Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-Wide Association Study Dissects the Genetic Architecture of Maize Husk Tightness

The husk is a leafy outer tissue that encloses a maize ear. Previously, we identified the optimum husk structure by measuring the husk length, husk layer number, husk thickness and husk width. Husk tightness (HTI) is a combined trait based on the above four husk measurements. Unveiling the genetic basis of HTI will aid in guiding the genetic improvement of maize for mechanical harvesting and for protecting the ear from pest damage and pathogen infection. Here, we used a maize associate population of 508 inbred lines with tropical, subtropical and temperate backgrounds to analyze the genetic architecture of HTI. Evaluating the phenotypic diversity in three different environments showed that HTI exhibited broad natural variations and a moderate heritability level of 0.41. A diversity analysis indicated that the inbred lines having a temperate background were more loosely related than those having a tropical or subtropical background. HTI showed significant negative correlations with husk thickness and width, which indicates that thicker and wider husks wrapped the ear tighter than thinner and slimmer husks. Combining husk traits with ∼1.25 million single nucleotide polymorphisms in a genome-wide association study revealed 27 variants that were significantly associated with HTI above the threshold of P < 7.26 × 10–6. We found 27 candidate genes for HTI that may participate in (1) husk senescence involving lipid peroxidation (GRMZM2G017616) and programmed cell death (GRMZM2G168898 and GRMZM2G035045); (2) husk morphogenesis involving cell division (GRMZM5G869246) and cell wall architecture (GRMZM2G319798); and (3) cell signal transduction involving protein phosphorylation (GRMZM2G149277 and GRMZM2G004207) and the ABSISIC ACID INSENSITIVE3/VIVIPAROUS1 transcription factor (GRMZM2G088427). These results provide useful information for understanding the genetic basis of husk development. Further studies of identified candidate genes will help elucidate the molecular pathways that regulate HTI in maize.
The role of Ca2+ and protein scaffolding in the formation in nature’s water oxidizing complex

The photosystem II (PSII) complex catalyzing the H2O-oxidation reaction of photosynthesis is highly prone to photodamage. Nature has evolved synthesis and repair mechanisms that include the photooxidative self-assembly, termed photoactivation, of the Mn4CaO5 metal cluster responsible for H2O-oxidation. Assembly is a multi-step light-driven process that proceeds with low quantum yield, involves a critical molecular rearrangement between light-activated steps, and is prone to photoinactivation and mis-assembly. A sensitive polarographic technique was used to track the assembly process under flash illumination as a function of the constituent Mn2+ and Ca2+ ions in genetically engineered samples to elucidate the action of Ca2+ and peripheral proteins. We show that the protein scaffolding that organizes this process is modulated allosterically by the assembly protein Psb27, which together with Ca2+, stabilizes the intermediates of photoactivation, a feature especially evident at long intervals between photoactivating flashes. Besides stabilizing intermediates, the Ca2+ ion is also critical to prevent photoinactivation due to inappropriate binding of Mn2+. Overexpression of Psb27, deletion of extrinsic protein PsbO, and excess Ca2+ characteristically modify these processes and retard the dark rearrangement. The results suggest the involvement of three metal binding sites, two Mn and one Ca with occupation of the Ca site by Ca2+ critical for the suppression of inactivation and the long-observed competition between Mn2+ and Ca2+ occurring at the second Mn site necessary for trapping the first stable assembly intermediates. Significance Statement The oxidation of water by the photosystem II is the foundation of bioproductivity on Earth and represents a blueprint for sustainable, carbon neutral technologies. Water oxidation is catalyzed by a metal cluster containing of 4 Mn and 1 Ca atoms linked via oxo bridges. The initial assembly is a complex sequential reaction harnessing the photochemical reaction center to photooxidatively incorporate Mn2+ and Ca2+ ions into the catalytic unit embedded in the protein matrix. This photoassembly is crucial for both de novo biosynthesis and as part of the ‘self-healing’ mechanism to cope with incessant photodamage that photosynthetic organisms experience. The results have implications for the natural mechanism as well as the highly desirable biomimetic devices currently envisioned for solar energy production.
Late fMRI Response Components Are Altered in Autism Spectrum Disorder

