Miracle-dz/UniFAR-FTUs huggingface dataset:
The blue light-dependent LOV-protein LdaP of Dinoroseobacter shibae acts as antirepressor of the PpsR repressor, regulating photosynthetic gene cluster expression

In the marine α-proteobacterium Dinoroseobacter shibae more than 40 genes of the aerobic anoxygenic photosynthesis are regulated in a light-dependent manner. A genome-wide screen of 5,605 clones from a D. shibae transposon library for loss of pigmentation and changes in bacteriochlorophyll absorbance identified 179 mutant clones. The gene encoding the LOV-domain containing protein Dshi_1135 was identified by its colorless phenotype. The mutant phenotype was complemented by the expression of a Dshi_1135-strep fusion protein in trans. The recombinantly produced and chromatographically purified Dshi_1135 protein was able to undergo a blue light-induced photocycle mediated by bound FMN. Transcriptome analyses revealed an essential role for Dshi_1135 in the light-dependent expression of the photosynthetic gene cluster. Interactomic studies identified the repressor protein PpsR as an interaction partner of Dshi_1135. The physical contact between PpsR and the Dshi_1135 protein was verified in vivo using the bacterial adenylate cyclase-based two-hybrid system. In addition, the antirepressor function of the Dshi_1135 protein was demonstrated in vivo testing of a bchF-lacZ reporter gene fusion in a heterologous Escherichia coli-based host system. We therefore propose to rename the Dshi_1135 protein to LdaP (light-dependent antirepressor of PpsR). Using the bacterial two-hybrid system, it was also shown that cobalamin (B12) is essential for the interaction of the antirepressor PpaA with PpsR. A regulatory model for the photosynthetic gene cluster in D. shibae was derived, including the repressor PpsR, the light-dependent antirepressor LdaP and the B12-dependent antirepressor PpaA.
Flows to Swedish Food Chain, Fertilizer Value, Effect on Mycorrhiza and Environmental Impact of Reuse

Phosphorus is an essential element for plants, animals and humans and is also a scarce resource as a raw material for fertilizer production. The flows of phosphorus to and from Swedish agriculture and food chain was investigated with a material flow analysis (MFA). The fertilizer value of recycled phosphorus in chemically precipitated sewage sludge, biological sludge, mineral fertilizer and ash was investigated in a three-year field experiment. The impact of different phosphorus fertilizers on arbuscular mycorrhiza (AM) was studied in field and pot experiments, and the environmental impact of different phosphorus fertilizers was evaluated by Life Cycle Assessment (LCA). The results showed that Sweden has a positive phosphorus balance, but that phosphorus is concentrated on farms with more than one animal unit per hectare. Furthermore, the calculations were made on recent production and if Sweden increases the level of self-sufficiency, more phosphorus would be needed in the system. In a long-term perspective, the form of phosphorus fertilizer used seems to be less important than maintaining soil phosphorus content to ensure phosphorus delivery to the crop when conditions in terms of moisture, temperature etc. are optimal. Easily soluble phosphorus in mineral fertilizer can be essential in a short-term perspective under dry conditions, or on phosphorus-deficient soils. This thesis shows that with balanced phosphorus fertilization, it is possible to achieve good yield without compromising the possibilities for AM fungi to colonize roots. Phosphorus recovery from ash is costly in terms of both energy and carbon dioxide emissions. The most efficient option for sewage sludge is to use it directly on farmland, but associated cadmium addition to soils can be a problem. The cadmium imports with food and feed to Sweden are currently unknown. Nitrogen is a valuable nutrient and is energy-demanding to replace, so fertilization systems that can keep nitrogen in usable form for production are preferable. It was concluded that the energy and carbon dioxide bound during photosynthesis should be assigned to agricultural production and not the product user, e.g. a sludge incineration facility. Production of bioenergy should include all products that contain energy bound by photosynthesis, not only products used for fuel and heating.
Novel Control Scheme of Three-Phase Six-Level Hybrid Flying-Capacitor Inverters With Self-Balancing Capability

