Miracle-dz/UniFAR-FTUs huggingface dataset:
Abscisic acid signaling is controlled by a BRANCHED1/HD-ZIP I cascade in Arabidopsis axillary buds

Significance Shoot-branching patterns affect key aspects of plant life and are important targets for crop breeding. However, we are still ignorant of the genetic mechanisms controlling locally an important decision during branch development: whether the axillary bud grows out to give a lateral shoot or remains dormant. Here we show that the TEOSINTE BRANCHED1, CYCLOIDEA, PCF (TCP) transcriptional regulator BRANCHED1 (BRC1), which acts inside axillary buds, binds and activates three genes encoding Homeodomain leucine zipper (HD-ZIP) transcription factors. These factors, together with BRC1, trigger a cascade leading to local abscisic acid (ABA) accumulation and response, essential for bud dormancy under light-limiting conditions. This finding demonstrates a direct relationship between BRC1 and ABA signaling and places ABA downstream of BRC1 in the control of axillary bud dormancy. Shoot-branching patterns determine key aspects of plant life and are important targets for crop breeding. However, we are still largely ignorant of the genetic networks controlling locally the most important decision during branch development: whether the axillary bud, or branch primordium, grows out to give a lateral shoot or remains dormant. Here we show that, inside the buds, the TEOSINTE BRANCHED1, CYCLOIDEA, PCF (TCP) transcription factor BRANCHED1 (BRC1) binds to and positively regulates the transcription of three related Homeodomain leucine zipper protein (HD-ZIP)-encoding genes: HOMEOBOX PROTEIN 21 (HB21), HOMEOBOX PROTEIN 40 (HB40), and HOMEOBOX PROTEIN 53 (HB53). These three genes, together with BRC1, enhance 9-CIS-EPOXICAROTENOID DIOXIGENASE 3 (NCED3) expression, lead to abscisic acid accumulation, and trigger hormone response, thus causing suppression of bud development. This TCP/HD-ZIP genetic module seems to be conserved in dicot and monocotyledonous species to prevent branching under light-limiting conditions.
The effect of life course socioeconomic position on crystallised cognitive ability in two large UK cohort studies: a structured modelling approach

Objectives This study systematically compared accumulation, sensitive period, critical period and social mobility models relating life course socioeconomic position (SEP) and adult crystallised cognitive ability, which has not been comprehensively investigated. Design Two prospective cohort studies. Participants Five thousand three hundred and sixty-two participants in the Medical Research Council National Survey of Health and Development (NSHD) Birth Cohort Study and 10 308 participants in the Whitehall II Occupational Cohort Study. Measures Childhood SEP was measured by father’s occupational SEP, early adulthood SEP by educational qualifications and adult SEP by own occupational SEP. Each life course model was compared with a saturated model. Results Using multiple imputation to account for missing data, the sensitive period model, which contained childhood, early adulthood and adult SEP terms, with different coefficients, provided the best fit for both men and women in the NSHD and Whitehall II cohorts. Early adulthood SEP had the largest coefficient in NSHD women, whereas for NSHD men early adulthood and adult SEP had similar coefficients. In Whitehall II adult SEP had the largest effect size for both men and women. Conclusions Sensitive period with all three time periods was the most appropriate life course models for adult crystallised cognitive ability in both cohorts, including an effect of childhood SEP. It is important to directly compare the life course models to determine which is the most appropriate.
Differential Attachment of Salmonella enterica and Enterohemorrhagic Escherichia coli to Alfalfa, Fenugreek, Lettuce, and Tomato Seeds

