Miracle-dz/UniFAR-FTUs huggingface dataset:
3D Printed Polyurethane Scaffolds for the Repair of Bone Defects

Critical-size bone defects are those that will not heal without intervention and can arise secondary to trauma, infection, and surgical resection of tumors. Treatment options are currently limited to filling the defect with autologous bone, of which there is not always an abundant supply, or ceramic pastes that only allow for limited osteo-inductive and -conductive capacity. In this study we investigate the repair of bone defects using a 3D printed LayFomm scaffold. LayFomm is a polymer blend of polyvinyl alcohol (PVA) and polyurethane (PU). It can be printed using the most common method of 3D printing, fused deposition modeling, before being washed in water-based solutions to remove the PVA. This leaves a more compliant, micro-porous PU elastomer. In vitro analysis of dental pulp stem cells seeded onto macro-porous scaffolds showed their ability to adhere, proliferate and form mineralized matrix on the scaffold in the presence of osteogenic media. Subcutaneous implantation of LayFomm in a rat model showed the formation of a vascularized fibrous capsule, but without a chronic inflammatory response. Implantation into a mandibular defect showed significantly increased mineralized tissue production when compared to a currently approved bone putty. While their mechanical properties are insufficient for use in load-bearing defects, these findings are promising for the use of polyurethane scaffolds in craniofacial bone regeneration.
Multi-Echo Quantitative Susceptibility Mapping for Strategically Acquired Gradient Echo (STAGE) Imaging

Purpose To develop a method to reconstruct quantitative susceptibility mapping (QSM) from multi-echo, multi-flip angle data collected using strategically acquired gradient echo (STAGE) imaging. Methods The proposed QSM reconstruction algorithm, referred to as “structurally constrained Susceptibility Weighted Imaging and Mapping” scSWIM, performs an ℓ1 and ℓ2 regularization-based reconstruction in a single step. The unique contrast of the T1 weighted enhanced (T1WE) image derived from STAGE imaging was used to extract reliable geometry constraints to protect the basal ganglia from over-smoothing. The multi-echo multi-flip angle data were used for improving the contrast-to-noise ratio in QSM through a weighted averaging scheme. The measured susceptibility values from scSWIM for both simulated and in vivo data were compared to the: original susceptibility model (for simulated data only), the multi orientation COSMOS (for in vivo data only), truncated k-space division (TKD), iterative susceptibility weighted imaging and mapping (iSWIM), and morphology enabled dipole inversion (MEDI) algorithms. Goodness of fit was quantified by measuring the root mean squared error (RMSE) and structural similarity index (SSIM). Additionally, scSWIM was assessed in ten healthy subjects. Results The unique contrast and tissue boundaries from T1WE and iSWIM enable the accurate definition of edges of high susceptibility regions. For the simulated brain model without the addition of microbleeds and calcium, the RMSE was best at 5.21ppb for scSWIM and 8.74ppb for MEDI thanks to the reduced streaking artifacts. However, by adding the microbleeds and calcium, MEDI’s performance dropped to 47.53ppb while scSWIM performance remained the same. The SSIM was highest for scSWIM (0.90) and then MEDI (0.80). The deviation from the expected susceptibility in deep gray matter structures for simulated data relative to the model (and for the in vivo data relative to COSMOS) as measured by the slope was lowest for scSWIM + 1%(−1%); MEDI + 2%(−11%) and then iSWIM −5%(−10%). Finally, scSWIM measurements in the basal ganglia of healthy subjects were in agreement with literature. Conclusion This study shows that using a data fidelity term and structural constraints results in reduced noise and streaking artifacts while preserving structural details. Furthermore, the use of STAGE imaging with multi-echo and multi-flip data helps to improve the signal-to-noise ratio in QSM data and yields less artifacts.
Persistent Last-mile Congestion: Not so Uncommon