In this paper, a novel control scheme is proposed for the recently developed six-level hybrid flying-capacitor inverter. In the conventional scheme, an auxiliary balancing circuit is required to regulate the voltages of split DC-link capacitors. This results in the increased device count and converter volume, and thus diminishes the competitiveness of this topology. In order to eliminate these auxiliary components, a novel control scheme is proposed based on zero-sequence voltage (ZSV) injection to the phase-shifted modulation voltages. This method has enabled a simultaneous control of all split DC-link and flying capacitor voltages through the regulation of closely-linked key parameters affecting these voltages, resulting in the self-balancing capability with low voltage ripples (lower than 10 % of the references). The proposed technique has been verified with simulation and experimental results.
Analysis and Detection of Jamming Attacks in an All-Optical Network

Existing supervisory schemes which can be used for detecting jamming attacks in all-optical networks are mostly based on average power detection and the use of pilot signals. We point out that these methods are not adequate to handle all types of jamming attacks. Based on a newly designed attack detection device at a network node, a novel attack detection scheme against jamming attacks is proposed. Preliminary results on the performance of the proposed attack detection scheme are given for both in-band and out-of-band jamming attacks. To analyze the performance of the attack detection scheme in further detail, we find, under certain conditions, the worst case in-band jamming attack scenarios which correspond to the smallest probabilities of being detected for a given value of average degraded bit error rate. We then investigate how our proposed attack detection scheme performs under the worst case in-band jamming attack scenarios. Finally, we make some modification to our attack detection scheme to improve its performance. Thesis Supervisor: Dr. Muriel M6dard Title: MIT Lincoln Laboratory Staff Thesis Supervisor: Robert G. Gallager Title: Professor of EECS Acknowledgments I wish to express my utmost gratitude to Dr. Muriel M6dard who closely supervised my master thesis from the very beginning to the very end. Her invaluable advice, her patience as well as her kindness helped make this work possible. I also wish to thank professor Robert Gallager for his insightful comments on various parts of the thesis, professor Amos Lapidoth for the research experience in my first year of the graduate study, and the MIT EECS Department together with the Advanced Networks Group of MIT Lincoln Laboratory who provided me with financial supports. This master thesis is devoted to my beloved family and my dearest Chaliga.
ESTIMATION OF THE ASYMMETRIC VERTICAL VARIATION OF THE SOUTHERN AND NORTHERN HEMISPHERES OF THE EARTH

In previous studies, the northern hemisphere of the Earth is considered to be in compression while the southern one is in expansion. In this study, based on three different methods, we calculate average vertical variations of the two hemispheres from velocity field data under the ITRF2008 (International Terrestrial Reference Frame 2008) solution. Results show that the northern hemisphere is in expansion at the rate about 1 mm/yr, while the compression rate of the southern hemisphere is one order smaller than the expansion rate of the northern one. After the post glacial rebound effect is subtracted, results show that the expansion and compression rates of the northern and southern hemispheres are 0.46 mm/yr and –0.19 mm/yr, respectively. Transformation between the velocity fields under ITRF2008 and ITRF2000 can explain why different authors have different conclusions about the expan­sion/compression pattern of one hemisphere or the other. Anyway, the entire Earth is expanding at a rate about 0.2 mm/yr, and this estimation coincides with results of our previous studies. The mean variation rates of the radii at different latitudes have been calculated.
Fine‐grained agglutinated elongate columnar stromatolites: Tieling Formation, ca 1420 Ma, North China