ABSTRACT Vegetable seeds have the potential to disseminate and transmit foodborne bacterial pathogens. This study was undertaken to assess the abilities of selected Salmonella and enterohemorrhagic Escherichia coli (EHEC) strains to attach to fungicide-treated versus untreated, and intact versus mechanically damaged, seeds of alfalfa, fenugreek, lettuce, and tomato. Surface-sanitized seeds (2 g) were exposed to four individual strains of Salmonella or EHEC at 20°C for 5 h. Contaminated seeds were rinsed twice, each with 10 ml of sterilized water, before being soaked overnight in 5 ml of phosphate-buffered saline at 4°C. The seeds were then vortexed vigorously for 1 min, and pathogen populations in seed rinse water and soaking buffer were determined using a standard plate count assay. In general, the Salmonella cells had higher attachment ratios than the EHEC cells. Lettuce seeds by unit weight had the highest numbers of attached Salmonella or EHEC cells, followed by tomato, alfalfa, and fenugreek seeds. In contrast, individual fenugreek seeds had more attached pathogen cells, followed by lettuce, alfalfa, and tomato seeds. Significantly more Salmonella and EHEC cells attached to mechanically damaged seeds than to intact seeds (P < 0.05). Although, on average, significantly more Salmonella and EHEC cells were recovered from untreated than fungicide-treated seeds (P < 0.05), fungicide treatment did not significantly affect the attachment of individual bacterial strains to vegetable seeds (P > 0.05), with a few exceptions. This study fills gaps in the current body of literature and helps explain bacterial interactions with vegetable seeds with differing surface characteristics. IMPORTANCE Vegetable seeds, specifically sprout seeds, have the potential to disseminate and transmit foodborne bacterial pathogens. This study investigated the interaction between two important bacterial pathogens, i.e., Salmonella and EHEC, and vegetable seeds with differing surface characteristics. This research helps understand whether seed surface structure, integrity, and fungicide treatment affect the interaction between bacterial cells and vegetable seeds.
Going Deeper: Autonomous Steering with Neural Memory Networks

Although autonomous driving is an area which has been extensively explored in computer vision, current deep learning based methods such as direct image to action mapping approaches are not able to generate accurate results, making their application questionable. This is largely due to the lack of capacity of the current state-of-the-art architectures to capture long term dependencies which can model different human preferences and their behaviour under different contexts. Our work explores a new paradigm in deep autonomous driving where the model incorporates both visual input as well as the steering wheel trajectory and attains a long term planning capacity via neural memory networks. Furthermore, this work investigates optimal feature fusion techniques to combine these multimodal information sources, without discarding the vital information that they offer. The effectiveness of the proposed architecture is illustrated using two publicly available datasets where in both cases the proposed model demonstrates human like behaviour under challenging situations including illumination variations, discontinuous shoulder lines, lane merges, and divided highways, outperforming the current state-of-the-art.
Deep Photometric Stereo Network

This paper presents a photometric stereo method based on deep learning. One of the major difficulties in photometric stereo is designing can appropriate reflectance model that is both capable of representing real-world reflectances and computationally tractable in terms of deriving surface normal. Unlike previous photometric stereo methods that rely on a simplified parametric image formation model, such as the Lambert's model, the proposed method aims at establishing a flexible mapping between complex reflectance observations and surface normal by the use of a deep neural network. As a result we propose a deep photometric stereo network (DPSN) that takes reflectance observations under varying light directions and infers the corresponding surface normal per pixel. To make the DPSN applicable to real-world objects, a database of measured bidirectional reflectance distribution functions (MERL BRDF database) has been used for training the network. Evaluation using simulation and real-world scenes shows effectiveness of the proposed approach over previous techniques.
A Nonconvex Optimization Framework for Low Rank Matrix Estimation

We study the estimation of low rank matrices via nonconvex optimization. Compared with convex relaxation, nonconvex optimization exhibits superior empirical performance for large scale instances of low rank matrix estimation. However, the understanding of its theoretical guarantees are limited. In this paper, we define the notion of projected oracle divergence based on which we establish sufficient conditions for the success of nonconvex optimization. We illustrate the consequences of this general framework for matrix sensing. In particular, we prove that a broad class of nonconvex optimization algorithms, including alternating minimization and gradient-type methods, geometrically converge to the global optimum and exactly recover the true low rank matrices under standard conditions.
The COMPASS-Like Complex Promotes Flowering and Panicle Branching in Rice1[OPEN]

