Genetic architecture of ecological divergence between Oryza rufipogon and Oryza nivara.

Ecological divergence due to habitat difference plays a prominent role in the formation of new species, but the genetic architecture during ecological speciation and the mechanism underlying phenotypic divergence remain less understood. Two wild ancestors of rice (Oryza rufipogon and Oryza nivara) are a progenitor-derivative species pair with ecological divergence and provide a unique system for studying ecological adaptation/speciation. Here, we constructed a high-resolution linkage map and conducted a quantitative trait locus (QTL) analysis of 19 phenotypic traits using an F2 population generated from a cross between the two Oryza species. We identified 113 QTLs associated with interspecific divergence of 16 quantitative traits, with effect sizes ranging from 1.61% to 34.1% in terms of the percentage of variation explained (PVE). The distribution of effect sizes of QTLs followed a negative exponential, suggesting that a few genes of large effect and many genes of small effect were responsible for the phenotypic divergence. We observed 18 clusters of QTLs (QTL hotspots) on 11 chromosomes, significantly more than that expected by chance, demonstrating the importance of coinheritance of loci/genes in ecological adaptation/speciation. Analysis of effect direction and v-test statistics revealed that interspecific differentiation of most traits was driven by divergent natural selection, supporting the argument that ecological adaptation/speciation would proceed rapidly under coordinated selection on multiple traits. Our findings provide new insights into the understanding of genetic architecture of ecological adaptation and speciation in plants and help effective manipulation of specific genes or gene cluster in rice breeding.

The Chinese Zodiac-in-Noise Test: An Internet-Based Speech-in-Noise Test for Large-Scale Hearing Screening.

OBJECTIVES: Motivated by the growing need for hearing screening in China, the present study has two objectives. First, to develop and validate a new test, called the Chinese Zodiac-in-noise (ZIN) test, for large-scale hearing screening in China. Second, to conduct a large-scale remote hearing screening in China, using the ZIN test developed. DESIGN: The ZIN test was developed following a similar procedure as the digits-in-noise test but emphasizes the importance of consonant recognition by employing the 12 zodiac animals in traditional Chinese culture as speech materials. It measures the speech reception threshold (SRT) using triplets of Chinese zodiac animals in speech-shaped noise with an adaptive procedure. RESULTS: Normative data of the test were obtained in a group of 140 normal-hearing listeners, and the performance of the test was validated by comparisons with pure-tone audiometry in 116 listeners with various hearing abilities. The ZIN test has a reference SRT of -11.0 ± 1.6 dB in normal-hearing listeners with a test-retest variability of 1.7 dB and can be completed in 3 minutes. The ZIN SRT is highly correlated with the better-ear pure-tone threshold ( r = 0.82). With a cutoff value of -7.7 dB, the ZIN test has a sensitivity of 0.85 and a specificity of 0.94 for detecting a hearing loss of 25 dB HL or more at the better ear.A large-scale remote hearing screening involving 30,552 participants was performed using the ZIN test. The large-scale study found a hearing loss proportion of 21.0% across the study sample, with a high proportion of 57.1% in the elderly study sample aged over 60 years. Age and gender were also observed to have associations with hearing loss, with older individuals and males being more likely to have hearing loss. CONCLUSIONS: The Chinese ZIN test is a valid and efficient solution for large-scale hearing screening in China. Its remote applications may improve access to hearing screening and enhance public awareness of hearing health.

[CT-Like MRI and Calcium-Suppressed Spectral CT Imaging of Multifocal Bone Infarcts in Both Lower Extremities:Report of One Case].

Bone infarction has a low incidence in clinical practice and mostly occurs in the metaphysis and diaphysis.Few studies report the advanced imaging technique for bone infarction.Here we reported the fast field echo resembling a CT using restricted echo-spacing and calcium-suppressed spectral CT imaging for a case of multifocal bone infarcts in both lower extremities,aiming to provide diagnostic experience for clinical practice.

[Atypical Cystic Meningioma:Report of One Case].

The diagnosis of atypical cystic meningioma is difficult because of the atypical MRI findings.This paper reported a case of atypical cystic meningioma and described the detailed MRI findings,which would provide valuable imaging evidence for the localization and classification of cystic meningioma.