Disrupted cortical neural inhibition has been hypothesized to be a primary contributor to the pathophysiology of autism spectrum disorder (ASD). This hypothesis predicts that ASD will be associated with an increase in neural responses. We tested this prediction by comparing fMRI response magnitudes to simultaneous visual, auditory, and motor stimulation in ASD and neurotypical (NT) individuals. No increases in the initial transient response in any brain region were observed in ASD, suggesting that there is no increase in overall cortical neural excitability. Most notably, there were widespread fMRI magnitude increases in the ASD response following stimulation offset, approximately 6–8 s after the termination of sensory and motor stimulation. In some regions, the higher fMRI offset response in ASD could be attributed to a lack of an “undershoot”—an often observed feature of fMRI responses believed to reflect inhibitory processing. Offset response magnitude was associated with reaction times (RT) in the NT group and may explain an overall reduced RT in the ASD group. Overall, our results suggest that increases in neural responsiveness are present in ASD but are confined to specific components of the neural response, are particularly strong following stimulation offset, and are linked to differences in RT.
Molecular Characterization of Cryptosporidium spp. in Brandt's Vole in China

Cryptosporidium spp. are important intestinal parasites that infect humans and various animals, including wildlife. Currently, few epidemiological data in wild rodents, especially in voles, are available. In the present study, a total of 678 Brandt's vole feces samples were collected from Maodeng Livestock Farm and East Ujimqin, Inner Mongolia. The overall prevalence of Cryptosporidium spp. was 18.7%. Significant differences were not found between genders but between locations and weight groups. Moreover, three known species/genotypes, C. suis, Cryptosporidium environmental sequence and muskrat genotype II, and a novel Cryptosporidium species/genotypes of Brandt's vole was identified. To the best of our knowledge, this is the first report of Cryptosporidium spp. infection in Brandt's vole worldwide. These findings imply Brandt's voles might be a potential source of human cryptosporidiosis.
Synaptische Plastizität im Subikulum und ihre Modulation durch Serotonin

The subiculum is the principal target of CA1 pyramidal cells and mediates hippocampal output to various cortical and subcortical regions of the brain. The majority of subicular pyramidal cells are burst-spiking neurons. Previous studies indicated that high frequency stimulation in subicular burst-spiking cells causes presynaptic NMDA-receptor dependent long-term potentiation (LTP) whereas low frequency stimulation induces postsynaptic NMDA-receptor-dependent longterm depression (LTD). In the present study, we investigate the effect of 5-hydroxytryptamine type 4 (5-HT4) receptor activation and blockade on both forms of synaptic plasticity in burst-spiking cells. We demonstrate that neither activation nor block of 5-HT4 receptors modulate the induction or expression of LTP. In contrast, activation of 5-HT4 receptors facilitates expression of LTD, and block of the 5-HT4 receptor prevents induction of short-term depression and LTD. As 5HT4 receptors are positively coupled to adenylate cyclase 1 (AC1), 5-HT4 receptors might modulate PKA activity through AC1. Since LTD is blocked in the presence of 5-HT4 receptor antagonists, our data are consistent with 5-HT4 receptor activation by ambient serotonin or intrinsically active 5-HT4 receptors. Our findings provide new insight into aminergic modulation of hippocampal output. Citation: Wawra M, Fidzinski P, Heinemann U, Mody I, Behr J (2014) 5-HT4-Receptors Modulate Induction of Long-Term Depression but Not Potentiation at Hippocampal Output Synapses in Acute Rat Brain Slices. PLoS ONE 9(2): e88085. doi:10.1371/journal.pone. 0088085 Editor: Thierry Amédée, Centre national de la recherche scientifique, University of Bordeaux, France Received July 18, 2013; Accepted January 6, 2014; Published February 5, 2014 Copyright: 2014 Wawra et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by German Research Foundation (DFG, www.dfg.de) grants to JB. (BE 2011/6-1) and MW. (GRK 1123, NeuroCure, www. neurocure.de). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: joachim.behr@charite.de
Parallelizing pruned landmark labeling: dealing with dependencies in graph algorithms

