several ecological hierarchies, including the individual, the community, and the landscape. Across these spatial scales herbivory appears to accelerate the ecosystem turnover of carbon and nitrogen by a combination of both plant‐ and animal‐based processes.
Combining low-latency communication protocols with multithreading for high performance DSM systems on clusters

With the development of clusters based on high performance networks, it is now possible to design efficient Distributed Shared Memory systems. In this paper we present the approach we choose to implement a high performance DSM system on top of a cluster by combining the use of low-latency communication protocols (MPI-BIP on Myrinet networks) with multithreading approach (PM2). We present our approach called Distributed Objects Shared MemOry System (DOSMOS system), its design and experiments performed on various communication libraries (PVM, MPI) and on various networks (Ethernet, Myrinet).
Purified polyoma virus medium T antigen has tyrosine-specific protein kinase activity but no significant phosphatidylinositol kinase activity

Medium T antigen, the transforming protein of polyoma virus, is associated with pp60c-src and strongly activates its tyrosine-specific protein kinase activity. We investigated whether the medium T-pp60c-src complex is also associated with an activity that phosphorylates the membrane phospholipid phosphatidylinositol, as shown for pp60v-src and p68v-ros, the transforming proteins of Rous sarcoma virus and avian sarcoma virus UR2, respectively. Medium T was purified by affinity chromatography from extracts of polyoma virus-infected mouse fibroblasts. It was bound to antibodies against a peptide corresponding to the carboxy terminus of medium T and released from the immune complex with an excess of the same peptide. In a second step, the partially purified medium T was bound to antibodies against another peptide corresponding to an internal region of medium T and released with excess peptide. Further purification was carried out with a monoclonal antibody against pp60c-src. Samples from each purification step were examined for protein kinase and phosphatidylinositol kinase activity. The highly purified preparations of the medium T-pp60c-src complex showed very low levels of phosphatidylinositol kinase activity, and no difference between medium T from transforming viruses and nontransforming hr-t mutants was detected. In contrast, protein kinase activity was associated with medium T purified from transforming viruses but not from hr-t mutants.
Impact of telephonic interviews on persistence and daily adherence to insulin treatment in insulin-naïve type 2 diabetes patients: dropout study

Objective The objective of this study is to evaluate the impact of sequential telephonic interviews on treatment persistence and daily adherence to insulin injections among insulin-naïve type 2 diabetes patients initiated on different insulin regimens in a 3-month period. Methods A total of 1,456 insulin-naïve patients with type 2 diabetes (mean [standard deviation, SD] age: 56.0 [12.0] years, 49.1% were females) initiated on insulin therapy and consecutively randomized to sequential (n=733) and single (n=723) telephonic interview groups were included. Data on insulin treatment and self-reported blood glucose values were obtained via telephone interview. Logistic regression analysis was performed for factors predicting increased likelihood of persistence and skipping an injection. Results Overall, 76.8% patients (83.2% in sequential vs 70.3% in single interview group, (P<0.001) remained on insulin treatment at the third month. Significantly higher rate for skipping doses was noted in basal bolus than in other regimens (27.0% vs 15.0% for premixed and 15.8% basal insulin, respectively, P<0.0001). Logistic regression analysis revealed sequential telephonic interview (odds ratio [OR], 1.531; 95% confidence interval [CI], 1.093–2.143; P=0.013), higher hemoglobin A1c levels (OR, 1.090; 95% CI, 0.999–1.189; P=0.049), and less negative appraisal of insulin therapy as significant predictors of higher persistence. Basal bolus regimen (OR, 1.583; 95% CI, 1.011–2.479; P=0.045) and higher hemoglobin A1c levels (OR, 1.114; 95% CI, 1.028–1.207; P=0.008) were the significant predictors of increased likelihood of skipping an injection. Conclusion Our findings revealed positive influence of sequential telephonic interview, although including no intervention in treatment, on achieving better treatment persistence in type 2 diabetes patients initiating insulin.
On Generalized Strong Vector Variational-Like Inequalities in Banach Spaces

The purpose of this paper is to study the solvability for a class of generalized strong vector variational-like inequalities in reflexive Banach spaces. Firstly, utilizing Brouwer's fixed point theorem, we prove the solvability for this class of generalized strong vector variational-like inequalities without monotonicity assumption under some quite mild conditions. Secondly, we introduce the new concept of pseudomonotonicity for vector multifunctions, and prove the solvability for this class of generalized strong vector variational-like inequalities for pseudomonotone vector multifunctions by using Fan's lemma and Nadler's theorem. Our results give an affirmative answer to an open problem proposed by Chen and Hou in 2000, and also extend and improve the corresponding results of Fang and Huang (2006).
Comparative Population Assessments of Nautilus sp. in the Philippines, Australia, Fiji, and American Samoa Using Baited Remote Underwater Video Systems