OsWDR5a and OsTrx1/SDG723 form the core components of the COMPASS-like complex to positively regulate the flowering time and panicle branching in rice. Flowering time (heading date) and panicle branch number are important agronomic traits that determine yield in rice (Oryza sativa). The activation of flowering requires histone methylation, but the roles of trimethylation of Lys 4 of histone 3 (H3K4me3) in modulating heading date and panicle development are unclear. Here, we showed that the COMPASS-like complex promotes flowering and panicle branching. The rice (Oryza sativa) WD40 protein OsWDR5a interacts with the TRITHORAX-like protein OsTrx1/SET domain group protein 723 (SDG723) to form the core components of the COMPASS-like complex. Plants in which OsWDR5a or OsTrx1 expression was decreased by RNA interference produced fewer secondary branches and less grain and exhibited a delayed heading date under long-day and short-day conditions, whereas loss of OsWDR5a function resulted in embryo lethality. OsWDR5a binds to Early heading date 1 to regulate its H3K4me3 and expression levels. Together, our results show that the COMPASS-like complex promotes flowering and panicle development and suggest that modulation of H3K4me3 levels by the COMPASS-like complex is critical for rice development.
Radiation track, DNA damage and response—a review

The purpose of this paper has been to review the current status and progress of the field of radiation biophysics, and draw attention to the fact that physics, in general, and radiation physics in particular, with the aid of mathematical modeling, can help elucidate biological mechanisms and cancer therapies. We hypothesize that concepts of condensed-matter physics along with the new genomic knowledge and technologies and mechanistic mathematical modeling in conjunction with advances in experimental DNA (Deoxyrinonucleic acid molecule) repair and cell signaling have now provided us with unprecedented opportunities in radiation biophysics to address problems in targeted cancer therapy, and genetic risk estimation in humans. Obviously, one is not dealing with ‘low-hanging fruit’, but it will be a major scientific achievement if it becomes possible to state, in another decade or so, that we can link mechanistically the stages between the initial radiation-induced DNA damage; in particular, at doses of radiation less than 2 Gy and with structural changes in genomic DNA as a precursor to cell inactivation and/or mutations leading to genetic diseases. The paper presents recent development in the physics of radiation track structure contained in the computer code system KURBUC, in particular for low-energy electrons in the condensed phase of water for which we provide a comprehensive discussion of the dielectric response function approach. The state-of-the-art in the simulation of proton and carbon ion tracks in the Bragg peak region is also presented. The paper presents a critical discussion of the models used for elastic scattering, and the validity of the trajectory approach in low-electron transport. Brief discussions of mechanistic and quantitative aspects of microdosimetry, DNA damage and DNA repair are also included as developed by the authors’ work.
Hemin, a heme oxygenase-1 inducer, restores the attenuated cardioprotective effect of ischemic preconditioning in isolated diabetic rat heart

Background: Attenuated cardioprotective effect of ischemic preconditioning (IPC) by reduced nitric oxide (NO) is a hallmark during diabetes mellitus (DM). Recently, we reported that the formation of caveolin–endothelial nitric oxide synthase (eNOS) complex decreases the release of NO, which is responsible for attenuation of IPC-induced cardioprotection in DM rat heart. Heme oxygenase-1 (HO-1) facilitates release of NO by disrupting caveolin–eNOS complex. The activity of HO-1 is decreased during DM. This study was designed to investigate the role of hemin (HO-1 inducer) in attenuated cardioprotective effect of IPC in isolated diabetic rat heart. Methods: DM was induced in male Wistar rat by single dose of streptozotocin. Cardioprotective effect was assessed in terms of myocardial infarct size and release of lactate dehydrogenase and creatine kinase in coronary effluent. The release of NO was estimated indirectly by measuring the release of nitrite in coronary effluent. Perfusion of sodium nitrite, a precursor of NO, was used as a positive control. Result: IPC-induced cardioprotection and increased release of nitrite were significantly attenuated in a diabetic rat as compared to a normal rat. Pretreatment with hemin and daidzein, a caveolin inhibitor, alone or in combination significantly restored the attenuated cardioprotection and increased the release of nitrite in diabetic rat heart. Zinc protoporphyrin, a HO-1 inhibitor, significantly abolished the observed cardioprotection and decreased the release of nitrite in hemin pretreated DM rat heart. Conclusion: Thus, it is suggested that hemin restores the attenuated cardioprotective effect in diabetic rat heart by increasing the activity of HO-1 and subsequently release of NO.
Somatostatin receptor expression in non-medullary thyroid carcinomas