Last-mile is the centerpiece of broadband connectivity, as poor last-mile performance generally translates to poor quality of experience. In this work we investigate last-mile latency using traceroute data from RIPE Atlas probes located in 646 ASes and focus on recurrent performance degradation. We find that in normal times probes in only 10% ASes experience persistent last-mile congestion but we recorded 55% more congested ASes during the COVID-19 outbreak. Persistent last-mile congestion is not uncommon, it is usually seen in large eyeball networks and may span years. With the help of CDN access log data, we dissect results for major ISPs in Japan, the most severely affected country in our study, and ascertain bottlenecks in the shared legacy infrastructure.
Diets of coyotes near the boundary of Saguaro National Monument and Tucson, Arizona

Suburban developments border the NW boundary of Saguaro National Monument East (SNM), a protected area for wildlife. Developments at this boundary have created an environment with potentially different sources of food for coyotes (Canis latrans). How coyotes use food resources at this boundary has not been described. Our objectives were to estimate and compare diets of coyotes living near suburban and rural areas of SNM to determine if suburban development influenced feeding patterns of coyotes in the Sonoran desert. To accomplish these objectives, we collected and analyzed coyote scats from an area of SNM that bordered a suburban landscape and compared them to scats from a rural area adjacent to SNM. The 14 km2 suburban area encompassed the NW corner of SNM. Housing density on adjacent residential lands was approximately 0.4 house/ ha. The 12.5 km2 rural area bordered the S boundary of SNM. Minimum airline distance between the two sites was 5.3 km. Topography and climate were similar in both areas. Similar sub-associations of Sonoran desert-scrub existed in both areas. Hunting, trapping, and livestock grazing were prohibited on the suburban site, but permitted on the rural site. Based on concurrent
Out of Sight, Not Out of Mind: A User-View on the Criticality of the Submarine Cable Network

Nearly all international data is carried by a mesh of submarine cables connecting virtually every region in the world. It is generally assumed that Internet services rely on this submarine cable network (SCN) for backend traffic, but that most users do not directly depend on it, as popular resources are either local or cached nearby. In this paper, we study the criticality of the SCN from the perspective of end users. We present a general methodology for analyzing the reliance on the SCN for a given region, and apply it to the most popular web resources accessed by users in 63 countries from every inhabited continent, collectively capturing ≈80% of the global Internet population. We find that as many as 64.33% of all web resources accessed from a specific country rely on the SCN. Despite the explosive growth of data center and CDN infrastructure around the world, at least 28.22% of the CDN-hosted resources traverse a submarine cable.
Manifestations of the Cretaceous High Arctic Large Igneous Province in Svalbard

Major Cretaceous Large Igneous Provinces (LIPs, e.g., Kerguelen and Ontong Java) show Aptian magmatic peaks and are linked to global mantle overturning and anomalous surface conditions. Widespread Cretaceous igneous activity in the High Arctic has recently been identified as a LIP. Exposed components on Svalbard, Franz Josef Island, adjacent shelf areas, Axel Heiberg and Ellesmere Islands, and perhaps North Greenland, cover several hundred thousand square kilometers and were peripheral to a LIP center at the Alpha Ridge. Manifestations of LIP development on Svalbard include (1) extensive sills, rare dikes, and extrusives in the east, (2) slow regression within the upper part of thick, black shales punctuated by locally abrupt uplift, with overlying coastal plain sandstones, (3) development of a regional, Late Cretaceous, low‐angle unconformity associated with a second regression, and (4) a widespread Early Aptian transition from quartz arenites to lithic arenites and feldspathic sandstones reflecting new northern volcanic source terranes. The unconformity likely reflects LIP thermal doming with >1 km of erosion. The sedimentologic record provides important insight into this LIP since much of it is inaccessible or eroded. Analysis of published geochronology indicates magmatism within a 135–90 Ma window, with more detailed interpretations being problematic. Two regressions suggest two pulses of igneous activity (Barremian and Albian). Multiple pulses have been documented for other LIPs and may result from a deep and large plume. Present evidence that magmatism was coeval in Svalbard and Franz Josef Land is inconsistent with a hotspot track hypothesis and suggestive of a large initial plume head.
Male zebra finches have limited ability to identify high-fecundity females

Lay Summary In species where males contribute substantially to parental care, males are expected to be choosy. Males should benefit from selecting a female of high fecundity, but it is unclear to what extent males are able to judge female fecundity before breeding. Here we show that male zebra finches seem to have only limited abilities to identify the better mate when faced with a choice between extremes in terms of female fecundity.
Small mammal abundance and seed predation across boundaries in a restored‐grazed woodland interface