The extant species of Nautilus and Allonautilus (Cephalopoda) inhabit fore-reef slope environments across a large geographic area of the tropical western Pacific and eastern Indian Oceans. While many aspects of their biology and behavior are now well-documented, uncertainties concerning their current populations and ecological role in the deeper, fore-reef slope environments remain. Given the historical to current day presence of nautilus fisheries at various locales across the Pacific and Indian Oceans, a comparative assessment of the current state of nautilus populations is critical to determine whether conservation measures are warranted. We used baited remote underwater video systems (BRUVS) to make quantitative photographic records as a means of estimating population abundance of Nautilus sp. at sites in the Philippine Islands, American Samoa, Fiji, and along an approximately 125 km transect on the fore reef slope of the Great Barrier Reef from east of Cairns to east of Lizard Island, Australia. Each site was selected based on its geography, historical abundance, and the presence (Philippines) or absence (other sites) of Nautilus fisheries The results from these observations indicate that there are significantly fewer nautiluses observable with this method in the Philippine Islands site. While there may be multiple possibilities for this difference, the most parsimonious is that the Philippine Islands population has been reduced due to fishing. When compared to historical trap records from the same site the data suggest there have been far more nautiluses at this site in the past. The BRUVS proved to be a valuable tool to measure Nautilus abundance in the deep sea (300–400 m) while reducing our overall footprint on the environment.
Bupleurum chinense Roots: a Bioactivity-Guided Approach toward Saponin-Type NF- κ B Inhibitors

Abstract The roots of Bupleurum chinense have a long history in traditional medicine to treat infectious diseases and inflammatory disorders. Two major compounds, saikosaponins A and D, were reported to exert potent anti-inflammatory activity by inhibiting NF-κB. In the present study, we isolated new saikosaponin analogues from the roots of B. chinese interfering with NF-κB activity in vitro. The methanol-soluble fraction of the dichloromethane extract of Radix Bupleuri was subjected to activity-guided isolation yielding 18 compounds, including triterpenoids and polyacetylenes. Their structures were determined by spectroscopic methods as saikogenin D (1), prosaikogenin D (2), saikosaponins B2 (3), W (4), B1 (5), Y (6), D (7), A (8), E (9), B4 (10), B3 (11), and T (12), saikodiyne A (13), D (14), E (15) and F (16), falcarindiol (17), and 1-linoleoyl-sn-glycero-3-phosphorylcholine (18). Among them, 4, 15, and 16 are new compounds, whereas 6, previously described as a semi-synthetic compound, is isolated from a natural source for the first time, and 13–17 are the first reports of polyacetylenes from this plant. Nine saponins/triterpenoids were tested for inhibition of NF-κB signaling in a cell-based NF-κB-dependent luciferase reporter gene model in vitro. Five of them (1, 2, 4, 6, and 8) showed strong (> 50%, at 30 µM) NF-κB inhibition, but also varying degrees of cytotoxicity, with compounds 1 and 4 (showing no significant cytotoxicity) presenting IC50 values of 14.0 µM and 14.1 µM in the cell-based assay, respectively.
Influence of dry‐season vegetation variability on Sahelian dust during 2002–2015

The drivers of dust emission interannual variability in North Africa, the largest dust source on Earth, are still debated. Early studies outlined the role of previous‐season rainfall and vegetation growth, while some recent studies emphasize the role of wind variability. Here we use a newly developed estimation of dry‐season nonphotosynthetic vegetation cover in the Sahel based on Moderate Resolution Imaging Spectroradiometer (MODIS) short‐wave infrared bands over the 2002–2015 period. The vegetation growth anomalies caused by variability of rainfall in June–September translate to anomalies of dry vegetation cover that persist throughout the dry season until May. These vegetation anomalies explain 43% (50%) of the year‐to‐year variance in Sahelian‐mean dry‐season aerosol optical depth (AOD) as derived from MODIS Deep Blue (Sun photometers). Similar explained variance is found with 10 m wind speed and dust uplift potential. The central Sahel proves more important than the western Sahel for dry‐season AOD variability.
A subresultant theory for Ore polynomials with applications

