julilili42/papers huggingface dataset:
Multi-level analysis of the interactions between REVOLUTA and MORE AXILLARY BRANCHES 2 in controlling plant development reveals parallel, independent and antagonistic functions
2020-01-01

Class III homeodomain leucine zipper (HD-ZIPIII) transcription factors play fundamental roles in controlling plant development. The known HD-ZIPIII target genes encode proteins involved in the production and dissipation of the auxin signal, HD-ZIPII transcription factors and components that feedback-regulate HD-ZIPIII expression or protein activity. Here we investigated the regulatory hierarchies of the control of MORE AXILLARY BRANCHES2 (MAX2) by the HD-ZIPIII protein REVOLUTA (REV). We found that REV can interact with the promoter of MAX2. In agreement had rev10D, gain-of-function mutants increased levels of MAX2 expression while rev loss-of-function mutants showed lower levels of MAX2 in some tissues. Like REV, plays MAX2 known roles in the control of plant architecture, photobiology and senescence which prompted us to initiate a multi-level analysis of growth phenotypes of hd-zipIII, max2 and respective higher order mutants thereof. Our data suggest a complex relationship of synergistic and antagonistic activities between REV and MAX2 and these interactions appear to depend on the developmental context and not all involve the direct regulation of MAX2 by REV.
Au54(Et3P)18Cl12: a structurally related cluster to Au32(Et3P)12Cl8 gives insight into the formation process
2020-01-01

<bold>Cluster fusion?</bold> A slight change in the synthetic procedure of Au<sub>32</sub>(Et<sub>3</sub>P)<sub>12</sub>Cl<sub>8</sub> leads to the metalloid gold cluster Au<sub>54</sub>(Et<sub>3</sub>P)<sub>18</sub>Cl<sub>12</sub>, giving further insight into the formation mechanism, showing new structural motifs within metalloid gold clusters
The anatomy of spatial neglect after posterior cerebral artery stroke
2020-01-01

Abstract Spatial neglect is a common consequence of stroke in the territory of the right middle cerebral artery. Damage to a perisylvian fronto-temporo-parietal network has been demonstrated to underlie this disorder. Less common, stroke to the posterior cerebral artery territory may also lead to spatial neglect. This study aimed to uncover the anatomical underpinnings of spatial neglect after posterior cerebral artery infarction. A sample of 50 posterior cerebral artery infarct patients was screened for spatial neglect. Neural correlates of neglect were investigated both with voxel-based lesion behaviour mapping and with region-of-interest analyses. Brain damage neither to the splenium, nor to the parahippocampal gyrus, nor to the thalamus was predictive of spatial neglect. Only damage to the perisylvian fronto-temporo-parietal network of spatial neglect was significantly associated with neglect severity. We conclude that both posterior and middle cerebral artery stroke induce spatial neglect after damage to the same perisylvian brain network. The findings contradict previous theories that postulated neural correlates of spatial neglect specifically supplied by the posterior cerebral artery. In posterior cerebral artery stroke patients, affected parts of this network are located at the border zone between the posterior and middle cerebral artery territories. Inter-individual variability in the localization of the border between both artery territories appears to mediate the occurrence of spatial neglect after posterior cerebral artery stroke.
Effects of the anti-oxidant PDTC in combination with a single bout of treadmill running on murine skeletal muscle
2020-01-01

<b>Objectives:</b> Skeletal muscle adaptation to physical activity is dependent on various factors. Important signaling mediators are reactive oxygen species (ROS). However, recent research suggests that ROS have both beneficial and deleterious effects on exercise adaptation, dependent on training intensity and training status, so that the question of whether anti-oxidants should be taken in connection with exercise cannot easily be answered. Thus, it is important to gain more insight into the complex roles of ROS in regulating training adaptation. <b>Methods:</b> The effects of ROS inhibition on skeletal muscle training adaptation were analyzed by applying the anti-oxidant PDTC, which is also an inhibitor of the ROS-activated transcription factor nuclear factor kappa B (NFκB), to juvenile mice in connection with a single bout of treadmill running. <b>Results:</b> We found that PDTC inhibits exercise-mediated induction of specific stress- and inflammation-associated genes. Other genes, specifically those encoding metabolic and mitochondrial factors, were affected to a lesser extent and there appeared to be little effect on the microRNA (miR) profile. <b>Discussion:</b> Our data suggest that anti-oxidants regulate distinct sets of adaptation-relevant genes, which might have important implications for the design of exercise-based preventive and therapeutic approaches.
Searching for neutrinoless double beta decay with GERDA
2020-01-01