The Mesoproterozoic Tieling Formation, near Jixian, northern China, contains thick beds of vertically branched, laterally elongate, columnar stromatolites. Carbonate mud is the primary component of both the stromatolites and their intervening matrix. Mud abundance is attributed to water column ‘whiting’ precipitation stimulated by cyanobacterial photosynthesis. Neomorphic microspar gives the stromatolites a ‘streaky’ microfabric and small mud flakes are common in the matrix. The columns consist of low‐relief, mainly non‐enveloping, laminae that show erosive truncation and well‐defined repetitive lamination. In plan view, the columns form disjunct elongate ridges <10 cm wide separated by narrow matrix‐filled runnels. The stromatolite surfaces were initially cohesive, rather than rigid, and prone to scour, and are interpreted as current aligned microbial mats that trapped carbonate mud. The pervasive ridge–runnel system suggests scale‐dependent biophysical feedback between: (i) carbonate mud supply; (ii) current duration, strength and direction; and (iii) growth and trapping by prolific mat growth. Together, these factors determined the size, morphology and arrangement of the stromatolite columns and their laminae, as well as their branching patterns, alignment and ridge–runnel spacing. Ridge–runnel surfaces resemble ripple mark patterns, but whether currents were parallel and/or normal to stromatolite alignment remains unclear. The formation and preservation of Tieling columns required plentiful supply of carbonate mud, mat‐building microbes well‐adapted to cope with this abundant sediment, and absence of both significant early lithification and bioturbation. These factors were time limited, and Tieling stromatolites closely resemble coeval examples in the Belt‐Purcell Supergroup of Laurentia. The dynamic interactions between mat growth, currents and sediment supply that determined the shape of Tieling columns contributed to the morphotypical diversity that characterizes mid–late Proterozoic branched stromatolites.
The Role of Ultrasonography and Magnetic Resonance Imaging in the Diagnosis of the Adherent Placenta: An Observational Study

Introduction Placenta accreta is an important factor responsible for maternal morbidity and mortality and is commonly associated with emergent postpartum hysterectomy. The precise prenatal diagnosis of affected pregnancies allows optimal obstetric management. Ultrasonography (USG) and magnetic resonance imaging (MRI) are the only diagnostic modalities available for the prenatal diagnosis of placenta accreta. Objective This study aims to evaluate the accuracy of USG and MRI in diagnosing adherent placenta. Methods Thirty females with placenta previa or a history of previous cesarean sections were evaluated with USG at 28-30 weeks, followed by MRI. The findings of USG and MRI were compared with the intra-operative findings (gold standard) as determined at surgery and by pathological examination. Results Abnormal bridging vessel (n = 24; 80%) was the most common finding seen on USG, whereas abnormal bulge (n = 22; 73.3%) and heterogenous placenta (n = 21; 70%) were the most common findings seen on MRI. The sensitivity of USG and MRI was in the range of 86.7%-92.9% and 92.9%-100%, respectively, in diagnosing three types of adherent placenta. The positive predictive values (PPV) of USG and MRI were in the range of 86.7%-86.7% and 93.8%-100%, respectively, in diagnosing three types of adherent placenta. The accuracy of USG and MRI was in the range of 86.7%-96.7% and 96.7%-100%, respectively, in diagnosing three types of adherent placenta. Conclusion MRI helps to accurately classify placental invasion according to depth, as can be seen from the results of the present study, where the MRI technique was more accurate in diagnosing three types of adherent placenta.
Hydrology of paraglacial catchments in a changing climate: impacts on biodiversity hotspots

Groundwater (GW) -fed streams are a common feature of paraglacial floodplains and are regarded as ‘biodiversity hotspots’, due to their role as valuable aquatic habitats. The hydrological dynamics which support GW-fed streams remain poorly understood. There is a need to improve understanding given paraglacial environments are extremely sensitive to the impacts of climate change. To address this significant knowledge gap site specific research was conducted on GW-fed streams within Denali National Park & Preserve, Alaska, during 2013 and 2014. Hydrometric, hydrochemical, hydrogeomorphic, and geophysical techniques were utilised to improve understanding of the hydrological dynamics and hydrogeomorphic controls that influence GW-fed stream occurrence. Paleochannels across paraglacial floodplains were identified as important preferential flow pathways (PFPs); and a first-order control upon GW-fed streams. In addition hillslope-runoff was established as an important hydrological flux to GW-fed streams. Colluvial deposits (e.g. talus cones) were highlighted as valuable hydrological stores on valleys-sides that made a direct contribution to streamflow. This research has raised concerns about the long-term stability of GW-fed streams in paraglacial environments due to changes in hydrogeomorphic controls (PFPs). It has also raised more immediate concerns about the short- to medium-term implications of shifting hydrologic regimes (e.g. declining winter snowpack) for GW-fed streams.
Rendimiento productivo e hígado graso en tilapia híbrida (Oreochromis spp): Influencia de dos fuentes de lípidos