Genome-wide analysis of Dof transcription factors and their response to cold stress in rice (Oryza sativa L.).

BACKGROUND: Rice (Oryza sativa L.) is a food crop for humans worldwide. However, temperature has an effect during the vegetative and reproductive stages. In high-latitude regions where rice is cultivated, cold stress is a major cause of yield loss and plant death. Research has identified a group of plant-specific transcription factors, DNA binding with one zinc fingers (DOFs), with a diverse range of functions, including stress signaling and stress response during plant growth. The aim of this study was to identify Dof genes in two rice subspecies, indica and japonica, and screen for Dof genes that may be involved in cold tolerance during plant growth. RESULTS: A total of 30 rice Dofs (OsDofs) were identified using bioinformatics and genome-wide analyses and phylogenetically analyzed. The 30 OsDOFs were classified into six subfamilies, and 24 motifs were identified based on protein sequence alignment. The chromosome locations of OsDofs were determined and nine gene duplication events were identified. A joint phylogenetic analysis was performed on DOF protein sequences obtained from four monocotyledon species to examine the evolutionary relationship of DOF proteins. Expression profiling of OsDofs from two japonica cultivars (Longdao5, which is cold-tolerant, and Longjing11, which is cold-sensitive) revealed that OsDof1 and OsDof19 are cold-inducible genes. We examined the seed setting rates in OsDof1- and OsDof19-overexpression and RNAi lines and found that OsDof1 showed a response to cold stress. CONCLUSIONS: Our investigation identified OsDof1 as a potential target for genetic breeding of rice with enhanced cold tolerance.

Speech intelligibility for various head orientations of a listener in an automobile using the speech transmission index.

As well as background noise and the acoustic conditions of the given space, speech intelligibility (SI) is affected by the binaural effect (BE), which is sensitive to the head orientation (HO) of the listener, especially in a small enclosed space such as an automobile. This study uses the speech transmission index (STI) to systematically investigate and predict SI for various HOs of the listener in an automobile. To explore the combined effects of reflections and BE on the auditory perception of speech, several groups of binaural room impulse responses for different speaker locations and HOs are measured in a listening room and an automobile, with the left-side front window (LFW) closed and open, and these are used to calculate the STI. The SI for various configurations is evaluated indirectly using a Chinese STI-SI model. The results show that reflections in the automobile help to increase the STI of the contralateral ear rather than the ipsilateral ear. The LFW is an important reflective boundary but does not always play a dominant role in the STI (SI). Moreover, the STI (SI) can be improved when the listener in the driver seat turns their head inward, i.e., at a negative HO.

Parallel Speciation of Wild Rice Associated with Habitat Shifts.

The occurrence of parallel speciation strongly implies the action of natural selection. However, it is unclear how general a phenomena parallel speciation is since it was only shown in a small number of animal species. In particular, the adaptive process and mechanisms underlying the process of parallel speciation remain elusive. Here, we used an integrative approach incorporating population genomics, common garden, and crossing experiments to investigate parallel speciation of the wild rice species Oryza nivara from O. rufipogon. We demonstrated that O. nivara originated multiple times from different O. rufipogon populations and revealed that different O. nivara populations have evolved similar phenotypes under divergent selection, a reflection of recurrent local adaptation of ancient O. rufipogon populations to dry habitats. Almost completed premating isolation was detected between O. nivara and O. rufipogon in the absence of any postmating barriers between and within these species. These results suggest that flowering time is a "magic" trait that contributes to both local adaptation and reproductive isolation in the origin of wild rice species. Our study thus demonstrates a convincing case of parallel ecological speciation as a consequence of adaptation to new environments.

Monitoring the Water Stress of an Indoor Living Wall System Using the "Triangle Method".

Living walls are important vertical greening systems with modular prevegetated structures. Studies have suggested that living walls have many social benefits as an ecological engineering technique with notable potential for reconciliation ecology. Despite these benefits, there are currently no mature workflows or technologies for monitoring the health status and water stress of living wall systems. To partially fill the current knowledge gap related to water stress, we acquired thermal, multispectral, and hyperspectral remote sensing data from an indoor living wall in the Cloud Forest of the Gardens by the Bay, Singapore. The surface temperature (Ts) and a normalized difference vegetation index (NDVI) were obtained from these data to construct a Ts-NDVI space for applying the "triangle method". A simple and effective algorithm was proposed to determine the dry and wet edges, the key components of the said method. The pixels associated with the dry and wet edges were then selected and highlighted to directly display the areas under water-stress conditions. Our results suggest that the proposed algorithm can provide a reasonable overview of the water-stress information of the living wall; therefore, our method can be simple and effective to monitor the health status of a living wall. Furthermore, our work confirms that the triangle method can be transferred from the outdoors to an indoor environment.