Abstract The GERmanium Detector Array (Gerda) experiment located at the INFN Gran Sasso Laboratory (Italy), is looking for the neutrinoless double beta decay of 76 Ge, by using high-purity germanium detectors made from isotopically enriched material. The combination of the novel experimental design, the careful material selection for radio-purity and the active/passive shielding techniques result in a very low residual background at the Q-value of the decay, about 10 −3 cts/(keV-kg-yr). This makes GERDA the first experiment in the field to be background-free for the complete design exposure of 100 kg-yr. A search for neutrinoless double beta decay was performed with a total exposure of 46.7 kg-yr: 23.2 kg-yr come from the second phase (Phase II) of the experiment, in which the background is reduced by about a factor of ten with respect to the previous phase. The analysis presented in this paper includes 12.4 kg-yr of new Phase II data. No evidence for a possible signal is found: the lower limit for the half-life of 76 Ge is 8.0 • 10 25 yr at 90% CL. The experimental median sensitivity is 5.8 • 10 25 yr. The experiment is currently taking data. As it is running in a background-free regime, its sensitivity grows linearly with exposure and it is expected to surpass 10 26 yr within 2018.
Increasing Warmth in Adolescents with Anorexia Nervosa: A Randomized Controlled Crossover Trial Examining the Efficacy of Mustard and Ginger Footbaths
2020-01-01

Objective . To analyze the thermogenic effects of footbaths with medicinal powders in adolescents with anorexia nervosa (AN) in comparison to healthy controls (HCs). Intervention and Outcomes . Forty‐one female participants (21 AN, 20 HCs; 14.22 ± 1.54 years) received three footbaths—warm water and mustard (MU, Sinapis nigra), warm water and ginger (GI, Zingiber officinale), or warm water only (WA), in random order within a crossover design. Data were collected before (t1), immediately after foot immersion (maximum 20 minutes) (t2), and after 10 minutes subsequently (t3). Actual skin temperature (high resolution thermography) and perceived warmth (HeWEF questionnaire) were assessed at each time point for various body parts. The primary outcome measure was self‐perceived warmth at the feet at t3. Secondary outcome measures were objective skin temperature and subjective warmth at the face, hands, and feet. Results . Perceived warmth at the feet at t3 was significantly higher after GI compared to WA (mean difference −1.02) and MU (−1.07), with no differences between those with AN and HC (−0.29). For the secondary outcome measures, a craniocaudal temperature gradient for the skin temperature (thermography) was noted at t1 for patients with AN and HC (AN with colder feet). The craniocaudal gradient for subjective warmth was only seen for patients with AN. Conclusion . Footbaths with ginger increased warmth perception at the feet longer than with mustard or warm water only for adolescents with AN as well as for HC. The impact of ginger footbaths on recovery of thermoregulatory disturbances in patients with AN repeated over extended periods merits further investigation.
Strong <inline-formula><tex-math id="M1">$ (L^2,L^\\gamma\\cap H_0^1) $</tex-math></inline-formula>-continuity in initial data of nonlinear reaction-diffusion equation in any space dimension
2020-01-01

