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Research on complete mitochondrial genomes can help in understanding the molecular evolution and phylogenetic relationships of various species. In this study, the complete mitogenome of Hua aristarchorum was characterized to supplement the limited mitogenomic information on the genus Hua. Three distinct assembly methods, GetOrganelle, NovoPlasty and SPAdes, were used to ensure reliable assembly. The 15,691 bp mitogenome contains 37 genes and an AT-rich region. Notably, the cytochrome c oxidase subunit I (COX1) gene, commonly used for species identification, appears to be slow-evolving and less variable, which may suggest the inclusion of rapidly evolving genes (NADH dehydrogenase subunit 6 [ND6] or NADH dehydrogenase subunit 2 [ND2]) as markers in diagnostic, detection, and population genetic studies of Cerithioidea. Moreover, we identified the unreliability of annotations (e.g., the absence of annotations for NADH dehydrogenase subunit 4L [ND4L] in NC_037771) and potential misidentifications (NC_023364) in public databases, which indicate that data from public databases should be manually curated in future research. Phylogenetic analyses of Cerithioidea based on different datasets generated identical trees using maximum likelihood and Bayesian inference methods. The results confirm that Semisulcospiridae is closely related to Pleuroceridae. The sequences of Semisulcospiridae clustered into three clades, of which H. aristarchorum is one; H. aristarchorum is sister to the other two clades. The findings of this study will contribute to a better understanding of the characteristics of the H. aristarchorum mitogenome and the phylogenetic relationships of Semisulcospiridae. The inclusion of further mitochondrial genome sequences will improve knowledge of the phylogeny and origin of Cerithioidea. [ABSTRACT FROM AUTHOR]

Background: Eligibility criteria are the primary strategy for screening the target participants of a clinical trial. Automated classification of clinical trial eligibility criteria text by using machine learning methods improves recruitment efficiency to reduce the cost of clinical research. However, existing methods suffer from poor classification performance due to the complexity and imbalance of eligibility criteria text data.Methods: An ensemble learning-based model with metric learning is proposed for eligibility criteria classification. The model integrates a set of pre-trained models including Bidirectional Encoder Representations from Transformers (BERT), A Robustly Optimized BERT Pretraining Approach (RoBERTa), XLNet, Pre-training Text Encoders as Discriminators Rather Than Generators (ELECTRA), and Enhanced Representation through Knowledge Integration (ERNIE). Focal Loss is used as a loss function to address the data imbalance problem. Metric learning is employed to train the embedding of each base model for feature distinguish. Soft Voting is applied to achieve final classification of the ensemble model. The dataset is from the standard evaluation task 3 of 5th China Health Information Processing Conference containing 38,341 eligibility criteria text in 44 categories.Results: Our ensemble method had an accuracy of 0.8497, a precision of 0.8229, and a recall of 0.8216 on the dataset. The macro F1-score was 0.8169, outperforming state-of-the-art baseline methods by 0.84% improvement on average. In addition, the performance improvement had a p-value of 2.152e-07 with a standard t-test, indicating that our model achieved a significant improvement.Conclusions: A model for classifying eligibility criteria text of clinical trials based on multi-model ensemble learning and metric learning was proposed. The experiments demonstrated that the classification performance was improved by our ensemble model significantly. In addition, metric learning was able to improve word embedding representation and the focal loss reduced the impact of data imbalance to model performance. [ABSTRACT FROM AUTHOR]

