Miracle-dz/UniFAR-FTUs huggingface dataset:
The lss Supernodulation Mutant of Medicago truncatula Reduces Expression of the SUNN Gene1[OA]

The number of nodules that form in a legume when interacting with compatible rhizobia is regulated by the plant. We report the identification of a mutant in nodule regulation in Medicago truncatula, like sunn supernodulator (lss), which displays shoot-controlled supernodulation and short roots, similar to sunn mutants. In contrast with the sunn-1 mutant, nodulation in the lss mutant is more extensive and is less sensitive to nitrate and ethylene, resembling the sunn-4 presumed null allele phenotype. Although the lss locus maps to the SUNN region of linkage group 4 and sunn and lss do not complement each other, there is no mutation in the genomic copy of the SUNN gene or in the 15-kb surrounding region in the lss mutant. However, expression of the SUNN gene in the shoots of lss plants is greatly reduced compared with wild-type plants. Analysis of cDNA from plants heterozygous for lss indicates that lss is a cis-acting factor affecting the expression of SUNN, and documented reversion events show it to be unstable, suggesting a possible reversible DNA rearrangement or an epigenetic change in the lss mutant. Assessment of the SUNN promoter revealed low levels of cytosine methylation in the 700-bp region proximal to the predicted transcription start site in both wild-type and lss plants, indicating that promoter hypermethylation is not responsible for the suppression of SUNN expression in lss. Thus, lss represents either a distal novel locus within the mapped region affecting SUNN expression or an uncharacterized epigenetic modification at the SUNN locus.
In Vivo Effect of Methylene Blue on Endothelium‐Dependent and Endothelium‐Independent Dilations of Brain Microvessels in Mice

Arterioles on the surface of the mouse brain were observed by in vivo TV microscopy. Four dilators were topically applied to relax the vessels in vivo. Two of the dilators were acetylcholine and bradykinin, whose action in this vascular bed is dependent upon production of endothelium-dependent relaxing factors. The other two dilators were sodium nitroprusside and 8-bromo-cGMP, whose action is not endothelium dependent. The dilations by acetylcholine, bradykinin, and nitroprusside were significantly depressed by 10-4 M methylene blue applied topically for 7 minutes prior to application of the dilators. The inhibitory effect was reversible, was greatest against acetylcholine, and was least against nitroprusside. These data parallel reports of methylene blue's action against these dilators when applied to large blood vessels in vitro. Our data appear to be the first microvascular data and the first in vivo data showing this effect. The data thus suggest that the mechanisms underlying dilation of cerebral arterioles and large extracerebral vessels are similar. The literature accounts for the effect of methylene blue on the basis of its action as an inhibitor of guanylate cyclase. Our data, including the failure of methylene blue to alter dilation by 8-bromo-cGMP, are in keeping with this hypothesis and with current beliefs that guanylate cyclase and cGMP have a central role in vasodilation. The data do not rule out the possibility that methylene blue has an additional action in the case of acetylcholine and inactivates the endothelium-dependent relaxing factor for that dilator.
Masked Types : Technical report

This paper presents a type-based solution to the long-standing problem of object initialization. Constructors, the conventional mechanism for object initialization, have semantics that are surprising to programmers and that lead to bugs. They also contribute to the problem of null-pointer exceptions, which make software less reliable. Masked types are a new type-state mechanism that explicitly tracks the initialization state of objects and prevents reading from uninitialized fields. In the resulting language, constructors are ordinary methods that operate on uninitialized objects, and no special default value ( null) is needed in the language. Initialization of cyclic data structures is achieved with the use of conditionally masked types. Masked types are modular and compatible with data abstraction. The type system is presented in a simplified object calculus and is proved to soundly prevent reading from uninitialized fields. Masked types have been implemented as an extension to Java, in which compilation simply erases extra type information. Experience using the extended language suggests that masked types work well on real code.
Design, implementation and performance evaluation of software OpenFlow flow counters in a bare metal commodity switch