The subresultant theory for univariate commutative polynomials is generalized to Ore polynomials. The generalization includes: the subresultant theorem, gap structure, and subresultant algorithm. Using this generalization, we de ne Sylvester's resultant of two Ore polynomials, derive the respective determinantal formulas for the greatest common right divisor and least common left multiple of two Ore polynomials, and present a fraction-free version of the noncommutative extended Euclidean algorithm.
Nutritional value of raw Canavalia ensiformis and its utilization as partial replacement for soybean meal in the diet of Clarias gariepinus (Burchell, 1822) fingerlings

Abstract The nutritional value of raw Jack bean meal (Canavalia ensiformis) as a partial substitute for soybeans meal was investigated in this study. Preliminary investigation on nutrient composition revealed that lysine, histidine, and phenylalanine were significantly higher in C. ensiformis seed meal compared to soybean meal. However, crude protein and other essential amino acids were significantly lower. Feeding trial was then conducted to investigate the effect of replacing about 40% soybeans meal (at 58.8% inclusion) with C. ensiformis in the diet of Clarias gariepinus. The result obtained after 56 days revealed that fingerlings could tolerate up to 20% replacement without significant effect on growth and nutrient utilization. Beyond this, growth was significantly reduced. Survivals of the fish also follow a similar trend as stated above. It was concluded that dietary inclusion of raw C. ensiform meal should not be beyond 11% (or 20% replacement for soybeans meal included at 58.8%) in the diet of C. gariepinus.
Early Carotid Atherosclerosis in Healthy Middle‐Aged Women: A Follow‐up Study

Background and Purpose Few longitudinal data about early atherosclerotic lesions of the carotid arteries are available in general populations. The main purpose of this study was to investigate risk factors for development and regression of intimal-medial thickening and atheromatous plaques. Methods Initial and 2-year examinations of the carotid arteries with high-resolution B-mode ultrasonography were performed in 308 apparently healthy women aged 45 to 55 years. The development of new atheromatous plaques and new intimal-medial thickening and the disappearance of preexisting plaques and intimal-medial thickening defined the four outcomes of interest. Results The development of plaques occurred more frequently in women with intimal-medial thickening than in women with normal carotid arteries at baseline (14.4% versus 7.2%, P<.053). A regression was seen in 21.7% of the women with preexisting plaques. Development of intimal-medial thickening occurred in 47.5% of the women with normal carotid arteries whereas 20.2% of the women with preexisting intimal-medial thickening showed a regression of their lesions. Multiple logistic regression showed that smoking (regression coefficient ±SE: 1.281 ±0.450; P<.005), baseline levels of systolic blood pressure (regression coefficient ±SE: 0.031 ±0.015; P<.04) and apolipoprotein B (regression coefficient ±SE: 0.016±0.007; P<.03) were independently associated with the development of plaques, whereas the presence of an intimal-medial thickening did not reach the significance level (regression coefficient ±SE: 0.639±0.436; P<.15). Independent predictors of the development of intimal-medial thickening were age (regression coefficient ±SE: 0.124±0.058; P<.04) and, with a borderline significance level, (log)triglyc-erides (regression coefficient ±SE: 0.854±0.451; P<.06). Low levels of low-density lipoprotein cholesterol (regression coefficient ±SE: 0.027±0.009; P<.004) were associated with its regression. Conclusions This longitudinal study emphasizes the interest of B-mode ultrasonography in the monitoring of early carotid lesions. It gives further support to the hypothesis that intimal-medial thickening may be an early indicator of the atherosclerotic process.
Nutritional risk and anthropometric evaluation in pediatric liver transplantation

OBJECTIVE: To analyze the nutritional status of pediatric patients after orthotopic liver transplantation and the relationship with short-term clinical outcome. METHOD: Anthropometric evaluations of 60 children and adolescents after orthotopic liver transplantation, during the first 24 hours in a tertiary pediatric intensive care unit. Nutritional status was determined from the Z score for the following indices: weight/age, height/age or length/age, weight/height or weight/length, body mass index/age, arm circumference/age and triceps skinfold/age. The severity of liver disease was evaluated using one of the two models which was adequated to the patients' age: 1. Pediatric End-stage Liver Disease, 2. Model for End-Stage Liver Disease. RESULTS: We found 50.0% undernutrition by height/age; 27.3% by weight/age; 11.1% by weight/height or weight/length; 10.0% by body mass index/age; 61.6% by arm circumference/age and 51.0% by triceps skinfold/age. There was no correlation between nutritional status and Pediatric End-stage Liver Disease or mortality. We found a negative correlation between arm circumference/age and length of hospitalization. CONCLUSION: Children with chronic liver diseases experience a significant degree of undernutrition, which makes nutritional support an important aspect of therapy. Despite the difficulties in assessment, anthropometric evaluation of the upper limbs is useful to evaluate nutritional status of children before or after liver transplantation.
Texas Wintergrass and Buffalograss Response to Seasonal Fires and Clipping