espanolCon el objeto de evaluar el efecto de dos fuentes de lipidos de origen animal y vegetal en el rendimiento productivo y la presentacion de higado graso en alevinos de tilapia hibrida (Oreochromis spp), se utilizaron seis dietas con aceite de pescado y aceite de soya como fuente de lipidos, con niveles de inclusion del 5%, 9% y 13% de cada uno, durante un periodo de 60 dias. Se determinaron parametros de rendimiento productivo e indices corporales (indice hepatosomatico-IHS, indice viscerosomatico-IVS). Adicionalmente se realizo evaluacion histopatologica del higado con tinciones diferenciales para lipidos y carbohidratos. Se observo un aumento significativo de peso (p EnglishWith the aim to evaluate the effect of animal and vegetable lipids on productive performance and development of fatty liver in fingerlings of hybrid tilapia (Oreochromis spp), six diets whit fish oil and soy bean oil as source of lipids were performed. The lipid levels were 5, 9 and 13% of each source, and the feeding period was 60 days. Values of productive performance parameters, hepatosomatic index-HIS and viscerosomatic index- IVS were determined. Additionally, liver histopathologic evaluation was performed with differential stains for lipids and carbohydrates. Weight increase of fish fed with 5, 9 and 13% of soy bean oil was observed as compared with those fed with 5 and 9% of fish oil. Soy bean oil at 13% in diets reduced the HSI of fish as compared with those fed with 5 and 9%. No differences were observed among treatments concerning SVI. The severity of fat infiltration was lower in fish fed diets with 5, 9 and 13% of soy bean oil. The present set of data allows to inferring that dietary soy bean oil, a n-6 polyunsaturated fatty acids rich nutrient, improves the productive performance and decreases the incidence of hepatic lipidosis of hybrid tilapias as compared with fish oil, a n-3 polyunsaturated fatty acids and long chain polyunsaturated fatty acids rich nutrient. portuguesCom fins de avaliar o efeito de duas fontes lipidicas, uma de origem animal e outra vegetal, sobre o desempenho produtivo e o desenvolvimento de figado gordo em alevinos de tilapia hibrida (Oreochromis spp), foram utilizadas seis dietas com oleo de peixe e oleo de soja como fonte de lipideos. Os niveis de inclusao foram 5, 9 e 13% de cada um, e a alimentacao ocorreu em um periodo de 60 dias. Foram determinados os parâmetros de rendimento produtivo, indices corporais (indice hepatossomatico-IHS, indice viscerosomatico indice-IVS). A avaliacao histopatologica do figado foi realizada utilizando-se coloracoes diferenciais para lipidios e carboidratos. Observou-se um aumento de peso significativo (p
Comment on: Kan et al. A Systematic Review and Meta-analysis of the Association Between Depression and Insulin Resistance. Diabetes Care 2013;36:480–489

Kan et al. (1) conducted a meta-analysis on the relationship between depression and insulin resistance (IR), targeting 25 datasets from 18 studies. They calculated the pooled odds ratio using random-effects models and observed a small but significant association between depression and IR. Before their results can be accepted, I would like to express two concerns in relation to their meta-analysis. First, Kan et al. included articles adopting different definitions for depression. In this connection, they mentioned that the magnitude …
They were robbed! Scoring by the middlemost to attenuate biased judging in boxing

Boxing has a long-standing problem with biased judging, impacting both professional and Olympic bouts. ''Robberies'', where boxers are widely seen as being denied rightful victories, threaten to drive fans and athletes away from the sport. To tackle this problem, we propose a minimalist adjustment in how boxing is scored: the winner would be decided by the majority of round-by-round victories according to the judges, rather than relying on the judges' overall bout scores. This approach, rooted in social choice theory and utilising majority rule and middlemost aggregation functions, creates a coordination problem for partisan judges and attenuates their influence. Our model analysis and simulations demonstrate the potential to significantly decrease the likelihood of a partisan judge swaying the result of a bout.
Characterization of the Clinically Approved MRI Tracer Resotran for Magnetic Particle Imaging in a Comparison Study