Intestinal microbiota is a critical determinant of growth and risk of metabolic diseases. Our previous studies showed that the locus rs16775833 within the DMRT1 gene is significantly associated with variation in the population structure of the gut microbiota, which is involved in determining the BW of the chicken. To assess the accuracy of correlation of rs16775833 located in the DMRT1 gene on microbial population and BW in birds, 2 genotypes GG and TT in the rs16775833 were identified in Chinese Yellow broiler breeders. We found that BW in the TT genotype group was significantly higher than in the GG genotype group at 7 and 13 wk of age in 777 female chickens. A full-length 16S rRNA sequencing approach was used to further evaluate the fecal bacterial composition of female broilers in 11 TT genotype chickens with high weight (HW-TT) and 11 GG genotype chickens with low weight (LW-GG) at 91 D of age. Partial least squares discriminant analysis revealed that the microbiota of the HW-TT and LW-GG females were clearly separated into 2 clusters. Furthermore, we identified 13 significantly different (P < 0.05) microbes at the genus level and 17 significantly different (P < 0.05) species between the HW-TT and LW-GG groups. Our data show that rs16775833 can modulate the microbial community structure and is associated with the BW of birds. To our knowledge, this is the first time that DMRT1 has been identified as a specific host factor, which is not only involved in sex determination but also has an effect on microbial function that might regulate animal growth. [ABSTRACT FROM AUTHOR]

We deposit Au films on single crystal sapphire substrates by sputtering and evaporation methods. The microstructure characteristics such as crystal textures, grain sizes, and fraction of contacted area of the films are examined by x-ray diffraction and transmission electron microscopy. The sputtered films have an average grain size of about 200 nm and perfectly attach to the substrates; the as-evaporated films partially attach to the substrate; the grain size varies from 10 to 30 nm, and after annealing, increases to 50 nm. Au2Al phase is observed in the annealed samples. The interfacial thermal resistance is measured by a frequency domain thermoreflectance method. The thermal resistance of the sputtered Au/sapphire interfaces is 35.5×10-9 m2 K W-1, and those of the evaporated samples are up to three times as large as this value. The change in interfacial thermal resistance is explained by the effect of detachment using a parallel arranged thermal resistance model, the effect of grain size, and the influence of chemical bonding at the interfaces. [ABSTRACT FROM AUTHOR]

Plasmodium falciparum causes malaria in humans with over 450,000 deaths annually. The asexual blood stage involves invasion of erythrocytes by merozoites, in which they grow and divide to release daughter merozoites, which in turn invade new erythrocytes perpetuating the cycle responsible for malaria. A key step in merozoite invasion is the essential binding of PfRh5/ CyRPA/PfRipr complex to basigin, a step linked to the formation of a pore between merozoites and erythrocytes. We show CyRPA interacts directly with PfRh5. An invasion inhibitory monoclonal antibody to CyRPA blocks binding of CyRPA to PfRh5 and complex formation thus illuminating the molecular mechanism for inhibition of parasite growth. We determined the crystal structures of CyRPA alone and in complex with an antibody Fab fragment. CyRPA has a six-bladed b-propeller fold, and we identify the region that interacts with PfRh5. This functionally conserved epitope is a potential target for vaccines against P. falciparum. [ABSTRACT FROM AUTHOR]

We investigated phonons with long mean free paths (MFPs) in amorphous Si (a-Si) and amorphous Ge (a-Ge). The thermal conductivity of a-Si and a-Ge thin films prepared by magnetron sputtering was found to depend on film thickness and deposition temperature. From the film thickness dependence, we conclude that phonons with MFPs longer than 100 nm contribute to heat transport in a-Si and a-Ge. Also, as deposition temperature was increased, phonons with MFPs ranging from 100 to 250 nm in a-Si and from 15 to 250 nm in a-Ge increased. [ABSTRACT FROM AUTHOR]

We measured the thermal conductivity of amorphous Ge films prepared by magnetron sputtering. The thermal conductivity was significantly higher than the value predicted by the minimum thermal conductivity model and increased with deposition temperature. We found that variations in sound velocity and Ge film density were not the main factors in the high thermal conductivity. Fast Fourier transform patterns of transmission electron micrographs revealed that short-range order in the Ge films was responsible for their high thermal conductivity. The results provide experimental evidences to understand the underlying nature of the variation of phonon mean free path in amorphous solids [ABSTRACT FROM AUTHOR]