To help compute shortest path distances over large graphs efficiently, 2-hop labeling has emerged as a major tool, with Pruned Landmark Labeling (PPL) as a popular algorithm. This paper demonstrates the first scalable parallel implementation of the PPL algorithm that produces the same results as the sequential algorithm. Based on theoretical analysis, we show how computations on each vertex can be performed in parallel while maintaining correctness, resulting in the Vertex-Centrix PLL (VC-PLL) algorithm. We also show a formulation of this algorithm based on linear algebra and argue why the use of a library based on linear algebra operations will not produce an efficient implementation. Next, we introduce a batched VC-PLL (BVC-PLL) algorithm to reduce the computational inefficiency in VC-PLL. We have carried out a parallel implementation of this method for modern clusters, combining shared memory and distributed memory parallelism, that can efficiently execute on graphs with more than a billion edges. We also demonstrate how BVC-PLL algorithm can be extended to handle directed graphs and weighted graphs and how the version for weighted graphs can benefit from SIMD parallelization.
Tree-liana relationships in a tropical evergreen forest at Varagalaiar, Anamalais, Western Ghats, India

In a 30-ha permanent plot of tropical evergreen forest at Varagalaiar, Indian Western Ghats, all trees ≥ 30 cm girth at breast height (gbh) were examined for the presence of lianas ≥ 1 cm dbh. The plot contained 13 445 trees in 152 species and 11 200 lianas in 75 species. Twenty-eight per cent of trees supported lianas and the mean number of lianas per tree was 0.38 ± 0.72. Association analysis between lianas and trees of 16 tree families and 20 abundant tree species indicated that tree susceptibility to lianas was better pronounced at species rather than at family level. Overall, at Varagalaiar site, the aggregation of lianas followed neither Poisson nor clumped distribution. Among the four dominant tree families Dipterocarpaceae and Clusiaceae fit to the negative binomial model better than Euphorbiaceae and Meliaceae. These four families differed in their susceptibility level with 34.6% , 36.7% , 24.1% and 27.7% of trees ≥ 30 cm gbh respectively supporting lianas. At the species level, the proportion of trees with lianas was positively correlated with the mean branch free bole height of trees ≥ 30-40 and ≥ 40 cm gbh classes, and the mean number of lianas per tree was also positively correlated with the mean branch bole height of trees ≥ 30 cm gbh. Of the 16 abundant families, Euphorbiaceae contributed 31% and dominated the lower canopy, but its susceptibility to lianas was lower when compared to most other families.
Inhibitory Effect of Buprofezin on the Progeny of Rice Weevil, Sitophilus oryzae L. (Coleoptera: Curculionidae)