In this paper, we designed, implemented, and evaluated the performance of software OpenFlow flow counters in a bare metal commodity switch. Normally, flow counters are implemented in hardware for line-rate operations and their number needs to be very large to support a large flow-based SDN network. Although these hardware counters operate very fast, they greatly increase the cost of an OpenFlow switch. In addition, due to the limited chip size of the switching ASIC used in an OpenFlow switch, the number of hardware counters cannot scale to a large number. To overcome these drawbacks, we designed and implemented software flow counters in a 48 port × 10 Gbps (port bandwidth) bare metal commodity switch and evaluated their performance and limitations. This paper also reports important findings obtained from this practical work.
Mutation of Residue Phe97 to Leu Disrupts the Central Allosteric Pathway in Scapharca Dimeric Hemoglobin*

Residue Phe97, which is thought to play a central role in the cooperative functioning ofScapharca dimeric hemoglobin, has been mutated to leucine to test its proposed role in mediating cooperative oxygen binding. This results in an 8-fold increase in oxygen affinity and a marked decrease in cooperativity. Kinetic measurements of ligand binding to the Leu97 mutant suggest an altered unliganded (deoxy) state, which has been confirmed by high resolution crystal structures in the unliganded and carbon monoxide-liganded states. Analysis of the structures at allosteric end points reveals them to be remarkably similar to the corresponding wild-type structures, with differences confined to the disposition of residue 97 side chain, F-helix geometry, and the interface water structure. Increased oxygen affinity results from the absence of the Phe97 side chain, whose tight packing in the heme pocket of the deoxy state normally restricts the heme from assuming a high affinity conformation. The absence of the Phe97 side chain is also associated with diminished cooperativity, since Leu97 packs in the heme pocket in both states. Residual cooperativity appears to be coupled with observed structural transitions and suggests that parallel pathways for communication exist in Scapharca dimeric hemoglobin.
A Review of Scrambler Therapy for Chronic Neuropathic Pain

Introduction: An increase in accidental death related to prescription opioid abuse prompts the identification of novel strategies to treat chronic pain at a low risk to patients and their communities. Scrambler therapy (ST) has recently emerged as a viable treatment option for patients with neuropathic pain (NP), prompting a systematic review of the literature. Materials and Methods: We conducted a literature search in PubMed, Embase, and other search engines with the key words scrambler therapy, Calmare®, and neuropathic pain. Results: Fifteen studies met the inclusion criteria for the literature review. Each of these studies reported varying degrees of pain reduction when patients were treated via ST. Discussion: ST appears to effectively treat a variety of NP syndromes; however further sham controlled studies are needed to validate this claim.
Glycemic control in adolescents with type 1 diabetes mellitus improves lipid serum levels and oxidative stress

Introduction: Atherosclerosis begins in childhood, and diabetes is a risk factor for coronary heart disease. Dyslipidemia is prevalent in children with type 1 diabetes mellitus (T1DM), with an association between elevated hemoglobin A1c (HbA1c), serum lipid levels, and oxidative stress. Our aim was to examine the effect of metabolic control on serum lipid levels and oxidative stress in adolescents with T1DM.
RSS-based indoor localisation using MDCF

As a low-cost distance measurement method, received signal strength (RSS) is often used for indoor wireless sensor localisation. However, RSS values can be easily influenced by multi-path fading, noise and other environmental parameters. This decreases the accuracy and stability of estimated distance. To improve localisation accuracy, this study proposes a multiplicative distance-correction factor (MDCF) to counteract the inaccuracy of estimated distance. In the same indoor environment, the product of this CF and estimated distance is regarded as a good approximation of real distance between unknown node and an anchor node. Then, two location estimated methods based on MDCF (MDCF-grid and MDCF-particle swarm optimisation) are proposed. The experimental results confirm that the proposed location estimation methods can significantly improve localisation accuracy without extra hardware in practical indoor scenarios.
Tryptophan and threonine requirements of young pigs and their effects on serum calcium, phosphorus and zinc concentrations.