&lt;p style='text-indent:20px;'&gt;In this paper we study the continuity in initial data of a classical reaction-diffusion equation with arbitrary &lt;inline-formula&gt;&lt;tex-math id="M2"&gt; &lt;/tex-math&gt;&lt;/inline-formula&gt; order nonlinearity and in any space dimension &lt;inline-formula&gt;&lt;tex-math id="M3"&gt; &lt;/tex-math&gt;&lt;/inline-formula&gt;. It is proved that the weak solutions can be &lt;inline-formula&gt;&lt;tex-math id="M4"&gt; &lt;/tex-math&gt;&lt;/inline-formula&gt;-continuous in initial data for arbitrarily large &lt;inline-formula&gt;&lt;tex-math id="M5"&gt; &lt;/tex-math&gt;&lt;/inline-formula&gt; (independent of the physical parameters of the system), i.e., can converge in the norm of any &lt;inline-formula&gt;&lt;tex-math id="M6"&gt; &lt;/tex-math&gt;&lt;/inline-formula&gt; as the corresponding initial values converge in &lt;inline-formula&gt;&lt;tex-math id="M7"&gt; &lt;/tex-math&gt;&lt;/inline-formula&gt;. In fact, the system is shown to be &lt;inline-formula&gt;&lt;tex-math id="M8"&gt; &lt;/tex-math&gt;&lt;/inline-formula&gt;-smoothing in a H&lt;inline-formula&gt;&lt;tex-math id="M9"&gt; &lt;/tex-math&gt;&lt;/inline-formula&gt;lder way. Applying this to the global attractor we find that, with external forcing only in &lt;inline-formula&gt;&lt;tex-math id="M10"&gt; &lt;/tex-math&gt;&lt;/inline-formula&gt;, the attractor &lt;inline-formula&gt;&lt;tex-math id="M11"&gt; &lt;/tex-math&gt;&lt;/inline-formula&gt; attracts bounded subsets of &lt;inline-formula&gt;&lt;tex-math id="M12"&gt; &lt;/tex-math&gt;&lt;/inline-formula&gt; in the norm of any &lt;inline-formula&gt;&lt;tex-math id="M13"&gt; &lt;/tex-math&gt;&lt;/inline-formula&gt;, and that every translation set &lt;inline-formula&gt;&lt;tex-math id="M14"&gt; &lt;/tex-math&gt;&lt;/inline-formula&gt; of &lt;inline-formula&gt;&lt;tex-math id="M15"&gt; &lt;/tex-math&gt;&lt;/inline-formula&gt; for any &lt;inline-formula&gt;&lt;tex-math id="M16"&gt; &lt;/tex-math&gt;&lt;/inline-formula&gt; is a finite dimensional compact subset of &lt;inline-formula&gt;&lt;tex-math id="M17"&gt; &lt;/tex-math&gt;&lt;/inline-formula&gt;. The main technique we employ is a combination of a Moser iteration and a decomposition of the nonlinearity, by which the interpolation inequalities are avoided and the new continuity result is obtained without any restrictions on the order &lt;inline-formula&gt;&lt;tex-math id="M18"&gt; &lt;/tex-math&gt;&lt;/inline-formula&gt; of the nonlinearity and the space dimension &lt;inline-formula&gt;&lt;tex-math id="M19"&gt; &lt;/tex-math&gt;&lt;/inline-formula&gt;.&lt;/p&gt;
Grammatical error detection in transcriptions of spoken English
2020-01-01

We describe the collection of transcription corrections and grammatical error annotations for the CrowdED Corpus of spoken English monologues on business topics. The corpus recordings were crowdsourced from native speakers of English and learners of English with German as their first language. The new transcriptions and annotations are obtained from different crowdworkers: we analyse the 1108 new crowdworker submissions and propose that they can be used for automatic transcription post-editing and grammatical error correction for speech. To further explore the data we train grammatical error detection models with various configurations including pre-trained and contextual word representations as input, additional features and auxiliary objectives, and extra training data from written error-annotated corpora. We find that a model concatenating pre-trained and contextual word representations as input performs best, and that additional information does not lead to further performance gains.
Could non-invasive brain-stimulation prevent neuronal degeneration upon ion channel re-distribution and ion accumulation after demyelination?
2020-01-01

Fast and efficient transmission of electrical signals in the nervous system is mediated through myelinated nerve fibers. In neuronal diseases such as multiple sclerosis, the conduction properties of axons are disturbed by the removal of the myelin sheath, leaving nerve cells at a higher risk of degenerating. In some cases, the protective myelin sheath of axons can be rebuilt by remyelination through oligodendroglial cells. In any case, however, changes in the ion channel organization occur and may help to restore impulse conduction after demyelination. On the other hand, changes in ion channel distribution may increase the energy demand of axons, thereby increasing the probability of axonal degeneration. Many attempts have been made or discussed in recent years to increase remyelination of affected axons in demyelinating diseases such as multiple sclerosis. These approaches range from pharmacological treatments that reduce inflammatory processes or block ion channels to the modulation of neuronal activity through electrical cortical stimulation. However, these treatments either affect the entire organism (pharmacological) or exert a very local effect (electrodes). Current results show that neuronal activity is a strong regulator of oligodendroglial development. To bridge the gap between global and very local treatments, non-invasive transcranial magnetic stimulation could be considered. Transcranial magnetic stimulation is externally applied to brain areas and experiments with repetitive transcranial magnetic stimulation show that the neuronal activity can be modulated depending on the stimulation parameters in both humans and animals. In this review, we discuss the possibilities of influencing ion channel distribution and increasing neuronal activity by transcranial magnetic stimulation as well as the effect of this modulation on oligodendroglial cells and their capacity to remyelinate previously demyelinated axons. Although the physiological mechanisms underlying the effects of transcranial magnetic stimulation clearly need further investigations, repetitive transcranial magnetic stimulation may be a promising approach for non-invasive neuronal modulation aiming at enhancing remyelination and thus reducing neurodegeneration.
Bioproduction of Anticancer Podophyllotoxin and Related Aryltretralin-Lignans in Hairy Root Cultures of Linum Flavum L.
2020-01-01