Gene deletion studies in mice have revealed critical roles for IL (interleukin)-4 and -13 in asthma development, with the latter controlling lung airways resistance and mucus secretion. We have now developed human neutralizing monoclonal antibodies against human IL-13Rα1 (IL-13 receptor α1) subunit that prevent activation of the receptor complex by both IL-4 and IL-13. We describe the crystal structures of the Fab fragment of antibody 10G5H6 alone and in complex with D3 (ectodomain 3) of IL-13Rα1. Although the structure showed significant domain swapping within aD3 dimer, we showed that Arg230, Phe233, Tyr250, Gln252 and Leu293 in each D3 monomer and Ser32, Asn102 and Trp103 in 10G5H6 Fab are the key interacting residues at the interface of the 10G5H6 Fab-D3 complex. One of the most striking contacts is the insertion of the ligand-contacting residue Leu293 of D3 into a deep pocket on the surface of 10G5H6 Fab, and this appears to be a central determinant of the high binding affinity and neutralizing activity of the antibody. [ABSTRACT FROM AUTHOR]

Mint adaptor proteins bind to the amyloid precursor protein (APP) and regulate APP processing associated with Alzheimer's disease; however, the molecular mechanisms underlying Mint regulation in APP binding and processing remain unclear. Biochemical, biophysical, and cellular experiments now show that the Minti phosphotyrosine binding (PTB) domain that binds to APP is intramolecularly inhibited by the adjacent C-terminal linker region. The crystal structure of a C-terminally extended Minti PTB fragment reveals that the linker region forms a short a-helix that folds back onto the PTB domain and sterically hinders APP binding. This intramolecular interaction is disrupted by mutation of Tyr633 within the Minti autoinhibitory helix leading to enhanced APP binding and a-amyloid production. Our findings suggest that an autoinhibitory mechanism in Minti is important for regulating APP processing and may provide novel therapies for Alzheimer's disease. [ABSTRACT FROM AUTHOR]

SNAREs are essential for intracellular membrane fusion. Using EPR, we determined the structure of the transmembrane domain (TMD) of the vesicle (v)-SNARE Snc2p involved in trafficking in yeast. Structural features of the TMD were used to design a v-SNARE mutant in which about half of the TMD was deleted. Liposomes containing this mutant induced outer leaflet mixing but not inner leaflet mixing when incubated with liposomes containing target membrane (t)-SNAREs. Hemifusion was also detected with wild-type SNAREs when low protein concentrations were reconstituted. Thus, these results show that SNARE-mediated fusion can transit through a hemifusion intermediate. [ABSTRACT FROM AUTHOR]

SNARE complex formation is essential for intracellular membrane fusion. Vesicle-associated (v-) SNARE intertwines with target membrane (t-) SNARE to form a coiled coil that bridges two membranes and facilitates fusion. For the SNARE family involved in neuronal communications, complex formation is tightly regulated by the v-SNARE-membrane interactions. However, it was found using EPR that complex formation is spontaneous for a different SNARE family that is involved in protein trafficking in yeast. Further, reconstituted yeast SNAREs promoted membrane fusion, different from the inhibited fusion for reconstituted neuronal SNAREs. The EPR structural analysis showed that none of the coiled-coil residues of yeast v-SNARE is buried in the hydrophobic layer of the membrane, making the entire coiled-coil motif accessible, again different from the deep insertion of the membrane-proximal region of neuronal v-SNARE into the bilayer. Importantly, yeast membrane fusion is constitutively active, while synaptic membrane fusion is regulated, consistent with the present results for two SNARE families. Thus, the v-SNARE-membrane interaction may be a major molecular determinant for regulated versus constitutive membrane fusion in cells. [ABSTRACT FROM AUTHOR]

The PII proteins from the cyanobacteria Synechococcus sp. PCC 7942 and Synechocystis sp. PCC 6803 have been crystallized and high-resolution structures have been obtained using X-ray crystallography. The core of these new structures is similar to that of the PII proteins from Escherichia coli, although the structures of the T- and C-loops differ. The T-loop of the Synechococcus protein is ordered, but appears to be stabilized by crystal contacts. The same loop in the Synechocystis protein is discordered. The C-termious of the Synechocystis protein is stabilized by hydrogen bonding to the same region of a crystallographically related molecule. The same terminus in the Synechococcus protein is stabilized by coordination with a metal ion. These observations are consistent with the idea that both the T-loop and the C-terminus of PII proteins are flexible in solution and that this flexibility may be important for receptor recognition. Sequence comparisons are used to identify regions of the sequence unique to the cyanobacteria. [ABSTRACT FROM AUTHOR]

Examines the usability of the structure of P[sub 11] with adenosine triphosphate. Inclusion of hexagonal crystal form; Emphasis of the level of glutamine synthetase activity; Models for the structures of the heterotrimers.