Four 28-d trials were conducted using a total of 432 pigs, with average initial weight across trials ranging from 6.3 to 9.7 kg, to estimate the tryptophan (trials 1 and 2) and threonine (trials 3 and 4) requirements of pigs fed low protein, corn-sunflower meal diets. The effect of tryptophan, threonine and protein level on serum calcium, phosphorus and zinc also was studied. The diets contained either 12 or 13% protein and were calculated to be adequate in all nutrients except crude protein and the amino acid being investigated. A lysine supplemented, 18% protein, corn-sunflower meal diet was included in all trials as a positive control. In trial 1, weight gains of pigs increased linearly (P less than .005) while feed conversion improved cubically (P less than .05) as dietary tryptophan increased from . 14 to . 22%. Pigs fed the 18% protein diet gained faster (P less than .05) and required less feed/gain than pigs fed low protein diets. In trial 2, weight gains improved quadratically (P less than .005) and feed conversion improved linearly (P less than .05) as dietary tryptophan increased from . 104 to . 204%. Serum phosphorus and zinc concentrations were lower (P less than .05) in pigs fed the 18% protein diet. In both trials, serum urea N responded quadratically (P less than .05) to increasing dietary tryptophan, and was lower (P less than .05) in pigs that were fed diets supplemented with L-tryptophan than in those fed the low protein basal or 18% protein diets. (ABSTRACT TRUNCATED AT 250 WORDS)
Physical layer network coding schemes for two-way relay

In this paper, various physical layer network coding (PNC) schemes are revisited for wireless two-way relay channel in single antenna case. The achievable rates are reviewed for AWGN channel and newly derived for fading channel for all these PNC schemes employing lattice codes and lattice decoding. A new transmit scheme using precoding is proposed over fading channel to achieve higher rates. It is revealed that for two-way relay channel, compute-and-forward can achieve the highest rate over both AWGN channel and fading channel. Thus it is the most suitable PNC scheme for two-way relay.
An interpretable graph-based image classifier

The generalization capability is usually recognized as the most desired feature of data-driven learning systems, such as classifiers. However, in many practical applications obtaining human-understandable information, relevant to the problem at hand, from the classidication model can be equally important. In this paper we propose a classification system able to fulfill these two requirements simultaneously for a generic image classification task. As a first preprocessing step, an input image to the classifier is represented by a labeled graph, relying on a segmentation algorithm. The graph is conceived to represent visual and topological information of the relevant segments of the image. Then, the graph is classified by a suited inductive inference engine. In the learning procedure all the training set images are represented by graphs, feeding a state-of-the-art classification system working on structured domains. The synthesis procedure consists in extracting characterizing subgraphs from the training set, which are used to embed the graphs into a vector space, enabling thus the applicability of well-known classifiers for feature-based patterns. Such characterizing subgraphs, which are derived in an unsupervised fashion, are interpretable by suitable field experts, allowing a semantic analysis of the discovered classification rules for the given problem at hand. The system is optimized with a genetic algorithm, which tunes the system parameters according to a cross-validation scheme. We show the validity of the approach by performing experiments considering some image classification problems derived from an on-line repository.
Elicited hippocampal theta rhythm: a screen for anxiolytic and procognitive drugs through changes in hippocampal function?

Hippocampal damage produces cognitive deficits similar to dementia and changes in emotional and motivated reactions similar to anxiolytic drugs. The gross electrical activity of the hippocampus contains a marked ‘theta rhythm’. This is a relatively high voltage sinusoidal waveform, resulting from synchronous phasic firing of cells, variation in which correlates with behavioural state. Like the hippocampus, theta has been linked to both cognitive and emotional functions. Critically, it has recently been shown that restoration of theta-like rhythmicity can restore lost cognitive function. We review the effects of systemic administration of drugs on hippocampal theta elicited by stimulation of the reticular formation. We conclude that reductions in the frequency of reticular-elicited theta provide what is currently the best in-vivo means of detecting antianxiety drugs. We also suggest that increases in the power of reticular-elicited theta could detect drugs useful in the treatment of disorders, such as dementia, that involve memory loss. We argue that these functionally distinct effects should be seen as indirect and that each results from a change in a single form of cognitive–emotional processing that particularly involves the hippocampus.
Stigmergic epistemology , stigmergic cognition Action editor :