OBJECTIVEPeptide receptor radionuclide therapy (PRRT) is dependent upon binding of radiolabelled peptides to their respective receptor expressing cells. The main objective of this study was to characterize the expression of somatostatin receptor (SSTR) subtypes in non-medullary thyroid cancers in order to be able to recommend the use of PRRT as a treatment option in patients with progressive local or metastatic disease.DESIGNWe constructed tissue microarrays from paraffin blocks prepared from 47 cases of non-medullary thyroid carcinomas and related normal thyroid tissue. Immunohistochemical staining was performed with five different polyclonal SSTR antibodies.RESULTSSSTR subtypes sst2 and sst3 were expressed in all non-medullary thyroid carcinomas, sst1 and sst5 in 75%, and sst4 in 38%. Coexpression of more than three subtypes was detected in 36 of the 47 cases. The expression of SSTR sub-types in normal thyroid tissue was low or absent.CONCLUSIONSNon-medullary thyroid carcinomas frequently express all SSTR subtypes. This expression provides a basis for further studies with the aim of exploring PRRT as a possible new treatment for iodine-131 refractory metastatic non-medullary thyroid carcinomas.
Recycling of Nd-Fe-B Magnets from Scrap Hard Disc Drives

A hydrogen-based treatment, including Hydrogen Decrepitation (HD) and Hydrogen Disproportionation-Desorption-Recombination (HDDR), was used as part of a recycling procedure for scrap neodymium-iron-boron magnets. Chemical methods of removing nickel coating out of magnets were tested, however ineffectively. Powders were obtained from magnets after the HD and were further processed by the HDDR. Finally, material with maximum energy product (BH)max of 74 kJ/m3 was produced. Chemical composition of magnets (MS, EDS), magnetic properties (VSM) and microstructure observations (SEM) were carried out.
Exploring the Impacts of Postharvest Processing on the Microbiota and Metabolite Profiles during Green Coffee Bean Production

ABSTRACT The postharvest treatment and processing of fresh coffee cherries can impact the quality of the unroasted green coffee beans. In the present case study, freshly harvested Arabica coffee cherries were processed through two different wet and dry methods to monitor differences in the microbial community structure and in substrate and metabolite profiles. The changes were followed throughout the postharvest processing chain, from harvest to drying, by implementing up-to-date techniques, encompassing multiple-step metagenomic DNA extraction, high-throughput sequencing, and multiphasic metabolite target analysis. During wet processing, a cohort of lactic acid bacteria (i.e., Leuconostoc, Lactococcus, and Lactobacillus) was the most commonly identified microbial group, along with enterobacteria and yeasts (Pichia and Starmerella). Several of the metabolites associated with lactic acid bacterial metabolism (e.g., lactic acid, acetic acid, and mannitol) produced in the mucilage were also found in the endosperm. During dry processing, acetic acid bacteria (i.e., Acetobacter and Gluconobacter) were most abundant, along with Pichia and non-Pichia (Candida, Starmerella, and Saccharomycopsis) yeasts. Accumulation of associated metabolites (e.g., gluconic acid and sugar alcohols) took place in the drying outer layers of the coffee cherries. Consequently, both wet and dry processing methods significantly influenced the microbial community structures and hence the composition of the final green coffee beans. This systematic approach to dissecting the coffee ecosystem contributes to a deeper understanding of coffee processing and might constitute a state-of-the-art framework for the further analysis and subsequent control of this complex biotechnological process. IMPORTANCE Coffee production is a long process, starting with the harvest of coffee cherries and the on-farm drying of their beans. In a later stage, the dried green coffee beans are roasted and ground in order to brew a cup of coffee. The on-farm, postharvest processing method applied can impact the quality of the green coffee beans. In the present case study, freshly harvested Arabica coffee cherries were processed through wet and dry processing in four distinct variations. The microorganisms present and the chemical profiles of the coffee beans were analyzed throughout the postharvest processing chain. The up-to-date techniques implemented facilitated the investigation of differences related to the method applied. For instance, different microbial groups were associated with wet and dry processing methods. Additionally, metabolites associated with the respective microorganisms accumulated on the final green coffee beans.
Random Order Contention Resolution Schemes