Objective. The availability of magnetic nanoparticles with medical approval for human intervention is fundamental to the clinical translation of magnetic particle imaging (MPI). In this work, we thoroughly evaluate and compare the magnetic properties of an magnetic resonance imaging (MRI) approved tracer to validate its performance for MPI in future human trials. Approach. We analyze whether the recently approved MRI tracer Resotran is suitable for MPI. In addition, we compare Resotran with the previously approved and extensively studied tracer Resovist, with Ferrotran, which is currently in a clinical phase III study, and with the tailored MPI tracer Perimag. Main results. Initial magnetic particle spectroscopy measurements indicate that Resotran exhibits performance characteristics akin to Resovist, but below Perimag. We provide data on four different tracers using dynamic light scattering, transmission electron microscopy, vibrating sample magnetometry measurements, magnetic particle spectroscopy to derive hysteresis, point spread functions, and a serial dilution, as well as system matrix based MPI measurements on a preclinical scanner (Bruker 25/20 FF), including reconstructed images. Significance. Numerous approved magnetic nanoparticles used as tracers in MRI lack the necessary magnetic properties essential for robust signal generation in MPI. The process of obtaining medical approval for dedicated MPI tracers optimized for signal performance is an arduous and costly endeavor, often only justifiable for companies with a well-defined clinical business case. Resotran is an approved tracer that has become available in Europe for MRI. In this work, we study the eligibility of Resotran for MPI in an effort to pave the way for human MPI trials.
Spatially-Attentive Patch-Hierarchical Network with Adaptive Sampling for Motion Deblurring

This paper tackles the problem of motion deblurring of dynamic scenes. Although end-to-end fully convolutional designs have recently advanced the state-of-the-art in non-uniform motion deblurring, their performance-complexity trade-off is still sub-optimal. Most existing approaches achieve a large receptive field by increasing the number of generic convolution layers and kernel size. In this work, we propose a pixel adaptive and feature attentive design for handling large blur variations across different spatial locations and process each test image adaptively. We design a content-aware global-local filtering module that significantly improves performance by considering not only global dependencies but also by dynamically exploiting neighboring pixel information. We further introduce a pixel-adaptive non-uniform sampling strategy that implicitly discovers the difficult-to-restore regions present in the image and, in turn, performs fine-grained refinement in a progressive manner. Extensive qualitative and quantitative comparisons with prior art on deblurring benchmarks demonstrate that our approach performs favorably against the state-of-the-art deblurring algorithms.
Distilling Morphology-Conditioned Hypernetworks for Efficient Universal Morphology Control

Learning a universal policy across different robot morphologies can significantly improve learning efficiency and enable zero-shot generalization to unseen morphologies. However, learning a highly performant universal policy requires sophisticated architectures like transformers (TF) that have larger memory and computational cost than simpler multi-layer perceptrons (MLP). To achieve both good performance like TF and high efficiency like MLP at inference time, we propose HyperDistill, which consists of: (1) A morphology-conditioned hypernetwork (HN) that generates robot-wise MLP policies, and (2) A policy distillation approach that is essential for successful training. We show that on UNIMAL, a benchmark with hundreds of diverse morphologies, HyperDistill performs as well as a universal TF teacher policy on both training and unseen test robots, but reduces model size by 6-14 times, and computational cost by 67-160 times in different environments. Our analysis attributes the efficiency advantage of HyperDistill at inference time to knowledge decoupling, i.e., the ability to decouple inter-task and intra-task knowledge, a general principle that could also be applied to improve inference efficiency in other domains.
Wetting ridge dissipation at large deformations

Liquid drops slide more slowly over soft, deformable substrates than over rigid solids. This phenomenon can be attributed to the viscoelastic dissipation induced by the moving wetting ridge, which inhibits a rapid motion, and is called"viscoelastic braking". Experiments on soft dynamical wetting have thus far been modelled using linear theory, assuming small deformations, which captures the essential scaling laws. Quantitatively, however, some important disparities have suggested the importance of large deformations induced by the sliding drops. Here we compute the dissipation occurring below a contact line moving at constant velocity over a viscoelastic substrate, for the first time explicitly accounting for large deformations. It is found that linear theory becomes inaccurate especially for thin layers, and we discuss our findings in the light of recent experiments.