The rice weevil Sitophilus oryzae (L.) (Coleoptera: Curculionidae), is an important pest of stored grains throughout the world. Different biopesticides and synthetic insecticides have been used for a long time to minimize the rice weevil infestation but their efficacy is not satisfactory yet. The climate and storage conditions are highly favorable for quick progeny which may be responsible for lower efficiency of insecticides and higher level of infestation. Insect growth regulators (IGRs) like buprofezin are the semi-synthetic insecticides, mimic the insectproduced hormones and don’t kill the insects directly but reduces pest populations by affecting mating behavior, reproduction, egg viability, pre and post embryonic development etc. Laboratory experiments were conducted from August to November 2012, to evaluate the efficacy of buprofezin on the mortality and the suppression of progeny production of rice weevil. Ten adult rice weevils were exposed on three types of rice grains (long, medium and short) treated with buprofezin at 100, 200 and 300 ppm. Mortality was counted at 15, 21 and 28 days after treatment while adult progeny was counted at 6, 7 and 8 weeks after buprofezin treatment to get a new generation. The data showed that buprofezin had no direct effect on the mortality of rice weevils regardless the concentrations. Buprofezin at 300 ppm in rice grains significantly inhibited progeny production while lower doses (200 and 100 ppm) had no significant effect but virtually reduces progeny number. Types of grains were not factor for increasing or decreasing the rice weevils populations. In conclusion, buprofezin caused decreasing progeny productivity by S. oryzae (L.) with increasing concentrations regardless the types of rice grains.
Pharmacological activities of Andrographis paniculata, Allium sativum and Adhatoda vasica

Andrographis paniculata, Allium sativum and Adhatoda vasica are the three important medicinal plants in which it is used for daily consumption by the user especially in the rural areas. Not only rural people are seeking for the medical benefits from the medicinal plants but also urban people because trying to eliminate the side effects of synthetic medicine on health. Research using these three plants should not stop here and must be extensively employed by the researchers and try to get more medical properties which is useful for the public. Andrographolide from Andrographis paniculata is the active component obtained from the aerial parts of this plant, having very bitter taste. It is a bicyclic diterpenoid lactone with multiple pharmacological activities. In 1997, garlic (Allium sativum) was the most widely used natural supplement in US house-holds. Garlic was shown to be used more than twice as much as any other natural supplement. Extract of Adhatoda vasica leaves has been used for the treatment of various diseases and disorders in Ayurved and Unani medicine. The plant has been used in the indigenous system of medicine in India for more than 2000 years. Compounds which are present in the plant/s which when consumed it promote the health of the consumers although some studies suggest that consumption may lead to toxic effect but in general it is safe to consume moderately. In many literature survey, researchers are trying the best to overcome the bacterial resistance by isolating compounds from the medicinal plants (one of the method) due to the resistance of bacterias towards synthetic chemicals. Overally this proved the importance of the medicinal plants. *Corresponding Author: Manoharan Sivananthan  siva8905@gmail.com International Journal of Biomolecules and Biomedicine (IJBB) ISSN: 2221-1063 (Print) 2222-503X (Online) Vol. 3, No. 2, p. 13-20, 2013 http://www.innspub. net
Financial Independence and Academic Achievement: Are There Key Factors of Transition to Adulthood for Young Higher Education Students in Colombia?

Autonomy is conceptualized as the need for agency, self-actualization, and independence. Nowadays, financial independence and academic achievement for young populations may be considered as key aspects in the transition to adulthood in response to some contextual demands of different cultural environments. By means of a multi-level model, the present study aims to determine the influence and contribution of factors at individual level (e.g., sex, age, socioeconomic status, family financial support, awarded scholarships, personal finance, student loans) and school level (e.g., program quality, online programs, face to face programs) on the academic achievement of young higher education Colombian students. Data come from the scores of the national standardized academic achievement test administered in 2018 in Colombia. The sample included 234,386 students enrolled in 3,389 higher education institutions in Colombia. After controlling the effects of program quality, and the student’s previous academic abilities and socio-economic conditions, results showed that students with scholarships had higher scores than financially dependent students (those who had student loans) and financially independent students (those who self-funded their studies or who worked during the week) who had low scores in the national standardized academic achievement test.
Modeling and optimizing NUMA effects and prefetching with machine learning