Contention resolution schemes have proven to be an incredibly powerful concept which allows tackling a broad class of problems. The framework has been initially designed to handle submodular optimization under various types of constraints, that is, intersections of exchange systems (including matroids), knapsacks, and unsplittable flows on trees. Later on, it turned out that this framework perfectly extends to optimization under uncertainty, like stochastic probing and online selection problems, which further can be applied to mechanism design. We add to this line of work by showing how to create contention resolution schemes for intersection of matroids and knapsacks when we work in the random order setting. More precisely, we do know the whole universe of elements in advance, but they appear in an order given by a random permutation. Upon arrival we need to irrevocably decide whether to take an element or not. We bring a novel technique for analyzing procedures in the random order setting that is based on the martingale theory. This unified approach makes it easier to combine constraints, and we do not need to rely on the monotonicity of contention resolution schemes, as it was the case before. Our paper fills the gaps, extends, and creates connections between many previous results and techniques. The main application of our framework is a k + 4 + epsilon approximation ratio for the Bayesian multi-parameter unit-demand mechanism design under the constraint of k matroids intersection, which improves upon the previous bounds of 4k – 2 and e(k + 1). Other results include improved approximation ratios for stochastic k-set packing and submodular stochastic probing over arbitrary non-negative submodular objective function, whereas previous results required the objective to be monotone.
Evaluation of anterior mediastinal solid tumors by CT perfusion: a preliminary study.

PURPOSE We aimed to assess the role of computed tomography (CT) perfusion in differentiation of thymoma from thymic hyperplasia, lymphoma, thymic carcinoma, and lung cancer invading anterior mediastinum. METHODS In this study, 25 patients with an anterior mediastinal lesion underwent CT perfusion imaging from January 2015 to February 2016. Diagnoses included thymoma (n=7), thymic hyperplasia (n=8), lymphoma (n=4), thymic carcinoma (n=3), and invasive lung cancer (n=3). Lymphoma, thymic carcinoma, and lung cancer were grouped as malignant tumors for statistical analysis. Values for blood flow, blood volume, and permeability surface were measured in CT perfusion. RESULTS Blood flow and blood volume values were higher in thymoma in comparison to thymic hyperplasia; however, the difference was not statistically significant. Blood volume values were significantly higher in thymoma (mean, 11.4 mL/100 mL; range, 5.2-20.2 mL/100 mL) compared with lymphoma (mean, 5.3 mL/100 mL; range, 2.5-7.2 mL/100 mL) (P = 0.023). Blood flow and blood volume values were significantly higher in thymoma compared with non-thymoma malignant tumors (P = 0.025). CONCLUSION CT perfusion is helpful in differentiating thymoma from non-thymoma malignancies including lymphoma, thymic carcinoma, and invasive lung cancer involving the anterior mediastinum.
Predictors of objective cough frequency in pulmonary sarcoidosis

Cough is a common symptom of pulmonary sarcoidosis. This study aimed to quantify cough frequency, and investigate its relationship with cough reflex sensitivity, pulmonary function and health status. 32 patients with pulmonary sarcoidosis were compared with 40 healthy controls. Cough reflex sensitivity to capsaicin, objective 24-h cough counts, cough-specific health status, cough severity and cough triggers were measured. The predictors of cough frequency in sarcoidosis were determined in a multivariate analysis. Objective cough frequency was significantly raised in patients with sarcoidosis compared with healthy controls (p<0.001) and patients with cough had an impaired health status. Patients with pulmonary sarcoidosis had a heightened cough reflex sensitivity compared with healthy controls (p<0.001). Only cough reflex sensitivity was significantly associated with objective cough frequency in multivariate analysis, explaining 42% of the variance (p<0.001). There was no association between cough frequency, lung function, number of organs involved, chest radiograph stage or serum angiotensin-converting enzyme levels. Cough is a common and significant symptom in patients with sarcoidosis. Ambulatory objective cough monitoring provides novel insights into the determinants of cough in sarcoidosis, suggesting that cough reflex sensitivity may be more important than lung function and other measures of disease severity, and this should be investigated further. Cough reflex hypersensitivity is an important determinant of objective cough frequency in sarcoidosis http://ow.ly/W4q9e