Podophyllotoxin (PPT) is the unique natural precursor of Etoposide, a topoisomerase II inhibitor drug, used in more than a dozen anticancer chemotherapy treatments. Etoposide is appearing on the list of essential medicines of the World Health Organization. PPT is still exclusively extracted from the rhizome of Podophyllum species, its main natural source. The supply of Podophyllum hexandrum plants is limited, since the occurrence of these plant species is scarce, collection is destructive, and the plants need a long regeneration period. As a consequence, this species is now endangered and listed on Appendix II of the Convention on International Trading of Endangered Species. Chemical synthesis of PPT is difficult due to the presence of four contiguous chiral centers and the presence of a base sensitive trans-lactone moiety. Alternatives are being actively searched, but so far, no wild plants have been described with similar PPT production capacity as compared to Podophyllum. However, several plants producing PPT or other related aryltetralin lignans (ATL) have been identified in recent decades, including the Linaceae. Given its high lignan accumulation capacity, Linum flavum is considered a promising alternative source of PPT and other related ATL. However, unlike the common flax L. usitatissimum, L. flavum has a low agricultural potential (e.g., slow growth and dehiscence of fruits). Therefore, in vitro cultures of plant cells and/or tissues provide an interesting alternative to whole L. flavum plants for the production of these valuable ATL. In particular, L. flavum hairy roots (HRs) accumulate high levels of ATL and it is also possible to further increase this ATL accumulation by the selection of the best genotype, optimization of cultures media and conditions and choice of carbon sources, use of plant growth regulators, elicitor treatments, or precursors’ addition. To date, the ATL accumulation levels can still be perceived insufficient for L. flavum HRs before being used as a commercially viable biotechnological production system. To reach this goal, a better knowledge of the mechanisms that regulate the metabolic flux of intermediates in the different branches of the ATL metabolic pathway will be an important prerequisite to direct the biosynthesis toward the production of a high amount of the desired PPT. In the future, metabolic engineering aiming at constructing the PPT pathway in a heterologous host is very appealing, but for that approach in-depth knowledge of the biosynthetic pathway toward PPT and other related ATL is necessary.
UniTuebingenCL at SemEval-2020 Task 7: Humor Detection in News Headlines
2020-01-01

This paper describes the work done by the team UniTuebingenCL for the SemEval 2020 Task 7: “Assessing the Funniness of Edited News Headlines”. We participated in both sub-tasks: sub-task A, given the original and the edited headline, predicting the mean funniness of the edited headline; and sub-task B, given the original headline and two edited versions, predicting which edited version is the funnier of the two. A Ridge Regression model using Elmo and Glove embeddings as well as Truncated Singular Value Decomposition was used as the final model. A long short term memory model recurrent network (LSTM) served as another approach for assessing the funniness of a headline. For the first sub-task, we experimented with the extraction of multiple features to achieve lower Root Mean Squared Error. The lowest Root Mean Squared Error achieved was 0.575 for sub-task A, and the highest Accuracy was 0.618 for sub-task B.
Rebound Phenomenon after Intravitreal Injection of Triamcinolone Acetonide for Macular Edema
2020-01-01

&lt;b&gt;&lt;i&gt;Introduction:&lt;/i&gt;&lt;/b&gt; The aim of this article was to report on a rebound phenomenon after intravitreal triamcinolone acetonide (IVTA) injection for macular edema secondary to diabetic retinopathy (DR) and central or branch retinal vein occlusion (CRVO/BRVO). &lt;b&gt;&lt;i&gt;Methods:&lt;/i&gt;&lt;/b&gt; The data were analyzed retrospectively. Complete ophthalmic examinations, including spectral domain optical coherence tomography, were performed before and 2 months after IVTA injection. The incidence of a rebound phenomenon was defined as an increase in central retinal thickness of &amp;#x3e;10% from baseline at 2 months after IVTA injection. &lt;b&gt;&lt;i&gt;Results:&lt;/i&gt;&lt;/b&gt; This retrospective study included 211 consecutive patients (268 eyes). One hundred ninety (71.2%), 39 (14.6%), and 39 (14.6%) eyes had macular edema (ME) due to DR, CRVO, and BRVO. In total, 9.7% of the eyes showed a rebound phenomenon (DR: 9.5%, CRVO: 5.2%, BRVO: 15.4%). The mean number of prior injections of vascular endothelial growth factor inhibitor or corticosteroid agent was statistically significantly higher in the rebound group (6.8 vs. 5.3) than in the nonrebound group (&lt;i&gt;p&lt;/i&gt; = 0.01). &lt;b&gt;&lt;i&gt;Conclusion:&lt;/i&gt;&lt;/b&gt; Our study shows that 9.7% of the eyes with ME secondary to DR and RVO developed a rebound phenomenon following IVTA injection, limiting its therapeutic effect. We found an increased number of prior intravitreal pharmacotherapy to be a risk factor for a rebound phenomenon.
P4-IPsec: Site-to-Site and Host-to-Site VPN With IPsec in P4-Based SDN
2020-01-01