Both NUMA thread/data placement and hardware prefetcher configuration have significant impacts on HPC performance. Optimizing both together leads to a large and complex design space that has previously been impractical to explore at runtime. In this work we deliver the performance benefits of optimizing both NUMA thread/data placement and prefetcher configuration at runtime through careful modeling and online profiling. To address the large design space, we propose a prediction model that reduces the amount of input information needed and the complexity of the prediction required. We do so by selecting a subset of performance counters and application configurations that provide the richest profile information as inputs, and by limiting the output predictions to a subset of configurations that cover most of the performance. Our model is robust and can choose near-optimal NUMA+Pre-fetcher configurations for applications from only two profile runs. We further demonstrate how to profile online with low overhead, resulting in a technique that delivers an average of 1.68X performance improvement over a locality-optimized NUMA baseline with all prefetchers enabled.
The Influence of Functional Flywheel Resistance Training on Movement Variability and Movement Velocity in Elite Rugby Players

The aim of this study was to identify the changes in movement variability and movement velocity during a six-week training period using a resistance horizontal forward–backward task without (NOBALL) or with (BALL) the constraint of catching and throwing a rugby ball in the forward phase. Eleven elite male rugby union players (mean ± SD: age 25.5 ± 2.0 years, height 1.83 ± 0.06 m, body mass 95 ± 18 kg, rugby practice 14 ± 3 years) performed eight repetitions of NOBALL and BALL conditions once a week in a rotational flywheel device. Velocity was recorded by an attached rotary encoder while acceleration data were used to calculate sample entropy (SampEn), multiscale entropy, and the complexity index. SampEn showed no significant decrease for NOBALL (ES = -0.64 ± 1.02) and significant decrease for BALL (ES = -1.71 ± 1.16; p < 0.007) conditions. Additionally, movement velocity showed a significant increase for NOBALL (ES = 1.02 ± 1.05; p < 0.047) and significant increase for BALL (ES = 1.25 ± 1.08; p < 0.025) between weeks 1 and 6. The complexity index showed higher levels of complexity in the BALL condition, specifically in the first three weeks. Movement velocity and complex dynamics were adapted to the constraints of the task after a four-week training period. Entropy measures seem a promising processing signal technique to identify when these exercise tasks should be changed.
Cogno-Vest: A Torso-Worn, Force Display to Experimentally Induce Specific Hallucinations and Related Bodily Sensations

Recent advances in virtual reality and robotic technologies have allowed researchers to explore the mechanisms underlying bodily aspects of self-consciousness which are largely attributed to the multisensory and sensorimotor processing of bodily signals (bodily self-consciousness, BSC). One key contribution to BSC, that is currently poorly addressed due to the lack of a wearable solution, concerns realistic collision sensations on the torso. Here, we introduce and validate a novel torso-worn force display, the Cogno-vest, to provide mechanical touch on the user’s back in a sensorimotor perception experiment. In a first empirical study, we characterized human finger poking (N=28). In order to match these poking characteristics and meet the wearability criteria, we used bi-directional, push-pull solenoids as a force actuator in the Cogno-vest. Subsequently, and based on an iterative, multidisciplinary design procedure, a bodyconforming, unisex, torso-worn force display was prototyped. Finally, we conducted a behavioral study that investigated BSC in 25 healthy participants by introducing conflicting sensorimotor signals between their hand and torso (back). Using the final reiteration of the Cogno-vest we successfully replicated previous findings on illusory states of BSC, characterized by presence hallucinations (PH) and passivity symptoms, and achieved higher illusion ratings compared to static conditions used in prior studies.
Replay bursts coincide with activation of the default mode and parietal alpha network

Our brains at rest spontaneously replay recently acquired information, but how this process is orchestrated to avoid interference with ongoing cognition is an open question. We investigated whether replay coincided with spontaneous patterns of whole brain activity. We found, in two separate datasets, that replay sequences were packaged into transient bursts occurring selectively during activation of the default mode network (DMN) and parietal alpha network. These networks were characterized by widespread synchronized oscillations coupled to increases in ripple band power, mechanisms that coordinate information flow between disparate cortical areas. Our data show a tight correspondence between two widely studied phenomena of neural physiology and suggest the DMN may coordinate replay bursts in a manner that minimizes interference with ongoing cognition.