Abstract There is increased interest in the use of summer-season fires to limit woody plant encroachment into grasslands, but effects of these fires on grasses are poorly understood. We quantified effects of repeated winter fires, repeated summer fires, and clipping (to simulate grazing) on aboveground total yield, live yield, and percentage of live tissue of C3 Texas wintergrass (Nassella leucotricha [Trin. & Rupr.] Pohl.), and C4 buffalograss (Buchloë dactyloides [Nutt.] Engelm.) in 2 experiments. Monospecific patches of each species were exposed to 1 of 3 fire treatments (no-fire, 2 winter fires in 3 years, or 2 summer fires in 3 years) and 1 of 2 clip treatments (no clip or clip once each spring). Experiment 1 evaluated effects of fire without grazing or clipping on late-growing season (late-season) yields. Late-season total yield of both species recovered from winter and summer fires within 1 or 2 growing seasons post-fire. By 3 years post-fire, Texas wintergrass late-season total yield was 2 times greater in the summer fire treatment than the winter fire or no-fire treatments, and buffalograss late-season total yield was 3 times greater in summer and winter fire treatments than in the no-fire treatment. Experiment 2 evaluated combined effects of fire and clipping the previous spring on spring-season yields. Clipping alone or with fire (summer or winter) reduced Texas wintergrass yields on more sample dates than occurred with buffalograss. By 3 years post-fire, buffalograss spring total yield was greater in all fire and fire + clip treatments than in the clip only or untreated controls. Results suggest: 1) both species were tolerant of summer fire, 2) fire in either season with or without clipping stimulated buffalograss production, and 3) buffalograss was more tolerant than Texas wintergrass to the combined effects of clipping + fire (either season).
Carmeltazite, ZrAl2Ti4O11, a New Mineral Trapped in Corundum from Volcanic Rocks of Mt Carmel, Northern Israel

The new mineral species carmeltazite, ideally ZrAl2Ti4O11, was discovered in pockets of trapped melt interstitial to, or included in, corundum xenocrysts from the Cretaceous Mt Carmel volcanics of northern Israel, associated with corundum, tistarite, anorthite, osbornite, an unnamed REE (Rare Earth Element) phase, in a Ca-Mg-Al-Si-O glass. In reflected light, carmeltazite is weakly to moderately bireflectant and weakly pleochroic from dark brown to dark green. Internal reflections are absent. Under crossed polars, the mineral is anisotropic, without characteristic rotation tints. Reflectance values for the four COM wavelengths (Rmin, Rmax (%) (λ in nm)) are: 21.8, 22.9 (471.1); 21.0, 21.6 (548.3), 19.9, 20.7 (586.6); and 18.5, 19.8 (652.3). Electron microprobe analysis (average of eight spot analyses) gave, on the basis of 11 oxygen atoms per formula unit and assuming all Ti and Sc as trivalent, the chemical formula (Ti3+3.60Al1.89Zr1.04Mg0.24Si0.13Sc0.06Ca0.05Y0.02Hf0.01)Σ=7.04O11. The simplified formula is ZrAl2Ti4O11, which requires ZrO2 24.03, Al2O3 19.88, and Ti2O3 56.09, totaling 100.00 wt %. The main diffraction lines, corresponding to multiple hkl indices, are (d in Å (relative visual intensity)): 5.04 (65), 4.09 (60), 2.961 (100), 2.885 (40), and 2.047 (60). The crystal structure study revealed carmeltazite to be orthorhombic, space group Pnma, with unit-cell parameters a = 14.0951 (9), b = 5.8123 (4), c = 10.0848 (7) Å, V = 826.2 (1) Å3, and Z = 4. The crystal structure was refined to a final R1 = 0.0216 for 1165 observed reflections with Fo > 4σ(Fo). Carmeltazite exhibits a structural arrangement similar to that observed in a defective spinel structure. The name carmeltazite derives from Mt Carmel (“CARMEL”) and from the dominant metals present in the mineral, i.e., Titanium, Aluminum and Zirconium (“TAZ”). The mineral and its name have been approved by the IMA Commission on New Minerals, Nomenclature and Classification (2018-103).