To know is to cognize, to cognize is to be a culturally bounded, rationality-bounded and environmentally located agent. Knowledge and cognition are thus dual aspects of human sociality. If social epistemology has the formation, acquisition, mediation, transmission and dissemination of knowledge in complex communities of knowers as its subject matter, then its third party character is essentially stigmergic. In its most generic formulation, stigmergy is the phenomenon of indirect communication mediated by modifications of the environment. Extending this notion one might conceive of social stigmergy as the extra-cranial analog of an artificial neural network providing epistemic structure. This paper recommends a stigmergic framework for social epistemology to account for the supposed tension between individual action, wants and beliefs and the social corpora. We also propose that the so-called ‘‘extended mind’’ thesis offers the requisite stigmergic cognitive analog to stigmergic knowledge. Stigmergy as a theory of interaction within complex systems theory is illustrated through an example that runs on a particle swarm optimization algorithm. 2007 Elsevier B.V. All rights reserved.
Bcl-2 Expression as a Predictive Marker of Hormone-Refractory Prostate Cancer Treated with Taxane-Based Chemotherapy

Purpose: Bcl-2 inhibits apoptosis, and its overexpression is associated with hormone refractory prostate cancer (HRPC). Bak and Bax are in the Bcl-2 family and counteract the antiapoptotic function of Bcl-2. Taxane-induced (paclitaxel and its analogue docetaxel) phosphorylation of Bcl-2 abolishes the potential antiapoptotic effect of Bcl-2. We hypothesized that (a) survival benefit in HRPC patients treated with taxanes is determined by the presence of Bcl-2 protein and (b) altered expression of Bak and Bax protein caused by genetic mutation is associated with biological aggressiveness of prostate cancer. Experimental Design: Forty localized prostate cancer and 30 HRPC cases were used in this study. Surgical specimens of localized prostate cancer and biopsy specimens of HRPC were used for immunostaining of Bcl-2, Bak, and Bax as well as DNA extraction. Mutations in the Bak and Bax genes were screened by single-strand conformational polymorphism, and confirmed by direct DNA sequencing. Results: Bcl-2–positive HRPC showed longer cause-specific survival in comparison with the counterparts. Multivariate analysis revealed that the level of Bcl-2 expression before treatment with taxane-based chemotherapy was an independent predictor for cause-specific survival (P < 0.01) and baseline prostate-specific antigen level was an independent predictor for progression-free survival (P < 0.01). Bax gene mutation was found in only one HRPC specimen. Conclusions: Bcl-2 expression in addition to prostate-specific antigen measurement before treatment could identify HRPC patients who may benefit from taxane-based chemotherapy. Mutation of the Bak and Bax genes is a rare event in prostate cancer.
A bHLH-Type Transcription Factor, ABA-INDUCIBLE BHLH-TYPE TRANSCRIPTION FACTOR/JA-ASSOCIATED MYC2-LIKE1, Acts as a Repressor to Negatively Regulate Jasmonate Signaling in Arabidopsis[C][W]

This work identifies the bHLH transcription factor, JA-ASSOCIATED MYC2-LIKE1 (JAM1), which negatively regulates jasmonate responses independently from known regulators, namely, JASMONATE-ZIM DOMAIN proteins. JAM1 is involved in JA-mediated male fertility and the defense response to insect attack and represses the transcription of the target genes of MYC2 by competing for the binding sequences. Jasmonates (JAs) are plant hormones that regulate the balance between plant growth and responses to biotic and abiotic stresses. Although recent studies have uncovered the mechanisms for JA-induced responses in Arabidopsis thaliana, the mechanisms by which plants attenuate the JA-induced responses remain elusive. Here, we report that a basic helix-loop-helix–type transcription factor, ABA-INDUCIBLE BHLH-TYPE TRANSCRIPTION FACTOR/JA-ASSOCIATED MYC2-LIKE1 (JAM1), acts as a transcriptional repressor and negatively regulates JA signaling. Gain-of-function transgenic plants expressing the chimeric repressor for JAM1 exhibited substantial reduction of JA responses, including JA-induced inhibition of root growth, accumulation of anthocyanin, and male fertility. These plants were also compromised in resistance to attack by the insect herbivore Spodoptera exigua. Conversely, jam1 loss-of-function mutants showed enhanced JA responsiveness, including increased resistance to insect attack. JAM1 and MYC2 competitively bind to the target sequence of MYC2, which likely provides the mechanism for negative regulation of JA signaling and suppression of MYC2 functions by JAM1. These results indicate that JAM1 negatively regulates JA signaling, thereby playing a pivotal role in fine-tuning of JA-mediated stress responses and plant growth.
Light-field imaging and heterogeneous light fields