Microsecond sensitivity to envelope interaural time differences in rats.

Currently, there is controversy around whether rats can use interaural time differences (ITDs) to localize sound. Here, naturalistic pulse train stimuli were used to evaluate the rat's sensitivity to onset and ongoing ITDs using a two-alternative forced choice sound lateralization task. Pulse rates between 50 Hz and 4.8 kHz with rectangular or Hanning windows were delivered with ITDs between ±175 µs over a near-field acoustic setup. Similar to other mammals, rats performed with 75% accuracy at ∼50 µs ITD, demonstrating that rats are highly sensitive to envelope ITDs.

Molecular cloning, identification of GSTs family in sunflower and their regulatory roles in biotic and abiotic stress.

Glutathione-S-transferase (GST) genes exist widely in plants and play major role in metabolic detoxification of exogenous chemical substances and oxidative stress. In this study, 14 sunflower GST genes (HaGSTs) were identified based on the sunflower transcriptome database that we had constructed. Full-length cDNA of 14 HaGTSs were isolated from total RNA by reverse transcription PCR (RT-PCR). Sunflower was received biotic stress (Sclerotinia sclerotiorum) and abiotic stress (NaCl, low-temperature, drought and wound). GST activity was measured by using the universal substrate. The results showed that most of the HaGSTs were up-regulated after NaCl and PEG6000-induced stresses, while a few HaGSTs were up-regulated after S. sclerotiorum, hypothermia and wound-induced stressed, and there was correlation between the changes of GST activity and the expression of HaGSTs, indicating that HaGSTs may play regulatory role in the biotic and abiotic stress responses. 14 HaGSTs from sunflower were identified, and the expression of HaGSTs were tissue-specific and played regulatory roles in both stress and abiotic stress.

Detection of exogenous gene doping of IGF-I by a real-time quantitative PCR assay.

Gene doping can be easily concealed since its product is similar to endogenous protein, making its effective detection very challenging. In this study, we selected insulin-like growth factor I (IGF-I) exogenous gene for gene doping detection. First, the synthetic IGF-I gene was subcloned to recombinant adeno-associated virus (rAAV) plasmid to produce recombinant rAAV2/IGF-I-GFP vectors. Second, in an animal model, rAAV2/IGF-I-GFP vectors were injected into the thigh muscle tissue of mice, and then muscle and blood specimens were sampled at different time points for total DNA isolation. Finally, real-time quantitative PCR was employed to detect the exogenous gene doping of IGF-I. In view of the characteristics of endogenous IGF-I gene sequences, a TaqMan probe was designed at the junction of exons 2 and 3 of IGF-I gene to distinguish it from the exogenous IGF-I gene. In addition, an internal reference control plasmid and its probe were used in PCR to rule out false-positive results through comparison of their threshold cycle (Ct) values. Thus, an accurate exogenous IGF-I gene detection approach was developed in this study.

Mandarin speech-in-noise and tone recognition using vocoder simulations of the temporal limits encoder for cochlear implants.

Temporal envelope-based signal processing strategies are widely used in cochlear-implant (CI) systems. It is well recognized that the inability to convey temporal fine structure (TFS) in the stimuli limits CI users' performance, but it is still unclear how to effectively deliver the TFS. A strategy known as the temporal limits encoder (TLE), which employs an approach to derive the amplitude modulator to generate the stimuli coded in an interleaved-sampling strategy, has recently been proposed. The TLE modulator contains information related to the original temporal envelope and a slow-varying TFS from the band signal. In this paper, theoretical analyses are presented to demonstrate the superiority of TLE compared with two existing strategies, the clinically available continuous-interleaved-sampling (CIS) strategy and the experimental harmonic-single-sideband-encoder strategy. Perceptual experiments with vocoder simulations in normal-hearing listeners are conducted to compare the performance of TLE and CIS on two tasks (i.e., Mandarin speech reception in babble noise and tone recognition in quiet). The performance of the TLE modulator is mostly better than (for most tone-band vocoders) or comparable to (for noise-band vocoders) the CIS modulator on both tasks. This work implies that there is some potential for improving the representation of TFS with CIs by using a TLE strategy.