Passive restoration is an effective tool for the maintenance and conservation of biodiversity. Often areas in recovery are immersed in a matrix of land uses, in which the expansion and intensification of human activities exert new visible pressures at their boundaries. The degree of connectivity between these areas and their peripheral lands can be analyzed by mobile link species, organisms that actively move in the landscape by connecting areas to one another through their functional roles. We focus our design on the interface generated by the long‐term restoration area and surrounding grazing lands. We analyze the changes on boundary structure, small mammal abundance, and on the function of native seed dispersal by these vertebrate species. We captured small mammals and determined seed removal of Prosopis flexuosa at three distances inside and outside a fence that delineates passively restored and currently grazed areas. Our results indicate that small rodents find more suitable habitats at the site under restoration than in grazing lands. The restored‐grazing interface shows a decrease in small mammal abundance from the protected area to the grazed lands. From a functional perspective, an increase in small mammal abundance results in an increase in their seed removal activity with implications for seed fate, because the long‐term recovery of vegetation could enhance seed predation on a native tree species.
Mechanical Implications of Creep and Partial Coupling on the World's Fastest Slipping Low‐Angle Normal Fault in Southeastern Papua New Guinea

We use densely spaced campaign GPS observations and laboratory friction experiments on fault rocks from one of the world's most rapidly slipping low‐angle normal faults, the Mai'iu fault in Papua New Guinea, to investigate the nature of interseismic deformation on active low‐angle normal faults. GPS velocities reveal 8.3 ± 1.2 mm/year of horizontal extension across the Mai'iu fault, and are fit well by dislocation models with shallow fault locking (above 2 km depth), or by deeper locking (from ~5–16 km depth) together with shallower creep. Laboratory friction experiments show that gouges from the shallowest portion of the fault zone are predominantly weak and velocity‐strengthening, while fault rocks deformed at greater depths are stronger and velocity‐weakening. Evaluating the geodetic and friction results together with geophysical and microstructural evidence for mixed‐mode seismic and aseismic slip at depth, we find that the Mai'iu fault is most likely strongly locked at depths of ~5–16 km and creeping updip and downdip of this region. Our results suggest that the Mai'iu fault and other active low‐angle normal faults can slip in large (Mw > 7) earthquakes despite near‐surface interseismic creep on frictionally stable clay‐rich gouges.
Growth and physiological responses of Shorea materialis Ridl. seedlings to various light regimes and fertilizer levels under nursery condition

Relative light intensity (RLI) is one of the most significant factors that affect plant growth by controlling physiological traits of plants in terms of photosynthesis, respiration, stomatal conductance, and chlorophyll synthesis, among others. An experiment was conducted in the shade house and open area to determine the effect of three light intensities, viz. 30%, 50% and 100% RLI, and three levels of NPK fertilizer, viz. 0,1 and 2 g. plant-1 month-1 on the growth and physiological traits of Shorea materialis seedlings. During the six-months study period, survival percentage, growth performance and chlorophyll content of the species were monitored every three months, while other physiological parameters, such as photosynthetic rate, stomatal conductance, and stomatal density were recorded at the end of the experiment. The results showed that survival percentage of the seedlings was not significantly affected by different light conditions and fertilizer levels, and it was 100% for all treatment combinations. On the other hand, growth and physiological properties except stomatal density were significantly affected by both the above factors. The seedlings growing under 30% to 50% RLI were significantly better than those under full sunlight, in terms of height increment, diameter increment, leaf number increment, chlorophyll content, photosynthetic rate and stomatal conductance. In addition, the seedlings treated with 1 g NPK were significantly better than the control for photosynthetic rate and stomatal conductance. However, the seedlings fertilized with 2 g NPK were significantly greater than the control, in the matter of height increment, leaf number increment, chlorophyll content. Generally, the species should be planted under 30 to 50% RLI with 1 to 2 g of NPK (monthly) to produce a healthy and high growth of the species.
Functional and phenotypic profiling of innate immunity during Salmonella infection