In this work, we present P4-IPsec, a concept for IPsec in software-defined networks (SDN) using P4 programmable data planes. The prototype implementation features ESP in tunnel mode and supports different cipher suites. P4-capable switches are programmed to serve as IPsec tunnel endpoints. We also provide a client agent to configure tunnel endpoints on Linux hosts so that site-to-site and host-to-site application scenarios can be supported which are the base for virtual private networks (VPNs). While traditional VPNs require complex key exchange protocols like IKE to set up and renew tunnel endpoints, P4-IPsec benefits from an SDN controller to accomplish these tasks. One goal of this experimental work is to investigate how well P4-IPsec can be implemented on existing P4 switches. We present a prototype for the BMv2 P4 software switch, evaluate its performance, and publish its source code on GitHub. We explain why we could not provide a useful implementation with the NetFPGA SUME board. For the Edgecore Wedge 100BF-32X Tofino-based switch, we presented two prototype implementations to cope with a missing crypto unit. As another contribution of this paper, we provide technological background of P4 and IPsec and give a comprehensive review of security applications in P4, IPsec in SDN, and IPsec data plane implementations. According to our knowledge, P4-IPsec is the first implementation of IPsec for P4-based SDN.
A conscious rethink: Why is brain tissue commonly preserved in the archaeological record? Commentary on: Petrone P, Pucci P, Niola M, et al. Heat-induced brain vitrification from the Vesuvius eruption in C.E. 79. N Engl J Med 2020;382:383-4. DOI: 10.1056/NEJMc1909867
2020-01-01

Brain tissue is ubiquitous in the archaeological record. Multiple, independent studies report the finding of black, resinous or shiny brain tissue, and Petrone et al. [2020 “Heat-induced Brain Vitrification from the Vesuvius Eruption in C.E. 79.” N Engl J Med. 382: 383–384; doi:10.1056/NEJMc1909867] raise the intriguing prospect of a role for vitrification in the preservation of ancient biomolecules. However, Petrone et al. (2020) have not made their raw data available, and no detailed laboratory or analytical methodology is offered. Issues of contamination and misinterpretation hampered a decade of research in biomolecular archaeology, such that addressing these sources of bias and facilitating validation of specious findings has become both routine and of paramount importance in the discipline. We argue that the evidence they present does not support their conclusion of heat-induced vitrification of human brain tissue, and that future studies should share palaeoproteomic data in an open access repository to facilitate comparative analysis of the recovery of ancient proteins and patterns of their degradation.
RNA Interactome Identification via RNA-BioID in Mouse Embryonic Fibroblasts
2020-01-01

Cytoplasmic localization of mRNAs is common to all organisms and serves the spatial expression of genes. Cis-acting RNA signals (mostly found in the mRNA's 3'-UTR), called zipcodes recruit trans-acting RNA-binding proteins that facilitate the localization of the mRNA. UV-cross-linking or affinity purification has been applied to identify such proteins but suffer from the need for stable RNA-protein binding or direct contact of protein and RNA. To identify stably or transiently interacting proteins that directly or indirectly associated with the localization elements and the body of the mRNA, we developed an <i>in vivo</i> proximity labeling method we call RNA-BioID. In RNA-BioID, we tether a fusion of the BirA* biotin ligase and the MS2 coat protein (MCP) at the 3'-UTR of MS2-tagged β-actin mRNA <i>in vivo</i>. Exposing BirA* expressing cells to biotin in the media and induces biotinylation of β-actin mRNA-associated proteins that can be isolated with streptavidin beads. This technique allowed us to identify by mass spectrometry analysis the β-actin mRNA 3'-UTR-interacting proteome in fibroblasts. The protocol can be useful to identify the interacting proteome of any mRNA in mammalian cells.