Repeated range expansions and inter-/postglacial recolonization routes of Sargentodoxa cuneata (Oliv.) Rehd. et Wils. (Lardizabalaceae) in subtropical China revealed by chloroplast phylogeography.

Most plant phylogeographic studies in subtropical China have stressed the importance of multiple refugia and limited admixture among refugia. Little attention has been paid to range expansion and recolonization routes in this region. In this study, we implemented a phylogeographic survey on Sargentodoxa cuneata, a widespread woody deciduous climber in subtropical China to determine if it conforms to the expansion-contraction (EC) model during the Pleistocene. Sequence variation of two chloroplast intergenic spacers (IGSs) in 369 individuals from 54 populations of S. cuneata was examined. Twenty-six chloroplast haplotypes were recovered. One of these (H5) occurred across the range of S. cuneata and was absent from only 13 populations. Sixteen of the 26 haplotypes were connected to H5 by one mutation and displayed a star-like pattern in the haplotype network. All chloroplast haplotypes clustered into two lineages (A and B) in a Bayesian tree, and most haplotypes (18 out of 26) originated during the mid-Pleistocene (0.63-1.07Ma). Demographic analyses detected a recent range expansion that occurred at 95.98ka (CI: 61.7-112.53ka) for Lineage A. The genetic signature of an ancient range expansion after the Middle Pleistocene Transition (MPT) was also evident. Three recolonization routes were identified in subtropical China. The results suggest that temperate plants in subtropical China may conform to the EC model to some extent. However, the genetic signature from multiple historical processes may complicate the phylogeographic patterns of organisms in the region due to the mild Pleistocene climate. This study provides a new perspective for understanding the evolutionary history of temperate plants in subtropical China.

A new approach to detection of incomplete antibodies using hydrogel chromatography medium.

In assays for incomplete antibody detection, several washing steps are required to remove unbound globulins which may cause false negatives. Here, we present an improved approach employing hydrogel chromatography medium (HCM) in the detection of incomplete antibodies. After a rapid single-step centrifugation, incomplete antibodies, attached to red blood cells (RBCs), were separated from the reaction mixture using HCM and sedimentation. This method obviates the need for multiple centrifugation steps found in conventional Tube-Coombs tests. The HCM-Coombs tests may have a wide range of applications for incomplete antibody detection.

[Proteomic analysis of U937 cells expressing Mycobacterium tuberculosis heat shock protein 16.3].

OBJECTIVE: To compare the protein expression differences between U937 macrophages expressing M. tuberculosis (MTB) Hsp16.3 protein and U937 macrophages expressing green fluorescent protein (GFP), and therefore to explore the protein expressions related to latent TB infection(LTBI). METHODS: U937 macrophages were infected with an integrase-deficient Lentivirus vector to transiently express MTB Hsp16.3, and green fluorescent protein (GFP) as a control. 2-DE was used to compare the differentially expressed proteins in the infected U937 cells. Then 5 significantly different expressed protein spots were identified by using mass spectrometry. RESULTS: The data of 6 protein spots in gel obtained from peptide mass fingerprinting were retrieved in protein database. They were identified as heat shock protein 70, actin, elongation factor I, peptidyl-prolyl cis-trans isomerase, ubiquitin-conjugation enzyme E2, and milk acyl glutathione lyase. CONCLUSION: The results showed that MTB specific protein intrusion resulted in changes of macrophage proteome expression, and this finding may help in understanding of the interaction between macrophages and MTB specific proteins.

Identification of latent tuberculosis infection-related microRNAs in human U937 macrophages expressing Mycobacterium tuberculosis Hsp16.3.