In traditional light-field analysis, images have matched spectral content which leads to constant intensity on epipolar plane image (EPI) manifolds. This kind of light field is termed homogeneous light field}. Heterogeneous light fields differ in that contributing images may have varying properties such as exposure selected or color filter applied. To be able to process heterogeneous light fields it is necessary to develop a computation method able to estimate orientations in heterogeneous EPI respectively. One alternative method to estimate orientation is the singular value decomposition. This analysis has resulted in new concepts for improving the structure tensor approach and yielded increased accuracy and greater applicability through exploitation of heterogeneous light fields.While the current structure tensor only estimates orientation with constant pixel intensity along the direction of orientation, the newly designed structure tensor is able to estimate orientations under changing intensity. Additionally, this improved structure tensor makes it possible to process acquired light fields with a higher reliability due to robustness against illumination changes. In order to use this improved structure tensor approach, it is important to design the light-field camera setup that the target scene covers the ±45° orientation range perfectly. This requirement leads directly to a relationship between camera setup for light-field capture and the frustum-shaped volume of interest. We show that higher-precision depth maps are achievable, which has a positive impact on the reliability of subsequent processing methods, especially for sRGB color reconstruction in color-filtered light fields. Aside this, a global shifting process is designed to overcome the basic range limitation of ±45° to estimate larger distances and to increase additionally the achievable precision in light-field processing. That enables the possibility to research spherical light fields, since the orientation range of spherical light fields typically overcomes the ±45° limit. Research in spherically acquired light fields has been conducted in collaboration with the German Center for Artificial Intelligence (DFKI) in Kaiserslautern.
A NOTE ON NOMINAL GDP TARGETING AND THE ZERO LOWER BOUND

I compare nominal gross domestic product (GDP) level targeting with strict price level targeting in a small New Keynesian model, with the central bank operating under optimal discretion and facing a zero lower bound on nominal interest rates. I show that, if the economy is only buffeted by purely temporary shocks to inflation, nominal GDP level targeting may be preferable because it requires the burden of the shocks to be shared by prices and output. However, in the presence of persistent supply and demand shocks, strict price level targeting may be superior because it induces greater policy inertia and improves the tradeoffs faced by the central bank. During lower bound episodes, somewhat paradoxically, nominal GDP level targeting leads to larger falls in nominal GDP.
Effects of prenatal exposure to valproic acid on the development of juvenile-typical social play in rats

Autism is a severe neurodevelopmental disorder characterized by qualitative impairments in social behavior, communication, and aberrant repetitive behaviors. A major focus of animal models of autism has been to mimic the social deficits of the disorder. The present study assessed whether rats exposed prenatally to valproic acid (VPA) show deficits in social play as juveniles that are consistent with the social deficits observed in autism. Dams were exposed to an acute dose of VPA on gestational day 12.5. Later, the playful interactions and associated ultrasonic vocalizations of the juveniles were examined. It was predicted that VPA-treated rats should play less than the controls. Characteristic of neurobehavioral insult at this early age, the VPA-treated juveniles showed significant increases in the frequency of body shakes and sexual mounting, but played at the same frequency as the controls. However, when playing, they were less likely to use tactics that facilitated bodily contact and vocalized less. These data suggest that prenatal VPA exposure disrupts some aspects of being able to communicate effectively and engage partners in dynamic interactions – deficits that are consistent with those observed in autism.