The C-terminal domain of adenylyltransferase (ATase) from Escherichia coli has been overexpressed, purified and crystallized in a form suitable for structure analysis. The domain is contained in a fragment that extends from residues 441–945 of the intact ATase. [ABSTRACT FROM AUTHOR]

The history and current status of materials data activities from handbook to database are reviewed, with introduction to some important products. Through an example of prediction of interfacial thermal resistance based on data and data science methods, we show the advantages and potential of material informatics to study material issues which are too complicated or time consuming for conventional theoretical and experimental methods. Materials big data is the fundamental of material informatics. The challenges and strategy to construct materials big data are discussed, and some solutions are proposed as the results of our experiences to construct National Institute for Materials Science (NIMS) materials databases. [ABSTRACT FROM AUTHOR]

Munc13-1 acts as a master regulator of neurotransmitter release, mediating docking- priming of synaptic vesicles and diverse presynaptic plasticity processes. It is unclear how the functions of the multiple domains of Munc13-1 are coordinated. The crystal structure of a Munc13-1 fragment including its C1, C2B and MUN domains (C1C2BMUN) reveals a 19.5 nm-long multi- helical structure with the C1 and C2B domains packed at one end. The similar orientations of the respective diacyglycerol- and Ca2+-binding sites of the C1 and C2B domains suggest that the two domains cooperate in plasma-membrane binding and that activation of Munc13-1 by Ca2+ and diacylglycerol during short-term presynaptic plasticity are closely interrelated. Electrophysiological experiments in mouse neurons support the functional importance of the domain interfaces observed in C1C2BMUN. The structure imposes key constraints for models of neurotransmitter release and suggests that Munc13-1 bridges the vesicle and plasma membranes from the periphery of the membrane-membrane interface. [ABSTRACT FROM AUTHOR]

In this study, we investigated the temperature dependence and size effect of the thermal boundary resistance at Si/Ge interfaces by non-equilibrium molecular dynamics (MD) simulations using the direct method with the Stillinger-Weber potential. The simulations were performed at four temperatures for two simulation cells of different sizes. The resulting thermal boundary resistance decreased with increasing temperature. The thermal boundary resistance was smaller for the large cell than for the small cell. Furthermore, the MD-predicted values were lower than the diffusion mismatch model (DMM)-predicted values. The phonon density of states (DOS) was calculated for all the cases to examine the underlying nature of the temperature dependence and size effect of thermal boundary resistance. We found that the phonon DOS was modified in the interface regions. The phonon DOS better matched between Si and Ge in the interface region than in the bulk region. Furthermore, in interface Si, the population of low-frequency phonons was found to increase with increasing temperature and cell size. We suggest that the increasing population of low-frequency phonons increased the phonon transmission coefficient at the interface, leading to the temperature dependence and size effect on thermal boundary resistance. [ABSTRACT FROM AUTHOR]

During the priming step that leaves synaptic vesicles ready for neurotransmitter release, the SNARE syntaxin-1 transitions from a closed conformation that binds Munc18-1 tightly to an open conformation within the highly stable SNARE complex. Control of this conformational transition is important for brain function, but the underlying mechanism is unknown. NMR and fluorescence experiments now show that the Munc13-1 MUN domain, which plays a central role in vesicle priming, markedly accelerates the transition from the syntaxin-1-Munc18-1 complex to the SNARE complex. This activity depends on weak interactions of the MUN domain with the syntaxin-1 SNARE motif, and probably with Munc18-1. Together with available physiological data, these results provide a defined molecular basis for synaptic vesicle priming, and they illustrate how weak protein-protein interactions can play crucial biological roles by promoting transitions between high-affinity macromolecular assemblies. [ABSTRACT FROM AUTHOR]