BACKGROUND: Latent tuberculosis infection (LTBI) relies on a homeostasis of macrophages and Mycobacterium tuberculosis (Mtb). The small heat shock protein, Mtb Hsp16.3 (also known as latency-associated antigen), plays an important role in Mtb persistence within macrophages. However, the mechanism of LTBI remains elusive. The aim of this study was to delineate LTBI-related miRNA expression in U937 macrophages expressing Mtb Hsp16.3 protein. U937 macrophages were infected with an integrase-deficient Lentivirus vector to transiently express Mtb Hsp16.3, and green fluorescent protein (GFP) as a control. We used a microRNA (miRNA) microarray chip containing more than 1000 probes to identify the significant differentially expressed miRNAs in the infected U937 cells, and employed real-time quantitative polymerase chain reaction (qRT-PCR) for validation. Furthermore, we confirmed these candidate LTBI-related miRNAs in peripheral blood mononuclear cells from subjects with LTBI and in healthy control individuals. Functional annotation prediction of miRNA target genes and pathway enrichment analyses were used to explore the putative links between these miRNAs and LTBI. RESULTS: Analysis of the miRNA expression profile identified 149 miRNAs that were differentially expressed in U937 macrophages expressing Mtb Hsp16.3 compared with the control expressing GFP. The expression level of seven miRNAs (miR-424-5p, miR-493-5p, miR-296-5p, miR-27b-3p, miR-377-5p, miR-3680-5p, miR-191-5p) were validated by qRT-PCR. The expression level of four miRNAs (miR-424-5p, miR-27b-3p, miR-377-5p, miR-3680-5p) in the peripheral blood mononuclear cells samples from LTBI and healthy participants reflected the altered patterns observed in the microarray profile. The bioinformatic analyses suggest that the miRNAs may regulate Mtb latent infection by affecting the development of macrophage cells. CONCLUSIONS: The results suggest that miRNA expression may play a considerable role in the pathogenesis of LTBI, and this would increase our understanding of the molecular basis of Hsp16.3-facilitated Mtb survival in macrophages.

Energy use in residential buildings for sustainable development: The fifth Solar Decathlon Europe revelations.

This research focuses on achieving sustainable development in residential buildings with energy use. Under the influence of the energy crisis and related problems, research on residential buildings for less energy use has great potential. The literature review, according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses, and including VOSviewer analysis, shows the research is increasing and meaningful. Solar Decathlon buildings are used as the main objects in this research. The fifth Solar Decathlon Europe energy use technologies are examined through onsite investigation and online searching. The Analytic Hierarchy Process method for multi-criteria decision analysis is used for sustainability assessment. Moreover, the Ladybug and ClimateStudio plugins simulated respectively the annual solar radiation and the best angle for receiving it. The main findings show that 34 kinds of technologies used in these buildings can be classified into two categories in three directions. Passive technologies should be applied and prioritized, but generating renewable energy is also important. Some infrequently used technologies are not insignificant. The research shows that the combination of technologies decides sustainability performance, but the quantity used does not. Furthermore, energy use also needs to be balanced and coordinated in combination with architectural aesthetics. This research on energy use in residential buildings is beneficial for achieving sustainable development.

Detectability of intracranial vessel wall atherosclerosis using black-blood spectral CT: a phantom and clinical study.