36 Introduction . 36 Materials & methods . 38 Results . 39 Discussion . 45 Acknowledgements . 47 DTU – Systems Biology PhD thesis Rikke Brandt viii References . 49 3 Salmonella Typhimurium-induced accumulation and regulation of plasmacytoid dendritic cells, myeloid dendritic cells and macrophages in gut-associated tissue during early-stage infection . 53 Abstract . 54. 54 Introduction . 54 Materials & methods . 55 Results . 57 Discussion . 68 References . 72 4 Integration of functional and genomic signatures from gut-associated bacteria reveals phylaspecific entities encoding immune inflammatory abilities . 77 Abstract . 78. 78 Introduction . 78 Materials & methods . 79 Results . 82 Discussion . 91 Acknowledgements . 95 References . 96 5 Summarising discussion. 102 References . 105 Appendix – Some putative prebiotics increase the severity of Salmonella enterica serovar Typhimurium infection in mice . 106 DTU – Systems Biology PhD thesis Rikke Brandt
Suitability of Wild Oat (Avena fatua), False Cleavers (Galium spurium), and Volunteer Canola (Brassica napus) for Harvest Weed Seed Control in Western Canada

As chemical management options for weeds become increasingly limited due to selection for herbicide resistance, investigation of additional nonchemical tools becomes necessary. Harvest weed seed control (HWSC) is a methodology of weed management that targets and destroys weed seeds that are otherwise dispersed by harvesters following threshing. It is not known whether problem weeds in western Canada retain their seeds in sufficient quantities until harvest at a height suitable for collection. A study was conducted at three sites over 2 yr to determine whether retention and height criteria were met by wild oat, false cleavers, and volunteer canola. Wild oat consistently shed seeds early, but seed retention was variable, averaging 56% at the time of wheat swathing, with continued losses until direct harvest of wheat and fababean. The majority of retained seeds were >45 cm above ground level, suitable for collection. Cleavers seed retention was highly variable by site-year, but generally greater than wild oat. The majority of seed was retained >15 cm above ground level and would be considered collectable. Canola seed typically had >95% retention, with the majority of seed retained >15 cm above ground level. The suitability ranking of the species for management with HWSC was canola > cleavers > wild oat. Efficacy of HWSC systems in western Canada will depend on the target species and site- and year-specific environmental conditions. Nomenclature: False cleavers, Galium spurium L. GALSP; volunteer canola, Brassica napus L. BRSNN; wild oat, Avena fatua L. AVEFA; fababean, Vicia faba L. ; wheat, Triticum aestivum L.
The Role of Blueschist Stored in Shallow Lithosphere in the Generation of Postcollisional Orogenic Magmas

In regions with small ocean plates and continental blocks, such as the Mediterranean in the Cenozoic and modern Indonesia, many blueschists may be stored at shallow depth in the mantle lithosphere that is newly formed during the amalgamation of small continental blocks and oceans. Melting of these blueschists at low pressures in the mixed lithosphere of this type during postcollisional relaxation may be involved in the generation of postcollisional orogenic magmas. Here, we have conducted a series of melting experiments on three blueschist samples with differing protoliths at 800–850°C, 2 GPa to investigate phase relations, mineral compositions, and trace element partitioning (using laser ablation‐inductively coupled plasma‐mass spectrometry [LA‐ICP‐MS]/nanoscale secondary ion mass spectrometry [NanoSIMS]), including the first results for clinozoisite. Dacitic/rhyolitic melts (SiO2 60 to 66 wt%) containing ~13 wt% volatiles are produced in all runs. Mn‐rich and Mn‐poor almandine garnets exhibit distinct rare earth element (REE) distribution patterns, while Mn‐rich garnets are effective preconcentrators of heavy REEs (HREEs) for later metamorphic processes. Melts produced from fluid‐affected blueschists of terrigenous origin show the most large‐ion lithophile element (LILE) enrichment, whereas those from terrigenous blueschists with no fluid history exhibit the lowest K/Th and Ba/Th and strongest Ce/Pb and Nb/U fractionations. Melts of blueschists derived from mid‐ocean ridge basalt (MORB) have relatively consistent, MORB‐like Ba/Th and Nb/U (~3) but the lowest Ce/Pb ratios (3.3). V/Sc and Zr/Hf ratios remain constant at ≥850°C regardless of the origin of the blueschist. Dehydration melting in new mantle lithosphere where blueschist is stored at shallow depth will significantly affect trace element behavior and should be considered carefully when examining chemical cycling and magmatism in postcollisional orogenic settings.
Bathing in Bacteria: Mycobacteria Relative Abundance on Showerhead Biofilms