During its brief twenty-five-year history, and under the close management of the central government, the postdoctoral training system in China has grown rapidly into a permanent element of the Chinese science and technology research system. Although designed to be attractive to elite Chinese Ph.D. talent both living abroad and in China, it turned out not to be. Over the years, Chinese students have demonstrated their preferences for foreign doctoral degrees, and return rates have been low. All the while, continued investment in science and technology has fed steady demand for postdoctoral researchers. Those who opt to return have commanded generous compensation packages for prestigious permanent positions, rather than settling for meagerly paid and temporary postdoctoral positions. For those who remain, a postdoctoral stint has evolved into a requirement for progressing along a research career path; however, their careers are often stymied by institutional preferences to hire returnees. As a result, the effectiveness of the postdoctoral system to boost the development of domestically trained talent is also not fully manifest. Although it is likely that the continued return of foreign talent will indeed ultimately boost the quality of research at Chinese institutions, the problem is the possible evolution of the cohort of domestically trained scientists into a subclass of highly trained scientists. In light of this, the continuing growth of the postdoctoral community in China is of concern, and significant change must be considered. To examine this question, we review the origins, structure, and governance of the postdoctoral system and examine the diversity and employability of postdoctoral scholars. [ABSTRACT FROM AUTHOR]

For harvesting energy from waste heat, the power generation densities and fabrication costs of thermoelectric generators (TEGs) are considered more important than their conversion efficiency because waste heat energy is essentially obtained free of charge. In this study, we propose a miniaturized planar Si-nanowire micro-thermoelectric generator (SiNW-μTEG) architecture, which could be simply fabricated using the complementary metal-oxide-semiconductor- compatible process. Compared with the conventional nanowire μTEGs, this SiNW-μTEG features the use of an exuded thermal field for power generation. Thus, there is no need to etch away the substrate to form suspended SiNWs, which leads to a low fabrication cost and well-protected SiNWs. We experimentally demonstrate that the power generation density of the SiNW-μTEGs was enhanced by four orders of magnitude when the SiNWs were shortened from 280 to 8 μm. Furthermore, we reduced the parasitic thermal resistance, which becomes significant in the shortened SiNW-μTEGs, by optimizing the fabrication process of AlN films as a thermally conductive layer. As a result, the power generation density of the SiNW-μTEGs was enhanced by an order of magnitude for reactive sputtering as compared to non-reactive sputtering process. A power density of 27.9 nW/cm2 has been achieved. By measuring the thermal conductivities of the two AlN films, we found that the reduction in the parasitic thermal resistance was caused by an increase in the thermal conductivity of the AlN film and a decrease in the thermal boundary resistance. [ABSTRACT FROM AUTHOR]

Neurotransmitter release depends critically on Munc18-1, Munc13, the Ca2+ sensor synaptotagmin-1, and the soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptors (SNAREs) syntaxin-1, synaptobrevin, and SNAP-25. In vitro reconstitutions have shown that syntaxin-1-SNAP-25 liposomes fuse efficiently with synaptobrevin liposomes in the presence of synaptotagmin-1-Ca2+, but neurotransmitter release also requires Munc18-1 and Munc13 in vivo. We found that Munc18-1 could displace SNAP-25 from syntaxin-1 and that fusion of syntaxin-1-Munc18-1 liposomes with synaptobrevin liposomes required Munc13, in addition to SNAP-25 and synaptotagmin-1-Ca2+. Moreover, when starting with syntaxin-1-SNAP-25 liposomes, NSF-α-SNAP disassembled the syntaxin-1-SNAP-25 heterodimers and abrogated fusion, which then required Munc18-1 and Munc13. We propose that fusion does not proceed through syntaxin-1-SNAP-25 heterodimers but starts with the syntaxin-1-Munc18-1 complex; Munc18-1 and Munc13 then orchestrate membrane fusion together with the SNAREs and synaptotagmin-1-Ca2+ in an NSF- and SNAP-resistant manner. [ABSTRACT FROM AUTHOR]