BACKGROUND: Computed tomography (CT) is the usual modality for diagnosing stroke, but conventional CT angiography reconstructions have limitations. METHODS: A phantom with tubes of known diameters and wall thickness was scanned for wall detectability, wall thickness, and contrast-to-noise ratio (CNR) on conventional and spectral black-blood (SBB) images. The clinical study included 34 stroke patients. Diagnostic certainty and conspicuity of normal/abnormal intracranial vessels using SBB were compared to conventional. Sensitivity/specificity/accuracy of SBB and conventional were compared for plaque detectability. CNR of the wall/lumen and quantitative comparison of remodeling index, plaque burden, and eccentricity were obtained for SBB imaging and high-resolution magnetic resonance imaging (hrMRI). RESULTS: The phantom study showed improved detectability of tube walls using SBB (108/108, 100% versus conventional 81/108, 75%, p < 0.001). CNRs were 75.9 ± 62.6 (mean ± standard deviation) for wall/lumen and 22.0 ± 17.1 for wall/water using SBB and 26.4 ± 15.3 and 101.6 ± 62.5 using conventional. Clinical study demonstrated (i) improved certainty and conspicuity of the vessels using SBB versus conventional (certainty, median score 3 versus 0; conspicuity, median score 3 versus 1 (p < 0.001)), (ii) improved sensitivity/specificity/accuracy of plaque (≥ 1.0 mm) detectability (0.944/0.981/0.962 versus 0.239/0.743/0.495) (p < 0.001), (iii) higher wall/lumen CNR of SBB of (78.3 ± 50.4/79.3 ± 96.7) versus hrMRI (18.9 ± 8.4/24.1 ± 14.1) (p < 0.001), and (iv) excellent reproducibility of remodeling index, plaque burden, and eccentricity using SBB versus hrMRI (intraclass correlation coefficient 0.85-0.94). CONCLUSIONS: SBB can enhance the detectability of intracranial plaques with an accuracy similar to that of hrMRI. RELEVANCE STATEMENT: This new spectral black-blood technique for the detection and characterization of intracranial vessel atherosclerotic disease could be a time-saving and cost-effective diagnostic step for clinical stroke patients. It may also facilitate prevention strategies for atherosclerosis. KEY POINTS: • Blooming artifacts can blur vessel wall morphology on conventional CT angiography. • Spectral black-blood (SBB) images are generated from material decomposition from spectral CT. • SBB images reduce blooming artifacts and noise and accurately detect small plaques.

Root damage of street trees in urban environments: An overview of its hazards, causes, and prevention and control measures.

Root damage from urban street trees represents a substantial concern arising from the conflict between root growth and limited growth spaces. Nonetheless, the phenomenon of root damage, which threatens the safety of urban facilities, appears to have received little scholarly attention. Moreover, the effectiveness of some proposed measures for root damage prevention and control has not yet received consistent evaluation. Accordingly, this review aims to examine root damage, including its causes and available prevention and control measures. Urban trees are found to have a high potential to exert root damage on infrastructures when the following factors exist. These include large and mature tree, fast-growing trees, trees planted in limited soil volumes, shallow-rooted tree with buttress roots, trees whose diameter at breast height exceeds 10 cm, old and cracked road paving, high soil surface moisture content, short distances between trees and sidewalks (<2 to 3 m), and underground pipes that are already broken and made of metals or stones. The phenotypic traits of trees may be the primary factor causing root damage when there is a mismatch between the root-soil requirements of urban street trees and the actual soil environment. The poor effectiveness of root damage prevention and control measures may be attributed to the lack of connection between the development of control measures and the mechanism of root damage.

Comparable Encoding, Comparable Perceptual Pattern: Acoustic and Electric Hearing.

Perception with electric neuroprostheses is sometimes expected to be simulated using properly designed physical stimuli. Here, we examined a new acoustic vocoder model for electric hearing with cochlear implants (CIs) and hypothesized that comparable speech encoding can lead to comparable perceptual patterns for CI and normal hearing (NH) listeners. Speech signals were encoded using FFT-based signal processing stages including band-pass filtering, temporal envelope extraction, maxima selection, and amplitude compression and quantization. These stages were specifically implemented in the same manner by an Advanced Combination Encoder (ACE) strategy in CI processors and Gaussian-enveloped Tones (GET) or Noise (GEN) vocoders for NH. Adaptive speech reception thresholds (SRTs) in noise were measured using four Mandarin sentence corpora. Initial consonant (11 monosyllables) and final vowel (20 monosyllables) recognition were also measured. NaÏve NH listeners were tested using vocoded speech with the proposed GET/GEN vocoders as well as conventional vocoders (controls). Experienced CI listeners were tested using their daily-used processors. Results showed that: 1) there was a significant training effect on GET vocoded speech perception; 2) the GEN vocoded scores (SRTs with four corpora and consonant and vowel recognition scores) as well as the phoneme-level confusion pattern matched with the CI scores better than controls. The findings suggest that the same signal encoding implementations may lead to similar perceptual patterns simultaneously in multiple perception tasks. This study highlights the importance of faithfully replicating all signal processing stages in the modeling of perceptual patterns in sensory neuroprostheses. This approach has the potential to enhance our understanding of CI perception and accelerate the engineering of prosthetic interventions. The GET/GEN MATLAB program is freely available athttps://github.com/BetterCI/GETVocoder.