Mycobacterium is a genus of Actinobacteria that contains many human pathogens, causing diseases such as tuberculosis, leprosy, and nontuberculous mycobacteria (NTM) lung disease. Diagnosed cases of NTM lung disease, are increasing rapidly across the United States. Recent studies have indicated that this respiratory infection is acquired through the inhalation of aerosolized mycobacteria derived from the biofilms found on the inside of household showerheads. To asses the factors that influence mycobacteria abundance on the interior biofilms of showerheads we analyzed bacterial and protistan communities from showerhead samples gathered across the United States. Further, we investigated water chemistry, specifically total chorine concentration and pH, and geographical variables to better understand the factors influencing the relative abundance of mycobacteria. After analyzing 191 samples, we found that Mycobacterium was the most common genus in showerhead biofilms, with a mean relative abundance of 19.2%. We found that mycobacteria were more abundant in biofilms with water sourced from municipal water than from well-water. This could be due to the higher chlorine content of municipal water, as mycobacteria are known to have mechanisms to resist chlorine. This is corroborated by the fact that mycobacteria were more abundant in samples with higher total chlorine concentrations. Mycobacterial abundances were not influenced by the pH of the water, the geographical location of the sample, or the relative abundance of free-living amoebas (FLA). Our results indicate that showerhead biofilms from chlorinated, municipal water supplies are more likely to contain mycobacteria. This indicates that individuals using these
Zur Frage der direkten oder indirekten Schädigung von Rebenwurzeln bei Befall durch die Reblaus ( Dactylosphaera vitifolii Shimer)

Is damage of phylloxera infested grapevine roots caused directly or indirectly? Disinfected eggs of phylloxera ( Dactylosphaera vitifolii SHIMER) were transferred to rooted explants of Vitis vinifera shoots (cv. Silvaner) reared under sterile conditions. Aerial rootlets which showed injuries in consequence of the insect's infestation proved to be free of microorganisms. lt is concluded, therefore, that damage of grapevine roots is pr imarily due to the activity of phylloxera itself, especially to abnormous growth and disturbance of metabolism in the affected plant tissues. Microorganisms occurring in root galls of naturally growing vines are considered to be secondary parasites or saprophytes.
MULTICORE SCHEDULING BASED ON LEARNING FROM OPTIMIZATION MODELS

Scheduling for multicore computer systems is a challenge since subsets of cores may share resources, such as a cache. Performance for workloads may therefore vary depending on which tasks are scheduled to run on the same subset of cores. There is therefore a need for contention-aware scheduling. Our study involves implementation of an optimal multicore scheduler which has perfect prediction of negative consequences of all combinations of tasks scheduled on the hardware platform we are using. It uses an Integer Program. We show that it is indeed optimal for our workloads, supporting its authors’ claims. We also implemented a scheduler which uses a combination of a machine learning model (M5 Prime) and Linear Programming to schedule tasks on CPU cores and compared it to a state-of-the-art scheduler known as Distributed Intensity (DI). Some workloads exhibited moderate improvements in unfairness, but not much in run-time. A scheduler based on another machine learning model was implemented, this time a Multilayer Perceptron (MLP). To do this, we had to generate workloads for the Optimal Scheduler, store its decision for various types of workloads, and train a Multilayer Perceptron model on this data. We then implemented a scheduler with the Multilayer Perceptron model, which tries to mimic the decision of the Optimal Scheduler. Our re-sults show that our scheduler is better than DI in 7 out of 9 test workloads (mostly by 10%), and approximately equal to the Optimal Scheduler in 6 out of 9 test workloads (exactly equal in 4). The MLP scheduler is faster than the Optimal Scheduler by a wide margin, and faster than the Linear Programming scheduler.